@article{913,
  abstract     = {Coordinated cell polarization in developing tissues is a recurrent theme in multicellular organisms. In plants, a directional distribution of the plant hormone auxin is at the core of many developmental programs. A feedback regulation of auxin on the polarized localization of PIN auxin transporters in individual cells has been proposed as a self-organizing mechanism for coordinated tissue polarization, but the molecular mechanisms linking auxin signalling to PIN-dependent auxin transport remain unknown. We performed a microarray-based approach to find regulators of the auxin-induced PIN relocation in the Arabidopsis thaliana root. We identified a subset of a family of phosphatidylinositol transfer proteins (PITP), the PATELLINs (PATL). Here, we show that PATLs are expressed in partially overlapping cells types in different tissues going through mitosis or initiating differentiation programs. PATLs are plasma membrane-associated proteins accumulated in Arabidopsis embryos, primary roots, lateral root primordia, and developing stomata. Higher order patl mutants display reduced PIN1 repolarization in response to auxin, shorter root apical meristem, and drastic defects in embryo and seedling development. This suggests PATLs redundantly play a crucial role in polarity and patterning in Arabidopsis.},
  author       = {Tejos, Ricardo and Rodríguez Furlán, Cecilia and Adamowski, Maciek and Sauer, Michael and Norambuena, Lorena and Friml, Jirí},
  issn         = {00219533},
  journal      = {Journal of Cell Science},
  number       = {2},
  publisher    = {Company of Biologists},
  title        = {{PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana}},
  doi          = {10.1242/jcs.204198},
  volume       = {131},
  year         = {2018},
}

@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},
}

@phdthesis{10,
  abstract     = {Genomic imprinting is an epigenetic process that leads to parent of origin-specific gene expression in a subset of genes. Imprinted genes are essential for brain development, and deregulation of imprinting is associated with neurodevelopmental diseases and the pathogenesis of psychiatric disorders. However, the cell-type specificity of imprinting at single cell resolution, and how imprinting and thus gene dosage regulates neuronal circuit assembly is still largely unknown. Here, MADM (Mosaic Analysis with Double Markers) technology was employed to assess genomic imprinting at single cell level. By visualizing MADM-induced uniparental disomies (UPDs) in distinct colors at single cell level in genetic mosaic animals, this experimental paradigm provides a unique quantitative platform to systematically assay the UPD-mediated imbalances in imprinted gene expression at unprecedented resolution. An experimental pipeline based on FACS, RNA-seq and bioinformatics analysis was established and applied to systematically map cell-type-specific ‘imprintomes’ in the mouse brain. The results revealed that parental-specific expression of imprinted genes per se is rarely cell-type-specific even at the individual cell level. Conversely, when we extended the comparison to downstream responses resulting from imbalanced imprinted gene expression, we discovered an unexpectedly high degree of cell-type specificity. Furthermore, we determined a novel function of genomic imprinting in cortical astrocyte production and in olfactory bulb (OB) granule cell generation. These results suggest important functional implication of genomic imprinting for generating cell-type diversity in the brain. In addition, MADM provides a powerful tool to study candidate genes by concomitant genetic manipulation and fluorescent labelling of single cells. MADM-based candidate gene approach was utilized to identify potential imprinted genes involved in the generation of cortical astrocytes and OB granule cells. We investigated p57Kip2, a maternally expressed gene and known cell cycle regulator. Although we found that p57Kip2 does not play a role in these processes, we detected an unexpected function of the paternal allele previously thought to be silent. Finally, we took advantage of a key property of MADM which is to allow unambiguous investigation of environmental impact on single cells. The experimental pipeline based on FACS and RNA-seq analysis of MADM-labeled cells was established to probe the functional differences of single cell loss of gene function compared to global loss of function on a transcriptional level. With this method, both common and distinct responses were isolated due to cell-autonomous and non-autonomous effects acting on genotypically identical cells. As a result, transcriptional changes were identified which result solely from the surrounding environment. Using the MADM technology to study genomic imprinting at single cell resolution, we have identified cell-type-specific gene expression, novel gene function and the impact of environment on single cell transcriptomes. Together, these provide important insights to the understanding of mechanisms regulating cell-type specificity and thus diversity in the brain.},
  author       = {Laukoter, Susanne},
  issn         = {2663-337X},
  pages        = {1 -- 139},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Role of genomic imprinting in cerebral cortex development}},
  doi          = {10.15479/AT:ISTA:th1057},
  year         = {2018},
}

@article{1012,
  abstract     = {We prove a new central limit theorem (CLT) for the difference of linear eigenvalue statistics of a Wigner random matrix H and its minor H and find that the fluctuation is much smaller than the fluctuations of the individual linear statistics, as a consequence of the strong correlation between the eigenvalues of H and H. In particular, our theorem identifies the fluctuation of Kerov's rectangular Young diagrams, defined by the interlacing eigenvalues ofH and H, around their asymptotic shape, the Vershik'Kerov'Logan'Shepp curve. Young diagrams equipped with the Plancherel measure follow the same limiting shape. For this, algebraically motivated, ensemble a CLT has been obtained in Ivanov and Olshanski [20] which is structurally similar to our result but the variance is different, indicating that the analogy between the two models has its limitations. Moreover, our theorem shows that Borodin's result [7] on the convergence of the spectral distribution of Wigner matrices to a Gaussian free field also holds in derivative sense.},
  author       = {Erdös, László and Schröder, Dominik J},
  issn         = {10737928},
  journal      = {International Mathematics Research Notices},
  number       = {10},
  pages        = {3255--3298},
  publisher    = {Oxford University Press},
  title        = {{Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues}},
  doi          = {10.1093/imrn/rnw330},
  volume       = {2018},
  year         = {2018},
}

@article{10286,
  abstract     = {In this paper, we evaluate clock signals generated in ring oscillators and self-timed rings and the way their jitter can be transformed into random numbers. We show that counting the periods of the jittery clock signal produces random numbers of significantly better quality than the methods in which the jittery signal is simply sampled (the case in almost all current methods). Moreover, we use the counter values to characterize and continuously monitor the source of randomness. However, instead of using the widely used statistical variance, we propose to use Allan variance to do so. There are two main advantages: Allan variance is insensitive to low frequency noises such as flicker noise that are known to be autocorrelated and significantly less circuitry is required for its computation than that used to compute commonly used variance. We also show that it is essential to use a differential principle of randomness extraction from the jitter based on the use of two identical oscillators to avoid autocorrelations originating from external and internal global jitter sources and that this fact is valid for both kinds of rings. Last but not least, we propose a method of statistical testing based on high order Markov model to show the reduced dependencies when the proposed randomness extraction is applied.},
  author       = {Allini, Elie Noumon and Skórski, Maciej and Petura, Oto and Bernard, Florent and Laban, Marek and Fischer, Viktor},
  issn         = {2569-2925},
  journal      = {IACR Transactions on Cryptographic Hardware and Embedded Systems},
  number       = {3},
  pages        = {214--242},
  publisher    = {International Association for Cryptologic Research},
  title        = {{Evaluation and monitoring of free running oscillators serving as source of randomness}},
  doi          = {10.13154/tches.v2018.i3.214-242},
  volume       = {2018},
  year         = {2018},
}

@article{104,
  abstract     = {The biotrophic pathogen Ustilago maydis, the causative agent of corn smut disease, infects one of the most important crops worldwide – Zea mays. To successfully colonize its host, U. maydis secretes proteins, known as effectors, that suppress plant defense responses and facilitate the establishment of biotrophy. In this work, we describe the U. maydis effector protein Cce1. Cce1 is essential for virulence and is upregulated during infection. Through microscopic analysis and in vitro assays, we show that Cce1 is secreted from hyphae during filamentous growth of the fungus. Strikingly, Δcce1 mutants are blocked at early stages of infection and induce callose deposition as a plant defense response. Cce1 is highly conserved among smut fungi and the Ustilago bromivora ortholog complemented the virulence defect of the SG200Δcce1 deletion strain. These data indicate that Cce1 is a core effector with apoplastic localization that is essential for U. maydis to infect its host.},
  author       = {Seitner, Denise and Uhse, Simon and Gallei, Michelle C and Djamei, Armin},
  journal      = {Molecular Plant Pathology},
  number       = {10},
  pages        = {2277 -- 2287},
  publisher    = {Wiley},
  title        = {{The core effector Cce1 is required for early infection of maize by Ustilago maydis}},
  doi          = {10.1111/mpp.12698},
  volume       = {19},
  year         = {2018},
}

@article{106,
  abstract     = {The goal of this article is to introduce the reader to the theory of intrinsic geometry of convex surfaces. We illustrate the power of the tools by proving a theorem on convex surfaces containing an arbitrarily long closed simple geodesic. Let us remind ourselves that a curve in a surface is called geodesic if every sufficiently short arc of the curve is length minimizing; if, in addition, it has no self-intersections, we call it simple geodesic. A tetrahedron with equal opposite edges is called isosceles. The axiomatic method of Alexandrov geometry allows us to work with the metrics of convex surfaces directly, without approximating it first by a smooth or polyhedral metric. Such approximations destroy the closed geodesics on the surface; therefore it is difficult (if at all possible) to apply approximations in the proof of our theorem. On the other hand, a proof in the smooth or polyhedral case usually admits a translation into Alexandrov’s language; such translation makes the result more general. In fact, our proof resembles a translation of the proof given by Protasov. Note that the main theorem implies in particular that a smooth convex surface does not have arbitrarily long simple closed geodesics. However we do not know a proof of this corollary that is essentially simpler than the one presented below.},
  author       = {Akopyan, Arseniy and Petrunin, Anton},
  journal      = {Mathematical Intelligencer},
  number       = {3},
  pages        = {26 -- 31},
  publisher    = {Springer},
  title        = {{Long geodesics on convex surfaces}},
  doi          = {10.1007/s00283-018-9795-5},
  volume       = {40},
  year         = {2018},
}

@article{1064,
  abstract     = {In 1945, A.W. Goodman and R.E. Goodman proved the following conjecture by P. Erdős: Given a family of (round) disks of radii r1, … , rn in the plane, it is always possible to cover them by a disk of radius R= ∑ ri, provided they cannot be separated into two subfamilies by a straight line disjoint from the disks. In this note we show that essentially the same idea may work for different analogues and generalizations of their result. In particular, we prove the following: Given a family of positive homothetic copies of a fixed convex body K⊂ Rd with homothety coefficients τ1, … , τn> 0 , it is always possible to cover them by a translate of d+12(∑τi)K, provided they cannot be separated into two subfamilies by a hyperplane disjoint from the homothets.},
  author       = {Akopyan, Arseniy and Balitskiy, Alexey and Grigorev, Mikhail},
  issn         = {14320444},
  journal      = {Discrete & Computational Geometry},
  number       = {4},
  pages        = {1001--1009},
  publisher    = {Springer},
  title        = {{On the circle covering theorem by A.W. Goodman and R.E. Goodman}},
  doi          = {10.1007/s00454-017-9883-x},
  volume       = {59},
  year         = {2018},
}

@article{12,
  abstract     = {Molding is a popular mass production method, in which the initial expenses for the mold are offset by the low per-unit production cost. However, the physical fabrication constraints of the molding technique commonly restrict the shape of moldable objects. For a complex shape, a decomposition of the object into moldable parts is a common strategy to address these constraints, with plastic model kits being a popular and illustrative example. However, conducting such a decomposition requires considerable expertise, and it depends on the technical aspects of the fabrication technique, as well as aesthetic considerations. We present an interactive technique to create such decompositions for two-piece molding, in which each part of the object is cast between two rigid mold pieces. Given the surface description of an object, we decompose its thin-shell equivalent into moldable parts by first performing a coarse decomposition and then utilizing an active contour model for the boundaries between individual parts. Formulated as an optimization problem, the movement of the contours is guided by an energy reflecting fabrication constraints to ensure the moldability of each part. Simultaneously, the user is provided with editing capabilities to enforce aesthetic guidelines. Our interactive interface provides control of the contour positions by allowing, for example, the alignment of part boundaries with object features. Our technique enables a novel workflow, as it empowers novice users to explore the design space, and it generates fabrication-ready two-piece molds that can be used either for casting or industrial injection molding of free-form objects.},
  author       = {Nakashima, Kazutaka and Auzinger, Thomas and Iarussi, Emmanuel and Zhang, Ran and Igarashi, Takeo and Bickel, Bernd},
  journal      = {ACM Transaction on Graphics},
  number       = {4},
  publisher    = {ACM},
  title        = {{CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds}},
  doi          = {10.1145/3197517.3201341},
  volume       = {37},
  year         = {2018},
}

@article{1215,
  abstract     = {Two generalizations of Itô formula to infinite-dimensional spaces are given.
The first one, in Hilbert spaces, extends the classical one by taking advantage of
cancellations when they occur in examples and it is applied to the case of a group
generator. The second one, based on the previous one and a limit procedure, is an Itô
formula in a special class of Banach spaces having a product structure with the noise
in a Hilbert component; again the key point is the extension due to a cancellation. This
extension to Banach spaces and in particular the specific cancellation are motivated
by path-dependent Itô calculus.},
  author       = {Flandoli, Franco and Russo, Francesco and Zanco, Giovanni A},
  journal      = {Journal of Theoretical Probability},
  number       = {2},
  pages        = {789--826},
  publisher    = {Springer},
  title        = {{Infinite-dimensional calculus under weak spatial regularity of the processes}},
  doi          = {10.1007/s10959-016-0724-2},
  volume       = {31},
  year         = {2018},
}

@article{13,
  abstract     = {We propose a new method for fabricating digital objects through reusable silicone molds. Molds are generated by casting liquid silicone into custom 3D printed containers called metamolds. Metamolds automatically define the cuts that are needed to extract the cast object from the silicone mold. The shape of metamolds is designed through a novel segmentation technique, which takes into account both geometric and topological constraints involved in the process of mold casting. Our technique is simple, does not require changing the shape or topology of the input objects, and only requires off-the- shelf materials and technologies. We successfully tested our method on a set of challenging examples with complex shapes and rich geometric detail. © 2018 Association for Computing Machinery.},
  author       = {Alderighi, Thomas and Malomo, Luigi and Giorgi, Daniela and Pietroni, Nico and Bickel, Bernd and Cignoni, Paolo},
  journal      = {ACM Trans. Graph.},
  number       = {4},
  publisher    = {ACM},
  title        = {{Metamolds: Computational design of silicone molds}},
  doi          = {10.1145/3197517.3201381},
  volume       = {37},
  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},
}