@article{17886, abstract = {Thin pancake-like neuronal networks cultured on top of a planar microelectrode array have been extensively tried out in neuroengineering, as a substrate for the mobile robot’s control unit, i.e., as a cyborg’s brain. Most of these attempts failed due to intricate self-organizing dynamics in the neuronal systems. In particular, the networks may exhibit an emergent spatial map of steady nucleation sites (“n-sites”) of spontaneous population spikes. Being unpredictable and independent of the surface electrode locations, the n-sites drastically change local ability of the network to generate spikes. Here, using a spiking neuronal network model with generative spatially-embedded connectome, we systematically show in simulations that the number, location, and relative activity of spontaneously formed n-sites (“the vitals”) crucially depend on the samplings of three distributions: (1) the network distribution of neuronal excitability, (2) the distribution of connections between neurons of the network, and (3) the distribution of maximal amplitudes of a single synaptic current pulse. Moreover, blocking the dynamics of a small fraction (about 4%) of non-pacemaker neurons having the highest excitability was enough to completely suppress the occurrence of population spikes and their n-sites. This key result is explained theoretically. Remarkably, the n-sites occur taking into account only short-term synaptic plasticity, i.e., without a Hebbian-type plasticity. As the spiking network model used in this study is strictly deterministic, all simulation results can be accurately reproduced. The model, which has already demonstrated a very high richness-to-complexity ratio, can also be directly extended into the three-dimensional case, e.g., for targeting peculiarities of spiking dynamics in cerebral (or brain) organoids. We recommend the model as an excellent illustrative tool for teaching network-level computational neuroscience, complementing a few benchmark models.}, author = {Zendrikov, Dmitrii and Paraskevov, Alexander}, issn = {1879-2782}, journal = {Neural Networks}, publisher = {Elsevier}, title = {{The vitals for steady nucleation maps of spontaneous spiking coherence in autonomous two-dimensional neuronal networks}}, doi = {10.1016/j.neunet.2024.106589}, volume = {180}, year = {2024}, } @article{17887, abstract = {We show convergence of the Navier-Stokes/Allen-Cahn system to a classical sharp interface model for the two-phase flow of two viscous incompressible fluids with same viscosities in a smooth bounded domain in two and three space dimensions as long as a smooth solution of the limit system exists. Moreover, we obtain error estimates with the aid of a relative entropy method. Our results hold provided that the mobility mε>0 in the Allen-Cahn equation tends to zero in a subcritical way, i.e., mε=m0εβ for some β∈(0,2) and m0>0 . The proof proceeds by showing via a relative entropy argument that the solution to the Navier-Stokes/Allen-Cahn system remains close to the solution of a perturbed version of the two-phase flow problem, augmented by an extra mean curvature flow term mεHΓt in the interface motion. In a second step, it is easy to see that the solution to the perturbed problem is close to the original two-phase flow.}, author = {Abels, Helmut and Fischer, Julian L and Moser, Maximilian}, issn = {1432-0673}, journal = {Archive for Rational Mechanics and Analysis}, number = {5}, publisher = {Springer Nature}, title = {{Approximation of classical two-phase flows of viscous incompressible fluids by a Navier–Stokes/Allen–Cahn system}}, doi = {10.1007/s00205-024-02020-9}, volume = {248}, year = {2024}, } @article{17888, abstract = {Context: Biotic resource exploitation is a critical determinant of species’ distributions. However, quantifying resource exploitation patterns through space and time can be difficult, complicating their incorporation in spatial ecology studies. Therefore, understanding the local drivers of spatial patterns of resource exploitation may contribute to better large-scale species distribution models. Objectives: We investigated (1) how the resource exploitation patterns of two trophic interactions (plant–insect) are explained by insect behaviour, resource aggregation, and potential insect-insect interactions. We also analyzed how (2) resource patch size and (3) resource accessibility in a heterogeneous landscape affected host exploitation patterns. Methods: We quantified nectar robbing by insects in the genus Bombus (bumblebees) and seed predation by Brachypterolus vestitus larvae (Antirrhinum beetle) on Antirrhinum majus L. (wild snapdragons) in the Pyrenees Mountains, Catalonia, Spain. We tested hypotheses about resource exploitation by integrating spatial analyses at multiple scales. Results: Both trophic interactions were aggregated, explained by the aggregation of their resource. At some scales, nectar robbing is more aggregated than the resource. Trophic interaction abundance is proportional to resource patch size, following the ideal free distribution model. Landscape features do not explain the locations exploited. Nectar robbing and seed predation occur together more often than expected. Conclusions: Our findings suggest that multiple biotic and ecological spatial factors may simultaneously affect resource exploitation at a local scale. These findings should be considered when developing agricultural projects, management plans and conservation policies.}, author = {Pocull Belles, Guillem and Baskett, Carina and Barton, Nicholas H}, issn = {1572-9761}, journal = {Landscape Ecology}, number = {9}, publisher = {Springer Nature}, title = {{Multiscale spatial analysis of two plant–insect interactions: Effects of landscape, resource distribution, and other insects}}, doi = {10.1007/s10980-024-01899-9}, volume = {39}, year = {2024}, } @article{17891, abstract = {Abstract Methods used in topological data analysis naturally capture higher-order interactions in point cloud data embedded in a metric space. This methodology was recently extended to data living in an information space, by which we mean a space measured with an information theoretical distance. One such setting is a finite collection of discrete probability distributions embedded in the probability simplex measured with the relative entropy (Kullback–Leibler divergence). More generally, one can work with a Bregman divergence parameterized by a different notion of entropy. While theoretical algorithms exist for this setup, there is a paucity of implementations for exploring and comparing geometric-topological properties of various information spaces. The interest of this work is therefore twofold. First, we propose the first robust algorithms and software for geometric and topological data analysis in information space. Perhaps surprisingly, despite working with Bregman divergences, our design reuses robust libraries for the Euclidean case. Second, using the new software, we take the first steps towards understanding the geometric-topological structure of these spaces. In particular, we compare them with the more familiar spaces equipped with the Euclidean and Fisher metrics.}, author = {Edelsbrunner, Herbert and Ölsböck, Katharina and Wagner, Hubert}, issn = {1099-4300}, journal = {Entropy}, number = {8}, publisher = {MDPI}, title = {{Understanding higher-order interactions in information space}}, doi = {10.3390/e26080637}, volume = {26}, year = {2024}, } @article{17892, abstract = {Enzyme-substrate kinetics form the basis of many biomolecular processes. The interplay between substrate binding and substrate geometry can give rise to long-range interactions between enzyme binding events. Here we study a general model of enzyme-substrate kinetics with restricted long-range interactions described by an exponent −𝛾. We employ a coherent-state path integral and renormalization group approach to calculate the first moment and two-point correlation function of the enzyme-binding profile. We show that starting from an empty substrate the average occupancy follows a power law with an exponent 1/(1−𝛾) over time. The correlation function decays algebraically with two distinct spatial regimes characterized by exponents −𝛾 on short distances and −(2/3)⁢(2−𝛾) on long distances. The crossover between both regimes scales inversely with the average substrate occupancy. Our work allows associating experimental measurements of bound enzyme locations with their binding kinetics and the spatial conformation of the substrate.}, author = {Olmeda, Fabrizio and Rulands, Steffen}, issn = {2470-0053}, journal = {Physical Review E}, number = {2}, publisher = {American Physical Society}, title = {{Field theory of enzyme-substrate systems with restricted long-range interactions}}, doi = {10.1103/PhysRevE.110.024404}, volume = {110}, year = {2024}, } @article{17896, abstract = {Broadband photodetectors that can decipher the wavelength (λ) and intensity (I) of an unknown incident light are urgently demanded. Photothermoelectric (PTE) detectors can achieve ultrabroadband photodetection surpassing the bandgap limitation; however, their practical application is severely hampered by the lack of deciphering strategy. In this work, we report a variable elimination method to decipher λ and I of the incident lights based on an integrated Ag2Se film-based PTE detector. Nanostructured Ag2Se films with controlled thickness are synthesized using an ion sputtering of Ag and a room-temperature selenization method and then assembled into a detector. Under identical illumination, Ag2Se films of different thicknesses produce varying output photothermal voltages, influenced by factors including λ. By establishing a direct relationship between the photothermal voltage and the absorption of Ag2Se films of varied thickness, we successfully eliminate variables independent of λ, thus determining λ. Subsequently, I is determined by the calibrated responsivity relationship using obtained λ. Our PTE detector achieves a broadband spectrum from 400 to 950 nm and high accuracy, with deviations as low as ∼2.63 and ∼0.53% for deciphered λ and I, respectively. This method allows for self-powered broadband decipherable photodetection without a complex device architecture or computational assistance, which could boost the research enthusiasm and promote the commercialization of PTE broadband detectors.}, author = {Zhou, Jiamin and Xu, Shengduo and Shuai, Yi and Sun, Qiang and Ma, Huangshui and Wang, Chao and Wu, Haijuan and Tan, Shanshan and Wang, Zegao and Yang, Lei}, issn = {1944-8252}, journal = {ACS Applied Materials and Interfaces}, number = {36}, pages = {47923--47930}, publisher = {American Chemical Society}, title = {{Decipher the wavelength and intensity using photothermoelectric detectors}}, doi = {10.1021/acsami.4c10489}, volume = {16}, year = {2024}, } @article{17897, abstract = {High-entropy materials (HEMs) offer a quasi-continuous spectrum of active sites and have generated great expectations in fields such as electrocatalysis and energy storage. Despite their potential, the complex composition and associated surface phenomena of HEMs pose challenges to their rational design and development. In this context, we have synthesized FeCoNiPdWP high entropy phosphide (HEP) nanoparticles using a low-temperature colloidal method, and explored their application as bifunctional electrocatalysts for the oxygen evolution and reduction reactions (OER/ORR). Our analysis provides a detailed understanding of the individual roles and transformations of each element during OER/ORR operation. Notably, the HEPs exhibit an exceptionally low OER overpotential of 227 mV at 10 mA cm−2, attributed to the reconstructed HEP surface into a FeCoNiPdW high entropy oxyhydroxide with high oxidation states of Fe, Co, and Ni serving as the active sites. Additionally, Pd and W play crucial roles in modulating the electronic structure to optimize the adsorption energy of oxygen intermediates. For the ORR, Pd emerges as the most active component. In the reconstructed catalyst, the strong d–d orbital coupling of especially Pd, Co, and W fine-tunes ORR electron transfer pathways, delivering an ORR half-wave potential of 0.81 V with a pure four-electron reduction mechanism. The practicality of these HEPs catalysts is showcased through the assembly of aqueous zinc–air batteries. These batteries demonstrate a superior specific capacity of 886 mA h gZn−1 and maintain excellent stability over more than 700 hours of continuous operation. Overall, this study not only elucidates the role of each element in HEMs but also establishes a foundational framework for the design and development of next-generation bifunctional oxygen catalysts, broadening the potential applications of these complex materials in advanced energy systems.}, author = {He, Ren and Wang, Shiqi and Yang, Linlin and Horta, Sharona and Ding, Yang and Di, Chong and Zhang, Xuesong and Xu, Ying and Ibáñez, Maria and Zhou, Yingtang and Mebs, Stefan and Dau, Holger and Hausmann, Jan Niklas and Huo, Wenyi and Menezes, Prashanth W. and Cabot, Andreu}, issn = {1754-5706}, journal = {Energy and Environmental Science}, number = {19}, pages = {7193--7208}, publisher = {Royal Society of Chemistry}, title = {{Active site switching on high entropy phosphides as bifunctional oxygen electrocatalysts for rechargeable/robust Zn-air battery}}, doi = {10.1039/d4ee01912a}, volume = {17}, year = {2024}, } @inbook{18052, abstract = {Sodium dodecyl sulfate-digested freeze-fracture replica labeling (SDS-FRL) is an electron microscope (EM) sample preparation technique which allows for high-resolution visualization of membrane proteins with high sensitivity. However, image acquisition of specific replica profiles such as synapses in a large field of EM view needs a valid experience and a long time for manual searching. Here, we describe how to utilize deep learning for automatizing image acquisition of specific profiles of interest in replica samples. This protocol facilitates the labor-intensive collection of EM images, in particular for rare profiles. We provide instructions for using SerialEM image acquisition software in conjunction with object detection by our newly developed deep learning software DarEM, to automatically acquire tilt series of all synapses in a selected region. We then show how to perform a mostly automated analysis of gold particle labeling in the acquired images by utilizing Darea software.}, author = {Kleindienst, David and Costanzo, Tommaso and Shigemoto, Ryuichi}, booktitle = {New Aspects in Analyzing the Synaptic Organization of the Brain}, editor = {Lübke, Joachim H.R. and Rollenhagen, Astrid}, isbn = {9781071640180}, issn = {1940-6045}, pages = {123--137}, publisher = {Springer Nature}, title = {{Automated Imaging and Analysis of Synapses in Freeze-Fracture Replica Samples with Deep Learning}}, doi = {10.1007/978-1-0716-4019-7_8}, year = {2024}, } @inbook{18058, abstract = {DNA cloning is a core technique in biomedical and biotechnological research and is used to assemble and modify DNA fragments at will. While DNA cloning has traditionally relied on restriction enzymes, recent homology-based methods offer improved protocols together with seamless and directional assembly of desired products, overcoming the main disadvantages of restriction enzyme DNA cloning. This chapter provides a historical perspective on DNA cloning, presents a detailed discussion on state-of-the-art in vitro and in vivo homology-based methodologies, covering the basics of how to perform all major plasmid modifications (sub-cloning, site-directed mutagenesis, insertions, and deletions), and gives examples of how to apply these techniques for complex DNA cloning projects.}, author = {Watson, Jake and Arroyo-Urea, Sandra and García-Nafría, Javier}, booktitle = {Handbook of Molecular Biotechnology}, editor = {Liu, Dongyou}, pages = {66--72}, publisher = {CRC Press}, title = {{DNA Cloning}}, doi = {10.1201/9781003055211-8}, year = {2024}, } @article{18063, abstract = {The developmental plasticity of the root system plays an essential role in the adaptation of plants to the environment. Among many other signals, auxin and its directional, intercellular transport are critical in regulating root growth and development. In particular, the PIN-FORMED2 (PIN2) auxin exporter acts as a key regulator of root gravitropic growth. Multiple regulators have been reported to be involved in PIN2-mediated root growth; however, our information remains incomplete. Here, we identified ROWY Bro1-domain proteins as important regulators of PIN2 sorting control. Genetic analysis revealed that Arabidopsis rowy1 single mutants and higher-order rowy1 rowy2 rowy3 triple mutants presented a wavy root growth phenotype. Cell biological experiments revealed that ROWY1 and PIN2 colocalized to the apical side of the plasma membrane in the root epidermis and that ROWYs are required for correct PM targeting of PIN2. In addition, ROWYs also affected PIN3 protein abundance in the stele, suggesting the potential involvement of additional PIN transporters as well as other proteins. A global transcriptome analysis revealed that ROWY genes are involved in the Fe2+ availability perception pathway. This work establishes ROWYs as important novel regulators of root gravitropic growth by connecting micronutrient availability to the proper subcellular targeting of PIN auxin transporters.}, author = {Peng, Yakun and Ji, Kangkang and Mao, Yanbo and Wang, Yiqun and Korbei, Barbara and Luschnig, Christian and Shen, Jinbo and Benková, Eva and Friml, Jiří and Tan, Shutang}, issn = {2399-3642}, journal = {Communications Biology}, publisher = {Springer Nature}, title = {{Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis}}, doi = {10.1038/s42003-024-06747-9}, volume = {7}, year = {2024}, } @article{18065, abstract = {We establish a close connection between acceleration and dynamical degree for one-frequency quasi-periodic compact cocycles, by showing that two vectors derived separately from each coincide. Based on this, we provide a dynamical classification of one-frequency quasi-periodic SO(3, R)-cocycles.}, author = {Hou, Xuanji and Pan, Yi and Zhou, Qi}, issn = {1090-2082}, journal = {Advances in Mathematics}, publisher = {Elsevier}, title = {{Dynamical classification of analytic one-frequency quasi-periodic SO(3,R)-cocycles}}, doi = {10.1016/j.aim.2024.109943}, volume = {457}, year = {2024}, } @inproceedings{18066, abstract = {Graph games lie at the algorithmic core of many automated design problems in computer science. These are games usually played between two players on a given graph, where the players keep moving a token along the edges according to pre-determined rules (turn-based, concurrent, etc.), and the winner is decided based on the infinite path (aka play) traversed by the token from a given initial position. In bidding games, the players initially get some monetary budgets which they need to use to bid for the privilege of moving the token at each step. Each round of bidding affects the players' available budgets, which is the only form of update that the budgets experience. We introduce bidding games with charging where the players can additionally improve their budgets during the game by collecting vertex-dependent monetary rewards, aka the "charges." Unlike traditional bidding games (where all charges are zero), bidding games with charging allow non-trivial recurrent behaviors. For example, a reachability objective may require multiple detours to vertices with high charges to earn additional budget. We show that, nonetheless, the central property of traditional bidding games generalizes to bidding games with charging: For each vertex there exists a threshold ratio, which is the necessary and sufficient fraction of the total budget for winning the game from that vertex. While the thresholds of traditional bidding games correspond to unique fixed points of linear systems of equations, in games with charging, these fixed points are no longer unique. This significantly complicates the proof of existence and the algorithmic computation of thresholds for infinite-duration objectives. We also provide the lower complexity bounds for computing thresholds for Rabin and Streett objectives, which are the first known lower bounds in any form of bidding games (with or without charging), and we solve the following repair problem for safety and reachability games that have unsatisfiable objectives: Can we distribute a given amount of charge to the players in a way such that the objective can be satisfied?}, author = {Avni, Guy and Goharshady, Ehsan Kafshdar and Henzinger, Thomas A and Mallik, Kaushik}, booktitle = {35th International Conference on Concurrency Theory}, isbn = {9783959773393}, issn = {1868-8969}, location = {Calgary, Canada}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Bidding games with charging}}, doi = {10.4230/LIPIcs.CONCUR.2024.8}, volume = {311}, year = {2024}, } @inproceedings{18067, abstract = {An automaton 𝒜 is history-deterministic if its nondeterminism can be resolved on the fly, only using the prefix of the word read so far. This mild form of nondeterminism has attracted particular attention for its applications in synthesis problems. An automaton 𝒜 is guidable with respect to a class C of automata if it can fairly simulate every automaton in C, whose language is contained in that of 𝒜. In other words, guidable automata are those for which inclusion and simulation coincide, making them particularly interesting for model-checking. We study the connection between these two notions, and specifically the question of when they coincide. For classes of automata on which they do, deciding guidability, an otherwise challenging decision problem, reduces to deciding history-determinism, a problem that is starting to be well-understood for many classes. We provide a selection of sufficient criteria for a class of automata to guarantee the coincidence of the notions, and use them to show that the notions coincide for the most common automata classes, among which are ω-regular automata and many infinite-state automata with safety and reachability acceptance conditions, including vector addition systems with states, one-counter nets, pushdown-, Parikh-, and timed-automata. We also demonstrate that history-determinism and guidability do not always coincide, for example, for the classes of timed automata with a fixed number of clocks.}, author = {Boker, Udi and Henzinger, Thomas A and Lehtinen, Karoliina and Prakash, Aditya}, booktitle = {35th International Conference on Concurrency Theory}, isbn = {9783959773393}, issn = {1868-8969}, location = {Calgary, Canada}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{History-determinism vs fair simulation}}, doi = {10.4230/LIPIcs.CONCUR.2024.12}, volume = {311}, year = {2024}, } @inproceedings{18068, abstract = {We study the following refinement relation between nondeterministic state-transition models: model ℬ strategically dominates model 𝒜 iff every deterministic refinement of 𝒜 is language contained in some deterministic refinement of ℬ. While language containment is trace inclusion, and the (fair) simulation preorder coincides with tree inclusion, strategic dominance falls strictly between the two and can be characterized as "strategy inclusion" between 𝒜 and ℬ: every strategy that resolves the nondeterminism of 𝒜 is dominated by a strategy that resolves the nondeterminism of ℬ. Strategic dominance can be checked in 2-ExpTime by a decidable first-order Presburger logic with quantification over words and strategies, called resolver logic. We give several other applications of resolver logic, including checking the co-safety, co-liveness, and history-determinism of boolean and quantitative automata, and checking the inclusion between hyperproperties that are specified by nondeterministic boolean and quantitative automata.}, author = {Henzinger, Thomas A and Mazzocchi, Nicolas Adrien and Sarac, Naci E}, booktitle = {35th International Conference on Concurrency Theory}, isbn = {9783959773393}, issn = {1868-8969}, location = {Calgary, Canada}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Strategic dominance: A new preorder for nondeterministic processes}}, doi = {10.4230/LIPIcs.CONCUR.2024.29}, volume = {311}, year = {2024}, } @article{18069, abstract = {We present results from the JWST First Reionization Epoch Spectroscopically Complete Observations survey on the star-forming sequence (SFS) of galaxies at 1.0 < z < 1.7, around the peak of the cosmic star formation history. Star formation rates (SFRs) are measured from the redshifted, relatively dust-insensitive Paschen-α emission line, and stellar mass measurements include the F444W (4.4 μm; rest-frame H) band. We find SFRs of galaxies with log(M*/M⊙) > 9.5 that are lower than found in many earlier studies by up to 0.6 dex, but in good agreement with recent results obtained with the Prospector fitting framework. The difference (log(SFR(Paα)-SFR(Prospector)) is −0.09 ± 0.04 dex at 1010−11M⊙. We also measure the empirical relation between Paschen-α luminosity and rest-frame H-band magnitude and find that the scatter is only 0.04 dex lower than that of the SFR–M* relation and is much lower than the systematic differences among relations in the literature due to various methods of converting observed measurements to physical properties. We additionally identify examples of sources—that, with standard cutoffs via the UVJ diagram, would be deemed quiescent—with significant (log(sSFR)> −11 yr−1), typically extended, Paschen-α emission. Our results may be indicative of the potential unification of methods used to derive the SFS with careful selection of star-forming galaxies and independent SFR and stellar mass indicators.}, author = {Neufeld, Chloe and Van Dokkum, Pieter and Asali, Yasmeen and Covelo-Paz, Alba and Leja, Joel and Lin, Jamie and Matthee, Jorryt J and Oesch, Pascal A. and Reddy, Naveen A. and Shivaei, Irene and Whitaker, Katherine E. and Wuyts, Stijn and Brammer, Gabriel and Marchesini, Danilo and Maseda, Michael V. and Naidu, Rohan P. and Nelson, Erica J. and Velichko, Anna and Weibel, Andrea and Xiao, Mengyuan}, issn = {1538-4357}, journal = {Astrophysical Journal}, number = {2}, publisher = {IOP Publishing}, title = {{FRESCO: The Paschen-α star-forming sequence at cosmic noon}}, doi = {10.3847/1538-4357/ad6158}, volume = {972}, year = {2024}, } @inproceedings{18070, abstract = {Parallel SGD in a shared-memory setting is oft-represented by the popular Hogwild! algorithm, in which lock-free updates are asynchronously performed by multiple computing processes. Unfortunately, scaling Hogwild! to distributed workers is largely unexplored. Specifically, it is unknown if any adaptation of Hogwild! to the popular decentralized multi-GPU setting offers any competitive speedup, either empirically or theoretically. In this work, we investigate the potential of decentralizing Hogwild! by incorporating simultaneously (a) asynchronous local gradient updates on the shared memory of GPUs, and (b) non-blocking asynchronous decentralized federated averaging. A naive direct implementation shows degradation in performance, arising from scheduling overheads and concurrent write conflicts on GPUs. To mitigate these drawbacks, we investigate and propose a new method, based on careful block selection rules, which update only portions of the parameter vectors. Our experiments show that the resulting decentralized training method exhibits improved throughput and competitive accuracy for standard image classification benchmarks on the CIFAR-10, CIFAR-100, and Imagenet datasets. On the theoretical side, we prove that our method guarantees sublinear ergodic convergence rates for non-convex objectives.}, author = {Chatterjee, Bapi and Kungurtsev, Vyacheslav and Alistarh, Dan-Adrian}, booktitle = {Proceedings of the 44th International Conference on Distributed Computing Systems}, isbn = {9798350386059}, issn = {2575-8411}, location = {Jersey City, NJ, United States}, pages = {857--868}, publisher = {IEEE}, title = {{Federated SGD with local asynchrony}}, doi = {10.1109/ICDCS60910.2024.00084}, year = {2024}, } @inproceedings{18071, abstract = {Recent advancements on DAG-based consensus protocols allow for blockchains with improved metrics and properties, such as throughput and censorship-resistance. Variants of the Bullshark [18] consensus protocol are adopted for practical use by the Sui blockchain, for improved latency. However, the protocol is leader-based, and is strongly affected by crashed leaders that can lead to various performance issues, for example, decreased transaction throughput. In this paper, we propose HammerHead, a DAG-based consensus protocol, that is inspired by Carousel [8] and provides Leader-Utilization. Our proposal differs from Carousel, which is built for a chained consensus protocol; in HammerHead chain quality is inherited by the DAG. HammerHead needs to preserve safety and liveness, despite validators committing leader vertices asynchronously. The key idea is to update leader schedules dynamically, based on the validators' scores during the previous schedule. We implement HammerHead and show a minor improvement in performance for cases without faults. The major improvements in comparison to Bullshark appear in faulty settings. Specifically, we show a drastic, 2x-latency improvement and up to 40% increased throughput when crash faults occur (100 validators, 33 faults).}, author = {Tsimos, Giorgos and Kichidis, Anastasios and Sonnino, Alberto and Kokoris Kogias, Eleftherios}, booktitle = {Proceedings - International Conference on Distributed Computing Systems}, isbn = {9798350386059}, issn = {2575-8411}, location = {Jersey City, NJ, United States}, pages = {1377--1387}, publisher = {IEEE}, title = {{HammerHead: Leader reputation for dynamic scheduling}}, doi = {10.1109/ICDCS60910.2024.00129}, year = {2024}, } @article{18072, abstract = {The individualization of chromosomes during early mitosis and their clustering upon exit from cell division are two key transitions that ensure efficient segregation of eukaryotic chromosomes. Both processes are regulated by the surfactant-like protein Ki-67, but how Ki-67 achieves these diametric functions has remained unknown. Here, we report that Ki-67 radically switches from a chromosome repellent to a chromosome attractant during anaphase in human cells. We show that Ki-67 dephosphorylation during mitotic exit and the simultaneous exposure of a conserved basic patch induce the RNA-dependent formation of a liquid-like condensed phase on the chromosome surface. Experiments and coarse-grained simulations support a model in which the coalescence of chromosome surfaces, driven by co-condensation of Ki-67 and RNA, promotes clustering of chromosomes. Our study reveals how the switch of Ki-67 from a surfactant to a liquid-like condensed phase can generate mechanical forces during genome segregation that are required for re-establishing nuclear-cytoplasmic compartmentalization after mitosis.}, author = {Hernandez-Armendariz, Alberto and Sorichetti, Valerio and Hayashi, Yuki and Koskova, Zuzana and Brunner, Andreas and Ellenberg, Jan and Šarić, Anđela and Cuylen-Haering, Sara}, issn = {1097-4164}, journal = {Molecular Cell}, number = {17}, pages = {P3254--3270.E9}, publisher = {Cell Press}, title = {{A liquid-like coat mediates chromosome clustering during mitotic exit}}, doi = {10.1016/j.molcel.2024.07.022}, volume = {84}, year = {2024}, } @article{18073, abstract = {Conserved signaling cascades monitor protein-folding homeostasis to ensure proper cellular function. One of the evolutionary conserved key players is IRE1, which maintains endoplasmic reticulum (ER) homeostasis through the unfolded protein response (UPR). Upon accumulation of misfolded proteins in the ER, IRE1 forms clusters on the ER membrane to initiate UPR signaling. What regulates IRE1 cluster formation is not fully understood. Here, we show that the ER lumenal domain (LD) of human IRE1α forms biomolecular condensates in vitro. IRE1α LD condensates were stabilized both by binding to unfolded polypeptides as well as by tethering to model membranes, suggesting their role in assembling IRE1α into signaling-competent stable clusters. Molecular dynamics simulations indicated that weak multivalent interactions drive IRE1α LD clustering. Mutagenesis experiments identified disordered regions in IRE1α LD to control its clustering in vitro and in cells. Importantly, dysregulated clustering of IRE1α mutants led to defects in IRE1α signaling. Our results revealed that disordered regions in IRE1α LD control its clustering and suggest their role as a common strategy in regulating protein assembly on membranes.}, author = {Kettel, Paulina and Marosits, Laura and Spinetti, Elena and Rechberger, Michael and Giannini, Caterina and Radler, Philipp and Niedermoser, Isabell and Fischer, Irmgard and Versteeg, Gijs A. and Loose, Martin and Covino, Roberto and Karagöz, G. Elif}, issn = {1460-2075}, journal = {EMBO Journal}, number = {20}, pages = {4668--4698}, publisher = {Embo Press}, title = {{Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering}}, doi = {10.1038/s44318-024-00207-0}, volume = {43}, year = {2024}, } @phdthesis{18076, abstract = {The new era of Ge has opened up new possibilities in quantum computing. The maturity of Ge spin qubits is unquestioned, while hybrid semiconductor-superconductor Ge circuits are on track to enter the game. Gate-tunable transmons (gatemons) employing semiconductor Josephson junctions have recently emerged as building blocks for such hybrid quantum circuits. In this thesis, we present a gatemon fabricated in planar Germanium. We induce superconductivity in a two-dimensional hole gas by evaporating aluminum atop a thin spacer, which separates the superconductor from the Ge quantum well. The Josephson junction is then integrated into an Xmon circuit and capacitively coupled to a transmission line resonator. We showcase the qubit tunability in a broad frequency range with resonator and two-tone spectroscopy. Time-domain characterizations reveal energy relaxation and coherence times up to 75 ns. Our results, combined with the recent advances in the spin qubit field, pave the way towards novel hybrid and protected qubits in a group IV, CMOS-compatible material.}, author = {Sagi, Oliver}, issn = {2663-337X}, pages = {111}, publisher = {Institute of Science and Technology Austria}, title = {{Hybrid circuits on planar Germanium}}, doi = {10.15479/at:ista:18076}, year = {2024}, }