@article{8384, abstract = {Previous research on animations of soap bubbles, films, and foams largely focuses on the motion and geometric shape of the bubble surface. These works neglect the evolution of the bubble’s thickness, which is normally responsible for visual phenomena like surface vortices, Newton’s interference patterns, capillary waves, and deformation-dependent rupturing of films in a foam. In this paper, we model these natural phenomena by introducing the film thickness as a reduced degree of freedom in the Navier-Stokes equations and deriving their equations of motion. We discretize the equations on a nonmanifold triangle mesh surface and couple it to an existing bubble solver. In doing so, we also introduce an incompressible fluid solver for 2.5D films and a novel advection algorithm for convecting fields across non-manifold surface junctions. Our simulations enhance state-of-the-art bubble solvers with additional effects caused by convection, rippling, draining, and evaporation of the thin film.}, author = {Ishida, Sadashige and Synak, Peter and Narita, Fumiya and Hachisuka, Toshiya and Wojtan, Christopher J}, issn = {15577368}, journal = {ACM Transactions on Graphics}, number = {4}, publisher = {Association for Computing Machinery}, title = {{A model for soap film dynamics with evolving thickness}}, doi = {10.1145/3386569.3392405}, volume = {39}, year = {2020}, } @inproceedings{7802, abstract = {The Massively Parallel Computation (MPC) model is an emerging model which distills core aspects of distributed and parallel computation. It has been developed as a tool to solve (typically graph) problems in systems where the input is distributed over many machines with limited space. Recent work has focused on the regime in which machines have sublinear (in $n$, the number of nodes in the input graph) space, with randomized algorithms presented for fundamental graph problems of Maximal Matching and Maximal Independent Set. However, there have been no prior corresponding deterministic algorithms. A major challenge underlying the sublinear space setting is that the local space of each machine might be too small to store all the edges incident to a single node. This poses a considerable obstacle compared to the classical models in which each node is assumed to know and have easy access to its incident edges. To overcome this barrier we introduce a new graph sparsification technique that deterministically computes a low-degree subgraph with additional desired properties. The degree of the nodes in this subgraph is small in the sense that the edges of each node can be now stored on a single machine. This low-degree subgraph also has the property that solving the problem on this subgraph provides \emph{significant} global progress, i.e., progress towards solving the problem for the original input graph. Using this framework to derandomize the well-known randomized algorithm of Luby [SICOMP'86], we obtain $O(\log \Delta+\log\log n)$-round deterministic MPC algorithms for solving the fundamental problems of Maximal Matching and Maximal Independent Set with $O(n^{\epsilon})$ space on each machine for any constant $\epsilon > 0$. Based on the recent work of Ghaffari et al. [FOCS'18], this additive $O(\log\log n)$ factor is conditionally essential. These algorithms can also be shown to run in $O(\log \Delta)$ rounds in the closely related model of CONGESTED CLIQUE, improving upon the state-of-the-art bound of $O(\log^2 \Delta)$ rounds by Censor-Hillel et al. [DISC'17].}, author = {Czumaj, Artur and Davies, Peter and Parter, Merav}, booktitle = {Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020)}, location = {Virtual Event, United States}, number = {7}, pages = {175--185}, publisher = {Association for Computing Machinery}, title = {{Graph sparsification for derandomizing massively parallel computation with low space}}, doi = {10.1145/3350755.3400282}, year = {2020}, } @inproceedings{7636, abstract = {Balanced search trees typically use key comparisons to guide their operations, and achieve logarithmic running time. By relying on numerical properties of the keys, interpolation search achieves lower search complexity and better performance. Although interpolation-based data structures were investigated in the past, their non-blocking concurrent variants have received very little attention so far. In this paper, we propose the first non-blocking implementation of the classic interpolation search tree (IST) data structure. For arbitrary key distributions, the data structure ensures worst-case O(log n + p) amortized time for search, insertion and deletion traversals. When the input key distributions are smooth, lookups run in expected O(log log n + p) time, and insertion and deletion run in expected amortized O(log log n + p) time, where p is a bound on the number of threads. To improve the scalability of concurrent insertion and deletion, we propose a novel parallel rebuilding technique, which should be of independent interest. We evaluate whether the theoretical improvements translate to practice by implementing the concurrent interpolation search tree, and benchmarking it on uniform and nonuniform key distributions, for dataset sizes in the millions to billions of keys. Relative to the state-of-the-art concurrent data structures, the concurrent interpolation search tree achieves performance improvements of up to 15% under high update rates, and of up to 50% under moderate update rates. Further, ISTs exhibit up to 2X less cache-misses, and consume 1.2 -- 2.6X less memory compared to the next best alternative on typical dataset sizes. We find that the results are surprisingly robust to distributional skew, which suggests that our data structure can be a promising alternative to classic concurrent search structures.}, author = {Brown, Trevor A and Prokopec, Aleksandar and Alistarh, Dan-Adrian}, booktitle = {Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming}, isbn = {9781450368186}, location = {San Diego, CA, United States}, pages = {276--291}, publisher = {Association for Computing Machinery}, title = {{Non-blocking interpolation search trees with doubly-logarithmic running time}}, doi = {10.1145/3332466.3374542}, year = {2020}, } @article{8385, abstract = {We present a method for animating yarn-level cloth effects using a thin-shell solver. We accomplish this through numerical homogenization: we first use a large number of yarn-level simulations to build a model of the potential energy density of the cloth, and then use this energy density function to compute forces in a thin shell simulator. We model several yarn-based materials, including both woven and knitted fabrics. Our model faithfully reproduces expected effects like the stiffness of woven fabrics, and the highly deformable nature and anisotropy of knitted fabrics. Our approach does not require any real-world experiments nor measurements; because the method is based entirely on simulations, it can generate entirely new material models quickly, without the need for testing apparatuses or human intervention. We provide data-driven models of several woven and knitted fabrics, which can be used for efficient simulation with an off-the-shelf cloth solver.}, author = {Sperl, Georg and Narain, Rahul and Wojtan, Christopher J}, issn = {15577368}, journal = {ACM Transactions on Graphics}, number = {4}, publisher = {Association for Computing Machinery}, title = {{Homogenized yarn-level cloth}}, doi = {10.1145/3386569.3392412}, volume = {39}, year = {2020}, } @article{7956, abstract = {When short-range attractions are combined with long-range repulsions in colloidal particle systems, complex microphases can emerge. Here, we study a system of isotropic particles, which can form lamellar structures or a disordered fluid phase when temperature is varied. We show that, at equilibrium, the lamellar structure crystallizes, while out of equilibrium, the system forms a variety of structures at different shear rates and temperatures above melting. The shear-induced ordering is analyzed by means of principal component analysis and artificial neural networks, which are applied to data of reduced dimensionality. Our results reveal the possibility of inducing ordering by shear, potentially providing a feasible route to the fabrication of ordered lamellar structures from isotropic particles.}, author = {Pȩkalski, J. and Rzadkowski, Wojciech and Panagiotopoulos, A. Z.}, issn = {10897690}, journal = {The Journal of chemical physics}, number = {20}, publisher = {AIP Publishing}, title = {{Shear-induced ordering in systems with competing interactions: A machine learning study}}, doi = {10.1063/5.0005194}, volume = {152}, year = {2020}, } @inproceedings{8382, abstract = {We present the first deterministic wait-free long-lived snapshot algorithm, using only read and write operations, that guarantees polylogarithmic amortized step complexity in all executions. This is the first non-blocking snapshot algorithm, using reads and writes only, that has sub-linear amortized step complexity in executions of arbitrary length. The key to our construction is a novel implementation of a 2-component max array object which may be of independent interest.}, author = {Baig, Mirza Ahad and Hendler, Danny and Milani, Alessia and Travers, Corentin}, booktitle = {Proceedings of the 39th Symposium on Principles of Distributed Computing}, isbn = {9781450375825}, location = {Virtual, Italy}, pages = {31--40}, publisher = {Association for Computing Machinery}, title = {{Long-lived snapshots with polylogarithmic amortized step complexity}}, doi = {10.1145/3382734.3406005}, year = {2020}, } @article{7428, abstract = {In the superconducting regime of FeTe(1−x)Sex, there exist two types of vortices which are distinguished by the presence or absence of zero-energy states in their core. To understand their origin, we examine the interplay of Zeeman coupling and superconducting pairings in three-dimensional metals with band inversion. Weak Zeeman fields are found to suppress intraorbital spin-singlet pairing, known to localize the states at the ends of the vortices on the surface. On the other hand, an orbital-triplet pairing is shown to be stable against Zeeman interactions, but leads to delocalized zero-energy Majorana modes which extend through the vortex. In contrast, the finite-energy vortex modes remain localized at the vortex ends even when the pairing is of orbital-triplet form. Phenomenologically, this manifests as an observed disappearance of zero-bias peaks within the cores of topological vortices upon an increase of the applied magnetic field. The presence of magnetic impurities in FeTe(1−x)Sex, which are attracted to the vortices, would lead to such Zeeman-induced delocalization of Majorana modes in a fraction of vortices that capture a large enough number of magnetic impurities. Our results provide an explanation for the dichotomy between topological and nontopological vortices recently observed in FeTe(1−x)Sex.}, author = {Ghazaryan, Areg and Lopes, P. L.S. and Hosur, Pavan and Gilbert, Matthew J. and Ghaemi, Pouyan}, issn = {24699969}, journal = {Physical Review B}, number = {2}, publisher = {American Physical Society}, title = {{Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors}}, doi = {10.1103/PhysRevB.101.020504}, volume = {101}, year = {2020}, } @article{8319, abstract = {We demonstrate that releasing atoms into free space from an optical lattice does not deteriorate cavity-generated spin squeezing for metrological purposes. In this work, an ensemble of 500000 spin-squeezed atoms in a high-finesse optical cavity with near-uniform atom-cavity coupling is prepared, released into free space, recaptured in the cavity, and probed. Up to ∼10 dB of metrologically relevant squeezing is retrieved for 700μs free-fall times, and decaying levels of squeezing are realized for up to 3 ms free-fall times. The degradation of squeezing results from loss of atom-cavity coupling homogeneity between the initial squeezed state generation and final collective state readout. A theoretical model is developed to quantify this degradation and this model is experimentally validated.}, author = {Wu, Yunfan and Krishnakumar, Rajiv and Martínez-Rincón, Julián and Malia, Benjamin K. and Hosten, Onur and Kasevich, Mark A.}, issn = {24699934}, journal = {Physical Review A}, number = {1}, publisher = {American Physical Society}, title = {{Retrieval of cavity-generated atomic spin squeezing after free-space release}}, doi = {10.1103/PhysRevA.102.012224}, volume = {102}, year = {2020}, } @article{15055, abstract = {Markov decision processes (MDPs) are the defacto framework for sequential decision making in the presence of stochastic uncertainty. A classical optimization criterion for MDPs is to maximize the expected discounted-sum payoff, which ignores low probability catastrophic events with highly negative impact on the system. On the other hand, risk-averse policies require the probability of undesirable events to be below a given threshold, but they do not account for optimization of the expected payoff. We consider MDPs with discounted-sum payoff with failure states which represent catastrophic outcomes. The objective of risk-constrained planning is to maximize the expected discounted-sum payoff among risk-averse policies that ensure the probability to encounter a failure state is below a desired threshold. Our main contribution is an efficient risk-constrained planning algorithm that combines UCT-like search with a predictor learned through interaction with the MDP (in the style of AlphaZero) and with a risk-constrained action selection via linear programming. We demonstrate the effectiveness of our approach with experiments on classical MDPs from the literature, including benchmarks with an order of 106 states.}, author = {Brázdil, Tomáš and Chatterjee, Krishnendu and Novotný, Petr and Vahala, Jiří}, issn = {2374-3468}, journal = {Proceedings of the 34th AAAI Conference on Artificial Intelligence}, keywords = {General Medicine}, location = {New York, NY, United States}, number = {06}, pages = {9794--9801}, publisher = {Association for the Advancement of Artificial Intelligence}, title = {{Reinforcement learning of risk-constrained policies in Markov decision processes}}, doi = {10.1609/aaai.v34i06.6531}, volume = {34}, year = {2020}, } @article{15057, abstract = {Vaccinia virus–related kinase (VRK) is an evolutionarily conserved nuclear protein kinase. VRK-1, the single Caenorhabditis elegans VRK ortholog, functions in cell division and germline proliferation. However, the role of VRK-1 in postmitotic cells and adult life span remains unknown. Here, we show that VRK-1 increases organismal longevity by activating the cellular energy sensor, AMP-activated protein kinase (AMPK), via direct phosphorylation. We found that overexpression of vrk-1 in the soma of adult C. elegans increased life span and, conversely, inhibition of vrk-1 decreased life span. In addition, vrk-1 was required for longevity conferred by mutations that inhibit C. elegans mitochondrial respiration, which requires AMPK. VRK-1 directly phosphorylated and up-regulated AMPK in both C. elegans and cultured human cells. Thus, our data show that the somatic nuclear kinase, VRK-1, promotes longevity through AMPK activation, and this function appears to be conserved between C. elegans and humans.}, author = {Park, Sangsoon and Artan, Murat and Han, Seung Hyun and Park, Hae-Eun H. and Jung, Yoonji and Hwang, Ara B. and Shin, Won Sik and Kim, Kyong-Tai and Lee, Seung-Jae V.}, issn = {2375-2548}, journal = {Science Advances}, number = {27}, publisher = {American Association for the Advancement of Science}, title = {{VRK-1 extends life span by activation of AMPK via phosphorylation}}, doi = {10.1126/sciadv.aaw7824}, volume = {6}, year = {2020}, } @article{15061, abstract = {The actin cytoskeleton, a dynamic network of actin filaments and associated F-actin–binding proteins, is fundamentally important in eukaryotes. α-Actinins are major F-actin bundlers that are inhibited by Ca2+ in nonmuscle cells. Here we report the mechanism of Ca2+-mediated regulation of Entamoeba histolytica α-actinin-2 (EhActn2) with features expected for the common ancestor of Entamoeba and higher eukaryotic α-actinins. Crystal structures of Ca2+-free and Ca2+-bound EhActn2 reveal a calmodulin-like domain (CaMD) uniquely inserted within the rod domain. Integrative studies reveal an exceptionally high affinity of the EhActn2 CaMD for Ca2+, binding of which can only be regulated in the presence of physiological concentrations of Mg2+. Ca2+ binding triggers an increase in protein multidomain rigidity, reducing conformational flexibility of F-actin–binding domains via interdomain cross-talk and consequently inhibiting F-actin bundling. In vivo studies uncover that EhActn2 plays an important role in phagocytic cup formation and might constitute a new drug target for amoebic dysentery.}, author = {Pinotsis, Nikos and Zielinska, Karolina and Babuta, Mrigya and Arolas, Joan L. and Kostan, Julius and Khan, Muhammad Bashir and Schreiner, Claudia and Testa Salmazo, Anita P and Ciccarelli, Luciano and Puchinger, Martin and Gkougkoulia, Eirini A. and Ribeiro, Euripedes de Almeida and Marlovits, Thomas C. and Bhattacharya, Alok and Djinovic-Carugo, Kristina}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences}, number = {36}, pages = {22101--22112}, publisher = {Proceedings of the National Academy of Sciences}, title = {{Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin}}, doi = {10.1073/pnas.1917269117}, volume = {117}, year = {2020}, } @article{15064, abstract = {We call a continuous self-map that reveals itself through a discrete set of point-value pairs a sampled dynamical system. Capturing the available information with chain maps on Delaunay complexes, we use persistent homology to quantify the evidence of recurrent behavior. We establish a sampling theorem to recover the eigenspaces of the endomorphism on homology induced by the self-map. Using a combinatorial gradient flow arising from the discrete Morse theory for Čech and Delaunay complexes, we construct a chain map to transform the problem from the natural but expensive Čech complexes to the computationally efficient Delaunay triangulations. The fast chain map algorithm has applications beyond dynamical systems.}, author = {Bauer, U. and Edelsbrunner, Herbert and Jablonski, Grzegorz and Mrozek, M.}, issn = {2367-1734}, journal = {Journal of Applied and Computational Topology}, number = {4}, pages = {455--480}, publisher = {Springer Nature}, title = {{Čech-Delaunay gradient flow and homology inference for self-maps}}, doi = {10.1007/s41468-020-00058-8}, volume = {4}, year = {2020}, } @article{15063, abstract = {We consider the least singular value of a large random matrix with real or complex i.i.d. Gaussian entries shifted by a constant z∈C. We prove an optimal lower tail estimate on this singular value in the critical regime where z is around the spectral edge, thus improving the classical bound of Sankar, Spielman and Teng (SIAM J. Matrix Anal. Appl. 28:2 (2006), 446–476) for the particular shift-perturbation in the edge regime. Lacking Brézin–Hikami formulas in the real case, we rely on the superbosonization formula (Comm. Math. Phys. 283:2 (2008), 343–395).}, author = {Cipolloni, Giorgio and Erdös, László and Schröder, Dominik J}, issn = {2690-1005}, journal = {Probability and Mathematical Physics}, keywords = {General Medicine}, number = {1}, pages = {101--146}, publisher = {Mathematical Sciences Publishers}, title = {{Optimal lower bound on the least singular value of the shifted Ginibre ensemble}}, doi = {10.2140/pmp.2020.1.101}, volume = {1}, year = {2020}, } @inproceedings{15074, abstract = {We introduce a new graph problem, the token dropping game, and we show how to solve it efficiently in a distributed setting. We use the token dropping game as a tool to design an efficient distributed algorithm for the stable orientation problem, which is a special case of the more general locally optimal semi-matching problem. The prior work by Czygrinow et al. (DISC 2012) finds a locally optimal semi-matching in O(Δ⁵) rounds in graphs of maximum degree Δ, which directly implies an algorithm with the same runtime for stable orientations. We improve the runtime to O(Δ⁴) for stable orientations and prove a lower bound of Ω(Δ) rounds.}, author = {Brandt, Sebastian and Keller, Barbara and Rybicki, Joel and Suomela, Jukka and Uitto, Jara}, booktitle = {34th International Symposium on Distributed Computing}, location = {Virtual}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Brief announcement: Efficient load-balancing through distributed token dropping}}, doi = {10.4230/LIPIcs.DISC.2020.40}, volume = {179}, year = {2020}, } @inproceedings{15077, abstract = {We consider the following dynamic load-balancing process: given an underlying graph G with n nodes, in each step t≥ 0, one unit of load is created, and placed at a randomly chosen graph node. In the same step, the chosen node picks a random neighbor, and the two nodes balance their loads by averaging them. We are interested in the expected gap between the minimum and maximum loads at nodes as the process progresses, and its dependence on n and on the graph structure. Variants of the above graphical balanced allocation process have been studied previously by Peres, Talwar, and Wieder [Peres et al., 2015], and by Sauerwald and Sun [Sauerwald and Sun, 2015]. These authors left as open the question of characterizing the gap in the case of cycle graphs in the dynamic case, where weights are created during the algorithm’s execution. For this case, the only known upper bound is of 𝒪(n log n), following from a majorization argument due to [Peres et al., 2015], which analyzes a related graphical allocation process. In this paper, we provide an upper bound of 𝒪 (√n log n) on the expected gap of the above process for cycles of length n. We introduce a new potential analysis technique, which enables us to bound the difference in load between k-hop neighbors on the cycle, for any k ≤ n/2. We complement this with a "gap covering" argument, which bounds the maximum value of the gap by bounding its value across all possible subsets of a certain structure, and recursively bounding the gaps within each subset. We provide analytical and experimental evidence that our upper bound on the gap is tight up to a logarithmic factor.}, author = {Alistarh, Dan-Adrian and Nadiradze, Giorgi and Sabour, Amirmojtaba}, booktitle = {47th International Colloquium on Automata, Languages, and Programming}, location = {Saarbrücken, Germany, Virtual}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Dynamic averaging load balancing on cycles}}, doi = {10.4230/LIPIcs.ICALP.2020.7}, volume = {168}, year = {2020}, } @inproceedings{15082, abstract = {Two plane drawings of geometric graphs on the same set of points are called disjoint compatible if their union is plane and they do not have an edge in common. For a given set S of 2n points two plane drawings of perfect matchings M1 and M2 (which do not need to be disjoint nor compatible) are disjoint tree-compatible if there exists a plane drawing of a spanning tree T on S which is disjoint compatible to both M1 and M2. We show that the graph of all disjoint tree-compatible perfect geometric matchings on 2n points in convex position is connected if and only if 2n ≥ 10. Moreover, in that case the diameter of this graph is either 4 or 5, independent of n.}, author = {Aichholzer, Oswin and Obmann, Julia and Patak, Pavel and Perz, Daniel and Tkadlec, Josef}, booktitle = {36th European Workshop on Computational Geometry}, location = {Würzburg, Germany, Virtual}, title = {{Disjoint tree-compatible plane perfect matchings}}, year = {2020}, } @article{6748, abstract = {Fitting a function by using linear combinations of a large number N of `simple' components is one of the most fruitful ideas in statistical learning. This idea lies at the core of a variety of methods, from two-layer neural networks to kernel regression, to boosting. In general, the resulting risk minimization problem is non-convex and is solved by gradient descent or its variants. Unfortunately, little is known about global convergence properties of these approaches. Here we consider the problem of learning a concave function f on a compact convex domain Ω⊆ℝd, using linear combinations of `bump-like' components (neurons). The parameters to be fitted are the centers of N bumps, and the resulting empirical risk minimization problem is highly non-convex. We prove that, in the limit in which the number of neurons diverges, the evolution of gradient descent converges to a Wasserstein gradient flow in the space of probability distributions over Ω. Further, when the bump width δ tends to 0, this gradient flow has a limit which is a viscous porous medium equation. Remarkably, the cost function optimized by this gradient flow exhibits a special property known as displacement convexity, which implies exponential convergence rates for N→∞, δ→0. Surprisingly, this asymptotic theory appears to capture well the behavior for moderate values of δ,N. Explaining this phenomenon, and understanding the dependence on δ,N in a quantitative manner remains an outstanding challenge.}, author = {Javanmard, Adel and Mondelli, Marco and Montanari, Andrea}, issn = {1941-7330}, journal = {Annals of Statistics}, number = {6}, pages = {3619--3642}, publisher = {Institute of Mathematical Statistics}, title = {{Analysis of a two-layer neural network via displacement convexity}}, doi = {10.1214/20-AOS1945}, volume = {48}, year = {2020}, } @article{8741, abstract = {In ecology, climate and other fields, (sub)systems have been identified that can transition into a qualitatively different state when a critical threshold or tipping point in a driving process is crossed. An understanding of those tipping elements is of great interest given the increasing influence of humans on the biophysical Earth system. Complex interactions exist between tipping elements, e.g. physical mechanisms connect subsystems of the climate system. Based on earlier work on such coupled nonlinear systems, we systematically assessed the qualitative long-term behaviour of interacting tipping elements. We developed an understanding of the consequences of interactions on the tipping behaviour allowing for tipping cascades to emerge under certain conditions. The (narrative) application of these qualitative results to real-world examples of interacting tipping elements indicates that tipping cascades with profound consequences may occur: the interacting Greenland ice sheet and thermohaline ocean circulation might tip before the tipping points of the isolated subsystems are crossed. The eutrophication of the first lake in a lake chain might propagate through the following lakes without a crossing of their individual critical nutrient input levels. The possibility of emerging cascading tipping dynamics calls for the development of a unified theory of interacting tipping elements and the quantitative analysis of interacting real-world tipping elements.}, author = {Klose, Ann Kristin and Karle, Volker and Winkelmann, Ricarda and Donges, Jonathan F.}, issn = {20545703}, journal = {Royal Society Open Science}, number = {6}, publisher = {The Royal Society}, title = {{Emergence of cascading dynamics in interacting tipping elements of ecology and climate: Cascading dynamics in tipping elements}}, doi = {10.1098/rsos.200599}, volume = {7}, year = {2020}, } @article{7687, abstract = {A working group, which was established within the Network of Repository Managers (RepManNet), has dealt with common certifications for repositories. In addition, current requirements of the research funding agencies FWF and EU were also taken into account. The Core Trust Seal was examined in more detail. For this purpose, a questionnaire was sent to those organizations that are already certified with CTS in Austria. The answers were summarized and evaluated anonymously. It is recommended to go for a repository certification. Moreover, the development of a DINI certificate in Austria is strongly suggested.}, author = {Ernst, Doris and Novotny, Gertraud and Schönher, Eva Maria}, issn = {1022-2588}, journal = {Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare}, number = {1}, pages = {46--59}, publisher = {Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare}, title = {{(Core Trust) Seal your repository!}}, doi = {10.31263/voebm.v73i1.3491}, volume = {73}, year = {2020}, } @inproceedings{15071, abstract = {A mesophilic methanogenic culture, designated JL01, was isolated from Holocene permafrost in the Russian Arctic [1]. After long-term extensive cultivation at 15°C it turned out to be a tied binary culture of archaeal (JL01) and bacterial (Sphaerochaeta associata GLS2) strains. Strain JL01 was a strict anaerobe and grew on methanol, acetate and methylamines as energy and carbon sources. Cells were irregular coccoid, non-motile, non-spore-forming, and Gram-stainpositive. Optimum conditions for growth were 24-28 oC, pH 6.8–7.3 and 0.075-0.1 M NaCl. Phylogenetic tree reconstructions based on 16S rRNA and concatenated alignment of broadly conserved protein-coding genes revealed its close relation to Methanosarcina mazei S-6 T (similarity 99.5%). The comparison of whole genomic sequences (ANI) of the isolate and the type strain of M.mazei was 98.5%, which is higher than the values recommended for new species. Thus strain JL01 (=VKM B-2370=JCM 31898) represents the first M. mazei isolated from permanently subzero Arcticsediments. The long-term co-cultivation of JL01 with S. associata GLS2T showed the methane production without any additional carbon and energy sources. Genome analysis of S. associata GLS2T revealed putative genes involved in methanochondroithin catabolism.}, author = {Oshurkova, Viktoriia and Troshina, Olga and Trubitsyn, Vladimir and Ryzhmanova, Yana and Bochkareva, Olga and Shcherbakova, Viktoria}, booktitle = {Proceedings of 1st International Electronic Conference on Microbiology}, location = {Virtual}, publisher = {MDPI}, title = {{Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T}}, doi = {10.3390/ecm2020-07116}, year = {2020}, }