@article{9570,
abstract = {We present conductance-matrix measurements in long, three-terminal hybrid superconductor-semiconductor nanowires, and compare with theoretical predictions of a magnetic-field-driven, topological quantum phase transition. By examining the nonlocal conductance, we identify the closure of the excitation gap in the bulk of the semiconductor before the emergence of zero-bias peaks, ruling out spurious gap-closure signatures from localized states. We observe that after the gap closes, nonlocal signals and zero-bias peaks fluctuate strongly at both ends, inconsistent with a simple picture of clean topological superconductivity.},
author = {Puglia, Denise and Martinez, E. A. and Ménard, G. C. and Pöschl, A. and Gronin, S. and Gardner, G. C. and Kallaher, R. and Manfra, M. J. and Marcus, C. M. and Higginbotham, Andrew P and Casparis, L.},
issn = {24699969},
journal = {Physical Review B},
number = {23},
publisher = {American Physical Society},
title = {{Closing of the induced gap in a hybrid superconductor-semiconductor nanowire}},
doi = {10.1103/PhysRevB.103.235201},
volume = {103},
year = {2021},
}
@article{9607,
abstract = {While high risk of failure is an inherent part of developing innovative therapies, it can be reduced by adherence to evidence-based rigorous research practices. Numerous analyses conducted to date have clearly identified measures that need to be taken to improve research rigor. Supported through the European Union's Innovative Medicines Initiative, the EQIPD consortium has developed a novel preclinical research quality system that can be applied in both public and private sectors and is free for anyone to use. The EQIPD Quality System was designed to be suited to boost innovation by ensuring the generation of robust and reliable preclinical data while being lean, effective and not becoming a burden that could negatively impact the freedom to explore scientific questions. EQIPD defines research quality as the extent to which research data are fit for their intended use. Fitness, in this context, is defined by the stakeholders, who are the scientists directly involved in the research, but also their funders, sponsors, publishers, research tool manufacturers and collaboration partners such as peers in a multi-site research project. The essence of the EQIPD Quality System is the set of 18 core requirements that can be addressed flexibly, according to user-specific needs and following a user-defined trajectory. The EQIPD Quality System proposes guidance on expectations for quality-related measures, defines criteria for adequate processes (i.e., performance standards) and provides examples of how such measures can be developed and implemented. However, it does not prescribe any pre-determined solutions. EQIPD has also developed tools (for optional use) to support users in implementing the system and assessment services for those research units that successfully implement the quality system and seek formal accreditation. Building upon the feedback from users and continuous improvement, a sustainable EQIPD Quality System will ultimately serve the entire community of scientists conducting non-regulated preclinical research, by helping them generate reliable data that are fit for their intended use.},
author = {Bespalov, Anton and Bernard, René and Gilis, Anja and Gerlach, Björn and Guillén, Javier and Castagné, Vincent and Lefevre, Isabel A. and Ducrey, Fiona and Monk, Lee and Bongiovanni, Sandrine and Altevogt, Bruce and Arroyo-Araujo, María and Bikovski, Lior and De Bruin, Natasja and Castaños-Vélez, Esmeralda and Dityatev, Alexander and Emmerich, Christoph H. and Fares, Raafat and Ferland-Beckham, Chantelle and Froger-Colléaux, Christelle and Gailus-Durner, Valerie and Hölter, Sabine M. and Hofmann, Martine Cj and Kabitzke, Patricia and Kas, Martien Jh and Kurreck, Claudia and Moser, Paul and Pietraszek, Malgorzata and Popik, Piotr and Potschka, Heidrun and Prado Montes De Oca, Ernesto and Restivo, Leonardo and Riedel, Gernot and Ritskes-Hoitinga, Merel and Samardzic, Janko and Schunn, Michael and Stöger, Claudia and Voikar, Vootele and Vollert, Jan and Wever, Kimberley E. and Wuyts, Kathleen and Macleod, Malcolm R. and Dirnagl, Ulrich and Steckler, Thomas},
issn = {2050084X},
journal = {eLife},
publisher = {eLife Sciences Publications},
title = {{Introduction to the EQIPD quality system}},
doi = {10.7554/eLife.63294},
volume = {10},
year = {2021},
}
@article{9569,
abstract = {We report the synthesis and characterization of graphene functionalized with iron (Fe3+) oxide (G-Fe3O4) nanohybrids for radio-frequency magnetic hyperthermia application. We adopted the wet chemical procedure, using various contents of Fe3O4 (magnetite) from 0–100% for making two-dimensional graphene–Fe3O4 nanohybrids. The homogeneous dispersal of Fe3O4 nanoparticles decorated on the graphene surface combined with their biocompatibility and high thermal conductivity make them an excellent material for magnetic hyperthermia. The morphological and magnetic properties of the nanohybrids were studied using scanning electron microscopy (SEM) and a vibrating sample magnetometer (VSM), respectively. The smart magnetic platforms were exposed to an alternating current (AC) magnetic field of 633 kHz and of strength 9.1 mT for studying their hyperthermic performance. The localized antitumor effects were investigated with artificial neural network modeling. A neural net time-series model was developed for the assessment of the best nanohybrid composition to serve the purpose with an accuracy close to 100%. Six Nonlinear Autoregressive with External Input (NARX) models were obtained, one for each of the components. The assessment of the accuracy of the predicted results has been done on the basis of Mean Squared Error (MSE). The highest Mean Squared Error value was obtained for the nanohybrid containing 45% magnetite and 55% graphene (F45G55) in the training phase i.e., 0.44703, which is where the model achieved optimal results after 71 epochs. The F45G55 nanohybrid was found to be the best for hyperthermia applications in low dosage with the highest specific absorption rate (SAR) and mean squared error values.},
author = {Dar, M. S. and Akram, Khush Bakhat and Sohail, Ayesha and Arif, Fatima and Zabihi, Fatemeh and Yang, Shengyuan and Munir, Shamsa and Zhu, Meifang and Abid, M. and Nauman, Muhammad},
issn = {2046-2069},
journal = {RSC Advances},
number = {35},
pages = {21702--21715},
publisher = {Royal Society of Chemistry},
title = {{Heat induction in two-dimensional graphene–Fe3O4 nanohybrids for magnetic hyperthermia applications with artificial neural network modeling}},
doi = {10.1039/d1ra03428f},
volume = {11},
year = {2021},
}
@article{9606,
abstract = {Sound propagation is a macroscopic manifestation of the interplay between the equilibrium thermodynamics and the dynamical transport properties of fluids. Here, for a two-dimensional system of ultracold fermions, we calculate the first and second sound velocities across the whole BCS-BEC crossover, and we analyze the system response to an external perturbation. In the low-temperature regime we reproduce the recent measurements [Phys. Rev. Lett. 124, 240403 (2020)] of the first sound velocity, which, due to the decoupling of density and entropy fluctuations, is the sole mode excited by a density probe. Conversely, a heat perturbation excites only the second sound, which, being sensitive to the superfluid depletion, vanishes in the deep BCS regime and jumps discontinuously to zero at the Berezinskii-Kosterlitz-Thouless superfluid transition. A mixing between the modes occurs only in the finite-temperature BEC regime, where our theory converges to the purely bosonic results.},
author = {Tononi, A. and Cappellaro, Alberto and Bighin, Giacomo and Salasnich, L.},
issn = {24699934},
journal = {Physical Review A},
number = {6},
publisher = {American Physical Society},
title = {{Propagation of first and second sound in a two-dimensional Fermi superfluid}},
doi = {10.1103/PhysRevA.103.L061303},
volume = {103},
year = {2021},
}
@article{9603,
abstract = {Mosaic analysis with double markers (MADM) offers one approach to visualize and concomitantly manipulate genetically defined cells in mice with single-cell resolution. MADM applications include the analysis of lineage, single-cell morphology and physiology, genomic imprinting phenotypes, and dissection of cell-autonomous gene functions in vivo in health and disease. Yet, MADM can only be applied to <25% of all mouse genes on select chromosomes to date. To overcome this limitation, we generate transgenic mice with knocked-in MADM cassettes near the centromeres of all 19 autosomes and validate their use across organs. With this resource, >96% of the entire mouse genome can now be subjected to single-cell genetic mosaic analysis. Beyond a proof of principle, we apply our MADM library to systematically trace sister chromatid segregation in distinct mitotic cell lineages. We find striking chromosome-specific biases in segregation patterns, reflecting a putative mechanism for the asymmetric segregation of genetic determinants in somatic stem cell division.},
author = {Contreras, Ximena and Amberg, Nicole and Davaatseren, Amarbayasgalan and Hansen, Andi H and Sonntag, Johanna and Andersen, Lill and Bernthaler, Tina and Streicher, Carmen and Heger, Anna-Magdalena and Johnson, Randy L. and Schwarz, Lindsay A. and Luo, Liqun and Rülicke, Thomas and Hippenmeyer, Simon},
issn = {22111247},
journal = {Cell Reports},
number = {12},
publisher = {Cell Press},
title = {{A genome-wide library of MADM mice for single-cell genetic mosaic analysis}},
doi = {10.1016/j.celrep.2021.109274},
volume = {35},
year = {2021},
}
@article{9601,
abstract = {In mammalian genomes, differentially methylated regions (DMRs) and histone marks including trimethylation of histone 3 lysine 27 (H3K27me3) at imprinted genes are asymmetrically inherited to control parentally-biased gene expression. However, neither parent-of-origin-specific transcription nor imprints have been comprehensively mapped at the blastocyst stage of preimplantation development. Here, we address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos. We find that seventy-one genes exhibit previously unreported parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted expressed). Uniparental expression of nBiX genes disappears soon after implantation. Micro-whole-genome bisulfite sequencing (µWGBS) of individual uniparental blastocysts detects 859 DMRs. We further find that 16% of nBiX genes are associated with a DMR, whereas most are associated with parentally-biased H3K27me3, suggesting a role for Polycomb-mediated imprinting in blastocysts. nBiX genes are clustered: five clusters contained at least one published imprinted gene, and five clusters exclusively contained nBiX genes. These data suggest that early development undergoes a complex program of stage-specific imprinting involving different tiers of regulation.},
author = {Santini, Laura and Halbritter, Florian and Titz-Teixeira, Fabian and Suzuki, Toru and Asami, Maki and Ma, Xiaoyan and Ramesmayer, Julia and Lackner, Andreas and Warr, Nick and Pauler, Florian and Hippenmeyer, Simon and Laue, Ernest and Farlik, Matthias and Bock, Christoph and Beyer, Andreas and Perry, Anthony C.F. and Leeb, Martin},
issn = {20411723},
journal = {Nature Communications},
number = {1},
publisher = {Springer Nature},
title = {{Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3}},
doi = {10.1038/s41467-021-23510-4},
volume = {12},
year = {2021},
}
@article{9602,
abstract = {An ordered graph is a graph with a linear ordering on its vertex set. We prove that for every positive integer k, there exists a constant ck > 0 such that any ordered graph G on n vertices with the property that neither G nor its complement contains an induced monotone path of size k, has either a clique or an independent set of size at least n^ck . This strengthens a result of Bousquet, Lagoutte, and Thomassé, who proved the analogous result for unordered graphs.
A key idea of the above paper was to show that any unordered graph on n vertices that does not contain an induced path of size k, and whose maximum degree is at most c(k)n for some small c(k) > 0, contains two disjoint linear size subsets with no edge between them. This approach fails for ordered graphs, because the analogous statement is false for k ≥ 3, by a construction of Fox. We provide some further examples showing that this statement also fails for ordered graphs avoiding other ordered trees.},
author = {Pach, János and Tomon, István},
issn = {00958956},
journal = {Journal of Combinatorial Theory. Series B},
pages = {21--37},
publisher = {Elsevier},
title = {{Erdős-Hajnal-type results for monotone paths}},
doi = {10.1016/j.jctb.2021.05.004},
volume = {151},
year = {2021},
}
@inproceedings{9604,
abstract = {Generalizing Lee’s inductive argument for counting the cells of higher order Voronoi tessellations in ℝ² to ℝ³, we get precise relations in terms of Morse theoretic quantities for piecewise constant functions on planar arrangements. Specifically, we prove that for a generic set of n ≥ 5 points in ℝ³, the number of regions in the order-k Voronoi tessellation is N_{k-1} - binom(k,2)n + n, for 1 ≤ k ≤ n-1, in which N_{k-1} is the sum of Euler characteristics of these function’s first k-1 sublevel sets. We get similar expressions for the vertices, edges, and polygons of the order-k Voronoi tessellation.},
author = {Biswas, Ranita and Cultrera di Montesano, Sebastiano and Edelsbrunner, Herbert and Saghafian, Morteza},
booktitle = {Leibniz International Proceedings in Informatics},
isbn = {9783959771849},
issn = {18688969},
location = {Online},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Counting cells of order-k voronoi tessellations in ℝ^{3} with morse theory}},
doi = {10.4230/LIPIcs.SoCG.2021.16},
volume = {189},
year = {2021},
}
@article{8909,
abstract = {Spin qubits are considered to be among the most promising candidates for building a quantum processor. Group IV hole spin qubits have moved into the focus of interest due to the ease of operation and compatibility with Si technology. In addition, Ge offers the option for monolithic superconductor-semiconductor integration. Here we demonstrate a hole spin qubit operating at fields below 10 mT, the critical field of Al, by exploiting the large out-of-plane hole g-factors in planar Ge and by encoding the qubit into the singlet-triplet states of a double quantum dot. We observe electrically controlled X and Z-rotations with tunable frequencies exceeding 100 MHz and dephasing times of 1μs which we extend beyond 15μs with echo techniques. These results show that Ge hole singlet triplet qubits outperform their electronic Si and GaAs based counterparts in speed and coherence, respectively. In addition, they are on par with Ge single spin qubits, but can be operated at much lower fields underlining their potential for on chip integration with superconducting technologies.},
author = {Jirovec, Daniel and Hofmann, Andrea C and Ballabio, Andrea and Mutter, Philipp M. and Tavani, Giulio and Botifoll, Marc and Crippa, Alessandro and Kukucka, Josip and Sagi, Oliver and Martins, Frederico and Saez Mollejo, Jaime and Prieto Gonzalez, Ivan and Borovkov, Maksim and Arbiol, Jordi and Chrastina, Daniel and Isella, Giovanni and Katsaros, Georgios},
issn = {1476-4660},
journal = {Nature Materials},
publisher = {Springer Nature},
title = {{A singlet triplet hole spin qubit in planar Ge}},
doi = {10.1038/s41563-021-01022-2},
year = {2021},
}
@misc{9323,
abstract = {This .zip File contains the data for figures presented in the main text and supplementary material of "A singlet triplet hole spin qubit in planar Ge" by D. Jirovec, et. al. The measurements were done using Labber Software and the data is stored in the hdf5 file format. The files can be opened using either the Labber Log Browser (https://labber.org/overview/) or Labber Python API (http://labber.org/online-doc/api/LogFile.html). A single file is acquired with QCodes and features the corresponding data type. XRD data are in .dat format and a code to open the data is provided. The code for simulations is as well provided in Python.},
author = {Jirovec, Daniel},
publisher = {IST Austria},
title = {{Research data for "A singlet-triplet hole spin qubit planar Ge"}},
doi = {10.15479/AT:ISTA:9323},
year = {2021},
}
@inproceedings{9356,
abstract = {In runtime verification, a monitor watches a trace of a system and, if possible, decides after observing each finite prefix whether or not the unknown infinite trace satisfies a given specification. We generalize the theory of runtime verification to monitors that attempt to estimate numerical values of quantitative trace properties (instead of attempting to conclude boolean values of trace specifications), such as maximal or average response time along a trace. Quantitative monitors are approximate: with every finite prefix, they can improve their estimate of the infinite trace's unknown property value. Consequently, quantitative monitors can be compared with regard to a precision-cost trade-off: better approximations of the property value require more monitor resources, such as states (in the case of finite-state monitors) or registers, and additional resources yield better approximations. We introduce a formal framework for quantitative and approximate monitoring, show how it conservatively generalizes the classical boolean setting for monitoring, and give several precision-cost trade-offs for monitors. For example, we prove that there are quantitative properties for which every additional register improves monitoring precision.},
author = {Henzinger, Thomas A and Sarac, Naci E},
booktitle = {Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science},
location = {Online},
publisher = {Association for Computing Machinery},
title = {{Quantitative and approximate monitoring}},
year = {2021},
}
@inproceedings{9592,
abstract = {The convex grabbing game is a game where two players, Alice and Bob, alternate taking extremal points from the convex hull of a point set on the plane. Rational weights are given to the points. The goal of each player is to maximize the total weight over all points that they obtain. We restrict the setting to the case of binary weights. We show a construction of an arbitrarily large odd-sized point set that allows Bob to obtain almost 3/4 of the total weight. This construction answers a question asked by Matsumoto, Nakamigawa, and Sakuma in [Graphs and Combinatorics, 36/1 (2020)]. We also present an arbitrarily large even-sized point set where Bob can obtain the entirety of the total weight. Finally, we discuss conjectures about optimum moves in the convex grabbing game for both players in general.},
author = {Dvorak, Martin and Nicholson, Sara},
booktitle = {Proceedings of the 33rd Canadian Conference on Computational Geometry},
keywords = {convex grabbing game, graph grabbing game, combinatorial game, convex geometry},
location = {Online},
title = {{Massively winning configurations in the convex grabbing game on the plane}},
year = {2021},
}
@article{8198,
abstract = {We investigate how the critical driving amplitude at the Floquet many-body localized (MBL) to ergodic phase transition differs between smooth and nonsmooth drives. To this end, we numerically study a disordered spin-1/2 chain which is periodically driven by a sine or square-wave drive over a wide range of driving frequencies. In both cases the critical driving amplitude increases monotonically with the frequency, and at large frequencies it is identical for the two drives. However, at low and intermediate frequencies the critical amplitude of the square-wave drive depends strongly on the frequency, while that of the sinusoidal drive is almost constant over a wide frequency range. By analyzing the density of drive-induced resonances we conclude that this difference is due to resonances induced by the higher harmonics which are present (absent) in the Fourier spectrum of the square-wave (sine) drive. Furthermore, we suggest a numerically efficient method for estimating the frequency dependence of the critical driving amplitudes for different drives which is based on calculating the density of drive-induced resonances. We conclude that delocalization occurs once the density of drive-induced resonances reaches a critical value determined only by the static system.},
author = {Diringer, Asaf A. and Gulden, Tobias},
issn = {24699969},
journal = {Physical Review B},
number = {21},
publisher = {American Physical Society},
title = {{Impact of drive harmonics on the stability of Floquet many-body localization}},
doi = {10.1103/PhysRevB.103.214204},
volume = {103},
year = {2021},
}
@article{8317,
abstract = {When can a polyomino piece of paper be folded into a unit cube? Prior work studied tree-like polyominoes, but polyominoes with holes remain an intriguing open problem. We present sufficient conditions for a polyomino with one or several holes to fold into a cube, and conditions under which cube folding is impossible. In particular, we show that all but five special “basic” holes guarantee foldability.},
author = {Aichholzer, Oswin and Akitaya, Hugo A. and Cheung, Kenneth C. and Demaine, Erik D. and Demaine, Martin L. and Fekete, Sándor P. and Kleist, Linda and Kostitsyna, Irina and Löffler, Maarten and Masárová, Zuzana and Mundilova, Klara and Schmidt, Christiane},
issn = {09257721},
journal = {Computational Geometry: Theory and Applications},
publisher = {Elsevier},
title = {{Folding polyominoes with holes into a cube}},
doi = {10.1016/j.comgeo.2020.101700},
volume = {93},
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 = {18728286},
journal = {Neurocomputing},
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},
year = {2021},
}
@article{9626,
abstract = {SnSe, a wide-bandgap semiconductor, has attracted significant attention from the thermoelectric (TE) community due to its outstanding TE performance deriving from the ultralow thermal conductivity and advantageous electronic structures. Here, we promoted the TE performance of n-type SnSe polycrystals through bandgap engineering and vacancy compensation. We found that PbTe can significantly reduce the wide bandgap of SnSe to reduce the impurity transition energy, largely enhancing the carrier concentration. Also, PbTe-induced crystal symmetry promotion increases the carrier mobility, preserving large Seebeck coefficient. Consequently, a maximum ZT of ∼1.4 at 793 K is obtained in Br doped SnSe–13%PbTe. Furthermore, we found that extra Sn in n-type SnSe can compensate for the intrinsic Sn vacancies and form electron donor-like metallic Sn nanophases. The Sn nanophases near the grain boundary could also reduce the intergrain energy barrier which largely enhances the carrier mobility. As a result, a maximum ZT value of ∼1.7 at 793 K and an average ZT (ZTave) of ∼0.58 in 300–793 K are achieved in Br doped Sn1.08Se–13%PbTe. Our findings provide a novel strategy to promote the TE performance in wide-bandgap semiconductors.},
author = {Su, Lizhong and Hong, Tao and Wang, Dongyang and Wang, Sining and Qin, Bingchao and Zhang, Mengmeng and Gao, Xiang and Chang, Cheng and Zhao, Li Dong},
issn = {25425293},
journal = {Materials Today Physics},
publisher = {Elsevier},
title = {{Realizing high doping efficiency and thermoelectric performance in n-type SnSe polycrystals via bandgap engineering and vacancy compensation}},
doi = {10.1016/j.mtphys.2021.100452},
volume = {20},
year = {2021},
}
@article{9438,
abstract = {Rigorous investigation of synaptic transmission requires analysis of unitary synaptic events by simultaneous recording from presynaptic terminals and postsynaptic target neurons. However, this has been achieved at only a limited number of model synapses, including the squid giant synapse and the mammalian calyx of Held. Cortical presynaptic terminals have been largely inaccessible to direct presynaptic recording, due to their small size. Here, we describe a protocol for improved subcellular patch-clamp recording in rat and mouse brain slices, with the synapse in a largely intact environment. Slice preparation takes ~2 h, recording ~3 h and post hoc morphological analysis 2 d. Single presynaptic hippocampal mossy fiber terminals are stimulated minimally invasively in the bouton-attached configuration, in which the cytoplasmic content remains unperturbed, or in the whole-bouton configuration, in which the cytoplasmic composition can be precisely controlled. Paired pre–postsynaptic recordings can be integrated with biocytin labeling and morphological analysis, allowing correlative investigation of synapse structure and function. Paired recordings can be obtained from mossy fiber terminals in slices from both rats and mice, implying applicability to genetically modified synapses. Paired recordings can also be performed together with axon tract stimulation or optogenetic activation, allowing comparison of unitary and compound synaptic events in the same target cell. Finally, paired recordings can be combined with spontaneous event analysis, permitting collection of miniature events generated at a single identified synapse. In conclusion, the subcellular patch-clamp techniques detailed here should facilitate analysis of biophysics, plasticity and circuit function of cortical synapses in the mammalian central nervous system.},
author = {Vandael, David H and Okamoto, Yuji and Borges Merjane, Carolina and Vargas Barroso, Victor M and Suter, Benjamin and Jonas, Peter M},
issn = {17502799},
journal = {Nature Protocols},
number = {6},
pages = {2947–2967},
publisher = {Springer Nature},
title = {{Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses}},
doi = {10.1038/s41596-021-00526-0},
volume = {16},
year = {2021},
}
@inproceedings{9605,
abstract = {Given a finite set A ⊂ ℝ^d, let Cov_{r,k} denote the set of all points within distance r to at least k points of A. Allowing r and k to vary, we obtain a 2-parameter family of spaces that grow larger when r increases or k decreases, called the multicover bifiltration. Motivated by the problem of computing the homology of this bifiltration, we introduce two closely related combinatorial bifiltrations, one polyhedral and the other simplicial, which are both topologically equivalent to the multicover bifiltration and far smaller than a Čech-based model considered in prior work of Sheehy. Our polyhedral construction is a bifiltration of the rhomboid tiling of Edelsbrunner and Osang, and can be efficiently computed using a variant of an algorithm given by these authors as well. Using an implementation for dimension 2 and 3, we provide experimental results. Our simplicial construction is useful for understanding the polyhedral construction and proving its correctness. },
author = {Corbet, René and Kerber, Michael and Lesnick, Michael and Osang, Georg F},
booktitle = {Leibniz International Proceedings in Informatics},
isbn = {9783959771849},
issn = {18688969},
location = {Online},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Computing the multicover bifiltration}},
doi = {10.4230/LIPIcs.SoCG.2021.27},
volume = {189},
year = {2021},
}
@article{9618,
abstract = {The control of nonequilibrium quantum dynamics in many-body systems is challenging because interactions typically lead to thermalization and a chaotic spreading throughout Hilbert space. We investigate nonequilibrium dynamics after rapid quenches in a many-body system composed of 3 to 200 strongly interacting qubits in one and two spatial dimensions. Using a programmable quantum simulator based on Rydberg atom arrays, we show that coherent revivals associated with so-called quantum many-body scars can be stabilized by periodic driving, which generates a robust subharmonic response akin to discrete time-crystalline order. We map Hilbert space dynamics, geometry dependence, phase diagrams, and system-size dependence of this emergent phenomenon, demonstrating new ways to steer complex dynamics in many-body systems and enabling potential applications in quantum information science.},
author = {Bluvstein, D. and Omran, A. and Levine, H. and Keesling, A. and Semeghini, G. and Ebadi, S. and Wang, T. T. and Michailidis, Alexios and Maskara, N. and Ho, W. W. and Choi, S. and Serbyn, Maksym and Greiner, M. and Vuletić, V. and Lukin, M. D.},
issn = {1095-9203},
journal = {Science},
keywords = {Multidisciplinary},
number = {6536},
pages = {1355--1359},
publisher = {AAAS},
title = {{Controlling quantum many-body dynamics in driven Rydberg atom arrays}},
doi = {10.1126/science.abg2530},
volume = {371},
year = {2021},
}
@article{9571,
abstract = {As the size and complexity of models and datasets grow, so does the need for communication-efficient variants of stochastic gradient descent that can be deployed to perform parallel model training. One popular communication-compression method for data-parallel SGD is QSGD (Alistarh et al., 2017), which quantizes and encodes gradients to reduce communication costs. The baseline variant of QSGD provides strong theoretical guarantees, however, for practical purposes, the authors proposed a heuristic variant which we call QSGDinf, which demonstrated impressive empirical gains for distributed training of large neural networks. In this paper, we build on this work to propose a new gradient quantization scheme, and show that it has both stronger theoretical guarantees than QSGD, and matches and exceeds the empirical performance of the QSGDinf heuristic and of other compression methods.},
author = {Ramezani-Kebrya, Ali and Faghri, Fartash and Markov, Ilya and Aksenov, Vitalii and Alistarh, Dan-Adrian and Roy, Daniel M.},
issn = {15337928},
journal = {Journal of Machine Learning Research},
number = {114},
pages = {1−43},
publisher = {Journal of Machine Learning Research},
title = {{NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization}},
volume = {22},
year = {2021},
}
@article{9629,
abstract = {Intestinal organoids derived from single cells undergo complex crypt–villus patterning and morphogenesis. However, the nature and coordination of the underlying forces remains poorly characterized. Here, using light-sheet microscopy and large-scale imaging quantification, we demonstrate that crypt formation coincides with a stark reduction in lumen volume. We develop a 3D biophysical model to computationally screen different mechanical scenarios of crypt morphogenesis. Combining this with live-imaging data and multiple mechanical perturbations, we show that actomyosin-driven crypt apical contraction and villus basal tension work synergistically with lumen volume reduction to drive crypt morphogenesis, and demonstrate the existence of a critical point in differential tensions above which crypt morphology becomes robust to volume changes. Finally, we identified a sodium/glucose cotransporter that is specific to differentiated enterocytes that modulates lumen volume reduction through cell swelling in the villus region. Together, our study uncovers the cellular basis of how cell fate modulates osmotic and actomyosin forces to coordinate robust morphogenesis.},
author = {Yang, Qiutan and Xue, Shi-lei and Chan, Chii Jou and Rempfler, Markus and Vischi, Dario and Maurer-Gutierrez, Francisca and Hiiragi, Takashi and Hannezo, Edouard B and Liberali, Prisca},
issn = {14764679},
journal = {Nature Cell Biology},
publisher = {Springer Nature},
title = {{Cell fate coordinates mechano-osmotic forces in intestinal crypt formation}},
doi = {10.1038/s41556-021-00700-2},
year = {2021},
}
@article{9642,
abstract = {Perineuronal nets (PNNs), components of the extracellular matrix, preferentially coat parvalbumin-positive interneurons and constrain critical-period plasticity in the adult cerebral cortex. Current strategies to remove PNN are long-lasting, invasive, and trigger neuropsychiatric symptoms. Here, we apply repeated anesthetic ketamine as a method with minimal behavioral effect. We find that this paradigm strongly reduces PNN coating in the healthy adult brain and promotes juvenile-like plasticity. Microglia are critically involved in PNN loss because they engage with parvalbumin-positive neurons in their defined cortical layer. We identify external 60-Hz light-flickering entrainment to recapitulate microglia-mediated PNN removal. Importantly, 40-Hz frequency, which is known to remove amyloid plaques, does not induce PNN loss, suggesting microglia might functionally tune to distinct brain frequencies. Thus, our 60-Hz light-entrainment strategy provides an alternative form of PNN intervention in the healthy adult brain.},
author = {Venturino, Alessandro and Schulz, Rouven and De Jesús-Cortés, Héctor and Maes, Margaret E and Nagy, Balint and Reilly-Andújar, Francis and Colombo, Gloria and Cubero, Ryan J and Schoot Uiterkamp, Florianne E and Bear, Mark F. and Siegert, Sandra},
issn = {22111247},
journal = {Cell Reports},
number = {1},
publisher = {Elsevier},
title = {{Microglia enable mature perineuronal nets disassembly upon anesthetic ketamine exposure or 60-Hz light entrainment in the healthy brain}},
doi = {10.1016/j.celrep.2021.109313},
volume = {36},
year = {2021},
}
@article{9641,
abstract = {At the encounter with a novel environment, contextual memory formation is greatly enhanced, accompanied with increased arousal and active exploration. Although this phenomenon has been widely observed in animal and human daily life, how the novelty in the environment is detected and contributes to contextual memory formation has lately started to be unveiled. The hippocampus has been studied for many decades for its largely known roles in encoding spatial memory, and a growing body of evidence indicates a differential involvement of dorsal and ventral hippocampal divisions in novelty detection. In this brief review article, we discuss the recent findings of the role of mossy cells in the ventral hippocampal moiety in novelty detection and put them in perspective with other novelty-related pathways in the hippocampus. We propose a mechanism for novelty-driven memory acquisition in the dentate gyrus by the direct projection of ventral mossy cells to dorsal dentate granule cells. By this projection, the ventral hippocampus sends novelty signals to the dorsal hippocampus, opening a gate for memory encoding in dentate granule cells based on information coming from the entorhinal cortex. We conclude that, contrary to the presently accepted functional independence, the dorsal and ventral hippocampi cooperate to link the novelty and contextual information, and this dorso-ventral interaction is crucial for the novelty-dependent memory formation.},
author = {Fredes, Felipe and Shigemoto, Ryuichi},
issn = {10959564},
journal = {Neurobiology of Learning and Memory},
publisher = {Elsevier},
title = {{The role of hippocampal mossy cells in novelty detection}},
doi = {10.1016/j.nlm.2021.107486},
volume = {183},
year = {2021},
}
@article{9679,
abstract = {The relative motion of three impenetrable particles on a ring, in our case two identical fermions and one impurity, is isomorphic to a triangular quantum billiard. Depending on the ratio κ of the impurity and fermion masses, the billiards can be integrable or non-integrable (also referred to in the main text as chaotic). To set the stage, we first investigate the energy level distributions of the billiards as a function of 1/κ ∈ [0, 1] and find no evidence of integrable cases beyond the limiting values 1/κ = 1 and 1/κ = 0. Then, we use machine learning tools to analyze properties of probability distributions of individual quantum states. We find that convolutional neural networks can correctly classify integrable and non-integrable states. The decisive features of the wave functions are the normalization and a large number of zero elements, corresponding to the existence of a nodal line. The network achieves typical accuracies of 97%, suggesting that machine learning tools can be used to analyze and classify the morphology of probability densities obtained in theory or experiment.},
author = {Huber, David and Marchukov, Oleksandr V. and Hammer, Hans Werner and Volosniev, Artem},
issn = {13672630},
journal = {New Journal of Physics},
number = {6},
publisher = {IOP Publishing},
title = {{Morphology of three-body quantum states from machine learning}},
doi = {10.1088/1367-2630/ac0576},
volume = {23},
year = {2021},
}
@article{9657,
abstract = {To overcome nitrogen deficiency, legume roots establish symbiotic interactions with nitrogen-fixing rhizobia that is fostered in specialized organs (nodules). Similar to other organs, nodule formation is determined by a local maximum of the phytohormone auxin at the primordium site. However, how auxin regulates nodule development remains poorly understood. Here, we found that in soybean, (Glycine max), dynamic auxin transport driven by PIN-FORMED (PIN) transporter GmPIN1 is involved in nodule primordium formation. GmPIN1 was specifically expressed in nodule primordium cells and GmPIN1 was polarly localized in these cells. Two nodulation regulators, (iso)flavonoids trigger expanded distribution of GmPIN1b to root cortical cells, and cytokinin rearranges GmPIN1b polarity. Gmpin1abc triple mutants generated with CRISPR-Cas9 showed impaired establishment of auxin maxima in nodule meristems and aberrant divisions in the nodule primordium cells. Moreover, overexpression of GmPIN1 suppressed nodule primordium initiation. GmPIN9d, an ortholog of Arabidopsis thaliana PIN2, acts together with GmPIN1 later in nodule development to acropetally transport auxin in vascular bundles, fine-tuning the auxin supply for nodule enlargement. Our findings reveal how PIN-dependent auxin transport modulates different aspects of soybean nodule development and suggest that establishment of auxin gradient is a prerequisite for the proper interaction between legumes and rhizobia.},
author = {Gao, Z and Chen, Z and Cui, Y and Ke, M and Xu, H and Xu, Q and Chen, J and Li, Y and Huang, L and Zhao, H and Huang, D and Mai, S and Xu, T and Liu, X and Li, S and Guan, Y and Yang, W and Friml, Jiří and Petrášek, J and Zhang, J and Chen, X},
issn = {1532-298x},
journal = {Plant Cell},
publisher = {American Society of Plant Biologists},
title = {{GmPIN-dependent polar auxin transport is involved in soybean nodule development}},
doi = {10.1093/plcell/koab183},
year = {2021},
}
@article{9656,
abstract = {Tropisms, growth responses to environmental stimuli such as light or gravity, are spectacular examples of adaptive plant development. The plant hormone auxin serves as a major coordinative signal. The PIN auxin exporters, through their dynamic polar subcellular localizations, redirect auxin fluxes in response to environmental stimuli and the resulting auxin gradients across organs underly differential cell elongation and bending. In this review, we discuss recent advances concerning regulations of PIN polarity during tropisms, focusing on PIN phosphorylation and trafficking. We also cover how environmental cues regulate PIN actions during tropisms, and a crucial role of auxin feedback on PIN polarity during bending termination. Finally, the interactions between different tropisms are reviewed to understand plant adaptive growth in the natural environment.},
author = {Han, Huibin and Adamowski, Maciek and Qi, Linlin and Alotaibi, SS and Friml, Jiří},
issn = {1469-8137},
journal = {New Phytologist},
publisher = {Wiley},
title = {{PIN-mediated polar auxin transport regulations in plant tropic responses}},
doi = {10.1111/nph.17617},
year = {2021},
}
@article{8910,
abstract = {A semiconducting nanowire fully wrapped by a superconducting shell has been proposed as a platform for obtaining Majorana modes at small magnetic fields. In this study, we demonstrate that the appearance of subgap states in such structures is actually governed by the junction region in tunneling spectroscopy measurements and not the full-shell nanowire itself. Short tunneling regions never show subgap states, whereas longer junctions always do. This can be understood in terms of quantum dots forming in the junction and hosting Andreev levels in the Yu-Shiba-Rusinov regime. The intricate magnetic field dependence of the Andreev levels, through both the Zeeman and Little-Parks effects, may result in robust zero-bias peaks—features that could be easily misinterpreted as originating from Majorana zero modes but are unrelated to topological superconductivity.},
author = {Valentini, Marco and Peñaranda, Fernando and Hofmann, Andrea C and Brauns, Matthias and Hauschild, Robert and Krogstrup, Peter and San-Jose, Pablo and Prada, Elsa and Aguado, Ramón and Katsaros, Georgios},
issn = {10959203},
journal = {Science},
number = {6550},
publisher = {American Association for the Advancement of Science},
title = {{Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states}},
doi = {10.1126/science.abf1513},
volume = {373},
year = {2021},
}
@article{9627,
abstract = {We compute the deficiency spaces of operators of the form 𝐻𝐴⊗̂ 𝐼+𝐼⊗̂ 𝐻𝐵, for symmetric 𝐻𝐴 and self-adjoint 𝐻𝐵. This enables us to construct self-adjoint extensions (if they exist) by means of von Neumann's theory. The structure of the deficiency spaces for this case was asserted already in Ibort et al. [Boundary dynamics driven entanglement, J. Phys. A: Math. Theor. 47(38) (2014) 385301], but only proven under the restriction of 𝐻𝐵 having discrete, non-degenerate spectrum.},
author = {Lenz, Daniel and Weinmann, Timon and Wirth, Melchior},
issn = {14643839},
journal = {Proceedings of the Edinburgh Mathematical Society},
pages = {1--15},
publisher = {Cambridge University Press},
title = {{Self-adjoint extensions of bipartite Hamiltonians}},
doi = {10.1017/S0013091521000080},
year = {2021},
}
@unpublished{9651,
abstract = {We introduce a hierachy of equivalence relations on the set of separated nets of a given Euclidean space, indexed by concave increasing functions ϕ:(0,∞)→(0,∞). Two separated nets are called ϕ-displacement equivalent if, roughly speaking, there is a bijection between them which, for large radii R, displaces points of norm at most R by something of order at most ϕ(R). We show that the spectrum of ϕ-displacement equivalence spans from the established notion of bounded displacement equivalence, which corresponds to bounded ϕ, to the indiscrete equivalence relation, coresponding to ϕ(R)∈Ω(R), in which all separated nets are equivalent. In between the two ends of this spectrum, the notions of ϕ-displacement equivalence are shown to be pairwise distinct with respect to the asymptotic classes of ϕ(R) for R→∞. We further undertake a comparison of our notion of ϕ-displacement equivalence with previously studied relations on separated nets. Particular attention is given to the interaction of the notions of ϕ-displacement equivalence with that of bilipschitz equivalence.},
author = {Dymond, Michael and Kaluza, Vojtech},
booktitle = {arXiv},
title = {{Divergence of separated nets with respect to displacement equivalence}},
year = {2021},
}
@article{9647,
abstract = {Gene expression is regulated by the set of transcription factors (TFs) that bind to the promoter. The ensuing regulating function is often represented as a combinational logic circuit, where output (gene expression) is determined by current input values (promoter bound TFs) only. However, the simultaneous arrival of TFs is a strong assumption, since transcription and translation of genes introduce intrinsic time delays and there is no global synchronisation among the arrival times of different molecular species at their targets. We present an experimentally implementable genetic circuit with two inputs and one output, which in the presence of small delays in input arrival, exhibits qualitatively distinct population-level phenotypes, over timescales that are longer than typical cell doubling times. From a dynamical systems point of view, these phenotypes represent long-lived transients: although they converge to the same value eventually, they do so after a very long time span. The key feature of this toy model genetic circuit is that, despite having only two inputs and one output, it is regulated by twenty-three distinct DNA-TF configurations, two of which are more stable than others (DNA looped states), one promoting and another blocking the expression of the output gene. Small delays in input arrival time result in a majority of cells in the population quickly reaching the stable state associated with the first input, while exiting of this stable state occurs at a slow timescale. In order to mechanistically model the behaviour of this genetic circuit, we used a rule-based modelling language, and implemented a grid-search to find parameter combinations giving rise to long-lived transients. Our analysis shows that in the absence of feedback, there exist path-dependent gene regulatory mechanisms based on the long timescale of transients. The behaviour of this toy model circuit suggests that gene regulatory networks can exploit event timing to create phenotypes, and it opens the possibility that they could use event timing to memorise events, without regulatory feedback. The model reveals the importance of (i) mechanistically modelling the transitions between the different DNA-TF states, and (ii) employing transient analysis thereof.},
author = {Petrov, Tatjana and Igler, Claudia and Sezgin, Ali and Henzinger, Thomas A and Guet, Calin C},
issn = {03043975},
journal = {Theoretical Computer Science},
publisher = {Elsevier},
title = {{Long lived transients in gene regulation}},
doi = {10.1016/j.tcs.2021.05.023},
year = {2021},
}
@inproceedings{9646,
abstract = {We consider the fundamental problem of deriving quantitative bounds on the probability that a given assertion is violated in a probabilistic program. We provide automated algorithms that obtain both lower and upper bounds on the assertion violation probability. The main novelty of our approach is that we prove new and dedicated fixed-point theorems which serve as the theoretical basis of our algorithms and enable us to reason about assertion violation bounds in terms of pre and post fixed-point functions. To synthesize such fixed-points, we devise algorithms that utilize a wide range of mathematical tools, including repulsing ranking supermartingales, Hoeffding's lemma, Minkowski decompositions, Jensen's inequality, and convex optimization. On the theoretical side, we provide (i) the first automated algorithm for lower-bounds on assertion violation probabilities, (ii) the first complete algorithm for upper-bounds of exponential form in affine programs, and (iii) provably and significantly tighter upper-bounds than the previous approaches. On the practical side, we show our algorithms can handle a wide variety of programs from the literature and synthesize bounds that are remarkably tighter than previous results, in some cases by thousands of orders of magnitude.},
author = {Wang, Jinyi and Sun, Yican and Fu, Hongfei and Chatterjee, Krishnendu and Goharshady, Amir Kafshdar},
booktitle = {Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation},
isbn = {9781450383912},
location = {Online},
pages = {1171--1186},
publisher = {Association for Computing Machinery},
title = {{Quantitative analysis of assertion violations in probabilistic programs}},
doi = {10.1145/3453483.3454102},
year = {2021},
}
@inproceedings{9645,
abstract = {We consider the fundamental problem of reachability analysis over imperative programs with real variables. Previous works that tackle reachability are either unable to handle programs consisting of general loops (e.g. symbolic execution), or lack completeness guarantees (e.g. abstract interpretation), or are not automated (e.g. incorrectness logic). In contrast, we propose a novel approach for reachability analysis that can handle general and complex loops, is complete, and can be entirely automated for a wide family of programs. Through the notion of Inductive Reachability Witnesses (IRWs), our approach extends ideas from both invariant generation and termination to reachability analysis.
We first show that our IRW-based approach is sound and complete for reachability analysis of imperative programs. Then, we focus on linear and polynomial programs and develop automated methods for synthesizing linear and polynomial IRWs. In the linear case, we follow the well-known approaches using Farkas' Lemma. Our main contribution is in the polynomial case, where we present a push-button semi-complete algorithm. We achieve this using a novel combination of classical theorems in real algebraic geometry, such as Putinar's Positivstellensatz and Hilbert's Strong Nullstellensatz. Finally, our experimental results show we can prove complex reachability objectives over various benchmarks that were beyond the reach of previous methods.},
author = {Asadi, Ali and Chatterjee, Krishnendu and Fu, Hongfei and Goharshady, Amir Kafshdar and Mahdavi, Mohammad},
booktitle = {Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation},
isbn = {9781450383912},
location = {Online},
pages = {772--787},
publisher = {Association for Computing Machinery},
title = {{Polynomial reachability witnesses via Stellensätze}},
doi = {10.1145/3453483.3454076},
year = {2021},
}
@inproceedings{9644,
abstract = {We present a new approach to proving non-termination of non-deterministic integer programs. Our technique is rather simple but efficient. It relies on a purely syntactic reversal of the program's transition system followed by a constraint-based invariant synthesis with constraints coming from both the original and the reversed transition system. The latter task is performed by a simple call to an off-the-shelf SMT-solver, which allows us to leverage the latest advances in SMT-solving. Moreover, our method offers a combination of features not present (as a whole) in previous approaches: it handles programs with non-determinism, provides relative completeness guarantees and supports programs with polynomial arithmetic. The experiments performed with our prototype tool RevTerm show that our approach, despite its simplicity and stronger theoretical guarantees, is at least on par with the state-of-the-art tools, often achieving a non-trivial improvement under a proper configuration of its parameters.},
author = {Chatterjee, Krishnendu and Goharshady, Ehsan Kafshdar and Novotný, Petr and Zikelic, Dorde},
booktitle = {Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation},
isbn = {9781450383912},
location = {Online},
pages = {1033--1048},
publisher = {Association for Computing Machinery},
title = {{Proving non-termination by program reversal}},
doi = {10.1145/3453483.3454093},
year = {2021},
}
@article{9649,
abstract = {Isomanifolds are the generalization of isosurfaces to arbitrary dimension and codimension, i.e. manifolds defined as the zero set of some multivariate vector-valued smooth function f : Rd → Rd−n. A natural (and efficient) way to approximate an isomanifold is to consider its Piecewise-Linear (PL) approximation based on a triangulation T of the ambient space Rd. In this paper, we give conditions under which the PL-approximation of an isomanifold is topologically equivalent to the isomanifold. The conditions are easy to satisfy in the sense that they can always be met by taking a sufficiently
fine triangulation T . This contrasts with previous results on the triangulation of manifolds where, in arbitrary dimensions, delicate perturbations are needed to guarantee topological correctness, which leads to strong limitations in practice. We further give a bound on the Fréchet distance between the original isomanifold and its PL-approximation. Finally we show analogous results for the PL-approximation of an isomanifold with boundary.},
author = {Boissonnat, Jean-Daniel and Wintraecken, Mathijs},
journal = {Foundations of Computational Mathematics },
publisher = {Springer Nature},
title = {{The topological correctness of PL approximations of isomanifolds}},
doi = {10.1007/s10208-021-09520-0},
year = {2021},
}
@inproceedings{9678,
abstract = {We introduce a new graph problem, the token dropping game, and we show how to solve it efficiently in a distributed setting. We use the token dropping game as a tool to design an efficient distributed algorithm for stable orientations and more generally for locally optimal semi-matchings. The prior work by Czygrinow et al. (DISC 2012) finds a stable orientation in O(Δ^5) rounds in graphs of maximum degree Δ, while we improve it to O(Δ^4) and also prove a lower bound of Ω(Δ). For the more general problem of locally optimal semi-matchings, the prior upper bound is O(S^5) and our new algorithm runs in O(C · S^4) rounds, which is an improvement for C = o(S); here C and S are the maximum degrees of customers and servers, respectively.},
author = {Brandt, Sebastian and Keller, Barbara and Rybicki, Joel and Suomela, Jukka and Uitto, Jara},
booktitle = {Annual ACM Symposium on Parallelism in Algorithms and Architectures},
isbn = {9781450380706},
location = { Virtual Event, United States},
pages = {129--139},
title = {{Efficient load-balancing through distributed token dropping}},
doi = {10.1145/3409964.3461785},
year = {2021},
}
@inproceedings{9441,
abstract = {Isomanifolds are the generalization of isosurfaces to arbitrary dimension and codimension, i.e. submanifolds of ℝ^d defined as the zero set of some multivariate multivalued smooth function f: ℝ^d → ℝ^{d-n}, where n is the intrinsic dimension of the manifold. A natural way to approximate a smooth isomanifold M is to consider its Piecewise-Linear (PL) approximation M̂ based on a triangulation 𝒯 of the ambient space ℝ^d. In this paper, we describe a simple algorithm to trace isomanifolds from a given starting point. The algorithm works for arbitrary dimensions n and d, and any precision D. Our main result is that, when f (or M) has bounded complexity, the complexity of the algorithm is polynomial in d and δ = 1/D (and unavoidably exponential in n). Since it is known that for δ = Ω (d^{2.5}), M̂ is O(D²)-close and isotopic to M, our algorithm produces a faithful PL-approximation of isomanifolds of bounded complexity in time polynomial in d. Combining this algorithm with dimensionality reduction techniques, the dependency on d in the size of M̂ can be completely removed with high probability. We also show that the algorithm can handle isomanifolds with boundary and, more generally, isostratifolds. The algorithm for isomanifolds with boundary has been implemented and experimental results are reported, showing that it is practical and can handle cases that are far ahead of the state-of-the-art. },
author = {Boissonnat, Jean-Daniel and Kachanovich, Siargey and Wintraecken, Mathijs},
booktitle = {37th International Symposium on Computational Geometry (SoCG 2021)},
isbn = {978-3-95977-184-9},
issn = {1868-8969},
location = {Virtual},
pages = {17:1--17:16},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Tracing isomanifolds in Rd in time polynomial in d using Coxeter-Freudenthal-Kuhn triangulations}},
doi = {10.4230/LIPIcs.SoCG.2021.17},
volume = {189},
year = {2021},
}
@inproceedings{9620,
abstract = {In this note, we introduce a distributed twist on the classic coupon collector problem: a set of m collectors wish to each obtain a set of n coupons; for this, they can each sample coupons uniformly at random, but can also meet in pairwise interactions, during which they can exchange coupons. By doing so, they hope to reduce the number of coupons that must be sampled by each collector in order to obtain a full set. This extension is natural when considering real-world manifestations of the coupon collector phenomenon, and has been remarked upon and studied empirically (Hayes and Hannigan 2006, Ahmad et al. 2014, Delmarcelle 2019).
We provide the first theoretical analysis for such a scenario. We find that “coupon collecting with friends” can indeed significantly reduce the number of coupons each collector must sample, and raises interesting connections to the more traditional variants of the problem. While our analysis is in most cases asymptotically tight, there are several open questions raised, regarding finer-grained analysis of both “coupon collecting with friends,” and of a long-studied variant of the original problem in which a collector requires multiple full sets of coupons.},
author = {Alistarh, Dan-Adrian and Davies, Peter},
booktitle = {Structural Information and Communication Complexity},
isbn = {9783030795269},
issn = {1611-3349},
location = {Wrocław, Poland},
pages = {3--12},
publisher = {Springer Nature},
title = {{Collecting coupons is faster with friends}},
doi = {10.1007/978-3-030-79527-6_1},
volume = {12810},
year = {2021},
}
@inproceedings{9200,
abstract = {Formal design of embedded and cyber-physical systems relies on mathematical modeling. In this paper, we consider the model class of hybrid automata whose dynamics are defined by affine differential equations. Given a set of time-series data, we present an algorithmic approach to synthesize a hybrid automaton exhibiting behavior that is close to the data, up to a specified precision, and changes in synchrony with the data. A fundamental problem in our synthesis algorithm is to check membership of a time series in a hybrid automaton. Our solution integrates reachability and optimization techniques for affine dynamical systems to obtain both a sufficient and a necessary condition for membership, combined in a refinement framework. The algorithm processes one time series at a time and hence can be interrupted, provide an intermediate result, and be resumed. We report experimental results demonstrating the applicability of our synthesis approach.},
author = {Garcia Soto, Miriam and Henzinger, Thomas A and Schilling, Christian},
booktitle = {HSCC '21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control},
isbn = {9781450383394},
keywords = {hybrid automaton, membership, system identification},
location = {Nashville, TN, United States},
pages = {2102.12734},
publisher = {Association for Computing Machinery},
title = {{Synthesis of hybrid automata with affine dynamics from time-series data}},
doi = {10.1145/3447928.3456704},
year = {2021},
}
@inproceedings{9345,
abstract = {Modeling a crystal as a periodic point set, we present a fingerprint consisting of density functionsthat facilitates the efficient search for new materials and material properties. We prove invarianceunder isometries, continuity, and completeness in the generic case, which are necessary featuresfor the reliable comparison of crystals. The proof of continuity integrates methods from discretegeometry and lattice theory, while the proof of generic completeness combines techniques fromgeometry with analysis. The fingerprint has a fast algorithm based on Brillouin zones and relatedinclusion-exclusion formulae. We have implemented the algorithm and describe its application tocrystal structure prediction.},
author = {Edelsbrunner, Herbert and Heiss, Teresa and Kurlin , Vitaliy and Smith, Philip and Wintraecken, Mathijs},
booktitle = {37th International Symposium on Computational Geometry (SoCG 2021)},
issn = {1868-8969},
location = {Virtual},
pages = {32:1--32:16},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{The density fingerprint of a periodic point set}},
doi = {10.4230/LIPIcs.SoCG.2021.32},
volume = {189},
year = {2021},
}
@inproceedings{9296,
abstract = { matching is compatible to two or more labeled point sets of size n with labels {1,…,n} if its straight-line drawing on each of these point sets is crossing-free. We study the maximum number of edges in a matching compatible to two or more labeled point sets in general position in the plane. We show that for any two labeled convex sets of n points there exists a compatible matching with ⌊2n−−√⌋ edges. More generally, for any ℓ labeled point sets we construct compatible matchings of size Ω(n1/ℓ) . As a corresponding upper bound, we use probabilistic arguments to show that for any ℓ given sets of n points there exists a labeling of each set such that the largest compatible matching has O(n2/(ℓ+1)) edges. Finally, we show that Θ(logn) copies of any set of n points are necessary and sufficient for the existence of a labeling such that any compatible matching consists only of a single edge.},
author = {Aichholzer, Oswin and Arroyo Guevara, Alan M and Masárová, Zuzana and Parada, Irene and Perz, Daniel and Pilz, Alexander and Tkadlec, Josef and Vogtenhuber, Birgit},
booktitle = {15th International Conference on Algorithms and Computation},
isbn = {9783030682101},
issn = {16113349},
location = {Yangon, Myanmar},
pages = {221--233},
publisher = {Springer Nature},
title = {{On compatible matchings}},
doi = {10.1007/978-3-030-68211-8_18},
volume = {12635},
year = {2021},
}
@inproceedings{9466,
abstract = {In this work, we apply the dynamical systems analysis of Hanrot et al. (CRYPTO’11) to a class of lattice block reduction algorithms that includes (natural variants of) slide reduction and block-Rankin reduction. This implies sharper bounds on the polynomial running times (in the query model) for these algorithms and opens the door to faster practical variants of slide reduction. We give heuristic arguments showing that such variants can indeed speed up slide reduction significantly in practice. This is confirmed by experimental evidence, which also shows that our variants are competitive with state-of-the-art reduction algorithms.},
author = {Walter, Michael},
booktitle = {Public-Key Cryptography – PKC 2021},
isbn = {9783030752446},
issn = {16113349},
location = {Virtual},
pages = {45--67},
publisher = {Springer Nature},
title = {{The convergence of slide-type reductions}},
doi = {10.1007/978-3-030-75245-3_3},
volume = {12710},
year = {2021},
}
@inproceedings{9210,
abstract = {Modern neural networks can easily fit their training set perfectly. Surprisingly, despite being “overfit” in this way, they tend to generalize well to future data, thereby defying the classic bias–variance trade-off of machine learning theory. Of the many possible explanations, a prevalent one is that training by stochastic gradient descent (SGD) imposes an implicit bias that leads it to learn simple functions, and these simple functions generalize well. However, the specifics of this implicit bias are not well understood.
In this work, we explore the smoothness conjecture which states that SGD is implicitly biased towards learning functions that are smooth. We propose several measures to formalize the intuitive notion of smoothness, and we conduct experiments to determine whether SGD indeed implicitly optimizes for these measures. Our findings rule out the possibility that smoothness measures based on first-order derivatives are being implicitly enforced. They are supportive, though, of the smoothness conjecture for measures based on second-order derivatives.},
author = {Volhejn, Vaclav and Lampert, Christoph},
booktitle = {42nd German Conference on Pattern Recognition },
isbn = {9783030712778},
issn = {16113349},
location = {Tübingen, Germany},
pages = {246--259},
publisher = {Springer},
title = {{Does SGD implicitly optimize for smoothness?}},
doi = {10.1007/978-3-030-71278-5_18},
volume = {12544 LNCS},
year = {2021},
}
@article{9640,
abstract = {Selection and random drift determine the probability that novel mutations fixate in a population. Population structure is known to affect the dynamics of the evolutionary process. Amplifiers of selection are population structures that increase the fixation probability of beneficial mutants compared to well-mixed populations. Over the past 15 years, extensive research has produced remarkable structures called strong amplifiers which guarantee that every beneficial mutation fixates with high probability. But strong amplification has come at the cost of considerably delaying the fixation event, which can slow down the overall rate of evolution. However, the precise relationship between fixation probability and time has remained elusive. Here we characterize the slowdown effect of strong amplification. First, we prove that all strong amplifiers must delay the fixation event at least to some extent. Second, we construct strong amplifiers that delay the fixation event only marginally as compared to the well-mixed populations. Our results thus establish a tight relationship between fixation probability and time: Strong amplification always comes at a cost of a slowdown, but more than a marginal slowdown is not needed.},
author = {Tkadlec, Josef and Pavlogiannis, Andreas and Chatterjee, Krishnendu and Nowak, Martin A.},
issn = {20411723},
journal = {Nature Communications},
number = {1},
publisher = {Springer Nature},
title = {{Fast and strong amplifiers of natural selection}},
doi = {10.1038/s41467-021-24271-w},
volume = {12},
year = {2021},
}
@phdthesis{9418,
abstract = {Deep learning is best known for its empirical success across a wide range of applications
spanning computer vision, natural language processing and speech. Of equal significance,
though perhaps less known, are its ramifications for learning theory: deep networks have
been observed to perform surprisingly well in the high-capacity regime, aka the overfitting
or underspecified regime. Classically, this regime on the far right of the bias-variance curve
is associated with poor generalisation; however, recent experiments with deep networks
challenge this view.
This thesis is devoted to investigating various aspects of underspecification in deep learning.
First, we argue that deep learning models are underspecified on two levels: a) any given
training dataset can be fit by many different functions, and b) any given function can be
expressed by many different parameter configurations. We refer to the second kind of
underspecification as parameterisation redundancy and we precisely characterise its extent.
Second, we characterise the implicit criteria (the inductive bias) that guide learning in the
underspecified regime. Specifically, we consider a nonlinear but tractable classification
setting, and show that given the choice, neural networks learn classifiers with a large margin.
Third, we consider learning scenarios where the inductive bias is not by itself sufficient to
deal with underspecification. We then study different ways of ‘tightening the specification’: i)
In the setting of representation learning with variational autoencoders, we propose a hand-
crafted regulariser based on mutual information. ii) In the setting of binary classification, we
consider soft-label (real-valued) supervision. We derive a generalisation bound for linear
networks supervised in this way and verify that soft labels facilitate fast learning. Finally, we
explore an application of soft-label supervision to the training of multi-exit models.},
author = {Bui Thi Mai, Phuong},
pages = {125},
publisher = {IST Austria},
title = {{Underspecification in Deep Learning}},
doi = {10.15479/AT:ISTA:9418},
year = {2021},
}
@inproceedings{9543,
abstract = {We consider the problem ofdistributed mean estimation (DME), in which n machines are each given a local d-dimensional vector xv∈Rd, and must cooperate to estimate the mean of their inputs μ=1n∑nv=1xv, while minimizing total communication cost. DME is a fundamental construct in distributed machine learning, and there has been considerable work on variants of this problem, especially in the context of distributed variance reduction for stochastic gradients in parallel SGD. Previous work typically assumes an upper bound on the norm of the input vectors, and achieves an error bound in terms of this norm. However, in many real applications, the input vectors are concentrated around the correct output μ, but μ itself has large norm. In such cases, previous output error bounds perform poorly. In this paper, we show that output error bounds need not depend on input norm. We provide a method of quantization which allows distributed mean estimation to be performed with solution quality dependent only on the distance between inputs, not on input norm, and show an analogous result for distributed variance reduction. The technique is based on a new connection with lattice theory. We also provide lower bounds showing that the communication to error trade-off of our algorithms is asymptotically optimal. As the lattices achieving optimal bounds under l2-norm can be computationally impractical, we also present an extension which leverages easy-to-use cubic lattices, and is loose only up to a logarithmic factor ind. We show experimentally that our method yields practical improvements for common applications, relative to prior approaches.},
author = {Davies, Peter and Gurunanthan, Vijaykrishna and Moshrefi, Niusha and Ashkboos, Saleh and Alistarh, Dan-Adrian},
booktitle = {9th International Conference on Learning Representations},
location = {Virtual},
title = {{New bounds for distributed mean estimation and variance reduction}},
year = {2021},
}
@inproceedings{9416,
abstract = {We study the inductive bias of two-layer ReLU networks trained by gradient flow. We identify a class of easy-to-learn (`orthogonally separable') datasets, and characterise the solution that ReLU networks trained on such datasets converge to. Irrespective of network width, the solution turns out to be a combination of two max-margin classifiers: one corresponding to the positive data subset and one corresponding to the negative data subset. The proof is based on the recently introduced concept of extremal sectors, for which we prove a number of properties in the context of orthogonal separability. In particular, we prove stationarity of activation patterns from some time onwards, which enables a reduction of the ReLU network to an ensemble of linear subnetworks.},
author = {Bui Thi Mai, Phuong and Lampert, Christoph},
booktitle = {9th International Conference on Learning Representations},
location = {Virtual},
title = {{The inductive bias of ReLU networks on orthogonally separable data}},
year = {2021},
}
@phdthesis{8934,
abstract = {In this thesis, we consider several of the most classical and fundamental problems in static analysis and formal verification, including invariant generation, reachability analysis, termination analysis of probabilistic programs, data-flow analysis, quantitative analysis of Markov chains and Markov decision processes, and the problem of data packing in cache management.
We use techniques from parameterized complexity theory, polyhedral geometry, and real algebraic geometry to significantly improve the state-of-the-art, in terms of both scalability and completeness guarantees, for the mentioned problems. In some cases, our results are the first theoretical improvements for the respective problems in two or three decades.},
author = {Goharshady, Amir Kafshdar},
issn = {2663-337X},
pages = {278},
publisher = {IST Austria},
title = {{Parameterized and algebro-geometric advances in static program analysis}},
doi = {10.15479/AT:ISTA:8934},
year = {2021},
}
@article{7956,
abstract = {When short-range attractions are combined with long-range repulsions in colloidal particle systems, complex microphases can emerge. Here, we study a system of isotropic particles, which can form lamellar structures or a disordered fluid phase when temperature is varied. We show that, at equilibrium, the lamellar structure crystallizes, while out of equilibrium, the system forms a variety of structures at different shear rates and temperatures above melting. The shear-induced ordering is analyzed by means of principal component analysis and artificial neural networks, which are applied to data of reduced dimensionality. Our results reveal the possibility of inducing ordering by shear, potentially providing a feasible route to the fabrication of ordered lamellar structures from isotropic particles.},
author = {Pȩkalski, J. and Rzadkowski, Wojciech and Panagiotopoulos, A. Z.},
issn = {10897690},
journal = {The Journal of chemical physics},
number = {20},
publisher = {AIP},
title = {{Shear-induced ordering in systems with competing interactions: A machine learning study}},
doi = {10.1063/5.0005194},
volume = {152},
year = {2020},
}
@article{7957,
abstract = {Neurodevelopmental disorders (NDDs) are a class of disorders affecting brain development and function and are characterized by wide genetic and clinical variability. In this review, we discuss the multiple factors that influence the clinical presentation of NDDs, with particular attention to gene vulnerability, mutational load, and the two-hit model. Despite the complex architecture of
mutational events associated with NDDs, the various proteins involved appear to converge on common pathways, such as synaptic plasticity/function, chromatin remodelers and the mammalian target of rapamycin (mTOR) pathway. A thorough understanding of the mechanisms behind these pathways will hopefully lead to the identification of candidates that could be targeted for treatment approaches.},
author = {Parenti, Ilaria and Garcia Rabaneda, Luis E and Schön, Hanna and Novarino, Gaia},
issn = {1878108X},
journal = {Trends in Neurosciences},
number = {8},
pages = {608--621},
publisher = {Elsevier},
title = {{Neurodevelopmental disorders: From genetics to functional pathways}},
doi = {10.1016/j.tins.2020.05.004},
volume = {43},
year = {2020},
}
@article{7960,
abstract = {Let A={A1,…,An} be a family of sets in the plane. For 0≤i2b be integers. We prove that if each k-wise or (k+1)-wise intersection of sets from A has at most b path-connected components, which all are open, then fk+1=0 implies fk≤cfk−1 for some positive constant c depending only on b and k. These results also extend to two-dimensional compact surfaces.},
author = {Kalai, Gil and Patakova, Zuzana},
issn = {14320444},
journal = {Discrete and Computational Geometry},
pages = {304--323},
publisher = {Springer Nature},
title = {{Intersection patterns of planar sets}},
doi = {10.1007/s00454-020-00205-z},
volume = {64},
year = {2020},
}
@article{7962,
abstract = {A string graph is the intersection graph of a family of continuous arcs in the plane. The intersection graph of a family of plane convex sets is a string graph, but not all string graphs can be obtained in this way. We prove the following structure theorem conjectured by Janson and Uzzell: The vertex set of almost all string graphs on n vertices can be partitioned into five cliques such that some pair of them is not connected by any edge (n→∞). We also show that every graph with the above property is an intersection graph of plane convex sets. As a corollary, we obtain that almost all string graphs on n vertices are intersection graphs of plane convex sets.},
author = {Pach, János and Reed, Bruce and Yuditsky, Yelena},
issn = {14320444},
journal = {Discrete and Computational Geometry},
number = {4},
pages = {888--917},
publisher = {Springer Nature},
title = {{Almost all string graphs are intersection graphs of plane convex sets}},
doi = {10.1007/s00454-020-00213-z},
volume = {63},
year = {2020},
}
@inproceedings{7966,
abstract = {For 1≤m≤n, we consider a natural m-out-of-n multi-instance scenario for a public-key encryption (PKE) scheme. An adversary, given n independent instances of PKE, wins if he breaks at least m out of the n instances. In this work, we are interested in the scaling factor of PKE schemes, SF, which measures how well the difficulty of breaking m out of the n instances scales in m. That is, a scaling factor SF=ℓ indicates that breaking m out of n instances is at least ℓ times more difficult than breaking one single instance. A PKE scheme with small scaling factor hence provides an ideal target for mass surveillance. In fact, the Logjam attack (CCS 2015) implicitly exploited, among other things, an almost constant scaling factor of ElGamal over finite fields (with shared group parameters).
For Hashed ElGamal over elliptic curves, we use the generic group model to argue that the scaling factor depends on the scheme's granularity. In low granularity, meaning each public key contains its independent group parameter, the scheme has optimal scaling factor SF=m; In medium and high granularity, meaning all public keys share the same group parameter, the scheme still has a reasonable scaling factor SF=√m. Our findings underline that instantiating ElGamal over elliptic curves should be preferred to finite fields in a multi-instance scenario.
As our main technical contribution, we derive new generic-group lower bounds of Ω(√(mp)) on the difficulty of solving both the m-out-of-n Gap Discrete Logarithm and the m-out-of-n Gap Computational Diffie-Hellman problem over groups of prime order p, extending a recent result by Yun (EUROCRYPT 2015). We establish the lower bound by studying the hardness of a related computational problem which we call the search-by-hypersurface problem.},
author = {Auerbach, Benedikt and Giacon, Federico and Kiltz, Eike},
booktitle = {Advances in Cryptology – EUROCRYPT 2020},
isbn = {9783030457266},
issn = {0302-9743},
pages = {475--506},
publisher = {Springer Nature},
title = {{Everybody’s a target: Scalability in public-key encryption}},
doi = {10.1007/978-3-030-45727-3_16},
volume = {12107},
year = {2020},
}
@article{7968,
abstract = {Organic materials are known to feature long spin-diffusion times, originating in a generally small spin–orbit coupling observed in these systems. From that perspective, chiral molecules acting as efficient spin selectors pose a puzzle that attracted a lot of attention in recent years. Here, we revisit the physical origins of chiral-induced spin selectivity (CISS) and propose a simple analytic minimal model to describe it. The model treats a chiral molecule as an anisotropic wire with molecular dipole moments aligned arbitrarily with respect to the wire’s axes and is therefore quite general. Importantly, it shows that the helical structure of the molecule is not necessary to observe CISS and other chiral nonhelical molecules can also be considered as potential candidates for the CISS effect. We also show that the suggested simple model captures the main characteristics of CISS observed in the experiment, without the need for additional constraints employed in the previous studies. The results pave the way for understanding other related physical phenomena where the CISS effect plays an essential role.},
author = {Ghazaryan, Areg and Paltiel, Yossi and Lemeshko, Mikhail},
issn = {1932-7447},
journal = {The Journal of Physical Chemistry C},
number = {21},
pages = {11716--11721},
publisher = {American Chemical Society},
title = {{Analytic model of chiral-induced spin selectivity}},
doi = {10.1021/acs.jpcc.0c02584},
volume = {124},
year = {2020},
}
@article{7971,
abstract = {Multilayer graphene lattices allow for an additional tunability of the band structure by the strong perpendicular electric field. In particular, the emergence of the new multiple Dirac points in ABA stacked trilayer graphene subject to strong transverse electric fields was proposed theoretically and confirmed experimentally. These new Dirac points dubbed “gullies” emerge from the interplay between strong electric field and trigonal warping. In this work, we first characterize the properties of new emergent Dirac points and show that the electric field can be used to tune the distance between gullies in the momentum space. We demonstrate that the band structure has multiple Lifshitz transitions and higher-order singularity of “monkey saddle” type. Following the characterization of the band structure, we consider the spectrum of Landau levels and structure of their wave functions. In the limit of strong electric fields when gullies are well separated in momentum space, they give rise to triply degenerate Landau levels. In the second part of this work, we investigate how degeneracy between three gully Landau levels is lifted in the presence of interactions. Within the Hartree-Fock approximation we show that the symmetry breaking state interpolates between the fully gully polarized state that breaks C3 symmetry at high displacement field and the gully symmetric state when the electric field is decreased. The discontinuous transition between these two states is driven by enhanced intergully tunneling and exchange. We conclude by outlining specific experimental predictions for the existence of such a symmetry-breaking state.},
author = {Rao, Peng and Serbyn, Maksym},
issn = {2469-9950},
journal = {Physical Review B},
number = {24},
publisher = {American Physical Society},
title = {{Gully quantum Hall ferromagnetism in biased trilayer graphene}},
doi = {10.1103/physrevb.101.245411},
volume = {101},
year = {2020},
}
@article{7985,
abstract = {The goal of limiting global warming to 1.5 °C requires a drastic reduction in CO2 emissions across many sectors of the world economy. Batteries are vital to this endeavor, whether used in electric vehicles, to store renewable electricity, or in aviation. Present lithium-ion technologies are preparing the public for this inevitable change, but their maximum theoretical specific capacity presents a limitation. Their high cost is another concern for commercial viability. Metal–air batteries have the highest theoretical energy density of all possible secondary battery technologies and could yield step changes in energy storage, if their practical difficulties could be overcome. The scope of this review is to provide an objective, comprehensive, and authoritative assessment of the intensive work invested in nonaqueous rechargeable metal–air batteries over the past few years, which identified the key problems and guides directions to solve them. We focus primarily on the challenges and outlook for Li–O2 cells but include Na–O2, K–O2, and Mg–O2 cells for comparison. Our review highlights the interdisciplinary nature of this field that involves a combination of materials chemistry, electrochemistry, computation, microscopy, spectroscopy, and surface science. The mechanisms of O2 reduction and evolution are considered in the light of recent findings, along with developments in positive and negative electrodes, electrolytes, electrocatalysis on surfaces and in solution, and the degradative effect of singlet oxygen, which is typically formed in Li–O2 cells.},
author = {Kwak, WJ and Sharon, D and Xia, C and Kim, H and Johnson, LR and Bruce, PG and Nazar, LF and Sun, YK and Frimer, AA and Noked, M and Freunberger, Stefan Alexander and Aurbach, D},
issn = {0009-2665},
journal = {Chemical Reviews},
number = {14},
pages = {6626--6683},
publisher = {American Chemical Society},
title = {{Lithium-oxygen batteries and related systems: Potential, status, and future}},
doi = {10.1021/acs.chemrev.9b00609},
volume = {120},
year = {2020},
}
@inproceedings{7989,
abstract = {We prove general topological Radon-type theorems for sets in ℝ^d, smooth real manifolds or finite dimensional simplicial complexes. Combined with a recent result of Holmsen and Lee, it gives fractional Helly theorem, and consequently the existence of weak ε-nets as well as a (p,q)-theorem. More precisely: Let X be either ℝ^d, smooth real d-manifold, or a finite d-dimensional simplicial complex. Then if F is a finite, intersection-closed family of sets in X such that the ith reduced Betti number (with ℤ₂ coefficients) of any set in F is at most b for every non-negative integer i less or equal to k, then the Radon number of F is bounded in terms of b and X. Here k is the smallest integer larger or equal to d/2 - 1 if X = ℝ^d; k=d-1 if X is a smooth real d-manifold and not a surface, k=0 if X is a surface and k=d if X is a d-dimensional simplicial complex. Using the recent result of the author and Kalai, we manage to prove the following optimal bound on fractional Helly number for families of open sets in a surface: Let F be a finite family of open sets in a surface S such that the intersection of any subfamily of F is either empty, or path-connected. Then the fractional Helly number of F is at most three. This also settles a conjecture of Holmsen, Kim, and Lee about an existence of a (p,q)-theorem for open subsets of a surface.},
author = {Patakova, Zuzana},
booktitle = {36th International Symposium on Computational Geometry},
isbn = {9783959771436},
issn = {18688969},
location = {Zürich, Switzerland},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Bounding radon number via Betti numbers}},
doi = {10.4230/LIPIcs.SoCG.2020.61},
volume = {164},
year = {2020},
}
@inproceedings{7990,
abstract = {Given a finite point set P in general position in the plane, a full triangulation is a maximal straight-line embedded plane graph on P. A partial triangulation on P is a full triangulation of some subset P' of P containing all extreme points in P. A bistellar flip on a partial triangulation either flips an edge, removes a non-extreme point of degree 3, or adds a point in P ⧵ P' as vertex of degree 3. The bistellar flip graph has all partial triangulations as vertices, and a pair of partial triangulations is adjacent if they can be obtained from one another by a bistellar flip. The goal of this paper is to investigate the structure of this graph, with emphasis on its connectivity. For sets P of n points in general position, we show that the bistellar flip graph is (n-3)-connected, thereby answering, for sets in general position, an open questions raised in a book (by De Loera, Rambau, and Santos) and a survey (by Lee and Santos) on triangulations. This matches the situation for the subfamily of regular triangulations (i.e., partial triangulations obtained by lifting the points and projecting the lower convex hull), where (n-3)-connectivity has been known since the late 1980s through the secondary polytope (Gelfand, Kapranov, Zelevinsky) and Balinski’s Theorem. Our methods also yield the following results (see the full version [Wagner and Welzl, 2020]): (i) The bistellar flip graph can be covered by graphs of polytopes of dimension n-3 (products of secondary polytopes). (ii) A partial triangulation is regular, if it has distance n-3 in the Hasse diagram of the partial order of partial subdivisions from the trivial subdivision. (iii) All partial triangulations are regular iff the trivial subdivision has height n-3 in the partial order of partial subdivisions. (iv) There are arbitrarily large sets P with non-regular partial triangulations, while every proper subset has only regular triangulations, i.e., there are no small certificates for the existence of non-regular partial triangulations (answering a question by F. Santos in the unexpected direction).},
author = {Wagner, Uli and Welzl, Emo},
booktitle = {36th International Symposium on Computational Geometry},
isbn = {9783959771436},
issn = {18688969},
location = {Zürich, Switzerland},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Connectivity of triangulation flip graphs in the plane (Part II: Bistellar flips)}},
doi = {10.4230/LIPIcs.SoCG.2020.67},
volume = {164},
year = {2020},
}
@inproceedings{7991,
abstract = {We define and study a discrete process that generalizes the convex-layer decomposition of a planar point set. Our process, which we call homotopic curve shortening (HCS), starts with a closed curve (which might self-intersect) in the presence of a set P⊂ ℝ² of point obstacles, and evolves in discrete steps, where each step consists of (1) taking shortcuts around the obstacles, and (2) reducing the curve to its shortest homotopic equivalent. We find experimentally that, if the initial curve is held fixed and P is chosen to be either a very fine regular grid or a uniformly random point set, then HCS behaves at the limit like the affine curve-shortening flow (ACSF). This connection between HCS and ACSF generalizes the link between "grid peeling" and the ACSF observed by Eppstein et al. (2017), which applied only to convex curves, and which was studied only for regular grids. We prove that HCS satisfies some properties analogous to those of ACSF: HCS is invariant under affine transformations, preserves convexity, and does not increase the total absolute curvature. Furthermore, the number of self-intersections of a curve, or intersections between two curves (appropriately defined), does not increase. Finally, if the initial curve is simple, then the number of inflection points (appropriately defined) does not increase.},
author = {Avvakumov, Sergey and Nivasch, Gabriel},
booktitle = {36th International Symposium on Computational Geometry},
isbn = {9783959771436},
issn = {18688969},
location = {Zürich, Switzerland},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Homotopic curve shortening and the affine curve-shortening flow}},
doi = {10.4230/LIPIcs.SoCG.2020.12},
volume = {164},
year = {2020},
}
@inproceedings{7992,
abstract = {Let K be a convex body in ℝⁿ (i.e., a compact convex set with nonempty interior). Given a point p in the interior of K, a hyperplane h passing through p is called barycentric if p is the barycenter of K ∩ h. In 1961, Grünbaum raised the question whether, for every K, there exists an interior point p through which there are at least n+1 distinct barycentric hyperplanes. Two years later, this was seemingly resolved affirmatively by showing that this is the case if p=p₀ is the point of maximal depth in K. However, while working on a related question, we noticed that one of the auxiliary claims in the proof is incorrect. Here, we provide a counterexample; this re-opens Grünbaum’s question. It follows from known results that for n ≥ 2, there are always at least three distinct barycentric cuts through the point p₀ ∈ K of maximal depth. Using tools related to Morse theory we are able to improve this bound: four distinct barycentric cuts through p₀ are guaranteed if n ≥ 3.},
author = {Patakova, Zuzana and Tancer, Martin and Wagner, Uli},
booktitle = {36th International Symposium on Computational Geometry},
isbn = {9783959771436},
issn = {18688969},
location = {Zürich, Switzerland},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Barycentric cuts through a convex body}},
doi = {10.4230/LIPIcs.SoCG.2020.62},
volume = {164},
year = {2020},
}
@inproceedings{7994,
abstract = {In the recent study of crossing numbers, drawings of graphs that can be extended to an arrangement of pseudolines (pseudolinear drawings) have played an important role as they are a natural combinatorial extension of rectilinear (or straight-line) drawings. A characterization of the pseudolinear drawings of K_n was found recently. We extend this characterization to all graphs, by describing the set of minimal forbidden subdrawings for pseudolinear drawings. Our characterization also leads to a polynomial-time algorithm to recognize pseudolinear drawings and construct the pseudolines when it is possible.},
author = {Arroyo Guevara, Alan M and Bensmail, Julien and Bruce Richter, R.},
booktitle = {36th International Symposium on Computational Geometry},
isbn = {9783959771436},
issn = {18688969},
location = {Zürich, Switzerland},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Extending drawings of graphs to arrangements of pseudolines}},
doi = {10.4230/LIPIcs.SoCG.2020.9},
volume = {164},
year = {2020},
}
@article{7995,
abstract = {When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple‐effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis , occur in North Atlantic rocky‐shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size‐assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment.},
author = {Perini, Samuel and Rafajlović, Marina and Westram, Anja M and Johannesson, Kerstin and Butlin, Roger K.},
issn = {15585646},
journal = {Evolution},
number = {7},
pages = {1482--1497},
publisher = {Wiley},
title = {{Assortative mating, sexual selection, and their consequences for gene flow in Littorina}},
doi = {10.1111/evo.14027},
volume = {74},
year = {2020},
}
@phdthesis{7996,
abstract = {Quantum computation enables the execution of algorithms that have exponential complexity. This might open the path towards the synthesis of new materials or medical drugs, optimization of transport or financial strategies etc., intractable on even the fastest classical computers. A quantum computer consists of interconnected two level quantum systems, called qubits, that satisfy DiVincezo’s criteria. Worldwide, there are ongoing efforts to find the qubit architecture which will unite quantum error correction compatible single and two qubit fidelities, long distance qubit to qubit coupling and
calability. Superconducting qubits have gone the furthest in this race, demonstrating an algorithm running on 53 coupled qubits, but still the fidelities are not even close to those required for realizing a single logical qubit. emiconductor qubits offer extremely good characteristics, but they are currently investigated across different platforms. Uniting those good characteristics into a single platform might be a big step towards the quantum computer realization.
Here we describe the implementation of a hole spin qubit hosted in a Ge hut wire double quantum dot. The high and tunable spin-orbit coupling together with a heavy hole state character is expected to allow fast spin manipulation and long coherence times. Furthermore large lever arms, for hut wire devices, should allow good coupling to superconducting resonators enabling efficient long distance spin to spin coupling and a sensitive gate reflectometry spin readout. The developed cryogenic setup (printed circuit board sample holders, filtering, high-frequency wiring) enabled us to perform low temperature spin dynamics experiments. Indeed, we measured the fastest single spin qubit Rabi frequencies reported so far, reaching 140 MHz, while the dephasing times of 130 ns oppose the long decoherence predictions. In order to further investigate this, a double quantum dot gate was connected directly to a lumped element
resonator which enabled gate reflectometry readout. The vanishing inter-dot transition signal, for increasing external magnetic field, revealed the spin nature of the measured quantity.},
author = {Kukucka, Josip},
issn = {2663-337X},
pages = {178},
publisher = {IST Austria},
title = {{Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing}},
doi = {10.15479/AT:ISTA:7996},
year = {2020},
}
@article{7999,
abstract = {Linking epigenetic marks to clinical outcomes improves insight into molecular processes, disease prediction, and therapeutic target identification. Here, a statistical approach is presented to infer the epigenetic architecture of complex disease, determine the variation captured by epigenetic effects, and estimate phenotype-epigenetic probe associations jointly. Implicitly adjusting for probe correlations, data structure (cell-count or relatedness), and single-nucleotide polymorphism (SNP) marker effects, improves association estimates and in 9,448 individuals, 75.7% (95% CI 71.70–79.3) of body mass index (BMI) variation and 45.6% (95% CI 37.3–51.9) of cigarette consumption variation was captured by whole blood methylation array data. Pathway-linked probes of blood cholesterol, lipid transport and sterol metabolism for BMI, and xenobiotic stimuli response for smoking, showed >1.5 times larger associations with >95% posterior inclusion probability. Prediction accuracy improved by 28.7% for BMI and 10.2% for smoking over a LASSO model, with age-, and tissue-specificity, implying associations are a phenotypic consequence rather than causal. },
author = {Trejo Banos, D and McCartney, DL and Patxot, M and Anchieri, L and Battram, T and Christiansen, C and Costeira, R and Walker, RM and Morris, SW and Campbell, A and Zhang, Q and Porteous, DJ and McRae, AF and Wray, NR and Visscher, PM and Haley, CS and Evans, KL and Deary, IJ and McIntosh, AM and Hemani, G and Bell, JT and Marioni, RE and Robinson, Matthew Richard},
issn = {2041-1723},
journal = {Nature Communications},
publisher = {Springer Nature},
title = {{Bayesian reassessment of the epigenetic architecture of complex traits}},
doi = {10.1038/s41467-020-16520-1},
volume = {11},
year = {2020},
}
@article{8001,
abstract = {Post-tetanic potentiation (PTP) is an attractive candidate mechanism for hippocampus-dependent short-term memory. Although PTP has a uniquely large magnitude at hippocampal mossy fiber-CA3 pyramidal neuron synapses, it is unclear whether it can be induced by natural activity and whether its lifetime is sufficient to support short-term memory. We combined in vivo recordings from granule cells (GCs), in vitro paired recordings from mossy fiber terminals and postsynaptic CA3 neurons, and “flash and freeze” electron microscopy. PTP was induced at single synapses and showed a low induction threshold adapted to sparse GC activity in vivo. PTP was mainly generated by enlargement of the readily releasable pool of synaptic vesicles, allowing multiplicative interaction with other plasticity forms. PTP was associated with an increase in the docked vesicle pool, suggesting formation of structural “pool engrams.” Absence of presynaptic activity extended the lifetime of the potentiation, enabling prolonged information storage in the hippocampal network.},
author = {Vandael, David H and Borges Merjane, Carolina and Zhang, Xiaomin and Jonas, Peter M},
issn = {10974199},
journal = {Neuron},
number = {3},
pages = {509--521},
publisher = {Elsevier},
title = {{Short-term plasticity at hippocampal mossy fiber synapses is induced by natural activity patterns and associated with vesicle pool engram formation}},
doi = {10.1016/j.neuron.2020.05.013},
volume = {107},
year = {2020},
}
@article{8002,
abstract = {Wound healing in plant tissues, consisting of rigid cell wall-encapsulated cells, represents a considerable challenge and occurs through largely unknown mechanisms distinct from those in animals. Owing to their inability to migrate, plant cells rely on targeted cell division and expansion to regenerate wounds. Strict coordination of these wound-induced responses is essential to ensure efficient, spatially restricted wound healing. Single-cell tracking by live imaging allowed us to gain mechanistic insight into the wound perception and coordination of wound responses after laser-based wounding in Arabidopsis root. We revealed a crucial contribution of the collapse of damaged cells in wound perception and detected an auxin increase specific to cells immediately adjacent to the wound. This localized auxin increase balances wound-induced cell expansion and restorative division rates in a dose-dependent manner, leading to tumorous overproliferation when the canonical TIR1 auxin signaling is disrupted. Auxin and wound-induced turgor pressure changes together also spatially define the activation of key components of regeneration, such as the transcription regulator ERF115. Our observations suggest that the wound signaling involves the sensing of collapse of damaged cells and a local auxin signaling activation to coordinate the downstream transcriptional responses in the immediate wound vicinity.},
author = {Hörmayer, Lukas and Montesinos López, Juan C and Marhavá, Petra and Benková, Eva and Yoshida, Saiko and Friml, Jiří},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
number = {26},
publisher = {Proceedings of the National Academy of Sciences},
title = {{Wounding-induced changes in cellular pressure and localized auxin signalling spatially coordinate restorative divisions in roots}},
doi = {10.1073/pnas.2003346117},
volume = {117},
year = {2020},
}
@article{8011,
abstract = {Relaxation to a thermal state is the inevitable fate of nonequilibrium interacting quantum systems without special conservation laws. While thermalization in one-dimensional systems can often be suppressed by integrability mechanisms, in two spatial dimensions thermalization is expected to be far more effective due to the increased phase space. In this work we propose a general framework for escaping or delaying the emergence of the thermal state in two-dimensional arrays of Rydberg atoms via the mechanism of quantum scars, i.e., initial states that fail to thermalize. The suppression of thermalization is achieved in two complementary ways: by adding local perturbations or by adjusting the driving Rabi frequency according to the local connectivity of the lattice. We demonstrate that these mechanisms allow us to realize robust quantum scars in various two-dimensional lattices, including decorated lattices with nonconstant connectivity. In particular, we show that a small decrease of the Rabi frequency at the corners of the lattice is crucial for mitigating the strong boundary effects in two-dimensional systems. Our results identify synchronization as an important tool for future experiments on two-dimensional quantum scars.},
author = {Michailidis, Alexios and Turner, C. J. and Papić, Z. and Abanin, D. A. and Serbyn, Maksym},
issn = {2643-1564},
journal = {Physical Review Research},
number = {2},
publisher = {American Physical Society},
title = {{Stabilizing two-dimensional quantum scars by deformation and synchronization}},
doi = {10.1103/physrevresearch.2.022065},
volume = {2},
year = {2020},
}
@inproceedings{8012,
abstract = {Asynchronous programs are notoriously difficult to reason about because they spawn computation tasks which take effect asynchronously in a nondeterministic way. Devising inductive invariants for such programs requires understanding and stating complex relationships between an unbounded number of computation tasks in arbitrarily long executions. In this paper, we introduce inductive sequentialization, a new proof rule that sidesteps this complexity via a sequential reduction, a sequential program that captures every behavior of the original program up to reordering of coarse-grained commutative actions. A sequential reduction of a concurrent program is easy to reason about since it corresponds to a simple execution of the program in an idealized synchronous environment, where processes act in a fixed order and at the same speed. We have implemented and integrated our proof rule in the CIVL verifier, allowing us to provably derive fine-grained implementations of asynchronous programs. We have successfully applied our proof rule to a diverse set of message-passing protocols, including leader election protocols, two-phase commit, and Paxos.},
author = {Kragl, Bernhard and Enea, Constantin and Henzinger, Thomas A and Mutluergil, Suha Orhun and Qadeer, Shaz},
booktitle = {Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation},
isbn = {9781450376136},
location = {London, United Kingdom},
pages = {227--242},
publisher = {Association for Computing Machinery},
title = {{Inductive sequentialization of asynchronous programs}},
doi = {10.1145/3385412.3385980},
year = {2020},
}
@phdthesis{8032,
abstract = {Algorithms in computational 3-manifold topology typically take a triangulation as an input and return topological information about the underlying 3-manifold. However, extracting the desired information from a triangulation (e.g., evaluating an invariant) is often computationally very expensive. In recent years this complexity barrier has been successfully tackled in some cases by importing ideas from the theory of parameterized algorithms into the realm of 3-manifolds. Various computationally hard problems were shown to be efficiently solvable for input triangulations that are sufficiently “tree-like.”
In this thesis we focus on the key combinatorial parameter in the above context: we consider the treewidth of a compact, orientable 3-manifold, i.e., the smallest treewidth of the dual graph of any triangulation thereof. By building on the work of Scharlemann–Thompson and Scharlemann–Schultens–Saito on generalized Heegaard splittings, and on the work of Jaco–Rubinstein on layered triangulations, we establish quantitative relations between the treewidth and classical topological invariants of a 3-manifold. In particular, among other results, we show that the treewidth of a closed, orientable, irreducible, non-Haken 3-manifold is always within a constant factor of its Heegaard genus.},
author = {Huszár, Kristóf},
isbn = {978-3-99078-006-0},
issn = {2663-337X},
pages = {xviii+120},
publisher = {IST Austria},
title = {{Combinatorial width parameters for 3-dimensional manifolds}},
doi = {10.15479/AT:ISTA:8032},
year = {2020},
}
@article{8036,
abstract = {When tiny soft ferromagnetic particles are placed along a liquid interface and exposed to a vertical magnetic field, the balance between capillary attraction and magnetic repulsion leads to self-organization into well-defined patterns. Here, we demonstrate experimentally that precessing magnetic fields induce metachronal waves on the periphery of these assemblies, similar to the ones observed in ciliates and some arthropods. The outermost layer of particles behaves like an array of cilia or legs whose sequential movement causes a net and controllable locomotion. This bioinspired many-particle swimming strategy is effective even at low Reynolds number, using only spatially uniform fields to generate the waves.},
author = {Collard, Ylona and Grosjean, Galien M and Vandewalle, Nicolas},
issn = {23993650},
journal = {Communications Physics},
publisher = {Springer Nature},
title = {{Magnetically powered metachronal waves induce locomotion in self-assemblies}},
doi = {10.1038/s42005-020-0380-9},
volume = {3},
year = {2020},
}
@article{8038,
abstract = {Microelectromechanical systems and integrated photonics provide the basis for many reliable and compact circuit elements in modern communication systems. Electro-opto-mechanical devices are currently one of the leading approaches to realize ultra-sensitive, low-loss transducers for an emerging quantum information technology. Here we present an on-chip microwave frequency converter based on a planar aluminum on silicon nitride platform that is compatible with slot-mode coupled photonic crystal cavities. We show efficient frequency conversion between two propagating microwave modes mediated by the radiation pressure interaction with a metalized dielectric nanobeam oscillator. We achieve bidirectional coherent conversion with a total device efficiency of up to ~60%, a dynamic range of 2 × 10^9 photons/s and an instantaneous bandwidth of up to 1.7 kHz. A high fidelity quantum state transfer would be possible if the drive dependent output noise of currently ~14 photons s^−1 Hz^−1 is further reduced. Such a silicon nitride based transducer is in situ reconfigurable and could be used for on-chip classical and quantum signal routing and filtering, both for microwave and hybrid microwave-optical applications.},
author = {Fink, Johannes M and Kalaee, M. and Norte, R. and Pitanti, A. and Painter, O.},
issn = {20589565},
journal = {Quantum Science and Technology},
number = {3},
publisher = {IOP Publishing},
title = {{Efficient microwave frequency conversion mediated by a photonics compatible silicon nitride nanobeam oscillator}},
doi = {10.1088/2058-9565/ab8dce},
volume = {5},
year = {2020},
}
@article{8039,
abstract = {In the present work, we report a solution-based strategy to produce crystallographically textured SnSe bulk nanomaterials and printed layers with optimized thermoelectric performance in the direction normal to the substrate. Our strategy is based on the formulation of a molecular precursor that can be continuously decomposed to produce a SnSe powder or printed into predefined patterns. The precursor formulation and decomposition conditions are optimized to produce pure phase 2D SnSe nanoplates. The printed layer and the bulk material obtained after hot press displays a clear preferential orientation of the crystallographic domains, resulting in an ultralow thermal conductivity of 0.55 W m–1 K–1 in the direction normal to the substrate. Such textured nanomaterials present highly anisotropic properties with the best thermoelectric performance in plane, i.e., in the directions parallel to the substrate, which coincide with the crystallographic bc plane of SnSe. This is an unfortunate characteristic because thermoelectric devices are designed to create/harvest temperature gradients in the direction normal to the substrate. We further demonstrate that this limitation can be overcome with the introduction of small amounts of tellurium in the precursor. The presence of tellurium allows one to reduce the band gap and increase both the charge carrier concentration and the mobility, especially the cross plane, with a minimal decrease of the Seebeck coefficient. These effects translate into record out of plane ZT values at 800 K.},
author = {Zhang, Yu and Liu, Yu and Xing, Congcong and Zhang, Ting and Li, Mengyao and Pacios, Mercè and Yu, Xiaoting and Arbiol, Jordi and Llorca, Jordi and Cadavid, Doris and Ibáñez, Maria and Cabot, Andreu},
issn = {19448252},
journal = {ACS Applied Materials and Interfaces},
number = {24},
pages = {27104--27111},
publisher = {American Chemical Society},
title = {{Tin selenide molecular precursor for the solution processing of thermoelectric materials and devices}},
doi = {10.1021/acsami.0c04331},
volume = {12},
year = {2020},
}
@article{8042,
abstract = {We consider systems of N bosons in a box of volume one, interacting through a repulsive two-body potential of the form κN3β−1V(Nβx). For all 0<β<1, and for sufficiently small coupling constant κ>0, we establish the validity of Bogolyubov theory, identifying the ground state energy and the low-lying excitation spectrum up to errors that vanish in the limit of large N.},
author = {Boccato, Chiara and Brennecke, Christian and Cenatiempo, Serena and Schlein, Benjamin},
issn = {14359855},
journal = {Journal of the European Mathematical Society},
number = {7},
pages = {2331--2403},
publisher = {European Mathematical Society},
title = {{The excitation spectrum of Bose gases interacting through singular potentials}},
doi = {10.4171/JEMS/966},
volume = {22},
year = {2020},
}
@article{8043,
abstract = {With decreasing Reynolds number, Re, turbulence in channel flow becomes spatio-temporally intermittent and self-organises into solitary stripes oblique to the mean flow direction. We report here the existence of localised nonlinear travelling wave solutions of the Navier–Stokes equations possessing this obliqueness property. Such solutions are identified numerically using edge tracking coupled with arclength continuation. All solutions emerge in saddle-node bifurcations at values of Re lower than the non-localised solutions. Relative periodic orbit solutions bifurcating from branches of travelling waves have also been computed. A complete parametric study is performed, including their stability, the investigation of their large-scale flow, and the robustness to changes of the numerical domain.},
author = {Paranjape, Chaitanya S and Duguet, Yohann and Hof, Björn},
issn = {14697645},
journal = {Journal of Fluid Mechanics},
publisher = {Cambridge University Press},
title = {{Oblique stripe solutions of channel flow}},
doi = {10.1017/jfm.2020.322},
volume = {897},
year = {2020},
}
@article{8057,
abstract = {Water-in-salt electrolytes based on highly concentrated bis(trifluoromethyl)sulfonimide (TFSI) promise aqueous electrolytes with stabilities approaching 3 V. However, especially with an electrode approaching the cathodic (reductive) stability, cycling stability is insufficient. While stability critically relies on a solid electrolyte interphase (SEI), the mechanism behind the cathodic stability limit remains unclear. Here, we reveal two distinct reduction potentials for the chemical environments of ‘free’ and ‘bound’ water and that both contribute to SEI formation. Free-water is reduced ~1V above bound water in a hydrogen evolution reaction (HER) and responsible for SEI formation via reactive intermediates of the HER; concurrent LiTFSI precipitation/dissolution establishes a dynamic interface. The free-water population emerges, therefore, as the handle to extend the cathodic limit of aqueous electrolytes and the battery cycling stability.},
author = {Bouchal, Roza and Li, Zhujie and Bongu, Chandra and Le Vot, Steven and Berthelot, Romain and Rotenberg, Benjamin and Favier, Frederic and Freunberger, Stefan Alexander and Salanne, Mathieu and Fontaine, Olivier},
issn = {0044-8249},
journal = {Angewandte Chemie},
number = {37},
pages = {16047--16051},
publisher = {Wiley},
title = {{Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte}},
doi = {10.1002/ange.202005378},
volume = {132},
year = {2020},
}
@unpublished{8063,
abstract = {We present a generative model of images that explicitly reasons over the set
of objects they show. Our model learns a structured latent representation that
separates objects from each other and from the background; unlike prior works,
it explicitly represents the 2D position and depth of each object, as well as
an embedding of its segmentation mask and appearance. The model can be trained
from images alone in a purely unsupervised fashion without the need for object
masks or depth information. Moreover, it always generates complete objects,
even though a significant fraction of training images contain occlusions.
Finally, we show that our model can infer decompositions of novel images into
their constituent objects, including accurate prediction of depth ordering and
segmentation of occluded parts.},
author = {Anciukevicius, Titas and Lampert, Christoph and Henderson, Paul M},
booktitle = {arXiv},
title = {{Object-centric image generation with factored depths, locations, and appearances}},
year = {2020},
}
@misc{8067,
abstract = {With the lithium-ion technology approaching its intrinsic limit with graphite-based anodes, lithium metal is recently receiving renewed interest from the battery community as potential high capacity anode for next-generation rechargeable batteries. In this focus paper, we review the main advances in this field since the first attempts in the
mid-1970s. Strategies for enabling reversible cycling and avoiding dendrite growth are thoroughly discussed, including specific applications in all-solid-state (polymeric and inorganic), Lithium-sulphur and Li-O2 (air) batteries. A particular attention is paid to review recent developments in regard of prototype manufacturing and current state-ofthe-art of these battery technologies with respect to the 2030 targets of the EU Integrated Strategic Energy Technology Plan (SET-Plan) Action 7.},
author = {Varzi, Alberto and Thanner, Katharina and Scipioni, Roberto and Di Lecce, Daniele and Hassoun, Jusef and Dörfler, Susanne and Altheus, Holger and Kaskel, Stefan and Prehal, Christian and Freunberger, Stefan Alexander},
issn = {2664-1690},
keywords = {Battery, Lithium metal, Lithium-sulphur, Lithium-air, All-solid-state},
pages = {63},
publisher = {IST Austria},
title = {{Current status and future perspectives of Lithium metal batteries}},
doi = {10.15479/AT:ISTA:8067},
year = {2020},
}
@article{8077,
abstract = {The projection methods with vanilla inertial extrapolation step for variational inequalities have been of interest to many authors recently due to the improved convergence speed contributed by the presence of inertial extrapolation step. However, it is discovered that these projection methods with inertial steps lose the Fejér monotonicity of the iterates with respect to the solution, which is being enjoyed by their corresponding non-inertial projection methods for variational inequalities. This lack of Fejér monotonicity makes projection methods with vanilla inertial extrapolation step for variational inequalities not to converge faster than their corresponding non-inertial projection methods at times. Also, it has recently been proved that the projection methods with vanilla inertial extrapolation step may provide convergence rates that are worse than the classical projected gradient methods for strongly convex functions. In this paper, we introduce projection methods with alternated inertial extrapolation step for solving variational inequalities. We show that the sequence of iterates generated by our methods converges weakly to a solution of the variational inequality under some appropriate conditions. The Fejér monotonicity of even subsequence is recovered in these methods and linear rate of convergence is obtained. The numerical implementations of our methods compared with some other inertial projection methods show that our method is more efficient and outperforms some of these inertial projection methods.},
author = {Shehu, Yekini and Iyiola, Olaniyi S.},
issn = {0168-9274},
journal = {Applied Numerical Mathematics},
pages = {315--337},
publisher = {Elsevier},
title = {{Projection methods with alternating inertial steps for variational inequalities: Weak and linear convergence}},
doi = {10.1016/j.apnum.2020.06.009},
volume = {157},
year = {2020},
}
@unpublished{8081,
abstract = {Here, we employ micro- and nanosized cellulose particles, namely paper fines and cellulose
nanocrystals, to induce hierarchical organization over a wide length scale. After processing
them into carbonaceous materials, we demonstrate that these hierarchically organized materials
outperform the best materials for supercapacitors operating with organic electrolytes reported
in literature in terms of specific energy/power (Ragone plot) while showing hardly any capacity
fade over 4,000 cycles. The highly porous materials feature a specific surface area as high as
2500 m2ˑg-1 and exhibit pore sizes in the range of 0.5 to 200 nm as proven by scanning electron
microscopy and N2 physisorption. The carbonaceous materials have been further investigated
by X-ray photoelectron spectroscopy and RAMAN spectroscopy. Since paper fines are an
underutilized side stream in any paper production process, they are a cheap and highly available
feedstock to prepare carbonaceous materials with outstanding performance in electrochemical
applications. },
author = {Hobisch, Mathias A. and Mourad, Eléonore and Fischer, Wolfgang J. and Prehal, Christian and Eyley, Samuel and Childress, Anthony and Zankel, Armin and Mautner, Andreas and Breitenbach, Stefan and Rao, Apparao M. and Thielemans, Wim and Freunberger, Stefan Alexander and Eckhart, Rene and Bauer, Wolfgang and Spirk, Stefan },
title = {{High specific capacitance supercapacitors from hierarchically organized all-cellulose composites}},
year = {2020},
}
@article{8084,
abstract = {Origin and functions of intermittent transitions among sleep stages, including brief awakenings and arousals, constitute a challenge to the current homeostatic framework for sleep regulation, focusing on factors modulating sleep over large time scales. Here we propose that the complex micro-architecture characterizing sleep on scales of seconds and minutes results from intrinsic non-equilibrium critical dynamics. We investigate θ- and δ-wave dynamics in control rats and in rats where the sleep-promoting ventrolateral preoptic nucleus (VLPO) is lesioned (male Sprague-Dawley rats). We demonstrate that bursts in θ and δ cortical rhythms exhibit complex temporal organization, with long-range correlations and robust duality of power-law (θ-bursts, active phase) and exponential-like (δ-bursts, quiescent phase) duration distributions, features typical of non-equilibrium systems self-organizing at criticality. We show that such non-equilibrium behavior relates to anti-correlated coupling between θ- and δ-bursts, persists across a range of time scales, and is independent of the dominant physiologic state; indications of a basic principle in sleep regulation. Further, we find that VLPO lesions lead to a modulation of cortical dynamics resulting in altered dynamical parameters of θ- and δ-bursts and significant reduction in θ–δ coupling. Our empirical findings and model simulations demonstrate that θ–δ coupling is essential for the emerging non-equilibrium critical dynamics observed across the sleep–wake cycle, and indicate that VLPO neurons may have dual role for both sleep and arousal/brief wake activation. The uncovered critical behavior in sleep- and wake-related cortical rhythms indicates a mechanism essential for the micro-architecture of spontaneous sleep-stage and arousal transitions within a novel, non-homeostatic paradigm of sleep regulation.},
author = {Lombardi, Fabrizio and Gómez-Extremera, Manuel and Bernaola-Galván, Pedro and Vetrivelan, Ramalingam and Saper, Clifford B. and Scammell, Thomas E. and Ivanov, Plamen Ch.},
issn = {0270-6474},
journal = {Journal of Neuroscience},
number = {1},
pages = {171--190},
publisher = {Society for Neuroscience},
title = {{Critical dynamics and coupling in bursts of cortical rhythms indicate non-homeostatic mechanism for sleep-stage transitions and dual role of VLPO neurons in both sleep and wake}},
doi = {10.1523/jneurosci.1278-19.2019},
volume = {40},
year = {2020},
}
@article{8091,
abstract = {In the setting of the fractional quantum Hall effect we study the effects of strong, repulsive two-body interaction potentials of short range. We prove that Haldane’s pseudo-potential operators, including their pre-factors, emerge as mathematically rigorous limits of such interactions when the range of the potential tends to zero while its strength tends to infinity. In a common approach the interaction potential is expanded in angular momentum eigenstates in the lowest Landau level, which amounts to taking the pre-factors to be the moments of the potential. Such a procedure is not appropriate for very strong interactions, however, in particular not in the case of hard spheres. We derive the formulas valid in the short-range case, which involve the scattering lengths of the interaction potential in different angular momentum channels rather than its moments. Our results hold for bosons and fermions alike and generalize previous results in [6], which apply to bosons in the lowest angular momentum channel. Our main theorem asserts the convergence in a norm-resolvent sense of the Hamiltonian on the whole Hilbert space, after appropriate energy scalings, to Hamiltonians with contact interactions in the lowest Landau level.},
author = {Seiringer, Robert and Yngvason, Jakob},
issn = {15729613},
journal = {Journal of Statistical Physics},
pages = {448--464},
publisher = {Springer},
title = {{Emergence of Haldane pseudo-potentials in systems with short-range interactions}},
doi = {10.1007/s10955-020-02586-0},
volume = {181},
year = {2020},
}
@inbook{8092,
abstract = {Image translation refers to the task of mapping images from a visual domain to another. Given two unpaired collections of images, we aim to learn a mapping between the corpus-level style of each collection, while preserving semantic content shared across the two domains. We introduce xgan, a dual adversarial auto-encoder, which captures a shared representation of the common domain semantic content in an unsupervised way, while jointly learning the domain-to-domain image translations in both directions. We exploit ideas from the domain adaptation literature and define a semantic consistency loss which encourages the learned embedding to preserve semantics shared across domains. We report promising qualitative results for the task of face-to-cartoon translation. The cartoon dataset we collected for this purpose, “CartoonSet”, is also publicly available as a new benchmark for semantic style transfer at https://google.github.io/cartoonset/index.html.},
author = {Royer, Amélie and Bousmalis, Konstantinos and Gouws, Stephan and Bertsch, Fred and Mosseri, Inbar and Cole, Forrester and Murphy, Kevin},
booktitle = {Domain Adaptation for Visual Understanding},
editor = {Singh, Richa and Vatsa, Mayank and Patel, Vishal M. and Ratha, Nalini},
isbn = {9783030306717},
pages = {33--49},
publisher = {Springer Nature},
title = {{XGAN: Unsupervised image-to-image translation for many-to-many mappings}},
doi = {10.1007/978-3-030-30671-7_3},
year = {2020},
}
@article{8093,
author = {Hippe, Andreas and Braun, Stephan Alexander and Oláh, Péter and Gerber, Peter Arne and Schorr, Anne and Seeliger, Stephan and Holtz, Stephanie and Jannasch, Katharina and Pivarcsi, Andor and Buhren, Bettina and Schrumpf, Holger and Kislat, Andreas and Bünemann, Erich and Steinhoff, Martin and Fischer, Jens and Lira, Sérgio A. and Boukamp, Petra and Hevezi, Peter and Stoecklein, Nikolas Hendrik and Hoffmann, Thomas and Alves, Frauke and Sleeman, Jonathan and Bauer, Thomas and Klufa, Jörg and Amberg, Nicole and Sibilia, Maria and Zlotnik, Albert and Müller-Homey, Anja and Homey, Bernhard},
issn = {15321827},
journal = {British Journal of Cancer},
pages = {942--954},
publisher = {Springer Nature},
title = {{EGFR/Ras-induced CCL20 production modulates the tumour microenvironment}},
doi = {10.1038/s41416-020-0943-2},
volume = {123},
year = {2020},
}
@misc{8097,
abstract = {Antibiotics that interfere with translation, when combined, interact in diverse and difficult-to-predict ways. Here, we explain these interactions by "translation bottlenecks": points in the translation cycle where antibiotics block ribosomal progression. To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using inducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks causes these interactions. We further show that growth laws, combined with drug uptake and binding kinetics, enable the direct prediction of a large fraction of observed interactions, yet fail to predict suppression. However, varying two translation bottlenecks simultaneously supports that dense traffic of ribosomes and competition for translation factors account for the previously unexplained suppression. These results highlight the importance of "continuous epistasis" in bacterial physiology.},
author = {Kavcic, Bor},
keywords = {Escherichia coli, antibiotic combinations, translation, growth laws, drug interactions, bacterial physiology, translation inhibitors},
publisher = {IST Austria},
title = {{Analysis scripts and research data for the paper "Mechanisms of drug interactions between translation-inhibiting antibiotics"}},
doi = {10.15479/AT:ISTA:8097},
year = {2020},
}
@article{8099,
abstract = {Sewall Wright developed FST for describing population differentiation and it has since been extended to many novel applications, including the detection of homomorphic sex chromosomes. However, there has been confusion regarding the expected estimate of FST for a fixed difference between the X‐ and Y‐chromosome when comparing males and females. Here, we attempt to resolve this confusion by contrasting two common FST estimators and explain why they yield different estimates when applied to the case of sex chromosomes. We show that this difference is true for many allele frequencies, but the situation characterized by fixed differences between the X‐ and Y‐chromosome is among the most extreme. To avoid additional confusion, we recommend that all authors using FST clearly state which estimator of FST their work uses.},
author = {Gammerdinger, William J and Toups, Melissa A and Vicoso, Beatriz},
issn = {1755-098X},
journal = {Molecular Ecology Resources},
number = {6},
pages = {1517--1525},
publisher = {Wiley},
title = {{Disagreement in FST estimators: A case study from sex chromosomes}},
doi = {10.1111/1755-0998.13210},
volume = {20},
year = {2020},
}
@article{8101,
abstract = {By rigorously accounting for mesoscale spatial correlations in donor/acceptor surface properties, we develop a scale-spanning model for same-material tribocharging. We find that mesoscale correlations affect not only the magnitude of charge transfer but also the fluctuations—suppressing otherwise overwhelming charge-transfer variability that is not observed experimentally. We furthermore propose a generic theoretical mechanism by which the mesoscale features might emerge, which is qualitatively consistent with other proposals in the literature.},
author = {Grosjean, Galien M and Wald, Sebastian and Sobarzo Ponce, Juan Carlos A and Waitukaitis, Scott R},
journal = {Physical Review Materials},
keywords = {electric charge, tribocharging, soft matter, granular materials, polymers},
number = {8},
publisher = {American Physical Society},
title = {{Quantitatively consistent scale-spanning model for same-material tribocharging}},
doi = {10.1103/PhysRevMaterials.4.082602},
volume = {4},
year = {2020},
}
@article{8105,
abstract = {Physical and biological systems often exhibit intermittent dynamics with bursts or avalanches (active states) characterized by power-law size and duration distributions. These emergent features are typical of systems at the critical point of continuous phase transitions, and have led to the hypothesis that such systems may self-organize at criticality, i.e. without any fine tuning of parameters. Since the introduction of the Bak-Tang-Wiesenfeld (BTW) model, the paradigm of self-organized criticality (SOC) has been very fruitful for the analysis of emergent collective behaviors in a number of systems, including the brain. Although considerable effort has been devoted in identifying and modeling scaling features of burst and avalanche statistics, dynamical aspects related to the temporal organization of bursts remain often poorly understood or controversial. Of crucial importance to understand the mechanisms responsible for emergent behaviors is the relationship between active and quiet periods, and the nature of the correlations. Here we investigate the dynamics of active (θ-bursts) and quiet states (δ-bursts) in brain activity during the sleep-wake cycle. We show the duality of power-law (θ, active phase) and exponential-like (δ, quiescent phase) duration distributions, typical of SOC, jointly emerge with power-law temporal correlations and anti-correlated coupling between active and quiet states. Importantly, we demonstrate that such temporal organization shares important similarities with earthquake dynamics, and propose that specific power-law correlations and coupling between active and quiet states are distinctive characteristics of a class of systems with self-organization at criticality.},
author = {Lombardi, Fabrizio and Wang, Jilin W.J.L. and Zhang, Xiyun and Ivanov, Plamen Ch},
issn = {2100-014X},
journal = {EPJ Web of Conferences},
publisher = {EDP Sciences},
title = {{Power-law correlations and coupling of active and quiet states underlie a class of complex systems with self-organization at criticality}},
doi = {10.1051/epjconf/202023000005},
volume = {230},
year = {2020},
}
@article{8112,
author = {Barton, Nicholas H},
issn = {1471-2970},
journal = {Philosophical Transactions of the Royal Society. Series B: Biological Sciences},
number = {1806},
publisher = {The Royal Society},
title = {{On the completion of speciation}},
doi = {10.1098/rstb.2019.0530},
volume = {375},
year = {2020},
}
@article{8127,
abstract = {Mechanistic modeling in neuroscience aims to explain observed phenomena in terms of underlying causes. However, determining which model parameters agree with complex and stochastic neural data presents a significant challenge. We address this challenge with a machine learning tool which uses deep neural density estimators—trained using model simulations—to carry out Bayesian inference and retrieve the full space of parameters compatible with raw data or selected data features. Our method is scalable in parameters and data features and can rapidly analyze new data after initial training. We demonstrate the power and flexibility of our approach on receptive fields, ion channels, and Hodgkin–Huxley models. We also characterize the space of circuit configurations giving rise to rhythmic activity in the crustacean stomatogastric ganglion, and use these results to derive hypotheses for underlying compensation mechanisms. Our approach will help close the gap between data-driven and theory-driven models of neural dynamics.},
author = {Gonçalves, Pedro J. and Lueckmann, Jan-Matthis and Deistler, Michael and Nonnenmacher, Marcel and Öcal, Kaan and Bassetto, Giacomo and Chintaluri, Chaitanya and Podlaski, William F. and Haddad, Sara A. and Vogels, Tim P and Greenberg, David S. and Macke, Jakob H.},
issn = {2050-084X},
journal = {eLife},
publisher = {eLife Sciences Publications},
title = {{Training deep neural density estimators to identify mechanistic models of neural dynamics}},
doi = {10.7554/eLife.56261},
volume = {9},
year = {2020},
}
@article{8130,
abstract = {We study the dynamics of a system of N interacting bosons in a disc-shaped trap, which is realised by an external potential that confines the bosons in one spatial dimension to an interval of length of order ε. The interaction is non-negative and scaled in such a way that its scattering length is of order ε/N, while its range is proportional to (ε/N)β with scaling parameter β∈(0,1]. We consider the simultaneous limit (N,ε)→(∞,0) and assume that the system initially exhibits Bose–Einstein condensation. We prove that condensation is preserved by the N-body dynamics, where the time-evolved condensate wave function is the solution of a two-dimensional non-linear equation. The strength of the non-linearity depends on the scaling parameter β. For β∈(0,1), we obtain a cubic defocusing non-linear Schrödinger equation, while the choice β=1 yields a Gross–Pitaevskii equation featuring the scattering length of the interaction. In both cases, the coupling parameter depends on the confining potential.},
author = {Bossmann, Lea},
issn = {0003-9527},
journal = {Archive for Rational Mechanics and Analysis},
number = {11},
pages = {541--606},
publisher = {Springer Nature},
title = {{Derivation of the 2d Gross–Pitaevskii equation for strongly confined 3d Bosons}},
doi = {10.1007/s00205-020-01548-w},
volume = {238},
year = {2020},
}
@article{8131,
abstract = {The possibility to generate construct valid animal models enabled the development and testing of therapeutic strategies targeting the core features of autism spectrum disorders (ASDs). At the same time, these studies highlighted the necessity of identifying sensitive developmental time windows for successful therapeutic interventions. Animal and human studies also uncovered the possibility to stratify the variety of ASDs in molecularly distinct subgroups, potentially facilitating effective treatment design. Here, we focus on the molecular pathways emerging as commonly affected by mutations in diverse ASD-risk genes, on their role during critical windows of brain development and the potential treatments targeting these biological processes.},
author = {Basilico, Bernadette and Morandell, Jasmin and Novarino, Gaia},
issn = {18790380},
journal = {Current Opinion in Genetics and Development},
number = {12},
pages = {126--137},
publisher = {Elsevier},
title = {{Molecular mechanisms for targeted ASD treatments}},
doi = {10.1016/j.gde.2020.06.004},
volume = {65},
year = {2020},
}
@article{8132,
abstract = {The WAVE regulatory complex (WRC) is crucial for assembly of the peripheral branched actin network constituting one of the main drivers of eukaryotic cell migration. Here, we uncover an essential role of the hematopoietic-specific WRC component HEM1 for immune cell development. Germline-encoded HEM1 deficiency underlies an inborn error of immunity with systemic autoimmunity, at cellular level marked by WRC destabilization, reduced filamentous actin, and failure to assemble lamellipodia. Hem1−/− mice display systemic autoimmunity, phenocopying the human disease. In the absence of Hem1, B cells become deprived of extracellular stimuli necessary to maintain the strength of B cell receptor signaling at a level permissive for survival of non-autoreactive B cells. This shifts the balance of B cell fate choices toward autoreactive B cells and thus autoimmunity.},
author = {Salzer, Elisabeth and Zoghi, Samaneh and Kiss, Máté G. and Kage, Frieda and Rashkova, Christina and Stahnke, Stephanie and Haimel, Matthias and Platzer, René and Caldera, Michael and Ardy, Rico Chandra and Hoeger, Birgit and Block, Jana and Medgyesi, David and Sin, Celine and Shahkarami, Sepideh and Kain, Renate and Ziaee, Vahid and Hammerl, Peter and Bock, Christoph and Menche, Jörg and Dupré, Loïc and Huppa, Johannes B. and Sixt, Michael K and Lomakin, Alexis and Rottner, Klemens and Binder, Christoph J. and Stradal, Theresia E.B. and Rezaei, Nima and Boztug, Kaan},
issn = {24709468},
journal = {Science Immunology},
number = {49},
publisher = {AAAS},
title = {{The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity}},
doi = {10.1126/sciimmunol.abc3979},
volume = {5},
year = {2020},
}
@article{8134,
abstract = {We prove an upper bound on the free energy of a two-dimensional homogeneous Bose gas in the thermodynamic limit. We show that for a2ρ ≪ 1 and βρ ≳ 1, the free energy per unit volume differs from the one of the non-interacting system by at most 4πρ2|lna2ρ|−1(2−[1−βc/β]2+) to leading order, where a is the scattering length of the two-body interaction potential, ρ is the density, β is the inverse temperature, and βc is the inverse Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity. In combination with the corresponding matching lower bound proved by Deuchert et al. [Forum Math. Sigma 8, e20 (2020)], this shows equality in the asymptotic expansion.},
author = {Mayer, Simon and Seiringer, Robert},
issn = {00222488},
journal = {Journal of Mathematical Physics},
number = {6},
publisher = {AIP},
title = {{The free energy of the two-dimensional dilute Bose gas. II. Upper bound}},
doi = {10.1063/5.0005950},
volume = {61},
year = {2020},
}
@inproceedings{8135,
abstract = {Discrete Morse theory has recently lead to new developments in the theory of random geometric complexes. This article surveys the methods and results obtained with this new approach, and discusses some of its shortcomings. It uses simulations to illustrate the results and to form conjectures, getting numerical estimates for combinatorial, topological, and geometric properties of weighted and unweighted Delaunay mosaics, their dual Voronoi tessellations, and the Alpha and Wrap complexes contained in the mosaics.},
author = {Edelsbrunner, Herbert and Nikitenko, Anton and Ölsböck, Katharina and Synak, Peter},
booktitle = {Topological Data Analysis},
isbn = {9783030434076},
issn = {21978549},
pages = {181--218},
publisher = {Springer Nature},
title = {{Radius functions on Poisson–Delaunay mosaics and related complexes experimentally}},
doi = {10.1007/978-3-030-43408-3_8},
volume = {15},
year = {2020},
}
@article{8138,
abstract = {Directional transport of the phytohormone auxin is a versatile, plant-specific mechanism regulating many aspects of plant development. The recently identified plant hormones, strigolactones (SLs), are implicated in many plant traits; among others, they modify the phenotypic output of PIN-FORMED (PIN) auxin transporters for fine-tuning of growth and developmental responses. Here, we show in pea and Arabidopsis that SLs target processes dependent on the canalization of auxin flow, which involves auxin feedback on PIN subcellular distribution. D14 receptor- and MAX2 F-box-mediated SL signaling inhibits the formation of auxin-conducting channels after wounding or from artificial auxin sources, during vasculature de novo formation and regeneration. At the cellular level, SLs interfere with auxin effects on PIN polar targeting, constitutive PIN trafficking as well as clathrin-mediated endocytosis. Our results identify a non-transcriptional mechanism of SL action, uncoupling auxin feedback on PIN polarity and trafficking, thereby regulating vascular tissue formation and regeneration.},
author = {Zhang, J and Mazur, E and Balla, J and Gallei, Michelle C and Kalousek, P and Medveďová, Z and Li, Y and Wang, Y and Prat, Tomas and Vasileva, Mina K and Reinöhl, V and Procházka, S and Halouzka, R and Tarkowski, P and Luschnig, C and Brewer, PB and Friml, Jiří},
issn = {2041-1723},
journal = {Nature Communications},
number = {1},
pages = {3508},
publisher = {Springer Nature},
title = {{Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization}},
doi = {10.1038/s41467-020-17252-y},
volume = {11},
year = {2020},
}
@article{8139,
abstract = {Clathrin-mediated endocytosis (CME) is a crucial cellular process implicated in many aspects of plant growth, development, intra- and inter-cellular signaling, nutrient uptake and pathogen defense. Despite these significant roles, little is known about the precise molecular details of how it functions in planta. In order to facilitate the direct quantitative study of plant CME, here we review current routinely used methods and present refined, standardized quantitative imaging protocols which allow the detailed characterization of CME at multiple scales in plant tissues. These include: (i) an efficient electron microscopy protocol for the imaging of Arabidopsis CME vesicles in situ, thus providing a method for the detailed characterization of the ultra-structure of clathrin-coated vesicles; (ii) a detailed protocol and analysis for quantitative live-cell fluorescence microscopy to precisely examine the temporal interplay of endocytosis components during single CME events; (iii) a semi-automated analysis to allow the quantitative characterization of global internalization of cargos in whole plant tissues; and (iv) an overview and validation of useful genetic and pharmacological tools to interrogate the molecular mechanisms and function of CME in intact plant samples.},
author = {Johnson, Alexander J and Gnyliukh, Nataliia and Kaufmann, Walter and Narasimhan, Madhumitha and Vert, G and Bednarek, SY and Friml, Jiří},
issn = {0021-9533},
journal = {Journal of Cell Science},
number = {15},
publisher = {The Company of Biologists},
title = {{Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis}},
doi = {10.1242/jcs.248062},
volume = {133},
year = {2020},
}
@article{8142,
abstract = {Cell production and differentiation for the acquisition of specific functions are key features of living systems. The dynamic network of cellular microtubules provides the necessary platform to accommodate processes associated with the transition of cells through the individual phases of cytogenesis. Here, we show that the plant hormone cytokinin fine‐tunes the activity of the microtubular cytoskeleton during cell differentiation and counteracts microtubular rearrangements driven by the hormone auxin. The endogenous upward gradient of cytokinin activity along the longitudinal growth axis in Arabidopsis thaliana roots correlates with robust rearrangements of the microtubule cytoskeleton in epidermal cells progressing from the proliferative to the differentiation stage. Controlled increases in cytokinin activity result in premature re‐organization of the microtubule network from transversal to an oblique disposition in cells prior to their differentiation, whereas attenuated hormone perception delays cytoskeleton conversion into a configuration typical for differentiated cells. Intriguingly, cytokinin can interfere with microtubules also in animal cells, such as leukocytes, suggesting that a cytokinin‐sensitive control pathway for the microtubular cytoskeleton may be at least partially conserved between plant and animal cells.},
author = {Montesinos López, Juan C and Abuzeineh, A and Kopf, Aglaja and Juanes Garcia, Alba and Ötvös, Krisztina and Petrášek, J and Sixt, Michael K and Benková, Eva},
issn = {0261-4189},
journal = {The Embo Journal},
number = {17},
publisher = {Embo Press},
title = {{Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage}},
doi = {10.15252/embj.2019104238},
volume = {39},
year = {2020},
}
@phdthesis{8155,
abstract = {In the thesis we focus on the interplay of the biophysics and evolution of gene regulation. We start by addressing how the type of prokaryotic gene regulation – activation and repression – affects spurious binding to DNA, also known as
transcriptional crosstalk. We propose that regulatory interference caused by excess regulatory proteins in the dense cellular medium – global crosstalk – could be a factor in determining which type of gene regulatory network is evolutionarily preferred. Next,we use a normative approach in eukaryotic gene regulation to describe minimal
non-equilibrium enhancer models that optimize so-called regulatory phenotypes. We find a class of models that differ from standard thermodynamic equilibrium models by a single parameter that notably increases the regulatory performance. Next chapter addresses the question of genotype-phenotype-fitness maps of higher dimensional phenotypes. We show that our biophysically realistic approach allows us to understand how the mechanisms of promoter function constrain genotypephenotype maps, and how they affect the evolutionary trajectories of promoters.
In the last chapter we ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using mathematical modeling, we show that amplifications can tune gene expression in many environments, including those where transcription factor-based schemes are
hard to evolve or maintain. },
author = {Grah, Rok},
issn = {2663-337X},
pages = {310},
publisher = {IST Austria},
title = {{Gene regulation across scales – how biophysical constraints shape evolution}},
doi = {10.15479/AT:ISTA:8155},
year = {2020},
}
@phdthesis{8156,
abstract = {We present solutions to several problems originating from geometry and discrete mathematics: existence of equipartitions, maps without Tverberg multiple points, and inscribing quadrilaterals. Equivariant obstruction theory is the natural topological approach to these type of questions. However, for the specific problems we consider it had yielded only partial or no results. We get our results by complementing equivariant obstruction theory with other techniques from topology and geometry.},
author = {Avvakumov, Sergey},
pages = {119},
publisher = {IST Austria},
title = {{Topological methods in geometry and discrete mathematics}},
doi = {10.15479/AT:ISTA:8156},
year = {2020},
}
@article{8162,
abstract = {In mammalian genomes, a subset of genes is regulated by genomic imprinting, resulting in silencing of one parental allele. Imprinting is essential for cerebral cortex development, but prevalence and functional impact in individual cells is unclear. Here, we determined allelic expression in cortical cell types and established a quantitative platform to interrogate imprinting in single cells. We created cells with uniparental chromosome disomy (UPD) containing two copies of either the maternal or the paternal chromosome; hence, imprinted genes will be 2-fold overexpressed or not expressed. By genetic labeling of UPD, we determined cellular phenotypes and transcriptional responses to deregulated imprinted gene expression at unprecedented single-cell resolution. We discovered an unexpected degree of cell-type specificity and a novel function of imprinting in the regulation of cortical astrocyte survival. More generally, our results suggest functional relevance of imprinted gene expression in glial astrocyte lineage and thus for generating cortical cell-type diversity.},
author = {Laukoter, Susanne and Pauler, Florian and Beattie, Robert J and Amberg, Nicole and Hansen, Andi H and Streicher, Carmen and Penz, Thomas and Bock, Christoph and Hippenmeyer, Simon},
issn = {0896-6273},
journal = {Neuron},
number = {6},
pages = {1160--1179.e9},
publisher = {Elsevier},
title = {{Cell-type specificity of genomic imprinting in cerebral cortex}},
doi = {10.1016/j.neuron.2020.06.031},
volume = {107},
year = {2020},
}
@article{8163,
abstract = {Fejes Tóth [3] studied approximations of smooth surfaces in three-space by piecewise flat triangular meshes with a given number of vertices on the surface that are optimal with respect to Hausdorff distance. He proves that this Hausdorff distance decreases inversely proportional with the number of vertices of the approximating mesh if the surface is convex. He also claims that this Hausdorff distance is inversely proportional to the square of the number of vertices for a specific non-convex surface, namely a one-sheeted hyperboloid of revolution bounded by two congruent circles. We refute this claim, and show that the asymptotic behavior of the Hausdorff distance is linear, that is the same as for convex surfaces.},
author = {Vegter, Gert and Wintraecken, Mathijs},
issn = {1588-2896},
journal = {Studia Scientiarum Mathematicarum Hungarica},
number = {2},
pages = {193--199},
publisher = {AKJournals},
title = {{Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes}},
doi = {10.1556/012.2020.57.2.1454},
volume = {57},
year = {2020},
}