@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}, } @article{7883, abstract = {All vertebrates have a spinal cord with dimensions and shape specific to their species. Yet how species‐specific organ size and shape are achieved is a fundamental unresolved question in biology. The formation and sculpting of organs begins during embryonic development. As it develops, the spinal cord extends in anterior–posterior direction in synchrony with the overall growth of the body. The dorsoventral (DV) and apicobasal lengths of the spinal cord neuroepithelium also change, while at the same time a characteristic pattern of neural progenitor subtypes along the DV axis is established and elaborated. At the basis of these changes in tissue size and shape are biophysical determinants, such as the change in cell number, cell size and shape, and anisotropic tissue growth. These processes are controlled by global tissue‐scale regulators, such as morphogen signaling gradients as well as mechanical forces. Current challenges in the field are to uncover how these tissue‐scale regulatory mechanisms are translated to the cellular and molecular level, and how regulation of distinct cellular processes gives rise to an overall defined size. Addressing these questions will help not only to achieve a better understanding of how size is controlled, but also of how tissue size is coordinated with the specification of pattern.}, author = {Kuzmicz-Kowalska, Katarzyna and Kicheva, Anna}, issn = {17597692}, journal = {Wiley Interdisciplinary Reviews: Developmental Biology}, publisher = {Wiley}, title = {{Regulation of size and scale in vertebrate spinal cord development}}, doi = {10.1002/wdev.383}, year = {2021}, } @article{7900, abstract = {Hartree–Fock theory has been justified as a mean-field approximation for fermionic systems. However, it suffers from some defects in predicting physical properties, making necessary a theory of quantum correlations. Recently, bosonization of many-body correlations has been rigorously justified as an upper bound on the correlation energy at high density with weak interactions. We review the bosonic approximation, deriving an effective Hamiltonian. We then show that for systems with Coulomb interaction this effective theory predicts collective excitations (plasmons) in accordance with the random phase approximation of Bohm and Pines, and with experimental observation.}, author = {Benedikter, Niels P}, issn = {1793-6659}, journal = {Reviews in Mathematical Physics}, number = {1}, publisher = {World Scientific}, title = {{Bosonic collective excitations in Fermi gases}}, doi = {10.1142/s0129055x20600090}, volume = {33}, year = {2021}, } @article{7901, abstract = {We derive rigorously the leading order of the correlation energy of a Fermi gas in a scaling regime of high density and weak interaction. The result verifies the prediction of the random-phase approximation. Our proof refines the method of collective bosonization in three dimensions. We approximately diagonalize an effective Hamiltonian describing approximately bosonic collective excitations around the Hartree–Fock state, while showing that gapless and non-collective excitations have only a negligible effect on the ground state energy.}, author = {Benedikter, Niels P and Nam, Phan Thành and Porta, Marcello and Schlein, Benjamin and Seiringer, Robert}, issn = {1432-1297}, journal = {Inventiones Mathematicae}, pages = {885--979}, publisher = {Springer}, title = {{Correlation energy of a weakly interacting Fermi gas}}, doi = {10.1007/s00222-021-01041-5}, volume = {225}, year = {2021}, } @article{7905, abstract = {We investigate a sheaf-theoretic interpretation of stratification learning from geometric and topological perspectives. Our main result is the construction of stratification learning algorithms framed in terms of a sheaf on a partially ordered set with the Alexandroff topology. We prove that the resulting decomposition is the unique minimal stratification for which the strata are homogeneous and the given sheaf is constructible. In particular, when we choose to work with the local homology sheaf, our algorithm gives an alternative to the local homology transfer algorithm given in Bendich et al. (Proceedings of the 23rd Annual ACM-SIAM Symposium on Discrete Algorithms, pp. 1355–1370, ACM, New York, 2012), and the cohomology stratification algorithm given in Nanda (Found. Comput. Math. 20(2), 195–222, 2020). Additionally, we give examples of stratifications based on the geometric techniques of Breiding et al. (Rev. Mat. Complut. 31(3), 545–593, 2018), illustrating how the sheaf-theoretic approach can be used to study stratifications from both topological and geometric perspectives. This approach also points toward future applications of sheaf theory in the study of topological data analysis by illustrating the utility of the language of sheaf theory in generalizing existing algorithms.}, author = {Brown, Adam and Wang, Bei}, issn = {1432-0444}, journal = {Discrete and Computational Geometry}, pages = {1166--1198}, publisher = {Springer Nature}, title = {{Sheaf-theoretic stratification learning from geometric and topological perspectives}}, doi = {10.1007/s00454-020-00206-y}, volume = {65}, year = {2021}, } @article{7925, abstract = {In this paper, we introduce a relaxed CQ method with alternated inertial step for solving split feasibility problems. We give convergence of the sequence generated by our method under some suitable assumptions. Some numerical implementations from sparse signal and image deblurring are reported to show the efficiency of our method.}, author = {Shehu, Yekini and Gibali, Aviv}, issn = {1862-4480}, journal = {Optimization Letters}, pages = {2109--2126}, publisher = {Springer Nature}, title = {{New inertial relaxed method for solving split feasibilities}}, doi = {10.1007/s11590-020-01603-1}, volume = {15}, year = {2021}, } @article{7939, abstract = {We design fast deterministic algorithms for distance computation in the Congested Clique model. Our key contributions include: A (2+ϵ)-approximation for all-pairs shortest paths in O(log2n/ϵ) rounds on unweighted undirected graphs. With a small additional additive factor, this also applies for weighted graphs. This is the first sub-polynomial constant-factor approximation for APSP in this model. A (1+ϵ)-approximation for multi-source shortest paths from O(n−−√) sources in O(log2n/ϵ) rounds on weighted undirected graphs. This is the first sub-polynomial algorithm obtaining this approximation for a set of sources of polynomial size. Our main techniques are new distance tools that are obtained via improved algorithms for sparse matrix multiplication, which we leverage to construct efficient hopsets and shortest paths. Furthermore, our techniques extend to additional distance problems for which we improve upon the state-of-the-art, including diameter approximation, and an exact single-source shortest paths algorithm for weighted undirected graphs in O~(n1/6) rounds. }, author = {Censor-Hillel, Keren and Dory, Michal and Korhonen, Janne and Leitersdorf, Dean}, issn = {1432-0452}, journal = {Distributed Computing}, pages = {463--487}, publisher = {Springer Nature}, title = {{Fast approximate shortest paths in the congested clique}}, doi = {10.1007/s00446-020-00380-5}, volume = {34}, year = {2021}, } @inbook{7941, abstract = {Expansion microscopy is a recently developed super-resolution imaging technique, which provides an alternative to optics-based methods such as deterministic approaches (e.g. STED) or stochastic approaches (e.g. PALM/STORM). The idea behind expansion microscopy is to embed the biological sample in a swellable gel, and then to expand it isotropically, thereby increasing the distance between the fluorophores. This approach breaks the diffraction barrier by simply separating the emission point-spread-functions of the fluorophores. The resolution attainable in expansion microscopy is thus directly dependent on the separation that can be achieved, i.e. on the expansion factor. The original implementation of the technique achieved an expansion factor of fourfold, for a resolution of 70–80 nm. The subsequently developed X10 method achieves an expansion factor of 10-fold, for a resolution of 25–30 nm. This technique can be implemented with minimal technical requirements on any standard fluorescence microscope, and is more easily applied for multi-color imaging than either deterministic or stochastic super-resolution approaches. This renders X10 expansion microscopy a highly promising tool for new biological discoveries, as discussed here, and as demonstrated by several recent applications.}, author = {Truckenbrodt, Sven M and Rizzoli, Silvio O.}, booktitle = {Methods in Cell Biology}, isbn = {978012820807-6}, issn = {0091-679X}, pages = {33--56}, publisher = {Elsevier}, title = {{Simple multi-color super-resolution by X10 microscopy}}, doi = {10.1016/bs.mcb.2020.04.016}, volume = {161}, year = {2021}, } @article{8196, abstract = {This paper aims to obtain a strong convergence result for a Douglas–Rachford splitting method with inertial extrapolation step for finding a zero of the sum of two set-valued maximal monotone operators without any further assumption of uniform monotonicity on any of the involved maximal monotone operators. Furthermore, our proposed method is easy to implement and the inertial factor in our proposed method is a natural choice. Our method of proof is of independent interest. Finally, some numerical implementations are given to confirm the theoretical analysis.}, author = {Shehu, Yekini and Dong, Qiao-Li and Liu, Lu-Lu and Yao, Jen-Chih}, issn = {1573-2924}, journal = {Optimization and Engineering}, pages = {2627--2653}, publisher = {Springer Nature}, title = {{New strong convergence method for the sum of two maximal monotone operators}}, doi = {10.1007/s11081-020-09544-5}, volume = {22}, 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}, } @article{13356, abstract = {Self-assembly of nanoparticles can be mediated by polymers, but has so far led almost exclusively to nanoparticle aggregates that are amorphous. Here, we employed Coulombic interactions to generate a range of composite materials from mixtures of charged nanoparticles and oppositely charged polymers. The assembly behavior of these nanoparticle/polymer composites depends on their order of addition: polymers added to nanoparticles give rise to stable aggregates, but nanoparticles added to polymers disassemble the initially formed aggregates. The amorphous aggregates were transformed into crystalline ones by transiently increasing the ionic strength of the solution. The morphology of the resulting crystals depended on the length of the polymer: short polymer chains mediated the self-assembly of nanoparticles into strongly faceted crystals, whereas long chains led to pseudospherical nanoparticle/polymer assemblies, within which the crystalline order of nanoparticles was retained.}, author = {Bian, Tong and Klajn, Rafal}, issn = {1749-6632}, journal = {Annals of the New York Academy of Sciences}, keywords = {History and Philosophy of Science, General Biochemistry, Genetics and Molecular Biology, General Neuroscience}, number = {1}, pages = {191--201}, publisher = {Wiley}, title = {{Morphology control in crystalline nanoparticle–polymer aggregates}}, doi = {10.1111/nyas.14674}, volume = {1505}, year = {2021}, } @article{13357, abstract = {Coulombic interactions can be used to assemble charged nanoparticles into higher-order structures, but the process requires oppositely charged partners that are similarly sized. The ability to mediate the assembly of such charged nanoparticles using structurally simple small molecules would greatly facilitate the fabrication of nanostructured materials and harnessing their applications in catalysis, sensing and photonics. Here we show that small molecules with as few as three electric charges can effectively induce attractive interactions between oppositely charged nanoparticles in water. These interactions can guide the assembly of charged nanoparticles into colloidal crystals of a quality previously only thought to result from their co-crystallization with oppositely charged nanoparticles of a similar size. Transient nanoparticle assemblies can be generated using positively charged nanoparticles and multiply charged anions that are enzymatically hydrolysed into mono- and/or dianions. Our findings demonstrate an approach for the facile fabrication, manipulation and further investigation of static and dynamic nanostructured materials in aqueous environments.}, author = {Bian, Tong and Gardin, Andrea and Gemen, Julius and Houben, Lothar and Perego, Claudio and Lee, Byeongdu and Elad, Nadav and Chu, Zonglin and Pavan, Giovanni M. and Klajn, Rafal}, issn = {1755-4349}, journal = {Nature Chemistry}, keywords = {General Chemical Engineering, General Chemistry}, number = {10}, pages = {940--949}, publisher = {Springer Nature}, title = {{Electrostatic co-assembly of nanoparticles with oppositely charged small molecules into static and dynamic superstructures}}, doi = {10.1038/s41557-021-00752-9}, volume = {13}, year = {2021}, }