@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{9810,
  author       = {Chaudhry, Waqas and Pleska, Maros and Shah, Nilang and Weiss, Howard and Mccall, Ingrid and Meyer, Justin and Gupta, Animesh and Guet, Calin C and Levin, Bruce},
  publisher    = {Public Library of Science},
  title        = {{Numerical data used in figures}},
  doi          = {10.1371/journal.pbio.2005971.s008},
  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{9831,
  abstract     = {Implementation of the inference method in Matlab, including three applications of the method: The first one for the model of ant motion, the second one for bacterial chemotaxis, and the third one for the motion of fish.},
  author       = {Bod’Ová, Katarína and Mitchell, Gabriel and Harpaz, Roy and Schneidman, Elad and Tkačik, Gašper},
  publisher    = {Public Library of Science},
  title        = {{Implementation of the inference method in Matlab}},
  doi          = {10.1371/journal.pone.0193049.s001},
  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},
}

@article{9915,
  abstract     = {The evolution of assortative mating is a key part of the speciation process. Stronger assortment, or greater divergence in mating traits, between species pairs with overlapping ranges is commonly observed, but possible causes of this pattern of reproductive character displacement are difficult to distinguish. We use a multidisciplinary approach to provide a rare example where it is possible to distinguish among hypotheses concerning the evolution of reproductive character displacement. We build on an earlier comparative analysis that illustrated a strong pattern of greater divergence in penis form between pairs of sister species with overlapping ranges than between allopatric sister-species pairs, in a large clade of marine gastropods (Littorinidae). We investigate both assortative mating and divergence in male genitalia in one of the sister-species pairs, discriminating among three contrasting processes each of which can generate a pattern of reproductive character displacement: reinforcement, reproductive interference and the Templeton effect. We demonstrate reproductive character displacement in assortative mating, but not in genital form between this pair of sister species and use demographic models to distinguish among the different processes. Our results support a model with no gene flow since secondary contact and thus favor reproductive interference as the cause of reproductive character displacement for mate choice, rather than reinforcement. High gene flow within species argues against the Templeton effect. Secondary contact appears to have had little impact on genital divergence.},
  author       = {Hollander, Johan and Montaño-Rendón, Mauricio and Bianco, Giuseppe and Yang, Xi and Westram, Anja M and Duvaux, Ludovic and Reid, David G. and Butlin, Roger K.},
  issn         = {2056-3744},
  journal      = {Evolution Letters},
  number       = {6},
  pages        = {557--566},
  publisher    = {Wiley},
  title        = {{Are assortative mating and genital divergence driven by reinforcement?}},
  doi          = {10.1002/evl3.85},
  volume       = {2},
  year         = {2018},
}

@article{9917,
  abstract     = {Adaptive divergence and speciation may happen despite opposition by gene flow. Identifying the genomic basis underlying divergence with gene flow is a major task in evolutionary genomics. Most approaches (e.g., outlier scans) focus on genomic regions of high differentiation. However, not all genomic architectures potentially underlying divergence are expected to show extreme differentiation. Here, we develop an approach that combines hybrid zone analysis (i.e., focuses on spatial patterns of allele frequency change) with system-specific simulations to identify loci inconsistent with neutral evolution. We apply this to a genome-wide SNP set from an ideally suited study organism, the intertidal snail Littorina saxatilis, which shows primary divergence between ecotypes associated with different shore habitats. We detect many SNPs with clinal patterns, most of which are consistent with neutrality. Among non-neutral SNPs, most are located within three large putative inversions differentiating ecotypes. Many non-neutral SNPs show relatively low levels of differentiation. We discuss potential reasons for this pattern, including loose linkage to selected variants, polygenic adaptation and a component of balancing selection within populations (which may be expected for inversions). Our work is in line with theory predicting a role for inversions in divergence, and emphasizes that genomic regions contributing to divergence may not always be accessible with methods purely based on allele frequency differences. These conclusions call for approaches that take spatial patterns of allele frequency change into account in other systems.},
  author       = {Westram, Anja M and Rafajlović, Marina and Chaube, Pragya and Faria, Rui and Larsson, Tomas and Panova, Marina and Ravinet, Mark and Blomberg, Anders and Mehlig, Bernhard and Johannesson, Kerstin and Butlin, Roger},
  issn         = {2056-3744},
  journal      = {Evolution Letters},
  number       = {4},
  pages        = {297--309},
  publisher    = {Wiley},
  title        = {{Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow}},
  doi          = {10.1002/evl3.74},
  volume       = {2},
  year         = {2018},
}

@misc{9929,
  abstract     = {The evolution of assortative mating is a key part of the speciation process. Stronger assortment, or greater divergence in mating traits, between species pairs with overlapping ranges is commonly observed, but possible causes of this pattern of reproductive character displacement are difficult to distinguish. We use a multidisciplinary approach to provide a rare example where it is possible to distinguish among hypotheses concerning the evolution of reproductive character displacement. We build on an earlier comparative analysis that illustrated a strong pattern of greater divergence in penis form between pairs of sister species with overlapping ranges than between allopatric sister-species pairs, in a large clade of marine gastropods (Littorinidae). We investigate both assortative mating and divergence in male genitalia in one of the sister-species pairs, discriminating among three contrasting processes each of which can generate a pattern of reproductive character displacement: reinforcement, reproductive interference and the Templeton effect. We demonstrate reproductive character displacement in assortative mating, but not in genital form between this pair of sister species and use demographic models to distinguish among the different processes. Our results support a model with no gene flow since secondary contact and thus favour reproductive interference as the cause of reproductive character displacement for mate choice, rather than reinforcement. High gene flow within species argues against the Templeton effect. Secondary contact appears to have had little impact on genital divergence.},
  author       = {Hollander, Johan and Montaño-Rendón, Mauricio and Bianco, Giuseppe and Yang, Xi and Westram, Anja M and Duvaux, Ludovic and Reid, David G. and Butlin, Roger K.},
  publisher    = {Dryad},
  title        = {{Data from: Are assortative mating and genital divergence driven by reinforcement?}},
  doi          = {10.5061/dryad.51sd2p5},
  year         = {2018},
}