TY - JOUR AB - As a bottleneck in the direct synthesis of hydrogen peroxide, the development of an efficient palladium-based catalyst has garnered great attention. However, elusive active centers and reaction mechanism issues inhibit further optimization of its performance. In this work, advanced microkinetic modeling with the adsorbate–adsorbate interaction and nanoparticle size effect based on first-principles calculations is developed. A full mechanism uncovering the significance of adsorbate–adsorbate interaction is determined on Pd nanoparticles. We demonstrate unambiguously that Pd(100) with main coverage species of O2 and H is beneficial to H2O2 production, being consistent with experimental operando observation, while H2O forms on Pd(111) covered by O species and Pd(211) covered by O and OH species. Kinetic analyses further enable quantitative estimation of the influence of temperature, pressure, and particle size. Large-size Pd nanoparticles are found to achieve a high H2O2 reaction rate when the operating conditions are moderate temperature and higher oxygen partial pressure. We reveal that specific facets of the Pd nanoparticles are crucial factors for their selectivity and activity. Consistent with the experiment, the production of H2O2 is discovered to be more favorable on Pd nanoparticles containing Pd(100) facets. The ratio of H2/O2 induces substantial variations in the coverage of intermediates of O2 and H on Pd(100), resulting in a change in product selectivity. AU - Zhao, Jinyan AU - Yao, Zihao AU - Bunting, Rhys AU - Hu, P. AU - Wang, Jianguo ID - 14663 IS - 22 JF - ACS Catalysis TI - Microkinetic modeling with size-dependent and adsorbate-adsorbate interactions for the direct synthesis of H₂O₂ over Pd nanoparticles VL - 13 ER - TY - JOUR AB - For large dimensional non-Hermitian random matrices X with real or complex independent, identically distributed, centered entries, we consider the fluctuations of f (X) as a matrix where f is an analytic function around the spectrum of X. We prove that for a generic bounded square matrix A, the quantity Tr f (X)A exhibits Gaussian fluctuations as the matrix size grows to infinity, which consists of two independent modes corresponding to the tracial and traceless parts of A. We find a new formula for the variance of the traceless part that involves the Frobenius norm of A and the L2-norm of f on the boundary of the limiting spectrum. AU - Erdös, László AU - Ji, Hong Chang ID - 14667 IS - 4 JF - Annales de l'institut Henri Poincare (B) Probability and Statistics SN - 0246-0203 TI - Functional CLT for non-Hermitian random matrices VL - 59 ER - TY - JOUR AB - We consider a class of polaron models, including the Fröhlich model, at zero total momentum, and show that at sufficiently weak coupling there are no excited eigenvalues below the essential spectrum. AU - Seiringer, Robert ID - 14662 IS - 3 JF - Journal of Spectral Theory SN - 1664-039X TI - Absence of excited eigenvalues for Fröhlich type polaron models at weak coupling VL - 13 ER - TY - JOUR AB - In order to demonstrate the stability of newly proposed iridium-based Ir2Cr(In,Sn) and IrRhCr(In,Sn) heusler alloys, we present ab-initio analysis of these alloys by examining various properties to prove their stability. The stability of these alloys can be inferred from different cohesive and formation energies as well as positive phonon frequencies. Their electronic structure results indicate that they are semi-metals in nature. The magnetic moments are computed using the Slater-Pauling formula and exhibit a high value, with the Cr atom contributing the most in all alloys. Mulliken’s charge analysis results show that our alloys contain a range of linkages, mainly ionic and covalent ones. The ductility and mechanical stability of these alloys are confirmed by elastic constants viz. Poisson’s ratio, Pugh’s ratio, and many different types of elastic moduli. AU - Gupta, Shyam Lal AU - Singh, Saurabh AU - Kumar, Sumit AU - Anupam, Unknown AU - Thakur, Samjeet Singh AU - Kumar, Ashish AU - Panwar, Sanjay AU - Diwaker, D. ID - 14652 JF - Physica B: Condensed Matter SN - 0921-4526 TI - Ab-initio stability of Iridium based newly proposed full and quaternary heusler alloys VL - 674 ER - TY - JOUR AB - Sleep plays a key role in preserving brain function, keeping the brain network in a state that ensures optimal computational capabilities. Empirical evidence indicates that such a state is consistent with criticality, where scale-free neuronal avalanches emerge. However, the relationship between sleep, emergent avalanches, and criticality remains poorly understood. Here we fully characterize the critical behavior of avalanches during sleep, and study their relationship with the sleep macro- and micro-architecture, in particular the cyclic alternating pattern (CAP). We show that avalanche size and duration distributions exhibit robust power laws with exponents approximately equal to −3/2 e −2, respectively. Importantly, we find that sizes scale as a power law of the durations, and that all critical exponents for neuronal avalanches obey robust scaling relations, which are consistent with the mean-field directed percolation universality class. Our analysis demonstrates that avalanche dynamics depends on the position within the NREM-REM cycles, with the avalanche density increasing in the descending phases and decreasing in the ascending phases of sleep cycles. Moreover, we show that, within NREM sleep, avalanche occurrence correlates with CAP activation phases, particularly A1, which are the expression of slow wave sleep propensity and have been proposed to be beneficial for cognitive processes. The results suggest that neuronal avalanches, and thus tuning to criticality, actively contribute to sleep development and play a role in preserving network function. Such findings, alongside characterization of the universality class for avalanches, open new avenues to the investigation of functional role of criticality during sleep with potential clinical application.Significance statementWe fully characterize the critical behavior of neuronal avalanches during sleep, and show that avalanches follow precise scaling laws that are consistent with the mean-field directed percolation universality class. The analysis provides first evidence of a functional relationship between avalanche occurrence, slow-wave sleep dynamics, sleep stage transitions and occurrence of CAP phase A during NREM sleep. Because CAP is considered one of the major guardians of NREM sleep that allows the brain to dynamically react to external perturbation and contributes to the cognitive consolidation processes occurring in sleep, our observations suggest that neuronal avalanches at criticality are associated with flexible response to external inputs and to cognitive processes, a key assumption of the critical brain hypothesis. AU - Scarpetta, Silvia AU - Morrisi, Niccolò AU - Mutti, Carlotta AU - Azzi, Nicoletta AU - Trippi, Irene AU - Ciliento, Rosario AU - Apicella, Ilenia AU - Messuti, Giovanni AU - Angiolelli, Marianna AU - Lombardi, Fabrizio AU - Parrino, Liborio AU - Vaudano, Anna Elisabetta ID - 12487 IS - 10 JF - iScience TI - Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture VL - 26 ER - TY - JOUR AB - Background: Fighting disease while fighting rivals exposes males to constraints and tradeoffs during male-male competition. We here tested how both the stage and intensity of infection with the fungal pathogen Metarhizium robertsii interfered with fighting success in Cardiocondyla obscurior ant males. Males of this species have evolved long lifespans during which they can gain many matings with the young queens of the colony, if successful in male-male competition. Since male fights occur inside the colony, the outcome of male-male competition can further be biased by interference of the colony’s worker force. Results: We found that severe, but not yet mild, infection strongly impaired male fighting success. In late-stage infection, this could be attributed to worker aggression directed towards the infected rather than the healthy male and an already very high male morbidity even in the absence of fighting. Shortly after pathogen exposure, however, male mortality was particularly increased during combat. Since these males mounted a strong immune response, their reduced fighting success suggests a trade-off between immune investment and competitive ability already early in the infection. Even if the males themselves showed no difference in the number of attacks they raised against their healthy rivals across infection stages and levels, severely infected males were thus losing in male-male competition from an early stage of infection on. Conclusions: Males of the ant C. obscurior have evolved high immune investment, triggering an effective immune response very fast after fungal exposure. This allows them to cope with mild pathogen exposures without cost to their success in male-male competition, and hence to gain multiple mating opportunities with the emerging virgin queens of the colony. Under severe infection, however, they are weak fighters and rarely survive a combat already at early infection when raising an immune response, as well as at progressed infection, when they are morbid and preferentially targeted by worker aggression. Workers thereby remove males that pose a future disease threat by biasing male-male competition. Our study thus revealed a novel social immunity mechanism how social insect workers protect the colony against disease risk. AU - Metzler, Sina AU - Kirchner, Jessica AU - Grasse, Anna V AU - Cremer, Sylvia ID - 12696 JF - BMC Ecology and Evolution SN - 2730-7182 TI - Trade-offs between immunity and competitive ability in fighting ant males VL - 23 ER - TY - JOUR AB - Understanding the response of Himalayan glaciers to global warming is vital because of their role as a water source for the Asian subcontinent. However, great uncertainties still exist on the climate drivers of past and present glacier changes across scales. Here, we analyse continuous hourly climate station data from a glacierized elevation (Pyramid station, Mount Everest) since 1994 together with other ground observations and climate reanalysis. We show that a decrease in maximum air temperature and precipitation occurred during the last three decades at Pyramid in response to global warming. Reanalysis data suggest a broader occurrence of this effect in the glacierized areas of the Himalaya. We hypothesize that the counterintuitive cooling is caused by enhanced sensible heat exchange and the associated increase in glacier katabatic wind, which draws cool air downward from higher elevations. The stronger katabatic winds have also lowered the elevation of local wind convergence, thereby diminishing precipitation in glacial areas and negatively affecting glacier mass balance. This local cooling may have partially preserved glaciers from melting and could help protect the periglacial environment. AU - Salerno, Franco AU - Guyennon, Nicolas AU - Yang, Kun AU - Shaw, Thomas AU - Lin, Changgui AU - Colombo, Nicola AU - Romano, Emanuele AU - Gruber, Stephan AU - Bolch, Tobias AU - Alessandri, Andrea AU - Cristofanelli, Paolo AU - Putero, Davide AU - Diolaiuti, Guglielmina AU - Tartari, Gianni AU - Verza, Gianpietro AU - Thakuri, Sudeep AU - Balsamo, Gianpaolo AU - Miles, Evan S. AU - Pellicciotti, Francesca ID - 14659 JF - Nature Geoscience SN - 1752-0894 TI - Local cooling and drying induced by Himalayan glaciers under global warming VL - 16 ER - TY - JOUR AB - AMPA glutamate receptors (AMPARs) mediate excitatory neurotransmission throughout the brain. Their signalling is uniquely diversified by brain region-specific auxiliary subunits, providing an opportunity for the development of selective therapeutics. AMPARs associated with TARP γ8 are enriched in the hippocampus, and are targets of emerging anti-epileptic drugs. To understand their therapeutic activity, we determined cryo-EM structures of the GluA1/2-γ8 receptor associated with three potent, chemically diverse ligands. We find that despite sharing a lipid-exposed and water-accessible binding pocket, drug action is differentially affected by binding-site mutants. Together with patch-clamp recordings and MD simulations we also demonstrate that ligand-triggered reorganisation of the AMPAR-TARP interface contributes to modulation. Unexpectedly, one ligand (JNJ-61432059) acts bifunctionally, negatively affecting GluA1 but exerting positive modulatory action on GluA2-containing AMPARs, in a TARP stoichiometry-dependent manner. These results further illuminate the action of TARPs, demonstrate the sensitive balance between positive and negative modulatory action, and provide a mechanistic platform for development of both positive and negative selective AMPAR modulators. AU - Zhang, Danyang AU - Lape, Remigijus AU - Shaikh, Saher A. AU - Kohegyi, Bianka K. AU - Watson, Jake AU - Cais, Ondrej AU - Nakagawa, Terunaga AU - Greger, Ingo H. ID - 12786 JF - Nature Communications TI - Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics VL - 14 ER - TY - DATA AB - See Readme File for further information. AU - Cremer, Sylvia ID - 12693 TI - Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males ER - TY - JOUR AB - Urban-living individuals are exposed to many environmental factors that may combine and interact to influence mental health. While individual factors of an urban environment have been investigated in isolation, no attempt has been made to model how complex, real-life exposure to living in the city relates to brain and mental health, and how this is moderated by genetic factors. Using the data of 156,075 participants from the UK Biobank, we carried out sparse canonical correlation analyses to investigate the relationships between urban environments and psychiatric symptoms. We found an environmental profile of social deprivation, air pollution, street network and urban land-use density that was positively correlated with an affective symptom group (r = 0.22, Pperm < 0.001), mediated by brain volume differences consistent with reward processing, and moderated by genes enriched for stress response, including CRHR1, explaining 2.01% of the variance in brain volume differences. Protective factors such as greenness and generous destination accessibility were negatively correlated with an anxiety symptom group (r = 0.10, Pperm < 0.001), mediated by brain regions necessary for emotion regulation and moderated by EXD3, explaining 1.65% of the variance. The third urban environmental profile was correlated with an emotional instability symptom group (r = 0.03, Pperm < 0.001). Our findings suggest that different environmental profiles of urban living may influence specific psychiatric symptom groups through distinct neurobiological pathways. AU - Xu, Jiayuan AU - Liu, Nana AU - Polemiti, Elli AU - Garcia-Mondragon, Liliana AU - Tang, Jie AU - Liu, Xiaoxuan AU - Lett, Tristram AU - Yu, Le AU - Nöthen, Markus M. AU - Feng, Jianfeng AU - Yu, Chunshui AU - Marquand, Andre AU - Schumann, Gunter AU - Walter, Henrik AU - Heinz, Andreas AU - Ralser, Markus AU - Twardziok, Sven AU - Vaidya, Nilakshi AU - Serin, Emin AU - Jentsch, Marcel AU - Hitchen, Esther AU - Eils, Roland AU - Taron, Ulrike Helene AU - Schütz, Tatjana AU - Schepanski, Kerstin AU - Banks, Jamie AU - Banaschewski, Tobias AU - Jansone, Karina AU - Christmann, Nina AU - Meyer-Lindenberg, Andreas AU - Tost, Heike AU - Holz, Nathalie AU - Schwarz, Emanuel AU - Stringaris, Argyris AU - Neidhart, Maja AU - Nees, Frauke AU - Siehl, Sebastian AU - A. Andreassen, Ole AU - T. Westlye, Lars AU - Van Der Meer, Dennis AU - Fernandez, Sara AU - Kjelkenes, Rikka AU - Ask, Helga AU - Rapp, Michael AU - Tschorn, Mira AU - Böttger, Sarah Jane AU - Novarino, Gaia AU - Marr, Lena AU - Slater, Mel AU - Viapiana, Guillem Feixas AU - Orosa, Francisco Eiroa AU - Gallego, Jaime AU - Pastor, Alvaro AU - Forstner, Andreas AU - Hoffmann, Per AU - M. Nöthen, Markus AU - J. Forstner, Andreas AU - Claus, Isabelle AU - Miller, Abbi AU - Heilmann-Heimbach, Stefanie AU - Sommer, Peter AU - Boye, Mona AU - Wilbertz, Johannes AU - Schmitt, Karen AU - Jirsa, Viktor AU - Petkoski, Spase AU - Pitel, Séverine AU - Otten, Lisa AU - Athanasiadis, Anastasios Polykarpos AU - Pearmund, Charlie AU - Spanlang, Bernhard AU - Alvarez, Elena AU - Sanchez, Mavi AU - Giner, Arantxa AU - Hese, Sören AU - Renner, Paul AU - Jia, Tianye AU - Gong, Yanting AU - Xia, Yunman AU - Chang, Xiao AU - Calhoun, Vince AU - Liu, Jingyu AU - Thompson, Paul AU - Clinton, Nicholas AU - Desrivieres, Sylvane AU - H. Young, Allan AU - Stahl, Bernd AU - Ogoh, George ID - 13168 JF - Nature Medicine SN - 1078-8956 TI - Effects of urban living environments on mental health in adults VL - 29 ER - TY - CONF AB - 3D printing based on continuous deposition of materials, such as filament-based 3D printing, has seen widespread adoption thanks to its versatility in working with a wide range of materials. An important shortcoming of this type of technology is its limited multi-material capabilities. While there are simple hardware designs that enable multi-material printing in principle, the required software is heavily underdeveloped. A typical hardware design fuses together individual materials fed into a single chamber from multiple inlets before they are deposited. This design, however, introduces a time delay between the intended material mixture and its actual deposition. In this work, inspired by diverse path planning research in robotics, we show that this mechanical challenge can be addressed via improved printer control. We propose to formulate the search for optimal multi-material printing policies in a reinforcement learning setup. We put forward a simple numerical deposition model that takes into account the non-linear material mixing and delayed material deposition. To validate our system we focus on color fabrication, a problem known for its strict requirements for varying material mixtures at a high spatial frequency. We demonstrate that our learned control policy outperforms state-of-the-art hand-crafted algorithms. AU - Liao, Kang AU - Tricard, Thibault AU - Piovarci, Michael AU - Seidel, Hans-Peter AU - Babaei, Vahid ID - 12976 KW - reinforcement learning KW - deposition KW - control KW - color KW - multi-filament SN - 1050-4729 T2 - 2023 IEEE International Conference on Robotics and Automation TI - Learning deposition policies for fused multi-material 3D printing VL - 2023 ER - TY - JOUR AB - Molecular compatibility between gametes is a prerequisite for successful fertilization. As long as a sperm and egg can recognize and bind each other via their surface proteins, gamete fusion may occur even between members of separate species, resulting in hybrids that can impact speciation. The egg membrane protein Bouncer confers species specificity to gamete interactions between medaka and zebrafish, preventing their cross-fertilization. Here, we leverage this specificity to uncover distinct amino acid residues and N-glycosylation patterns that differentially influence the function of medaka and zebrafish Bouncer and contribute to cross-species incompatibility. Curiously, in contrast to the specificity observed for medaka and zebrafish Bouncer, seahorse and fugu Bouncer are compatible with both zebrafish and medaka sperm, in line with the pervasive purifying selection that dominates Bouncer’s evolution. The Bouncer-sperm interaction is therefore the product of seemingly opposing evolutionary forces that, for some species, restrict fertilization to closely related fish, and for others, allow broad gamete compatibility that enables hybridization. AU - Gert, Krista R.B. AU - Panser, Karin AU - Surm, Joachim AU - Steinmetz, Benjamin S. AU - Schleiffer, Alexander AU - Jovine, Luca AU - Moran, Yehu AU - Kondrashov, Fyodor AU - Pauli, Andrea ID - 13164 JF - Nature Communications TI - Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries VL - 14 ER - TY - JOUR AB - Let P be a nontorsion point on an elliptic curve defined over a number field K and consider the sequence {Bn}n∈N of the denominators of x(nP). We prove that every term of the sequence of the Bn has a primitive divisor for n greater than an effectively computable constant that we will explicitly compute. This constant will depend only on the model defining the curve. AU - Verzobio, Matteo ID - 12313 IS - 2 JF - Pacific Journal of Mathematics TI - Some effectivity results for primitive divisors of elliptic divisibility sequences VL - 325 ER - TY - JOUR AB - We prove a characterization of the Dirichlet–Ferguson measure over an arbitrary finite diffuse measure space. We provide an interpretation of this characterization in analogy with the Mecke identity for Poisson point processes. AU - Dello Schiavo, Lorenzo AU - Lytvynov, Eugene ID - 13145 JF - Electronic Communications in Probability TI - A Mecke-type characterization of the Dirichlet–Ferguson measure VL - 28 ER - TY - JOUR AB - We study the problem of high-dimensional multiple packing in Euclidean space. Multiple packing is a natural generalization of sphere packing and is defined as follows. Let N > 0 and L ∈ Z ≽2 . A multiple packing is a set C of points in R n such that any point in R n lies in the intersection of at most L – 1 balls of radius √ nN around points in C . Given a well-known connection with coding theory, multiple packings can be viewed as the Euclidean analog of list-decodable codes, which are well-studied for finite fields. In this paper, we derive the best known lower bounds on the optimal density of list-decodable infinite constellations for constant L under a stronger notion called average-radius multiple packing. To this end, we apply tools from high-dimensional geometry and large deviation theory. AU - Zhang, Yihan AU - Vatedka, Shashank ID - 12838 IS - 7 JF - IEEE Transactions on Information Theory SN - 0018-9448 TI - Multiple packing: Lower bounds via infinite constellations VL - 69 ER - TY - CONF AB - A machine-learned system that is fair in static decision-making tasks may have biased societal impacts in the long-run. This may happen when the system interacts with humans and feedback patterns emerge, reinforcing old biases in the system and creating new biases. While existing works try to identify and mitigate long-run biases through smart system design, we introduce techniques for monitoring fairness in real time. Our goal is to build and deploy a monitor that will continuously observe a long sequence of events generated by the system in the wild, and will output, with each event, a verdict on how fair the system is at the current point in time. The advantages of monitoring are two-fold. Firstly, fairness is evaluated at run-time, which is important because unfair behaviors may not be eliminated a priori, at design-time, due to partial knowledge about the system and the environment, as well as uncertainties and dynamic changes in the system and the environment, such as the unpredictability of human behavior. Secondly, monitors are by design oblivious to how the monitored system is constructed, which makes them suitable to be used as trusted third-party fairness watchdogs. They function as computationally lightweight statistical estimators, and their correctness proofs rely on the rigorous analysis of the stochastic process that models the assumptions about the underlying dynamics of the system. We show, both in theory and experiments, how monitors can warn us (1) if a bank’s credit policy over time has created an unfair distribution of credit scores among the population, and (2) if a resource allocator’s allocation policy over time has made unfair allocations. Our experiments demonstrate that the monitors introduce very low overhead. We believe that runtime monitoring is an important and mathematically rigorous new addition to the fairness toolbox. AU - Henzinger, Thomas A AU - Karimi, Mahyar AU - Kueffner, Konstantin AU - Mallik, Kaushik ID - 13228 SN - 9781450372527 T2 - FAccT '23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency TI - Runtime monitoring of dynamic fairness properties ER - TY - JOUR AB - Recently the leading order of the correlation energy of a Fermi gas in a coupled mean-field and semiclassical scaling regime has been derived, under the assumption of an interaction potential with a small norm and with compact support in Fourier space. We generalize this result to large interaction potentials, requiring only |⋅|V^∈ℓ1(Z3). Our proof is based on approximate, collective bosonization in three dimensions. Significant improvements compared to recent work include stronger bounds on non-bosonizable terms and more efficient control on the bosonization of the kinetic energy. AU - Benedikter, Niels P AU - Porta, Marcello AU - Schlein, Benjamin AU - Seiringer, Robert ID - 13225 IS - 4 JF - Archive for Rational Mechanics and Analysis SN - 0003-9527 TI - Correlation energy of a weakly interacting Fermi gas with large interaction potential VL - 247 ER - TY - JOUR AB - We consider the ground state and the low-energy excited states of a system of N identical bosons with interactions in the mean-field scaling regime. For the ground state, we derive a weak Edgeworth expansion for the fluctuations of bounded one-body operators, which yields corrections to a central limit theorem to any order in 1/N−−√. For suitable excited states, we show that the limiting distribution is a polynomial times a normal distribution, and that higher-order corrections are given by an Edgeworth-type expansion. AU - Bossmann, Lea AU - Petrat, Sören P ID - 13226 IS - 4 JF - Letters in Mathematical Physics SN - 0377-9017 TI - Weak Edgeworth expansion for the mean-field Bose gas VL - 113 ER - TY - JOUR AB - Currently available quantum processors are dominated by noise, which severely limits their applicability and motivates the search for new physical qubit encodings. In this work, we introduce the inductively shunted transmon, a weakly flux-tunable superconducting qubit that offers charge offset protection for all levels and a 20-fold reduction in flux dispersion compared to the state-of-the-art resulting in a constant coherence over a full flux quantum. The parabolic confinement provided by the inductive shunt as well as the linearity of the geometric superinductor facilitates a high-power readout that resolves quantum jumps with a fidelity and QND-ness of >90% and without the need for a Josephson parametric amplifier. Moreover, the device reveals quantum tunneling physics between the two prepared fluxon ground states with a measured average decay time of up to 3.5 h. In the future, fast time-domain control of the transition matrix elements could offer a new path forward to also achieve full qubit control in the decay-protected fluxon basis. AU - Hassani, Farid AU - Peruzzo, Matilda AU - Kapoor, Lucky AU - Trioni, Andrea AU - Zemlicka, Martin AU - Fink, Johannes M ID - 13227 JF - Nature Communications TI - Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours VL - 14 ER - TY - CONF AB - We consider the problem of reconstructing the signal and the hidden variables from observations coming from a multi-layer network with rotationally invariant weight matrices. The multi-layer structure models inference from deep generative priors, and the rotational invariance imposed on the weights generalizes the i.i.d. Gaussian assumption by allowing for a complex correlation structure, which is typical in applications. In this work, we present a new class of approximate message passing (AMP) algorithms and give a state evolution recursion which precisely characterizes their performance in the large system limit. In contrast with the existing multi-layer VAMP (ML-VAMP) approach, our proposed AMP – dubbed multilayer rotationally invariant generalized AMP (ML-RI-GAMP) – provides a natural generalization beyond Gaussian designs, in the sense that it recovers the existing Gaussian AMP as a special case. Furthermore, ML-RI-GAMP exhibits a significantly lower complexity than ML-VAMP, as the computationally intensive singular value decomposition is replaced by an estimation of the moments of the design matrices. Finally, our numerical results show that this complexity gain comes at little to no cost in the performance of the algorithm. AU - Xu, Yizhou AU - Hou, Tian Qi AU - Liang, Shan Suo AU - Mondelli, Marco ID - 13321 SN - 9798350301496 T2 - 2023 IEEE Information Theory Workshop TI - Approximate message passing for multi-layer estimation in rotationally invariant models ER - TY - JOUR AB - In this study, we propose a computational framework for optimizing the continuity of the toolpath in fabricating surface models on an extrusion-based 3D printer. Toolpath continuity is a critical issue that influences both the quality and the efficiency of extrusion-based fabrication. Transfer moves lead to rough and bumpy surfaces, where this phenomenon worsens for materials with large viscosity, like clay. The effects of continuity on the surface models are even more severe in terms of the quality of the surface and the stability of the model. We introduce a criterion called the one–path patch (OPP) to represent a patch on the surface of the shell that can be traversed along one path by considering the constraints on fabrication. We study the properties of the OPPs and their merging operations to propose a bottom-up OPP merging procedure to decompose the given shell surface into a minimal number of OPPs, and to generate the “as-continuous-as-possible” (ACAP) toolpath. Furthermore, we augment the path planning algorithm with a curved-layer printing scheme that reduces staircase defects and improves the continuity of the toolpath by connecting multiple segments. We evaluated the ACAP algorithm on ceramic and thermoplastic materials, and the results showed that it improves the fabrication of surface models in terms of both efficiency and surface quality. AU - Zhong, Fanchao AU - Xu, Yonglai AU - Zhao, Haisen AU - Lu, Lin ID - 13265 IS - 3 JF - ACM Transactions on Graphics SN - 0730-0301 TI - As-Continuous-As-Possible extrusion-based fabrication of surface models VL - 42 ER - TY - JOUR AB - Bohnenblust–Hille inequalities for Boolean cubes have been proven with dimension-free constants that grow subexponentially in the degree (Defant et al. in Math Ann 374(1):653–680, 2019). Such inequalities have found great applications in learning low-degree Boolean functions (Eskenazis and Ivanisvili in Proceedings of the 54th annual ACM SIGACT symposium on theory of computing, pp 203–207, 2022). Motivated by learning quantum observables, a qubit analogue of Bohnenblust–Hille inequality for Boolean cubes was recently conjectured in Rouzé et al. (Quantum Talagrand, KKL and Friedgut’s theorems and the learnability of quantum Boolean functions, 2022. arXiv preprint arXiv:2209.07279). The conjecture was resolved in Huang et al. (Learning to predict arbitrary quantum processes, 2022. arXiv preprint arXiv:2210.14894). In this paper, we give a new proof of these Bohnenblust–Hille inequalities for qubit system with constants that are dimension-free and of exponential growth in the degree. As a consequence, we obtain a junta theorem for low-degree polynomials. Using similar ideas, we also study learning problems of low degree quantum observables and Bohr’s radius phenomenon on quantum Boolean cubes. AU - Volberg, Alexander AU - Zhang, Haonan ID - 13318 JF - Mathematische Annalen SN - 0025-5831 TI - Noncommutative Bohnenblust–Hille inequalities ER - TY - JOUR AB - In this paper, we prove the convexity of trace functionals (A,B,C)↦Tr|BpACq|s, for parameters (p, q, s) that are best possible, where B and C are any n-by-n positive-definite matrices, and A is any n-by-n matrix. We also obtain the monotonicity versions of trace functionals of this type. As applications, we extend some results in Carlen et al. (Linear Algebra Appl 490:174–185, 2016), Hiai and Petz (Publ Res Inst Math Sci 48(3):525-542, 2012) and resolve a conjecture in Al-Rashed and Zegarliński (Infin Dimens Anal Quantum Probab Relat Top 17(4):1450029, 2014) in the matrix setting. Other conjectures in Al-Rashed and Zegarliński (Infin Dimens Anal Quantum Probab Relat Top 17(4):1450029, 2014) will also be discussed. We also show that some related trace functionals are not concave in general. Such concavity results were expected to hold in different problems. AU - Zhang, Haonan ID - 13271 JF - Annales Henri Poincare SN - 1424-0637 TI - Some convexity and monotonicity results of trace functionals ER - TY - JOUR AB - Many human interactions feature the characteristics of social dilemmas where individual actions have consequences for the group and the environment. The feedback between behavior and environment can be studied with the framework of stochastic games. In stochastic games, the state of the environment can change, depending on the choices made by group members. Past work suggests that such feedback can reinforce cooperative behaviors. In particular, cooperation can evolve in stochastic games even if it is infeasible in each separate repeated game. In stochastic games, participants have an interest in conditioning their strategies on the state of the environment. Yet in many applications, precise information about the state could be scarce. Here, we study how the availability of information (or lack thereof) shapes evolution of cooperation. Already for simple examples of two state games we find surprising effects. In some cases, cooperation is only possible if there is precise information about the state of the environment. In other cases, cooperation is most abundant when there is no information about the state of the environment. We systematically analyze all stochastic games of a given complexity class, to determine when receiving information about the environment is better, neutral, or worse for evolution of cooperation. AU - Kleshnina, Maria AU - Hilbe, Christian AU - Simsa, Stepan AU - Chatterjee, Krishnendu AU - Nowak, Martin A. ID - 13258 JF - Nature Communications TI - The effect of environmental information on evolution of cooperation in stochastic games VL - 14 ER - TY - JOUR AB - Motivation: Boolean networks are simple but efficient mathematical formalism for modelling complex biological systems. However, having only two levels of activation is sometimes not enough to fully capture the dynamics of real-world biological systems. Hence, the need for multi-valued networks (MVNs), a generalization of Boolean networks. Despite the importance of MVNs for modelling biological systems, only limited progress has been made on developing theories, analysis methods, and tools that can support them. In particular, the recent use of trap spaces in Boolean networks made a great impact on the field of systems biology, but there has been no similar concept defined and studied for MVNs to date. Results: In this work, we generalize the concept of trap spaces in Boolean networks to that in MVNs. We then develop the theory and the analysis methods for trap spaces in MVNs. In particular, we implement all proposed methods in a Python package called trapmvn. Not only showing the applicability of our approach via a realistic case study, we also evaluate the time efficiency of the method on a large collection of real-world models. The experimental results confirm the time efficiency, which we believe enables more accurate analysis on larger and more complex multi-valued models. AU - Trinh, Van Giang AU - Benhamou, Belaid AU - Henzinger, Thomas A AU - Pastva, Samuel ID - 13263 IS - Supplement_1 JF - Bioinformatics SN - 1367-4803 TI - Trap spaces of multi-valued networks: Definition, computation, and applications VL - 39 ER - TY - JOUR AB - Although budding yeast has been extensively used as a model organism for studying organelle functions and intracellular vesicle trafficking, whether it possesses an independent endocytic early/sorting compartment that sorts endocytic cargos to the endo-lysosomal pathway or the recycling pathway has long been unclear. The structure and properties of the endocytic early/sorting compartment differ significantly between organisms; in plant cells, the trans-Golgi network (TGN) serves this role, whereas in mammalian cells a separate intracellular structure performs this function. The yeast syntaxin homolog Tlg2p, widely localizing to the TGN and endosomal compartments, is presumed to act as a Q-SNARE for endocytic vesicles, but which compartment is the direct target for endocytic vesicles remained unanswered. Here we demonstrate by high-speed and high-resolution 4D imaging of fluorescently labeled endocytic cargos that the Tlg2p-residing compartment within the TGN functions as the early/sorting compartment. After arriving here, endocytic cargos are recycled to the plasma membrane or transported to the yeast Rab5-residing endosomal compartment through the pathway requiring the clathrin adaptors GGAs. Interestingly, Gga2p predominantly localizes at the Tlg2p-residing compartment, and the deletion of GGAs has little effect on another TGN region where Sec7p is present but suppresses dynamics of the Tlg2-residing early/sorting compartment, indicating that the Tlg2p- and Sec7p-residing regions are discrete entities in the mutant. Thus, the Tlg2p-residing region seems to serve as an early/sorting compartment and function independently of the Sec7p-residing region within the TGN. AU - Toshima, Junko Y. AU - Tsukahara, Ayana AU - Nagano, Makoto AU - Tojima, Takuro AU - Siekhaus, Daria E AU - Nakano, Akihiko AU - Toshima, Jiro ID - 13316 JF - eLife TI - The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network VL - 12 ER - TY - JOUR AB - We prove the Eigenstate Thermalisation Hypothesis (ETH) for local observables in a typical translation invariant system of quantum spins with L-body interactions, where L is the number of spins. This mathematically verifies the observation first made by Santos and Rigol (Phys Rev E 82(3):031130, 2010, https://doi.org/10.1103/PhysRevE.82.031130) that the ETH may hold for systems with additional translational symmetries for a naturally restricted class of observables. We also present numerical support for the same phenomenon for Hamiltonians with local interaction. AU - Sugimoto, Shoki AU - Henheik, Sven Joscha AU - Riabov, Volodymyr AU - Erdös, László ID - 13317 IS - 7 JF - Journal of Statistical Physics SN - 0022-4715 TI - Eigenstate thermalisation hypothesis for translation invariant spin systems VL - 190 ER - TY - JOUR AB - We present a numerical analysis of spin-1/2 fermions in a one-dimensional harmonic potential in the presence of a magnetic point-like impurity at the center of the trap. The model represents a few-body analogue of a magnetic impurity in the vicinity of an s-wave superconductor. Already for a few particles we find a ground-state level crossing between sectors with different fermion parities. We interpret this crossing as a few-body precursor of a quantum phase transition, which occurs when the impurity "breaks" a Cooper pair. This picture is further corroborated by analyzing density-density correlations in momentum space. Finally, we discuss how the system may be realized with existing cold-atoms platforms. AU - Rammelmüller, Lukas AU - Huber, David AU - Čufar, Matija AU - Brand, Joachim AU - Hammer, Hans-Werner AU - Volosniev, Artem ID - 13278 IS - 1 JF - SciPost Physics KW - General Physics and Astronomy SN - 2542-4653 TI - Magnetic impurity in a one-dimensional few-fermion system VL - 14 ER - TY - JOUR AB - Viscous flows through pipes and channels are steady and ordered until, with increasing velocity, the laminar motion catastrophically breaks down and gives way to turbulence. How this apparently discontinuous change from low- to high-dimensional motion can be rationalized within the framework of the Navier-Stokes equations is not well understood. Exploiting geometrical properties of transitional channel flow we trace turbulence to far lower Reynolds numbers (Re) than previously possible and identify the complete path that reversibly links fully turbulent motion to an invariant solution. This precursor of turbulence destabilizes rapidly with Re, and the accompanying explosive increase in attractor dimension effectively marks the transition between deterministic and de facto stochastic dynamics. AU - Paranjape, Chaitanya S AU - Yalniz, Gökhan AU - Duguet, Yohann AU - Budanur, Nazmi B AU - Hof, Björn ID - 13274 IS - 3 JF - Physical Review Letters KW - General Physics and Astronomy SN - 0031-9007 TI - Direct path from turbulence to time-periodic solutions VL - 131 ER - TY - JOUR AB - Chromosomes in the eukaryotic nucleus are highly compacted. However, for many functional processes, including transcription initiation, the pairwise motion of distal chromosomal elements such as enhancers and promoters is essential and necessitates dynamic fluidity. Here, we used a live-imaging assay to simultaneously measure the positions of pairs of enhancers and promoters and their transcriptional output while systematically varying the genomic separation between these two DNA loci. Our analysis reveals the coexistence of a compact globular organization and fast subdiffusive dynamics. These combined features cause an anomalous scaling of polymer relaxation times with genomic separation leading to long-ranged correlations. Thus, encounter times of DNA loci are much less dependent on genomic distance than predicted by existing polymer models, with potential consequences for eukaryotic gene expression. AU - Brückner, David AU - Chen, Hongtao AU - Barinov, Lev AU - Zoller, Benjamin AU - Gregor, Thomas ID - 13261 IS - 6652 JF - Science TI - Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome VL - 380 ER - TY - GEN AU - Kleshnina, Maria ID - 13336 TI - kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games ER - TY - JOUR AB - The ages of solar-like stars have been at the center of many studies such as exoplanet characterization or Galactic-archeology. While ages are usually computed from stellar evolution models, relations linking ages to other stellar properties, such as rotation and magnetic activity, have been investigated. With the large catalog of 55,232 rotation periods, Prot, and photometric magnetic activity index, Sph from Kepler data, we have the opportunity to look for such magneto-gyro-chronology relations. Stellar ages are obtained with two stellar evolution codes that include treatment of angular momentum evolution, hence using Prot as input in addition to classical atmospheric parameters. We explore two different ways of predicting stellar ages on three subsamples with spectroscopic observations: solar analogs, late-F and G dwarfs, and K dwarfs. We first perform a Bayesian analysis to derive relations between Sph and ages between 1 and 5 Gyr, and other stellar properties. For late-F and G dwarfs, and K dwarfs, the multivariate regression favors the model with Prot and Sph with median differences of 0.1% and 0.2%, respectively. We also apply Machine Learning techniques with a Random Forest algorithm to predict ages up to 14 Gyr with the same set of input parameters. For late-F, G and K dwarfs together, predicted ages are on average within 5.3% of the model ages and improve to 3.1% when including Prot. These are very promising results for a quick age estimation for solar-like stars with photometric observations, especially with current and future space missions. AU - Mathur, Savita AU - Claytor, Zachary R. AU - Santos, Ângela R. G. AU - García, Rafael A. AU - Amard, Louis AU - Bugnet, Lisa Annabelle AU - Corsaro, Enrico AU - Bonanno, Alfio AU - Breton, Sylvain N. AU - Godoy-Rivera, Diego AU - Pinsonneault, Marc H. AU - van Saders, Jennifer ID - 13443 IS - 2 JF - The Astrophysical Journal KW - Space and Planetary Science KW - Astronomy and Astrophysics SN - 0004-637X TI - Magnetic activity evolution of solar-like stars. I. Sph–age relation derived from Kepler observations VL - 952 ER - TY - JOUR AB - Plants can regenerate their bodies via de novo establishment of shoot apical meristems (SAMs) from pluripotent callus. Only a small fraction of callus cells is eventually specified into SAMs but the molecular mechanisms underlying fate specification remain obscure. The expression of WUSCHEL (WUS) is an early hallmark of SAM fate acquisition. Here, we show that a WUS paralog, WUSCHEL-RELATED HOMEOBOX 13 (WOX13), negatively regulates SAM formation from callus in Arabidopsis thaliana. WOX13 promotes non-meristematic cell fate via transcriptional repression of WUS and other SAM regulators and activation of cell wall modifiers. Our Quartz-Seq2–based single cell transcriptome revealed that WOX13 plays key roles in determining cellular identity of callus cell population. We propose that reciprocal inhibition between WUS and WOX13 mediates critical cell fate determination in pluripotent cell population, which has a major impact on regeneration efficiency. AU - Ogura, Nao AU - Sasagawa, Yohei AU - Ito, Tasuku AU - Tameshige, Toshiaki AU - Kawai, Satomi AU - Sano, Masaki AU - Doll, Yuki AU - Iwase, Akira AU - Kawamura, Ayako AU - Suzuki, Takamasa AU - Nikaido, Itoshi AU - Sugimoto, Keiko AU - Ikeuchi, Momoko ID - 13259 IS - 27 JF - Science Advances TI - WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus VL - 9 ER - TY - JOUR AB - Conflicts and natural disasters affect entire populations of the countries involved and, in addition to the thousands of lives destroyed, have a substantial negative impact on the scientific advances these countries provide. The unprovoked invasion of Ukraine by Russia, the devastating earthquake in Turkey and Syria, and the ongoing conflicts in the Middle East are just a few examples. Millions of people have been killed or displaced, their futures uncertain. These events have resulted in extensive infrastructure collapse, with loss of electricity, transportation, and access to services. Schools, universities, and research centers have been destroyed along with decades’ worth of data, samples, and findings. Scholars in disaster areas face short- and long-term problems in terms of what they can accomplish now for obtaining grants and for employment in the long run. In our interconnected world, conflicts and disasters are no longer a local problem but have wide-ranging impacts on the entire world, both now and in the future. Here, we focus on the current and ongoing impact of war on the scientific community within Ukraine and from this draw lessons that can be applied to all affected countries where scientists at risk are facing hardship. We present and classify examples of effective and feasible mechanisms used to support researchers in countries facing hardship and discuss how these can be implemented with help from the international scientific community and what more is desperately needed. Reaching out, providing accessible training opportunities, and developing collaborations should increase inclusion and connectivity, support scientific advancements within affected communities, and expedite postwar and disaster recovery. AU - Wolfsberger, Walter AU - Chhugani, Karishma AU - Shchubelka, Khrystyna AU - Frolova, Alina AU - Salyha, Yuriy AU - Zlenko, Oksana AU - Arych, Mykhailo AU - Dziuba, Dmytro AU - Parkhomenko, Andrii AU - Smolanka, Volodymyr AU - Gümüş, Zeynep H. AU - Sezgin, Efe AU - Diaz-Lameiro, Alondra AU - Toth, Viktor R. AU - Maci, Megi AU - Bortz, Eric AU - Kondrashov, Fyodor AU - Morton, Patricia M. AU - Łabaj, Paweł P. AU - Romero, Veronika AU - Hlávka, Jakub AU - Mangul, Serghei AU - Oleksyk, Taras K. ID - 13976 JF - GigaScience TI - Scientists without borders: Lessons from Ukraine VL - 12 ER - TY - JOUR AB - We construct families of log K3 surfaces and study the arithmetic of their members. We use this to produce explicit surfaces with an order 5 Brauer–Manin obstruction to the integral Hasse principle. AU - Lyczak, Julian ID - 13973 IS - 2 JF - Annales de l'Institut Fourier SN - 0373-0956 TI - Order 5 Brauer–Manin obstructions to the integral Hasse principle on log K3 surfaces VL - 73 ER - TY - JOUR AB - The Tverberg theorem is one of the cornerstones of discrete geometry. It states that, given a set X of at least (d+1)(r−1)+1 points in Rd, one can find a partition X=X1∪⋯∪Xr of X, such that the convex hulls of the Xi, i=1,…,r, all share a common point. In this paper, we prove a trengthening of this theorem that guarantees a partition which, in addition to the above, has the property that the boundaries of full-dimensional convex hulls have pairwise nonempty intersections. Possible generalizations and algorithmic aspects are also discussed. As a concrete application, we show that any n points in the plane in general position span ⌊n/3⌋ vertex-disjoint triangles that are pairwise crossing, meaning that their boundaries have pairwise nonempty intersections; this number is clearly best possible. A previous result of Álvarez-Rebollar et al. guarantees ⌊n/6⌋pairwise crossing triangles. Our result generalizes to a result about simplices in Rd, d≥2. AU - Fulek, Radoslav AU - Gärtner, Bernd AU - Kupavskii, Andrey AU - Valtr, Pavel AU - Wagner, Uli ID - 13974 JF - Discrete and Computational Geometry SN - 0179-5376 TI - The crossing Tverberg theorem ER - TY - JOUR AB - We consider the spectrum of random Laplacian matrices of the form Ln=An−Dn where An is a real symmetric random matrix and Dn is a diagonal matrix whose entries are equal to the corresponding row sums of An. If An is a Wigner matrix with entries in the domain of attraction of a Gaussian distribution, the empirical spectral measure of Ln is known to converge to the free convolution of a semicircle distribution and a standard real Gaussian distribution. We consider real symmetric random matrices An with independent entries (up to symmetry) whose row sums converge to a purely non-Gaussian infinitely divisible distribution, which fall into the class of Lévy–Khintchine random matrices first introduced by Jung [Trans Am Math Soc, 370, (2018)]. Our main result shows that the empirical spectral measure of Ln converges almost surely to a deterministic limit. A key step in the proof is to use the purely non-Gaussian nature of the row sums to build a random operator to which Ln converges in an appropriate sense. This operator leads to a recursive distributional equation uniquely describing the Stieltjes transform of the limiting empirical spectral measure. AU - Campbell, Andrew J AU - O’Rourke, Sean ID - 13975 JF - Journal of Theoretical Probability SN - 0894-9840 TI - Spectrum of Lévy–Khintchine random laplacian matrices ER - TY - JOUR AB - The magnetotropic susceptibility is the thermodynamic coefficient associated with the rotational anisotropy of the free energy in an external magnetic field and is closely related to the magnetic susceptibility. It emerges naturally in frequency-shift measurements of oscillating mechanical cantilevers, which are becoming an increasingly important tool in the quantitative study of the thermodynamics of modern condensed-matter systems. Here we discuss the basic properties of the magnetotropic susceptibility as they relate to the experimental aspects of frequency-shift measurements, as well as to the interpretation of those experiments in terms of the intrinsic properties of the system under study. AU - Shekhter, A. AU - Mcdonald, R. D. AU - Ramshaw, B. J. AU - Modic, Kimberly A ID - 13257 IS - 3 JF - Physical Review B SN - 2469-9950 TI - Magnetotropic susceptibility VL - 108 ER - TY - JOUR AB - This Special Collection is dedicated to the field of photocatalytic synthesis and contains a diverse selection of original research contributions. It includes studies on catalyst development, mechanistic investigations, method development and the use of enabling technologies, illustrating the many facets of state-of-the-art research in photocatalytic synthesis. Further, emerging topics are surveyed and discussed in three reviews and a concept article. AU - Næsborg, Line AU - Pieber, Bartholomäus AU - Wenger, Oliver S. ID - 13972 JF - ChemCatChem SN - 1867-3880 TI - Special Collection: Photocatalytic synthesis ER - TY - JOUR AB - The use of multimodal readout mechanisms next to label-free real-time monitoring of biomolecular interactions can provide valuable insight into surface-based reaction mechanisms. To this end, the combination of an electrolyte-gated field-effect transistor (EG-FET) with a fiber optic-coupled surface plasmon resonance (FO-SPR) probe serving as gate electrode has been investigated to deconvolute surface mass and charge density variations associated to surface reactions. However, applying an electrochemical potential on such gold-coated FO-SPR gate electrodes can induce gradual morphological changes of the thin gold film, leading to an irreversible blue-shift of the SPR wavelength and a substantial signal drift. We show that mild annealing leads to optical and electronic signal stabilization (20-fold lower signal drift than as-sputtered fiber optic gates) and improved overall analytical performance characteristics. The thermal treatment prevents morphological changes of the thin gold-film occurring during operation, hence providing reliable and stable data immediately upon gate voltage application. Thus, the readout output of both transducing principles, the optical FO-SPR and electronic EG-FET, stays constant throughout the whole sensing time-window and the long-term effect of thermal treatment is also improved, providing stable signals even after 1 year of storage. Annealing should therefore be considered a necessary modification for applying fiber optic gate electrodes in real-time multimodal investigations of surface reactions at the solid-liquid interface. AU - Hasler, Roger AU - Steger-Polt, Marie Helene AU - Reiner-Rozman, Ciril AU - Fossati, Stefan AU - Lee, Seungho AU - Aspermair, Patrik AU - Kleber, Christoph AU - Ibáñez, Maria AU - Dostalek, Jakub AU - Knoll, Wolfgang ID - 13968 JF - Frontiers in Physics TI - Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing VL - 11 ER - TY - JOUR AB - Long-time and large-data existence of weak solutions for initial- and boundary-value problems concerning three-dimensional flows of incompressible fluids is nowadays available not only for Navier–Stokes fluids but also for various fluid models where the relation between the Cauchy stress tensor and the symmetric part of the velocity gradient is nonlinear. The majority of such studies however concerns models where such a dependence is explicit (the stress is a function of the velocity gradient), which makes the class of studied models unduly restrictive. The same concerns boundary conditions, or more precisely the slipping mechanisms on the boundary, where the no-slip is still the most preferred condition considered in the literature. Our main objective is to develop a robust mathematical theory for unsteady internal flows of implicitly constituted incompressible fluids with implicit relations between the tangential projections of the velocity and the normal traction on the boundary. The theory covers numerous rheological models used in chemistry, biorheology, polymer and food industry as well as in geomechanics. It also includes, as special cases, nonlinear slip as well as stick–slip boundary conditions. Unlike earlier studies, the conditions characterizing admissible classes of constitutive equations are expressed by means of tools of elementary calculus. In addition, a fully constructive proof (approximation scheme) is incorporated. Finally, we focus on the question of uniqueness of such weak solutions. AU - Bulíček, Miroslav AU - Málek, Josef AU - Maringová, Erika ID - 14042 IS - 3 JF - Journal of Mathematical Fluid Mechanics SN - 1422-6928 TI - On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary VL - 25 ER - TY - JOUR AB - Tissue morphogenesis and patterning during development involve the segregation of cell types. Segregation is driven by differential tissue surface tensions generated by cell types through controlling cell-cell contact formation by regulating adhesion and actomyosin contractility-based cellular cortical tensions. We use vertebrate tissue cell types and zebrafish germ layer progenitors as in vitro models of 3-dimensional heterotypic segregation and developed a quantitative analysis of their dynamics based on 3D time-lapse microscopy. We show that general inhibition of actomyosin contractility by the Rho kinase inhibitor Y27632 delays segregation. Cell type-specific inhibition of non-muscle myosin2 activity by overexpression of myosin assembly inhibitor S100A4 reduces tissue surface tension, manifested in decreased compaction during aggregation and inverted geometry observed during segregation. The same is observed when we express a constitutively active Rho kinase isoform to ubiquitously keep actomyosin contractility high at cell-cell and cell-medium interfaces and thus overriding the interface-specific regulation of cortical tensions. Tissue surface tension regulation can become an effective tool in tissue engineering. AU - Méhes, Elod AU - Mones, Enys AU - Varga, Máté AU - Zsigmond, Áron AU - Biri-Kovács, Beáta AU - Nyitray, László AU - Barone, Vanessa AU - Krens, Gabriel AU - Heisenberg, Carl-Philipp J AU - Vicsek, Tamás ID - 14041 JF - Communications Biology TI - 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation VL - 6 ER - TY - JOUR AB - Membranes are essential for life. They act as semi-permeable boundaries that define cells and organelles. In addition, their surfaces actively participate in biochemical reaction networks, where they confine proteins, align reaction partners, and directly control enzymatic activities. Membrane-localized reactions shape cellular membranes, define the identity of organelles, compartmentalize biochemical processes, and can even be the source of signaling gradients that originate at the plasma membrane and reach into the cytoplasm and nucleus. The membrane surface is, therefore, an essential platform upon which myriad cellular processes are scaffolded. In this review, we summarize our current understanding of the biophysics and biochemistry of membrane-localized reactions with particular focus on insights derived from reconstituted and cellular systems. We discuss how the interplay of cellular factors results in their self-organization, condensation, assembly, and activity, and the emergent properties derived from them. AU - Leonard, Thomas A. AU - Loose, Martin AU - Martens, Sascha ID - 14039 IS - 15 JF - Developmental Cell SN - 1534-5807 TI - The membrane surface as a platform that organizes cellular and biochemical processes VL - 58 ER - TY - JOUR AB - Robust oxygenic photosynthesis requires a suite of accessory factors to ensure efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex. The highly conserved Ycf48 assembly factor binds to the newly synthesized D1 reaction center polypeptide and promotes the initial steps of PSII assembly, but its binding site is unclear. Here we use cryo-electron microscopy to determine the structure of a cyanobacterial PSII D1/D2 reaction center assembly complex with Ycf48 attached. Ycf48, a 7-bladed beta propeller, binds to the amino-acid residues of D1 that ultimately ligate the water-oxidising Mn4CaO5 cluster, thereby preventing the premature binding of Mn2+ and Ca2+ ions and protecting the site from damage. Interactions with D2 help explain how Ycf48 promotes assembly of the D1/D2 complex. Overall, our work provides valuable insights into the early stages of PSII assembly and the structural changes that create the binding site for the Mn4CaO5 cluster. AU - Zhao, Ziyu AU - Vercellino, Irene AU - Knoppová, Jana AU - Sobotka, Roman AU - Murray, James W. AU - Nixon, Peter J. AU - Sazanov, Leonid A AU - Komenda, Josef ID - 14040 JF - Nature Communications TI - The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis VL - 14 ER - TY - CONF AB - A classic solution technique for Markov decision processes (MDP) and stochastic games (SG) is value iteration (VI). Due to its good practical performance, this approximative approach is typically preferred over exact techniques, even though no practical bounds on the imprecision of the result could be given until recently. As a consequence, even the most used model checkers could return arbitrarily wrong results. Over the past decade, different works derived stopping criteria, indicating when the precision reaches the desired level, for various settings, in particular MDP with reachability, total reward, and mean payoff, and SG with reachability.In this paper, we provide the first stopping criteria for VI on SG with total reward and mean payoff, yielding the first anytime algorithms in these settings. To this end, we provide the solution in two flavours: First through a reduction to the MDP case and second directly on SG. The former is simpler and automatically utilizes any advances on MDP. The latter allows for more local computations, heading towards better practical efficiency.Our solution unifies the previously mentioned approaches for MDP and SG and their underlying ideas. To achieve this, we isolate objective-specific subroutines as well as identify objective-independent concepts. These structural concepts, while surprisingly simple, form the very essence of the unified solution. AU - Kretinsky, Jan AU - Meggendorfer, Tobias AU - Weininger, Maximilian ID - 13967 SN - 1043-6871 T2 - 38th Annual ACM/IEEE Symposium on Logic in Computer Science TI - Stopping criteria for value iteration on stochastic games with quantitative objectives VL - 2023 ER - TY - JOUR AB - Many modes and mechanisms of epigenetic inheritance have been elucidated in eukaryotes. Most of them are relatively short-term, generally not exceeding one or a few organismal generations. However, emerging evidence indicates that one mechanism, cytosine DNA methylation, can mediate epigenetic inheritance over much longer timescales, which are mostly or completely inaccessible in the laboratory. Here we discuss the evidence for, and mechanisms and implications of, such long-term epigenetic inheritance. We argue that compelling evidence supports the long-term epigenetic inheritance of gene body methylation, at least in the model angiosperm Arabidopsis thaliana, and that variation in such methylation can therefore serve as an epigenetic basis for phenotypic variation in natural populations. AU - Hollwey, Elizabeth AU - Briffa, Amy AU - Howard, Martin AU - Zilberman, Daniel ID - 13965 IS - 8 JF - Current Opinion in Genetics and Development SN - 0959-437X TI - Concepts, mechanisms and implications of long-term epigenetic inheritance VL - 81 ER - TY - THES AB - Females and males across species are subject to divergent selective pressures arising from di↵erent reproductive interests and ecological niches. This often translates into a intricate array of sex-specific natural and sexual selection on traits that have a shared genetic basis between both sexes, causing a genetic sexual conflict. The resolution of this conflict mostly relies on the evolution of sex-specific expression of the shared genes, leading to phenotypic sexual dimorphism. Such sex-specific gene expression is thought to evolve via modifications of the genetic networks ultimately linked to sex-determining transcription factors. Although much empirical and theoretical evidence supports this standard picture of the molecular basis of sexual conflict resolution, there still are a few open questions regarding the complex array of selective forces driving phenotypic di↵erentiation between the sexes, as well as the molecular mechanisms underlying sexspecific adaptation. I address some of these open questions in my PhD thesis. First, how do patterns of phenotypic sexual dimorphism vary within populations, as a response to the temporal and spatial changes in sex-specific selective forces? To tackle this question, I analyze the patterns of sex-specific phenotypic variation along three life stages and across populations spanning the whole geographical range of Rumex hastatulus, a wind-pollinated angiosperm, in the first Chapter of the thesis. Second, how do gene expression patterns lead to phenotypic dimorphism, and what are the molecular mechanisms underlying the observed transcriptomic variation? I address this question by examining the sex- and tissue-specific expression variation in newly-generated datasets of sex-specific expression in heads and gonads of Drosophila melanogaster. I additionally used two complementary approaches for the study of the genetic basis of sex di↵erences in gene expression in the second and third Chapters of the thesis. Third, how does intersex correlation, thought to be one of the main aspects constraining the ability for the two sexes to decouple, interact with the evolution of sexual dimorphism? I develop models of sex-specific stabilizing selection, mutation and drift to formalize common intuition regarding the patterns of covariation between intersex correlation and sexual dimorphism in the fourth Chapter of the thesis. Alltogether, the work described in this PhD thesis provides useful insights into the links between genetic, transcriptomic and phenotypic layers of sex-specific variation, and contributes to our general understanding of the dynamics of sexual dimorphism evolution. AU - Puixeu Sala, Gemma ID - 14058 SN - 2663-337X TI - The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation ER - TY - JOUR AB - The regulatory architecture of gene expression is known to differ substantially between sexes in Drosophila, but most studies performed so far used whole-body data and only single crosses, which may have limited their scope to detect patterns that are robust across tissues and biological replicates. Here, we use allele-specific gene expression of parental and reciprocal hybrid crosses between 6 Drosophila melanogaster inbred lines to quantify cis- and trans-regulatory variation in heads and gonads of both sexes separately across 3 replicate crosses. Our results suggest that female and male heads, as well as ovaries, have a similar regulatory architecture. On the other hand, testes display more and substantially different cis-regulatory effects, suggesting that sex differences in the regulatory architecture that have been previously observed may largely derive from testis-specific effects. We also examine the difference in cis-regulatory variation of genes across different levels of sex bias in gonads and heads. Consistent with the idea that intersex correlations constrain expression and can lead to sexual antagonism, we find more cis variation in unbiased and moderately biased genes in heads. In ovaries, reduced cis variation is observed for male-biased genes, suggesting that cis variants acting on these genes in males do not lead to changes in ovary expression. Finally, we examine the dominance patterns of gene expression and find that sex- and tissue-specific patterns of inheritance as well as trans-regulatory variation are highly variable across biological crosses, although these were performed in highly controlled experimental conditions. This highlights the importance of using various genetic backgrounds to infer generalizable patterns. AU - Puixeu Sala, Gemma AU - Macon, Ariana AU - Vicoso, Beatriz ID - 14077 IS - 8 JF - G3: Genes, Genomes, Genetics KW - Genetics (clinical) KW - Genetics KW - Molecular Biology SN - 2160-1836 TI - Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster VL - 13 ER - TY - JOUR AB - Epithelial barrier function is commonly analyzed using transepithelial electrical resistance, which measures ion flux across a monolayer, or by adding traceable macromolecules and monitoring their passage across the monolayer. Although these methods measure changes in global barrier function, they lack the sensitivity needed to detect local or transient barrier breaches, and they do not reveal the location of barrier leaks. Therefore, we previously developed a method that we named the zinc-based ultrasensitive microscopic barrier assay (ZnUMBA), which overcomes these limitations, allowing for detection of local tight junction leaks with high spatiotemporal resolution. Here, we present expanded applications for ZnUMBA. ZnUMBA can be used in Xenopus embryos to measure the dynamics of barrier restoration and actin accumulation following laser injury. ZnUMBA can also be effectively utilized in developing zebrafish embryos as well as cultured monolayers of Madin–Darby canine kidney (MDCK) II epithelial cells. ZnUMBA is a powerful and flexible method that, with minimal optimization, can be applied to multiple systems to measure dynamic changes in barrier function with spatiotemporal precision. AU - Higashi, Tomohito AU - Stephenson, Rachel E. AU - Schwayer, Cornelia AU - Huljev, Karla AU - Higashi, Atsuko Y. AU - Heisenberg, Carl-Philipp J AU - Chiba, Hideki AU - Miller, Ann L. ID - 14082 IS - 15 JF - Journal of Cell Science SN - 0021-9533 TI - ZnUMBA - a live imaging method to detect local barrier breaches VL - 136 ER - TY - JOUR AB - Most permissionless blockchains inherently suffer from throughput limitations. Layer-2 systems, such as side-chains or Rollups, have been proposed as a possible strategy to overcome this limitation. Layer-2 systems interact with the main-chain in two ways. First, users can move funds from/to the main-chain to/from the layer-2. Second, layer-2 systems periodically synchronize with the main-chain to keep some form of log of their activity on the main-chain - this log is key for security. Due to this interaction with the main-chain, which is necessary and recurrent, layer-2 systems impose some load on the main-chain. The impact of such load on the main-chain has been, so far, poorly understood. In addition to that, layer-2 approaches typically sacrifice decentralization and security in favor of higher throughput. This paper presents an experimental study that analyzes the current state of Ethereum layer-2 projects. Our goal is to assess the load they impose on Ethereum and to understand their scalability potential in the long-run. Our analysis shows that the impact of any given layer-2 on the main-chain is the result of both technical aspects (how state is logged on the main-chain) and user behavior (how often users decide to transfer funds between the layer-2 and the main-chain). Based on our observations, we infer that without efficient mechanisms that allow users to transfer funds in a secure and fast manner directly from one layer-2 project to another, current layer-2 systems will not be able to scale Ethereum effectively, regardless of their technical solutions. Furthermore, from our results, we conclude that the layer-2 systems that offer similar security guarantees as Ethereum have limited scalability potential, while approaches that offer better performance, sacrifice security and lead to an increase in centralization which runs against the end-goals of permissionless blockchains. AU - Neiheiser, Ray AU - Inacio, Gustavo AU - Rech, Luciana AU - Montez, Carlos AU - Matos, Miguel AU - Rodrigues, Luis ID - 13988 JF - IEEE Access KW - General Engineering KW - General Materials Science KW - General Computer Science KW - Electrical and Electronic Engineering SN - 2169-3536 TI - Practical limitations of Ethereum’s layer-2 VL - 11 ER -