@article{12082, abstract = {Proximity-dependent protein labeling provides a powerful in vivo strategy to characterize the interactomes of specific proteins. We previously optimized a proximity labeling protocol for Caenorhabditis elegans using the highly active biotin ligase TurboID. A significant constraint on the sensitivity of TurboID is the presence of abundant endogenously biotinylated proteins that take up bandwidth in the mass spectrometer, notably carboxylases that use biotin as a cofactor. In C. elegans, these comprise POD-2/acetyl-CoA carboxylase alpha, PCCA-1/propionyl-CoA carboxylase alpha, PYC-1/pyruvate carboxylase, and MCCC-1/methylcrotonyl-CoA carboxylase alpha. Here, we developed ways to remove these carboxylases prior to streptavidin purification and mass spectrometry by engineering their corresponding genes to add a C-terminal His10 tag. This allows us to deplete them from C. elegans lysates using immobilized metal affinity chromatography. To demonstrate the method's efficacy, we use it to expand the interactome map of the presynaptic active zone protein ELKS-1. We identify many known active zone proteins, including UNC-10/RIM, SYD-2/liprin-alpha, SAD-1/BRSK1, CLA-1/CLArinet, C16E9.2/Sentryn, as well as previously uncharacterized potentially synaptic proteins such as the ortholog of human angiomotin, F59C12.3 and the uncharacterized protein R148.3. Our approach provides a quick and inexpensive solution to a common contaminant problem in biotin-dependent proximity labeling. The approach may be applicable to other model organisms and will enable deeper and more complete analysis of interactors for proteins of interest.}, author = {Artan, Murat and Hartl, Markus and Chen, Weiqiang and De Bono, Mario}, issn = {1083-351X}, journal = {Journal of Biological Chemistry}, number = {9}, publisher = {Elsevier}, title = {{Depletion of endogenously biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in Caenorhabditis elegans}}, doi = {10.1016/j.jbc.2022.102343}, volume = {298}, year = {2022}, } @article{12083, abstract = {We consider the many-body time evolution of weakly interacting bosons in the mean field regime for initial coherent states. We show that bounded k-particle operators, corresponding to dependent random variables, satisfy both a law of large numbers and a central limit theorem.}, author = {Rademacher, Simone Anna Elvira}, issn = {0022-2488}, journal = {Journal of Mathematical Physics}, number = {8}, publisher = {AIP Publishing}, title = {{Dependent random variables in quantum dynamics}}, doi = {10.1063/5.0086712}, volume = {63}, year = {2022}, } @article{12084, abstract = {Neuronal networks encode information through patterns of activity that define the networks’ function. The neurons’ activity relies on specific connectivity structures, yet the link between structure and function is not fully understood. Here, we tackle this structure-function problem with a new conceptual approach. Instead of manipulating the connectivity directly, we focus on upper triangular matrices, which represent the network dynamics in a given orthonormal basis obtained by the Schur decomposition. This abstraction allows us to independently manipulate the eigenspectrum and feedforward structures of a connectivity matrix. Using this method, we describe a diverse repertoire of non-normal transient amplification, and to complement the analysis of the dynamical regimes, we quantify the geometry of output trajectories through the effective rank of both the eigenvector and the dynamics matrices. Counter-intuitively, we find that shrinking the eigenspectrum’s imaginary distribution leads to highly amplifying regimes in linear and long-lasting dynamics in nonlinear networks. We also find a trade-off between amplification and dimensionality of neuronal dynamics, i.e., trajectories in neuronal state-space. Networks that can amplify a large number of orthogonal initial conditions produce neuronal trajectories that lie in the same subspace of the neuronal state-space. Finally, we examine networks of excitatory and inhibitory neurons. We find that the strength of global inhibition is directly linked with the amplitude of amplification, such that weakening inhibitory weights also decreases amplification, and that the eigenspectrum’s imaginary distribution grows with an increase in the ratio between excitatory-to-inhibitory and excitatory-to-excitatory connectivity strengths. Consequently, the strength of global inhibition reveals itself as a strong signature for amplification and a potential control mechanism to switch dynamical regimes. Our results shed a light on how biological networks, i.e., networks constrained by Dale’s law, may be optimised for specific dynamical regimes.}, author = {Christodoulou, Georgia and Vogels, Tim P and Agnes, Everton J.}, issn = {1553-7358}, journal = {PLoS Computational Biology}, number = {8}, publisher = {Public Library of Science}, title = {{Regimes and mechanisms of transient amplification in abstract and biological neural networks}}, doi = {10.1371/journal.pcbi.1010365}, volume = {18}, year = {2022}, } @article{12085, abstract = {Molecular catch bonds are ubiquitous in biology and essential for processes like leucocyte extravasion1 and cellular mechanosensing2. Unlike normal (slip) bonds, catch bonds strengthen under tension. The current paradigm is that this feature provides ‘strength on demand3’, thus enabling cells to increase rigidity under stress1,4,5,6. However, catch bonds are often weaker than slip bonds because they have cryptic binding sites that are usually buried7,8. Here we show that catch bonds render reconstituted cytoskeletal actin networks stronger than slip bonds, even though the individual bonds are weaker. Simulations show that slip bonds remain trapped in stress-free areas, whereas weak binding allows catch bonds to mitigate crack initiation by moving to high-tension areas. This ‘dissociation on demand’ explains how cells combine mechanical strength with the adaptability required for shape change, and is relevant to diseases where catch bonding is compromised7,9, including focal segmental glomerulosclerosis10 caused by the α-actinin-4 mutant studied here. We surmise that catch bonds are the key to create life-like materials.}, author = {Mulla, Yuval and Avellaneda Sarrió, Mario and Roland, Antoine and Baldauf, Lucia and Jung, Wonyeong and Kim, Taeyoon and Tans, Sander J. and Koenderink, Gijsje H.}, issn = {1476-4660}, journal = {Nature Materials}, number = {9}, pages = {1019--1023}, publisher = {Springer Nature}, title = {{Weak catch bonds make strong networks}}, doi = {10.1038/s41563-022-01288-0}, volume = {21}, year = {2022}, } @inproceedings{12088, abstract = {We present a quantum-enabled microwave-telecom interface with bidirectional conversion efficiencies up to 15% and added input noise quanta as low as 0.16. Moreover, we observe evidence for electro-optic laser cooling and vacuum amplification.}, author = {Sahu, Rishabh and Hease, William J and Rueda Sanchez, Alfredo R and Arnold, Georg M and Qiu, Liu and Fink, Johannes M}, booktitle = {Conference on Lasers and Electro-Optics}, isbn = {9781557528209}, location = {San Jose, CA, United States}, publisher = {Optica Publishing Group}, title = {{Realizing a quantum-enabled interconnect between microwave and telecom light}}, doi = {10.1364/CLEO_QELS.2022.FW4D.4}, year = {2022}, } @inproceedings{12101, abstract = {Spatial games form a widely-studied class of games from biology and physics modeling the evolution of social behavior. Formally, such a game is defined by a square (d by d) payoff matrix M and an undirected graph G. Each vertex of G represents an individual, that initially follows some strategy i ∈ {1,2,…,d}. In each round of the game, every individual plays the matrix game with each of its neighbors: An individual following strategy i meeting a neighbor following strategy j receives a payoff equal to the entry (i,j) of M. Then, each individual updates its strategy to its neighbors' strategy with the highest sum of payoffs, and the next round starts. The basic computational problems consist of reachability between configurations and the average frequency of a strategy. For general spatial games and graphs, these problems are in PSPACE. In this paper, we examine restricted setting: the game is a prisoner’s dilemma; and G is a subgraph of grid. We prove that basic computational problems for spatial games with prisoner’s dilemma on a subgraph of a grid are PSPACE-hard.}, author = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus and Jecker, Ismael R and Svoboda, Jakub}, booktitle = {42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science}, isbn = {9783959772617}, issn = {1868-8969}, location = {Madras, India}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Complexity of spatial games}}, doi = {10.4230/LIPIcs.FSTTCS.2022.11}, volume = {250}, year = {2022}, } @inproceedings{12102, abstract = {Given a Markov chain M = (V, v_0, δ), with state space V and a starting state v_0, and a probability threshold ε, an ε-core is a subset C of states that is left with probability at most ε. More formally, C ⊆ V is an ε-core, iff ℙ[reach (V\C)] ≤ ε. Cores have been applied in a wide variety of verification problems over Markov chains, Markov decision processes, and probabilistic programs, as a means of discarding uninteresting and low-probability parts of a probabilistic system and instead being able to focus on the states that are likely to be encountered in a real-world run. In this work, we focus on the problem of computing a minimal ε-core in a Markov chain. Our contributions include both negative and positive results: (i) We show that the decision problem on the existence of an ε-core of a given size is NP-complete. This solves an open problem posed in [Jan Kretínský and Tobias Meggendorfer, 2020]. We additionally show that the problem remains NP-complete even when limited to acyclic Markov chains with bounded maximal vertex degree; (ii) We provide a polynomial time algorithm for computing a minimal ε-core on Markov chains over control-flow graphs of structured programs. A straightforward combination of our algorithm with standard branch prediction techniques allows one to apply the idea of cores to find a subset of program lines that are left with low probability and then focus any desired static analysis on this core subset.}, author = {Ahmadi, Ali and Chatterjee, Krishnendu and Goharshady, Amir Kafshdar and Meggendorfer, Tobias and Safavi Hemami, Roodabeh and Zikelic, Dorde}, booktitle = {42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science}, isbn = {9783959772617}, issn = {1868-8969}, location = {Madras, India}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Algorithms and hardness results for computing cores of Markov chains}}, doi = {10.4230/LIPIcs.FSTTCS.2022.29}, volume = {250}, year = {2022}, } @article{12107, abstract = {The sensitivity of coarse-grained daily extreme precipitation to sea surface temperature is analyzed using satellite precipitation estimates over the 300–302.5 K range. A theoretical scaling is proposed, linking changes in coarse-grained precipitation to changes in fine-scale hourly precipitation area fraction and changes in conditional fine-scale precipitation rates. The analysis reveals that the extreme coarse-grained precipitation scaling with temperature (∼7%/K) is dominated by the fine-scale precipitating fraction scaling (∼6.5%/K) when using a 3 mm/h fine-scale threshold to delineate the precipitating fraction. These results are shown to be robust to the selection of the precipitation product and to the percentile used to characterize the extreme. This new coarse-grained scaling is further related to the well-known scaling for fine-scale precipitation extremes, and suggests a compensation between thermodynamic and dynamic contributions or that both contributions are small with respect to that of fractional coverage. These results suggest that processes responsible for the changes in fractional coverage are to be accounted for to assess the sensitivity of coarse-grained extreme daily precipitation to surface temperature.}, author = {Roca, Rémy and De Meyer, Victorien and Muller, Caroline J}, issn = {1944-8007}, journal = {Geophysical Research Letters}, number = {24}, publisher = {Wiley}, title = {{Precipitating fraction, not intensity, explains extreme coarse-grained precipitation Clausius-Clapeyron scaling with sea surface temperature over tropical oceans}}, doi = {10.1029/2022GL100624}, volume = {49}, year = {2022}, } @article{12108, abstract = {The sequential exchange of filament composition to increase filament curvature was proposed as a mechanism for how some biological polymers deform and cut membranes. The relationship between the filament composition and its mechanical effect is lacking. We develop a kinetic model for the assembly of composite filaments that includes protein–membrane adhesion, filament mechanics and membrane mechanics. We identify the physical conditions for such a membrane remodeling and show this mechanism of sequential polymer assembly lowers the energetic barrier for membrane deformation.}, author = {Meadowcroft, Billie and Palaia, Ivan and Pfitzner, Anna Katharina and Roux, Aurélien and Baum, Buzz and Šarić, Anđela}, issn = {1079-7114}, journal = {Physical Review Letters}, number = {26}, publisher = {American Physical Society}, title = {{Mechanochemical rules for shape-shifting filaments that remodel membranes}}, doi = {10.1103/PhysRevLett.129.268101}, volume = {129}, year = {2022}, } @article{12109, abstract = {Kelvin probe force microscopy (KPFM) is a powerful tool for studying contact electrification (CE) at the nanoscale, but converting KPFM voltage maps to charge density maps is nontrivial due to long-range forces and complex system geometry. Here we present a strategy using finite-element method (FEM) simulations to determine the Green's function of the KPFM probe/insulator/ground system, which allows us to quantitatively extract surface charge. Testing our approach with synthetic data, we find that accounting for the atomic force microscope (AFM) tip, cone, and cantilever is necessary to recover a known input and that existing methods lead to gross miscalculation or even the incorrect sign of the underlying charge. Applying it to experimental data, we demonstrate its capacity to extract realistic surface charge densities and fine details from contact-charged surfaces. Our method gives a straightforward recipe to convert qualitative KPFM voltage data into quantitative charge data over a range of experimental conditions, enabling quantitative CE at the nanoscale.}, author = {Pertl, Felix and Sobarzo Ponce, Juan Carlos A and Shafeek, Lubuna B and Cramer, Tobias and Waitukaitis, Scott R}, issn = {2475-9953}, journal = {Physical Review Materials}, number = {12}, publisher = {American Physical Society}, title = {{Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach}}, doi = {10.1103/PhysRevMaterials.6.125605}, volume = {6}, year = {2022}, } @article{12110, abstract = {A recently proposed approach for avoiding the ultraviolet divergence of Hamiltonians with particle creation is based on interior-boundary conditions (IBCs). The approach works well in the non-relativistic case, i.e., for the Laplacian operator. Here, we study how the approach can be applied to Dirac operators. While this has successfully been done already in one space dimension, and more generally for codimension-1 boundaries, the situation of point sources in three dimensions corresponds to a codimension-3 boundary. One would expect that, for such a boundary, Dirac operators do not allow for boundary conditions because they are known not to allow for point interactions in 3D, which also correspond to a boundary condition. Indeed, we confirm this expectation here by proving that there is no self-adjoint operator on a (truncated) Fock space that would correspond to a Dirac operator with an IBC at configurations with a particle at the origin. However, we also present a positive result showing that there are self-adjoint operators with an IBC (on the boundary consisting of configurations with a particle at the origin) that are away from those configurations, given by a Dirac operator plus a sufficiently strong Coulomb potential.}, author = {Henheik, Sven Joscha and Tumulka, Roderich}, issn = {0022-2488}, journal = {Journal of Mathematical Physics}, number = {12}, publisher = {AIP Publishing}, title = {{Interior-boundary conditions for the Dirac equation at point sources in three dimensions}}, doi = {10.1063/5.0104675}, volume = {63}, year = {2022}, } @article{12111, abstract = {Quantum impurities exhibit fascinating many-body phenomena when the small interacting impurity changes the physics of a large noninteracting environment. The characterisation of such strongly correlated nonperturbative effects is particularly challenging due to the infinite size of the environment, and the inability of local correlators to capture the buildup of long-ranged entanglement in the system. Here, we harness an entanglement-based observable—the purity of the impurity—as a witness for the formation of strong correlations. We showcase the utility of our scheme by exactly solving the open Kondo box model in the small box limit, and thus describe all-electronic dot-cavity devices. Specifically, we conclusively characterize the metal-to-insulator phase transition in the system and identify how the (conducting) dot-lead Kondo singlet is quenched by an (insulating) intraimpurity singlet formation. Furthermore, we propose an experimentally feasible tomography protocol for the measurement of the purity, which motivates the observation of impurity physics through their entanglement build up.}, author = {Stocker, Lidia and Sack, Stefan and Ferguson, Michael S. and Zilberberg, Oded}, issn = {2643-1564}, journal = {Physical Review Research}, number = {4}, publisher = {American Physical Society}, title = {{Entanglement-based observables for quantum impurities}}, doi = {10.1103/PhysRevResearch.4.043177}, volume = {4}, year = {2022}, } @article{12116, abstract = {Russia’s unprovoked attack on Ukraine has destroyed civilian infrastructure, including universities, research centers, and other academic infrastructure (1). Many Ukrainian scholars and researchers remain in Ukraine, and their work has suffered from major setbacks (2–4). We call on international scientists and institutions to support them.}, author = {Chhugani, Karishma and Frolova, Alina and Salyha, Yuriy and Fiscutean, Andrada and Zlenko, Oksana and Reinsone, Sanita and Wolfsberger, Walter W. and Ivashchenko, Oleksandra V. and Maci, Megi and Dziuba, Dmytro and Parkhomenko, Andrii and Bortz, Eric and Kondrashov, Fyodor and Łabaj, Paweł P. and Romero, Veronika and Hlávka, Jakub and Oleksyk, Taras K. and Mangul, Serghei}, issn = {1095-9203}, journal = {Science}, number = {6626}, pages = {1285--1286}, publisher = {American Association for the Advancement of Science}, title = {{Remote opportunities for scholars in Ukraine}}, doi = {10.1126/science.adg0797}, volume = {378}, year = {2022}, } @article{12117, abstract = {To understand how potential gene manipulations affect in vitro microglia, we provide a set of short protocols to evaluate microglia identity and function. We detail steps for immunostaining to determine microglia identity. We describe three functional assays for microglia: phagocytosis, calcium response following ATP stimulation, and cytokine expression upon inflammatory stimuli. We apply these protocols to human induced-pluripotent-stem-cell (hiPSC)-derived microglia, but they can be also applied to other in vitro microglial models including primary mouse microglia. For complete details on the use and execution of this protocol, please refer to Bartalska et al. (2022).1}, author = {Hübschmann, Verena and Korkut, Medina and Siegert, Sandra}, issn = {2666-1667}, journal = {STAR Protocols}, keywords = {General Immunology and Microbiology, General Biochemistry, Genetics and Molecular Biology, General Neuroscience}, number = {4}, publisher = {Elsevier}, title = {{Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay}}, doi = {10.1016/j.xpro.2022.101866}, volume = {3}, year = {2022}, } @article{12118, abstract = {Hybrid semiconductor–superconductor devices hold great promise for realizing topological quantum computing with Majorana zero modes1,2,3,4,5. However, multiple claims of Majorana detection, based on either tunnelling6,7,8,9,10 or Coulomb blockade (CB) spectroscopy11,12, remain disputed. Here we devise an experimental protocol that allows us to perform both types of measurement on the same hybrid island by adjusting its charging energy via tunable junctions to the normal leads. This method reduces ambiguities of Majorana detections by checking the consistency between CB spectroscopy and zero-bias peaks in non-blockaded transport. Specifically, we observe junction-dependent, even–odd modulated, single-electron CB peaks in InAs/Al hybrid nanowires without concomitant low-bias peaks in tunnelling spectroscopy. We provide a theoretical interpretation of the experimental observations in terms of low-energy, longitudinally confined island states rather than overlapping Majorana modes. Our results highlight the importance of combined measurements on the same device for the identification of topological Majorana zero modes.}, author = {Valentini, Marco and Borovkov, Maksim and Prada, Elsa and Martí-Sánchez, Sara and Botifoll, Marc and Hofmann, Andrea C and Arbiol, Jordi and Aguado, Ramón and San-Jose, Pablo and Katsaros, Georgios}, issn = {1476-4687}, journal = {Nature}, keywords = {Multidisciplinary}, number = {7940}, pages = {442--447}, publisher = {Springer Nature}, title = {{Majorana-like Coulomb spectroscopy in the absence of zero-bias peaks}}, doi = {10.1038/s41586-022-05382-w}, volume = {612}, year = {2022}, } @article{12119, abstract = {Intravascular neutrophils and platelets collaborate in maintaining host integrity, but their interaction can also trigger thrombotic complications. We report here that cooperation between neutrophil and platelet lineages extends to the earliest stages of platelet formation by megakaryocytes in the bone marrow. Using intravital microscopy, we show that neutrophils “plucked” intravascular megakaryocyte extensions, termed proplatelets, to control platelet production. Following CXCR4-CXCL12-dependent migration towards perisinusoidal megakaryocytes, plucking neutrophils actively pulled on proplatelets and triggered myosin light chain and extracellular-signal-regulated kinase activation through reactive oxygen species. By these mechanisms, neutrophils accelerate proplatelet growth and facilitate continuous release of platelets in steady state. Following myocardial infarction, plucking neutrophils drove excessive release of young, reticulated platelets and boosted the risk of recurrent ischemia. Ablation of neutrophil plucking normalized thrombopoiesis and reduced recurrent thrombosis after myocardial infarction and thrombus burden in venous thrombosis. We establish neutrophil plucking as a target to reduce thromboischemic events.}, author = {Petzold, Tobias and Zhang, Zhe and Ballesteros, Iván and Saleh, Inas and Polzin, Amin and Thienel, Manuela and Liu, Lulu and Ul Ain, Qurrat and Ehreiser, Vincent and Weber, Christian and Kilani, Badr and Mertsch, Pontus and Götschke, Jeremias and Cremer, Sophie and Fu, Wenwen and Lorenz, Michael and Ishikawa-Ankerhold, Hellen and Raatz, Elisabeth and El-Nemr, Shaza and Görlach, Agnes and Marhuenda, Esther and Stark, Konstantin and Pircher, Joachim and Stegner, David and Gieger, Christian and Schmidt-Supprian, Marc and Gärtner, Florian R and Almendros, Isaac and Kelm, Malte and Schulz, Christian and Hidalgo, Andrés and Massberg, Steffen}, issn = {1074-7613}, journal = {Immunity}, keywords = {Infectious Diseases, Immunology, Immunology and Allergy}, number = {12}, pages = {2285--2299.e7}, publisher = {Elsevier}, title = {{Neutrophil “plucking” on megakaryocytes drives platelet production and boosts cardiovascular disease}}, doi = {10.1016/j.immuni.2022.10.001}, volume = {55}, year = {2022}, } @article{12120, abstract = {Plant root architecture flexibly adapts to changing nitrate (NO3−) availability in the soil; however, the underlying molecular mechanism of this adaptive development remains under-studied. To explore the regulation of NO3−-mediated root growth, we screened for low-nitrate-resistant mutant (lonr) and identified mutants that were defective in the NAC transcription factor NAC075 (lonr1) as being less sensitive to low NO3− in terms of primary root growth. We show that NAC075 is a mobile transcription factor relocating from the root stele tissues to the endodermis based on NO3− availability. Under low-NO3− availability, the kinase CBL-interacting protein kinase 1 (CIPK1) is activated, and it phosphorylates NAC075, restricting its movement from the stele, which leads to the transcriptional regulation of downstream target WRKY53, consequently leading to adapted root architecture. Our work thus identifies an adaptive mechanism involving translocation of transcription factor based on nutrient availability and leading to cell-specific reprogramming of plant root growth.}, author = {Xiao, Huixin and Hu, Yumei and Wang, Yaping and Cheng, Jinkui and Wang, Jinyi and Chen, Guojingwei and Li, Qian and Wang, Shuwei and Wang, Yalu and Wang, Shao-Shuai and Wang, Yi and Xuan, Wei and Li, Zhen and Guo, Yan and Gong, Zhizhong and Friml, Jiří and Zhang, Jing}, issn = {1534-5807}, journal = {Developmental Cell}, keywords = {Developmental Biology, Cell Biology, General Biochemistry, Genetics and Molecular Biology, Molecular Biology}, number = {23}, pages = {2638--2651.e6}, publisher = {Elsevier}, title = {{Nitrate availability controls translocation of the transcription factor NAC075 for cell-type-specific reprogramming of root growth}}, doi = {10.1016/j.devcel.2022.11.006}, volume = {57}, year = {2022}, } @article{12121, abstract = {Autophagosomes are double-membraned vesicles that traffic harmful or unwanted cellular macromolecules to the vacuole for recycling. Although autophagosome biogenesis has been extensively studied, autophagosome maturation, i.e., delivery and fusion with the vacuole, remains largely unknown in plants. Here, we have identified an autophagy adaptor, CFS1, that directly interacts with the autophagosome marker ATG8 and localizes on both membranes of the autophagosome. Autophagosomes form normally in Arabidopsis thaliana cfs1 mutants, but their delivery to the vacuole is disrupted. CFS1’s function is evolutionarily conserved in plants, as it also localizes to the autophagosomes and plays a role in autophagic flux in the liverwort Marchantia polymorpha. CFS1 regulates autophagic flux by bridging autophagosomes with the multivesicular body-localized ESCRT-I component VPS23A, leading to the formation of amphisomes. Similar to CFS1-ATG8 interaction, disrupting the CFS1-VPS23A interaction blocks autophagic flux and renders plants sensitive to nitrogen starvation. Altogether, our results reveal a conserved vacuolar sorting hub that regulates autophagic flux in plants.}, author = {Zhao, Jierui and Bui, Mai Thu and Ma, Juncai and Künzl, Fabian and Picchianti, Lorenzo and De La Concepcion, Juan Carlos and Chen, Yixuan and Petsangouraki, Sofia and Mohseni, Azadeh and García-Leon, Marta and Gomez, Marta Salas and Giannini, Caterina and Gwennogan, Dubois and Kobylinska, Roksolana and Clavel, Marion and Schellmann, Swen and Jaillais, Yvon and Friml, Jiří and Kang, Byung-Ho and Dagdas, Yasin}, issn = {1540-8140}, journal = {Journal of Cell Biology}, keywords = {Cell Biology}, number = {12}, publisher = {Rockefeller University Press}, title = {{Plant autophagosomes mature into amphisomes prior to their delivery to the central vacuole}}, doi = {10.1083/jcb.202203139}, volume = {221}, year = {2022}, } @article{12128, abstract = {We introduce a machine-learning (ML) framework for high-throughput benchmarking of diverse representations of chemical systems against datasets of materials and molecules. The guiding principle underlying the benchmarking approach is to evaluate raw descriptor performance by limiting model complexity to simple regression schemes while enforcing best ML practices, allowing for unbiased hyperparameter optimization, and assessing learning progress through learning curves along series of synchronized train-test splits. The resulting models are intended as baselines that can inform future method development, in addition to indicating how easily a given dataset can be learnt. Through a comparative analysis of the training outcome across a diverse set of physicochemical, topological and geometric representations, we glean insight into the relative merits of these representations as well as their interrelatedness.}, author = {Poelking, Carl and Faber, Felix A and Cheng, Bingqing}, issn = {2632-2153}, journal = {Machine Learning: Science and Technology}, keywords = {Artificial Intelligence, Human-Computer Interaction, Software}, number = {4}, publisher = {IOP Publishing}, title = {{BenchML: An extensible pipelining framework for benchmarking representations of materials and molecules at scale}}, doi = {10.1088/2632-2153/ac4d11}, volume = {3}, year = {2022}, } @article{12129, abstract = {Given a finite point set P in general position in the plane, a full triangulation of P is a maximal straight-line embedded plane graph on P. A partial triangulation of P is a full triangulation of some subset P′ of P containing all extreme points in P. A bistellar flip on a partial triangulation either flips an edge (called edge flip), removes a non-extreme point of degree 3, or adds a point in P∖P′ as vertex of degree 3. The bistellar flip graph has all partial triangulations as vertices, and a pair of partial triangulations is adjacent if they can be obtained from one another by a bistellar flip. The edge flip graph is defined with full triangulations as vertices, and edge flips determining the adjacencies. Lawson showed in the early seventies that these graphs are connected. The goal of this paper is to investigate the structure of these graphs, with emphasis on their vertex connectivity. For sets P of n points in the plane in general position, we show that the edge flip graph is ⌈n/2−2⌉-vertex connected, and the bistellar flip graph is (n−3)-vertex connected; both results are tight. The latter bound matches the situation for the subfamily of regular triangulations (i.e., partial triangulations obtained by lifting the points to 3-space and projecting back the lower convex hull), where (n−3)-vertex connectivity has been known since the late eighties through the secondary polytope due to Gelfand, Kapranov, & Zelevinsky and Balinski’s Theorem. For the edge flip-graph, we additionally show that the vertex connectivity is at least as large as (and hence equal to) the minimum degree (i.e., the minimum number of flippable edges in any full triangulation), provided that n is large enough. Our methods also yield several other results: (i) The edge flip graph can be covered by graphs of polytopes of dimension ⌈n/2−2⌉ (products of associahedra) and the bistellar flip graph can be covered by graphs of polytopes of dimension n−3 (products of secondary polytopes). (ii) A partial triangulation is regular, if it has distance n−3 in the Hasse diagram of the partial order of partial subdivisions from the trivial subdivision. (iii) All partial triangulations of a point set are regular iff the partial order of partial subdivisions has height n−3. (iv) There are arbitrarily large sets P with non-regular partial triangulations and such that every proper subset has only regular triangulations, i.e., there are no small certificates for the existence of non-regular triangulations.}, author = {Wagner, Uli and Welzl, Emo}, issn = {1432-0444}, journal = {Discrete & Computational Geometry}, keywords = {Computational Theory and Mathematics, Discrete Mathematics and Combinatorics, Geometry and Topology, Theoretical Computer Science}, number = {4}, pages = {1227--1284}, publisher = {Springer Nature}, title = {{Connectivity of triangulation flip graphs in the plane}}, doi = {10.1007/s00454-022-00436-2}, volume = {68}, year = {2022}, }