TY - COMP AU - Hauschild, Robert ID - 14926 TI - Matlab script for analysis of clone dispersal ER - TY - JOUR AB - Tropical precipitation extremes and their changes with surface warming are investigated using global storm resolving simulations and high-resolution observations. The simulations demonstrate that the mesoscale organization of convection, a process that cannot be physically represented by conventional global climate models, is important for the variations of tropical daily accumulated precipitation extremes. In both the simulations and observations, daily precipitation extremes increase in a more organized state, in association with larger, but less frequent, storms. Repeating the simulations for a warmer climate results in a robust increase in monthly-mean daily precipitation extremes. Higher precipitation percentiles have a greater sensitivity to convective organization, which is predicted to increase with warming. Without changes in organization, the strongest daily precipitation extremes over the tropical oceans increase at a rate close to Clausius-Clapeyron (CC) scaling. Thus, in a future warmer state with increased organization, the strongest daily precipitation extremes over oceans increase at a faster rate than CC scaling. AU - Bao, Jiawei AU - Stevens, Bjorn AU - Kluft, Lukas AU - Muller, Caroline J ID - 15047 IS - 8 JF - Science Advances TI - Intensification of daily tropical precipitation extremes from more organized convection VL - 10 ER - TY - JOUR AB - The superior colliculus (SC) in the mammalian midbrain is essential for multisensory integration and is composed of a rich diversity of excitatory and inhibitory neurons and glia. However, the developmental principles directing the generation of SC cell-type diversity are not understood. Here, we pursued systematic cell lineage tracing in silico and in vivo, preserving full spatial information, using genetic mosaic analysis with double markers (MADM)-based clonal analysis with single-cell sequencing (MADM-CloneSeq). The analysis of clonally related cell lineages revealed that radial glial progenitors (RGPs) in SC are exceptionally multipotent. Individual resident RGPs have the capacity to produce all excitatory and inhibitory SC neuron types, even at the stage of terminal division. While individual clonal units show no pre-defined cellular composition, the establishment of appropriate relative proportions of distinct neuronal types occurs in a PTEN-dependent manner. Collectively, our findings provide an inaugural framework at the single-RGP/-cell level of the mammalian SC ontogeny. AU - Cheung, Giselle T AU - Pauler, Florian AU - Koppensteiner, Peter AU - Krausgruber, Thomas AU - Streicher, Carmen AU - Schrammel, Martin AU - Özgen, Natalie Y AU - Ivec, Alexis AU - Bock, Christoph AU - Shigemoto, Ryuichi AU - Hippenmeyer, Simon ID - 12875 IS - 2 JF - Neuron SN - 0896-6273 TI - Multipotent progenitors instruct ontogeny of the superior colliculus VL - 112 ER - TY - JOUR AB - Poxviruses are among the largest double-stranded DNA viruses, with members such as variola virus, monkeypox virus and the vaccination strain vaccinia virus (VACV). Knowledge about the structural proteins that form the viral core has remained sparse. While major core proteins have been annotated via indirect experimental evidence, their structures have remained elusive and they could not be assigned to individual core features. Hence, which proteins constitute which layers of the core, such as the palisade layer and the inner core wall, has remained enigmatic. Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach in combination with AlphaFold molecular modeling, that trimers formed by the cleavage product of VACV protein A10 are the key component of the palisade layer. This allows us to place previously obtained descriptions of protein interactions within the core wall into perspective and to provide a detailed model of poxvirus core architecture. Importantly, we show that interactions within A10 trimers are likely generalizable over members of orthopox- and parapoxviruses. AU - Datler, Julia AU - Hansen, Jesse AU - Thader, Andreas AU - Schlögl, Alois AU - Bauer, Lukas W AU - Hodirnau, Victor-Valentin AU - Schur, Florian KM ID - 14979 JF - Nature Structural & Molecular Biology KW - Molecular Biology KW - Structural Biology SN - 1545-9993 TI - Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores ER - TY - JOUR AB - Contraction and flow of the actin cell cortex have emerged as a common principle by which cells reorganize their cytoplasm and take shape. However, how these cortical flows interact with adjacent cytoplasmic components, changing their form and localization, and how this affects cytoplasmic organization and cell shape remains unclear. Here we show that in ascidian oocytes, the cooperative activities of cortical actomyosin flows and deformation of the adjacent mitochondria-rich myoplasm drive oocyte cytoplasmic reorganization and shape changes following fertilization. We show that vegetal-directed cortical actomyosin flows, established upon oocyte fertilization, lead to both the accumulation of cortical actin at the vegetal pole of the zygote and compression and local buckling of the adjacent elastic solid-like myoplasm layer due to friction forces generated at their interface. Once cortical flows have ceased, the multiple myoplasm buckles resolve into one larger buckle, which again drives the formation of the contraction pole—a protuberance of the zygote’s vegetal pole where maternal mRNAs accumulate. Thus, our findings reveal a mechanism where cortical actomyosin network flows determine cytoplasmic reorganization and cell shape by deforming adjacent cytoplasmic components through friction forces. AU - Caballero Mancebo, Silvia AU - Shinde, Rushikesh AU - Bolger-Munro, Madison AU - Peruzzo, Matilda AU - Szep, Gregory AU - Steccari, Irene AU - Labrousse Arias, David AU - Zheden, Vanessa AU - Merrin, Jack AU - Callan-Jones, Andrew AU - Voituriez, Raphaël AU - Heisenberg, Carl-Philipp J ID - 14846 JF - Nature Physics SN - 1745-2473 TI - Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization ER - TY - JOUR AB - Key innovations are fundamental to biological diversification, but their genetic basis is poorly understood. A recent transition from egg-laying to live-bearing in marine snails (Littorina spp.) provides the opportunity to study the genetic architecture of an innovation that has evolved repeatedly across animals. Individuals do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical analysis revealed numerous small genomic regions where all live-bearers carry the same core haplotype. Candidate regions show evidence for live-bearer–specific positive selection and are enriched for genes that are differentially expressed between egg-laying and live-bearing reproductive systems. Ages of selective sweeps suggest that live-bearer–specific alleles accumulated over more than 200,000 generations. Our results suggest that new functions evolve through the recruitment of many alleles rather than in a single evolutionary step. AU - Stankowski, Sean AU - Zagrodzka, Zuzanna B. AU - Garlovsky, Martin D. AU - Pal, Arka AU - Shipilina, Daria AU - Garcia Castillo, Diego Fernando AU - Lifchitz, Hila AU - Le Moan, Alan AU - Leder, Erica AU - Reeve, James AU - Johannesson, Kerstin AU - Westram, Anja M AU - Butlin, Roger K. ID - 14796 IS - 6678 JF - Science TI - The genetic basis of a recent transition to live-bearing in marine snails VL - 383 ER - TY - THES AB - This thesis consists of four distinct pieces of work within theoretical biology, with two themes in common: the concept of optimization in biological systems, and the use of information-theoretic tools to quantify biological stochasticity and statistical uncertainty. Chapter 2 develops a statistical framework for studying biological systems which we believe to be optimized for a particular utility function, such as retinal neurons conveying information about visual stimuli. We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the expected utility. We explore how such priors aid inference of system parameters with limited data and enable optimality hypothesis testing: is the utility higher than by chance? Chapter 3 examines the ultimate biological optimization process: evolution by natural selection. As some individuals survive and reproduce more successfully than others, populations evolve towards fitter genotypes and phenotypes. We formalize this as accumulation of genetic information, and use population genetics theory to study how much such information can be accumulated per generation and maintained in the face of random mutation and genetic drift. We identify the population size and fitness variance as the key quantities that control information accumulation and maintenance. Chapter 4 reuses the concept of genetic information from Chapter 3, but from a different perspective: we ask how much genetic information organisms actually need, in particular in the context of gene regulation. For example, how much information is needed to bind transcription factors at correct locations within the genome? Population genetics provides us with a refined answer: with an increasing population size, populations achieve higher fitness by maintaining more genetic information. Moreover, regulatory parameters experience selection pressure to optimize the fitness-information trade-off, i.e. minimize the information needed for a given fitness. This provides an evolutionary derivation of the optimization priors introduced in Chapter 2. Chapter 5 proves an upper bound on mutual information between a signal and a communication channel output (such as neural activity). Mutual information is an important utility measure for biological systems, but its practical use can be difficult due to the large dimensionality of many biological channels. Sometimes, a lower bound on mutual information is computed by replacing the high-dimensional channel outputs with decodes (signal estimates). Our result provides a corresponding upper bound, provided that the decodes are the maximum posterior estimates of the signal. AU - Hledik, Michal ID - 15020 KW - Theoretical biology KW - Optimality KW - Evolution KW - Information SN - 2663 - 337X TI - Genetic information and biological optimization ER - TY - GEN AB - Eva Benkova received a PhD in Biophysics at the Institute of Biophysics of the Czech Academy of Sciences in 1998. After working as a postdoc at the Max Planck Institute in Cologne and the Center for Plant Molecular Biology (ZMBP) in Tübingen, she became a group leader at the Plant Systems Biology Department of the Vlaams Instituut voor Biotechnologie (VIB) in Gent. In 2012, she transitioned to an Assistant Professor position at the Institute of Science and Technology Austria (ISTA) where she was later promoted to Professor. Since 2021, she has served as the Dean of the ISTA Graduate School. As a plant developmental biologist, she focuses on unraveling the molecular mechanisms and principles that underlie hormonal interactions in plants. In her current work, she explores the intricate connections between hormones and regulatory pathways that mediate the perception of environmental stimuli, including abiotic stress and nitrate availability. AU - Benková, Eva ID - 14842 IS - 1 T2 - Current Biology TI - Eva Benkova VL - 34 ER - TY - JOUR AB - GABAB receptor (GBR) activation inhibits neurotransmitter release in axon terminals in the brain, except in medial habenula (MHb) terminals, which show robust potentiation. However, mechanisms underlying this enigmatic potentiation remain elusive. Here, we report that GBR activation on MHb terminals induces an activity-dependent transition from a facilitating, tonic to a depressing, phasic neurotransmitter release mode. This transition is accompanied by a 4.1-fold increase in readily releasable vesicle pool (RRP) size and a 3.5-fold increase of docked synaptic vesicles (SVs) at the presynaptic active zone (AZ). Strikingly, the depressing phasic release exhibits looser coupling distance than the tonic release. Furthermore, the tonic and phasic release are selectively affected by deletion of synaptoporin (SPO) and Ca 2+ -dependent activator protein for secretion 2 (CAPS2), respectively. SPO modulates augmentation, the short-term plasticity associated with tonic release, and CAPS2 retains the increased RRP for initial responses in phasic response trains. The cytosolic protein CAPS2 showed a SV-associated distribution similar to the vesicular transmembrane protein SPO, and they were colocalized in the same terminals. We developed the “Flash and Freeze-fracture” method, and revealed the release of SPO-associated vesicles in both tonic and phasic modes and activity-dependent recruitment of CAPS2 to the AZ during phasic release, which lasted several minutes. Overall, these results indicate that GBR activation translocates CAPS2 to the AZ along with the fusion of CAPS2-associated SVs, contributing to persistency of the RRP increase. Thus, we identified structural and molecular mechanisms underlying tonic and phasic neurotransmitter release and their transition by GBR activation in MHb terminals. AU - Koppensteiner, Peter AU - Bhandari, Pradeep AU - Önal, Hüseyin C AU - Borges Merjane, Carolina AU - Le Monnier, Elodie AU - Roy, Utsa AU - Nakamura, Yukihiro AU - Sadakata, Tetsushi AU - Sanbo, Makoto AU - Hirabayashi, Masumi AU - Rhee, JeongSeop AU - Brose, Nils AU - Jonas, Peter M AU - Shigemoto, Ryuichi ID - 15084 IS - 8 JF - Proceedings of the National Academy of Sciences SN - 0027-8424 TI - GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles VL - 121 ER - TY - JOUR AB - Direct reciprocity is a powerful mechanism for cooperation in social dilemmas. The very logic of reciprocity, however, seems to require that individuals are symmetric, and that everyone has the same means to influence each others’ payoffs. Yet in many applications, individuals are asymmetric. Herein, we study the effect of asymmetry in linear public good games. Individuals may differ in their endowments (their ability to contribute to a public good) and in their productivities (how effective their contributions are). Given the individuals’ productivities, we ask which allocation of endowments is optimal for cooperation. To this end, we consider two notions of optimality. The first notion focuses on the resilience of cooperation. The respective endowment distribution ensures that full cooperation is feasible even under the most adverse conditions. The second notion focuses on efficiency. The corresponding endowment distribution maximizes group welfare. Using analytical methods, we fully characterize these two endowment distributions. This analysis reveals that both optimality notions favor some endowment inequality: More productive players ought to get higher endowments. Yet the two notions disagree on how unequal endowments are supposed to be. A focus on resilience results in less inequality. With additional simulations, we show that the optimal endowment allocation needs to account for both the resilience and the efficiency of cooperation. AU - Hübner, Valentin AU - Staab, Manuel AU - Hilbe, Christian AU - Chatterjee, Krishnendu AU - Kleshnina, Maria ID - 15083 IS - 10 JF - Proceedings of the National Academy of Sciences SN - 0027-8424 TI - Efficiency and resilience of cooperation in asymmetric social dilemmas VL - 121 ER - TY - GEN AB - in the research article "Efficiency and resilience of cooperation in asymmetric social dilemmas" (by Valentin Hübner, Manuel Staab, Christian Hilbe, Krishnendu Chatterjee, and Maria Kleshnina). We used different implementations for the case of two and three players, both described below. AU - Hübner, Valentin AU - Kleshnina, Maria ID - 15108 TI - Computer code for "Efficiency and resilience of cooperation in asymmetric social dilemmas" ER - TY - JOUR AB - Global storm-resolving models (GSRMs) use strongly refined horizontal grids compared with the climate models typically used in the Coupled Model Intercomparison Project (CMIP) but employ comparable vertical grid spacings. Here, we study how changes in the vertical grid spacing and adjustments to the integration time step affect the basic climate quantities simulated by the ICON-Sapphire atmospheric GSRM. Simulations are performed over a 45 d period for five different vertical grids with between 55 and 540 vertical layers and maximum tropospheric vertical grid spacings of between 800 and 50 m, respectively. The effects of changes in the vertical grid spacing are compared with the effects of reducing the horizontal grid spacing from 5 to 2.5 km. For most of the quantities considered, halving the vertical grid spacing has a smaller effect than halving the horizontal grid spacing, but it is not negligible. Each halving of the vertical grid spacing, along with the necessary reductions in time step length, increases cloud liquid water by about 7 %, compared with an approximate 16 % decrease for halving the horizontal grid spacing. The effect is due to both the vertical grid refinement and the time step reduction. There is no tendency toward convergence in the range of grid spacings tested here. The cloud ice amount also increases with a refinement in the vertical grid, but it is hardly affected by the time step length and does show a tendency to converge. While the effect on shortwave radiation is globally dominated by the altered reflection due to the change in the cloud liquid water content, the effect on longwave radiation is more difficult to interpret because changes in the cloud ice concentration and cloud fraction are anticorrelated in some regions. The simulations show that using a maximum tropospheric vertical grid spacing larger than 400 m would increase the truncation error strongly. Computing time investments in a further vertical grid refinement can affect the truncation errors of GSRMs similarly to comparable investments in horizontal refinement, because halving the vertical grid spacing is generally cheaper than halving the horizontal grid spacing. However, convergence of boundary layer cloud properties cannot be expected, even for the smallest maximum tropospheric grid spacing of 50 m used in this study. AU - Schmidt, Hauke AU - Rast, Sebastian AU - Bao, Jiawei AU - Cassim, Amrit AU - Fang, Shih Wei AU - Jimenez-De La Cuesta, Diego AU - Keil, Paul AU - Kluft, Lukas AU - Kroll, Clarissa AU - Lang, Theresa AU - Niemeier, Ulrike AU - Schneidereit, Andrea AU - Williams, Andrew I.L. AU - Stevens, Bjorn ID - 15097 IS - 4 JF - Geoscientific Model Development SN - 1991-959X TI - Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model VL - 17 ER - TY - JOUR AB - In this note, we prove a formula for the cancellation exponent kv,n between division polynomials ψn and ϕn associated with a sequence {nP}n∈N of points on an elliptic curve E defined over a discrete valuation field K. The formula greatly generalizes the previously known special cases and treats also the case of non-standard Kodaira types for non-perfect residue fields. AU - Naskręcki, Bartosz AU - Verzobio, Matteo ID - 12311 JF - Proceedings of the Royal Society of Edinburgh Section A: Mathematics KW - Elliptic curves KW - Néron models KW - division polynomials KW - height functions KW - discrete valuation rings SN - 0308-2105 TI - Common valuations of division polynomials ER - TY - JOUR AB - Speciation is a key evolutionary process that is not yet fully understood. Combining population genomic and ecological data from multiple diverging pairs of marine snails (Littorina) supports the search for speciation mechanisms. Placing pairs on a one-dimensional speciation continuum, from undifferentiated populations to species, obscured the complexity of speciation. Adding multiple axes helped to describe either speciation routes or reproductive isolation in the snails. Divergent ecological selection repeatedly generated barriers between ecotypes, but appeared less important in completing speciation while genetic incompatibilities played a key role. Chromosomal inversions contributed to genomic barriers, but with variable impact. A multidimensional (hypercube) approach supported framing of questions and identification of knowledge gaps and can be useful to understand speciation in many other systems. AU - Johannesson, Kerstin AU - Faria, Rui AU - Le Moan, Alan AU - Rafajlović, Marina AU - Westram, Anja M AU - Butlin, Roger K. AU - Stankowski, Sean ID - 15099 JF - Trends in Genetics SN - 0168-9525 TI - Diverse pathways to speciation revealed by marine snails ER - TY - JOUR AB - The paper is devoted to the analysis of the global well-posedness and the interior regularity of the 2D Navier–Stokes equations with inhomogeneous stochastic boundary conditions. The noise, white in time and coloured in space, can be interpreted as the physical law describing the driving mechanism on the atmosphere–ocean interface, i.e. as a balance of the shear stress of the ocean and the horizontal wind force. AU - Agresti, Antonio AU - Luongo, Eliseo ID - 15098 JF - Mathematische Annalen SN - 0025-5831 TI - Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions ER - TY - JOUR AB - The coupling between Ca2+ channels and release sensors is a key factor defining the signaling properties of a synapse. However, the coupling nanotopography at many synapses remains unknown, and it is unclear how it changes during development. To address these questions, we examined coupling at the cerebellar inhibitory basket cell (BC)-Purkinje cell (PC) synapse. Biophysical analysis of transmission by paired recording and intracellular pipette perfusion revealed that the effects of exogenous Ca2+ chelators decreased during development, despite constant reliance of release on P/Q-type Ca2+ channels. Structural analysis by freeze-fracture replica labeling (FRL) and transmission electron microscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters throughout development, whereas docked vesicles were only clustered at later developmental stages. Modeling suggested a developmental transformation from a more random to a more clustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches a point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic transmission. AU - Chen, JingJing AU - Kaufmann, Walter AU - Chen, Chong AU - Arai, Itaru AU - Kim, Olena AU - Shigemoto, Ryuichi AU - Jonas, Peter M ID - 14843 JF - Neuron SN - 0896-6273 TI - Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse ER - TY - THES AU - Chen, JingJing ID - 15101 SN - 2663 - 337X TI - Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse ER - TY - JOUR AB - Quantum computers are increasing in size and quality but are still very noisy. Error mitigation extends the size of the quantum circuits that noisy devices can meaningfully execute. However, state-of-the-art error mitigation methods are hard to implement and the limited qubit connectivity in superconducting qubit devices restricts most applications to the hardware's native topology. Here we show a quantum approximate optimization algorithm (QAOA) on nonplanar random regular graphs with up to 40 nodes enabled by a machine learning-based error mitigation. We use a swap network with careful decision-variable-to-qubit mapping and a feed-forward neural network to optimize a depth-two QAOA on up to 40 qubits. We observe a meaningful parameter optimization for the largest graph which requires running quantum circuits with 958 two-qubit gates. Our paper emphasizes the need to mitigate samples, and not only expectation values, in quantum approximate optimization. These results are a step towards executing quantum approximate optimization at a scale that is not classically simulable. Reaching such system sizes is key to properly understanding the true potential of heuristic algorithms like QAOA. AU - Sack, Stefan AU - Egger, Daniel J. ID - 15122 IS - 1 JF - Physical Review Research SN - 2643-1564 TI - Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation VL - 6 ER - TY - JOUR AB - Cell division in all domains of life requires the orchestration of many proteins, but in Archaea most of the machinery remains poorly characterized. Here we investigate the FtsZ-based cell division mechanism in Haloferax volcanii and find proteins containing photosynthetic reaction centre (PRC) barrel domains that play an essential role in archaeal cell division. We rename these proteins cell division protein B 1 (CdpB1) and CdpB2. Depletions and deletions in their respective genes cause severe cell division defects, generating drastically enlarged cells. Fluorescence microscopy of tagged FtsZ1, FtsZ2 and SepF in CdpB1 and CdpB2 mutant strains revealed an unusually disordered divisome that is not organized into a distinct ring-like structure. Biochemical analysis shows that SepF forms a tripartite complex with CdpB1/2 and crystal structures suggest that these two proteins might form filaments, possibly aligning SepF and the FtsZ2 ring during cell division. Overall our results indicate that PRC-domain proteins play essential roles in FtsZ-based cell division in Archaea. AU - Nußbaum, Phillip AU - Kureisaite-Ciziene, Danguole AU - Bellini, Dom AU - Van Der Does, Chris AU - Kojic, Marko AU - Taib, Najwa AU - Yeates, Anna AU - Tourte, Maxime AU - Gribaldo, Simonetta AU - Loose, Martin AU - Löwe, Jan AU - Albers, Sonja Verena ID - 15118 IS - 3 JF - Nature Microbiology TI - Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division VL - 9 ER - TY - JOUR AB - In this paper we consider an SPDE where the leading term is a second order operator with periodic boundary conditions, coefficients which are measurable in (t,ω) , and Hölder continuous in space. Assuming stochastic parabolicity conditions, we prove Lp((0,T)×Ω,tκdt;Hσ,q(Td)) -estimates. The main novelty is that we do not require p=q . Moreover, we allow arbitrary σ∈R and weights in time. Such mixed regularity estimates play a crucial role in applications to nonlinear SPDEs which is clear from our previous work. To prove our main results we develop a general perturbation theory for SPDEs. Moreover, we prove a new result on pointwise multiplication in spaces with fractional smoothness. AU - Agresti, Antonio AU - Veraar, Mark ID - 15119 IS - 1 JF - Annales de l'institut Henri Poincare Probability and Statistics SN - 0246-0203 TI - Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions VL - 60 ER - TY - JOUR AB - Entire chromosomes are typically only transmitted vertically from one generation to the next. The horizontal transfer of such chromosomes has long been considered improbable, yet gained recent support in several pathogenic fungi where it may affect the fitness or host specificity. To date, it is unknown how these transfers occur, how common they are and whether they can occur between different species. In this study, we show multiple independent instances of horizontal transfers of the same accessory chromosome between two distinct strains of the asexual entomopathogenic fungusMetarhizium robertsiiduring experimental co-infection of its insect host, the Argentine ant. Notably, only the one chromosome – but no other – was transferred from the donor to the recipient strain. The recipient strain, now harboring the accessory chromosome, exhibited a competitive advantage under certain host conditions. By phylogenetic analysis we further demonstrate that the same accessory chromosome was horizontally transferred in a natural environment betweenM. robertsiiand another congeneric insect pathogen,M. guizhouense. Hence horizontal chromosome transfer is not limited to the observed frequent events within species during experimental infections but also occurs naturally across species. The transferred accessory chromosome contains genes that might be involved in its preferential horizontal transfer, encoding putative histones and histone-modifying enzymes, but also putative virulence factors that may support its establishment. Our study reveals that both intra- and interspecies horizontal transfer of entire chromosomes is more frequent than previously assumed, likely representing a not uncommon mechanism for gene exchange.Significance StatementThe enormous success of bacterial pathogens has been attributed to their ability to exchange genetic material between one another. Similarly, in eukaryotes, horizontal transfer of genetic material allowed the spread of virulence factors across species. The horizontal transfer of whole chromosomes could be an important pathway for such exchange of genetic material, but little is known about the origin of transferable chromosomes and how frequently they are exchanged. Here, we show that the transfer of accessory chromosomes - chromosomes that are non-essential but may provide fitness benefits - is common during fungal co-infections and is even possible between distant pathogenic species, highlighting the importance of horizontal gene transfer via chromosome transfer also for the evolution and function of eukaryotic pathogens. AU - Habig, Michael AU - Grasse, Anna V AU - Müller, Judith AU - Stukenbrock, Eva H. AU - Leitner, Hanna AU - Cremer, Sylvia ID - 14478 IS - 11 JF - Proceedings of the National Academy of Sciences of the United States of America SN - 0027-8424 TI - Frequent horizontal chromosome transfer between asexual fungal insect pathogens VL - 121 ER - TY - JOUR AB - Given a fixed finite metric space (V,μ), the {\em minimum 0-extension problem}, denoted as 0-Ext[μ], is equivalent to the following optimization problem: minimize function of the form minx∈Vn∑ifi(xi)+∑ijcijμ(xi,xj) where cij,cvi are given nonnegative costs and fi:V→R are functions given by fi(xi)=∑v∈Vcviμ(xi,v). The computational complexity of 0-Ext[μ] has been recently established by Karzanov and by Hirai: if metric μ is {\em orientable modular} then 0-Ext[μ] can be solved in polynomial time, otherwise 0-Ext[μ] is NP-hard. To prove the tractability part, Hirai developed a theory of discrete convex functions on orientable modular graphs generalizing several known classes of functions in discrete convex analysis, such as L♮-convex functions. We consider a more general version of the problem in which unary functions fi(xi) can additionally have terms of the form cuv;iμ(xi,{u,v}) for {u,v}∈F, where set F⊆(V2) is fixed. We extend the complexity classification above by providing an explicit condition on (μ,F) for the problem to be tractable. In order to prove the tractability part, we generalize Hirai's theory and define a larger class of discrete convex functions. It covers, in particular, another well-known class of functions, namely submodular functions on an integer lattice. Finally, we improve the complexity of Hirai's algorithm for solving 0-Ext on orientable modular graphs. AU - Dvorak, Martin AU - Kolmogorov, Vladimir ID - 10045 JF - Mathematical Programming KW - minimum 0-extension problem KW - metric labeling problem KW - discrete metric spaces KW - metric extensions KW - computational complexity KW - valued constraint satisfaction problems KW - discrete convex analysis KW - L-convex functions SN - 0025-5610 TI - Generalized minimum 0-extension problem and discrete convexity ER - TY - JOUR AB - We present an auction algorithm using multiplicative instead of constant weight updates to compute a (1-E)-approximate maximum weight matching (MWM) in a bipartite graph with n vertices and m edges in time 0(mE-1), beating the running time of the fastest known approximation algorithm of Duan and Pettie [JACM ’14] that runs in 0(mE-1 log E-1). Our algorithm is very simple and it can be extended to give a dynamic data structure that maintains a (1-E)-approximate maximum weight matching under (1) one-sided vertex deletions (with incident edges) and (2) one-sided vertex insertions (with incident edges sorted by weight) to the other side. The total time time used is 0(mE-1), where m is the sum of the number of initially existing and inserted edges. AU - Zheng, Da Wei AU - Henzinger, Monika H ID - 15121 JF - Mathematical Programming SN - 0025-5610 TI - Multiplicative auction algorithm for approximate maximum weight bipartite matching ER - TY - JOUR AB - As a key liquid organic hydrogen carrier, investigating the decomposition of formic acid (HCOOH) on the Pd (1 1 1) transition metal surface is imperative for harnessing hydrogen energy. Despite a multitude of studies, the major mechanisms and key intermediates involved in the dehydrogenation process of formic acid remain a great topic of debate due to ambiguous adsorbate interactions. In this research, we develop an advanced microkinetic model based on first-principles calculations, accounting for adsorbate–adsorbate interactions. Our study unveils a comprehensive mechanism for the Pd (1 1 1) surface, highlighting the significance of coverage effects in formic acid dehydrogenation. Our findings unequivocally demonstrate that H coverage on the Pd (1 1 1) surface renders formic acid more susceptible to decompose into H2 and CO2 through COOH intermediates. Consistent with experimental results, the selectivity of H2 in the decomposition of formic acid on the Pd (1 1 1) surface approaches 100 %. Considering the influence of H coverage, our kinetic analysis aligns perfectly with experimental values at a temperature of 373 K. AU - Yao, Zihao AU - Liu, Xu AU - Bunting, Rhys AU - Wang, Jianguo ID - 15114 JF - Chemical Engineering Science SN - 0009-2509 TI - Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling VL - 291 ER - TY - JOUR AB - Water is known to play an important role in collagen self-assembly, but it is still largely unclear how water–collagen interactions influence the assembly process and determine the fibril network properties. Here, we use the H2O/D2O isotope effect on the hydrogen-bond strength in water to investigate the role of hydration in collagen self-assembly. We dissolve collagen in H2O and D2O and compare the growth kinetics and the structure of the collagen assemblies formed in these water isotopomers. Surprisingly, collagen assembly occurs ten times faster in D2O than in H2O, and collagen in D2O self-assembles into much thinner fibrils, that form a more inhomogeneous and softer network, with a fourfold reduction in elastic modulus when compared to H2O. Combining spectroscopic measurements with atomistic simulations, we show that collagen in D2O is less hydrated than in H2O. This partial dehydration lowers the enthalpic penalty for water removal and reorganization at the collagen–water interface, increasing the self-assembly rate and the number of nucleation centers, leading to thinner fibrils and a softer network. Coarse-grained simulations show that the acceleration in the initial nucleation rate can be reproduced by the enhancement of electrostatic interactions. These results show that water acts as a mediator between collagen monomers, by modulating their interactions so as to optimize the assembly process and, thus, the final network properties. We believe that isotopically modulating the hydration of proteins can be a valuable method to investigate the role of water in protein structural dynamics and protein self-assembly. AU - Giubertoni, Giulia AU - Feng, Liru AU - Klein, Kevin AU - Giannetti, Guido AU - Rutten, Luco AU - Choi, Yeji AU - Van Der Net, Anouk AU - Castro-Linares, Gerard AU - Caporaletti, Federico AU - Micha, Dimitra AU - Hunger, Johannes AU - Deblais, Antoine AU - Bonn, Daniel AU - Sommerdijk, Nico AU - Šarić, Anđela AU - Ilie, Ioana M. AU - Koenderink, Gijsje H. AU - Woutersen, Sander ID - 15116 IS - 11 JF - Proceedings of the National Academy of Sciences of the United States of America SN - 0027-8424 TI - Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration VL - 121 ER - TY - JOUR AB - The hippocampal mossy fiber synapse, formed between axons of dentate gyrus granule cells and dendrites of CA3 pyramidal neurons, is a key synapse in the trisynaptic circuitry of the hippocampus. Because of its comparatively large size, this synapse is accessible to direct presynaptic recording, allowing a rigorous investigation of the biophysical mechanisms of synaptic transmission and plasticity. Furthermore, because of its placement in the very center of the hippocampal memory circuit, this synapse seems to be critically involved in several higher network functions, such as learning, memory, pattern separation, and pattern completion. Recent work based on new technologies in both nanoanatomy and nanophysiology, including presynaptic patch-clamp recording, paired recording, super-resolution light microscopy, and freeze-fracture and “flash-and-freeze” electron microscopy, has provided new insights into the structure, biophysics, and network function of this intriguing synapse. This brings us one step closer to answering a fundamental question in neuroscience: how basic synaptic properties shape higher network computations. AU - Vandael, David H AU - Jonas, Peter M ID - 15117 IS - 6687 JF - Science TI - Structure, biophysics, and circuit function of a "giant" cortical presynaptic terminal VL - 383 ER - TY - THES AB - Point sets, geometric networks, and arrangements of hyperplanes are fundamental objects in discrete geometry that have captivated mathematicians for centuries, if not millennia. This thesis seeks to cast new light on these structures by illustrating specific instances where a topological perspective, specifically through discrete Morse theory and persistent homology, provides valuable insights. At first glance, the topology of these geometric objects might seem uneventful: point sets essentially lack of topology, arrangements of hyperplanes are a decomposition of Rd, which is a contractible space, and the topology of a network primarily involves the enumeration of connected components and cycles within the network. However, beneath this apparent simplicity, there lies an array of intriguing structures, a small subset of which will be uncovered in this thesis. Focused on three case studies, each addressing one of the mentioned objects, this work will showcase connections that intertwine topology with diverse fields such as combinatorial geometry, algorithms and data structures, and emerging applications like spatial biology. AU - Cultrera di Montesano, Sebastiano ID - 15094 SN - 2663 - 337X TI - Persistence and Morse theory for discrete geometric structures ER - TY - CONF AB - We present a dynamic data structure for maintaining the persistent homology of a time series of real numbers. The data structure supports local operations, including the insertion and deletion of an item and the cutting and concatenating of lists, each in time O(log n + k), in which n counts the critical items and k the changes in the augmented persistence diagram. To achieve this, we design a tailor-made tree structure with an unconventional representation, referred to as banana tree, which may be useful in its own right. AU - Cultrera di Montesano, Sebastiano AU - Edelsbrunner, Herbert AU - Henzinger, Monika H AU - Ost, Lara ED - Woodruff, David P. ID - 15093 T2 - Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA) TI - Dynamically maintaining the persistent homology of time series ER - TY - GEN AB - Motivated by applications in the medical sciences, we study finite chromatic sets in Euclidean space from a topological perspective. Based on the persistent homology for images, kernels and cokernels, we design provably stable homological quantifiers that describe the geometric micro- and macro-structure of how the color classes mingle. These can be efficiently computed using chromatic variants of Delaunay and alpha complexes, and code that does these computations is provided. AU - Cultrera di Montesano, Sebastiano AU - Draganov, Ondrej AU - Edelsbrunner, Herbert AU - Saghafian, Morteza ID - 15091 T2 - arXiv TI - Chromatic alpha complexes ER - TY - JOUR AB - The brain’s functionality is developed and maintained through synaptic plasticity. As synapses undergo plasticity, they also affect each other. The nature of such ‘co-dependency’ is difficult to disentangle experimentally, because multiple synapses must be monitored simultaneously. To help understand the experimentally observed phenomena, we introduce a framework that formalizes synaptic co-dependency between different connection types. The resulting model explains how inhibition can gate excitatory plasticity while neighboring excitatory–excitatory interactions determine the strength of long-term potentiation. Furthermore, we show how the interplay between excitatory and inhibitory synapses can account for the quick rise and long-term stability of a variety of synaptic weight profiles, such as orientation tuning and dendritic clustering of co-active synapses. In recurrent neuronal networks, co-dependent plasticity produces rich and stable motor cortex-like dynamics with high input sensitivity. Our results suggest an essential role for the neighborly synaptic interaction during learning, connecting micro-level physiology with network-wide phenomena. AU - Agnes, Everton J. AU - Vogels, Tim P ID - 15171 JF - Nature Neuroscience SN - 1097-6256 TI - Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks ER - TY - JOUR AB - We propose a novel approach to concentration for non-independent random variables. The main idea is to “pretend” that the random variables are independent and pay a multiplicative price measuring how far they are from actually being independent. This price is encapsulated in the Hellinger integral between the joint and the product of the marginals, which is then upper bounded leveraging tensorisation properties. Our bounds represent a natural generalisation of concentration inequalities in the presence of dependence: we recover exactly the classical bounds (McDiarmid’s inequality) when the random variables are independent. Furthermore, in a “large deviations” regime, we obtain the same decay in the probability as for the independent case, even when the random variables display non-trivial dependencies. To show this, we consider a number of applications of interest. First, we provide a bound for Markov chains with finite state space. Then, we consider the Simple Symmetric Random Walk, which is a non-contracting Markov chain, and a non-Markovian setting in which the stochastic process depends on its entire past. To conclude, we propose an application to Markov Chain Monte Carlo methods, where our approach leads to an improved lower bound on the minimum burn-in period required to reach a certain accuracy. In all of these settings, we provide a regime of parameters in which our bound fares better than what the state of the art can provide. AU - Esposito, Amedeo Roberto AU - Mondelli, Marco ID - 15172 JF - IEEE Transactions on Information Theory SN - 0018-9448 TI - Concentration without independence via information measures ER - TY - JOUR AB - The James Webb Space Telescope is revealing a new population of dust-reddened broad-line active galactic nuclei (AGN) at redshifts z ≳ 5. Here we present deep NIRSpec/Prism spectroscopy from the Cycle 1 Treasury program Ultradeep NIRSpec and NIRCam ObserVations before the Epoch of Reionization (UNCOVER) of 15 AGN candidates selected to be compact, with red continua in the rest-frame optical but with blue slopes in the UV. From NIRCam photometry alone, they could have been dominated by dusty star formation or an AGN. Here we show that the majority of the compact red sources in UNCOVER are dust-reddened AGN: 60% show definitive evidence for broad-line Hα with a FWHM > 2000 km s −1, 20% of the current data are inconclusive, and 20% are brown dwarf stars. We propose an updated photometric criterion to select red z > 5 AGN that excludes brown dwarfs and is expected to yield >80% AGN. Remarkably, among all zphot > 5 galaxies with F277W – F444W > 1 in UNCOVER at least 33% are AGN regardless of compactness, climbing to at least 80% AGN for sources with F277W – F444W > 1.6. The confirmed AGN have black hole masses of 107–109M⊙. While their UV luminosities (−16 > MUV > −20 AB mag) are low compared to UV-selected AGN at these epochs, consistent with percent-level scattered AGN light or low levels of unobscured star formation, the inferred bolometric luminosities are typical of 107–109M⊙ black holes radiating at ∼10%–40% the Eddington limit. The number densities are surprisingly high at ∼10−5 Mpc−3 mag−1, 100 times more common than the faintest UV-selected quasars, while accounting for ∼1% of the UV-selected galaxies. While their UV faintness suggests they may not contribute strongly to reionization, their ubiquity poses challenges to models of black hole growth. AU - Greene, Jenny E. AU - Labbe, Ivo AU - Goulding, Andy D. AU - Furtak, Lukas J. AU - Chemerynska, Iryna AU - Kokorev, Vasily AU - Dayal, Pratika AU - Volonteri, Marta AU - Williams, Christina C. AU - Wang, Bingjie AU - Setton, David J. AU - Burgasser, Adam J. AU - Bezanson, Rachel AU - Atek, Hakim AU - Brammer, Gabriel AU - Cutler, Sam E. AU - Feldmann, Robert AU - Fujimoto, Seiji AU - Glazebrook, Karl AU - De Graaff, Anna AU - Khullar, Gourav AU - Leja, Joel AU - Marchesini, Danilo AU - Maseda, Michael V. AU - Matthee, Jorryt J AU - Miller, Tim B. AU - Naidu, Rohan P. AU - Nanayakkara, Themiya AU - Oesch, Pascal A. AU - Pan, Richard AU - Papovich, Casey AU - Price, Sedona H. AU - Van Dokkum, Pieter AU - Weaver, John R. AU - Whitaker, Katherine E. AU - Zitrin, Adi ID - 15170 JF - Astrophysical Journal SN - 0004-637X TI - UNCOVER spectroscopy confirms the surprising ubiquity of active galactic nuclei in red sources at z > 5 VL - 964 ER - TY - CONF AB - A linearly ordered (LO) k-colouring of a hypergraph is a colouring of its vertices with colours 1, … , k such that each edge contains a unique maximal colour. Deciding whether an input hypergraph admits LO k-colouring with a fixed number of colours is NP-complete (and in the special case of graphs, LO colouring coincides with the usual graph colouring). Here, we investigate the complexity of approximating the "linearly ordered chromatic number" of a hypergraph. We prove that the following promise problem is NP-complete: Given a 3-uniform hypergraph, distinguish between the case that it is LO 3-colourable, and the case that it is not even LO 4-colourable. We prove this result by a combination of algebraic, topological, and combinatorial methods, building on and extending a topological approach for studying approximate graph colouring introduced by Krokhin, Opršal, Wrochna, and Živný (2023). AU - Filakovský, Marek AU - Nakajima, Tamio Vesa AU - Opršal, Jakub AU - Tasinato, Gianluca AU - Wagner, Uli ID - 15168 SN - 9783959773119 T2 - 41st International Symposium on Theoretical Aspects of Computer Science TI - Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs VL - 289 ER - TY - JOUR AB - Primary implant stability, which refers to the stability of the implant during the initial healing period is a crucial factor in determining the long-term success of the implant and lays the foundation for secondary implant stability achieved through osseointegration. Factors affecting primary stability include implant design, surgical technique, and patient-specific factors like bone quality and morphology. In vivo, the cyclic nature of anatomical loading puts osteosynthesis locking screws under dynamic loads, which can lead to the formation of micro cracks and defects that slowly degrade the mechanical connection between the bone and screw, thus compromising the initial stability and secondary stability of the implant. Monotonic quasi-static loading used for testing the holding capacity of implanted screws is not well suited to capture this behavior since it cannot capture the progressive deterioration of peri‑implant bone at small displacements. In order to address this issue, this study aims to determine a critical point of loss of primary implant stability in osteosynthesis locking screws under cyclic overloading by investigating the evolution of damage, dissipated energy, and permanent deformation. A custom-made test setup was used to test implanted 2.5 mm locking screws under cyclic overloading test. For each loading cycle, maximum forces and displacement were recorded as well as initial and final cycle displacements and used to calculate damage and energy dissipation evolution. The results of this study demonstrate that for axial, shear, and mixed loading significant damage and energy dissipation can be observed at approximately 20 % of the failure force. Additionally, at this load level, permanent deformations on the screw-bone interface were found to be in the range of 50 to 150 mm which promotes osseointegration and secondary implant stability. This research can assist surgeons in making informed preoperative decisions by providing a better understanding of the critical point of loss of primary implant stability, thus improving the long-term success of the implant and overall patient satisfaction. AU - Silva-Henao, Juan D. AU - Schober, Sophie AU - Pahr, Dieter H. AU - Reisinger, Andreas G. ID - 15164 JF - Medical Engineering and Physics SN - 1350-4533 TI - Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading VL - 126 ER - TY - JOUR AB - Interpretation of extracellular recordings can be challenging due to the long range of electric field. This challenge can be mitigated by estimating the current source density (CSD). Here we introduce kCSD-python, an open Python package implementing Kernel Current Source Density (kCSD) method and related tools to facilitate CSD analysis of experimental data and the interpretation of results. We show how to counter the limitations imposed by noise and assumptions in the method itself. kCSD-python allows CSD estimation for an arbitrary distribution of electrodes in 1D, 2D, and 3D, assuming distributions of sources in tissue, a slice, or in a single cell, and includes a range of diagnostic aids. We demonstrate its features in a Jupyter Notebook tutorial which illustrates a typical analytical workflow and main functionalities useful in validating analysis results. AU - Chintaluri, Chaitanya AU - Bejtka, Marta AU - Sredniawa, Wladyslaw AU - Czerwinski, Michal AU - Dzik, Jakub M. AU - Jedrzejewska-Szmek, Joanna AU - Wojciki, Daniel K. ID - 15169 IS - 3 JF - PLoS Computational Biology SN - 1553-734X TI - kCSD-python, reliable current source density estimation with quality control VL - 20 ER - TY - JOUR AB - We perform a diagrammatic analysis of the energy of a mobile impurity immersed in a strongly interacting two-component Fermi gas to second order in the impurity-bath interaction. These corrections demonstrate divergent behavior in the limit of large impurity momentum. We show the fundamental processes responsible for these logarithmically divergent terms. We study the problem in the general case without any assumptions regarding the fermion-fermion interactions in the bath. We show that the divergent term can be summed up to all orders in the Fermi-Fermi interaction and that the resulting expression is equivalent to the one obtained in the few-body calculation. Finally, we provide a perturbative calculation to the second order in the Fermi-Fermi interaction, and we show the diagrams responsible for these terms. AU - Al Hyder, Ragheed AU - Chevy, F. AU - Leyronas, X. ID - 15167 IS - 3 JF - Physical Review A SN - 2469-9926 TI - Exploring beyond-mean-field logarithmic divergences in Fermi-polaron energy VL - 109 ER - TY - JOUR AB - For some k∈Z≥0∪{∞}, we call a linear forest k-bounded if each of its components has at most k edges. We will say a (k,ℓ)-bounded linear forest decomposition of a graph G is a partition of E(G) into the edge sets of two linear forests Fk,Fℓ where Fk is k-bounded and Fℓ is ℓ-bounded. We show that the problem of deciding whether a given graph has such a decomposition is NP-complete if both k and ℓ are at least 2, NP-complete if k≥9 and ℓ=1, and is in P for (k,ℓ)=(2,1). Before this, the only known NP-complete cases were the (2,2) and (3,3) cases. Our hardness result answers a question of Bermond et al. from 1984. We also show that planar graphs of girth at least nine decompose into a linear forest and a matching, which in particular is stronger than 3-edge-colouring such graphs. AU - Campbell, Rutger AU - Hörsch, Florian AU - Moore, Benjamin ID - 15163 IS - 6 JF - Discrete Mathematics SN - 0012-365X TI - Decompositions into two linear forests of bounded lengths VL - 347 ER - TY - JOUR AB - Characterizing the prevalence and properties of faint active galactic nuclei (AGNs) in the early Universe is key for understanding the formation of supermassive black holes (SMBHs) and determining their role in cosmic reionization. We perform a spectroscopic search for broad Hα emitters at z ≈ 4–6 using deep JWST/NIRCam imaging and wide field slitless spectroscopy from the EIGER and FRESCO surveys. We identify 20 Hα lines at z = 4.2–5.5 that have broad components with line widths from ∼1200–3700 km s−1, contributing ∼30%–90% of the total line flux. We interpret these broad components as being powered by accretion onto SMBHs with implied masses ∼107–8M⊙. In the UV luminosity range MUV,AGN+host = −21 to −18, we measure number densities of ≈10−5 cMpc−3. This is an order of magnitude higher than expected from extrapolating quasar UV luminosity functions (LFs). Yet, such AGN are found in only <1% of star-forming galaxies at z ∼ 5. The number density discrepancy is much lower when compared to the broad Hα LF. The SMBH mass function agrees with large cosmological simulations. In two objects, we detect complex Hα profiles that we tentatively interpret as caused by absorption signatures from dense gas fueling SMBH growth and outflows. We may be witnessing early AGN feedback that will clear dust-free pathways through which more massive blue quasars are seen. We uncover a strong correlation between reddening and the fraction of total galaxy luminosity arising from faint AGN. This implies that early SMBH growth is highly obscured and that faint AGN are only minor contributors to cosmic reionization. AU - Matthee, Jorryt J AU - Naidu, Rohan P. AU - Brammer, Gabriel AU - Chisholm, John AU - Eilers, Anna-Christina AU - Goulding, Andy AU - Greene, Jenny AU - Kashino, Daichi AU - Labbe, Ivo AU - Lilly, Simon J. AU - Mackenzie, Ruari AU - Oesch, Pascal A. AU - Weibel, Andrea AU - Wuyts, Stijn AU - Xiao, Mengyuan AU - Bordoloi, Rongmon AU - Bouwens, Rychard AU - van Dokkum, Pieter AU - Illingworth, Garth AU - Kramarenko, Ivan AU - Maseda, Michael V. AU - Mason, Charlotte AU - Meyer, Romain A. AU - Nelson, Erica J. AU - Reddy, Naveen A. AU - Shivaei, Irene AU - Simcoe, Robert A. AU - Yue, Minghao ID - 15180 IS - 2 JF - The Astrophysical Journal KW - Space and Planetary Science KW - Astronomy and Astrophysics SN - 0004-637X TI - Little Red Dots: An abundant population of faint active galactic nuclei at z ∼ 5 revealed by the EIGER and FRESCO JWST surveys VL - 963 ER - TY - JOUR AB - The fungal bioluminescence pathway can be reconstituted in other organisms allowing luminescence imaging without exogenously supplied substrate. The pathway starts from hispidin biosynthesis—a step catalyzed by a large fungal polyketide synthase that requires a posttranslational modification for activity. Here, we report identification of alternative compact hispidin synthases encoded by a phylogenetically diverse group of plants. A hybrid bioluminescence pathway that combines plant and fungal genes is more compact, not dependent on availability of machinery for posttranslational modifications, and confers autonomous bioluminescence in yeast, mammalian, and plant hosts. The compact size of plant hispidin synthases enables additional modes of delivery of autoluminescence, such as delivery with viral vectors. AU - Palkina, Kseniia A. AU - Karataeva, Tatiana A. AU - Perfilov, Maxim M. AU - Fakhranurova, Liliia I. AU - Markina, Nadezhda M. AU - Gonzalez Somermeyer, Louisa AU - Garcia-Perez, Elena AU - Vazquez-Vilar, Marta AU - Rodriguez-Rodriguez, Marta AU - Vazquez-Vilriales, Victor AU - Shakhova, Ekaterina S. AU - Mitiouchkina, Tatiana AU - Belozerova, Olga A. AU - Kovalchuk, Sergey I. AU - Alekberova, Anna AU - Malyshevskaia, Alena K. AU - Bugaeva, Evgenia N. AU - Guglya, Elena B. AU - Balakireva, Anastasia AU - Sytov, Nikita AU - Bezlikhotnova, Anastasia AU - Boldyreva, Daria I. AU - Babenko, Vladislav V. AU - Kondrashov, Fyodor AU - Choob, Vladimir V. AU - Orzaez, Diego AU - Yampolsky, Ilia V. AU - Mishin, Alexander S. AU - Sarkisyan, Karen S. ID - 15179 IS - 10 JF - Science Advances SN - 2375-2548 TI - A hybrid pathway for self-sustained luminescence VL - 10 ER - TY - JOUR AB - The elimination of rain evaporation in the planetary boundary layer (PBL) has been found to lead to convective self‐aggregation (CSA) even without radiative feedback, but the precise mechanisms underlying this phenomenon remain unclear. We conducted cloud‐resolving simulations with two domain sizes and progressively reduced rain evaporation in the PBL. Surprisingly, CSA only occurred when rain evaporation was almost completely removed. The additional convective heating resulting from the reduction of evaporative cooling in the moist patch was found to be the trigger, thereafter a dry subsidence intrusion into the PBL in the dry patch takes over and sets CSA in motion. Temperature and moisture anomalies oppose each other in their buoyancy effects, hence explaining the need for almost total rain evaporation removal. We also found radiative cooling and not cold pools to be the leading cause for the comparative ease of CSA to take place in the larger domain. AU - Hwong, Yi-Ling AU - Muller, Caroline J ID - 15186 IS - 6 JF - Geophysical Research Letters KW - General Earth and Planetary Sciences KW - Geophysics SN - 0094-8276 TI - The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation VL - 51 ER - TY - JOUR AB - We demonstrate the failure of the adiabatic Born-Oppenheimer approximation to describe the ground state of a quantum impurity within an ultracold Fermi gas despite substantial mass differences between the bath and impurity species. Increasing repulsion leads to the appearance of nonadiabatic couplings between the fast bath and slow impurity degrees of freedom, which reduce the parity symmetry of the latter according to the pseudo Jahn-Teller effect. The presence of this mechanism is associated to a conical intersection involving the impurity position and the inverse of the interaction strength, which acts as a synthetic dimension. We elucidate the presence of these effects via a detailed ground-state analysis involving the comparison of ab initio fully correlated simulations with effective models. Our study suggests ultracold atomic ensembles as potent emulators of complex molecular phenomena. AU - Becker, A. AU - Koutentakis, Georgios AU - Schmelcher, P. ID - 15181 IS - 1 JF - Physical Review Research SN - 2643-1564 TI - Synthetic dimension-induced pseudo Jahn-Teller effect in one-dimensional confined fermions VL - 6 ER - TY - JOUR AB - Thermoelectric materials convert heat into electricity, with a broad range of applications near room temperature (RT). However, the library of RT high-performance materials is limited. Traditional high-temperature synthetic methods constrain the range of materials achievable, hindering the ability to surpass crystal structure limitations and engineer defects. Here, a solution-based synthetic approach is introduced, enabling RT synthesis of powders and exploration of densification at lower temperatures to influence the material's microstructure. The approach is exemplified by Ag2Se, an n-type alternative to bismuth telluride. It is demonstrated that the concentration of Ag interstitials, grain boundaries, and dislocations are directly correlated to the sintering temperature, and achieve a figure of merit of 1.1 from RT to 100 °C after optimization. Moreover, insights into and resolve Ag2Se's challenges are provided, including stoichiometry issues leading to irreproducible performances. This work highlights the potential of RT solution synthesis in expanding the repertoire of high-performance thermoelectric materials for practical applications. AU - Kleinhanns, Tobias AU - Milillo, Francesco AU - Calcabrini, Mariano AU - Fiedler, Christine AU - Horta, Sharona AU - Balazs, Daniel AU - Strumolo, Marissa J. AU - Hasler, Roger AU - Llorca, Jordi AU - Tkadletz, Michael AU - Brutchey, Richard L. AU - Ibáñez, Maria ID - 15182 JF - Advanced Energy Materials SN - 1614-6832 TI - A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se ER - TY - JOUR AB - Current knowledge suggests a drought Indian monsoon (perhaps a severe one) when the El Nino Southern Oscillation and Pacific Decadal Oscillation each exhibit positive phases (a joint positive phase). For the monsoons, which are exceptions in this regard, we found northeast India often gets excess pre-monsoon rainfall. Further investigation reveals that this excess pre-monsoon rainfall is produced by the interaction of the large-scale circulation associated with the joint phase with the mountains in northeast India. We posit that a warmer troposphere, a consequence of excess rainfall over northeast India, drives a stronger monsoon circulation and enhances monsoon rainfall over central India. Hence, we argue that pre-monsoon rainfall over northeast India can be used for seasonal monsoon rainfall prediction over central India. Most importantly, its predictive value is at its peak when the Pacific Ocean exhibits a joint positive phase and the threat of extreme drought monsoon looms over India. AU - Goswami, Bidyut B ID - 15165 IS - 5 JF - Geophysical Research Letters SN - 0094-8276 TI - A pre-monsoon signal of false alarms of Indian monsoon droughts VL - 51 ER - TY - JOUR AB - Reducing defects boosts room-temperature performance of a thermoelectric device AU - Navita, Navita AU - Ibáñez, Maria ID - 15166 IS - 6688 JF - Science SN - 0036-8075 TI - Electron highways are cooler VL - 383 ER - TY - JOUR AB - The extracellular matrix (ECM) serves as a scaffold for cells and plays an essential role in regulating numerous cellular processes, including cell migration and proliferation. Due to limitations in specimen preparation for conventional room-temperature electron microscopy, we lack structural knowledge on how ECM components are secreted, remodeled, and interact with surrounding cells. We have developed a 3D-ECM platform compatible with sample thinning by cryo-focused ion beam milling, the lift-out extraction procedure, and cryo-electron tomography. Our workflow implements cell-derived matrices (CDMs) grown on EM grids, resulting in a versatile tool closely mimicking ECM environments. This allows us to visualize ECM for the first time in its hydrated, native context. Our data reveal an intricate network of extracellular fibers, their positioning relative to matrix-secreting cells, and previously unresolved structural entities. Our workflow and results add to the structural atlas of the ECM, providing novel insights into its secretion and assembly. AU - Zens, Bettina AU - Fäßler, Florian AU - Hansen, Jesse AU - Hauschild, Robert AU - Datler, Julia AU - Hodirnau, Victor-Valentin AU - Zheden, Vanessa AU - Alanko, Jonna H AU - Sixt, Michael K AU - Schur, Florian KM ID - 15146 IS - 6 JF - Journal of Cell Biology SN - 0021-9525 TI - Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix VL - 223 ER - TY - JOUR AB - We prove an upper bound on the ground state energy of the dilute spin-polarized Fermi gas capturing the leading correction to the kinetic energy resulting from repulsive interactions. One of the main ingredients in the proof is a rigorous implementation of the fermionic cluster expansion of Gaudin et al. (1971) [15]. AU - Lauritsen, Asbjørn Bækgaard AU - Seiringer, Robert ID - 14931 IS - 7 JF - Journal of Functional Analysis SN - 0022-1236 TI - Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion VL - 286 ER - TY - CHAP AB - The mammary gland consists of a bilayered epithelial structure with an extensively branched morphology. The majority of this epithelial tree is laid down during puberty, during which actively proliferating terminal end buds repeatedly elongate and bifurcate to form the basic structure of the ductal tree. Mammary ducts consist of a basal and luminal cell layer with a multitude of identified sub-lineages within both layers. The understanding of how these different cell lineages are cooperatively driving branching morphogenesis is a problem of crossing multiple scales, as this requires information on the macroscopic branched structure of the gland, as well as data on single-cell dynamics driving the morphogenic program. Here we describe a method to combine genetic lineage tracing with whole-gland branching analysis. Quantitative data on the global organ structure can be used to derive a model for mammary gland branching morphogenesis and provide a backbone on which the dynamics of individual cell lineages can be simulated and compared to lineage-tracing approaches. Eventually, these quantitative models and experiments allow to understand the couplings between the macroscopic shape of the mammary gland and the underlying single-cell dynamics driving branching morphogenesis. AU - Hannezo, Edouard B AU - Scheele, Colinda L.G.J. ED - Margadant, Coert ID - 12428 SN - 9781071628867 T2 - Cell Migration in Three Dimensions TI - A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland VL - 2608 ER - TY - JOUR AB - Brownian motion of a mobile impurity in a bath is affected by spin-orbit coupling (SOC). Here, we discuss a Caldeira-Leggett-type model that can be used to propose and interpret quantum simulators of this problem in cold Bose gases. First, we derive a master equation that describes the model and explore it in a one-dimensional (1D) setting. To validate the standard assumptions needed for our derivation, we analyze available experimental data without SOC; as a byproduct, this analysis suggests that the quench dynamics of the impurity is beyond the 1D Bose-polaron approach at temperatures currently accessible in a cold-atom laboratory—motion of the impurity is mainly driven by dissipation. For systems with SOC, we demonstrate that 1D spin-orbit coupling can be gauged out even in the presence of dissipation—the information about SOC is incorporated in the initial conditions. Observables sensitive to this information (such as spin densities) can be used to study formation of steady spin polarization domains during quench dynamics. AU - Ghazaryan, Areg AU - Cappellaro, Alberto AU - Lemeshko, Mikhail AU - Volosniev, Artem ID - 12534 IS - 1 JF - Physical Review Research SN - 2643-1564 TI - Dissipative dynamics of an impurity with spin-orbit coupling VL - 5 ER - TY - JOUR AB - Post-translational histone modifications modulate chromatin activity to affect gene expression. How chromatin states underlie lineage choice in single cells is relatively unexplored. We develop sort-assisted single-cell chromatin immunocleavage (sortChIC) and map active (H3K4me1 and H3K4me3) and repressive (H3K27me3 and H3K9me3) histone modifications in the mouse bone marrow. During differentiation, hematopoietic stem and progenitor cells (HSPCs) acquire active chromatin states mediated by cell-type-specifying transcription factors, which are unique for each lineage. By contrast, most alterations in repressive marks during differentiation occur independent of the final cell type. Chromatin trajectory analysis shows that lineage choice at the chromatin level occurs at the progenitor stage. Joint profiling of H3K4me1 and H3K9me3 demonstrates that cell types within the myeloid lineage have distinct active chromatin but share similar myeloid-specific heterochromatin states. This implies a hierarchical regulation of chromatin during hematopoiesis: heterochromatin dynamics distinguish differentiation trajectories and lineages, while euchromatin dynamics reflect cell types within lineages. AU - Zeller, Peter AU - Yeung, Jake AU - Viñas Gaza, Helena AU - de Barbanson, Buys Anton AU - Bhardwaj, Vivek AU - Florescu, Maria AU - van der Linden, Reinier AU - van Oudenaarden, Alexander ID - 12158 JF - Nature Genetics KW - Genetics SN - 1061-4036 TI - Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis VL - 55 ER - TY - CONF AB - Turn-based stochastic games (aka simple stochastic games) are two-player zero-sum games played on directed graphs with probabilistic transitions. The goal of player-max is to maximize the probability to reach a target state against the adversarial player-min. These games lie in NP ∩ coNP and are among the rare combinatorial problems that belong to this complexity class for which the existence of polynomial-time algorithm is a major open question. While randomized sub-exponential time algorithm exists, all known deterministic algorithms require exponential time in the worst-case. An important open question has been whether faster algorithms can be obtained parametrized by the treewidth of the game graph. Even deterministic sub-exponential time algorithm for constant treewidth turn-based stochastic games has remain elusive. In this work our main result is a deterministic algorithm to solve turn-based stochastic games that, given a game with n states, treewidth at most t, and the bit-complexity of the probabilistic transition function log D, has running time O ((tn2 log D)t log n). In particular, our algorithm is quasi-polynomial time for games with constant or poly-logarithmic treewidth. AU - Chatterjee, Krishnendu AU - Meggendorfer, Tobias AU - Saona Urmeneta, Raimundo J AU - Svoboda, Jakub ID - 12676 SN - 9781611977554 T2 - Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms TI - Faster algorithm for turn-based stochastic games with bounded treewidth ER -