@article{9229, author = {Danzl, Johann G}, issn = {2500-2295}, journal = {Opera Medica et Physiologica}, number = {S1}, pages = {11}, publisher = {Lobachevsky State University of Nizhny Novgorod}, title = {{Diffraction-unlimited optical imaging for synaptic physiology}}, doi = {10.20388/omp2018.00s1.001}, volume = {4}, year = {2018}, } @article{9471, abstract = {The DEMETER (DME) DNA glycosylase catalyzes genome-wide DNA demethylation and is required for endosperm genomic imprinting and embryo viability. Targets of DME-mediated DNA demethylation reside in small, euchromatic, AT-rich transposons and at the boundaries of large transposons, but how DME interacts with these diverse chromatin states is unknown. The STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1) subunit of the chromatin remodeler FACT (facilitates chromatin transactions), was previously shown to be involved in the DME-dependent regulation of genomic imprinting in Arabidopsis endosperm. Therefore, to investigate the interaction between DME and chromatin, we focused on the activity of the two FACT subunits, SSRP1 and SUPPRESSOR of TY16 (SPT16), during reproduction in Arabidopsis. We found that FACT colocalizes with nuclear DME in vivo, and that DME has two classes of target sites, the first being euchromatic and accessible to DME, but the second, representing over half of DME targets, requiring the action of FACT for DME-mediated DNA demethylation genome-wide. Our results show that the FACT-dependent DME targets are GC-rich heterochromatin domains with high nucleosome occupancy enriched with H3K9me2 and H3K27me1. Further, we demonstrate that heterochromatin-associated linker histone H1 specifically mediates the requirement for FACT at a subset of DME-target loci. Overall, our results demonstrate that FACT is required for DME targeting by facilitating its access to heterochromatin.}, author = {Frost, Jennifer M. and Kim, M. Yvonne and Park, Guen Tae and Hsieh, Ping-Hung and Nakamura, Miyuki and Lin, Samuel J. H. and Yoo, Hyunjin and Choi, Jaemyung and Ikeda, Yoko and Kinoshita, Tetsu and Choi, Yeonhee and Zilberman, Daniel and Fischer, Robert L.}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences}, keywords = {Multidisciplinary}, number = {20}, pages = {E4720--E4729}, publisher = {National Academy of Sciences}, title = {{FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis}}, doi = {10.1073/pnas.1713333115}, volume = {115}, year = {2018}, } @article{95, abstract = {Electrostatic charging of insulating fine particles can be responsible for numerous phenomena ranging from lightning in volcanic plumes to dust explosions. However, even basic aspects of how fine particles become charged are still unclear. Studying particle charging is challenging because it usually involves the complexities associated with many-particle collisions. To address these issues, we introduce a method based on acoustic levitation, which makes it possible to initiate sequences of repeated collisions of a single submillimeter particle with a flat plate, and to precisely measure the particle charge in situ after each collision. We show that collisional charge transfer between insulators is dependent on the hydrophobicity of the contacting surfaces. We use glass, which we modify by attaching nonpolar molecules to the particle, the plate, or both. We find that hydrophilic surfaces develop significant positive charges after contacting hydrophobic surfaces. Moreover, we demonstrate that charging between a hydrophilic and a hydrophobic surface is suppressed in an acidic environment and enhanced in a basic one. Application of an electric field during each collision is found to modify the charge transfer, again depending on surface hydrophobicity. We discuss these results within the context of contact charging due to ion transfer, and we show that they lend strong support to OH− ions as the charge carriers.}, author = {Lee, Victor and James, Nicole and Waitukaitis, Scott R and Jaeger, Heinrich}, journal = {Physical Review Materials}, number = {3}, publisher = {American Physical Society}, title = {{Collisional charging of individual submillimeter particles: Using ultrasonic levitation to initiate and track charge transfer}}, doi = {10.1103/PhysRevMaterials.2.035602}, volume = {2}, year = {2018}, } @article{9565, abstract = {Let D(n,p) be the random directed graph on n vertices where each of the n(n-1) possible arcs is present independently with probability p. A celebrated result of Frieze shows that if p≥(logn+ω(1))/n then D(n,p) typically has a directed Hamilton cycle, and this is best possible. In this paper, we obtain a strengthening of this result, showing that under the same condition, the number of directed Hamilton cycles in D(n,p) is typically n!(p(1+o(1)))n. We also prove a hitting-time version of this statement, showing that in the random directed graph process, as soon as every vertex has in-/out-degrees at least 1, there are typically n!(logn/n(1+o(1)))n directed Hamilton cycles.}, author = {Ferber, Asaf and Kwan, Matthew Alan and Sudakov, Benny}, issn = {1098-2418}, journal = {Random Structures and Algorithms}, number = {4}, pages = {592--603}, publisher = {Wiley}, title = {{Counting Hamilton cycles in sparse random directed graphs}}, doi = {10.1002/rsa.20815}, volume = {53}, year = {2018}, } @article{9567, abstract = {Let P be a graph property which is preserved by removal of edges, and consider the random graph process that starts with the empty n-vertex graph and then adds edges one-by-one, each chosen uniformly at random subject to the constraint that P is not violated. These types of random processes have been the subject of extensive research over the last 20 years, having striking applications in extremal combinatorics, and leading to the discovery of important probabilistic tools. In this paper we consider the k-matching-free process, where P is the property of not containing a matching of size k. We are able to analyse the behaviour of this process for a wide range of values of k; in particular we prove that if k=o(n) or if n−2k=o(n−−√/logn) then this process is likely to terminate in a k-matching-free graph with the maximum possible number of edges, as characterised by Erdős and Gallai. We also show that these bounds on k are essentially best possible, and we make a first step towards understanding the behaviour of the process in the intermediate regime.}, author = {Krivelevich, Michael and Kwan, Matthew Alan and Loh, Po‐Shen and Sudakov, Benny}, issn = {1098-2418}, journal = {Random Structures and Algorithms}, number = {4}, pages = {692--716}, publisher = {Wiley}, title = {{The random k‐matching‐free process}}, doi = {10.1002/rsa.20814}, volume = {53}, year = {2018}, } @article{9568, abstract = {An intercalate in a Latin square is a 2×2 Latin subsquare. Let N be the number of intercalates in a uniformly random n×n Latin square. We prove that asymptotically almost surely N≥(1−o(1))n2/4, and that EN≤(1+o(1))n2/2 (therefore asymptotically almost surely N≤fn2 for any f→∞). This significantly improves the previous best lower and upper bounds. We also give an upper tail bound for the number of intercalates in two fixed rows of a random Latin square. In addition, we discuss a problem of Linial and Luria on low-discrepancy Latin squares.}, author = {Kwan, Matthew Alan and Sudakov, Benny}, issn = {1098-2418}, journal = {Random Structures and Algorithms}, number = {2}, pages = {181--196}, publisher = {Wiley}, title = {{Intercalates and discrepancy in random Latin squares}}, doi = {10.1002/rsa.20742}, volume = {52}, year = {2018}, } @article{9587, abstract = {We say a family of sets is intersecting if any two of its sets intersect, and we say it is trivially intersecting if there is an element which appears in every set of the family. In this paper we study the maximum size of a non-trivially intersecting family in a natural “multi-part” setting. Here the ground set is divided into parts, and one considers families of sets whose intersection with each part is of a prescribed size. Our work is motivated by classical results in the single-part setting due to Erdős, Ko and Rado, and Hilton and Milner, and by a theorem of Frankl concerning intersecting families in this multi-part setting. In the case where the part sizes are sufficiently large we determine the maximum size of a non-trivially intersecting multi-part family, disproving a conjecture of Alon and Katona.}, author = {Kwan, Matthew Alan and Sudakov, Benny and Vieira, Pedro}, issn = {0097-3165}, journal = {Journal of Combinatorial Theory Series A}, pages = {44--60}, publisher = {Elsevier}, title = {{Non-trivially intersecting multi-part families}}, doi = {10.1016/j.jcta.2017.12.001}, volume = {156}, year = {2018}, } @article{9659, abstract = {The curvature dependence of interfacial free energy, which is crucial in quantitatively predicting nucleation kinetics and the stability of bubbles and droplets, is quantified by the Tolman length δ. For solid-liquid interfaces, however, δ has never been computed directly due to various theoretical and practical challenges. Here we perform a direct evaluation of the Tolman length from atomistic simulations of a solid-liquid planar interface in out-of-equilibrium conditions, by first computing the surface tension from the amplitude of thermal capillary fluctuations of a localized version of the Gibbs dividing surface and by then calculating how much the surface energy changes when it is defined relative to the equimolar dividing surface. We computed δ for a model potential, and found a good agreement with the values indirectly inferred from nucleation simulations. The agreement not only validates our approach but also suggests that the nucleation free energy of the system can be perfectly described using classical nucleation theory if the Tolman length is taken into account.}, author = {Cheng, Bingqing and Ceriotti, Michele}, issn = {1089-7690}, journal = {The Journal of Chemical Physics}, number = {23}, publisher = {AIP Publishing}, title = {{Communication: Computing the Tolman length for solid-liquid interfaces}}, doi = {10.1063/1.5038396}, volume = {148}, year = {2018}, } @article{9665, abstract = {We investigate the thermodynamics and kinetics of a hydrogen interstitial in magnetic α-iron, taking account of the quantum fluctuations of the proton as well as the anharmonicities of lattice vibrations and hydrogen hopping. We show that the diffusivity of hydrogen in the lattice of bcc iron deviates strongly from an Arrhenius behavior at and below room temperature. We compare a quantum transition state theory to explicit ring polymer molecular dynamics in the calculation of diffusivity. We then address the trapping of hydrogen by a vacancy as a prototype lattice defect. By a sequence of steps in a thought experiment, each involving a thermodynamic integration, we are able to separate out the binding free energy of a proton to a defect into harmonic and anharmonic, and classical and quantum contributions. We find that about 30% of a typical binding free energy of hydrogen to a lattice defect in iron is accounted for by finite temperature effects, and about half of these arise from quantum proton fluctuations. This has huge implications for the comparison between thermal desorption and permeation experiments and standard electronic structure theory. The implications are even greater for the interpretation of muon spin resonance experiments.}, author = {Cheng, Bingqing and Paxton, Anthony T. and Ceriotti, Michele}, issn = {1079-7114}, journal = {Physical Review Letters}, number = {22}, publisher = {American Physical Society}, title = {{Hydrogen diffusion and trapping in α-iron: The role of quantum and anharmonic fluctuations}}, doi = {10.1103/physrevlett.120.225901}, volume = {120}, year = {2018}, } @article{9668, abstract = {Estimating the homogeneous ice nucleation rate from undercooled liquid water is crucial for understanding many important physical phenomena and technological applications, and challenging for both experiments and theory. From a theoretical point of view, difficulties arise due to the long time scales required, as well as the numerous nucleation pathways involved to form ice nuclei with different stacking disorders. We computed the homogeneous ice nucleation rate at a physically relevant undercooling for a single-site water model, taking into account the diffuse nature of ice–water interfaces, stacking disorders in ice nuclei, and the addition rate of particles to the critical nucleus. We disentangled and investigated the relative importance of all the terms, including interfacial free energy, entropic contributions and the kinetic prefactor, that contribute to the overall nucleation rate. Breaking down the problem into pieces not only provides physical insights into ice nucleation, but also sheds light on the long-standing discrepancy between different theoretical predictions, as well as between theoretical and experimental determinations of the nucleation rate. Moreover, we pinpoint the main shortcomings and suggest strategies to systematically improve the existing simulation methods.}, author = {Cheng, Bingqing and Dellago, Christoph and Ceriotti, Michele}, issn = {1463-9084}, journal = {Physical Chemistry Chemical Physics}, number = {45}, pages = {28732--28740}, publisher = {Royal Society of Chemistry}, title = {{Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics}}, doi = {10.1039/c8cp04561e}, volume = {20}, year = {2018}, } @article{9687, abstract = {The Gibbs free energy is the fundamental thermodynamic potential underlying the relative stability of different states of matter under constant-pressure conditions. However, computing this quantity from atomic-scale simulations is far from trivial, so the potential energy of a system is often used as a proxy. In this paper, we use a combination of thermodynamic integration methods to accurately evaluate the Gibbs free energies associated with defects in crystals, including the vacancy formation energy in bcc iron, and the stacking fault energy in fcc nickel, iron, and cobalt. We quantify the importance of entropic and anharmonic effects in determining the free energies of defects at high temperatures, and show that the potential energy approximation as well as the harmonic approximation may produce inaccurate or even qualitatively wrong results. Our calculations manifest the necessity to employ accurate free energy methods such as thermodynamic integration to estimate the stability of crystallographic defects at high temperatures.}, author = {Cheng, Bingqing and Ceriotti, Michele}, issn = {2469-9969}, journal = {Physical Review B}, number = {5}, publisher = {American Physical Society}, title = {{Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids}}, doi = {10.1103/physrevb.97.054102}, volume = {97}, year = {2018}, } @misc{9807, abstract = {Table S1. Genes with highest betweenness. Table S2. Local and Master regulators up-regulated. Table S3. Local and Master regulators down-regulated (XLSX 23 kb).}, author = {Higareda Almaraz, Juan and Karbiener, Michael and Giroud, Maude and Pauler, Florian and Gerhalter, Teresa and Herzig, Stephan and Scheideler, Marcel}, publisher = {Springer Nature}, title = {{Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes}}, doi = {10.6084/m9.figshare.7295339.v1}, year = {2018}, } @misc{9808, abstract = {Table S4. Counts per Gene per Million Reads Mapped. (XLSX 2751 kb).}, author = {Higareda Almaraz, Juan and Karbiener, Michael and Giroud, Maude and Pauler, Florian and Gerhalter, Teresa and Herzig, Stephan and Scheideler, Marcel}, publisher = {Springer Nature}, title = {{Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes}}, doi = {10.6084/m9.figshare.7295369.v1}, year = {2018}, } @misc{9811, abstract = {This document contains additional supporting evidence presented as supplemental tables. (XLSX 50Â kb)}, author = {Zapata, Luis and Pich, Oriol and Serrano, Luis and Kondrashov, Fyodor and Ossowski, Stephan and Schaefer, Martin}, publisher = {Springer Nature}, title = {{Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome}}, doi = {10.6084/m9.figshare.6401390.v1}, year = {2018}, } @misc{9812, abstract = {This document contains the full list of genes with their respective significance and dN/dS values. (TXT 4499Â kb)}, author = {Zapata, Luis and Pich, Oriol and Serrano, Luis and Kondrashov, Fyodor and Ossowski, Stephan and Schaefer, Martin}, publisher = {Springer Nature}, title = {{Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome}}, doi = {10.6084/m9.figshare.6401414.v1}, year = {2018}, } @misc{9813, abstract = {File S1 contains figures that clarify the following features: (i) effect of population size on the average number/frequency of SI classes, (ii) changes in the minimal completeness deficit in time for a single class, and (iii) diversification diagrams for all studied pathways, including the summary figure for k = 8. File S2 contains the code required for a stochastic simulation of the SLF system with an example. This file also includes the output in the form of figures and tables.}, author = {Bod'ová, Katarína and Priklopil, Tadeas and Field, David and Barton, Nicholas H and Pickup, Melinda}, publisher = {Genetics Society of America}, title = {{Supplemental material for Bodova et al., 2018}}, doi = {10.25386/genetics.6148304.v1}, year = {2018}, } @misc{9837, abstract = {Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients.}, author = {Faria, Rui and Chaube, Pragya and Morales, Hernán E. and Larsson, Tomas and Lemmon, Alan R. and Lemmon, Emily M. and Rafajlović, Marina and Panova, Marina and Ravinet, Mark and Johannesson, Kerstin and Westram, Anja M and Butlin, Roger K.}, publisher = {Dryad}, title = {{Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes}}, doi = {10.5061/dryad.72cg113}, year = {2018}, } @misc{9838, abstract = {Facial shape is the basis for facial recognition and categorization. Facial features reflect the underlying geometry of the skeletal structures. Here we reveal that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped by signals generated by neural structures: brain and olfactory epithelium. Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal capsule, whereas the formation of a capsule roof is controlled by signals from the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned out to be important for shaping membranous facial bones during development. This suggests that conserved neurosensory structures could benefit from protection and have evolved signals inducing cranial cartilages encasing them. Experiments with mutant mice revealed that the genomic regulatory regions controlling production of SHH in the nervous system contribute to facial cartilage morphogenesis, which might be a mechanism responsible for the adaptive evolution of animal faces and snouts.}, author = {Kaucka, Marketa and Petersen, Julian and Tesarova, Marketa and Szarowska, Bara and Kastriti, Maria Eleni and Xie, Meng and Kicheva, Anna and Annusver, Karl and Kasper, Maria and Symmons, Orsolya and Pan, Leslie and Spitz, Francois and Kaiser, Jozef and Hovorakova, Maria and Zikmund, Tomas and Sunadome, Kazunori and Matise, Michael P and Wang, Hui and Marklund, Ulrika and Abdo, Hind and Ernfors, Patrik and Maire, Pascal and Wurmser, Maud and Chagin, Andrei S and Fried, Kaj and Adameyko, Igor}, publisher = {Dryad}, title = {{Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage}}, doi = {10.5061/dryad.f1s76f2}, year = {2018}, } @misc{9840, abstract = {Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity.}, author = {Payne, Pavel and Geyrhofer, Lukas and Barton, Nicholas H and Bollback, Jonathan P}, publisher = {Dryad}, title = {{Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations}}, doi = {10.5061/dryad.42n44}, year = {2018}, } @misc{9841, abstract = {Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects. Dramatic adaptive changes in genes underlying the production and perception of pheromones confirm the importance of chemical communication in the termites. These are accompanied by major changes in gene regulation and the molecular evolution of caste determination. Many of these results parallel molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific solutions are remarkably different, thus revealing a striking case of convergence in one of the major evolutionary transitions in biological complexity.}, author = {Harrison, Mark C. and Jongepier, Evelien and Robertson, Hugh M. and Arning, Nicolas and Bitard-Feildel, Tristan and Chao, Hsu and Childers, Christopher P. and Dinh, Huyen and Doddapaneni, Harshavardhan and Dugan, Shannon and Gowin, Johannes and Greiner, Carolin and Han, Yi and Hu, Haofu and Hughes, Daniel S. T. and Huylmans, Ann K and Kemena, Carsten and Kremer, Lukas P. M. and Lee, Sandra L. and Lopez-Ezquerra, Alberto and Mallet, Ludovic and Monroy-Kuhn, Jose M. and Moser, Annabell and Murali, Shwetha C. and Muzny, Donna M. and Otani, Saria and Piulachs, Maria-Dolors and Poelchau, Monica and Qu, Jiaxin and Schaub, Florentine and Wada-Katsumata, Ayako and Worley, Kim C. and Xie, Qiaolin and Ylla, Guillem and Poulsen, Michael and Gibbs, Richard A. and Schal, Coby and Richards, Stephen and Belles, Xavier and Korb, Judith and Bornberg-Bauer, Erich}, publisher = {Dryad}, title = {{Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality}}, doi = {10.5061/dryad.51d4r}, year = {2018}, }