@article{384, abstract = {Can orthologous proteins differ in terms of their ability to be secreted? To answer this question, we investigated the distribution of signal peptides within the orthologous groups of Enterobacterales. Parsimony analysis and sequence comparisons revealed a large number of signal peptide gain and loss events, in which signal peptides emerge or disappear in the course of evolution. Signal peptide losses prevail over gains, an effect which is especially pronounced in the transition from the free-living or commensal to the endosymbiotic lifestyle. The disproportionate decline in the number of signal peptide-containing proteins in endosymbionts cannot be explained by the overall reduction of their genomes. Signal peptides can be gained and lost either by acquisition/elimination of the corresponding N-terminal regions or by gradual accumulation of mutations. The evolutionary dynamics of signal peptides in bacterial proteins represents a powerful mechanism of functional diversification.}, author = {Hönigschmid, Peter and Bykova, Nadya and Schneider, René and Ivankov, Dmitry and Frishman, Dmitrij}, journal = {Genome Biology and Evolution}, number = {3}, pages = {928 -- 938}, publisher = {Oxford University Press}, title = {{Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss}}, doi = {10.1093/gbe/evy049}, volume = {10}, year = {2018}, } @article{563, abstract = {In continuous populations with local migration, nearby pairs of individuals have on average more similar genotypes than geographically well separated pairs. A barrier to gene flow distorts this classical pattern of isolation by distance. Genetic similarity is decreased for sample pairs on different sides of the barrier and increased for pairs on the same side near the barrier. Here, we introduce an inference scheme that utilizes this signal to detect and estimate the strength of a linear barrier to gene flow in two-dimensions. We use a diffusion approximation to model the effects of a barrier on the geographical spread of ancestry backwards in time. This approach allows us to calculate the chance of recent coalescence and probability of identity by descent. We introduce an inference scheme that fits these theoretical results to the geographical covariance structure of bialleleic genetic markers. It can estimate the strength of the barrier as well as several demographic parameters. We investigate the power of our inference scheme to detect barriers by applying it to a wide range of simulated data. We also showcase an example application to a Antirrhinum majus (snapdragon) flower color hybrid zone, where we do not detect any signal of a strong genome wide barrier to gene flow.}, author = {Ringbauer, Harald and Kolesnikov, Alexander and Field, David and Barton, Nicholas H}, journal = {Genetics}, number = {3}, pages = {1231--1245}, publisher = {Genetics Society of America}, title = {{Estimating barriers to gene flow from distorted isolation-by-distance patterns}}, doi = {10.1534/genetics.117.300638}, volume = {208}, year = {2018}, } @article{135, abstract = {The Fluid Implicit Particle method (FLIP) reduces numerical dissipation by combining particles with grids. To improve performance, the subsequent narrow band FLIP method (NB‐FLIP) uses a FLIP‐based fluid simulation only near the liquid surface and a traditional grid‐based fluid simulation away from the surface. This spatially‐limited FLIP simulation significantly reduces the number of particles and alleviates a computational bottleneck. In this paper, we extend the NB‐FLIP idea even further, by allowing a simulation to transition between a FLIP‐like fluid simulation and a grid‐based simulation in arbitrary locations, not just near the surface. This approach leads to even more savings in memory and computation, because we can concentrate the particles only in areas where they are needed. More importantly, this new method allows us to seamlessly transition to smooth implicit surface geometry wherever the particle‐based simulation is unnecessary. Consequently, our method leads to a practical algorithm for avoiding the noisy surface artifacts associated with particle‐based liquid simulations, while simultaneously maintaining the benefits of a FLIP simulation in regions of dynamic motion.}, author = {Sato, Takahiro and Wojtan, Christopher J and Thuerey, Nils and Igarashi, Takeo and Ando, Ryoichi}, issn = {0167-7055}, journal = {Computer Graphics Forum}, number = {2}, pages = {169 -- 177}, publisher = {Wiley}, title = {{Extended narrow band FLIP for liquid simulations}}, doi = {10.1111/cgf.13351}, volume = {37}, year = {2018}, } @article{316, abstract = {Self-incompatibility (SI) is a genetically based recognition system that functions to prevent self-fertilization and mating among related plants. An enduring puzzle in SI is how the high diversity observed in nature arises and is maintained. Based on the underlying recognition mechanism, SI can be classified into two main groups: self- and non-self recognition. Most work has focused on diversification within self-recognition systems despite expected differences between the two groups in the evolutionary pathways and outcomes of diversification. Here, we use a deterministic population genetic model and stochastic simulations to investigate how novel S-haplotypes evolve in a gametophytic non-self recognition (SRNase/S Locus F-box (SLF)) SI system. For this model the pathways for diversification involve either the maintenance or breakdown of SI and can vary in the order of mutations of the female (SRNase) and male (SLF) components. We show analytically that diversification can occur with high inbreeding depression and self-pollination, but this varies with evolutionary pathway and level of completeness (which determines the number of potential mating partners in the population), and in general is more likely for lower haplotype number. The conditions for diversification are broader in stochastic simulations of finite population size. However, the number of haplotypes observed under high inbreeding and moderate to high self-pollination is less than that commonly observed in nature. Diversification was observed through pathways that maintain SI as well as through self-compatible intermediates. Yet the lifespan of diversified haplotypes was sensitive to their level of completeness. By examining diversification in a non-self recognition SI system, this model extends our understanding of the evolution and maintenance of haplotype diversity observed in a self recognition system common in flowering plants.}, author = {Bodova, Katarina and Priklopil, Tadeas and Field, David and Barton, Nicholas H and Pickup, Melinda}, journal = {Genetics}, number = {3}, pages = {861--883}, publisher = {Genetics Society of America}, title = {{Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system}}, doi = {10.1534/genetics.118.300748}, volume = {209}, year = {2018}, } @article{190, abstract = {The German cockroach, Blattella germanica, is a worldwide pest that infests buildings, including homes, restaurants, and hospitals, often living in unsanitary conditions. As a disease vector and producer of allergens, this species has major health and economic impacts on humans. Factors contributing to the success of the German cockroach include its resistance to a broad range of insecticides, immunity to many pathogens, and its ability, as an extreme generalist omnivore, to survive on most food sources. The recently published genome shows that B. germanica has an exceptionally high number of protein coding genes. In this study, we investigate the functions of the 93 significantly expanded gene families with the aim to better understand the success of B. germanica as a major pest despite such inhospitable conditions. We find major expansions in gene families with functions related to the detoxification of insecticides and allelochemicals, defense against pathogens, digestion, sensory perception, and gene regulation. These expansions might have allowed B. germanica to develop multiple resistance mechanisms to insecticides and pathogens, and enabled a broad, flexible diet, thus explaining its success in unsanitary conditions and under recurrent chemical control. The findings and resources presented here provide insights for better understanding molecular mechanisms that will facilitate more effective cockroach control.}, author = {Harrison, Mark and Arning, Nicolas and Kremer, Lucas and Ylla, Guillem and Belles, Xavier and Bornberg Bauer, Erich and Huylmans, Ann K and Jongepier, Evelien and Puilachs, Maria and Richards, Stephen and Schal, Coby}, journal = {Journal of Experimental Zoology Part B: Molecular and Developmental Evolution}, pages = {254--264}, publisher = {Wiley}, title = {{Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest}}, doi = {10.1002/jez.b.22824}, volume = {330}, year = {2018}, } @article{404, abstract = {We construct martingale solutions to stochastic thin-film equations by introducing a (spatial) semidiscretization and establishing convergence. The discrete scheme allows for variants of the energy and entropy estimates in the continuous setting as long as the discrete energy does not exceed certain threshold values depending on the spatial grid size $h$. Using a stopping time argument to prolongate high-energy paths constant in time, arbitrary moments of coupled energy/entropy functionals can be controlled. Having established Hölder regularity of approximate solutions, the convergence proof is then based on compactness arguments---in particular on Jakubowski's generalization of Skorokhod's theorem---weak convergence methods, and recent tools on martingale convergence. }, author = {Fischer, Julian L and Grün, Günther}, journal = {SIAM Journal on Mathematical Analysis}, number = {1}, pages = {411 -- 455}, publisher = {Society for Industrial and Applied Mathematics }, title = {{Existence of positive solutions to stochastic thin-film equations}}, doi = {10.1137/16M1098796}, volume = {50}, 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}, } @article{5780, abstract = {Bioluminescence is found across the entire tree of life, conferring a spectacular set of visually oriented functions from attracting mates to scaring off predators. Half a dozen different luciferins, molecules that emit light when enzymatically oxidized, are known. However, just one biochemical pathway for luciferin biosynthesis has been described in full, which is found only in bacteria. Here, we report identification of the fungal luciferase and three other key enzymes that together form the biosynthetic cycle of the fungal luciferin from caffeic acid, a simple and widespread metabolite. Introduction of the identified genes into the genome of the yeast Pichia pastoris along with caffeic acid biosynthesis genes resulted in a strain that is autoluminescent in standard media. We analyzed evolution of the enzymes of the luciferin biosynthesis cycle and found that fungal bioluminescence emerged through a series of events that included two independent gene duplications. The retention of the duplicated enzymes of the luciferin pathway in nonluminescent fungi shows that the gene duplication was followed by functional sequence divergence of enzymes of at least one gene in the biosynthetic pathway and suggests that the evolution of fungal bioluminescence proceeded through several closely related stepping stone nonluminescent biochemical reactions with adaptive roles. The availability of a complete eukaryotic luciferin biosynthesis pathway provides several applications in biomedicine and bioengineering.}, author = {Kotlobay, Alexey A. and Sarkisyan, Karen and Mokrushina, Yuliana A. and Marcet-Houben, Marina and Serebrovskaya, Ekaterina O. and Markina, Nadezhda M. and Gonzalez Somermeyer, Louisa and Gorokhovatsky, Andrey Y. and Vvedensky, Andrey and Purtov, Konstantin V. and Petushkov, Valentin N. and Rodionova, Natalja S. and Chepurnyh, Tatiana V. and Fakhranurova, Liliia and Guglya, Elena B. and Ziganshin, Rustam and Tsarkova, Aleksandra S. and Kaskova, Zinaida M. and Shender, Victoria and Abakumov, Maxim and Abakumova, Tatiana O. and Povolotskaya, Inna S. and Eroshkin, Fedor M. and Zaraisky, Andrey G. and Mishin, Alexander S. and Dolgov, Sergey V. and Mitiouchkina, Tatiana Y. and Kopantzev, Eugene P. and Waldenmaier, Hans E. and Oliveira, Anderson G. and Oba, Yuichi and Barsova, Ekaterina and Bogdanova, Ekaterina A. and Gabaldón, Toni and Stevani, Cassius V. and Lukyanov, Sergey and Smirnov, Ivan V. and Gitelson, Josef I. and Kondrashov, Fyodor and Yampolsky, Ilia V.}, issn = {00278424}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {50}, pages = {12728--12732}, publisher = {National Academy of Sciences}, title = {{Genetically encodable bioluminescent system from fungi}}, doi = {10.1073/pnas.1803615115}, volume = {115}, year = {2018}, } @article{428, abstract = {The plant hormone gibberellic acid (GA) is a crucial regulator of growth and development. The main paradigm of GA signaling puts forward transcriptional regulation via the degradation of DELLA transcriptional repressors. GA has also been shown to regulate tropic responses by modulation of the plasma membrane incidence of PIN auxin transporters by an unclear mechanism. Here we uncovered the cellular and molecular mechanisms by which GA redirects protein trafficking and thus regulates cell surface functionality. Photoconvertible reporters revealed that GA balances the protein traffic between the vacuole degradation route and recycling back to the cell surface. Low GA levels promote vacuolar delivery and degradation of multiple cargos, including PIN proteins, whereas high GA levels promote their recycling to the plasma membrane. This GA effect requires components of the retromer complex, such as Sorting Nexin 1 (SNX1) and its interacting, microtubule (MT)-associated protein, the Cytoplasmic Linker-Associated Protein (CLASP1). Accordingly, GA regulates the subcellular distribution of SNX1 and CLASP1, and the intact MT cytoskeleton is essential for the GA effect on trafficking. This GA cellular action occurs through DELLA proteins that regulate the MT and retromer presumably via their interaction partners Prefoldins (PFDs). Our study identified a branching of the GA signaling pathway at the level of DELLA proteins, which, in parallel to regulating transcription, also target by a nontranscriptional mechanism the retromer complex acting at the intersection of the degradation and recycling trafficking routes. By this mechanism, GA can redirect receptors and transporters to the cell surface, thus coregulating multiple processes, including PIN-dependent auxin fluxes during tropic responses.}, author = {Salanenka, Yuliya and Verstraeten, Inge and Löfke, Christian and Tabata, Kaori and Naramoto, Satoshi and Glanc, Matous and Friml, Jirí}, journal = {PNAS}, number = {14}, pages = { 3716 -- 3721}, publisher = {National Academy of Sciences}, title = {{Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane}}, doi = {10.1073/pnas.1721760115}, volume = {115}, year = {2018}, } @article{62, abstract = {Imaging is a dominant strategy for data collection in neuroscience, yielding stacks of images that often scale to gigabytes of data for a single experiment. Machine learning algorithms from computer vision can serve as a pair of virtual eyes that tirelessly processes these images, automatically detecting and identifying microstructures. Unlike learning methods, our Flexible Learning-free Reconstruction of Imaged Neural volumes (FLoRIN) pipeline exploits structure-specific contextual clues and requires no training. This approach generalizes across different modalities, including serially-sectioned scanning electron microscopy (sSEM) of genetically labeled and contrast enhanced processes, spectral confocal reflectance (SCoRe) microscopy, and high-energy synchrotron X-ray microtomography (μCT) of large tissue volumes. We deploy the FLoRIN pipeline on newly published and novel mouse datasets, demonstrating the high biological fidelity of the pipeline’s reconstructions. FLoRIN reconstructions are of sufficient quality for preliminary biological study, for example examining the distribution and morphology of cells or extracting single axons from functional data. Compared to existing supervised learning methods, FLoRIN is one to two orders of magnitude faster and produces high-quality reconstructions that are tolerant to noise and artifacts, as is shown qualitatively and quantitatively.}, author = {Shabazi, Ali and Kinnison, Jeffery and Vescovi, Rafael and Du, Ming and Hill, Robert and Jösch, Maximilian A and Takeno, Marc and Zeng, Hongkui and Da Costa, Nuno and Grutzendler, Jaime and Kasthuri, Narayanan and Scheirer, Walter}, journal = {Scientific Reports}, number = {1}, publisher = {Nature Publishing Group}, title = {{Flexible learning-free segmentation and reconstruction of neural volumes}}, doi = {10.1038/s41598-018-32628-3}, volume = {8}, year = {2018}, } @article{437, abstract = {Dendritic cells (DCs) are sentinels of the adaptive immune system that reside in peripheral organs of mammals. Upon pathogen encounter, they undergo maturation and up-regulate the chemokine receptor CCR7 that guides them along gradients of its chemokine ligands CCL19 and 21 to the next draining lymph node. There, DCs present peripherally acquired antigen to naïve T cells, thereby triggering adaptive immunity.}, author = {Leithner, Alexander F and Renkawitz, Jörg and De Vries, Ingrid and Hauschild, Robert and Haecker, Hans and Sixt, Michael K}, journal = {European Journal of Immunology}, number = {6}, pages = {1074 -- 1077}, publisher = {Wiley-Blackwell}, title = {{Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration}}, doi = {10.1002/eji.201747358}, volume = {48}, year = {2018}, } @article{617, abstract = {Insects are exposed to a variety of potential pathogens in their environment, many of which can severely impact fitness and health. Consequently, hosts have evolved resistance and tolerance strategies to suppress or cope with infections. Hosts utilizing resistance improve fitness by clearing or reducing pathogen loads, and hosts utilizing tolerance reduce harmful fitness effects per pathogen load. To understand variation in, and selective pressures on, resistance and tolerance, we asked to what degree they are shaped by host genetic background, whether plasticity in these responses depends upon dietary environment, and whether there are interactions between these two factors. Females from ten wild-type Drosophila melanogaster genotypes were kept on high- or low-protein (yeast) diets and infected with one of two opportunistic bacterial pathogens, Lactococcus lactis or Pseudomonas entomophila. We measured host resistance as the inverse of bacterial load in the early infection phase. The relationship (slope) between fly fecundity and individual-level bacteria load provided our fecundity tolerance measure. Genotype and dietary yeast determined host fecundity and strongly affected survival after infection with pathogenic P. entomophila. There was considerable genetic variation in host resistance, a commonly found phenomenon resulting from for example varying resistance costs or frequency-dependent selection. Despite this variation and the reproductive cost of higher P. entomophila loads, fecundity tolerance did not vary across genotypes. The absence of genetic variation in tolerance may suggest that at this early infection stage, fecundity tolerance is fixed or that any evolved tolerance mechanisms are not expressed under these infection conditions.}, author = {Kutzer, Megan and Kurtz, Joachim and Armitage, Sophie}, issn = {1420-9101}, journal = {Journal of Evolutionary Biology}, number = {1}, pages = {159 -- 171}, publisher = {Wiley}, title = {{Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance}}, doi = {10.1111/jeb.13211}, volume = {31}, year = {2018}, } @article{5888, abstract = {Despite the remarkable number of scientific breakthroughs of the last 100 years, the treatment of neurodevelopmental disorders (e.g., autism spectrum disorder, intellectual disability) remains a great challenge. Recent advancements in genomics, such as whole-exome or whole-genome sequencing, have enabled scientists to identify numerous mutations underlying neurodevelopmental disorders. Given the few hundred risk genes that have been discovered, the etiological variability and the heterogeneous clinical presentation, the need for genotype — along with phenotype- based diagnosis of individual patients has become a requisite. In this review we look at recent advancements in genomic analysis and their translation into clinical practice.}, author = {Tarlungeanu, Dora-Clara and Novarino, Gaia}, issn = {2092-6413}, journal = {Experimental & Molecular Medicine}, number = {8}, publisher = {Springer Nature}, title = {{Genomics in neurodevelopmental disorders: an avenue to personalized medicine}}, doi = {10.1038/s12276-018-0129-7}, volume = {50}, year = {2018}, } @article{295, abstract = {We prove upper and lower bounds on the ground-state energy of the ideal two-dimensional anyon gas. Our bounds are extensive in the particle number, as for fermions, and linear in the statistics parameter (Formula presented.). The lower bounds extend to Lieb–Thirring inequalities for all anyons except bosons.}, author = {Lundholm, Douglas and Seiringer, Robert}, journal = {Letters in Mathematical Physics}, number = {11}, pages = {2523--2541}, publisher = {Springer}, title = {{Fermionic behavior of ideal anyons}}, doi = {10.1007/s11005-018-1091-y}, volume = {108}, year = {2018}, } @article{555, abstract = {Conventional wisdom has it that proteins fold and assemble into definite structures, and that this defines their function. Glycosaminoglycans (GAGs) are different. In most cases the structures they form have a low degree of order, even when interacting with proteins. Here, we discuss how physical features common to all GAGs — hydrophilicity, charge, linearity and semi-flexibility — underpin the overall properties of GAG-rich matrices. By integrating soft matter physics concepts (e.g. polymer brushes and phase separation) with our molecular understanding of GAG–protein interactions, we can better comprehend how GAG-rich matrices assemble, what their properties are, and how they function. Taking perineuronal nets (PNNs) — a GAG-rich matrix enveloping neurons — as a relevant example, we propose that microphase separation determines the holey PNN anatomy that is pivotal to PNN functions.}, author = {Richter, Ralf and Baranova, Natalia and Day, Anthony and Kwok, Jessica}, journal = {Current Opinion in Structural Biology}, pages = {65 -- 74}, publisher = {Elsevier}, title = {{Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets?}}, doi = {10.1016/j.sbi.2017.12.002}, volume = {50}, year = {2018}, } @article{448, 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 and Jongepier, Evelien and Robertson, Hugh and Arning, Nicolas and Bitard Feildel, Tristan and Chao, Hsu and Childers, Christopher and Dinh, Huyen and Doddapaneni, Harshavardhan and Dugan, Shannon and Gowin, Johannes and Greiner, Carolin and Han, Yi and Hu, Haofu and Hughes, Daniel and Huylmans, Ann K and Kemena, Karsten and Kremer, Lukas and Lee, Sandra and López Ezquerra, Alberto and Mallet, Ludovic and Monroy Kuhn, Jose and Moser, Annabell and Murali, Shwetha and Muzny, Donna and Otani, Saria and Piulachs, Maria and Poelchau, Monica and Qu, Jiaxin and Schaub, Florentine and Wada Katsumata, Ayako and Worley, Kim and Xie, Qiaolin and Ylla, Guillem and Poulsen, Michael and Gibbs, Richard and Schal, Coby and Richards, Stephen and Belles, Xavier and Korb, Judith and Bornberg Bauer, Erich}, journal = {Nature Ecology and Evolution}, number = {3}, pages = {557--566}, publisher = {Springer Nature}, title = {{Hemimetabolous genomes reveal molecular basis of termite eusociality}}, doi = {10.1038/s41559-017-0459-1}, volume = {2}, year = {2018}, } @article{723, abstract = {Escaping local optima is one of the major obstacles to function optimisation. Using the metaphor of a fitness landscape, local optima correspond to hills separated by fitness valleys that have to be overcome. We define a class of fitness valleys of tunable difficulty by considering their length, representing the Hamming path between the two optima and their depth, the drop in fitness. For this function class we present a runtime comparison between stochastic search algorithms using different search strategies. The (1+1) EA is a simple and well-studied evolutionary algorithm that has to jump across the valley to a point of higher fitness because it does not accept worsening moves (elitism). In contrast, the Metropolis algorithm and the Strong Selection Weak Mutation (SSWM) algorithm, a famous process in population genetics, are both able to cross the fitness valley by accepting worsening moves. We show that the runtime of the (1+1) EA depends critically on the length of the valley while the runtimes of the non-elitist algorithms depend crucially on the depth of the valley. Moreover, we show that both SSWM and Metropolis can also efficiently optimise a rugged function consisting of consecutive valleys.}, author = {Oliveto, Pietro and Paixao, Tiago and Pérez Heredia, Jorge and Sudholt, Dirk and Trubenova, Barbora}, journal = {Algorithmica}, number = {5}, pages = {1604 -- 1633}, publisher = {Springer}, title = {{How to escape local optima in black box optimisation when non elitism outperforms elitism}}, doi = {10.1007/s00453-017-0369-2}, volume = {80}, year = {2018}, } @article{321, abstract = {The twelve papers in this special section focus on learning systems with shared information for computer vision and multimedia communication analysis. In the real world, a realistic setting for computer vision or multimedia recognition problems is that we have some classes containing lots of training data and many classes containing a small amount of training data. Therefore, how to use frequent classes to help learning rare classes for which it is harder to collect the training data is an open question. Learning with shared information is an emerging topic in machine learning, computer vision and multimedia analysis. There are different levels of components that can be shared during concept modeling and machine learning stages, such as sharing generic object parts, sharing attributes, sharing transformations, sharing regularization parameters and sharing training examples, etc. Regarding the specific methods, multi-task learning, transfer learning and deep learning can be seen as using different strategies to share information. These learning with shared information methods are very effective in solving real-world large-scale problems.}, author = {Darrell, Trevor and Lampert, Christoph and Sebe, Nico and Wu, Ying and Yan, Yan}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, number = {5}, pages = {1029 -- 1031}, publisher = {IEEE}, title = {{Guest editors' introduction to the special section on learning with Shared information for computer vision and multimedia analysis}}, doi = {10.1109/TPAMI.2018.2804998}, volume = {40}, 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}, } @inproceedings{397, abstract = {Concurrent sets with range query operations are highly desirable in applications such as in-memory databases. However, few set implementations offer range queries. Known techniques for augmenting data structures with range queries (or operations that can be used to build range queries) have numerous problems that limit their usefulness. For example, they impose high overhead or rely heavily on garbage collection. In this work, we show how to augment data structures with highly efficient range queries, without relying on garbage collection. We identify a property of epoch-based memory reclamation algorithms that makes them ideal for implementing range queries, and produce three algorithms, which use locks, transactional memory and lock-free techniques, respectively. Our algorithms are applicable to more data structures than previous work, and are shown to be highly efficient on a large scale Intel system. }, author = {Arbel Raviv, Maya and Brown, Trevor A}, isbn = {978-1-4503-4982-6}, location = {Vienna, Austria}, number = {1}, pages = {14 -- 27}, publisher = {ACM}, title = {{Harnessing epoch-based reclamation for efficient range queries}}, doi = {10.1145/3178487.3178489}, volume = {53}, year = {2018}, }