@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}, } @misc{13063, abstract = {We develop a Bayesian model (BayesRR-RC) that provides robust SNP-heritability estimation, an alternative to marker discovery, and accurate genomic prediction, taking 22 seconds per iteration to estimate 8.4 million SNP-effects and 78 SNP-heritability parameters in the UK Biobank. We find that only $\leq$ 10\% of the genetic variation captured for height, body mass index, cardiovascular disease, and type 2 diabetes is attributable to proximal regulatory regions within 10kb upstream of genes, while 12-25% is attributed to coding regions, 32-44% to introns, and 22-28% to distal 10-500kb upstream regions. Up to 24% of all cis and coding regions of each chromosome are associated with each trait, with over 3,100 independent exonic and intronic regions and over 5,400 independent regulatory regions having >95% probability of contributing >0.001% to the genetic variance of these four traits. Our open-source software (GMRM) provides a scalable alternative to current approaches for biobank data.}, author = {Robinson, Matthew Richard}, publisher = {Dryad}, title = {{Probabilistic inference of the genetic architecture of functional enrichment of complex traits}}, doi = {10.5061/dryad.sqv9s4n51}, year = {2021}, } @misc{13068, abstract = {Source data and source code for the graphs in "Spatiotemporal dynamics of self-organized branching pancreatic cancer-derived organoids".}, author = {Randriamanantsoa, Samuel and Papargyriou, Aristeidis and Maurer, Carlo and Peschke, Katja and Schuster, Maximilian and Zecchin, Giulia and Steiger, Katja and Öllinger, Rupert and Saur, Dieter and Scheel, Christina and Rad, Roland and Hannezo, Edouard B and Reichert, Maximilian and Bausch, Andreas R.}, publisher = {Zenodo}, title = {{Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids}}, doi = {10.5281/ZENODO.5148117}, year = {2021}, } @misc{13069, abstract = {To survive elevated temperatures, ectotherms adjust the fluidity of membranes by fine-tuning lipid desaturation levels in a process previously described to be cell-autonomous. We have discovered that, in Caenorhabditis elegans, neuronal Heat shock Factor 1 (HSF-1), the conserved master regulator of the heat shock response (HSR)- causes extensive fat remodelling in peripheral tissues. These changes include a decrease in fat desaturase and acid lipase expression in the intestine, and a global shift in the saturation levels of plasma membrane’s phospholipids. The observed remodelling of plasma membrane is in line with ectothermic adaptive responses and gives worms a cumulative advantage to warm temperatures. We have determined that at least six TAX-2/TAX-4 cGMP gated channel expressing sensory neurons and TGF-β/BMP are required for signalling across tissues to modulate fat desaturation. We also find neuronal hsf-1 is not only sufficient but also partially necessary to control the fat remodelling response and for survival at warm temperatures. This is the first study to show that a thermostat-based mechanism can cell non-autonomously coordinate membrane saturation and composition across tissues in a multicellular animal.}, author = {Chauve, Laetitia and Hodge, Francesca and Murdoch, Sharlene and Masoudzadeh, Fatemah and Mann, Harry-Jack and Lopez-Clavijo, Andrea and Okkenhaug, Hanneke and West, Greg and Sousa, Bebiana C. and Segonds-Pichon, Anne and Li, Cheryl and Wingett, Steven and Kienberger, Hermine and Kleigrewe, Karin and de Bono, Mario and Wakelam, Michael and Casanueva, Olivia}, publisher = {Zenodo}, title = {{Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans}}, doi = {10.5281/ZENODO.5519410}, year = {2021}, } @misc{13072, abstract = {CpGs and corresponding mean weights for DNAm-based prediction of cognitive abilities (6 traits)}, author = {McCartney, Daniel L and Hillary, Robert F and Conole, Eleanor LS and Trejo Banos, Daniel and Gadd, Danni A and Walker, Rosie M and Nangle, Cliff and Flaig, Robin and Campbell, Archie and Murray, Alison D and Munoz Maniega, Susana and del C Valdes-Hernandez, Maria and Harris, Mathew A and Bastin, Mark E and Wardlaw, Joanna M and Harris, Sarah E and Porteous, David J and Tucker-Drob, Elliot M and McIntosh, Andrew M and Evans, Kathryn L and Deary, Ian J and Cox, Simon R and Robinson, Matthew Richard and Marioni, Riccardo E}, publisher = {Zenodo}, title = {{Blood-based epigenome-wide analyses of cognitive abilities}}, doi = {10.5281/ZENODO.5794028}, year = {2021}, } @misc{13080, abstract = {Data for the manuscript 'Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire' ([2006.01275] Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire (arxiv.org)) We upload a pdf with extended data sets, and the raw data for these extended datasets as well.}, author = {Puglia, Denise and Martinez, Esteban and Menard, Gerbold and Pöschl, Andreas and Gronin, Sergei and Gardner, Geoffrey and Kallaher, Ray and Manfra, Michael and Marcus, Charles and Higginbotham, Andrew P and Casparis, Lucas}, publisher = {Zenodo}, title = {{Data for 'Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire}}, doi = {10.5281/ZENODO.4592435}, year = {2021}, } @inproceedings{13146, abstract = {A recent line of work has analyzed the theoretical properties of deep neural networks via the Neural Tangent Kernel (NTK). In particular, the smallest eigenvalue of the NTK has been related to the memorization capacity, the global convergence of gradient descent algorithms and the generalization of deep nets. However, existing results either provide bounds in the two-layer setting or assume that the spectrum of the NTK matrices is bounded away from 0 for multi-layer networks. In this paper, we provide tight bounds on the smallest eigenvalue of NTK matrices for deep ReLU nets, both in the limiting case of infinite widths and for finite widths. In the finite-width setting, the network architectures we consider are fairly general: we require the existence of a wide layer with roughly order of N neurons, N being the number of data samples; and the scaling of the remaining layer widths is arbitrary (up to logarithmic factors). To obtain our results, we analyze various quantities of independent interest: we give lower bounds on the smallest singular value of hidden feature matrices, and upper bounds on the Lipschitz constant of input-output feature maps.}, author = {Nguyen, Quynh and Mondelli, Marco and Montufar, Guido}, booktitle = {Proceedings of the 38th International Conference on Machine Learning}, isbn = {9781713845065}, issn = {2640-3498}, location = {Virtual}, pages = {8119--8129}, publisher = {ML Research Press}, title = {{Tight bounds on the smallest Eigenvalue of the neural tangent kernel for deep ReLU networks}}, volume = {139}, year = {2021}, } @inproceedings{13147, abstract = {We investigate fast and communication-efficient algorithms for the classic problem of minimizing a sum of strongly convex and smooth functions that are distributed among n different nodes, which can communicate using a limited number of bits. Most previous communication-efficient approaches for this problem are limited to first-order optimization, and therefore have \emph{linear} dependence on the condition number in their communication complexity. We show that this dependence is not inherent: communication-efficient methods can in fact have sublinear dependence on the condition number. For this, we design and analyze the first communication-efficient distributed variants of preconditioned gradient descent for Generalized Linear Models, and for Newton’s method. Our results rely on a new technique for quantizing both the preconditioner and the descent direction at each step of the algorithms, while controlling their convergence rate. We also validate our findings experimentally, showing faster convergence and reduced communication relative to previous methods.}, author = {Alimisis, Foivos and Davies, Peter and Alistarh, Dan-Adrian}, booktitle = {Proceedings of the 38th International Conference on Machine Learning}, isbn = {9781713845065}, issn = {2640-3498}, location = {Virtual}, pages = {196--206}, publisher = {ML Research Press}, title = {{Communication-efficient distributed optimization with quantized preconditioners}}, volume = {139}, 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}, } @article{13358, abstract = {DNA nanotechnology offers a versatile toolbox for precise spatial and temporal manipulation of matter on the nanoscale. However, rendering DNA-based systems responsive to light has remained challenging. Herein, we describe the remote manipulation of native (non-photoresponsive) chiral plasmonic molecules (CPMs) using light. Our strategy is based on the use of a photoresponsive medium comprising a merocyanine-based photoacid. Upon exposure to visible light, the medium decreases its pH, inducing the formation of DNA triplex links, leading to a spatial reconfiguration of the CPMs. The process can be reversed simply by turning the light off and it can be repeated for multiple cycles. The degree of the overall chirality change in an ensemble of CPMs depends on the CPM fraction undergoing reconfiguration, which, remarkably, depends on and can be tuned by the intensity of incident light. Such a dynamic, remotely controlled system could aid in further advancing DNA-based devices and nanomaterials.}, author = {Ryssy, Joonas and Natarajan, Ashwin K. and Wang, Jinhua and Lehtonen, Arttu J. and Nguyen, Minh‐Kha and Klajn, Rafal and Kuzyk, Anton}, issn = {1521-3773}, journal = {Angewandte Chemie International Edition}, keywords = {General Chemistry, Catalysis}, number = {11}, pages = {5859--5863}, publisher = {Wiley}, title = {{Light‐responsive dynamic DNA‐origami‐based plasmonic assemblies}}, doi = {10.1002/anie.202014963}, volume = {60}, year = {2021}, }