@article{8997, abstract = {Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems.}, author = {Kavcic, Bor and Tkačik, Gašper and Bollenbach, Tobias}, issn = {1553-7358}, journal = {PLOS Computational Biology}, keywords = {Modelling and Simulation, Genetics, Molecular Biology, Antibiotics, Drug interactions}, publisher = {Public Library of Science}, title = {{Minimal biophysical model of combined antibiotic action}}, doi = {10.1371/journal.pcbi.1008529}, volume = {17}, year = {2021}, } @article{8999, abstract = {In many basic shear flows, such as pipe, Couette, and channel flow, turbulence does not arise from an instability of the laminar state, and both dynamical states co-exist. With decreasing flow speed (i.e., decreasing Reynolds number) the fraction of fluid in laminar motion increases while turbulence recedes and eventually the entire flow relaminarizes. The first step towards understanding the nature of this transition is to determine if the phase change is of either first or second order. In the former case, the turbulent fraction would drop discontinuously to zero as the Reynolds number decreases while in the latter the process would be continuous. For Couette flow, the flow between two parallel plates, earlier studies suggest a discontinuous scenario. In the present study we realize a Couette flow between two concentric cylinders which allows studies to be carried out in large aspect ratios and for extensive observation times. The presented measurements show that the transition in this circular Couette geometry is continuous suggesting that former studies were limited by finite size effects. A further characterization of this transition, in particular its relation to the directed percolation universality class, requires even larger system sizes than presently available. }, author = {Avila, Kerstin and Hof, Björn}, issn = {1099-4300}, journal = {Entropy}, number = {1}, publisher = {MDPI}, title = {{Second-order phase transition in counter-rotating taylor-couette flow experiment}}, doi = {10.3390/e23010058}, volume = {23}, year = {2021}, } @article{6965, abstract = {The central object of investigation of this paper is the Hirzebruch class, a deformation of the Todd class, given by Hirzebruch (for smooth varieties). The generalization for singular varieties is due to Brasselet–Schürmann–Yokura. Following the work of Weber, we investigate its equivariant version for (possibly singular) toric varieties. The local decomposition of the Hirzebruch class to the fixed points of the torus action and a formula for the local class in terms of the defining fan are recalled. After this review part, we prove the positivity of local Hirzebruch classes for all toric varieties, thus proving false the alleged counterexample given by Weber.}, author = {Rychlewicz, Kamil P}, issn = {1469-2120}, journal = {Bulletin of the London Mathematical Society}, number = {2}, pages = {560--574}, publisher = {Wiley}, title = {{The positivity of local equivariant Hirzebruch class for toric varieties}}, doi = {10.1112/blms.12442}, volume = {53}, year = {2021}, } @misc{6995, abstract = {Human brain organoids represent a powerful tool for the study of human neurological diseases particularly those that impact brain growth and structure. However, many neurological diseases lack obvious anatomical abnormalities, yet significantly impact neural network functions, raising the question of whether organoids possess sufficient neural network architecture and complexity to model these conditions. Here, we explore the network level functions of brain organoids using calcium sensor imaging and extracellular recording approaches that together reveal the existence of complex oscillatory network behaviors reminiscent of intact brain preparations. We further demonstrate strikingly abnormal epileptiform network activity in organoids derived from a Rett Syndrome patient despite only modest anatomical differences from isogenically matched controls, and rescue with an unconventional neuromodulatory drug Pifithrin-α. Together, these findings provide an essential foundation for the utilization of human brain organoids to study intact and disordered human brain network formation and illustrate their utility in therapeutic discovery.}, author = {Samarasinghe, Ranmal A. and Miranda, Osvaldo and Buth, Jessie E. and Mitchell, Simon and Ferando, Isabella and Watanabe, Momoko and Kurdian, Arinnae and Golshani, Peyman and Plath, Kathrin and Lowry, William E. and Parent, Jack M. and Mody, Istvan and Novitch, Bennett G.}, issn = {1546-1726}, pages = {32}, publisher = {Springer Nature}, title = {{Identification of neural oscillations and epileptiform changes in human brain organoids}}, doi = {10.1038/s41593-021-00906-5}, volume = {24}, year = {2021}, } @article{7463, abstract = {Resting-state brain activity is characterized by the presence of neuronal avalanches showing absence of characteristic size. Such evidence has been interpreted in the context of criticality and associated with the normal functioning of the brain. A distinctive attribute of systems at criticality is the presence of long-range correlations. Thus, to verify the hypothesis that the brain operates close to a critical point and consequently assess deviations from criticality for diagnostic purposes, it is of primary importance to robustly and reliably characterize correlations in resting-state brain activity. Recent works focused on the analysis of narrow-band electroencephalography (EEG) and magnetoencephalography (MEG) signal amplitude envelope, showing evidence of long-range temporal correlations (LRTC) in neural oscillations. However, brain activity is a broadband phenomenon, and a significant piece of information useful to precisely discriminate between normal (critical) and pathological behavior (non-critical), may be encoded in the broadband spatio-temporal cortical dynamics. Here we propose to characterize the temporal correlations in the broadband brain activity through the lens of neuronal avalanches. To this end, we consider resting-state EEG and long-term MEG recordings, extract the corresponding neuronal avalanche sequences, and study their temporal correlations. We demonstrate that the broadband resting-state brain activity consistently exhibits long-range power-law correlations in both EEG and MEG recordings, with similar values of the scaling exponents. Importantly, although we observe that the avalanche size distribution depends on scale parameters, scaling exponents characterizing long-range correlations are quite robust. In particular, they are independent of the temporal binning (scale of analysis), indicating that our analysis captures intrinsic characteristics of the underlying dynamics. Because neuronal avalanches constitute a fundamental feature of neural systems with universal characteristics, the proposed approach may serve as a general, systems- and experiment-independent procedure to infer the existence of underlying long-range correlations in extended neural systems, and identify pathological behaviors in the complex spatio-temporal interplay of cortical rhythms.}, author = {Lombardi, Fabrizio and Shriki, Oren and Herrmann, Hans J and de Arcangelis, Lucilla}, issn = {1872-8286}, journal = {Neurocomputing}, pages = {657--666}, publisher = {Elsevier}, title = {{Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches}}, doi = {10.1016/j.neucom.2020.05.126}, volume = {461}, year = {2021}, } @article{7551, abstract = {Novelty facilitates formation of memories. The detection of novelty and storage of contextual memories are both mediated by the hippocampus, yet the mechanisms that link these two functions remain to be defined. Dentate granule cells (GCs) of the dorsal hippocampus fire upon novelty exposure forming engrams of contextual memory. However, their key excitatory inputs from the entorhinal cortex are not responsive to novelty and are insufficient to make dorsal GCs fire reliably. Here we uncover a powerful glutamatergic pathway to dorsal GCs from ventral hippocampal mossy cells (MCs) that relays novelty, and is necessary and sufficient for driving dorsal GCs activation. Furthermore, manipulation of ventral MCs activity bidirectionally regulates novelty-induced contextual memory acquisition. Our results show that ventral MCs activity controls memory formation through an intra-hippocampal interaction mechanism gated by novelty.}, author = {Fredes Tolorza, Felipe A and Silva Sifuentes, Maria A and Koppensteiner, Peter and Kobayashi, Kenta and Jösch, Maximilian A and Shigemoto, Ryuichi}, journal = {Current Biology}, number = {1}, pages = {P25--38.E5}, publisher = {Elsevier}, title = {{Ventro-dorsal hippocampal pathway gates novelty-induced contextual memory formation}}, doi = {10.1016/j.cub.2020.09.074}, volume = {31}, year = {2021}, } @article{7553, abstract = {Normative theories and statistical inference provide complementary approaches for the study of biological systems. A normative theory postulates that organisms have adapted to efficiently solve essential tasks, and proceeds to mathematically work out testable consequences of such optimality; parameters that maximize the hypothesized organismal function can be derived ab initio, without reference to experimental data. In contrast, statistical inference focuses on efficient utilization of data to learn model parameters, without reference to any a priori notion of biological function, utility, or fitness. Traditionally, these two approaches were developed independently and applied separately. Here we unify them in a coherent Bayesian framework that embeds a normative theory into a family of maximum-entropy “optimization priors.” This family defines a smooth interpolation between a data-rich inference regime (characteristic of “bottom-up” statistical models), and a data-limited ab inito prediction regime (characteristic of “top-down” normative theory). We demonstrate the applicability of our framework using data from the visual cortex, and argue that the flexibility it affords is essential to address a number of fundamental challenges relating to inference and prediction in complex, high-dimensional biological problems.}, author = {Mlynarski, Wiktor F and Hledik, Michal and Sokolowski, Thomas R and Tkačik, Gašper}, journal = {Neuron}, number = {7}, pages = {1227--1241.e5}, publisher = {Cell Press}, title = {{Statistical analysis and optimality of neural systems}}, doi = {10.1016/j.neuron.2021.01.020}, volume = {109}, year = {2021}, } @article{7685, abstract = {We consider a gas of interacting bosons trapped in a box of side length one in the Gross–Pitaevskii limit. We review the proof of the validity of Bogoliubov’s prediction for the ground state energy and the low-energy excitation spectrum. This note is based on joint work with C. Brennecke, S. Cenatiempo and B. Schlein.}, author = {Boccato, Chiara}, issn = {0129-055X}, journal = {Reviews in Mathematical Physics}, number = {1}, publisher = {World Scientific}, title = {{The excitation spectrum of the Bose gas in the Gross-Pitaevskii regime}}, doi = {10.1142/S0129055X20600065}, volume = {33}, year = {2021}, } @inproceedings{14332, abstract = {Learning data representations that are useful for various downstream tasks is a cornerstone of artificial intelligence. While existing methods are typically evaluated on downstream tasks such as classification or generative image quality, we propose to assess representations through their usefulness in downstream control tasks, such as reaching or pushing objects. By training over 10,000 reinforcement learning policies, we extensively evaluate to what extent different representation properties affect out-of-distribution (OOD) generalization. Finally, we demonstrate zero-shot transfer of these policies from simulation to the real world, without any domain randomization or fine-tuning. This paper aims to establish the first systematic characterization of the usefulness of learned representations for real-world OOD downstream tasks.}, author = {Träuble, Frederik and Dittadi, Andrea and Wuthrich, Manuel and Widmaier, Felix and Gehler, Peter Vincent and Winther, Ole and Locatello, Francesco and Bachem, Olivier and Schölkopf, Bernhard and Bauer, Stefan}, booktitle = {ICML 2021 Workshop on Unsupervised Reinforcement Learning}, location = {Virtual}, title = {{Representation learning for out-of-distribution generalization in reinforcement learning}}, year = {2021}, } @article{14800, abstract = {Research on two-dimensional (2D) materials has been explosively increasing in last seventeen years in varying subjects including condensed matter physics, electronic engineering, materials science, and chemistry since the mechanical exfoliation of graphene in 2004. Starting from graphene, 2D materials now have become a big family with numerous members and diverse categories. The unique structural features and physicochemical properties of 2D materials make them one class of the most appealing candidates for a wide range of potential applications. In particular, we have seen some major breakthroughs made in the field of 2D materials in last five years not only in developing novel synthetic methods and exploring new structures/properties but also in identifying innovative applications and pushing forward commercialisation. In this review, we provide a critical summary on the recent progress made in the field of 2D materials with a particular focus on last five years. After a brief background introduction, we first discuss the major synthetic methods for 2D materials, including the mechanical exfoliation, liquid exfoliation, vapor phase deposition, and wet-chemical synthesis as well as phase engineering of 2D materials belonging to the field of phase engineering of nanomaterials (PEN). We then introduce the superconducting/optical/magnetic properties and chirality of 2D materials along with newly emerging magic angle 2D superlattices. Following that, the promising applications of 2D materials in electronics, optoelectronics, catalysis, energy storage, solar cells, biomedicine, sensors, environments, etc. are described sequentially. Thereafter, we present the theoretic calculations and simulations of 2D materials. Finally, after concluding the current progress, we provide some personal discussions on the existing challenges and future outlooks in this rapidly developing field. }, author = {Chang, Cheng and Chen, Wei and Chen, Ye and Chen, Yonghua and Chen, Yu and Ding, Feng and Fan, Chunhai and Fan, Hong Jin and Fan, Zhanxi and Gong, Cheng and Gong, Yongji and He, Qiyuan and Hong, Xun and Hu, Sheng and Hu, Weida and Huang, Wei and Huang, Yuan and Ji, Wei and Li, Dehui and Li, Lain Jong and Li, Qiang and Lin, Li and Ling, Chongyi and Liu, Minghua and Liu, Nan and Liu, Zhuang and Loh, Kian Ping and Ma, Jianmin and Miao, Feng and Peng, Hailin and Shao, Mingfei and Song, Li and Su, Shao and Sun, Shuo and Tan, Chaoliang and Tang, Zhiyong and Wang, Dingsheng and Wang, Huan and Wang, Jinlan and Wang, Xin and Wang, Xinran and Wee, Andrew T.S. and Wei, Zhongming and Wu, Yuen and Wu, Zhong Shuai and Xiong, Jie and Xiong, Qihua and Xu, Weigao and Yin, Peng and Zeng, Haibo and Zeng, Zhiyuan and Zhai, Tianyou and Zhang, Han and Zhang, Hui and Zhang, Qichun and Zhang, Tierui and Zhang, Xiang and Zhao, Li Dong and Zhao, Meiting and Zhao, Weijie and Zhao, Yunxuan and Zhou, Kai Ge and Zhou, Xing and Zhou, Yu and Zhu, Hongwei and Zhang, Hua and Liu, Zhongfan}, issn = {1001-4861}, journal = {Acta Physico-Chimica Sinica}, number = {12}, publisher = {Peking University}, title = {{Recent progress on two-dimensional materials}}, doi = {10.3866/PKU.WHXB202108017}, volume = {37}, year = {2021}, } @article{14889, abstract = {We consider the Fröhlich Hamiltonian with large coupling constant α. For initial data of Pekar product form with coherent phonon field and with the electron minimizing the corresponding energy, we provide a norm approximation of the evolution, valid up to times of order α2. The approximation is given in terms of a Pekar product state, evolved through the Landau-Pekar equations, corrected by a Bogoliubov dynamics taking quantum fluctuations into account. This allows us to show that the Landau-Pekar equations approximately describe the evolution of the electron- and one-phonon reduced density matrices under the Fröhlich dynamics up to times of order α2.}, author = {Leopold, Nikolai K and Mitrouskas, David Johannes and Rademacher, Simone Anna Elvira and Schlein, Benjamin and Seiringer, Robert}, issn = {2578-5885}, journal = {Pure and Applied Analysis}, number = {4}, pages = {653--676}, publisher = {Mathematical Sciences Publishers}, title = {{Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly coupled polaron}}, doi = {10.2140/paa.2021.3.653}, volume = {3}, year = {2021}, } @article{14890, abstract = {We consider a system of N interacting bosons in the mean-field scaling regime and construct corrections to the Bogoliubov dynamics that approximate the true N-body dynamics in norm to arbitrary precision. The N-independent corrections are given in terms of the solutions of the Bogoliubov and Hartree equations and satisfy a generalized form of Wick's theorem. We determine the n-point correlation functions of the excitations around the condensate, as well as the reduced densities of the N-body system, to arbitrary accuracy, given only the knowledge of the two-point functions of a quasi-free state and the solution of the Hartree equation. In this way, the complex problem of computing all n-point correlation functions for an interacting N-body system is essentially reduced to the problem of solving the Hartree equation and the PDEs for the Bogoliubov two-point functions.}, author = {Bossmann, Lea and Petrat, Sören P and Pickl, Peter and Soffer, Avy}, issn = {2578-5885}, journal = {Pure and Applied Analysis}, number = {4}, pages = {677--726}, publisher = {Mathematical Sciences Publishers}, title = {{Beyond Bogoliubov dynamics}}, doi = {10.2140/paa.2021.3.677}, volume = {3}, year = {2021}, } @inbook{14984, abstract = {Hybrid zones are narrow geographic regions where different populations, races or interbreeding species meet and mate, producing mixed ‘hybrid’ offspring. They are relatively common and can be found in a diverse range of organisms and environments. The study of hybrid zones has played an important role in our understanding of the origin of species, with hybrid zones having been described as ‘natural laboratories’. This is because they allow us to study,in situ, the conditions and evolutionary forces that enable divergent taxa to remain distinct despite some ongoing gene exchange between them.}, author = {Stankowski, Sean and Shipilina, Daria and Westram, Anja M}, booktitle = {Encyclopedia of Life Sciences}, isbn = {9780470016176}, publisher = {Wiley}, title = {{Hybrid Zones}}, doi = {10.1002/9780470015902.a0029355}, volume = {2}, year = {2021}, } @inbook{14987, abstract = {The goal of zero-shot learning is to construct a classifier that can identify object classes for which no training examples are available. When training data for some of the object classes is available but not for others, the name generalized zero-shot learning is commonly used. In a wider sense, the phrase zero-shot is also used to describe other machine learning-based approaches that require no training data from the problem of interest, such as zero-shot action recognition or zero-shot machine translation.}, author = {Lampert, Christoph}, booktitle = {Computer Vision}, editor = {Ikeuchi, Katsushi}, isbn = {9783030634155}, pages = {1395--1397}, publisher = {Springer}, title = {{Zero-Shot Learning}}, doi = {10.1007/978-3-030-63416-2_874}, year = {2021}, } @misc{14988, abstract = {Raw data generated from the publication - The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis by Johnson et al., 2021 In PNAS}, author = {Johnson, Alexander J}, publisher = {Zenodo}, title = {{Raw data from Johnson et al, PNAS, 2021}}, doi = {10.5281/ZENODO.5747100}, year = {2021}, } @article{15013, abstract = {We consider random n×n matrices X with independent and centered entries and a general variance profile. We show that the spectral radius of X converges with very high probability to the square root of the spectral radius of the variance matrix of X when n tends to infinity. We also establish the optimal rate of convergence, that is a new result even for general i.i.d. matrices beyond the explicitly solvable Gaussian cases. The main ingredient is the proof of the local inhomogeneous circular law [arXiv:1612.07776] at the spectral edge.}, author = {Alt, Johannes and Erdös, László and Krüger, Torben H}, issn = {2690-1005}, journal = {Probability and Mathematical Physics}, number = {2}, pages = {221--280}, publisher = {Mathematical Sciences Publishers}, title = {{Spectral radius of random matrices with independent entries}}, doi = {10.2140/pmp.2021.2.221}, volume = {2}, year = {2021}, } @misc{13057, abstract = {This dataset comprises all data shown in the figures of the submitted article "Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction". Additional raw data are available from the corresponding author on reasonable request.}, author = {Peruzzo, Matilda and Hassani, Farid and Szep, Grisha and Trioni, Andrea and Redchenko, Elena and Zemlicka, Martin and Fink, Johannes M}, publisher = {Zenodo}, title = {{Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction}}, doi = {10.5281/ZENODO.5592103}, year = {2021}, } @misc{13058, abstract = {The zip file includes source data used in the main text of the manuscript "Theory of branching morphogenesis by local interactions and global guidance", as well as a representative Jupyter notebook to reproduce the main figures. A sample script for the simulations of branching and annihilating random walks is also included (Sample_script_for_simulations_of_BARWs.ipynb) to generate exemplary branched networks under external guidance. A detailed description of the simulation setup is provided in the supplementary information of the manuscipt.}, author = {Ucar, Mehmet C}, publisher = {Zenodo}, title = {{Source data for the manuscript "Theory of branching morphogenesis by local interactions and global guidance"}}, doi = {10.5281/ZENODO.5257160}, year = {2021}, } @misc{13061, abstract = {Infections early in life can have enduring effects on an organism’s development and immunity. In this study, we show that this equally applies to developing “superorganisms” – incipient social insect colonies. When we exposed newly mated Lasius niger ant queens to a low pathogen dose, their colonies grew more slowly than controls before winter, but reached similar sizes afterwards. Independent of exposure, queen hibernation survival improved when the ratio of pupae to workers was small. Queens that reared fewer pupae before worker emergence exhibited lower pathogen levels, indicating that high brood rearing efforts interfere with the ability of the queen’s immune system to suppress pathogen proliferation. Early-life queen pathogen-exposure also improved the immunocompetence of her worker offspring, as demonstrated by challenging the workers to the same pathogen a year later. Transgenerational transfer of the queen’s pathogen experience to her workforce can hence durably reduce the disease susceptibility of the whole superorganism.}, author = {Casillas Perez, Barbara E and Pull, Christopher and Naiser, Filip and Naderlinger, Elisabeth and Matas, Jiri and Cremer, Sylvia}, publisher = {Dryad}, title = {{Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies}}, doi = {10.5061/DRYAD.7PVMCVDTJ}, year = {2021}, } @misc{13062, abstract = {This paper analyzes the conditions for local adaptation in a metapopulation with infinitely many islands under a model of hard selection, where population size depends on local fitness. Each island belongs to one of two distinct ecological niches or habitats. Fitness is influenced by an additive trait which is under habitat-dependent directional selection. Our analysis is based on the diffusion approximation and accounts for both genetic drift and demographic stochasticity. By neglecting linkage disequilibria, it yields the joint distribution of allele frequencies and population size on each island. We find that under hard selection, the conditions for local adaptation in a rare habitat are more restrictive for more polygenic traits: even moderate migration load per locus at very many loci is sufficient for population sizes to decline. This further reduces the efficacy of selection at individual loci due to increased drift and because smaller populations are more prone to swamping due to migration, causing a positive feedback between increasing maladaptation and declining population sizes. Our analysis also highlights the importance of demographic stochasticity, which exacerbates the decline in numbers of maladapted populations, leading to population collapse in the rare habitat at significantly lower migration than predicted by deterministic arguments.}, author = {Szep, Eniko and Sachdeva, Himani and Barton, Nicholas H}, publisher = {Dryad}, title = {{Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model}}, doi = {10.5061/DRYAD.8GTHT76P1}, year = {2021}, }