@article{14843, abstract = {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.}, author = {Chen, JingJing and Kaufmann, Walter and Chen, Chong and Arai, Itaru and Kim, Olena and Shigemoto, Ryuichi and Jonas, Peter M}, issn = {1097-4199}, journal = {Neuron}, publisher = {Elsevier}, title = {{Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse}}, doi = {10.1016/j.neuron.2023.12.002}, year = {2024}, } @phdthesis{15101, author = {Chen, JingJing}, issn = {2663 - 337X}, pages = {84}, publisher = {Institute of Science and Technology Austria}, title = {{Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse}}, doi = {10.15479/at:ista:15101}, year = {2024}, } @article{15122, abstract = {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.}, author = {Sack, Stefan and Egger, Daniel J.}, issn = {2643-1564}, journal = {Physical Review Research}, number = {1}, publisher = {American Physical Society}, title = {{Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation}}, doi = {10.1103/PhysRevResearch.6.013223}, volume = {6}, year = {2024}, } @article{15118, abstract = {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.}, author = {Nußbaum, Phillip and Kureisaite-Ciziene, Danguole and Bellini, Dom and Van Der Does, Chris and Kojic, Marko and Taib, Najwa and Yeates, Anna and Tourte, Maxime and Gribaldo, Simonetta and Loose, Martin and Löwe, Jan and Albers, Sonja Verena}, issn = {2058-5276}, journal = {Nature Microbiology}, number = {3}, pages = {698--711}, publisher = {Springer Nature}, title = {{Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division}}, doi = {10.1038/s41564-024-01600-5}, volume = {9}, year = {2024}, } @article{15119, abstract = {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.}, author = {Agresti, Antonio and Veraar, Mark}, issn = {0246-0203}, journal = {Annales de l'institut Henri Poincare Probability and Statistics}, number = {1}, pages = {413--430}, publisher = {Institute of Mathematical Statistics}, title = {{Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions}}, doi = {10.1214/22-AIHP1333}, volume = {60}, year = {2024}, } @article{14478, abstract = {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.}, author = {Habig, Michael and Grasse, Anna V and Müller, Judith and Stukenbrock, Eva H. and Leitner, Hanna and Cremer, Sylvia}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {11}, publisher = {Proceedings of the National Academy of Sciences}, title = {{Frequent horizontal chromosome transfer between asexual fungal insect pathogens}}, doi = {10.1073/pnas.2316284121}, volume = {121}, year = {2024}, } @article{10045, abstract = {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. }, author = {Dvorak, Martin and Kolmogorov, Vladimir}, issn = {1436-4646}, journal = {Mathematical Programming}, keywords = {minimum 0-extension problem, metric labeling problem, discrete metric spaces, metric extensions, computational complexity, valued constraint satisfaction problems, discrete convex analysis, L-convex functions}, publisher = {Springer Nature}, title = {{Generalized minimum 0-extension problem and discrete convexity}}, doi = {10.1007/s10107-024-02064-5}, year = {2024}, } @article{15121, abstract = {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.}, author = {Zheng, Da Wei and Henzinger, Monika H}, issn = {1436-4646}, journal = {Mathematical Programming}, publisher = {Springer Nature}, title = {{Multiplicative auction algorithm for approximate maximum weight bipartite matching}}, doi = {10.1007/s10107-024-02066-3}, year = {2024}, } @article{15114, abstract = {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.}, author = {Yao, Zihao and Liu, Xu and Bunting, Rhys and Wang, Jianguo}, issn = {0009-2509}, journal = {Chemical Engineering Science}, publisher = {Elsevier}, title = {{Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling}}, doi = {10.1016/j.ces.2024.119959}, volume = {291}, year = {2024}, } @article{15116, abstract = {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.}, author = {Giubertoni, Giulia and Feng, Liru and Klein, Kevin and Giannetti, Guido and Rutten, Luco and Choi, Yeji and Van Der Net, Anouk and Castro-Linares, Gerard and Caporaletti, Federico and Micha, Dimitra and Hunger, Johannes and Deblais, Antoine and Bonn, Daniel and Sommerdijk, Nico and Šarić, Anđela and Ilie, Ioana M. and Koenderink, Gijsje H. and Woutersen, Sander}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {11}, publisher = {Proceedings of the National Academy of Sciences}, title = {{Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration}}, doi = {10.1073/pnas.2313162121}, volume = {121}, year = {2024}, } @misc{15126, abstract = {This zip file contains data, and analysis for the paper "Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration".}, author = {Giubertoni, G. and Woutersen, S.}, publisher = {Figshare}, title = {{Dataset Collagen Self Assembly in H2O and D2O}}, doi = {10.21942/UVA.24829896}, year = {2024}, } @article{15117, abstract = {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.}, author = {Vandael, David H and Jonas, Peter M}, issn = {1095-9203}, journal = {Science}, number = {6687}, pages = {eadg6757}, publisher = {AAAS}, title = {{Structure, biophysics, and circuit function of a "giant" cortical presynaptic terminal}}, doi = {10.1126/science.adg6757}, volume = {383}, year = {2024}, } @phdthesis{15094, abstract = {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. }, author = {Cultrera di Montesano, Sebastiano}, issn = {2663 - 337X}, pages = {108}, publisher = {Institute of Science and Technology Austria}, title = {{Persistence and Morse theory for discrete geometric structures}}, doi = {10.15479/at:ista:15094}, year = {2024}, } @inproceedings{15093, abstract = {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.}, author = {Cultrera di Montesano, Sebastiano and Edelsbrunner, Herbert and Henzinger, Monika H and Ost, Lara}, booktitle = {Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA)}, editor = {Woodruff, David P.}, location = {Alexandria, VA, USA}, pages = {243 -- 295}, publisher = {Society for Industrial and Applied Mathematics}, title = {{Dynamically maintaining the persistent homology of time series}}, doi = {10.1137/1.9781611977912.11}, year = {2024}, } @unpublished{15091, abstract = {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.}, author = {Cultrera di Montesano, Sebastiano and Draganov, Ondrej and Edelsbrunner, Herbert and Saghafian, Morteza}, booktitle = {arXiv}, title = {{Chromatic alpha complexes}}, year = {2024}, } @article{15171, abstract = {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.}, author = {Agnes, Everton J. and Vogels, Tim P}, issn = {1546-1726}, journal = {Nature Neuroscience}, publisher = {Springer Nature}, title = {{Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks}}, doi = {10.1038/s41593-024-01597-4}, year = {2024}, } @article{15172, abstract = {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.}, author = {Esposito, Amedeo Roberto and Mondelli, Marco}, issn = {1557-9654}, journal = {IEEE Transactions on Information Theory}, publisher = {IEEE}, title = {{Concentration without independence via information measures}}, doi = {10.1109/TIT.2024.3367767}, year = {2024}, } @article{15170, abstract = {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.}, author = {Greene, Jenny E. and Labbe, Ivo and Goulding, Andy D. and Furtak, Lukas J. and Chemerynska, Iryna and Kokorev, Vasily and Dayal, Pratika and Volonteri, Marta and Williams, Christina C. and Wang, Bingjie and Setton, David J. and Burgasser, Adam J. and Bezanson, Rachel and Atek, Hakim and Brammer, Gabriel and Cutler, Sam E. and Feldmann, Robert and Fujimoto, Seiji and Glazebrook, Karl and De Graaff, Anna and Khullar, Gourav and Leja, Joel and Marchesini, Danilo and Maseda, Michael V. and Matthee, Jorryt J and Miller, Tim B. and Naidu, Rohan P. and Nanayakkara, Themiya and Oesch, Pascal A. and Pan, Richard and Papovich, Casey and Price, Sedona H. and Van Dokkum, Pieter and Weaver, John R. and Whitaker, Katherine E. and Zitrin, Adi}, issn = {1538-4357}, journal = {Astrophysical Journal}, publisher = {IOP Publishing}, title = {{UNCOVER spectroscopy confirms the surprising ubiquity of active galactic nuclei in red sources at z > 5}}, doi = {10.3847/1538-4357/ad1e5f}, volume = {964}, year = {2024}, } @inproceedings{15168, abstract = {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).}, author = {Filakovský, Marek and Nakajima, Tamio Vesa and Opršal, Jakub and Tasinato, Gianluca and Wagner, Uli}, booktitle = {41st International Symposium on Theoretical Aspects of Computer Science}, isbn = {9783959773119}, issn = {1868-8969}, location = {Clermont-Ferrand, France}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs}}, doi = {10.4230/LIPIcs.STACS.2024.34}, volume = {289}, year = {2024}, } @article{15164, abstract = {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.}, author = {Silva-Henao, Juan D. and Schober, Sophie and Pahr, Dieter H. and Reisinger, Andreas G.}, issn = {1873-4030}, journal = {Medical Engineering and Physics}, publisher = {Elsevier}, title = {{Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading}}, doi = {10.1016/j.medengphy.2024.104143}, volume = {126}, year = {2024}, } @article{15169, abstract = {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.}, author = {Chintaluri, Chaitanya and Bejtka, Marta and Sredniawa, Wladyslaw and Czerwinski, Michal and Dzik, Jakub M. and Jedrzejewska-Szmek, Joanna and Wojciki, Daniel K.}, issn = {1553-7358}, journal = {PLoS Computational Biology}, number = {3}, publisher = {Public Library of Science}, title = {{kCSD-python, reliable current source density estimation with quality control}}, doi = {10.1371/journal.pcbi.1011941}, volume = {20}, year = {2024}, } @article{15167, abstract = {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.}, author = {Al Hyder, Ragheed and Chevy, F. and Leyronas, X.}, issn = {2469-9934}, journal = {Physical Review A}, number = {3}, publisher = {American Physical Society}, title = {{Exploring beyond-mean-field logarithmic divergences in Fermi-polaron energy}}, doi = {10.1103/PhysRevA.109.033315}, volume = {109}, year = {2024}, } @article{15163, abstract = {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.}, author = {Campbell, Rutger and Hörsch, Florian and Moore, Benjamin}, issn = {0012-365X}, journal = {Discrete Mathematics}, number = {6}, publisher = {Elsevier}, title = {{Decompositions into two linear forests of bounded lengths}}, doi = {10.1016/j.disc.2024.113962}, volume = {347}, year = {2024}, } @article{15180, abstract = {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.}, author = {Matthee, Jorryt J and Naidu, Rohan P. and Brammer, Gabriel and Chisholm, John and Eilers, Anna-Christina and Goulding, Andy and Greene, Jenny and Kashino, Daichi and Labbe, Ivo and Lilly, Simon J. and Mackenzie, Ruari and Oesch, Pascal A. and Weibel, Andrea and Wuyts, Stijn and Xiao, Mengyuan and Bordoloi, Rongmon and Bouwens, Rychard and van Dokkum, Pieter and Illingworth, Garth and Kramarenko, Ivan and Maseda, Michael V. and Mason, Charlotte and Meyer, Romain A. and Nelson, Erica J. and Reddy, Naveen A. and Shivaei, Irene and Simcoe, Robert A. and Yue, Minghao}, issn = {1538-4357}, journal = {The Astrophysical Journal}, keywords = {Space and Planetary Science, Astronomy and Astrophysics}, number = {2}, publisher = {American Astronomical Society}, title = {{Little Red Dots: An abundant population of faint active galactic nuclei at z ∼ 5 revealed by the EIGER and FRESCO JWST surveys}}, doi = {10.3847/1538-4357/ad2345}, volume = {963}, year = {2024}, } @article{15179, abstract = {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.}, author = {Palkina, Kseniia A. and Karataeva, Tatiana A. and Perfilov, Maxim M. and Fakhranurova, Liliia I. and Markina, Nadezhda M. and Gonzalez Somermeyer, Louisa and Garcia-Perez, Elena and Vazquez-Vilar, Marta and Rodriguez-Rodriguez, Marta and Vazquez-Vilriales, Victor and Shakhova, Ekaterina S. and Mitiouchkina, Tatiana and Belozerova, Olga A. and Kovalchuk, Sergey I. and Alekberova, Anna and Malyshevskaia, Alena K. and Bugaeva, Evgenia N. and Guglya, Elena B. and Balakireva, Anastasia and Sytov, Nikita and Bezlikhotnova, Anastasia and Boldyreva, Daria I. and Babenko, Vladislav V. and Kondrashov, Fyodor and Choob, Vladimir V. and Orzaez, Diego and Yampolsky, Ilia V. and Mishin, Alexander S. and Sarkisyan, Karen S.}, issn = {2375-2548}, journal = {Science Advances}, number = {10}, publisher = {American Association for the Advancement of Science}, title = {{A hybrid pathway for self-sustained luminescence}}, doi = {10.1126/sciadv.adk1992}, volume = {10}, year = {2024}, } @article{15186, abstract = {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.}, author = {Hwong, Yi-Ling and Muller, Caroline J}, issn = {1944-8007}, journal = {Geophysical Research Letters}, keywords = {General Earth and Planetary Sciences, Geophysics}, number = {6}, publisher = {American Geophysical Union}, title = {{The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation}}, doi = {10.1029/2023gl106523}, volume = {51}, year = {2024}, } @article{15181, abstract = {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.}, author = {Becker, A. and Koutentakis, Georgios and Schmelcher, P.}, issn = {2643-1564}, journal = {Physical Review Research}, number = {1}, publisher = {American Physical Society}, title = {{Synthetic dimension-induced pseudo Jahn-Teller effect in one-dimensional confined fermions}}, doi = {10.1103/physrevresearch.6.013257}, volume = {6}, year = {2024}, } @article{15182, abstract = {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.}, author = {Kleinhanns, Tobias and Milillo, Francesco and Calcabrini, Mariano and Fiedler, Christine and Horta, Sharona and Balazs, Daniel and Strumolo, Marissa J. and Hasler, Roger and Llorca, Jordi and Tkadletz, Michael and Brutchey, Richard L. and Ibáñez, Maria}, issn = {1614-6840}, journal = {Advanced Energy Materials}, publisher = {Wiley}, title = {{A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se}}, doi = {10.1002/aenm.202400408}, year = {2024}, } @article{15165, abstract = {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.}, author = {Goswami, Bidyut B}, issn = {1944-8007}, journal = {Geophysical Research Letters}, number = {5}, publisher = {Wiley}, title = {{A pre-monsoon signal of false alarms of Indian monsoon droughts}}, doi = {10.1029/2023GL106569}, volume = {51}, year = {2024}, } @article{15166, abstract = {Reducing defects boosts room-temperature performance of a thermoelectric device}, author = {Navita, Navita and Ibáñez, Maria}, issn = {1095-9203}, journal = {Science}, number = {6688}, pages = {1184}, publisher = {American Association for the Advancement of Science}, title = {{Electron highways are cooler}}, doi = {10.1126/science.ado4077}, volume = {383}, year = {2024}, } @article{15146, abstract = {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.}, author = {Zens, Bettina and Fäßler, Florian and Hansen, Jesse and Hauschild, Robert and Datler, Julia and Hodirnau, Victor-Valentin and Zheden, Vanessa and Alanko, Jonna H and Sixt, Michael K and Schur, Florian KM}, issn = {1540-8140}, journal = {Journal of Cell Biology}, number = {6}, publisher = {Rockefeller University Press}, title = {{Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix}}, doi = {10.1083/jcb.202309125}, volume = {223}, year = {2024}, } @article{14931, abstract = {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].}, author = {Lauritsen, Asbjørn Bækgaard and Seiringer, Robert}, issn = {1096--0783}, journal = {Journal of Functional Analysis}, number = {7}, publisher = {Elsevier}, title = {{Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion}}, doi = {10.1016/j.jfa.2024.110320}, volume = {286}, year = {2024}, } @inbook{12428, abstract = {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.}, author = {Hannezo, Edouard B and Scheele, Colinda L.G.J.}, booktitle = {Cell Migration in Three Dimensions}, editor = {Margadant, Coert}, isbn = {9781071628867}, issn = {1940-6029}, pages = {183--205}, publisher = {Springer Nature}, title = {{A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland}}, doi = {10.1007/978-1-0716-2887-4_12}, volume = {2608}, year = {2023}, } @article{12534, abstract = {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.}, author = {Ghazaryan, Areg and Cappellaro, Alberto and Lemeshko, Mikhail and Volosniev, Artem}, issn = {2643-1564}, journal = {Physical Review Research}, number = {1}, publisher = {American Physical Society}, title = {{Dissipative dynamics of an impurity with spin-orbit coupling}}, doi = {10.1103/physrevresearch.5.013029}, volume = {5}, year = {2023}, } @article{12158, abstract = {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.}, author = {Zeller, Peter and Yeung, Jake and Viñas Gaza, Helena and de Barbanson, Buys Anton and Bhardwaj, Vivek and Florescu, Maria and van der Linden, Reinier and van Oudenaarden, Alexander}, issn = {1546-1718}, journal = {Nature Genetics}, keywords = {Genetics}, pages = {333--345}, publisher = {Springer Nature}, title = {{Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis}}, doi = {10.1038/s41588-022-01260-3}, volume = {55}, year = {2023}, } @inproceedings{12676, abstract = {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.}, author = {Chatterjee, Krishnendu and Meggendorfer, Tobias and Saona Urmeneta, Raimundo J and Svoboda, Jakub}, booktitle = {Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms}, isbn = {9781611977554}, location = {Florence, Italy}, pages = {4590--4605}, publisher = {Society for Industrial and Applied Mathematics}, title = {{Faster algorithm for turn-based stochastic games with bounded treewidth}}, doi = {10.1137/1.9781611977554.ch173}, year = {2023}, } @inbook{12720, abstract = {Here we describe the in vivo DNA assembly approach, where molecular cloning procedures are performed using an E. coli recA-independent recombination pathway, which assembles linear fragments of DNA with short homologous termini. This pathway is present in all standard laboratory E. coli strains and, by bypassing the need for in vitro DNA assembly, allows simplified molecular cloning to be performed without the plasmid instability issues associated with specialized recombination-cloning bacterial strains. The methodology requires specific primer design and can perform all standard plasmid modifications (insertions, deletions, mutagenesis, and sub-cloning) in a rapid, simple, and cost-efficient manner, as it does not require commercial kits or specialized bacterial strains. Additionally, this approach can be used to perform complex procedures such as multiple modifications to a plasmid, as up to 6 linear fragments can be assembled in vivo by this recombination pathway. Procedures generally require less than 3 h, involving PCR amplification, DpnI digestion of template DNA, and transformation, upon which circular plasmids are assembled. In this chapter we describe the requirements, procedure, and potential pitfalls when using this technique, as well as protocol variations to overcome the most common issues.}, author = {Arroyo-Urea, Sandra and Watson, Jake and García-Nafría, Javier}, booktitle = {DNA Manipulation and Analysis}, editor = {Scarlett, Garry}, isbn = {978-1-0716-3003-7}, issn = {1940-6029}, pages = {33--44}, publisher = {Springer Nature}, title = {{Molecular Cloning Using In Vivo DNA Assembly}}, doi = {10.1007/978-1-0716-3004-4_3}, volume = {2633}, year = {2023}, } @inproceedings{12735, abstract = {Asynchronous programming has gained significant popularity over the last decade: support for this programming pattern is available in many popular languages via libraries and native language implementations, typically in the form of coroutines or the async/await construct. Instead of programming via shared memory, this concept assumes implicit synchronization through message passing. The key data structure enabling such communication is the rendezvous channel. Roughly, a rendezvous channel is a blocking queue of size zero, so both send(e) and receive() operations wait for each other, performing a rendezvous when they meet. To optimize the message passing pattern, channels are usually equipped with a fixed-size buffer, so sends do not suspend and put elements into the buffer until its capacity is exceeded. This primitive is known as a buffered channel. This paper presents a fast and scalable algorithm for both rendezvous and buffered channels. Similarly to modern queues, our solution is based on an infinite array with two positional counters for send(e) and receive() operations, leveraging the unconditional Fetch-And-Add instruction to update them. Yet, the algorithm requires non-trivial modifications of this classic pattern, in order to support the full channel semantics, such as buffering and cancellation of waiting requests. We compare the performance of our solution to that of the Kotlin implementation, as well as against other academic proposals, showing up to 9.8× speedup. To showcase its expressiveness and performance, we also integrated the proposed algorithm into the standard Kotlin Coroutines library, replacing the previous channel implementations.}, author = {Koval, Nikita and Alistarh, Dan-Adrian and Elizarov, Roman}, booktitle = {Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming}, isbn = {9798400700156}, location = {Montreal, QC, Canada}, pages = {107--118}, publisher = {Association for Computing Machinery}, title = {{Fast and scalable channels in Kotlin Coroutines}}, doi = {10.1145/3572848.3577481}, year = {2023}, } @misc{12736, abstract = {Although a wide variety of handcrafted concurrent data structures have been proposed, there is considerable interest in universal approaches (Universal Constructions or UCs) for building concurrent data structures. UCs (semi-)automatically convert a sequential data structure into a concurrent one. The simplest approach uses locks [3, 6] that protect a sequential data structure and allow only one process to access it at a time. However, the resulting data structure is blocking. Most work on UCs instead focuses on obtaining non-blocking progress guarantees such as obstruction-freedom, lock-freedom or wait-freedom. Many non-blocking UCs have appeared. Key examples include the seminal wait-free UC [2] by Herlihy, a NUMA-aware UC [10] by Yi et al., and an efficient UC for large objects [1] by Fatourou et al.}, author = {Aksenov, Vitaly and Brown, Trevor A and Fedorov, Alexander and Kokorin, Ilya}, booktitle = {Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming}, isbn = {9798400700156}, location = {Montreal, QB, Canada}, pages = {438--440}, publisher = {Association for Computing Machinery}, title = {{Unexpected scaling in path copying trees}}, doi = {10.1145/3572848.3577512}, year = {2023}, } @inproceedings{12760, abstract = {Dynamic programming (DP) is one of the fundamental paradigms in algorithm design. However, many DP algorithms have to fill in large DP tables, represented by two-dimensional arrays, which causes at least quadratic running times and space usages. This has led to the development of improved algorithms for special cases when the DPs satisfy additional properties like, e.g., the Monge property or total monotonicity. In this paper, we consider a new condition which assumes (among some other technical assumptions) that the rows of the DP table are monotone. Under this assumption, we introduce a novel data structure for computing (1 + ϵ)-approximate DP solutions in near-linear time and space in the static setting, and with polylogarithmic update times when the DP entries change dynamically. To the best of our knowledge, our new condition is incomparable to previous conditions and is the first which allows to derive dynamic algorithms based on existing DPs. Instead of using two-dimensional arrays to store the DP tables, we store the rows of the DP tables using monotone piecewise constant functions. This allows us to store length-n DP table rows with entries in [0, W] using only polylog(n, W) bits, and to perform operations, such as (min, +)-convolution or rounding, on these functions in polylogarithmic time. We further present several applications of our data structure. For bicriteria versions of k-balanced graph partitioning and simultaneous source location, we obtain the first dynamic algorithms with subpolynomial update times, as well as the first static algorithms using only near-linear time and space. Additionally, we obtain the currently fastest algorithm for fully dynamic knapsack.}, author = {Henzinger, Monika H and Neumann, Stefan and Räcke, Harald and Schmid, Stefan}, booktitle = {40th International Symposium on Theoretical Aspects of Computer Science}, isbn = {9783959772662}, issn = {1868-8969}, location = {Hamburg, Germany}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Dynamic maintenance of monotone dynamic programs and applications}}, doi = {10.4230/LIPIcs.STACS.2023.36}, volume = {254}, year = {2023}, } @phdthesis{12716, abstract = {The process of detecting and evaluating sensory information to guide behaviour is termed perceptual decision-making (PDM), and is critical for the ability of an organism to interact with its external world. Individuals with autism, a neurodevelopmental condition primarily characterised by social and communication difficulties, frequently exhibit altered sensory processing and PDM difficulties are widely reported. Recent technological advancements have pushed forward our understanding of the genetic changes accompanying this condition, however our understanding of how these mutations affect the function of specific neuronal circuits and bring about the corresponding behavioural changes remains limited. Here, we use an innate PDM task, the looming avoidance response (LAR) paradigm, to identify a convergent behavioural abnormality across three molecularly distinct genetic mouse models of autism (Cul3, Setd5 and Ptchd1). Although mutant mice can rapidly detect threatening visual stimuli, their responses are consistently delayed, requiring longer to initiate an appropriate response than their wild-type siblings. Mutant animals show abnormal adaptation in both their stimulus- evoked escape responses and exploratory dynamics following repeated stimulus presentations. Similarly delayed behavioural responses are observed in wild-type animals when faced with more ambiguous threats, suggesting the mutant phenotype could arise from a dysfunction in the flexible control of this PDM process. Our knowledge of the core neuronal circuitry mediating the LAR facilitated a detailed dissection of the neuronal mechanisms underlying the behavioural impairment. In vivo extracellular recording revealed that visual responses were unaffected within a key brain region for the rapid processing of visual threats, the superior colliculus (SC), indicating that the behavioural delay was unlikely to originate from sensory impairments. Delayed behavioural responses were recapitulated in the Setd5 model following optogenetic stimulation of the excitatory output neurons of the SC, which are known to mediate escape initiation through the activation of cells in the underlying dorsal periaqueductal grey (dPAG). In vitro patch-clamp recordings of dPAG cells uncovered a stark hypoexcitability phenotype in two out of the three genetic models investigated (Setd5 and Ptchd1), that in Setd5, is mediated by the misregulation of voltage-gated potassium channels. Overall, our results show that the ability to use visual information to drive efficient escape responses is impaired in three diverse genetic mouse models of autism and that, in one of the models studied, this behavioural delay likely originates from differences in the intrinsic excitability of a key subcortical node, the dPAG. Furthermore, this work showcases the use of an innate behavioural paradigm to mechanistically dissect PDM processes in autism.}, author = {Burnett, Laura}, issn = {2663-337X}, pages = {178}, publisher = {Institute of Science and Technology Austria}, title = {{To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism}}, doi = {10.15479/at:ista:12716}, year = {2023}, } @inproceedings{12854, abstract = {The main idea behind BUBAAK is to run multiple program analyses in parallel and use runtime monitoring and enforcement to observe and control their progress in real time. The analyses send information about (un)explored states of the program and discovered invariants to a monitor. The monitor processes the received data and can force an analysis to stop the search of certain program parts (which have already been analyzed by other analyses), or to make it utilize a program invariant found by another analysis. At SV-COMP 2023, the implementation of data exchange between the monitor and the analyses was not yet completed, which is why BUBAAK only ran several analyses in parallel, without any coordination. Still, BUBAAK won the meta-category FalsificationOverall and placed very well in several other (sub)-categories of the competition.}, author = {Chalupa, Marek and Henzinger, Thomas A}, booktitle = {Tools and Algorithms for the Construction and Analysis of Systems}, isbn = {9783031308192}, issn = {1611-3349}, location = {Paris, France}, pages = {535--540}, publisher = {Springer Nature}, title = {{Bubaak: Runtime monitoring of program verifiers}}, doi = {10.1007/978-3-031-30820-8_32}, volume = {13994}, year = {2023}, } @unpublished{12846, abstract = {We present a formula for the signed area of a spherical polygon via prequantization. In contrast to the traditional formula based on the Gauss-Bonnet theorem that requires measuring angles, the new formula mimics Green's theorem and is applicable to a wider range of degenerate spherical curves and polygons.}, author = {Chern, Albert and Ishida, Sadashige}, booktitle = {arXiv}, title = {{Area formula for spherical polygons via prequantization}}, doi = {10.48550/arXiv.2303.14555}, year = {2023}, } @inproceedings{12856, abstract = {As the complexity and criticality of software increase every year, so does the importance of run-time monitoring. Third-party monitoring, with limited knowledge of the monitored software, and best-effort monitoring, which keeps pace with the monitored software, are especially valuable, yet underexplored areas of run-time monitoring. Most existing monitoring frameworks do not support their combination because they either require access to the monitored code for instrumentation purposes or the processing of all observed events, or both. We present a middleware framework, VAMOS, for the run-time monitoring of software which is explicitly designed to support third-party and best-effort scenarios. The design goals of VAMOS are (i) efficiency (keeping pace at low overhead), (ii) flexibility (the ability to monitor black-box code through a variety of different event channels, and the connectability to monitors written in different specification languages), and (iii) ease-of-use. To achieve its goals, VAMOS combines aspects of event broker and event recognition systems with aspects of stream processing systems. We implemented a prototype toolchain for VAMOS and conducted experiments including a case study of monitoring for data races. The results indicate that VAMOS enables writing useful yet efficient monitors, is compatible with a variety of event sources and monitor specifications, and simplifies key aspects of setting up a monitoring system from scratch.}, author = {Chalupa, Marek and Mühlböck, Fabian and Muroya Lei, Stefanie and Henzinger, Thomas A}, booktitle = {Fundamental Approaches to Software Engineering}, isbn = {9783031308253}, issn = {1611-3349}, location = {Paris, France}, pages = {260--281}, publisher = {Springer Nature}, title = {{Vamos: Middleware for best-effort third-party monitoring}}, doi = {10.1007/978-3-031-30826-0_15}, volume = {13991}, year = {2023}, } @misc{12407, abstract = {As the complexity and criticality of software increase every year, so does the importance of run-time monitoring. Third-party monitoring, with limited knowledge of the monitored software, and best-effort monitoring, which keeps pace with the monitored software, are especially valuable, yet underexplored areas of run-time monitoring. Most existing monitoring frameworks do not support their combination because they either require access to the monitored code for instrumentation purposes or the processing of all observed events, or both. We present a middleware framework, VAMOS, for the run-time monitoring of software which is explicitly designed to support third-party and best-effort scenarios. The design goals of VAMOS are (i) efficiency (keeping pace at low overhead), (ii) flexibility (the ability to monitor black-box code through a variety of different event channels, and the connectability to monitors written in different specification languages), and (iii) ease-of-use. To achieve its goals, VAMOS combines aspects of event broker and event recognition systems with aspects of stream processing systems. We implemented a prototype toolchain for VAMOS and conducted experiments including a case study of monitoring for data races. The results indicate that VAMOS enables writing useful yet efficient monitors, is compatible with a variety of event sources and monitor specifications, and simplifies key aspects of setting up a monitoring system from scratch.}, author = {Chalupa, Marek and Mühlböck, Fabian and Muroya Lei, Stefanie and Henzinger, Thomas A}, issn = {2664-1690}, keywords = {runtime monitoring, best effort, third party}, pages = {38}, publisher = {Institute of Science and Technology Austria}, title = {{VAMOS: Middleware for Best-Effort Third-Party Monitoring}}, doi = {10.15479/AT:ISTA:12407}, year = {2023}, } @inbook{12866, abstract = {Autism spectrum disorder (ASD) and epilepsy are frequently comorbid neurodevelopmental disorders. Extensive research has demonstrated shared pathological pathways, etiologies, and phenotypes. Many risk factors for these disorders, like genetic mutations and environmental pressures, are linked to changes in childhood brain development, which is a critical period for their manifestation. Decades of research have yielded many signatures for ASD and epilepsy, some shared and others unique or opposing. The anatomical, physiological, and behavioral correlates of these disorders are discussed in this chapter in the context of understanding shared pathological pathways. We end with important takeaways on the presentation, prevention, intervention, and policy changes for ASD and epilepsy. This chapter aims to explore the complexity of these disorders, both in etiology and phenotypes, with the further goal of appreciating the expanse of unknowns still to explore about the brain.}, author = {Currin, Christopher and Beyer, Chad}, booktitle = {Encyclopedia of Child and Adolescent Health}, editor = {Halpern-Felsher, Bonnie}, isbn = {9780128188736}, pages = {86--98}, publisher = {Elsevier}, title = {{Altered childhood brain development in autism and epilepsy}}, doi = {10.1016/b978-0-12-818872-9.00129-1}, year = {2023}, } @phdthesis{12809, abstract = {Understanding the mechanisms of learning and memory formation has always been one of the main goals in neuroscience. Already Pavlov (1927) in his early days has used his classic conditioning experiments to study the neural mechanisms governing behavioral adaptation. What was not known back then was that the part of the brain that is largely responsible for this type of associative learning is the cerebellum. Since then, plenty of theories on cerebellar learning have emerged. Despite their differences, one thing they all have in common is that learning relies on synaptic and intrinsic plasticity. The goal of my PhD project was to unravel the molecular mechanisms underlying synaptic plasticity in two synapses that have been shown to be implicated in motor learning, in an effort to understand how learning and memory formation are processed in the cerebellum. One of the earliest and most well-known cerebellar theories postulates that motor learning largely depends on long-term depression at the parallel fiber-Purkinje cell (PC-PC) synapse. However, the discovery of other types of plasticity in the cerebellar circuitry, like long-term potentiation (LTP) at the PC-PC synapse, potentiation of molecular layer interneurons (MLIs), and plasticity transfer from the cortex to the cerebellar/ vestibular nuclei has increased the popularity of the idea that multiple sites of plasticity might be involved in learning. Still a lot remains unknown about the molecular mechanisms responsible for these types of plasticity and whether they occur during physiological learning. In the first part of this thesis we have analyzed the variation and nanodistribution of voltagegated calcium channels (VGCCs) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid type glutamate receptors (AMPARs) on the parallel fiber-Purkinje cell synapse after vestibuloocular reflex phase reversal adaptation, a behavior that has been suggested to rely on PF-PC LTP. We have found that on the last day of adaptation there is no learning trace in form of VGCCs nor AMPARs variation at the PF-PC synapse, but instead a decrease in the number of PF-PC synapses. These data seem to support the view that learning is only stored in the cerebellar cortex in an initial learning phase, being transferred later to the vestibular nuclei. Next, we have studied the role of MLIs in motor learning using a relatively simple and well characterized behavioral paradigm – horizontal optokinetic reflex (HOKR) adaptation. We have found behavior-induced MLI potentiation in form of release probability increase that could be explained by the increase of VGCCs at the presynaptic side. Our results strengthen the idea of distributed cerebellar plasticity contributing to learning and provide a novel mechanism for release probability increase. }, author = {Alcarva, Catarina}, issn = {2663 - 337X}, pages = {115}, publisher = {Institute of Science and Technology Austria}, title = {{Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning}}, doi = {10.15479/at:ista:12809}, year = {2023}, } @article{12668, abstract = {Background: Plant and animal embryogenesis have conserved and distinct features. Cell fate transitions occur during embryogenesis in both plants and animals. The epigenomic processes regulating plant embryogenesis remain largely elusive. Results: Here, we elucidate chromatin and transcriptomic dynamics during embryogenesis of the most cultivated crop, hexaploid wheat. Time-series analysis reveals stage-specific and proximal–distal distinct chromatin accessibility and dynamics concordant with transcriptome changes. Following fertilization, the remodeling kinetics of H3K4me3, H3K27ac, and H3K27me3 differ from that in mammals, highlighting considerable species-specific epigenomic dynamics during zygotic genome activation. Polycomb repressive complex 2 (PRC2)-mediated H3K27me3 deposition is important for embryo establishment. Later H3K27ac, H3K27me3, and chromatin accessibility undergo dramatic remodeling to establish a permissive chromatin environment facilitating the access of transcription factors to cis-elements for fate patterning. Embryonic maturation is characterized by increasing H3K27me3 and decreasing chromatin accessibility, which likely participates in restricting totipotency while preventing extensive organogenesis. Finally, epigenomic signatures are correlated with biased expression among homeolog triads and divergent expression after polyploidization, revealing an epigenomic contributor to subgenome diversification in an allohexaploid genome. Conclusions: Collectively, we present an invaluable resource for comparative and mechanistic analysis of the epigenomic regulation of crop embryogenesis.}, author = {Zhao, Long and Yang, Yiman and Chen, Jinchao and Lin, Xuelei and Zhang, Hao and Wang, Hao and Wang, Hongzhe and Bie, Xiaomin and Jiang, Jiafu and Feng, Xiaoqi and Fu, Xiangdong and Zhang, Xiansheng and Du, Zhuo and Xiao, Jun}, issn = {1474-760X}, journal = {Genome Biology}, publisher = {Springer Nature}, title = {{Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat}}, doi = {10.1186/s13059-022-02844-2}, volume = {24}, year = {2023}, } @article{12920, abstract = {The multicomponent approach allows to incorporate several functionalities into a single covalent organic framework (COF) and consequently allows the construction of bifunctional materials for cooperative catalysis. The well-defined structure of such multicomponent COFs is furthermore ideally suited for structure-activity relationship studies. We report a series of multicomponent COFs that contain acridine- and 2,2’-bipyridine linkers connected through 1,3,5-benzenetrialdehyde derivatives. The acridine motif is responsible for broad light absorption, while the bipyridine unit enables complexation of nickel catalysts. These features enable the usage of the framework materials as catalysts for light-mediated carbon−heteroatom cross-couplings. Variation of the node units shows that the catalytic activity correlates to the keto-enamine tautomer isomerism. This allows switching between high charge-carrier mobility and persistent, localized charge-separated species depending on the nodes, a tool to tailor the materials for specific reactions. Moreover, nickel-loaded COFs are recyclable and catalyze cross-couplings even using red light irradiation.}, author = {Traxler, Michael and Reischauer, Susanne and Vogl, Sarah and Roeser, Jérôme and Rabeah, Jabor and Penschke, Christopher and Saalfrank, Peter and Pieber, Bartholomäus and Thomas, Arne}, issn = {1521-3765}, journal = {Chemistry – A European Journal}, keywords = {General Chemistry, Catalysis, Organic Chemistry}, number = {4}, publisher = {Wiley}, title = {{Programmable photocatalytic activity of multicomponent covalent organic frameworks used as metallaphotocatalysts}}, doi = {10.1002/chem.202202967}, volume = {29}, year = {2023}, } @article{12921, abstract = {Visible-light photocatalysis provides numerous useful methodologies for synthetic organic chemistry. However, the mechanisms of these reactions are often not fully understood. Common mechanistic experiments mainly aim to characterize excited state properties of photocatalysts and their interaction with other species. Recently, in situ reaction monitoring using dedicated techniques was shown to be well-suited for the identification of intermediates and to obtain kinetic insights, thereby providing more holistic pictures of the reactions of interest. This minireview surveys these technologies and discusses selected examples where reaction monitoring was used to elucidate the mechanism of photocatalytic reactions.}, author = {Madani, Amiera and Pieber, Bartholomäus}, issn = {1867-3899}, journal = {ChemCatChem}, keywords = {Inorganic Chemistry, Organic Chemistry, Physical and Theoretical Chemistry, Catalysis}, number = {7}, publisher = {Wiley}, title = {{In situ reaction monitoring in photocatalytic organic synthesis}}, doi = {10.1002/cctc.202201583}, volume = {15}, year = {2023}, }