@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{21081, abstract = {Macrocyclic peptides are an important class of bioactive substances. When inserting an aromatic foldamer segment in a macrocyclic peptide, the strong folding propensity of the former may influence the conformation and alter the properties of the latter. Such an insertion is relevant because some foldamer–peptide hybrids have recently been shown to be tolerated by the ribosome, prior to forming macrocycles, and can thus be produced using an in vitro translation system. We have investigated the interplay of peptide and foldamer conformations in such hybrid macrocycles. We show that foldamer helical folding always prevails and stands as a viable means to stretch, i.e. unfold, peptides in a solvent dependent manner. Conversely, the peptide systematically has a reciprocal influence and gives rise to strong foldamer helix handedness bias as well as foldamer helix stabilisation. The hybrid macrocycles also show resistance towards proteolytic degradation.}, author = {Dengler, Sebastian and Mandal, Pradeep K and Allmendinger, Lars and Douat, Céline and Huc, Ivan}, issn = {2041-6539}, journal = {Chemical Science}, number = {33}, pages = {11004--11012}, publisher = {Royal Society of Chemistry}, title = {{Conformational interplay in hybrid peptide–helical aromatic foldamer macrocycles}}, doi = {10.1039/d1sc03640h}, volume = {12}, year = {2021}, } @article{21082, abstract = {A novel chiral aromatic δ-amino acid building block was shown to fully induce handedness in quinoline oligoamide foldamers with the possibility of further increasing the bias by combining multiples of these units in the same sequence. Through its incorporation within the helix, both N- and C-termini are still accessible for further functionalisation.}, author = {Bindl, Daniel and Heinemann, Elisabeth and Mandal, Pradeep K and Huc, Ivan}, issn = {1364-548X}, journal = {Chemical Communications}, number = {46}, pages = {5662--5665}, publisher = {Royal Society of Chemistry}, title = {{Quantitative helix handedness bias through a single H vs. CH3 stereochemical differentiation}}, doi = {10.1039/d1cc01452h}, volume = {57}, year = {2021}, } @article{21552, abstract = {We present full-Maxwell topology-optimization design of a single-piece multilayer metalens, about 10 wavelengths λ in thickness, which simultaneously focuses over a 60° angular range and a 23% spectral bandwidth without suffering chromatic or angular aberration, a “plan-achromat.” At all angles and frequencies, it achieves diffraction-limited focusing (Strehl ratio >0.8) and an absolute focusing efficiency of >50%. Both 2D and 3D axisymmetric designs are presented, optimized over ∼105 degrees of freedom. We also demonstrate shortening the lens-to-sensor distance while producing the same image as for a longer “virtual” focal length and maintaining plan-achromaticity. These proof-of-concept designs demonstrate the ultra-compact multifunctionality that can be achieved by exploiting the full wave physics of subwavelength designs and motivate future work on design and fabrication of multilayer metaoptics.}, author = {Lin, Zin and Roques-Carmes, Charles and Christiansen, Rasmus E. and Soljačić, Marin and Johnson, Steven G.}, issn = {1077-3118}, journal = {Applied Physics Letters}, number = {4}, publisher = {AIP Publishing}, title = {{Computational inverse design for ultra-compact single-piece metalenses free of chromatic and angular aberration}}, doi = {10.1063/5.0035419}, volume = {118}, year = {2021}, } @article{21559, abstract = {Being a general wave phenomenon, bound states in the continuum (BICs) appear in acoustic, hydrodynamic, and photonic systems of various dimensionalities. Here, we report the first experimental observation of an accidental electromagnetic BIC in a one-dimensional periodic chain of coaxial ceramic disks. We show that the accidental BIC manifests itself as a narrow peak in the transmission spectra of the chain placed between two loop antennas. We demonstrate a linear growth of the radiative quality factor of the BICs with the number of disks that is well described with the developed tight-binding model. We estimate the number of disks when the radiation losses become negligible in comparison to material absorption and, therefore, the chain can be considered as practically infinite. The presented analysis is supported by near-field measurements of the BIC profile. The obtained results provide useful guidelines for practical implementations of structures with BICs opening up horizons for the development of radio-frequency and optical metadevices.}, author = {Sidorenko, M.S. and Sergaeva, O.N. and Sadrieva, Z.F. and Roques-Carmes, Charles and Muraev, P.S. and Maksimov, D.N. and Bogdanov, A.A.}, issn = {2331-7019}, journal = {Physical Review Applied}, number = {3}, publisher = {American Physical Society }, title = {{Observation of an accidental bound state in the continuum in a chain of dielectric disks}}, doi = {10.1103/physrevapplied.15.034041}, volume = {15}, year = {2021}, } @inproceedings{21565, abstract = {Dielectric resonators are open systems whose eigenmodes couple to the radiation continuum resulting in nonzero radiation losses. For a long time, it was believed that only guided modes with frequencies below the light line were decoupled from the radiation continuum [1] . In the early 2000’s, several counterexamples of perfectly localized states – i.e. totally decoupled from the radiation continuum – at frequencies above the light line were proposed in dielectric gratings and photonic crystal waveguides [2] . Such states are known as bound states in the continuum (BIC) .}, author = {Sidorenko, M. S. and Sergaeva, O. N. and Sadrieva, Z. F. and Roques-Carmes, Charles and Muraev, P. S. and Maksimov, D. N. and Bogdanov, A. A.}, booktitle = {2021 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference}, location = {Munich, Germany}, publisher = {IEEE}, title = {{Accidental bound state in the continuum in a chain of dielectric disks}}, doi = {10.1109/cleo/europe-eqec52157.2021.9592618}, year = {2021}, } @inproceedings{21574, abstract = {Combinatorial problems, such as the Ising problem, are hard to solve with conventional electronics. Photonic systems have recently been proposed as an efficient platform to solve these problems faster and more efficiently, thus calling for the development of featured algorithms to run on photonic machines. A few recent findings, including the Photonic Recurrent Ising Sampler, a photonic machine that recurrently solves arbitrary Ising problems, will be presented in this talk, along with their experimental realizations in various platforms.}, author = {Roques-Carmes, Charles and Shen, Yichen and Prabhu, Mihika and Englund, Dirk and Joannopoulos, John and Soljacic, Marin}, booktitle = {AI and Optical Data Sciences II}, location = {Virtual}, publisher = {SPIE}, title = {{Heuristic algorithms to solve combinatorial problems with photonics}}, doi = {10.1117/12.2579334}, volume = {11703}, year = {2021}, } @inproceedings{21575, abstract = {Periodic wavelength-scale surface patterns have long been used in the context of lasing and spontaneous emission to enhance emission by light trapping (distributed Bragg resonances). Buried within these well-known devices, however, are theoretical mysteries that are still being unravelled. A periodic surface grating actually creates a continuum of resonant modes, so what determines which single mode (if any) lases? Technically, what determines the stability of a periodic lasing mode: is it only the finite size of a surface that allows single-mode lasing, or can it arise for arbitrarily large structures? More generally, if one continuously deforms an unpatterned surface to maximize light emission, how is the symmetry broken and what optimal structures arise? We address these questions by combining new computational techniques for modeling and large-scale optimization of incoherent emission and lasing with new analytical results arising from perturbation and stability theory.}, author = {Benzaouia, Mohammed and Yao, Wenjie and Cerjan, Alexander and Lin, Zin and Roques-Carmes, Charles and Verdugo, Francesc and Christiansen, Rasmus E. and Johnson, Steven G.}, booktitle = {Active Photonic Platforms XIII}, location = {San Diego, CA, United States}, pages = {117960L}, publisher = {SPIE}, title = {{Foundations of lasing and emission from surface-patterned structures}}, doi = {10.1117/12.2595792}, volume = {11796}, year = {2021}, } @inproceedings{21622, abstract = {We develop a general framework to describe non-equilibrium radiation by materials in nanophotonic structures (such as photoluminescence/cathodoluminescence/scintillation). We demonstrate the concept experimentally, enhancing and shaping cathodoluminescence from a silica photonic crystal.}, author = {Roques-Carmes, Charles and Rivera, Nicholas and Ghorashi, Ali and Kooi, Steven E. and Yang, Yi and Lin, Zin and Beroz, Justin and Joannopoulos, John D. and Kaminer, Ido and Johnson, Steven and Soljačić, Marin}, booktitle = {Conference on Lasers and Electro-Optics}, location = {San Jose, CA, United States}, publisher = {Optica Publishing Group}, title = {{A general framework for shaping luminescence in materials}}, doi = {10.1364/cleo_qels.2021.fm1l.5}, year = {2021}, } @inproceedings{21623, abstract = {We present a method to overcome the Manley-Rowe limit in a Q-factor engineered multimodal nonlinear cavity. Cascading nonlinear processes enable continuous-wave terahertz generation with a theoretical conversion efficiency of 98.8%.}, author = {Salamin, Yannick and Roques-Carmes, Charles and Lin, Zin and Johnson, Steven G. and Soljačić, Marin}, booktitle = {Conference on Lasers and Electro-Optics}, location = {San Jose, CA, United States}, publisher = {Optica Publishing Group}, title = {{Overcoming the Manley-Rowe limit for CW terahertz generation in Q-engineered multimodal cavity}}, doi = {10.1364/cleo_qels.2021.ftu2j.3}, year = {2021}, } @article{21805, abstract = {Donor–acceptor Stenhouse adducts (DASAs) are visible‐light‐responsive photoswitches with a variety of emerging applications in photoresponsive materials. Their two‐step modular synthesis, centered on the nucleophilic ring opening of an activated furan, makes DASAs readily accessible. However, the use of less reactive donors or acceptors renders the process slow and low yielding, which has limited their development. We demonstrate here that 1,1,1,3,3,3‐hexafluoro‐2‐propanol (HFIP) promotes the ring‐opening reaction and stabilizes the open isomer, allowing greatly reduced reaction times and increased yields for known derivatives. In addition, it provides access to previously unattainable DASA‐based photoswitches and DASA–polymer conjugates. The role of HFIP and the photochromic properties of a set of new DASAs is probed using a combination of 1H NMR and UV/Vis spectroscopy. The use of sterically hindered, electron‐poor amines enabled the dark equilibrium to be decoupled from closed‐isomer half‐lives for the first time.}, author = {Clerc, Michèle and Stricker, Friedrich J and Ulrich, Sebastian and Sroda, Miranda and Bruns, Nico and Boesel, Luciano F. and Read de Alaniz, Javier}, issn = {1521-3773}, journal = {Angewandte Chemie International Edition}, number = {18}, pages = {10219--10227}, publisher = {Wiley}, title = {{Promoting the furan ring‐opening reaction to access new donor-acceptor Stenhouse adducts with hexafluoroisopropanol}}, doi = {10.1002/anie.202100115}, volume = {60}, year = {2021}, }