@article{7563, abstract = {We introduce “state space persistence analysis” for deducing the symbolic dynamics of time series data obtained from high-dimensional chaotic attractors. To this end, we adapt a topological data analysis technique known as persistent homology for the characterization of state space projections of chaotic trajectories and periodic orbits. By comparing the shapes along a chaotic trajectory to those of the periodic orbits, state space persistence analysis quantifies the shape similarity of chaotic trajectory segments and periodic orbits. We demonstrate the method by applying it to the three-dimensional Rössler system and a 30-dimensional discretization of the Kuramoto–Sivashinsky partial differential equation in (1+1) dimensions. One way of studying chaotic attractors systematically is through their symbolic dynamics, in which one partitions the state space into qualitatively different regions and assigns a symbol to each such region.1–3 This yields a “coarse-grained” state space of the system, which can then be reduced to a Markov chain encoding all possible transitions between the states of the system. While it is possible to obtain the symbolic dynamics of low-dimensional chaotic systems with standard tools such as Poincaré maps, when applied to high-dimensional systems such as turbulent flows, these tools alone are not sufficient to determine symbolic dynamics.4,5 In this paper, we develop “state space persistence analysis” and demonstrate that it can be utilized to infer the symbolic dynamics in very high-dimensional settings.}, author = {Yalniz, Gökhan and Budanur, Nazmi B}, issn = {1089-7682}, journal = {Chaos}, number = {3}, publisher = {AIP Publishing}, title = {{Inferring symbolic dynamics of chaotic flows from persistence}}, doi = {10.1063/1.5122969}, volume = {30}, year = {2020}, } @article{7554, abstract = {Slicing a Voronoi tessellation in ${R}^n$ with a $k$-plane gives a $k$-dimensional weighted Voronoi tessellation, also known as a power diagram or Laguerre tessellation. Mapping every simplex of the dual weighted Delaunay mosaic to the radius of the smallest empty circumscribed sphere whose center lies in the $k$-plane gives a generalized discrete Morse function. Assuming the Voronoi tessellation is generated by a Poisson point process in ${R}^n$, we study the expected number of simplices in the $k$-dimensional weighted Delaunay mosaic as well as the expected number of intervals of the Morse function, both as functions of a radius threshold. As a by-product, we obtain a new proof for the expected number of connected components (clumps) in a line section of a circular Boolean model in ${R}^n$.}, author = {Edelsbrunner, Herbert and Nikitenko, Anton}, issn = {10957219}, journal = {Theory of Probability and its Applications}, number = {4}, pages = {595--614}, publisher = {SIAM}, title = {{Weighted Poisson–Delaunay mosaics}}, doi = {10.1137/S0040585X97T989726}, volume = {64}, year = {2020}, } @article{7570, abstract = {The relaxation of few-body quantum systems can strongly depend on the initial state when the system’s semiclassical phase space is mixed; i.e., regions of chaotic motion coexist with regular islands. In recent years, there has been much effort to understand the process of thermalization in strongly interacting quantum systems that often lack an obvious semiclassical limit. The time-dependent variational principle (TDVP) allows one to systematically derive an effective classical (nonlinear) dynamical system by projecting unitary many-body dynamics onto a manifold of weakly entangled variational states. We demonstrate that such dynamical systems generally possess mixed phase space. When TDVP errors are small, the mixed phase space leaves a footprint on the exact dynamics of the quantum model. For example, when the system is initialized in a state belonging to a stable periodic orbit or the surrounding regular region, it exhibits persistent many-body quantum revivals. As a proof of principle, we identify new types of “quantum many-body scars,” i.e., initial states that lead to long-time oscillations in a model of interacting Rydberg atoms in one and two dimensions. Intriguingly, the initial states that give rise to most robust revivals are typically entangled states. On the other hand, even when TDVP errors are large, as in the thermalizing tilted-field Ising model, initializing the system in a regular region of phase space leads to a surprising slowdown of thermalization. Our work establishes TDVP as a method for identifying interacting quantum systems with anomalous dynamics in arbitrary dimensions. Moreover, the mixed phase space classical variational equations allow one to find slowly thermalizing initial conditions in interacting models. Our results shed light on a link between classical and quantum chaos, pointing toward possible extensions of the classical Kolmogorov-Arnold-Moser theorem to quantum systems.}, author = {Michailidis, Alexios and Turner, C. J. and Papić, Z. and Abanin, D. A. and Serbyn, Maksym}, issn = {2160-3308}, journal = {Physical Review X}, number = {1}, publisher = {American Physical Society}, title = {{Slow quantum thermalization and many-body revivals from mixed phase space}}, doi = {10.1103/physrevx.10.011055}, volume = {10}, year = {2020}, } @article{7582, abstract = {Small RNAs (smRNA, 19–25 nucleotides long), which are transcribed by RNA polymerase II, regulate the expression of genes involved in a multitude of processes in eukaryotes. miRNA biogenesis and the proteins involved in the biogenesis pathway differ across plant and animal lineages. The major proteins constituting the biogenesis pathway, namely, the Dicers (DCL/DCR) and Argonautes (AGOs), have been extensively studied. However, the accessory proteins (DAWDLE (DDL), SERRATE (SE), and TOUGH (TGH)) of the pathway that differs across the two lineages remain largely uncharacterized. We present the first detailed report on the molecular evolution and divergence of these proteins across eukaryotes. Although DDL is present in eukaryotes and prokaryotes, SE and TGH appear to be specific to eukaryotes. The addition/deletion of specific domains and/or domain-specific sequence divergence in the three proteins points to the observed functional divergence of these proteins across the two lineages, which correlates with the differences in miRNA length across the two lineages. Our data enhance the current understanding of the structure–function relationship of these proteins and reveals previous unexplored crucial residues in the three proteins that can be used as a basis for further functional characterization. The data presented here on the number of miRNAs in crown eukaryotic lineages are consistent with the notion of the expansion of the number of miRNA-coding genes in animal and plant lineages correlating with organismal complexity. Whether this difference in functionally correlates with the diversification (or presence/absence) of the three proteins studied here or the miRNA signaling in the plant and animal lineages is unclear. Based on our results of the three proteins studied here and previously available data concerning the evolution of miRNA genes in the plant and animal lineages, we believe that miRNAs probably evolved once in the ancestor to crown eukaryotes and have diversified independently in the eukaryotes.}, author = {Moturu, Taraka Ramji and Sinha, Sansrity and Salava, Hymavathi and Thula, Sravankumar and Nodzyński, Tomasz and Vařeková, Radka Svobodová and Friml, Jiří and Simon, Sibu}, issn = {22237747}, journal = {Plants}, number = {3}, publisher = {MDPI}, title = {{Molecular evolution and diversification of proteins involved in miRNA maturation pathway}}, doi = {10.3390/plants9030299}, volume = {9}, year = {2020}, } @article{7593, abstract = {Heterozygous loss of human PAFAH1B1 (coding for LIS1) results in the disruption of neurogenesis and neuronal migration via dysregulation of microtubule (MT) stability and dynein motor function/localization that alters mitotic spindle orientation, chromosomal segregation, and nuclear migration. Recently, human induced pluripotent stem cell (iPSC) models revealed an important role for LIS1 in controlling the length of terminal cell divisions of outer radial glial (oRG) progenitors, suggesting cellular functions of LIS1 in regulating neural progenitor cell (NPC) daughter cell separation. Here we examined the late mitotic stages NPCs in vivo and mouse embryonic fibroblasts (MEFs) in vitro from Pafah1b1-deficient mutants. Pafah1b1-deficient neocortical NPCs and MEFs similarly exhibited cleavage plane displacement with mislocalization of furrow-associated markers, associated with actomyosin dysfunction and cell membrane hyper-contractility. Thus, it suggests LIS1 acts as a key molecular link connecting MTs/dynein and actomyosin, ensuring that cell membrane contractility is tightly controlled to execute proper daughter cell separation.}, author = {Moon, Hyang Mi and Hippenmeyer, Simon and Luo, Liqun and Wynshaw-Boris, Anthony}, issn = {2050-084X}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{LIS1 determines cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility}}, doi = {10.7554/elife.51512}, volume = {9}, year = {2020}, } @article{7600, abstract = {Directional intercellular transport of the phytohormone auxin mediated by PIN FORMED (PIN) efflux carriers plays essential roles in both coordinating patterning processes and integrating multiple external cues by rapidly redirecting auxin fluxes. Multilevel regulations of PIN activity under internal and external cues are complicated; however, the underlying molecular mechanism remains elusive. Here we demonstrate that 3’-Phosphoinositide-Dependent Protein Kinase1 (PDK1), which is conserved in plants and mammals, functions as a molecular hub integrating the upstream lipid signalling and the downstream substrate activity through phosphorylation. Genetic analysis uncovers that loss-of-function Arabidopsis mutant pdk1.1 pdk1.2 exhibits a plethora of abnormalities in organogenesis and growth, due to the defective PIN-dependent auxin transport. Further cellular and biochemical analyses reveal that PDK1 phosphorylates D6 Protein Kinase to facilitate its activity towards PIN proteins. Our studies establish a lipid-dependent phosphorylation cascade connecting membrane composition-based cellular signalling with plant growth and patterning by regulating morphogenetic auxin fluxes.}, author = {Tan, Shutang and Zhang, Xixi and Kong, Wei and Yang, Xiao-Li and Molnar, Gergely and Vondráková, Zuzana and Filepová, Roberta and Petrášek, Jan and Friml, Jiří and Xue, Hong-Wei}, issn = {20550278}, journal = {Nature Plants}, pages = {556--569}, publisher = {Springer Nature}, title = {{The lipid code-dependent phosphoswitch PDK1–D6PK activates PIN-mediated auxin efflux in Arabidopsis}}, doi = {10.1038/s41477-020-0648-9}, volume = {6}, year = {2020}, } @article{7603, abstract = {Plants are exposed to a variety of abiotic and biotic stresses that may result in DNA damage. Endogenous processes - such as DNA replication, DNA recombination, respiration, or photosynthesis - are also a threat to DNA integrity. It is therefore essential to understand the strategies plants have developed for DNA damage detection, signaling, and repair. Alternative splicing (AS) is a key post-transcriptional process with a role in regulation of gene expression. Recent studies demonstrate that the majority of intron-containing genes in plants are alternatively spliced, highlighting the importance of AS in plant development and stress response. Not only does AS ensure a versatile proteome and influence the abundance and availability of proteins greatly, it has also emerged as an important player in the DNA damage response (DDR) in animals. Despite extensive studies of DDR carried out in plants, its regulation at the level of AS has not been comprehensively addressed. Here, we provide some insights into the interplay between AS and DDR in plants.}, author = {Nimeth, Barbara Anna and Riegler, Stefan and Kalyna, Maria}, issn = {1664462X}, journal = {Frontiers in Plant Science}, publisher = {Frontiers}, title = {{Alternative splicing and DNA damage response in plants}}, doi = {10.3389/fpls.2020.00091}, volume = {11}, year = {2020}, } @article{7586, abstract = {CLC chloride/proton exchangers may support acidification of endolysosomes and raise their luminal Cl− concentration. Disruption of endosomal ClC‐3 causes severe neurodegeneration. To assess the importance of ClC‐3 Cl−/H+ exchange, we now generate Clcn3unc/unc mice in which ClC‐3 is converted into a Cl− channel. Unlike Clcn3−/− mice, Clcn3unc/unc mice appear normal owing to compensation by ClC‐4 with which ClC‐3 forms heteromers. ClC‐4 protein levels are strongly reduced in Clcn3−/−, but not in Clcn3unc/unc mice because ClC‐3unc binds and stabilizes ClC‐4 like wild‐type ClC‐3. Although mice lacking ClC‐4 appear healthy, its absence in Clcn3unc/unc/Clcn4−/− mice entails even stronger neurodegeneration than observed in Clcn3−/− mice. A fraction of ClC‐3 is found on synaptic vesicles, but miniature postsynaptic currents and synaptic vesicle acidification are not affected in Clcn3unc/unc or Clcn3−/− mice before neurodegeneration sets in. Both, Cl−/H+‐exchange activity and the stabilizing effect on ClC‐4, are central to the biological function of ClC‐3.}, author = {Weinert, Stefanie and Gimber, Niclas and Deuschel, Dorothea and Stuhlmann, Till and Puchkov, Dmytro and Farsi, Zohreh and Ludwig, Carmen F. and Novarino, Gaia and López-Cayuqueo, Karen I. and Planells-Cases, Rosa and Jentsch, Thomas J.}, issn = {14602075}, journal = {EMBO Journal}, publisher = {EMBO Press}, title = {{Uncoupling endosomal CLC chloride/proton exchange causes severe neurodegeneration}}, doi = {10.15252/embj.2019103358}, volume = {39}, year = {2020}, } @article{7618, abstract = {This short note aims to study quantum Hellinger distances investigated recently by Bhatia et al. (Lett Math Phys 109:1777–1804, 2019) with a particular emphasis on barycenters. We introduce the family of generalized quantum Hellinger divergences that are of the form ϕ(A,B)=Tr((1−c)A+cB−AσB), where σ is an arbitrary Kubo–Ando mean, and c∈(0,1) is the weight of σ. We note that these divergences belong to the family of maximal quantum f-divergences, and hence are jointly convex, and satisfy the data processing inequality. We derive a characterization of the barycenter of finitely many positive definite operators for these generalized quantum Hellinger divergences. We note that the characterization of the barycenter as the weighted multivariate 1/2-power mean, that was claimed in Bhatia et al. (2019), is true in the case of commuting operators, but it is not correct in the general case. }, author = {Pitrik, Jozsef and Virosztek, Daniel}, issn = {1573-0530}, journal = {Letters in Mathematical Physics}, number = {8}, pages = {2039--2052}, publisher = {Springer Nature}, title = {{Quantum Hellinger distances revisited}}, doi = {10.1007/s11005-020-01282-0}, volume = {110}, year = {2020}, } @article{7632, abstract = {The posterior parietal cortex (PPC) and frontal motor areas comprise a cortical network supporting goal-directed behaviour, with functions including sensorimotor transformations and decision making. In primates, this network links performed and observed actions via mirror neurons, which fire both when individuals perform an action and when they observe the same action performed by a conspecific. Mirror neurons are believed to be important for social learning, but it is not known whether mirror-like neurons occur in similar networks in other social species, such as rodents, or if they can be measured in such models using paradigms where observers passively view a demonstrator. Therefore, we imaged Ca2+ responses in PPC and secondary motor cortex (M2) while mice performed and observed pellet-reaching and wheel-running tasks, and found that cell populations in both areas robustly encoded several naturalistic behaviours. However, neural responses to the same set of observed actions were absent, although we verified that observer mice were attentive to performers and that PPC neurons responded reliably to visual cues. Statistical modelling also indicated that executed actions outperformed observed actions in predicting neural responses. These results raise the possibility that sensorimotor action recognition in rodents could take place outside of the parieto-frontal circuit, and underscore that detecting socially-driven neural coding depends critically on the species and behavioural paradigm used.}, author = {Tombaz, Tuce and Dunn, Benjamin A. and Hovde, Karoline and Cubero, Ryan J and Mimica, Bartul and Mamidanna, Pranav and Roudi, Yasser and Whitlock, Jonathan R.}, issn = {20452322}, journal = {Scientific reports}, number = {1}, publisher = {Springer Nature}, title = {{Action representation in the mouse parieto-frontal network}}, doi = {10.1038/s41598-020-62089-6}, volume = {10}, year = {2020}, } @article{7622, abstract = {The International Young Physicists' Tournament (IYPT) continued in 2018 in Beijing, China and 2019 in Warsaw, Poland with its 31st and 32nd editions. The IYPT is a modern scientific competition for teams of high school students, also known as the Physics World Cup. It involves long-term theoretical and experimental work focused on solving 17 publicly announced open-ended problems in teams of five. On top of that, teams have to present their solutions in front of other teams and a scientific jury, and get opposed and reviewed by their peers. Here we present a brief information about the competition with a specific focus on one of the IYPT 2018 tasks, the 'Ring Oiler'. This seemingly simple mechanical problem appeared to be of such a complexity that even the dozens of participating teams and jurying scientists were not able to solve all of its subtleties.}, author = {Plesch, Martin and Plesník, Samuel and Ruzickova, Natalia}, issn = {13616404}, journal = {European Journal of Physics}, number = {3}, publisher = {IOP Publishing}, title = {{The IYPT and the 'Ring Oiler' problem}}, doi = {10.1088/1361-6404/ab6414}, volume = {41}, year = {2020}, } @article{7623, abstract = {A two-dimensional mathematical model for cells migrating without adhesion capabilities is presented and analyzed. Cells are represented by their cortex, which is modeled as an elastic curve, subject to an internal pressure force. Net polymerization or depolymerization in the cortex is modeled via local addition or removal of material, driving a cortical flow. The model takes the form of a fully nonlinear degenerate parabolic system. An existence analysis is carried out by adapting ideas from the theory of gradient flows. Numerical simulations show that these simple rules can account for the behavior observed in experiments, suggesting a possible mechanical mechanism for adhesion-independent motility.}, author = {Jankowiak, Gaspard and Peurichard, Diane and Reversat, Anne and Schmeiser, Christian and Sixt, Michael K}, issn = {02182025}, journal = {Mathematical Models and Methods in Applied Sciences}, number = {3}, pages = {513--537}, publisher = {World Scientific}, title = {{Modeling adhesion-independent cell migration}}, doi = {10.1142/S021820252050013X}, volume = {30}, year = {2020}, } @article{7646, abstract = {In plant cells, environmental stressors promote changes in connectivity between the cortical ER and the PM. Although this process is tightly regulated in space and time, the molecular signals and structural components mediating these changes in inter-organelle communication are only starting to be characterized. In this report, we confirm the presence of a putative tethering complex containing the synaptotagmins 1 and 5 (SYT1 and SYT5) and the Ca2+ and lipid binding protein 1 (CLB1/SYT7). This complex is enriched at ER-PM contact sites (EPCS), have slow responses to changes in extracellular Ca2+, and display severe cytoskeleton-dependent rearrangements in response to the trivalent lanthanum (La3+) and gadolinium (Gd3+) rare earth elements (REEs). Although REEs are generally used as non-selective cation channel blockers at the PM, here we show that the slow internalization of REEs into the cytosol underlies the activation of the Ca2+/Calmodulin intracellular signaling, the accumulation of phosphatidylinositol-4-phosphate (PI4P) at the PM, and the cytoskeleton-dependent rearrangement of the SYT1/SYT5 EPCS complexes. We propose that the observed EPCS rearrangements act as a slow adaptive response to sustained stress conditions, and that this process involves the accumulation of stress-specific phosphoinositides species at the PM.}, author = {Lee, E and Vila Nova Santana, B and Samuels, E and Benitez-Fuente, F and Corsi, E and Botella, MA and Perez-Sancho, J and Vanneste, S and Friml, Jiří and Macho, A and Alves Azevedo, A and Rosado, A}, issn = {1460-2431}, journal = {Journal of Experimental Botany}, number = {14}, pages = {3986–3998}, publisher = {Oxford University Press}, title = {{Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis}}, doi = {10.1093/jxb/eraa138}, volume = {71}, year = {2020}, } @article{7656, abstract = {We propose that correlations among neurons are generically strong enough to organize neural activity patterns into a discrete set of clusters, which can each be viewed as a population codeword. Our reasoning starts with the analysis of retinal ganglion cell data using maximum entropy models, showing that the population is robustly in a frustrated, marginally sub-critical, or glassy, state. This leads to an argument that neural populations in many other brain areas might share this structure. Next, we use latent variable models to show that this glassy state possesses well-defined clusters of neural activity. Clusters have three appealing properties: (i) clusters exhibit error correction, i.e., they are reproducibly elicited by the same stimulus despite variability at the level of constituent neurons; (ii) clusters encode qualitatively different visual features than their constituent neurons; and (iii) clusters can be learned by downstream neural circuits in an unsupervised fashion. We hypothesize that these properties give rise to a “learnable” neural code which the cortical hierarchy uses to extract increasingly complex features without supervision or reinforcement.}, author = {Berry, Michael J. and Tkačik, Gašper}, issn = {16625188}, journal = {Frontiers in Computational Neuroscience}, publisher = {Frontiers}, title = {{Clustering of neural activity: A design principle for population codes}}, doi = {10.3389/fncom.2020.00020}, volume = {14}, year = {2020}, } @article{7638, abstract = {Following on from our recent work, we investigate a stochastic approach to non-equilibrium quantum spin systems. We show how the method can be applied to a variety of physical observables and for different initial conditions. We provide exact formulae of broad applicability for the time-dependence of expectation values and correlation functions following a quantum quench in terms of averages over classical stochastic processes. We further explore the behavior of the classical stochastic variables in the presence of dynamical quantum phase transitions, including results for their distributions and correlation functions. We provide details on the numerical solution of the associated stochastic differential equations, and examine the growth of fluctuations in the classical description. We discuss the strengths and limitations of the current implementation of the stochastic approach and the potential for further development.}, author = {De Nicola, Stefano and Doyon, B. and Bhaseen, M. J.}, issn = {17425468}, journal = {Journal of Statistical Mechanics: Theory and Experiment}, number = {1}, publisher = {IOP Publishing}, title = {{Non-equilibrium quantum spin dynamics from classical stochastic processes}}, doi = {10.1088/1742-5468/ab6093}, volume = {2020}, year = {2020}, } @article{7637, abstract = {The evolution of finitely many particles obeying Langevin dynamics is described by Dean–Kawasaki equations, a class of stochastic equations featuring a non-Lipschitz multiplicative noise in divergence form. We derive a regularised Dean–Kawasaki model based on second order Langevin dynamics by analysing a system of particles interacting via a pairwise potential. Key tools of our analysis are the propagation of chaos and Simon's compactness criterion. The model we obtain is a small-noise stochastic perturbation of the undamped McKean–Vlasov equation. We also provide a high-probability result for existence and uniqueness for our model.}, author = {Cornalba, Federico and Shardlow, Tony and Zimmer, Johannes}, issn = {13616544}, journal = {Nonlinearity}, number = {2}, pages = {864--891}, publisher = {IOP Publishing}, title = {{From weakly interacting particles to a regularised Dean-Kawasaki model}}, doi = {10.1088/1361-6544/ab5174}, volume = {33}, year = {2020}, } @article{7664, abstract = {Metabotropic γ-aminobutyric acid (GABAB) receptors contribute to the control of network activity and information processing in hippocampal circuits by regulating neuronal excitability and synaptic transmission. The dysfunction in the dentate gyrus (DG) has been implicated in Alzheimer´s disease (AD). Given the involvement of GABAB receptors in AD, to determine their subcellular localisation and possible alteration in granule cells of the DG in a mouse model of AD at 12 months of age, we used high-resolution immunoelectron microscopic analysis. Immunohistochemistry at the light microscopic level showed that the regional and cellular expression pattern of GABAB1 was similar in an AD model mouse expressing mutated human amyloid precursor protein and presenilin1 (APP/PS1) and in age-matched wild type mice. High-resolution immunoelectron microscopy revealed a distance-dependent gradient of immunolabelling for GABAB receptors, increasing from proximal to distal dendrites in both wild type and APP/PS1 mice. However, the overall density of GABAB receptors at the neuronal surface of these postsynaptic compartments of granule cells was significantly reduced in APP/PS1 mice. Parallel to this reduction in surface receptors, we found a significant increase in GABAB1 at cytoplasmic sites. GABAB receptors were also detected at presynaptic sites in the molecular layer of the DG. We also found a decrease in plasma membrane GABAB receptors in axon terminals contacting dendritic spines of granule cells, which was more pronounced in the outer than in the inner molecular layer. Altogether, our data showing post- and presynaptic reduction in surface GABAB receptors in the DG suggest the alteration of the GABAB-mediated modulation of excitability and synaptic transmission in granule cells, which may contribute to the cognitive dysfunctions in the APP/PS1 model of AD}, author = {Martín-Belmonte, Alejandro and Aguado, Carolina and Alfaro-Ruíz, Rocío and Moreno-Martínez, Ana Esther and De La Ossa, Luis and Martínez-Hernández, José and Buisson, Alain and Shigemoto, Ryuichi and Fukazawa, Yugo and Luján, Rafael}, issn = {14220067}, journal = {International journal of molecular sciences}, number = {7}, publisher = {MDPI}, title = {{Density of GABAB receptors is reduced in granule cells of the hippocampus in a mouse model of Alzheimer's disease}}, doi = {10.3390/ijms21072459}, volume = {21}, year = {2020}, } @article{7665, abstract = {Acute brain slice preparation is a powerful experimental model for investigating the characteristics of synaptic function in the brain. Although brain tissue is usually cut at ice-cold temperature (CT) to facilitate slicing and avoid neuronal damage, exposure to CT causes molecular and architectural changes of synapses. To address these issues, we investigated ultrastructural and electrophysiological features of synapses in mouse acute cerebellar slices prepared at ice-cold and physiological temperature (PT). In the slices prepared at CT, we found significant spine loss and reconstruction, synaptic vesicle rearrangement and decrease in synaptic proteins, all of which were not detected in slices prepared at PT. Consistent with these structural findings, slices prepared at PT showed higher release probability. Furthermore, preparation at PT allows electrophysiological recording immediately after slicing resulting in higher detectability of long-term depression (LTD) after motor learning compared with that at CT. These results indicate substantial advantages of the slice preparation at PT for investigating synaptic functions in different physiological conditions.}, author = {Eguchi, Kohgaku and Velicky, Philipp and Hollergschwandtner, Elena and Itakura, Makoto and Fukazawa, Yugo and Danzl, Johann G and Shigemoto, Ryuichi}, issn = {16625102}, journal = {Frontiers in Cellular Neuroscience}, publisher = {Frontiers Media}, title = {{Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions}}, doi = {10.3389/fncel.2020.00063}, volume = {14}, year = {2020}, } @article{7663, abstract = {Wood, as the most abundant carbon dioxide storing bioresource, is currently driven beyond its traditional use through creative innovations and nanotechnology. For many properties the micro- and nanostructure plays a crucial role and one key challenge is control and detection of chemical and physical processes in the confined microstructure and nanopores of the wooden cell wall. In this study, correlative Raman and atomic force microscopy show high potential for tracking in situ molecular rearrangement of wood polymers during compression. More water molecules (interpreted as wider cellulose microfibril distances) and disentangling of hemicellulose chains are detected in the opened cell wall regions, whereas an increase of lignin is revealed in the compressed areas. These results support a new more “loose” cell wall model based on flexible lignin nanodomains and advance our knowledge of the molecular reorganization during deformation of wood for optimized processing and utilization.}, author = {Felhofer, Martin and Bock, Peter and Singh, Adya and Prats Mateu, Batirtze and Zirbs, Ronald and Gierlinger, Notburga}, issn = {15306992}, journal = {Nano Letters}, number = {4}, pages = {2647--2653}, publisher = {American Chemical Society}, title = {{Wood deformation leads to rearrangement of molecules at the nanoscale}}, doi = {10.1021/acs.nanolett.0c00205}, volume = {20}, year = {2020}, } @article{7666, abstract = {Generalizing the decomposition of a connected planar graph into a tree and a dual tree, we prove a combinatorial analog of the classic Helmholtz–Hodge decomposition of a smooth vector field. Specifically, we show that for every polyhedral complex, K, and every dimension, p, there is a partition of the set of p-cells into a maximal p-tree, a maximal p-cotree, and a collection of p-cells whose cardinality is the p-th reduced Betti number of K. Given an ordering of the p-cells, this tri-partition is unique, and it can be computed by a matrix reduction algorithm that also constructs canonical bases of cycle and boundary groups.}, author = {Edelsbrunner, Herbert and Ölsböck, Katharina}, issn = {14320444}, journal = {Discrete and Computational Geometry}, pages = {759--775}, publisher = {Springer Nature}, title = {{Tri-partitions and bases of an ordered complex}}, doi = {10.1007/s00454-020-00188-x}, volume = {64}, year = {2020}, } @article{7683, abstract = {For any free oriented Borel–Moore homology theory A, we construct an associative product on the A-theory of the stack of Higgs torsion sheaves over a projective curve C. We show that the resulting algebra AHa0C admits a natural shuffle presentation, and prove it is faithful when A is replaced with usual Borel–Moore homology groups. We also introduce moduli spaces of stable triples, heavily inspired by Nakajima quiver varieties, whose A-theory admits an AHa0C-action. These triples can be interpreted as certain sheaves on PC(ωC⊕OC). In particular, we obtain an action of AHa0C on the cohomology of Hilbert schemes of points on T∗C.}, author = {Minets, Sasha}, issn = {14209020}, journal = {Selecta Mathematica, New Series}, number = {2}, publisher = {Springer Nature}, title = {{Cohomological Hall algebras for Higgs torsion sheaves, moduli of triples and sheaves on surfaces}}, doi = {10.1007/s00029-020-00553-x}, volume = {26}, year = {2020}, } @article{7672, abstract = {Large overpotentials upon discharge and charge of Li-O2 cells have motivated extensive research into heterogeneous solid electrocatalysts or non-carbon electrodes with the aim to improve rate capability, round-trip efficiency and cycle life. These features are equally governed by parasitic reactions, which are now recognized to be caused by the highly reactive singlet oxygen (1O2). However, the link between the presence of electrocatalysts and 1O2 formation in metal-O2 cells is unknown. Here, we show that, compared to pristine carbon black electrodes, a representative selection of electrocatalysts or non-carbon electrodes (noble metal, transition metal compounds) may both slightly reduce or severely increase the 1O2 formation. The individual reaction steps, where the surfaces impact the 1O2 yield are deciphered, showing that 1O2 yield from superoxide disproportionation as well as the decomposition of trace H2O2 are sensitive to catalysts. Transition metal compounds in general are prone to increase 1O2.}, author = {Samojlov, Aleksej and Schuster, David and Kahr, Jürgen and Freunberger, Stefan Alexander}, journal = {Electrochimica Acta}, number = {12}, publisher = {Elsevier}, title = {{Surface and catalyst driven singlet oxygen formation in Li-O2 cells}}, doi = {10.1016/j.electacta.2020.137175}, volume = {362}, year = {2020}, } @article{7684, author = {Gridchyn, Igor and Schönenberger, Philipp and O'Neill, Joseph and Csicsvari, Jozsef L}, issn = {10974199}, journal = {Neuron}, number = {2}, pages = {291--300.e6}, publisher = {Elsevier}, title = {{Assembly-specific disruption of hippocampal replay leads to selective memory deficit}}, doi = {10.1016/j.neuron.2020.01.021}, volume = {106}, year = {2020}, } @article{7788, abstract = {Mutations in NDUFS4, which encodes an accessory subunit of mitochondrial oxidative phosphorylation (OXPHOS) complex I (CI), induce Leigh syndrome (LS). LS is a poorly understood pediatric disorder featuring brain-specific anomalies and early death. To study the LS pathomechanism, we here compared OXPHOS proteomes between various Ndufs4−/− mouse tissues. Ndufs4−/− animals displayed significantly lower CI subunit levels in brain/diaphragm relative to other tissues (liver/heart/kidney/skeletal muscle), whereas other OXPHOS subunit levels were not reduced. Absence of NDUFS4 induced near complete absence of the NDUFA12 accessory subunit, a 50% reduction in other CI subunit levels, and an increase in specific CI assembly factors. Among the latter, NDUFAF2 was most highly increased. Regarding NDUFS4, NDUFA12 and NDUFAF2, identical results were obtained in Ndufs4−/− mouse embryonic fibroblasts (MEFs) and NDUFS4-mutated LS patient cells. Ndufs4−/− MEFs contained active CI in situ but blue-native-PAGE highlighted that NDUFAF2 attached to an inactive CI subcomplex (CI-830) and inactive assemblies of higher MW. In NDUFA12-mutated LS patient cells, NDUFA12 absence did not reduce NDUFS4 levels but triggered NDUFAF2 association to active CI. BN-PAGE revealed no such association in LS patient fibroblasts with mutations in other CI subunit-encoding genes where NDUFAF2 was attached to CI-830 (NDUFS1, NDUFV1 mutation) or not detected (NDUFS7 mutation). Supported by enzymological and CI in silico structural analysis, we conclude that absence of NDUFS4 induces near complete absence of NDUFA12 but not vice versa, and that NDUFAF2 stabilizes active CI in Ndufs4−/− mice and LS patient cells, perhaps in concert with mitochondrial inner membrane lipids.}, author = {Adjobo-Hermans, Merel J.W. and De Haas, Ria and Willems, Peter H.G.M. and Wojtala, Aleksandra and Van Emst-De Vries, Sjenet E. and Wagenaars, Jori A. and Van Den Brand, Mariel and Rodenburg, Richard J. and Smeitink, Jan A.M. and Nijtmans, Leo G. and Sazanov, Leonid A and Wieckowski, Mariusz R. and Koopman, Werner J.H.}, issn = {18792650}, journal = {Biochimica et Biophysica Acta - Bioenergetics}, number = {8}, publisher = {Elsevier}, title = {{NDUFS4 deletion triggers loss of NDUFA12 in Ndufs4−/− mice and Leigh syndrome patients: A stabilizing role for NDUFAF2}}, doi = {10.1016/j.bbabio.2020.148213}, volume = {1861}, year = {2020}, } @article{7789, abstract = {During embryonic and postnatal development, organs and tissues grow steadily to achieve their final size at the end of puberty. However, little is known about the cellular dynamics that mediate postnatal growth. By combining in vivo clonal lineage tracing, proliferation kinetics, single-cell transcriptomics, andin vitro micro-pattern experiments, we resolved the cellular dynamics taking place during postnatal skin epidermis expansion. Our data revealed that harmonious growth is engineered by a single population of developmental progenitors presenting a fixed fate imbalance of self-renewing divisions with an ever-decreasing proliferation rate. Single-cell RNA sequencing revealed that epidermal developmental progenitors form a more uniform population compared with adult stem and progenitor cells. Finally, we found that the spatial pattern of cell division orientation is dictated locally by the underlying collagen fiber orientation. Our results uncover a simple design principle of organ growth where progenitors and differentiated cells expand in harmony with their surrounding tissues.}, author = {Dekoninck, Sophie and Hannezo, Edouard B and Sifrim, Alejandro and Miroshnikova, Yekaterina A. and Aragona, Mariaceleste and Malfait, Milan and Gargouri, Souhir and De Neunheuser, Charlotte and Dubois, Christine and Voet, Thierry and Wickström, Sara A. and Simons, Benjamin D. and Blanpain, Cédric}, issn = {10974172}, journal = {Cell}, number = {3}, pages = {604--620.e22}, publisher = {Elsevier}, title = {{Defining the design principles of skin epidermis postnatal growth}}, doi = {10.1016/j.cell.2020.03.015}, volume = {181}, year = {2020}, } @article{7793, abstract = {Hormonal signalling in animals often involves direct transcription factor-hormone interactions that modulate gene expression. In contrast, plant hormone signalling is most commonly based on de-repression via the degradation of transcriptional repressors. Recently, we uncovered a non-canonical signalling mechanism for the plant hormone auxin whereby auxin directly affects the activity of the atypical auxin response factor (ARF), ETTIN towards target genes without the requirement for protein degradation. Here we show that ETTIN directly binds auxin, leading to dissociation from co-repressor proteins of the TOPLESS/TOPLESS-RELATED family followed by histone acetylation and induction of gene expression. This mechanism is reminiscent of animal hormone signalling as it affects the activity towards regulation of target genes and provides the first example of a DNA-bound hormone receptor in plants. Whilst auxin affects canonical ARFs indirectly by facilitating degradation of Aux/IAA repressors, direct ETTIN-auxin interactions allow switching between repressive and de-repressive chromatin states in an instantly-reversible manner.}, author = {Kuhn, André and Ramans Harborough, Sigurd and McLaughlin, Heather M and Natarajan, Bhavani and Verstraeten, Inge and Friml, Jiří and Kepinski, Stefan and Østergaard, Lars}, issn = {2050-084X}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{Direct ETTIN-auxin interaction controls chromatin states in gynoecium development}}, doi = {10.7554/elife.51787}, volume = {9}, year = {2020}, } @article{7790, abstract = {We prove a lower bound for the free energy (per unit volume) of the two-dimensional Bose gas in the thermodynamic limit. We show that the free energy at density 𝜌 and inverse temperature 𝛽 differs from the one of the noninteracting system by the correction term 𝜋𝜌𝜌𝛽𝛽 . Here, is the scattering length of the interaction potential, and 𝛽 is the inverse Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity. The result is valid in the dilute limit 𝜌 and if 𝛽𝜌 .}, author = {Deuchert, Andreas and Mayer, Simon and Seiringer, Robert}, issn = {20505094}, journal = {Forum of Mathematics, Sigma}, publisher = {Cambridge University Press}, title = {{The free energy of the two-dimensional dilute Bose gas. I. Lower bound}}, doi = {10.1017/fms.2020.17}, volume = {8}, year = {2020}, } @article{7805, abstract = {Plants as non-mobile organisms constantly integrate varying environmental signals to flexibly adapt their growth and development. Local fluctuations in water and nutrient availability, sudden changes in temperature or other abiotic and biotic stresses can trigger changes in the growth of plant organs. Multiple mutually interconnected hormonal signaling cascades act as essential endogenous translators of these exogenous signals in the adaptive responses of plants. Although the molecular backbones of hormone transduction pathways have been identified, the mechanisms underlying their interactions are largely unknown. Here, using genome wide transcriptome profiling we identify an auxin and cytokinin cross-talk component; SYNERGISTIC ON AUXIN AND CYTOKININ 1 (SYAC1), whose expression in roots is strictly dependent on both of these hormonal pathways. We show that SYAC1 is a regulator of secretory pathway, whose enhanced activity interferes with deposition of cell wall components and can fine-tune organ growth and sensitivity to soil pathogens.}, author = {Hurny, Andrej and Cuesta, Candela and Cavallari, Nicola and Ötvös, Krisztina and Duclercq, Jerome and Dokládal, Ladislav and Montesinos López, Juan C and Gallemi, Marçal and Semeradova, Hana and Rauter, Thomas and Stenzel, Irene and Persiau, Geert and Benade, Freia and Bhalearo, Rishikesh and Sýkorová, Eva and Gorzsás, András and Sechet, Julien and Mouille, Gregory and Heilmann, Ingo and De Jaeger, Geert and Ludwig-Müller, Jutta and Benková, Eva}, issn = {20411723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance}}, doi = {10.1038/s41467-020-15895-5}, volume = {11}, year = {2020}, } @article{7882, abstract = {A few-body cluster is a building block of a many-body system in a gas phase provided the temperature at most is of the order of the binding energy of this cluster. Here we illustrate this statement by considering a system of tubes filled with dipolar distinguishable particles. We calculate the partition function, which determines the probability to find a few-body cluster at a given temperature. The input for our calculations—the energies of few-body clusters—is estimated using the harmonic approximation. We first describe and demonstrate the validity of our numerical procedure. Then we discuss the results featuring melting of the zero-temperature many-body state into a gas of free particles and few-body clusters. For temperature higher than its binding energy threshold, the dimers overwhelmingly dominate the ensemble, where the remaining probability is in free particles. At very high temperatures free (harmonic oscillator trap-bound) particle dominance is eventually reached. This structure evolution appears both for one and two particles in each layer providing crucial information about the behavior of ultracold dipolar gases. The investigation addresses the transition region between few- and many-body physics as a function of temperature using a system of ten dipoles in five tubes.}, author = {Armstrong, Jeremy R. and Jensen, Aksel S. and Volosniev, Artem and Zinner, Nikolaj T.}, issn = {22277390}, journal = {Mathematics}, number = {4}, publisher = {MDPI}, title = {{Clusters in separated tubes of tilted dipoles}}, doi = {10.3390/math8040484}, volume = {8}, year = {2020}, } @article{7804, abstract = {Besides pro-inflammatory roles, the ancient cytokine interleukin-17 (IL-17) modulates neural circuit function. We investigate IL-17 signaling in neurons, and the extent it can alter organismal phenotypes. We combine immunoprecipitation and mass spectrometry to biochemically characterize endogenous signaling complexes that function downstream of IL-17 receptors in C. elegans neurons. We identify the paracaspase MALT-1 as a critical output of the pathway. MALT1 mediates signaling from many immune receptors in mammals, but was not previously implicated in IL-17 signaling or nervous system function. C. elegans MALT-1 forms a complex with homologs of Act1 and IRAK and appears to function both as a scaffold and a protease. MALT-1 is expressed broadly in the C. elegans nervous system, and neuronal IL-17–MALT-1 signaling regulates multiple phenotypes, including escape behavior, associative learning, immunity and longevity. Our data suggest MALT1 has an ancient role modulating neural circuit function downstream of IL-17 to remodel physiology and behavior.}, author = {Flynn, Sean M. and Chen, Changchun and Artan, Murat and Barratt, Stephen and Crisp, Alastair and Nelson, Geoffrey M. and Peak-Chew, Sew Yeu and Begum, Farida and Skehel, Mark and De Bono, Mario}, issn = {20411723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity}}, doi = {10.1038/s41467-020-15872-y}, volume = {11}, year = {2020}, } @article{7875, abstract = {Cells navigating through complex tissues face a fundamental challenge: while multiple protrusions explore different paths, the cell needs to avoid entanglement. How a cell surveys and then corrects its own shape is poorly understood. Here, we demonstrate that spatially distinct microtubule dynamics regulate amoeboid cell migration by locally promoting the retraction of protrusions. In migrating dendritic cells, local microtubule depolymerization within protrusions remote from the microtubule organizing center triggers actomyosin contractility controlled by RhoA and its exchange factor Lfc. Depletion of Lfc leads to aberrant myosin localization, thereby causing two effects that rate-limit locomotion: (1) impaired cell edge coordination during path finding and (2) defective adhesion resolution. Compromised shape control is particularly hindering in geometrically complex microenvironments, where it leads to entanglement and ultimately fragmentation of the cell body. We thus demonstrate that microtubules can act as a proprioceptive device: they sense cell shape and control actomyosin retraction to sustain cellular coherence.}, author = {Kopf, Aglaja and Renkawitz, Jörg and Hauschild, Robert and Girkontaite, Irute and Tedford, Kerry and Merrin, Jack and Thorn-Seshold, Oliver and Trauner, Dirk and Häcker, Hans and Fischer, Klaus Dieter and Kiermaier, Eva and Sixt, Michael K}, issn = {1540-8140}, journal = {The Journal of Cell Biology}, number = {6}, publisher = {Rockefeller University Press}, title = {{Microtubules control cellular shape and coherence in amoeboid migrating cells}}, doi = {10.1083/jcb.201907154}, volume = {219}, year = {2020}, } @article{7888, abstract = {Embryonic stem cell cultures are thought to self-organize into embryoid bodies, able to undergo symmetry-breaking, germ layer specification and even morphogenesis. Yet, it is unclear how to reconcile this remarkable self-organization capacity with classical experiments demonstrating key roles for extrinsic biases by maternal factors and/or extraembryonic tissues in embryogenesis. Here, we show that zebrafish embryonic tissue explants, prepared prior to germ layer induction and lacking extraembryonic tissues, can specify all germ layers and form a seemingly complete mesendoderm anlage. Importantly, explant organization requires polarized inheritance of maternal factors from dorsal-marginal regions of the blastoderm. Moreover, induction of endoderm and head-mesoderm, which require peak Nodal-signaling levels, is highly variable in explants, reminiscent of embryos with reduced Nodal signals from the extraembryonic tissues. Together, these data suggest that zebrafish explants do not undergo bona fide self-organization, but rather display features of genetically encoded self-assembly, where intrinsic genetic programs control the emergence of order.}, author = {Schauer, Alexandra and Nunes Pinheiro, Diana C and Hauschild, Robert and Heisenberg, Carl-Philipp J}, issn = {2050-084X}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{Zebrafish embryonic explants undergo genetically encoded self-assembly}}, doi = {10.7554/elife.55190}, volume = {9}, year = {2020}, } @article{7877, abstract = {The NIPBL/MAU2 heterodimer loads cohesin onto chromatin. Mutations inNIPBLaccount for most cases ofthe rare developmental disorder Cornelia de Lange syndrome (CdLS). Here we report aMAU2 variant causing CdLS, a deletion of seven amino acids that impairs the interaction between MAU2 and the NIPBL N terminus.Investigating this interaction, we discovered that MAU2 and the NIPBL N terminus are largely dispensable fornormal cohesin and NIPBL function in cells with a NIPBL early truncating mutation. Despite a predicted fataloutcome of an out-of-frame single nucleotide duplication inNIPBL, engineered in two different cell lines,alternative translation initiation yields a form of NIPBL missing N-terminal residues. This form cannot interactwith MAU2, but binds DNA and mediates cohesin loading. Altogether, our work reveals that cohesin loading can occur independently of functional NIPBL/MAU2 complexes and highlights a novel mechanism protectiveagainst out-of-frame mutations that is potentially relevant for other genetic conditions.}, author = {Parenti, Ilaria and Diab, Farah and Gil, Sara Ruiz and Mulugeta, Eskeatnaf and Casa, Valentina and Berutti, Riccardo and Brouwer, Rutger W.W. and Dupé, Valerie and Eckhold, Juliane and Graf, Elisabeth and Puisac, Beatriz and Ramos, Feliciano and Schwarzmayr, Thomas and Gines, Macarena Moronta and Van Staveren, Thomas and Van Ijcken, Wilfred F.J. and Strom, Tim M. and Pié, Juan and Watrin, Erwan and Kaiser, Frank J. and Wendt, Kerstin S.}, issn = {22111247}, journal = {Cell Reports}, number = {7}, publisher = {Elsevier}, title = {{MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome}}, doi = {10.1016/j.celrep.2020.107647}, volume = {31}, year = {2020}, } @article{7878, abstract = {Type 1 metabotropic glutamate receptors (mGluR1s) are key elements in neuronal signaling. While their function is well documented in slices, requirements for their activation in vivo are poorly understood. We examine this question in adult mice in vivo using 2-photon imaging of cerebellar molecular layer interneurons (MLIs) expressing GCaMP. In anesthetized mice, parallel fiber activation evokes beam-like Cai rises in postsynaptic MLIs which depend on co-activation of mGluR1s and ionotropic glutamate receptors (iGluRs). In awake mice, blocking mGluR1 decreases Cai rises associated with locomotion. In vitro studies and freeze-fracture electron microscopy show that the iGluR-mGluR1 interaction is synergistic and favored by close association of the two classes of receptors. Altogether our results suggest that mGluR1s, acting in synergy with iGluRs, potently contribute to processing cerebellar neuronal signaling under physiological conditions.}, author = {Bao, Jin and Graupner, Michael and Astorga, Guadalupe and Collin, Thibault and Jalil, Abdelali and Indriati, Dwi Wahyu and Bradley, Jonathan and Shigemoto, Ryuichi and Llano, Isabel}, issn = {2050084X}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo}}, doi = {10.7554/eLife.56839}, volume = {9}, year = {2020}, } @article{7880, abstract = {Following its evoked release, dopamine (DA) signaling is rapidly terminated by presynaptic reuptake, mediated by the cocaine-sensitive DA transporter (DAT). DAT surface availability is dynamically regulated by endocytic trafficking, and direct protein kinase C (PKC) activation acutely diminishes DAT surface expression by accelerating DAT internalization. Previous cell line studies demonstrated that PKC-stimulated DAT endocytosis requires both Ack1 inactivation, which releases a DAT-specific endocytic brake, and the neuronal GTPase, Rit2, which binds DAT. However, it is unknown whether Rit2 is required for PKC-stimulated DAT endocytosis in DAergic terminals or whether there are region- and/or sex-dependent differences in PKC-stimulated DAT trafficking. Moreover, the mechanisms by which Rit2 controls PKC-stimulated DAT endocytosis are unknown. Here, we directly examined these important questions. Ex vivo studies revealed that PKC activation acutely decreased DAT surface expression selectively in ventral, but not dorsal, striatum. AAV-mediated, conditional Rit2 knockdown in DAergic neurons impacted baseline DAT surface:intracellular distribution in DAergic terminals from female ventral, but not dorsal, striatum. Further, Rit2 was required for PKC-stimulated DAT internalization in both male and female ventral striatum. FRET and surface pulldown studies in cell lines revealed that PKC activation drives DAT-Rit2 surface dissociation and that the DAT N terminus is required for both PKC-mediated DAT-Rit2 dissociation and DAT internalization. Finally, we found that Rit2 and Ack1 independently converge on DAT to facilitate PKC-stimulated DAT endocytosis. Together, our data provide greater insight into mechanisms that mediate PKC-regulated DAT internalization and reveal unexpected region-specific differences in PKC-stimulated DAT trafficking in bona fide DAergic terminals. }, author = {Fagan, Rita R. and Kearney, Patrick J. and Sweeney, Carolyn G. and Luethi, Dino and Schoot Uiterkamp, Florianne E and Schicker, Klaus and Alejandro, Brian S. and O'Connor, Lauren C. and Sitte, Harald H. and Melikian, Haley E.}, issn = {1083351X}, journal = {Journal of Biological Chemistry}, number = {16}, pages = {5229--5244}, publisher = {ASBMB Publications}, title = {{Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact}}, doi = {10.1074/jbc.RA120.012628}, volume = {295}, year = {2020}, } @article{7876, abstract = {In contrast to lymph nodes, the lymphoid regions of the spleen—the white pulp—are located deep within the organ, yielding the trafficking paths of T cells in the white pulp largely invisible. In an intravital microscopy tour de force reported in this issue of Immunity, Chauveau et al. show that T cells perform unidirectional, perivascular migration through the enigmatic marginal zone bridging channels. }, author = {Sixt, Michael K and Lämmermann, Tim}, issn = {10974180}, journal = {Immunity}, number = {5}, pages = {721--723}, publisher = {Elsevier}, title = {{T cells: Bridge-and-channel commute to the white pulp}}, doi = {10.1016/j.immuni.2020.04.020}, volume = {52}, year = {2020}, } @article{7909, abstract = {Cell migration entails networks and bundles of actin filaments termed lamellipodia and microspikes or filopodia, respectively, as well as focal adhesions, all of which recruit Ena/VASP family members hitherto thought to antagonize efficient cell motility. However, we find these proteins to act as positive regulators of migration in different murine cell lines. CRISPR/Cas9-mediated loss of Ena/VASP proteins reduced lamellipodial actin assembly and perturbed lamellipodial architecture, as evidenced by changed network geometry as well as reduction of filament length and number that was accompanied by abnormal Arp2/3 complex and heterodimeric capping protein accumulation. Loss of Ena/VASP function also abolished the formation of microspikes normally embedded in lamellipodia, but not of filopodia capable of emanating without lamellipodia. Ena/VASP-deficiency also impaired integrin-mediated adhesion accompanied by reduced traction forces exerted through these structures. Our data thus uncover novel Ena/VASP functions of these actin polymerases that are fully consistent with their promotion of cell migration.}, author = {Damiano-Guercio, Julia and Kurzawa, Laëtitia and Müller, Jan and Dimchev, Georgi A and Schaks, Matthias and Nemethova, Maria and Pokrant, Thomas and Brühmann, Stefan and Linkner, Joern and Blanchoin, Laurent and Sixt, Michael K and Rottner, Klemens and Faix, Jan}, issn = {2050084X}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion}}, doi = {10.7554/eLife.55351}, volume = {9}, year = {2020}, } @article{7908, abstract = {Volatile anesthetics are widely used for surgery, but neuronal mechanisms of anesthesia remain unidentified. At the calyx of Held in brainstem slices from rats of either sex, isoflurane at clinical doses attenuated EPSCs by decreasing the release probability and the number of readily releasable vesicles. In presynaptic recordings of Ca2+ currents and exocytic capacitance changes, isoflurane attenuated exocytosis by inhibiting Ca2+ currents evoked by a short presynaptic depolarization, whereas it inhibited exocytosis evoked by a prolonged depolarization via directly blocking exocytic machinery downstream of Ca2+ influx. Since the length of presynaptic depolarization can simulate the frequency of synaptic inputs, isoflurane anesthesia is likely mediated by distinct dual mechanisms, depending on input frequencies. In simultaneous presynaptic and postsynaptic action potential recordings, isoflurane impaired the fidelity of repetitive spike transmission, more strongly at higher frequencies. Furthermore, in the cerebrum of adult mice, isoflurane inhibited monosynaptic corticocortical spike transmission, preferentially at a higher frequency. We conclude that dual presynaptic mechanisms operate for the anesthetic action of isoflurane, of which direct inhibition of exocytic machinery plays a low-pass filtering role in spike transmission at central excitatory synapses.}, author = {Wang, Han Ying and Eguchi, Kohgaku and Yamashita, Takayuki and Takahashi, Tomoyuki}, issn = {15292401}, journal = {Journal of Neuroscience}, number = {21}, pages = {4103--4115}, publisher = {Society for Neuroscience}, title = {{Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms}}, doi = {10.1523/JNEUROSCI.2946-19.2020}, volume = {40}, year = {2020}, } @article{7931, abstract = {In the course of sample preparation for Next Generation Sequencing (NGS), DNA is fragmented by various methods. Fragmentation shows a persistent bias with regard to the cleavage rates of various dinucleotides. With the exception of CpG dinucleotides the previously described biases were consistent with results of the DNA cleavage in solution. Here we computed cleavage rates of all dinucleotides including the methylated CpG and unmethylated CpG dinucleotides using data of the Whole Genome Sequencing datasets of the 1000 Genomes project. We found that the cleavage rate of CpG is significantly higher for the methylated CpG dinucleotides. Using this information, we developed a classifier for distinguishing cancer and healthy tissues based on their CpG islands statuses of the fragmentation. A simple Support Vector Machine classifier based on this algorithm shows an accuracy of 84%. The proposed method allows the detection of epigenetic markers purely based on mechanochemical DNA fragmentation, which can be detected by a simple analysis of the NGS sequencing data.}, author = {Uroshlev, Leonid A. and Abdullaev, Eldar T. and Umarova, Iren R. and Il’Icheva, Irina A. and Panchenko, Larisa A. and Polozov, Robert V. and Kondrashov, Fyodor and Nechipurenko, Yury D. and Grokhovsky, Sergei L.}, issn = {20452322}, journal = {Scientific Reports}, publisher = {Springer Nature}, title = {{A method for identification of the methylation level of CpG islands from NGS data}}, doi = {10.1038/s41598-020-65406-1}, volume = {10}, year = {2020}, } @article{7933, abstract = {We study a mobile quantum impurity, possessing internal rotational degrees of freedom, confined to a ring in the presence of a many-particle bosonic bath. By considering the recently introduced rotating polaron problem, we define the Hamiltonian and examine the energy spectrum. The weak-coupling regime is studied by means of a variational ansatz in the truncated Fock space. The corresponding spectrum indicates that there emerges a coupling between the internal and orbital angular momenta of the impurity as a consequence of the phonon exchange. We interpret the coupling as a phonon-mediated spin-orbit coupling and quantify it by using a correlation function between the internal and the orbital angular momentum operators. The strong-coupling regime is investigated within the Pekar approach, and it is shown that the correlation function of the ground state shows a kink at a critical coupling, that is explained by a sharp transition from the noninteracting state to the states that exhibit strong interaction with the surroundings. The results might find applications in such fields as spintronics or topological insulators where spin-orbit coupling is of crucial importance.}, author = {Maslov, Mikhail and Lemeshko, Mikhail and Yakaboylu, Enderalp}, issn = {24699969}, journal = {Physical Review B}, number = {18}, publisher = {American Physical Society}, title = {{Synthetic spin-orbit coupling mediated by a bosonic environment}}, doi = {10.1103/PhysRevB.101.184104}, volume = {101}, year = {2020}, } @article{7942, abstract = {An understanding of the missing antinodal electronic excitations in the pseudogap state is essential for uncovering the physics of the underdoped cuprate high-temperature superconductors1,2,3,4,5,6. The majority of high-temperature experiments performed thus far, however, have been unable to discern whether the antinodal states are rendered unobservable due to their damping or whether they vanish due to their gapping7,8,9,10,11,12,13,14,15,16,17,18. Here, we distinguish between these two scenarios by using quantum oscillations to examine whether the small Fermi surface pocket, found to occupy only 2% of the Brillouin zone in the underdoped cuprates19,20,21,22,23,24, exists in isolation against a majority of completely gapped density of states spanning the antinodes, or whether it is thermodynamically coupled to a background of ungapped antinodal states. We find that quantum oscillations associated with the small Fermi surface pocket exhibit a signature sawtooth waveform characteristic of an isolated two-dimensional Fermi surface pocket25,26,27,28,29,30,31,32. This finding reveals that the antinodal states are destroyed by a hard gap that extends over the majority of the Brillouin zone, placing strong constraints on a drastic underlying origin of quasiparticle disappearance over almost the entire Brillouin zone in the pseudogap regime7,8,9,10,11,12,13,14,15,16,17,18.}, author = {Hartstein, Máté and Hsu, Yu Te and Modic, Kimberly A and Porras, Juan and Loew, Toshinao and Tacon, Matthieu Le and Zuo, Huakun and Wang, Jinhua and Zhu, Zengwei and Chan, Mun K. and Mcdonald, Ross D. and Lonzarich, Gilbert G. and Keimer, Bernhard and Sebastian, Suchitra E. and Harrison, Neil}, issn = {17452481}, journal = {Nature Physics}, pages = {841--847}, publisher = {Springer Nature}, title = {{Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors}}, doi = {10.1038/s41567-020-0910-0}, volume = {16}, year = {2020}, } @article{7948, abstract = {In agricultural systems, nitrate is the main source of nitrogen available for plants. Besides its role as a nutrient, nitrate has been shown to act as a signal molecule for plant growth, development and stress responses. In Arabidopsis, the NRT1.1 nitrate transceptor represses lateral root (LR) development at low nitrate availability by promoting auxin basipetal transport out of the LR primordia (LRPs). In addition, our present study shows that NRT1.1 acts as a negative regulator of the TAR2 auxin biosynthetic gene expression in the root stele. This is expected to repress local auxin biosynthesis and thus to reduce acropetal auxin supply to the LRPs. Moreover, NRT1.1 also negatively affects expression of the LAX3 auxin influx carrier, thus preventing cell wall remodeling required for overlying tissues separation during LRP emergence. Both NRT1.1-mediated repression of TAR2 and LAX3 are suppressed at high nitrate availability, resulting in the nitrate induction of TAR2 and LAX3 expression that is required for optimal stimulation of LR development by nitrate. Altogether, our results indicate that the NRT1.1 transceptor coordinately controls several crucial auxin-associated processes required for LRP development, and as a consequence that NRT1.1 plays a much more integrated role than previously anticipated in regulating the nitrate response of root system architecture.}, author = {Maghiaoui, A and Bouguyon, E and Cuesta, Candela and Perrine-Walker, F and Alcon, C and Krouk, G and Benková, Eva and Nacry, P and Gojon, A and Bach, L}, issn = {1460-2431}, journal = {Journal of Experimental Botany}, number = {15}, pages = {4480--4494}, publisher = {Oxford University Press}, title = {{The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis and transport to regulate root branching in response to nitrate}}, doi = {10.1093/jxb/eraa242}, volume = {71}, year = {2020}, } @article{7940, abstract = {We prove that the Yangian associated to an untwisted symmetric affine Kac–Moody Lie algebra is isomorphic to the Drinfeld double of a shuffle algebra. The latter is constructed in [YZ14] as an algebraic formalism of cohomological Hall algebras. As a consequence, we obtain the Poincare–Birkhoff–Witt (PBW) theorem for this class of affine Yangians. Another independent proof of the PBW theorem is given recently by Guay, Regelskis, and Wendlandt [GRW18].}, author = {Yang, Yaping and Zhao, Gufang}, issn = {1531586X}, journal = {Transformation Groups}, pages = {1371--1385}, publisher = {Springer Nature}, title = {{The PBW theorem for affine Yangians}}, doi = {10.1007/s00031-020-09572-6}, volume = {25}, year = {2020}, } @misc{9708, abstract = {This research data supports 'Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors'. A Readme file for plotting each figure is provided.}, author = {Hartstein, Mate and Hsu, Yu-Te and Modic, Kimberly A and Porras, Juan and Loew, Toshinao and Le Tacon, Matthieu and Zuo, Huakun and Wang, Jinhua and Zhu, Zengwei and Chan, Mun and McDonald, Ross and Lonzarich, Gilbert and Keimer, Bernhard and Sebastian, Suchitra and Harrison, Neil}, publisher = {Apollo - University of Cambridge}, title = {{Accompanying dataset for 'Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors'}}, doi = {10.17863/cam.50169}, year = {2020}, } @inproceedings{7955, abstract = {Simple stochastic games are turn-based 2½-player games with a reachability objective. The basic question asks whether one player can ensure reaching a given target with at least a given probability. A natural extension is games with a conjunction of such conditions as objective. Despite a plethora of recent results on the analysis of systems with multiple objectives, the decidability of this basic problem remains open. In this paper, we present an algorithm approximating the Pareto frontier of the achievable values to a given precision. Moreover, it is an anytime algorithm, meaning it can be stopped at any time returning the current approximation and its error bound.}, author = {Ashok, Pranav and Chatterjee, Krishnendu and Kretinsky, Jan and Weininger, Maximilian and Winkler, Tobias}, booktitle = {Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science }, isbn = {9781450371049}, location = {Saarbrücken, Germany}, pages = {102--115}, publisher = {Association for Computing Machinery}, title = {{Approximating values of generalized-reachability stochastic games}}, doi = {10.1145/3373718.3394761}, 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}, } @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{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}, } @misc{8809, 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 Rafajlovic, Marina and Westram, Anja M and Johannesson, Kerstin and Butlin, Roger}, publisher = {Dryad}, title = {{Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina}}, doi = {10.5061/dryad.qrfj6q5cn}, 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{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{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{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}, } @misc{9326, abstract = {The mitochondrial respiratory chain, formed by five protein complexes, utilizes energy from catabolic processes to synthesize ATP. Complex I, the first and the largest protein complex of the chain, harvests electrons from NADH to reduce quinone, while pumping protons across the mitochondrial membrane. Detailed knowledge of the working principle of such coupled charge-transfer processes remains, however, fragmentary due to bottlenecks in understanding redox-driven conformational transitions and their interplay with the hydrated proton pathways. Complex I from Thermus thermophilus encases 16 subunits with nine iron–sulfur clusters, reduced by electrons from NADH. Here, employing the latest crystal structure of T. thermophilus complex I, we have used microsecond-scale molecular dynamics simulations to study the chemo-mechanical coupling between redox changes of the iron–sulfur clusters and conformational transitions across complex I. First, we identify the redox switches within complex I, which allosterically couple the dynamics of the quinone binding pocket to the site of NADH reduction. Second, our free-energy calculations reveal that the affinity of the quinone, specifically menaquinone, for the binding-site is higher than that of its reduced, menaquinol forma design essential for menaquinol release. Remarkably, the barriers to diffusive menaquinone dynamics are lesser than that of the more ubiquitous ubiquinone, and the naphthoquinone headgroup of the former furnishes stronger binding interactions with the pocket, favoring menaquinone for charge transport in T. thermophilus. Our computations are consistent with experimentally validated mutations and hierarchize the key residues into three functional classes, identifying new mutation targets. Third, long-range hydrogen-bond networks connecting the quinone-binding site to the transmembrane subunits are found to be responsible for proton pumping. Put together, the simulations reveal the molecular design principles linking redox reactions to quinone turnover to proton translocation in complex I.}, author = {Gupta, Chitrak and Khaniya, Umesh and Chan, Chun and Dehez, Francois and Shekhar, Mrinal and Gunner, M. R. and Sazanov, Leonid A and Chipot, Christophe and Singharoy, Abhishek}, publisher = {American Chemical Society}, title = {{Charge transfer and chemo-mechanical coupling in respiratory complex I}}, doi = {10.1021/jacs.9b13450.s002}, 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{8093, abstract = {Background: The activation of the EGFR/Ras-signalling pathway in tumour cells induces a distinct chemokine repertoire, which in turn modulates the tumour microenvironment. Methods: The effects of EGFR/Ras on the expression and translation of CCL20 were analysed in a large set of epithelial cancer cell lines and tumour tissues by RT-qPCR and ELISA in vitro. CCL20 production was verified by immunohistochemistry in different tumour tissues and correlated with clinical data. The effects of CCL20 on endothelial cell migration and tumour-associated vascularisation were comprehensively analysed with chemotaxis assays in vitro and in CCR6-deficient mice in vivo. Results: Tumours facilitate progression by the EGFR/Ras-induced production of CCL20. Expression of the chemokine CCL20 in tumours correlates with advanced tumour stage, increased lymph node metastasis and decreased survival in patients. Microvascular endothelial cells abundantly express the specific CCL20 receptor CCR6. CCR6 signalling in endothelial cells induces angiogenesis. CCR6-deficient mice show significantly decreased tumour growth and tumour-associated vascularisation. The observed phenotype is dependent on CCR6 deficiency in stromal cells but not within the immune system. Conclusion: We propose that the chemokine axis CCL20–CCR6 represents a novel and promising target to interfere with the tumour microenvironment, and opens an innovative multimodal strategy for cancer therapy.}, 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 = {1532-1827}, 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}, } @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}, } @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}, } @article{8133, abstract = {The molecular factors which control circulating levels of inflammatory proteins are not well understood. Furthermore, association studies between molecular probes and human traits are often performed by linear model-based methods which may fail to account for complex structure and interrelationships within molecular datasets.In this study, we perform genome- and epigenome-wide association studies (GWAS/EWAS) on the levels of 70 plasma-derived inflammatory protein biomarkers in healthy older adults (Lothian Birth Cohort 1936; n = 876; Olink® inflammation panel). We employ a Bayesian framework (BayesR+) which can account for issues pertaining to data structure and unknown confounding variables (with sensitivity analyses using ordinary least squares- (OLS) and mixed model-based approaches). We identified 13 SNPs associated with 13 proteins (n = 1 SNP each) concordant across OLS and Bayesian methods. We identified 3 CpG sites spread across 3 proteins (n = 1 CpG each) that were concordant across OLS, mixed-model and Bayesian analyses. Tagged genetic variants accounted for up to 45% of variance in protein levels (for MCP2, 36% of variance alone attributable to 1 polymorphism). Methylation data accounted for up to 46% of variation in protein levels (for CXCL10). Up to 66% of variation in protein levels (for VEGFA) was explained using genetic and epigenetic data combined. We demonstrated putative causal relationships between CD6 and IL18R1 with inflammatory bowel disease and between IL12B and Crohn’s disease. Our data may aid understanding of the molecular regulation of the circulating inflammatory proteome as well as causal relationships between inflammatory mediators and disease.}, author = {Hillary, Robert F. and Trejo-Banos, Daniel and Kousathanas, Athanasios and Mccartney, Daniel L. and Harris, Sarah E. and Stevenson, Anna J. and Patxot, Marion and Ojavee, Sven Erik and Zhang, Qian and Liewald, David C. and Ritchie, Craig W. and Evans, Kathryn L. and Tucker-Drob, Elliot M. and Wray, Naomi R. and Mcrae, Allan F. and Visscher, Peter M. and Deary, Ian J. and Robinson, Matthew Richard and Marioni, Riccardo E.}, issn = {1756994X}, journal = {Genome Medicine}, number = {1}, publisher = {Springer Nature}, title = {{Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults}}, doi = {10.1186/s13073-020-00754-1}, volume = {12}, 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{8126, abstract = {Cortical areas comprise multiple types of inhibitory interneurons with stereotypical connectivity motifs, but their combined effect on postsynaptic dynamics has been largely unexplored. Here, we analyse the response of a single postsynaptic model neuron receiving tuned excitatory connections alongside inhibition from two plastic populations. Depending on the inhibitory plasticity rule, synapses remain unspecific (flat), become anti-correlated to, or mirror excitatory synapses. Crucially, the neuron’s receptive field, i.e., its response to presynaptic stimuli, depends on the modulatory state of inhibition. When both inhibitory populations are active, inhibition balances excitation, resulting in uncorrelated postsynaptic responses regardless of the inhibitory tuning profiles. Modulating the activity of a given inhibitory population produces strong correlations to either preferred or non-preferred inputs, in line with recent experimental findings showing dramatic context-dependent changes of neurons’ receptive fields. We thus confirm that a neuron’s receptive field doesn’t follow directly from the weight profiles of its presynaptic afferents.}, author = {Agnes, Everton J. and Luppi, Andrea I. and Vogels, Tim P}, issn = {1529-2401}, journal = {The Journal of Neuroscience}, number = {50}, pages = {9634--9649}, publisher = {Society for Neuroscience}, title = {{Complementary inhibitory weight profiles emerge from plasticity and allow attentional switching of receptive fields}}, doi = {10.1523/JNEUROSCI.0276-20.2020}, volume = {40}, year = {2020}, } @misc{9706, abstract = {Additional file 2: Supplementary Tables. The association of pre-adjusted protein levels with biological and technical covariates. Protein levels were adjusted for age, sex, array plate and four genetic principal components (population structure) prior to analyses. Significant associations are emboldened. (Table S1). pQTLs associated with inflammatory biomarker levels from Bayesian penalised regression model (Posterior Inclusion Probability > 95%). (Table S2). All pQTLs associated with inflammatory biomarker levels from ordinary least squares regression model (P < 7.14 × 10− 10). (Table S3). Summary of lambda values relating to ordinary least squares GWAS and EWAS performed on inflammatory protein levels (n = 70) in Lothian Birth Cohort 1936 study. (Table S4). Conditionally significant pQTLs associated with inflammatory biomarker levels from ordinary least squares regression model (P < 7.14 × 10− 10). (Table S5). Comparison of variance explained by ordinary least squares and Bayesian penalised regression models for concordantly identified SNPs. (Table S6). Estimate of heritability for blood protein levels as well as proportion of variance explained attributable to different prior mixtures. (Table S7). Comparison of heritability estimates from Ahsan et al. (maximum likelihood) and Hillary et al. (Bayesian penalised regression). (Table S8). List of concordant SNPs identified by linear model and Bayesian penalised regression and whether they have been previously identified as eQTLs. (Table S9). Bayesian tests of colocalisation for cis pQTLs and cis eQTLs. (Table S10). Sherlock algorithm: Genes whose expression are putatively associated with circulating inflammatory proteins that harbour pQTLs. (Table S11). CpGs associated with inflammatory protein biomarkers as identified by Bayesian model (Bayesian model; Posterior Inclusion Probability > 95%). (Table S12). CpGs associated with inflammatory protein biomarkers as identified by linear model (limma) at P < 5.14 × 10− 10. (Table S13). CpGs associated with inflammatory protein biomarkers as identified by mixed linear model (OSCA) at P < 5.14 × 10− 10. (Table S14). Estimate of variance explained for blood protein levels by DNA methylation as well as proportion of explained attributable to different prior mixtures - BayesR+. (Table S15). Comparison of variance in protein levels explained by genome-wide DNA methylation data by mixed linear model (OSCA) and Bayesian penalised regression model (BayesR+). (Table S16). Variance in circulating inflammatory protein biomarker levels explained by common genetic and methylation data (joint and conditional estimates from BayesR+). Ordered by combined variance explained by genetic and epigenetic data - smallest to largest. Significant results from t-tests comparing distributions for variance explained by methylation or genetics alone versus combined estimate are emboldened. (Table S17). Genetic and epigenetic factors identified by BayesR+ when conditioning on all SNPs and CpGs together. (Table S18). Mendelian Randomisation analyses to assess whether proteins with concordantly identified genetic signals are causally associated with Alzheimer’s disease risk. (Table S19).}, author = {Hillary, Robert F. and Trejo-Banos, Daniel and Kousathanas, Athanasios and McCartney, Daniel L. and Harris, Sarah E. and Stevenson, Anna J. and Patxot, Marion and Ojavee, Sven Erik and Zhang, Qian and Liewald, David C. and Ritchie, Craig W. and Evans, Kathryn L. and Tucker-Drob, Elliot M. and Wray, Naomi R. and McRae, Allan F. and Visscher, Peter M. and Deary, Ian J. and Robinson, Matthew Richard and Marioni, Riccardo E. }, publisher = {Springer Nature}, title = {{Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults}}, doi = {10.6084/m9.figshare.12629697.v1}, 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 Publishing}, title = {{The free energy of the two-dimensional dilute Bose gas. II. Upper bound}}, doi = {10.1063/5.0005950}, volume = {61}, 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{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{8168, abstract = {Speciation, that is, the evolution of reproductive barriers eventually leading to complete isolation, is a crucial process generating biodiversity. Recent work has contributed much to our understanding of how reproductive barriers begin to evolve, and how they are maintained in the face of gene flow. However, little is known about the transition from partial to strong reproductive isolation (RI) and the completion of speciation. We argue that the evolution of strong RI is likely to involve different processes, or new interactions among processes, compared with the evolution of the first reproductive barriers. Transition to strong RI may be brought about by changing external conditions, for example, following secondary contact. However, the increasing levels of RI themselves create opportunities for new barriers to evolve and, and interaction or coupling among barriers. These changing processes may depend on genomic architecture and leave detectable signals in the genome. We outline outstanding questions and suggest more theoretical and empirical work, considering both patterns and processes associated with strong RI, is needed to understand how speciation is completed.}, author = {Kulmuni, Jonna and Butlin, Roger K. and Lucek, Kay and Savolainen, Vincent and Westram, Anja M}, issn = {1471-2970}, journal = {Philosophical Transactions of the Royal Society. Series B: Biological sciences}, number = {1806}, publisher = {The Royal Society}, title = {{Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers}}, doi = {10.1098/rstb.2019.0528}, volume = {375}, year = {2020}, } @article{8167, abstract = {The evolution of strong reproductive isolation (RI) is fundamental to the origins and maintenance of biological diversity, especially in situations where geographical distributions of taxa broadly overlap. But what is the history behind strong barriers currently acting in sympatry? Using whole-genome sequencing and single nucleotide polymorphism genotyping, we inferred (i) the evolutionary relationships, (ii) the strength of RI, and (iii) the demographic history of divergence between two broadly sympatric taxa of intertidal snail. Despite being cryptic, based on external morphology, Littorina arcana and Littorina saxatilis differ in their mode of female reproduction (egg-laying versus brooding), which may generate a strong post-zygotic barrier. We show that egg-laying and brooding snails are closely related, but genetically distinct. Genotyping of 3092 snails from three locations failed to recover any recent hybrid or backcrossed individuals, confirming that RI is strong. There was, however, evidence for a very low level of asymmetrical introgression, suggesting that isolation remains incomplete. The presence of strong, asymmetrical RI was further supported by demographic analysis of these populations. Although the taxa are currently broadly sympatric, demographic modelling suggests that they initially diverged during a short period of geographical separation involving very low gene flow. Our study suggests that some geographical separation may kick-start the evolution of strong RI, facilitating subsequent coexistence of taxa in sympatry. The strength of RI needed to achieve sympatry and the subsequent effect of sympatry on RI remain open questions.}, author = {Stankowski, Sean and Westram, Anja M and Zagrodzka, Zuzanna B. and Eyres, Isobel and Broquet, Thomas and Johannesson, Kerstin and Butlin, Roger K.}, issn = {1471-2970}, journal = {Philosophical Transactions of the Royal Society. Series B: Biological Sciences}, number = {1806}, publisher = {The Royal Society}, title = {{The evolution of strong reproductive isolation between sympatric intertidal snails}}, doi = {10.1098/rstb.2019.0545}, volume = {375}, year = {2020}, } @article{8170, abstract = {Alignment of OCS, CS2, and I2 molecules embedded in helium nanodroplets is measured as a function of time following rotational excitation by a nonresonant, comparatively weak ps laser pulse. The distinct peaks in the power spectra, obtained by Fourier analysis, are used to determine the rotational, B, and centrifugal distortion, D, constants. For OCS, B and D match the values known from IR spectroscopy. For CS2 and I2, they are the first experimental results reported. The alignment dynamics calculated from the gas-phase rotational Schrödinger equation, using the experimental in-droplet B and D values, agree in detail with the measurement for all three molecules. The rotational spectroscopy technique for molecules in helium droplets introduced here should apply to a range of molecules and complexes.}, author = {Chatterley, Adam S. and Christiansen, Lars and Schouder, Constant A. and Jørgensen, Anders V. and Shepperson, Benjamin and Cherepanov, Igor and Bighin, Giacomo and Zillich, Robert E. and Lemeshko, Mikhail and Stapelfeldt, Henrik}, issn = {10797114}, journal = {Physical Review Letters}, number = {1}, publisher = {American Physical Society}, title = {{Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains}}, doi = {10.1103/PhysRevLett.125.013001}, volume = {125}, year = {2020}, } @inproceedings{8194, abstract = {Fixed-point arithmetic is a popular alternative to floating-point arithmetic on embedded systems. Existing work on the verification of fixed-point programs relies on custom formalizations of fixed-point arithmetic, which makes it hard to compare the described techniques or reuse the implementations. In this paper, we address this issue by proposing and formalizing an SMT theory of fixed-point arithmetic. We present an intuitive yet comprehensive syntax of the fixed-point theory, and provide formal semantics for it based on rational arithmetic. We also describe two decision procedures for this theory: one based on the theory of bit-vectors and the other on the theory of reals. We implement the two decision procedures, and evaluate our implementations using existing mature SMT solvers on a benchmark suite we created. Finally, we perform a case study of using the theory we propose to verify properties of quantized neural networks.}, author = {Baranowski, Marek and He, Shaobo and Lechner, Mathias and Nguyen, Thanh Son and Rakamarić, Zvonimir}, booktitle = {Automated Reasoning}, isbn = {9783030510732}, issn = {16113349}, location = {Paris, France}, pages = {13--31}, publisher = {Springer Nature}, title = {{An SMT theory of fixed-point arithmetic}}, doi = {10.1007/978-3-030-51074-9_2}, volume = {12166}, year = {2020}, } @article{8220, abstract = {Understanding to what extent stem cell potential is a cell-intrinsic property or an emergent behavior coming from global tissue dynamics and geometry is a key outstanding question of systems and stem cell biology. Here, we propose a theory of stem cell dynamics as a stochastic competition for access to a spatially localized niche, giving rise to a stochastic conveyor-belt model. Cell divisions produce a steady cellular stream which advects cells away from the niche, while random rearrangements enable cells away from the niche to be favorably repositioned. Importantly, even when assuming that all cells in a tissue are molecularly equivalent, we predict a common (“universal”) functional dependence of the long-term clonal survival probability on distance from the niche, as well as the emergence of a well-defined number of functional stem cells, dependent only on the rate of random movements vs. mitosis-driven advection. We test the predictions of this theory on datasets of pubertal mammary gland tips and embryonic kidney tips, as well as homeostatic intestinal crypts. Importantly, we find good agreement for the predicted functional dependency of the competition as a function of position, and thus functional stem cell number in each organ. This argues for a key role of positional fluctuations in dictating stem cell number and dynamics, and we discuss the applicability of this theory to other settings.}, author = {Corominas-Murtra, Bernat and Scheele, Colinda L.G.J. and Kishi, Kasumi and Ellenbroek, Saskia I.J. and Simons, Benjamin D. and Van Rheenen, Jacco and Hannezo, Edouard B}, issn = {10916490}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {29}, pages = {16969--16975}, publisher = {National Academy of Sciences}, title = {{Stem cell lineage survival as a noisy competition for niche access}}, doi = {10.1073/pnas.1921205117}, volume = {117}, year = {2020}, } @article{8199, abstract = {We investigate a mechanism to transiently stabilize topological phenomena in long-lived quasi-steady states of isolated quantum many-body systems driven at low frequencies. We obtain an analytical bound for the lifetime of the quasi-steady states which is exponentially large in the inverse driving frequency. Within this lifetime, the quasi-steady state is characterized by maximum entropy subject to the constraint of fixed number of particles in the system's Floquet-Bloch bands. In such a state, all the non-universal properties of these bands are washed out, hence only the topological properties persist.}, author = {Gulden, Tobias and Berg, Erez and Rudner, Mark Spencer and Lindner, Netanel}, issn = {2542-4653}, journal = {SciPost Physics}, publisher = {SciPost Foundation}, title = {{Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps}}, doi = {10.21468/scipostphys.9.1.015}, volume = {9}, year = {2020}, } @article{8261, abstract = {Dentate gyrus granule cells (GCs) connect the entorhinal cortex to the hippocampal CA3 region, but how they process spatial information remains enigmatic. To examine the role of GCs in spatial coding, we measured excitatory postsynaptic potentials (EPSPs) and action potentials (APs) in head-fixed mice running on a linear belt. Intracellular recording from morphologically identified GCs revealed that most cells were active, but activity level varied over a wide range. Whereas only ∼5% of GCs showed spatially tuned spiking, ∼50% received spatially tuned input. Thus, the GC population broadly encodes spatial information, but only a subset relays this information to the CA3 network. Fourier analysis indicated that GCs received conjunctive place-grid-like synaptic input, suggesting code conversion in single neurons. GC firing was correlated with dendritic complexity and intrinsic excitability, but not extrinsic excitatory input or dendritic cable properties. Thus, functional maturation may control input-output transformation and spatial code conversion.}, author = {Zhang, Xiaomin and Schlögl, Alois and Jonas, Peter M}, issn = {0896-6273}, journal = {Neuron}, number = {6}, pages = {1212--1225}, publisher = {Elsevier}, title = {{Selective routing of spatial information flow from input to output in hippocampal granule cells}}, doi = {10.1016/j.neuron.2020.07.006}, volume = {107}, year = {2020}, } @article{8268, abstract = {Modern scientific instruments produce vast amounts of data, which can overwhelm the processing ability of computer systems. Lossy compression of data is an intriguing solution, but comes with its own drawbacks, such as potential signal loss, and the need for careful optimization of the compression ratio. In this work, we focus on a setting where this problem is especially acute: compressive sensing frameworks for interferometry and medical imaging. We ask the following question: can the precision of the data representation be lowered for all inputs, with recovery guarantees and practical performance Our first contribution is a theoretical analysis of the normalized Iterative Hard Thresholding (IHT) algorithm when all input data, meaning both the measurement matrix and the observation vector are quantized aggressively. We present a variant of low precision normalized IHT that, under mild conditions, can still provide recovery guarantees. The second contribution is the application of our quantization framework to radio astronomy and magnetic resonance imaging. We show that lowering the precision of the data can significantly accelerate image recovery. We evaluate our approach on telescope data and samples of brain images using CPU and FPGA implementations achieving up to a 9x speedup with negligible loss of recovery quality.}, author = {Gurel, Nezihe Merve and Kara, Kaan and Stojanov, Alen and Smith, Tyler and Lemmin, Thomas and Alistarh, Dan-Adrian and Puschel, Markus and Zhang, Ce}, issn = {19410476}, journal = {IEEE Transactions on Signal Processing}, pages = {4268--4282}, publisher = {IEEE}, title = {{Compressive sensing using iterative hard thresholding with low precision data representation: Theory and applications}}, doi = {10.1109/TSP.2020.3010355}, volume = {68}, 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}, issn = {2475-9953}, 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{8325, abstract = {Let 𝐹:ℤ2→ℤ be the pointwise minimum of several linear functions. The theory of smoothing allows us to prove that under certain conditions there exists the pointwise minimal function among all integer-valued superharmonic functions coinciding with F “at infinity”. We develop such a theory to prove existence of so-called solitons (or strings) in a sandpile model, studied by S. Caracciolo, G. Paoletti, and A. Sportiello. Thus we made a step towards understanding the phenomena of the identity in the sandpile group for planar domains where solitons appear according to experiments. We prove that sandpile states, defined using our smoothing procedure, move changeless when we apply the wave operator (that is why we call them solitons), and can interact, forming triads and nodes. }, author = {Kalinin, Nikita and Shkolnikov, Mikhail}, issn = {14320916}, journal = {Communications in Mathematical Physics}, number = {9}, pages = {1649--1675}, publisher = {Springer Nature}, title = {{Sandpile solitons via smoothing of superharmonic functions}}, doi = {10.1007/s00220-020-03828-8}, volume = {378}, year = {2020}, } @article{8318, abstract = {Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in complex I is not known. Here we report five crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like compounds. We also determined cryo-EM structures of major and minor native states of the complex, differing in the position of the peripheral arm. Crystal structures show that binding of quinone-like compounds (but not of NADH) leads to a related global conformational change, accompanied by local re-arrangements propagating from the quinone site to the nearest proton channel. Normal mode and molecular dynamics analyses indicate that these are likely to represent the first steps in the proton translocation mechanism. Our results suggest that quinone binding and chemistry play a key role in the coupling mechanism of complex I.}, author = {Gutierrez-Fernandez, Javier and Kaszuba, Karol and Minhas, Gurdeep S. and Baradaran, Rozbeh and Tambalo, Margherita and Gallagher, David T. and Sazanov, Leonid A}, issn = {20411723}, journal = {Nature Communications}, number = {1}, publisher = {Springer Nature}, title = {{Key role of quinone in the mechanism of respiratory complex I}}, doi = {10.1038/s41467-020-17957-0}, volume = {11}, year = {2020}, } @article{8323, author = {Pach, János}, issn = {14320444}, journal = {Discrete and Computational Geometry}, pages = {571--574}, publisher = {Springer Nature}, title = {{A farewell to Ricky Pollack}}, doi = {10.1007/s00454-020-00237-5}, volume = {64}, year = {2020}, } @article{8336, abstract = {Plant hormone cytokinins are perceived by a subfamily of sensor histidine kinases (HKs), which via a two-component phosphorelay cascade activate transcriptional responses in the nucleus. Subcellular localization of the receptors proposed the endoplasmic reticulum (ER) membrane as a principal cytokinin perception site, while study of cytokinin transport pointed to the plasma membrane (PM)-mediated cytokinin signalling. Here, by detailed monitoring of subcellular localizations of the fluorescently labelled natural cytokinin probe and the receptor ARABIDOPSIS HISTIDINE KINASE 4 (CRE1/AHK4) fused to GFP reporter, we show that pools of the ER-located cytokinin receptors can enter the secretory pathway and reach the PM in cells of the root apical meristem, and the cell plate of dividing meristematic cells. Brefeldin A (BFA) experiments revealed vesicular recycling of the receptor and its accumulation in BFA compartments. We provide a revised view on cytokinin signalling and the possibility of multiple sites of perception at PM and ER.}, author = {Kubiasova, Karolina and Montesinos López, Juan C and Šamajová, Olga and Nisler, Jaroslav and Mik, Václav and Semeradova, Hana and Plíhalová, Lucie and Novák, Ondřej and Marhavý, Peter and Cavallari, Nicola and Zalabák, David and Berka, Karel and Doležal, Karel and Galuszka, Petr and Šamaj, Jozef and Strnad, Miroslav and Benková, Eva and Plíhal, Ondřej and Spíchal, Lukáš}, issn = {20411723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Cytokinin fluoroprobe reveals multiple sites of cytokinin perception at plasma membrane and endoplasmic reticulum}}, doi = {10.1038/s41467-020-17949-0}, volume = {11}, year = {2020}, } @article{8337, abstract = {Cytokinins are mobile multifunctional plant hormones with roles in development and stress resilience. Although their Histidine Kinase receptors are substantially localised to the endoplasmic reticulum, cellular sites of cytokinin perception and importance of spatially heterogeneous cytokinin distribution continue to be debated. Here we show that cytokinin perception by plasma membrane receptors is an effective additional path for cytokinin response. Readout from a Two Component Signalling cytokinin-specific reporter (TCSn::GFP) closely matches intracellular cytokinin content in roots, yet we also find cytokinins in extracellular fluid, potentially enabling action at the cell surface. Cytokinins covalently linked to beads that could not pass the plasma membrane increased expression of both TCSn::GFP and Cytokinin Response Factors. Super-resolution microscopy of GFP-labelled receptors and diminished TCSn::GFP response to immobilised cytokinins in cytokinin receptor mutants, further indicate that receptors can function at the cell surface. We argue that dual intracellular and surface locations may augment flexibility of cytokinin responses.}, author = {Antoniadi, Ioanna and Novák, Ondřej and Gelová, Zuzana and Johnson, Alexander J and Plíhal, Ondřej and Simerský, Radim and Mik, Václav and Vain, Thomas and Mateo-Bonmatí, Eduardo and Karady, Michal and Pernisová, Markéta and Plačková, Lenka and Opassathian, Korawit and Hejátko, Jan and Robert, Stéphanie and Friml, Jiří and Doležal, Karel and Ljung, Karin and Turnbull, Colin}, issn = {20411723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Cell-surface receptors enable perception of extracellular cytokinins}}, doi = {10.1038/s41467-020-17700-9}, volume = {11}, 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{8361, abstract = {With the lithium-ion technology approaching its intrinsic limit with graphite-based anodes, Li 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 (inorganic and polymeric), Lithium–Sulfur (Li–S) and Lithium-O2 (air) batteries. A particular attention is paid to recent developments of these battery technologies and their current state 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 = {0378-7753}, journal = {Journal of Power Sources}, number = {12}, publisher = {Elsevier}, title = {{Current status and future perspectives of lithium metal batteries}}, doi = {10.1016/j.jpowsour.2020.228803}, volume = {480}, year = {2020}, } @article{8529, abstract = {Practical quantum networks require low-loss and noise-resilient optical interconnects as well as non-Gaussian resources for entanglement distillation and distributed quantum computation. The latter could be provided by superconducting circuits but existing solutions to interface the microwave and optical domains lack either scalability or efficiency, and in most cases the conversion noise is not known. In this work we utilize the unique opportunities of silicon photonics, cavity optomechanics and superconducting circuits to demonstrate a fully integrated, coherent transducer interfacing the microwave X and the telecom S bands with a total (internal) bidirectional transduction efficiency of 1.2% (135%) at millikelvin temperatures. The coupling relies solely on the radiation pressure interaction mediated by the femtometer-scale motion of two silicon nanobeams reaching a Vπ as low as 16 μV for sub-nanowatt pump powers. Without the associated optomechanical gain, we achieve a total (internal) pure conversion efficiency of up to 0.019% (1.6%), relevant for future noise-free operation on this qubit-compatible platform.}, author = {Arnold, Georg M and Wulf, Matthias and Barzanjeh, Shabir and Redchenko, Elena and Rueda Sanchez, Alfredo R and Hease, William J and Hassani, Farid and Fink, Johannes M}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Biochemistry, Genetics and Molecular Biology, General Physics and Astronomy, General Chemistry}, publisher = {Springer Nature}, title = {{Converting microwave and telecom photons with a silicon photonic nanomechanical interface}}, doi = {10.1038/s41467-020-18269-z}, volume = {11}, year = {2020}, } @article{8535, abstract = {We propose a method to enhance the visual detail of a water surface simulation. Our method works as a post-processing step which takes a simulation as input and increases its apparent resolution by simulating many detailed Lagrangian water waves on top of it. We extend linear water wave theory to work in non-planar domains which deform over time, and we discretize the theory using Lagrangian wave packets attached to spline curves. The method is numerically stable and trivially parallelizable, and it produces high frequency ripples with dispersive wave-like behaviors customized to the underlying fluid simulation.}, author = {Skrivan, Tomas and Soderstrom, Andreas and Johansson, John and Sprenger, Christoph and Museth, Ken and Wojtan, Christopher J}, issn = {15577368}, journal = {ACM Transactions on Graphics}, number = {4}, publisher = {Association for Computing Machinery}, title = {{Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces}}, doi = {10.1145/3386569.3392466}, volume = {39}, year = {2020}, } @article{8539, abstract = {Cohomological and K-theoretic stable bases originated from the study of quantum cohomology and quantum K-theory. Restriction formula for cohomological stable bases played an important role in computing the quantum connection of cotangent bundle of partial flag varieties. In this paper we study the K-theoretic stable bases of cotangent bundles of flag varieties. We describe these bases in terms of the action of the affine Hecke algebra and the twisted group algebra of KostantKumar. Using this algebraic description and the method of root polynomials, we give a restriction formula of the stable bases. We apply it to obtain the restriction formula for partial flag varieties. We also build a relation between the stable basis and the Casselman basis in the principal series representations of the Langlands dual group. As an application, we give a closed formula for the transition matrix between Casselman basis and the characteristic functions.}, author = {Su, C. and Zhao, Gufang and Zhong, C.}, issn = {0012-9593}, journal = {Annales Scientifiques de l'Ecole Normale Superieure}, number = {3}, pages = {663--671}, publisher = {Société Mathématique de France}, title = {{On the K-theory stable bases of the springer resolution}}, doi = {10.24033/asens.2431}, volume = {53}, year = {2020}, } @misc{13056, abstract = {This datasets comprises all data shown in plots of the submitted article "Converting microwave and telecom photons with a silicon photonic nanomechanical interface". Additional raw data are available from the corresponding author on reasonable request.}, author = {Arnold, Georg M and Wulf, Matthias and Barzanjeh, Shabir and Redchenko, Elena and Rueda Sanchez, Alfredo R and Hease, William J and Hassani, Farid and Fink, Johannes M}, publisher = {Zenodo}, title = {{Converting microwave and telecom photons with a silicon photonic nanomechanical interface}}, doi = {10.5281/ZENODO.3961561}, year = {2020}, } @article{8579, abstract = {Copper (Cu) is an essential trace element for all living organisms and used as cofactor in key enzymes of important biological processes, such as aerobic respiration or superoxide dismutation. However, due to its toxicity, cells have developed elaborate mechanisms for Cu homeostasis, which balance Cu supply for cuproprotein biogenesis with the need to remove excess Cu. This review summarizes our current knowledge on bacterial Cu homeostasis with a focus on Gram-negative bacteria and describes the multiple strategies that bacteria use for uptake, storage and export of Cu. We furthermore describe general mechanistic principles that aid the bacterial response to toxic Cu concentrations and illustrate dedicated Cu relay systems that facilitate Cu delivery for cuproenzyme biogenesis. Progress in understanding how bacteria avoid Cu poisoning while maintaining a certain Cu quota for cell proliferation is of particular importance for microbial pathogens because Cu is utilized by the host immune system for attenuating pathogen survival in host cells.}, author = {Andrei, Andreea and Öztürk, Yavuz and Khalfaoui-Hassani, Bahia and Rauch, Juna and Marckmann, Dorian and Trasnea, Petru Iulian and Daldal, Fevzi and Koch, Hans-Georg}, issn = {20770375}, journal = {Membranes}, number = {9}, publisher = {MDPI}, title = {{Cu homeostasis in bacteria: The ins and outs}}, doi = {10.3390/membranes10090242}, volume = {10}, year = {2020}, } @article{8592, abstract = {Glioblastoma is the most malignant cancer in the brain and currently incurable. It is urgent to identify effective targets for this lethal disease. Inhibition of such targets should suppress the growth of cancer cells and, ideally also precancerous cells for early prevention, but minimally affect their normal counterparts. Using genetic mouse models with neural stem cells (NSCs) or oligodendrocyte precursor cells (OPCs) as the cells‐of‐origin/mutation, it is shown that the susceptibility of cells within the development hierarchy of glioma to the knockout of insulin‐like growth factor I receptor (IGF1R) is determined not only by their oncogenic states, but also by their cell identities/states. Knockout of IGF1R selectively disrupts the growth of mutant and transformed, but not normal OPCs, or NSCs. The desirable outcome of IGF1R knockout on cell growth requires the mutant cells to commit to the OPC identity regardless of its development hierarchical status. At the molecular level, oncogenic mutations reprogram the cellular network of OPCs and force them to depend more on IGF1R for their growth. A new‐generation brain‐penetrable, orally available IGF1R inhibitor harnessing tumor OPCs in the brain is also developed. The findings reveal the cellular window of IGF1R targeting and establish IGF1R as an effective target for the prevention and treatment of glioblastoma.}, author = {Tian, Anhao and Kang, Bo and Li, Baizhou and Qiu, Biying and Jiang, Wenhong and Shao, Fangjie and Gao, Qingqing and Liu, Rui and Cai, Chengwei and Jing, Rui and Wang, Wei and Chen, Pengxiang and Liang, Qinghui and Bao, Lili and Man, Jianghong and Wang, Yan and Shi, Yu and Li, Jin and Yang, Minmin and Wang, Lisha and Zhang, Jianmin and Hippenmeyer, Simon and Zhu, Junming and Bian, Xiuwu and Wang, Ying‐Jie and Liu, Chong}, issn = {2198-3844}, journal = {Advanced Science}, keywords = {General Engineering, General Physics and Astronomy, General Materials Science, Medicine (miscellaneous), General Chemical Engineering, Biochemistry, Genetics and Molecular Biology (miscellaneous)}, number = {21}, publisher = {Wiley}, title = {{Oncogenic state and cell identity combinatorially dictate the susceptibility of cells within glioma development hierarchy to IGF1R targeting}}, doi = {10.1002/advs.202001724}, volume = {7}, year = {2020}, } @article{8568, abstract = {Aqueous iodine based electrochemical energy storage is considered a potential candidate to improve sustainability and performance of current battery and supercapacitor technology. It harnesses the redox activity of iodide, iodine, and polyiodide species in the confined geometry of nanoporous carbon electrodes. However, current descriptions of the electrochemical reaction mechanism to interconvert these species are elusive. Here we show that electrochemical oxidation of iodide in nanoporous carbons forms persistent solid iodine deposits. Confinement slows down dissolution into triiodide and pentaiodide, responsible for otherwise significant self-discharge via shuttling. The main tools for these insights are in situ Raman spectroscopy and in situ small and wide-angle X-ray scattering (in situ SAXS/WAXS). In situ Raman confirms the reversible formation of triiodide and pentaiodide. In situ SAXS/WAXS indicates remarkable amounts of solid iodine deposited in the carbon nanopores. Combined with stochastic modeling, in situ SAXS allows quantifying the solid iodine volume fraction and visualizing the iodine structure on 3D lattice models at the sub-nanometer scale. Based on the derived mechanism, we demonstrate strategies for improved iodine pore filling capacity and prevention of self-discharge, applicable to hybrid supercapacitors and batteries.}, author = {Prehal, Christian and Fitzek, Harald and Kothleitner, Gerald and Presser, Volker and Gollas, Bernhard and Freunberger, Stefan Alexander and Abbas, Qamar}, issn = {2041-1723}, journal = {Nature Communications}, keywords = {General Biochemistry, Genetics and Molecular Biology, General Physics and Astronomy, General Chemistry}, publisher = {Springer Nature}, title = {{Persistent and reversible solid iodine electrodeposition in nanoporous carbons}}, doi = {10.1038/s41467-020-18610-6}, volume = {11}, year = {2020}, } @article{8643, abstract = {The parabigeminal nucleus (PBG) is the mammalian homologue to the isthmic complex of other vertebrates. Optogenetic stimulation of the PBG induces freezing and escape in mice, a result thought to be caused by a PBG projection to the central nucleus of the amygdala. However, the isthmic complex, including the PBG, has been classically considered satellite nuclei of the Superior Colliculus (SC), which upon stimulation of its medial part also triggers fear and avoidance reactions. As the PBG-SC connectivity is not well characterized, we investigated whether the topology of the PBG projection to the SC could be related to the behavioral consequences of PBG stimulation. To that end, we performed immunohistochemistry, in situ hybridization and neural tracer injections in the SC and PBG in a diurnal rodent, the Octodon degus. We found that all PBG neurons expressed both glutamatergic and cholinergic markers and were distributed in clearly defined anterior (aPBG) and posterior (pPBG) subdivisions. The pPBG is connected reciprocally and topographically to the ipsilateral SC, whereas the aPBG receives afferent axons from the ipsilateral SC and projected exclusively to the contralateral SC. This contralateral projection forms a dense field of terminals that is restricted to the medial SC, in correspondence with the SC representation of the aerial binocular field which, we also found, in O. degus prompted escape reactions upon looming stimulation. Therefore, this specialized topography allows binocular interactions in the SC region controlling responses to aerial predators, suggesting a link between the mechanisms by which the SC and PBG produce defensive behaviors.}, author = {Deichler, Alfonso and Carrasco, Denisse and Lopez-Jury, Luciana and Vega Zuniga, Tomas A and Marquez, Natalia and Mpodozis, Jorge and Marin, Gonzalo}, issn = {20452322}, journal = {Scientific Reports}, publisher = {Springer Nature}, title = {{A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents}}, doi = {10.1038/s41598-020-72848-0}, volume = {10}, year = {2020}, } @article{8645, abstract = {Epistasis, the context-dependence of the contribution of an amino acid substitution to fitness, is common in evolution. To detect epistasis, fitness must be measured for at least four genotypes: the reference genotype, two different single mutants and a double mutant with both of the single mutations. For higher-order epistasis of the order n, fitness has to be measured for all 2n genotypes of an n-dimensional hypercube in genotype space forming a ‘combinatorially complete dataset’. So far, only a handful of such datasets have been produced by manual curation. Concurrently, random mutagenesis experiments have produced measurements of fitness and other phenotypes in a high-throughput manner, potentially containing a number of combinatorially complete datasets. We present an effective recursive algorithm for finding all hypercube structures in random mutagenesis experimental data. To test the algorithm, we applied it to the data from a recent HIS3 protein dataset and found all 199 847 053 unique combinatorially complete genotype combinations of dimensionality ranging from 2 to 12. The algorithm may be useful for researchers looking for higher-order epistasis in their high-throughput experimental data.}, author = {Esteban, Laura A and Lonishin, Lyubov R and Bobrovskiy, Daniil M and Leleytner, Gregory and Bogatyreva, Natalya S and Kondrashov, Fyodor and Ivankov, Dmitry N }, issn = {1460-2059}, journal = {Bioinformatics}, number = {6}, pages = {1960--1962}, publisher = {Oxford Academic}, title = {{HypercubeME: Two hundred million combinatorially complete datasets from a single experiment}}, doi = {10.1093/bioinformatics/btz841}, volume = {36}, year = {2020}, } @article{8597, abstract = {Error analysis and data visualization of positive COVID-19 cases in 27 countries have been performed up to August 8, 2020. This survey generally observes a progression from early exponential growth transitioning to an intermediate power-law growth phase, as recently suggested by Ziff and Ziff. The occurrence of logistic growth after the power-law phase with lockdowns or social distancing may be described as an effect of avoidance. A visualization of the power-law growth exponent over short time windows is qualitatively similar to the Bhatia visualization for pandemic progression. Visualizations like these can indicate the onset of second waves and may influence social policy.}, author = {Merrin, Jack}, issn = {14783975}, journal = {Physical Biology}, number = {6}, publisher = {IOP Publishing}, title = {{Differences in power law growth over time and indicators of COVID-19 pandemic progression worldwide}}, doi = {10.1088/1478-3975/abb2db}, volume = {17}, year = {2020}, } @article{8674, abstract = {Extrasynaptic actions of glutamate are limited by high-affinity transporters expressed by perisynaptic astroglial processes (PAPs): this helps maintain point-to-point transmission in excitatory circuits. Memory formation in the brain is associated with synaptic remodeling, but how this affects PAPs and therefore extrasynaptic glutamate actions is poorly understood. Here, we used advanced imaging methods, in situ and in vivo, to find that a classical synaptic memory mechanism, long-term potentiation (LTP), triggers withdrawal of PAPs from potentiated synapses. Optical glutamate sensors combined with patch-clamp and 3D molecular localization reveal that LTP induction thus prompts spatial retreat of astroglial glutamate transporters, boosting glutamate spillover and NMDA-receptor-mediated inter-synaptic cross-talk. The LTP-triggered PAP withdrawal involves NKCC1 transporters and the actin-controlling protein cofilin but does not depend on major Ca2+-dependent cascades in astrocytes. We have therefore uncovered a mechanism by which a memory trace at one synapse could alter signal handling by multiple neighboring connections.}, author = {Henneberger, Christian and Bard, Lucie and Panatier, Aude and Reynolds, James P. and Kopach, Olga and Medvedev, Nikolay I. and Minge, Daniel and Herde, Michel K. and Anders, Stefanie and Kraev, Igor and Heller, Janosch P. and Rama, Sylvain and Zheng, Kaiyu and Jensen, Thomas P. and Sanchez-Romero, Inmaculada and Jackson, Colin J. and Janovjak, Harald L and Ottersen, Ole Petter and Nagelhus, Erlend Arnulf and Oliet, Stephane H.R. and Stewart, Michael G. and Nägerl, U. VAlentin and Rusakov, Dmitri A. }, issn = {10974199}, journal = {Neuron}, number = {5}, pages = {P919--936.E11}, publisher = {Elsevier}, title = {{LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia}}, doi = {10.1016/j.neuron.2020.08.030}, volume = {108}, year = {2020}, } @article{8652, abstract = {Nature creates electrons with two values of the spin projection quantum number. In certain applications, it is important to filter electrons with one spin projection from the rest. Such filtering is not trivial, since spin-dependent interactions are often weak, and cannot lead to any substantial effect. Here we propose an efficient spin filter based upon scattering from a two-dimensional crystal, which is made of aligned point magnets. The polarization of the outgoing electron flux is controlled by the crystal, and reaches maximum at specific values of the parameters. In our scheme, polarization increase is accompanied by higher reflectivity of the crystal. High transmission is feasible in scattering from a quantum cavity made of two crystals. Our findings can be used for studies of low-energy spin-dependent scattering from two-dimensional ordered structures made of magnetic atoms or aligned chiral molecules.}, author = {Ghazaryan, Areg and Lemeshko, Mikhail and Volosniev, Artem}, issn = {2399-3650}, journal = {Communications Physics}, publisher = {Springer Nature}, title = {{Filtering spins by scattering from a lattice of point magnets}}, doi = {10.1038/s42005-020-00445-8}, volume = {3}, year = {2020}, } @article{8669, abstract = {Pancreatic islets play an essential role in regulating blood glucose level. Although the molecular pathways underlying islet cell differentiation are beginning to be resolved, the cellular basis of islet morphogenesis and fate allocation remain unclear. By combining unbiased and targeted lineage tracing, we address the events leading to islet formation in the mouse. From the statistical analysis of clones induced at multiple embryonic timepoints, here we show that, during the secondary transition, islet formation involves the aggregation of multiple equipotent endocrine progenitors that transition from a phase of stochastic amplification by cell division into a phase of sublineage restriction and limited islet fission. Together, these results explain quantitatively the heterogeneous size distribution and degree of polyclonality of maturing islets, as well as dispersion of progenitors within and between islets. Further, our results show that, during the secondary transition, α- and β-cells are generated in a contemporary manner. Together, these findings provide insight into the cellular basis of islet development.}, author = {Sznurkowska, Magdalena K. and Hannezo, Edouard B and Azzarelli, Roberta and Chatzeli, Lemonia and Ikeda, Tatsuro and Yoshida, Shosei and Philpott, Anna and Simons, Benjamin D}, issn = {20411723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Tracing the cellular basis of islet specification in mouse pancreas}}, doi = {10.1038/s41467-020-18837-3}, volume = {11}, year = {2020}, } @article{8672, abstract = {Cell fate transitions are key to development and homeostasis. It is thus essential to understand the cellular mechanisms controlling fate transitions. Cell division has been implicated in fate decisions in many stem cell types, including neuronal and epithelial progenitors. In other stem cells, such as embryonic stem (ES) cells, the role of division remains unclear. Here, we show that exit from naive pluripotency in mouse ES cells generally occurs after a division. We further show that exit timing is strongly correlated between sister cells, which remain connected by cytoplasmic bridges long after division, and that bridge abscission progressively accelerates as cells exit naive pluripotency. Finally, interfering with abscission impairs naive pluripotency exit, and artificially inducing abscission accelerates it. Altogether, our data indicate that a switch in the division machinery leading to faster abscission regulates pluripotency exit. Our study identifies abscission as a key cellular process coupling cell division to fate transitions.}, author = {Chaigne, Agathe and Labouesse, Céline and White, Ian J. and Agnew, Meghan and Hannezo, Edouard B and Chalut, Kevin J. and Paluch, Ewa K.}, issn = {18781551}, journal = {Developmental Cell}, number = {2}, pages = {195--208}, publisher = {Elsevier}, title = {{Abscission couples cell division to embryonic stem cell fate}}, doi = {10.1016/j.devcel.2020.09.001}, volume = {55}, year = {2020}, } @article{8697, abstract = {In the computation of the material properties of random alloys, the method of 'special quasirandom structures' attempts to approximate the properties of the alloy on a finite volume with higher accuracy by replicating certain statistics of the random atomic lattice in the finite volume as accurately as possible. In the present work, we provide a rigorous justification for a variant of this method in the framework of the Thomas–Fermi–von Weizsäcker (TFW) model. Our approach is based on a recent analysis of a related variance reduction method in stochastic homogenization of linear elliptic PDEs and the locality properties of the TFW model. Concerning the latter, we extend an exponential locality result by Nazar and Ortner to include point charges, a result that may be of independent interest.}, author = {Fischer, Julian L and Kniely, Michael}, issn = {13616544}, journal = {Nonlinearity}, number = {11}, pages = {5733--5772}, publisher = {IOP Publishing}, title = {{Variance reduction for effective energies of random lattices in the Thomas-Fermi-von Weizsäcker model}}, doi = {10.1088/1361-6544/ab9728}, volume = {33}, year = {2020}, } @article{8680, abstract = {Animal development entails the organization of specific cell types in space and time, and spatial patterns must form in a robust manner. In the zebrafish spinal cord, neural progenitors form stereotypic patterns despite noisy morphogen signaling and large-scale cellular rearrangements during morphogenesis and growth. By directly measuring adhesion forces and preferences for three types of endogenous neural progenitors, we provide evidence for the differential adhesion model in which differences in intercellular adhesion mediate cell sorting. Cell type–specific combinatorial expression of different classes of cadherins (N-cadherin, cadherin 11, and protocadherin 19) results in homotypic preference ex vivo and patterning robustness in vivo. Furthermore, the differential adhesion code is regulated by the sonic hedgehog morphogen gradient. We propose that robust patterning during tissue morphogenesis results from interplay between adhesion-based self-organization and morphogen-directed patterning.}, author = {Tsai, Tony Y.-C. and Sikora, Mateusz K and Xia, Peng and Colak-Champollion, Tugba and Knaut, Holger and Heisenberg, Carl-Philipp J and Megason, Sean G.}, issn = {1095-9203}, journal = {Science}, keywords = {Multidisciplinary}, number = {6512}, pages = {113--116}, publisher = {American Association for the Advancement of Science}, title = {{An adhesion code ensures robust pattern formation during tissue morphogenesis}}, doi = {10.1126/science.aba6637}, volume = {370}, year = {2020}, } @article{8670, abstract = {The α–z Rényi relative entropies are a two-parameter family of Rényi relative entropies that are quantum generalizations of the classical α-Rényi relative entropies. In the work [Adv. Math. 365, 107053 (2020)], we decided the full range of (α, z) for which the data processing inequality (DPI) is valid. In this paper, we give algebraic conditions for the equality in DPI. For the full range of parameters (α, z), we give necessary conditions and sufficient conditions. For most parameters, we give equivalent conditions. This generalizes and strengthens the results of Leditzky et al. [Lett. Math. Phys. 107, 61–80 (2017)].}, author = {Zhang, Haonan}, issn = {00222488}, journal = {Journal of Mathematical Physics}, number = {10}, publisher = {AIP Publishing}, title = {{Equality conditions of data processing inequality for α-z Rényi relative entropies}}, doi = {10.1063/5.0022787}, volume = {61}, year = {2020}, }