@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}, } @article{12919, abstract = {We report the visible light photocatalytic cleavage of trityl thioethers or ethers under pH-neutral conditions. The method results in the formation of the respective symmetrical disulfides and alcohols in moderate to excellent yield. The protocol only requires the addition of a suitable photocatalyst and light rendering it orthogonal to several functionalities, including acid labile protective groups. The same conditions can be used to directly convert trityl-protected thiols into unsymmetrical disulfides or selenosulfides, and to cleave trityl resins in solid phase organic synthesis.}, author = {Murakami, Sho and Brudy, Cosima and Bachmann, Moritz and Takemoto, Yoshiji and Pieber, Bartholomäus}, issn = {1437-210X}, journal = {Synthesis}, keywords = {Organic Chemistry, Catalysis}, number = {09}, pages = {1367--1374}, publisher = {Georg Thieme Verlag}, title = {{Photocatalytic cleavage of trityl protected thiols and alcohols}}, doi = {10.1055/a-1979-5933}, volume = {55}, year = {2023}, } @inproceedings{13048, abstract = {In this paper we introduce a pruning of the medial axis called the (λ,α)-medial axis (axλα). We prove that the (λ,α)-medial axis of a set K is stable in a Gromov-Hausdorff sense under weak assumptions. More formally we prove that if K and K′ are close in the Hausdorff (dH) sense then the (λ,α)-medial axes of K and K′ are close as metric spaces, that is the Gromov-Hausdorff distance (dGH) between the two is 1/4-Hölder in the sense that dGH (axλα(K),axλα(K′)) ≲ dH(K,K′)1/4. The Hausdorff distance between the two medial axes is also bounded, by dH (axλα(K),λα(K′)) ≲ dH(K,K′)1/2. These quantified stability results provide guarantees for practical computations of medial axes from approximations. Moreover, they provide key ingredients for studying the computability of the medial axis in the context of computable analysis.}, author = {Lieutier, André and Wintraecken, Mathijs}, booktitle = {Proceedings of the 55th Annual ACM Symposium on Theory of Computing}, isbn = {9781450399135}, location = {Orlando, FL, United States}, pages = {1768--1776}, publisher = {Association for Computing Machinery}, title = {{Hausdorff and Gromov-Hausdorff stable subsets of the medial axis}}, doi = {10.1145/3564246.3585113}, year = {2023}, } @inproceedings{13053, abstract = {Deep neural networks (DNNs) often have to be compressed, via pruning and/or quantization, before they can be deployed in practical settings. In this work we propose a new compression-aware minimizer dubbed CrAM that modifies the optimization step in a principled way, in order to produce models whose local loss behavior is stable under compression operations such as pruning. Thus, dense models trained via CrAM should be compressible post-training, in a single step, without significant accuracy loss. Experimental results on standard benchmarks, such as residual networks for ImageNet classification and BERT models for language modelling, show that CrAM produces dense models that can be more accurate than the standard SGD/Adam-based baselines, but which are stable under weight pruning: specifically, we can prune models in one-shot to 70-80% sparsity with almost no accuracy loss, and to 90% with reasonable (∼1%) accuracy loss, which is competitive with gradual compression methods. Additionally, CrAM can produce sparse models which perform well for transfer learning, and it also works for semi-structured 2:4 pruning patterns supported by GPU hardware. The code for reproducing the results is available at this https URL .}, author = {Peste, Elena-Alexandra and Vladu, Adrian and Kurtic, Eldar and Lampert, Christoph and Alistarh, Dan-Adrian}, booktitle = {11th International Conference on Learning Representations }, location = {Kigali, Rwanda }, title = {{CrAM: A Compression-Aware Minimizer}}, year = {2023}, } @inproceedings{13143, abstract = {GIMPS and PrimeGrid are large-scale distributed projects dedicated to searching giant prime numbers, usually of special forms like Mersenne and Proth primes. The numbers in the current search-space are millions of digits large and the participating volunteers need to run resource-consuming primality tests. Once a candidate prime N has been found, the only way for another party to independently verify the primality of N used to be by repeating the expensive primality test. To avoid the need for second recomputation of each primality test, these projects have recently adopted certifying mechanisms that enable efficient verification of performed tests. However, the mechanisms presently in place only detect benign errors and there is no guarantee against adversarial behavior: a malicious volunteer can mislead the project to reject a giant prime as being non-prime. In this paper, we propose a practical, cryptographically-sound mechanism for certifying the non-primality of Proth numbers. That is, a volunteer can – parallel to running the primality test for N – generate an efficiently verifiable proof at a little extra cost certifying that N is not prime. The interactive protocol has statistical soundness and can be made non-interactive using the Fiat-Shamir heuristic. Our approach is based on a cryptographic primitive called Proof of Exponentiation (PoE) which, for a group G, certifies that a tuple (x,y,T)∈G2×N satisfies x2T=y (Pietrzak, ITCS 2019 and Wesolowski, J. Cryptol. 2020). In particular, we show how to adapt Pietrzak’s PoE at a moderate additional cost to make it a cryptographically-sound certificate of non-primality.}, author = {Hoffmann, Charlotte and Hubáček, Pavel and Kamath, Chethan and Pietrzak, Krzysztof Z}, booktitle = {Public-Key Cryptography - PKC 2023}, isbn = {9783031313677}, issn = {1611-3349}, location = {Atlanta, GA, United States}, pages = {530--553}, publisher = {Springer Nature}, title = {{Certifying giant nonprimes}}, doi = {10.1007/978-3-031-31368-4_19}, volume = {13940}, year = {2023}, } @inproceedings{13142, abstract = {Reinforcement learning has received much attention for learning controllers of deterministic systems. We consider a learner-verifier framework for stochastic control systems and survey recent methods that formally guarantee a conjunction of reachability and safety properties. Given a property and a lower bound on the probability of the property being satisfied, our framework jointly learns a control policy and a formal certificate to ensure the satisfaction of the property with a desired probability threshold. Both the control policy and the formal certificate are continuous functions from states to reals, which are learned as parameterized neural networks. While in the deterministic case, the certificates are invariant and barrier functions for safety, or Lyapunov and ranking functions for liveness, in the stochastic case the certificates are supermartingales. For certificate verification, we use interval arithmetic abstract interpretation to bound the expected values of neural network functions.}, author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Lechner, Mathias and Zikelic, Dorde}, booktitle = {Tools and Algorithms for the Construction and Analysis of Systems }, isbn = {9783031308222}, issn = {1611-3349}, location = {Paris, France}, pages = {3--25}, publisher = {Springer Nature}, title = {{A learner-verifier framework for neural network controllers and certificates of stochastic systems}}, doi = {10.1007/978-3-031-30823-9_1}, volume = {13993}, year = {2023}, } @inproceedings{13141, abstract = {We automatically compute a new class of environment assumptions in two-player turn-based finite graph games which characterize an “adequate cooperation” needed from the environment to allow the system player to win. Given an ω-regular winning condition Φ for the system player, we compute an ω-regular assumption Ψ for the environment player, such that (i) every environment strategy compliant with Ψ allows the system to fulfill Φ (sufficiency), (ii) Ψ can be fulfilled by the environment for every strategy of the system (implementability), and (iii) Ψ does not prevent any cooperative strategy choice (permissiveness). For parity games, which are canonical representations of ω-regular games, we present a polynomial-time algorithm for the symbolic computation of adequately permissive assumptions and show that our algorithm runs faster and produces better assumptions than existing approaches—both theoretically and empirically. To the best of our knowledge, for ω -regular games, we provide the first algorithm to compute sufficient and implementable environment assumptions that are also permissive.}, author = {Anand, Ashwani and Mallik, Kaushik and Nayak, Satya Prakash and Schmuck, Anne Kathrin}, booktitle = {TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems}, isbn = {9783031308192}, issn = {1611-3349}, location = {Paris, France}, pages = {211--228}, publisher = {Springer Nature}, title = {{Computing adequately permissive assumptions for synthesis}}, doi = {10.1007/978-3-031-30820-8_15}, volume = {13994}, year = {2023}, } @phdthesis{12826, abstract = {During navigation, animals can infer the structure of the environment by computing the optic flow cues elicited by their own movements, and subsequently use this information to instruct proper locomotor actions. These computations require a panoramic assessment of the visual environment in order to disambiguate similar sensory experiences that may require distinct behavioral responses. The estimation of the global motion patterns is therefore essential for successful navigation. Yet, our understanding of the algorithms and implementations that enable coherent panoramic visual perception remains scarce. Here I pursue this problem by dissecting the functional aspects of interneuronal communication in the lobula plate tangential cell network in Drosophila melanogaster. The results presented in the thesis demonstrate that the basis for effective interpretation of the optic flow in this circuit are stereotyped synaptic connections that mediate the formation of distinct subnetworks, each extracting a particular pattern of global motion. Firstly, I show that gap junctions are essential for a correct interpretation of binocular motion cues by horizontal motion-sensitive cells. HS cells form electrical synapses with contralateral H2 neurons that are involved in detecting yaw rotation and translation. I developed an FlpStop-mediated mutant of a gap junction protein ShakB that disrupts these electrical synapses. While the loss of electrical synapses does not affect the tuning of the direction selectivity in HS neurons, it severely alters their sensitivity to horizontal motion in the contralateral side. These physiological changes result in an inappropriate integration of binocular motion cues in walking animals. While wild-type flies form a binocular perception of visual motion by non-linear integration of monocular optic flow cues, the mutant flies sum the monocular inputs linearly. These results indicate that rather than averaging signals in neighboring neurons, gap-junctions operate in conjunction with chemical synapses to mediate complex non-linear optic flow computations. Secondly, I show that stochastic manipulation of neuronal activity in the lobula plate tangential cell network is a powerful approach to study the neuronal implementation of optic flow-based navigation in flies. Tangential neurons form multiple subnetworks, each mediating course-stabilizing response to a particular global pattern of visual motion. Application of genetic mosaic techniques can provide sparse optogenetic activation of HS cells in numerous combinations. These distinct combinations of activated neurons drive an array of distinct behavioral responses, providing important insights into how visuomotor transformation is performed in the lobula plate tangential cell network. This approach can be complemented by stochastic silencing of tangential neurons, enabling direct assessment of the functional role of individual tangential neurons in the processing of specific visual motion patterns. Taken together, the findings presented in this thesis suggest that establishing specific activity patterns of tangential cells via stereotyped synaptic connectivity is a key to efficient optic flow-based navigation in Drosophila melanogaster.}, author = {Pokusaeva, Victoria}, issn = {2663 - 337X}, pages = {106}, publisher = {Institute of Science and Technology Austria}, title = {{Neural control of optic flow-based navigation in Drosophila melanogaster}}, doi = {10.15479/at:ista:12826}, year = {2023}, } @article{12086, abstract = {We present a simple algorithm for computing higher-order Delaunay mosaics that works in Euclidean spaces of any finite dimensions. The algorithm selects the vertices of the order-k mosaic from incrementally constructed lower-order mosaics and uses an algorithm for weighted first-order Delaunay mosaics as a black-box to construct the order-k mosaic from its vertices. Beyond this black-box, the algorithm uses only combinatorial operations, thus facilitating easy implementation. We extend this algorithm to compute higher-order α-shapes and provide open-source implementations. We present experimental results for properties of higher-order Delaunay mosaics of random point sets.}, author = {Edelsbrunner, Herbert and Osang, Georg F}, issn = {1432-0541}, journal = {Algorithmica}, pages = {277--295}, publisher = {Springer Nature}, title = {{A simple algorithm for higher-order Delaunay mosaics and alpha shapes}}, doi = {10.1007/s00453-022-01027-6}, volume = {85}, year = {2023}, } @article{12104, abstract = {We study ergodic decompositions of Dirichlet spaces under intertwining via unitary order isomorphisms. We show that the ergodic decomposition of a quasi-regular Dirichlet space is unique up to a unique isomorphism of the indexing space. Furthermore, every unitary order isomorphism intertwining two quasi-regular Dirichlet spaces is decomposable over their ergodic decompositions up to conjugation via an isomorphism of the corresponding indexing spaces.}, author = {Dello Schiavo, Lorenzo and Wirth, Melchior}, issn = {1424-3202}, journal = {Journal of Evolution Equations}, number = {1}, publisher = {Springer Nature}, title = {{Ergodic decompositions of Dirichlet forms under order isomorphisms}}, doi = {10.1007/s00028-022-00859-7}, volume = {23}, year = {2023}, } @article{11434, abstract = {The Indian summer monsoon rainfall (ISMR) has been declining since the 1950s. However, since 2002 it is reported to have revived. For these observed changes in the ISMR, several explanations have been reported. Among these explanations, however, the role of the eastern equatorial Indian Ocean (EEIO) is missing despite being one of the warmest regions in the Indian Ocean, and monotonously warming. A recent study reported that EEIO warming impacts the rainfall over northern India. Here we report that warming in the EEIO weakens the low-level Indian summer monsoon circulation and reduces ISMR. A warm EEIO drives easterly winds in the Indo–Pacific sector as a Gill response. The warm EEIO also enhances nocturnal convection offshore the western coast of Sumatra. The latent heating associated with the increased convection augments the Gill response and the resultant circulation opposes the monsoon low-level circulation and weakens the seasonal rainfall.}, author = {Goswami, Bidyut B}, issn = {1432-0894}, journal = {Climate Dynamics}, pages = {427--442}, publisher = {Springer Nature}, title = {{Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend}}, doi = {10.1007/s00382-022-06337-7}, volume = {60}, year = {2023}, } @inproceedings{12467, abstract = {Safety and liveness are elementary concepts of computation, and the foundation of many verification paradigms. The safety-liveness classification of boolean properties characterizes whether a given property can be falsified by observing a finite prefix of an infinite computation trace (always for safety, never for liveness). In quantitative specification and verification, properties assign not truth values, but quantitative values to infinite traces (e.g., a cost, or the distance to a boolean property). We introduce quantitative safety and liveness, and we prove that our definitions induce conservative quantitative generalizations of both (1)~the safety-progress hierarchy of boolean properties and (2)~the safety-liveness decomposition of boolean properties. In particular, we show that every quantitative property can be written as the pointwise minimum of a quantitative safety property and a quantitative liveness property. Consequently, like boolean properties, also quantitative properties can be min-decomposed into safety and liveness parts, or alternatively, max-decomposed into co-safety and co-liveness parts. Moreover, quantitative properties can be approximated naturally. We prove that every quantitative property that has both safe and co-safe approximations can be monitored arbitrarily precisely by a monitor that uses only a finite number of states.}, author = {Henzinger, Thomas A and Mazzocchi, Nicolas Adrien and Sarac, Naci E}, booktitle = {26th International Conference Foundations of Software Science and Computation Structures}, isbn = {9783031308284}, issn = {1611-3349}, location = {Paris, France}, pages = {349--370}, publisher = {Springer Nature}, title = {{Quantitative safety and liveness}}, doi = {10.1007/978-3-031-30829-1_17}, volume = {13992}, year = {2023}, } @article{13179, abstract = {Writing concurrent code that is both correct and efficient is notoriously difficult. Thus, programmers often prefer to use synchronization abstractions, which render code simpler and easier to reason about. Despite a wealth of work on this topic, there is still a gap between the rich semantics provided by synchronization abstractions in modern programming languages—specifically, fair FIFO ordering of synchronization requests and support for abortable operations—and frameworks for implementing it correctly and efficiently. Supporting such semantics is critical given the rising popularity of constructs for asynchronous programming, such as coroutines, which abort frequently and are cheaper to suspend and resume compared to native threads. This paper introduces a new framework called CancellableQueueSynchronizer (CQS), which enables simple yet efficient implementations of a wide range of fair and abortable synchronization primitives: mutexes, semaphores, barriers, count-down latches, and blocking pools. Our main contribution is algorithmic, as implementing both fairness and abortability efficiently at this level of generality is non-trivial. Importantly, all our algorithms, including the CQS framework and the primitives built on top of it, come with formal proofs in the Iris framework for Coq for many of their properties. These proofs are modular, so it is easy to show correctness for new primitives implemented on top of CQS. From a practical perspective, implementation of CQS for native threads on the JVM improves throughput by up to two orders of magnitude over Java’s AbstractQueuedSynchronizer, the only practical abstraction offering similar semantics. Further, we successfully integrated CQS as a core component of the popular Kotlin Coroutines library, validating the framework’s practical impact and expressiveness in a real-world environment. In sum, CancellableQueueSynchronizer is the first framework to combine expressiveness with formal guarantees and solid practical performance. Our approach should be extensible to other languages and families of synchronization primitives.}, author = {Koval, Nikita and Khalanskiy, Dmitry and Alistarh, Dan-Adrian}, issn = {2475-1421}, journal = {Proceedings of the ACM on Programming Languages}, publisher = {Association for Computing Machinery }, title = {{CQS: A formally-verified framework for fair and abortable synchronization}}, doi = {10.1145/3591230}, volume = {7}, year = {2023}, } @article{13180, abstract = {We study the density of everywhere locally soluble diagonal quadric surfaces, parameterised by rational points that lie on a split quadric surface}, author = {Browning, Timothy D and Lyczak, Julian and Sarapin, Roman}, issn = {1944-4184}, journal = {Involve}, number = {2}, pages = {331--342}, publisher = {Mathematical Sciences Publishers}, title = {{Local solubility for a family of quadrics over a split quadric surface}}, doi = {10.2140/involve.2023.16.331}, volume = {16}, year = {2023}, } @inproceedings{13162, author = {Elefante, Stefano and Stadlbauer, Stephan and Alexander, Michael F and Schlögl, Alois}, booktitle = {ASHPC23 - Austrian-Slovenian HPC Meeting 2023}, location = {Maribor, Slovenia}, pages = {42--42}, publisher = {EuroCC}, title = {{Cryo-EM software packages: A sys-admins point of view}}, year = {2023}, } @inproceedings{13161, author = {Schlögl, Alois and Elefante, Stefano and Hodirnau, Victor-Valentin}, booktitle = {ASHPC23 - Austrian-Slovenian HPC Meeting 2023}, location = {Maribor, Slovenia}, pages = {59--59}, publisher = {EuroCC}, title = {{Running Windows-applications on a Linux HPC cluster using WINE}}, year = {2023}, } @article{13251, abstract = {A rotating organic cation and a dynamically disordered soft inorganic cage are the hallmark features of organic-inorganic lead-halide perovskites. Understanding the interplay between these two subsystems is a challenging problem, but it is this coupling that is widely conjectured to be responsible for the unique behavior of photocarriers in these materials. In this work, we use the fact that the polarizability of the organic cation strongly depends on the ambient electrostatic environment to put the molecule forward as a sensitive probe of the local crystal fields inside the lattice cell. We measure the average polarizability of the C/N–H bond stretching mode by means of infrared spectroscopy, which allows us to deduce the character of the motion of the cation molecule, find the magnitude of the local crystal field, and place an estimate on the strength of the hydrogen bond between the hydrogen and halide atoms. Our results pave the way for understanding electric fields in lead-halide perovskites using infrared bond spectroscopy.}, author = {Wei, Yujing and Volosniev, Artem and Lorenc, Dusan and Zhumekenov, Ayan A. and Bakr, Osman M. and Lemeshko, Mikhail and Alpichshev, Zhanybek}, issn = {1948-7185}, journal = {The Journal of Physical Chemistry Letters}, keywords = {General Materials Science, Physical and Theoretical Chemistry}, number = {27}, pages = {6309--6314}, publisher = {American Chemical Society}, title = {{Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites}}, doi = {10.1021/acs.jpclett.3c01158}, volume = {14}, year = {2023}, } @inproceedings{13292, abstract = {The operator precedence languages (OPLs) represent the largest known subclass of the context-free languages which enjoys all desirable closure and decidability properties. This includes the decidability of language inclusion, which is the ultimate verification problem. Operator precedence grammars, automata, and logics have been investigated and used, for example, to verify programs with arithmetic expressions and exceptions (both of which are deterministic pushdown but lie outside the scope of the visibly pushdown languages). In this paper, we complete the picture and give, for the first time, an algebraic characterization of the class of OPLs in the form of a syntactic congruence that has finitely many equivalence classes exactly for the operator precedence languages. This is a generalization of the celebrated Myhill-Nerode theorem for the regular languages to OPLs. As one of the consequences, we show that universality and language inclusion for nondeterministic operator precedence automata can be solved by an antichain algorithm. Antichain algorithms avoid determinization and complementation through an explicit subset construction, by leveraging a quasi-order on words, which allows the pruning of the search space for counterexample words without sacrificing completeness. Antichain algorithms can be implemented symbolically, and these implementations are today the best-performing algorithms in practice for the inclusion of finite automata. We give a generic construction of the quasi-order needed for antichain algorithms from a finite syntactic congruence. This yields the first antichain algorithm for OPLs, an algorithm that solves the ExpTime-hard language inclusion problem for OPLs in exponential time.}, author = {Henzinger, Thomas A and Kebis, Pavol and Mazzocchi, Nicolas Adrien and Sarac, Naci E}, booktitle = {50th International Colloquium on Automata, Languages, and Programming}, isbn = {9783959772785}, issn = {1868-8969}, location = {Paderborn, Germany}, pages = {129:1----129:20}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Regular methods for operator precedence languages}}, doi = {10.4230/LIPIcs.ICALP.2023.129}, volume = {261}, year = {2023}, } @article{13277, abstract = {Recent experimental advances have inspired the development of theoretical tools to describe the non-equilibrium dynamics of quantum systems. Among them an exact representation of quantum spin systems in terms of classical stochastic processes has been proposed. Here we provide first steps towards the extension of this stochastic approach to bosonic systems by considering the one-dimensional quantum quartic oscillator. We show how to exactly parameterize the time evolution of this prototypical model via the dynamics of a set of classical variables. We interpret these variables as stochastic processes, which allows us to propose a novel way to numerically simulate the time evolution of the system. We benchmark our findings by considering analytically solvable limits and providing alternative derivations of known results.}, author = {Tucci, Gennaro and De Nicola, Stefano and Wald, Sascha and Gambassi, Andrea}, issn = {2666-9366}, journal = {SciPost Physics Core}, keywords = {Statistical and Nonlinear Physics, Atomic and Molecular Physics, and Optics, Nuclear and High Energy Physics, Condensed Matter Physics}, number = {2}, publisher = {SciPost Foundation}, title = {{Stochastic representation of the quantum quartic oscillator}}, doi = {10.21468/scipostphyscore.6.2.029}, volume = {6}, year = {2023}, } @article{13276, abstract = {We introduce a generic and accessible implementation of an exact diagonalization method for studying few-fermion models. Our aim is to provide a testbed for the newcomers to the field as well as a stepping stone for trying out novel optimizations and approximations. This userguide consists of a description of the algorithm, and several examples in varying orders of sophistication. In particular, we exemplify our routine using an effective-interaction approach that fixes the low-energy physics. We benchmark this approach against the existing data, and show that it is able to deliver state-of-the-art numerical results at a significantly reduced computational cost.}, author = {Rammelmüller, Lukas and Huber, David and Volosniev, Artem}, issn = {2949-804X}, journal = {SciPost Physics Codebases}, publisher = {SciPost Foundation}, title = {{A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D}}, doi = {10.21468/scipostphyscodeb.12}, year = {2023}, } @misc{13275, abstract = {We introduce a generic and accessible implementation of an exact diagonalization method for studying few-fermion models. Our aim is to provide a testbed for the newcomers to the field as well as a stepping stone for trying out novel optimizations and approximations. This userguide consists of a description of the algorithm, and several examples in varying orders of sophistication. In particular, we exemplify our routine using an effective-interaction approach that fixes the low-energy physics. We benchmark this approach against the existing data, and show that it is able to deliver state-of-the-art numerical results at a significantly reduced computational cost.}, author = {Rammelmüller, Lukas and Huber, David and Volosniev, Artem}, publisher = {SciPost Foundation}, title = {{Codebase release 1.0 for FermiFCI}}, doi = {10.21468/scipostphyscodeb.12-r1.0}, year = {2023}, }