@article{8723, abstract = {Deep learning at scale is dominated by communication time. Distributing samples across nodes usually yields the best performance, but poses scaling challenges due to global information dissemination and load imbalance across uneven sample lengths. State-of-the-art decentralized optimizers mitigate the problem, but require more iterations to achieve the same accuracy as their globally-communicating counterparts. We present Wait-Avoiding Group Model Averaging (WAGMA) SGD, a wait-avoiding stochastic optimizer that reduces global communication via subgroup weight exchange. The key insight is a combination of algorithmic changes to the averaging scheme and the use of a group allreduce operation. We prove the convergence of WAGMA-SGD, and empirically show that it retains convergence rates similar to Allreduce-SGD. For evaluation, we train ResNet-50 on ImageNet; Transformer for machine translation; and deep reinforcement learning for navigation at scale. Compared with state-of-the-art decentralized SGD variants, WAGMA-SGD significantly improves training throughput (e.g., 2.1× on 1,024 GPUs for reinforcement learning), and achieves the fastest time-to-solution (e.g., the highest score using the shortest training time for Transformer).}, author = {Li, Shigang and Tal Ben-Nun, Tal Ben-Nun and Nadiradze, Giorgi and Girolamo, Salvatore Di and Dryden, Nikoli and Alistarh, Dan-Adrian and Hoefler, Torsten}, issn = {1045-9219}, journal = {IEEE Transactions on Parallel and Distributed Systems}, number = {7}, publisher = {IEEE}, title = {{Breaking (global) barriers in parallel stochastic optimization with wait-avoiding group averaging}}, doi = {10.1109/TPDS.2020.3040606}, volume = {32}, year = {2021}, } @article{8742, abstract = {We develop a version of Ekedahl’s geometric sieve for integral quadratic forms of rank at least five. As one ranges over the zeros of such quadratic forms, we use the sieve to compute the density of coprime values of polynomials, and furthermore, to address a question about local solubility in families of varieties parameterised by the zeros.}, author = {Browning, Timothy D and Heath-Brown, Roger}, issn = {1435-5337}, journal = {Forum Mathematicum}, number = {1}, pages = {147--165}, publisher = {De Gruyter}, title = {{The geometric sieve for quadrics}}, doi = {10.1515/forum-2020-0074}, volume = {33}, year = {2021}, } @article{8743, abstract = {Montane cloud forests are areas of high endemism, and are one of the more vulnerable terrestrial ecosystems to climate change. Thus, understanding how they both contribute to the generation of biodiversity, and will respond to ongoing climate change, are important and related challenges. The widely accepted model for montane cloud forest dynamics involves upslope forcing of their range limits with global climate warming. However, limited climate data provides some support for an alternative model, where range limits are forced downslope with climate warming. Testing between these two models is challenging, due to the inherent limitations of climate and pollen records. We overcome this with an alternative source of historical information, testing between competing model predictions using genomic data and demographic analyses for a species of beetle tightly associated to an oceanic island cloud forest. Results unequivocally support the alternative model: populations that were isolated at higher elevation peaks during the Last Glacial Maximum are now in contact and hybridizing at lower elevations. Our results suggest that genomic data are a rich source of information to further understand how montane cloud forest biodiversity originates, and how it is likely to be impacted by ongoing climate change.}, author = {Salces-Castellano, Antonia and Stankowski, Sean and Arribas, Paula and Patino, Jairo and Karger, Dirk N. and Butlin, Roger and Emerson, Brent C.}, issn = {1558-5646}, journal = {Evolution}, number = {2}, pages = {231--244}, publisher = {Wiley}, title = {{Long-term cloud forest response to climate warming revealed by insect speciation history}}, doi = {10.1111/evo.14111}, volume = {75}, year = {2021}, } @article{8757, abstract = {Traditional scientific conferences and seminar events have been hugely disrupted by the COVID-19 pandemic, paving the way for virtual forms of scientific communication to take hold and be put to the test.}, author = {Bozelos, Panagiotis and Vogels, Tim P}, issn = {1471-0048}, journal = {Nature Reviews Neuroscience}, number = {1}, pages = {1--2}, publisher = {Springer Nature}, title = {{Talking science, online}}, doi = {10.1038/s41583-020-00408-6}, volume = {22}, year = {2021}, } @article{8773, abstract = {Let g be a complex semisimple Lie algebra. We give a classification of contravariant forms on the nondegenerate Whittaker g-modules Y(χ,η) introduced by Kostant. We prove that the set of all contravariant forms on Y(χ,η) forms a vector space whose dimension is given by the cardinality of the Weyl group of g. We also describe a procedure for parabolically inducing contravariant forms. As a corollary, we deduce the existence of the Shapovalov form on a Verma module, and provide a formula for the dimension of the space of contravariant forms on the degenerate Whittaker modules M(χ,η) introduced by McDowell.}, author = {Brown, Adam and Romanov, Anna}, issn = {1088-6826}, journal = {Proceedings of the American Mathematical Society}, keywords = {Applied Mathematics, General Mathematics}, number = {1}, pages = {37--52}, publisher = {American Mathematical Society}, title = {{Contravariant forms on Whittaker modules}}, doi = {10.1090/proc/15205}, volume = {149}, year = {2021}, } @article{8792, abstract = {This paper is concerned with a non-isothermal Cahn-Hilliard model based on a microforce balance. The model was derived by A. Miranville and G. Schimperna starting from the two fundamental laws of Thermodynamics, following M. Gurtin's two-scale approach. The main working assumptions are made on the behaviour of the heat flux as the absolute temperature tends to zero and to infinity. A suitable Ginzburg-Landau free energy is considered. Global-in-time existence for the initial-boundary value problem associated to the entropy formulation and, in a subcase, also to the weak formulation of the model is proved by deriving suitable a priori estimates and by showing weak sequential stability of families of approximating solutions. At last, some highlights are given regarding a possible approximation scheme compatible with the a-priori estimates available for the system.}, author = {Marveggio, Alice and Schimperna, Giulio}, issn = {1090-2732}, journal = {Journal of Differential Equations}, number = {2}, pages = {924--970}, publisher = {Elsevier}, title = {{On a non-isothermal Cahn-Hilliard model based on a microforce balance}}, doi = {10.1016/j.jde.2020.10.030}, volume = {274}, year = {2021}, } @article{8816, abstract = {Area-dependent quantum field theory is a modification of two-dimensional topological quantum field theory, where one equips each connected component of a bordism with a positive real number—interpreted as area—which behaves additively under glueing. As opposed to topological theories, in area-dependent theories the state spaces can be infinite-dimensional. We introduce the notion of regularised Frobenius algebras in Hilbert spaces and show that area-dependent theories are in one-to-one correspondence to commutative regularised Frobenius algebras. We also provide a state sum construction for area-dependent theories. Our main example is two-dimensional Yang–Mills theory with compact gauge group, which we treat in detail.}, author = {Runkel, Ingo and Szegedy, Lorant}, issn = {1432-0916}, journal = {Communications in Mathematical Physics}, number = {1}, pages = {83–117}, publisher = {Springer Nature}, title = {{Area-dependent quantum field theory}}, doi = {10.1007/s00220-020-03902-1}, volume = {381}, year = {2021}, } @article{8817, abstract = {The paper introduces an inertial extragradient subgradient method with self-adaptive step sizes for solving equilibrium problems in real Hilbert spaces. Weak convergence of the proposed method is obtained under the condition that the bifunction is pseudomonotone and Lipchitz continuous. Linear convergence is also given when the bifunction is strongly pseudomonotone and Lipchitz continuous. Numerical implementations and comparisons with other related inertial methods are given using test problems including a real-world application to Nash–Cournot oligopolistic electricity market equilibrium model.}, author = {Shehu, Yekini and Iyiola, Olaniyi S. and Thong, Duong Viet and Van, Nguyen Thi Cam}, issn = {1432-5217}, journal = {Mathematical Methods of Operations Research}, number = {2}, pages = {213--242}, publisher = {Springer Nature}, title = {{An inertial subgradient extragradient algorithm extended to pseudomonotone equilibrium problems}}, doi = {10.1007/s00186-020-00730-w}, volume = {93}, year = {2021}, } @article{8818, abstract = {The hippocampus has a major role in encoding and consolidating long-term memories, and undergoes plastic changes during sleep1. These changes require precise homeostatic control by subcortical neuromodulatory structures2. The underlying mechanisms of this phenomenon, however, remain unknown. Here, using multi-structure recordings in macaque monkeys, we show that the brainstem transiently modulates hippocampal network events through phasic pontine waves known as pontogeniculooccipital waves (PGO waves). Two physiologically distinct types of PGO wave appear to occur sequentially, selectively influencing high-frequency ripples and low-frequency theta events, respectively. The two types of PGO wave are associated with opposite hippocampal spike-field coupling, prompting periods of high neural synchrony of neural populations during periods of ripple and theta instances. The coupling between PGO waves and ripples, classically associated with distinct sleep stages, supports the notion that a global coordination mechanism of hippocampal sleep dynamics by cholinergic pontine transients may promote systems and synaptic memory consolidation as well as synaptic homeostasis.}, author = {Ramirez Villegas, Juan F and Besserve, Michel and Murayama, Yusuke and Evrard, Henry C. and Oeltermann, Axel and Logothetis, Nikos K.}, issn = {1476-4687}, journal = {Nature}, number = {7840}, pages = {96--102}, publisher = {Springer Nature}, title = {{Coupling of hippocampal theta and ripples with pontogeniculooccipital waves}}, doi = {10.1038/s41586-020-2914-4}, volume = {589}, year = {2021}, } @article{8824, abstract = {Plants are able to orient their growth according to gravity, which ultimately controls both shoot and root architecture.1 Gravitropism is a dynamic process whereby gravistimulation induces the asymmetric distribution of the plant hormone auxin, leading to asymmetric growth, organ bending, and subsequent reset of auxin distribution back to the original pre-gravistimulation situation.1, 2, 3 Differential auxin accumulation during the gravitropic response depends on the activity of polarly localized PIN-FORMED (PIN) auxin-efflux carriers.1, 2, 3, 4 In particular, the timing of this dynamic response is regulated by PIN2,5,6 but the underlying molecular mechanisms are poorly understood. Here, we show that MEMBRANE ASSOCIATED KINASE REGULATOR2 (MAKR2) controls the pace of the root gravitropic response. We found that MAKR2 is required for the PIN2 asymmetry during gravitropism by acting as a negative regulator of the cell-surface signaling mediated by the receptor-like kinase TRANSMEMBRANE KINASE1 (TMK1).2,7, 8, 9, 10 Furthermore, we show that the MAKR2 inhibitory effect on TMK1 signaling is antagonized by auxin itself, which triggers rapid MAKR2 membrane dissociation in a TMK1-dependent manner. Our findings suggest that the timing of the root gravitropic response is orchestrated by the reversible inhibition of the TMK1 signaling pathway at the cell surface.}, author = {Marquès-Bueno, MM and Armengot, L and Noack, LC and Bareille, J and Rodriguez Solovey, Lesia and Platre, MP and Bayle, V and Liu, M and Opdenacker, D and Vanneste, S and Möller, BK and Nimchuk, ZL and Beeckman, T and Caño-Delgado, AI and Friml, Jiří and Jaillais, Y}, issn = {1879-0445}, journal = {Current Biology}, number = {1}, publisher = {Elsevier}, title = {{Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism}}, doi = {10.1016/j.cub.2020.10.011}, volume = {31}, year = {2021}, } @article{8911, abstract = {In the worldwide endeavor for disruptive quantum technologies, germanium is emerging as a versatile material to realize devices capable of encoding, processing, or transmitting quantum information. These devices leverage special properties of the germanium valence-band states, commonly known as holes, such as their inherently strong spin-orbit coupling and the ability to host superconducting pairing correlations. In this Review, we initially introduce the physics of holes in low-dimensional germanium structures with key insights from a theoretical perspective. We then examine the material science progress underpinning germanium-based planar heterostructures and nanowires. We review the most significant experimental results demonstrating key building blocks for quantum technology, such as an electrically driven universal quantum gate set with spin qubits in quantum dots and superconductor-semiconductor devices for hybrid quantum systems. We conclude by identifying the most promising prospects toward scalable quantum information processing. }, author = {Scappucci, Giordano and Kloeffel, Christoph and Zwanenburg, Floris A. and Loss, Daniel and Myronov, Maksym and Zhang, Jian-Jun and Franceschi, Silvano De and Katsaros, Georgios and Veldhorst, Menno}, issn = {2058-8437}, journal = {Nature Reviews Materials}, pages = {926–943 }, publisher = {Springer Nature}, title = {{The germanium quantum information route}}, doi = {10.1038/s41578-020-00262-z}, volume = {6}, year = {2021}, } @article{8927, abstract = {The recent outbreak of coronavirus disease 2019 (COVID‐19), caused by the Severe Acute Respiratory Syndrome Coronavirus‐2 (SARS‐CoV‐2) has resulted in a world‐wide pandemic. Disseminated lung injury with the development of acute respiratory distress syndrome (ARDS) is the main cause of mortality in COVID‐19. Although liver failure does not seem to occur in the absence of pre‐existing liver disease, hepatic involvement in COVID‐19 may correlate with overall disease severity and serve as a prognostic factor for the development of ARDS. The spectrum of liver injury in COVID‐19 may range from direct infection by SARS‐CoV‐2, indirect involvement by systemic inflammation, hypoxic changes, iatrogenic causes such as drugs and ventilation to exacerbation of underlying liver disease. This concise review discusses the potential pathophysiological mechanisms for SARS‐CoV‐2 hepatic tropism as well as acute and possibly long‐term liver injury in COVID‐19.}, author = {Nardo, Alexander D. and Schneeweiss-Gleixner, Mathias and Bakail, May M and Dixon, Emmanuel D. and Lax, Sigurd F. and Trauner, Michael}, issn = {1478-3231}, journal = {Liver International}, number = {1}, pages = {20--32}, publisher = {Wiley}, title = {{Pathophysiological mechanisms of liver injury in COVID-19}}, doi = {10.1111/liv.14730}, volume = {41}, year = {2021}, } @article{8940, abstract = {We quantise Whitney’s construction to prove the existence of a triangulation for any C^2 manifold, so that we get an algorithm with explicit bounds. We also give a new elementary proof, which is completely geometric.}, author = {Boissonnat, Jean-Daniel and Kachanovich, Siargey and Wintraecken, Mathijs}, issn = {1432-0444}, journal = {Discrete & Computational Geometry}, keywords = {Theoretical Computer Science, Computational Theory and Mathematics, Geometry and Topology, Discrete Mathematics and Combinatorics}, number = {1}, pages = {386--434}, publisher = {Springer Nature}, title = {{Triangulating submanifolds: An elementary and quantified version of Whitney’s method}}, doi = {10.1007/s00454-020-00250-8}, volume = {66}, year = {2021}, } @article{8992, abstract = {The phytohormone auxin plays a central role in shaping plant growth and development. With decades of genetic and biochemical studies, numerous core molecular components and their networks, underlying auxin biosynthesis, transport, and signaling, have been identified. Notably, protein phosphorylation, catalyzed by kinases and oppositely hydrolyzed by phosphatases, has been emerging to be a crucial type of post-translational modification, regulating physiological and developmental auxin output at all levels. In this review, we comprehensively discuss earlier and recent advances in our understanding of genetics, biochemistry, and cell biology of the kinases and phosphatases participating in auxin action. We provide insights into the mechanisms by which reversible protein phosphorylation defines developmental auxin responses, discuss current challenges, and provide our perspectives on future directions involving the integration of the control of protein phosphorylation into the molecular auxin network.}, author = {Tan, Shutang and Luschnig, Christian and Friml, Jiří}, issn = {1752-9867}, journal = {Molecular Plant}, number = {1}, pages = {151--165}, publisher = {Elsevier}, title = {{Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling}}, doi = {10.1016/j.molp.2020.11.004}, volume = {14}, year = {2021}, } @article{8997, abstract = {Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems.}, author = {Kavcic, Bor and Tkačik, Gašper and Bollenbach, Tobias}, issn = {1553-7358}, journal = {PLOS Computational Biology}, keywords = {Modelling and Simulation, Genetics, Molecular Biology, Antibiotics, Drug interactions}, publisher = {Public Library of Science}, title = {{Minimal biophysical model of combined antibiotic action}}, doi = {10.1371/journal.pcbi.1008529}, volume = {17}, year = {2021}, } @article{8999, abstract = {In many basic shear flows, such as pipe, Couette, and channel flow, turbulence does not arise from an instability of the laminar state, and both dynamical states co-exist. With decreasing flow speed (i.e., decreasing Reynolds number) the fraction of fluid in laminar motion increases while turbulence recedes and eventually the entire flow relaminarizes. The first step towards understanding the nature of this transition is to determine if the phase change is of either first or second order. In the former case, the turbulent fraction would drop discontinuously to zero as the Reynolds number decreases while in the latter the process would be continuous. For Couette flow, the flow between two parallel plates, earlier studies suggest a discontinuous scenario. In the present study we realize a Couette flow between two concentric cylinders which allows studies to be carried out in large aspect ratios and for extensive observation times. The presented measurements show that the transition in this circular Couette geometry is continuous suggesting that former studies were limited by finite size effects. A further characterization of this transition, in particular its relation to the directed percolation universality class, requires even larger system sizes than presently available. }, author = {Avila, Kerstin and Hof, Björn}, issn = {1099-4300}, journal = {Entropy}, number = {1}, publisher = {MDPI}, title = {{Second-order phase transition in counter-rotating taylor-couette flow experiment}}, doi = {10.3390/e23010058}, volume = {23}, year = {2021}, } @article{9002, abstract = { We prove that, for the binary erasure channel (BEC), the polar-coding paradigm gives rise to codes that not only approach the Shannon limit but do so under the best possible scaling of their block length as a function of the gap to capacity. This result exhibits the first known family of binary codes that attain both optimal scaling and quasi-linear complexity of encoding and decoding. Our proof is based on the construction and analysis of binary polar codes with large kernels. When communicating reliably at rates within ε>0 of capacity, the code length n often scales as O(1/εμ), where the constant μ is called the scaling exponent. It is known that the optimal scaling exponent is μ=2, and it is achieved by random linear codes. The scaling exponent of conventional polar codes (based on the 2×2 kernel) on the BEC is μ=3.63. This falls far short of the optimal scaling guaranteed by random codes. Our main contribution is a rigorous proof of the following result: for the BEC, there exist ℓ×ℓ binary kernels, such that polar codes constructed from these kernels achieve scaling exponent μ(ℓ) that tends to the optimal value of 2 as ℓ grows. We furthermore characterize precisely how large ℓ needs to be as a function of the gap between μ(ℓ) and 2. The resulting binary codes maintain the recursive structure of conventional polar codes, and thereby achieve construction complexity O(n) and encoding/decoding complexity O(nlogn).}, author = {Fazeli, Arman and Hassani, Hamed and Mondelli, Marco and Vardy, Alexander}, issn = {1557-9654}, journal = {IEEE Transactions on Information Theory}, number = {9}, pages = {5693--5710}, publisher = {IEEE}, title = {{Binary linear codes with optimal scaling: Polar codes with large kernels}}, doi = {10.1109/TIT.2020.3038806}, volume = {67}, year = {2021}, } @article{9009, abstract = {Recent advancements in live cell imaging technologies have identified the phenomenon of intracellular propagation of late apoptotic events, such as cytochrome c release and caspase activation. The mechanism, prevalence, and speed of apoptosis propagation remain unclear. Additionally, no studies have demonstrated propagation of the pro-apoptotic protein, BAX. To evaluate the role of BAX in intracellular apoptotic propagation, we used high speed live-cell imaging to visualize fluorescently tagged-BAX recruitment to mitochondria in four immortalized cell lines. We show that propagation of mitochondrial BAX recruitment occurs in parallel to cytochrome c and SMAC/Diablo release and is affected by cellular morphology, such that cells with processes are more likely to exhibit propagation. The initiation of propagation events is most prevalent in the distal tips of processes, while the rate of propagation is influenced by the 2-dimensional width of the process. Propagation was rarely observed in the cell soma, which exhibited near synchronous recruitment of BAX. Propagation velocity is not affected by mitochondrial volume in segments of processes, but is negatively affected by mitochondrial density. There was no evidence of a propagating wave of increased levels of intracellular calcium ions. Alternatively, we did observe a uniform increase in superoxide build-up in cellular mitochondria, which was released as a propagating wave simultaneously with the propagating recruitment of BAX to the mitochondrial outer membrane.}, author = {Grosser, Joshua A. and Maes, Margaret E and Nickells, Robert W.}, issn = {1573-675X}, journal = {Apoptosis}, number = {2}, pages = {132--145}, publisher = {Springer Nature}, title = {{Characteristics of intracellular propagation of mitochondrial BAX recruitment during apoptosis}}, doi = {10.1007/s10495-020-01654-w}, volume = {26}, year = {2021}, } @article{9020, abstract = {We study dynamics and thermodynamics of ion transport in narrow, water-filled channels, considered as effective 1D Coulomb systems. The long range nature of the inter-ion interactions comes about due to the dielectric constants mismatch between the water and the surrounding medium, confining the electric filed to stay mostly within the water-filled channel. Statistical mechanics of such Coulomb systems is dominated by entropic effects which may be accurately accounted for by mapping onto an effective quantum mechanics. In presence of multivalent ions the corresponding quantum mechanics appears to be non-Hermitian. In this review we discuss a framework for semiclassical calculations for the effective non-Hermitian Hamiltonians. Non-Hermiticity elevates WKB action integrals from the real line to closed cycles on a complex Riemann surfaces where direct calculations are not attainable. We circumvent this issue by applying tools from algebraic topology, such as the Picard-Fuchs equation. We discuss how its solutions relate to the thermodynamics and correlation functions of multivalent solutions within narrow, water-filled channels. }, author = {Gulden, Tobias and Kamenev, Alex}, issn = {1099-4300}, journal = {Entropy}, number = {1}, publisher = {MDPI}, title = {{Dynamics of ion channels via non-hermitian quantum mechanics}}, doi = {10.3390/e23010125}, volume = {23}, year = {2021}, } @article{9036, abstract = {In this short note, we prove that the square root of the quantum Jensen-Shannon divergence is a true metric on the cone of positive matrices, and hence in particular on the quantum state space.}, author = {Virosztek, Daniel}, issn = {0001-8708}, journal = {Advances in Mathematics}, keywords = {General Mathematics}, number = {3}, publisher = {Elsevier}, title = {{The metric property of the quantum Jensen-Shannon divergence}}, doi = {10.1016/j.aim.2021.107595}, volume = {380}, year = {2021}, }