TY - JOUR AB - Background: Drosophila albomicans is a unique model organism for studying both sex chromosome and B chromosome evolution. A pair of its autosomes comprising roughly 40% of the whole genome has fused to the ancient X and Y chromosomes only about 0.12 million years ago, thereby creating the youngest and most gene-rich neo-sex system reported to date. This species also possesses recently derived B chromosomes that show non-Mendelian inheritance and significantly influence fertility.Methods: We sequenced male flies with B chromosomes at 124.5-fold genome coverage using next-generation sequencing. To characterize neo-Y specific changes and B chromosome sequences, we also sequenced inbred female flies derived from the same strain but without B's at 28.5-fold.Results: We assembled a female genome and placed 53% of the sequence and 85% of the annotated proteins into specific chromosomes, by comparison with the 12 Drosophila genomes. Despite its very recent origin, the non-recombining neo-Y chromosome shows various signs of degeneration, including a significant enrichment of non-functional genes compared to the neo-X, and an excess of tandem duplications relative to other chromosomes. We also characterized a B-chromosome linked scaffold that contains an actively transcribed unit and shows sequence similarity to the subcentromeric regions of both the ancient X and the neo-X chromosome.Conclusions: Our results provide novel insights into the very early stages of sex chromosome evolution and B chromosome origination, and suggest an unprecedented connection between the births of these two systems in D. albomicans. AU - Zhou, Qi AU - Zhu, Hongmei AU - Huang, Quanfei AU - Zhao, Li AU - Zhang, Guo J AU - Roy, Scott W AU - Beatriz Vicoso AU - Xuan, Zhaolin AU - Ruan, Jue AU - Zhang, Yue AU - Zhao, Ruoping AU - Ye, Chen AU - Zhang, Xiuqing AU - Wang, Jùn AU - Wang, Wen AU - Bachtrog, Doris ID - 2073 IS - 1 JF - BMC Genomics TI - Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans VL - 13 ER - TY - JOUR AB - We introduce an algorithm and representation for fabricating 3D shape abstractions using mutually intersecting planar cut-outs. The planes have prefabricated slits at their intersections and are assembled by sliding them together. Often such abstractions are used as a sculptural art form or in architecture and are colloquially called ‘cardboard sculptures’. Based on an analysis of construction rules, we propose an extended binary space partitioning tree as an efficient representation of such cardboard models which allows us to quickly evaluate the feasibility of newly added planar elements. The complexity of insertion order quickly increases with the number of planar elements and manual analysis becomes intractable. We provide tools for generating cardboard sculptures with guaranteed constructibility. In combination with a simple optimization and sampling strategy for new elements, planar shape abstraction models can be designed by iteratively adding elements. As an output, we obtain a fabrication plan that can be printed or sent to a laser cutter. We demonstrate the complete process by designing and fabricating cardboard models of various well-known 3D shapes. AU - Hildebrand, Kristian AU - Bernd Bickel AU - Alexa, Marc ID - 2079 IS - 2pt3 JF - Computer Graphics Forum TI - crdbrd: Shape fabrication by sliding planar slices VL - 31 ER - TY - JOUR AB - Although facial hair plays an important role in individual expression, facial-hair reconstruction is not addressed by current facecapture systems. Our research addresses this limitation with an algorithm that treats hair and skin surface capture together in a coupled fashion so that a high-quality representation of hair fibers as well as the underlying skin surface can be reconstructed. We propose a passive, camera-based system that is robust against arbitrary motion since all data is acquired within the time period of a single exposure. Our reconstruction algorithm detects and traces hairs in the captured images and reconstructs them in 3D using a multiview stereo approach. Our coupled skin-reconstruction algorithm uses information about the detected hairs to deliver a skin surface that lies underneath all hairs irrespective of occlusions. In dense regions like eyebrows, we employ a hair-synthesis method to create hair fibers that plausibly match the image data. We demonstrate our scanning system on a number of individuals and show that it can successfully reconstruct a variety of facial-hair styles together with the underlying skin surface. AU - Beeler, Thabo AU - Bernd Bickel AU - Noris, Gioacchino AU - Beardsley, Paul A AU - Marschner, Steve AU - Sumner, Robert W AU - Groß, Markus S ID - 2103 IS - 4 JF - ACM Transactions on Graphics TI - Coupled 3D reconstruction of sparse facial hair and skin VL - 31 ER - TY - JOUR AB - Articulated deformable characters are widespread in computer animation. Unfortunately, we lack methods for their automatic fabrication using modern additive manufacturing (AM) technologies. We propose a method that takes a skinned mesh as input, then estimates a fabricatable single-material model that approximates the 3D kinematics of the corresponding virtual articulated character in a piecewise linear manner. We first extract a set of potential joint locations. From this set, together with optional, user-specified range constraints, we then estimate mechanical friction joints that satisfy inter-joint non-penetration and other fabrication constraints. To avoid brittle joint designs, we place joint centers on an approximate medial axis representation of the input geometry, and maximize each joint's minimal cross-sectional area. We provide several demonstrations, manufactured as single, assembled pieces using 3D printers. AU - Bac̈her, Moritz AU - Bernd Bickel AU - James, Doug L AU - Pfister, Hanspeter ID - 2101 IS - 4 JF - ACM Transactions on Graphics TI - Fabricating articulated characters from skinned meshes VL - 31 ER - TY - JOUR AB - We propose a complete process for designing, simulating, and fabricating synthetic skin for an animatronics character that mimics the face of a given subject and its expressions. The process starts with measuring the elastic properties of a material used to manufacture synthetic soft tissue. Given these measurements we use physicsbased simulation to predict the behavior of a face when it is driven by the underlying robotic actuation. Next, we capture 3D facial expressions for a given target subject. As the key component of our process, we present a novel optimization scheme that determines the shape of the synthetic skin as well as the actuation parameters that provide the best match to the target expressions. We demonstrate this computational skin design by physically cloning a real human face onto an animatronics figure. AU - Bernd Bickel AU - Kaufmann, Peter AU - Skouras, Mélina AU - Thomaszewski, Bernhard AU - Bradley, Derek J AU - Beeler, Thabo AU - Jackson, Philip V AU - Marschner, Steve AU - Matusik, Wojciech AU - Groß, Markus S ID - 2102 IS - 4 JF - ACM Transactions on Graphics TI - Physical face cloning VL - 31 ER - TY - CONF AB - Progress in cloth simulation for computer animation and apparel design has led to a multitude of deformation models, each with its own way of relating geometry, deformation, and forces. As simulators improve, differences between these models become more important, but it is difficult to choose a model and a set of parameters to match a given real material simply by looking at simulation results. This paper provides measurement and fitting methods that allow nonlinear models to be fit to the observed deformation of a particular cloth sample. Unlike standard textile testing, our system measures complex 3D deformations of a sheet of cloth, not just one-dimensional force-displacement curves, so it works under a wider range of deformation conditions. The fitted models are then evaluated by comparison to measured deformations with motions very different from those used for fitting. AU - Miguel, Eder AU - Bradley, Derek J AU - Thomaszewski, Bernhard AU - Bernd Bickel AU - Matusik, Wojciech AU - Otaduy, Miguel A AU - Marschner, Steve ID - 2106 IS - 2 TI - Data-driven estimation of cloth simulation models VL - 31 ER - TY - CONF AB - In recent years, various methods have been introduced to exploit pre-recorded data to improve the performance and/or realism of dynamic deformations, but their differences and similarities have not been adequately analyzed or discussed. So far, the proposed methods have been explored mainly in the research context. They have not been adopted by the computer graphics industry. This course bridges the gap between research labs and industry to present a unifying theory and understanding of data-driven methods for dynamic deformations that may inspire development of novel solutions. It focuses on application of data-driven methods to three areas of computer animation: dynamic deformation of faces, soft volumetric tissue, and cloth. And it describes how to approach these challenges in a data-driven manner, classifies the various methods, and demonstrates how data-driven methods can work in other settings. AU - Otaduy, Miguel A AU - Bernd Bickel AU - Bradley, Derek J AU - Wang, Huamin ID - 2104 TI - Data-driven simulation methods in computer graphics: Cloth, tissue and faces ER - TY - CONF AU - Skouras, Mélina AU - Thomaszewski, Bernhard AU - Bernd Bickel AU - Groß, Markus S ID - 2105 IS - 2 TI - Computational design of rubber balloons VL - 31 ER - TY - JOUR AB - We consider a class of stochastic PDEs of Burgers type in spatial dimension 1, driven by space–time white noise. Even though it is well known that these equations are well posed, it turns out that if one performs a spatial discretization of the nonlinearity in the “wrong” way, then the sequence of approximate equations does converge to a limit, but this limit exhibits an additional correction term. This correction term is proportional to the local quadratic cross-variation (in space) of the gradient of the conserved quantity with the solution itself. This can be understood as a consequence of the fact that for any fixed time, the law of the solution is locally equivalent to Wiener measure, where space plays the role of time. In this sense, the correction term is similar to the usual Itô–Stratonovich correction term that arises when one considers different temporal discretizations of stochastic ODEs. AU - Hairer, Martin M AU - Jan Maas ID - 2125 IS - 4 JF - Annals of Probability TI - A spatial version of the Itô-Stratonovich correction VL - 40 ER - TY - JOUR AB - We study a new notion of Ricci curvature that applies to Markov chains on discrete spaces. This notion relies on geodesic convexity of the entropy and is analogous to the one introduced by Lott, Sturm, and Villani for geodesic measure spaces. In order to apply to the discrete setting, the role of the Wasserstein metric is taken over by a different metric, having the property that continuous time Markov chains are gradient flows of the entropy. Using this notion of Ricci curvature we prove discrete analogues of fundamental results by Bakry–Émery and Otto–Villani. Further, we show that Ricci curvature bounds are preserved under tensorisation. As a special case we obtain the sharp Ricci curvature lower bound for the discrete hypercube. AU - Erbar, Matthias AU - Jan Maas ID - 2127 IS - 3 JF - Archive for Rational Mechanics and Analysis TI - Ricci curvature of finite Markov chains via convexity of the entropy VL - 206 ER - TY - JOUR AB - We introduce a technique for handling Whitney decompositions in Gaussian harmonic analysis and apply it to the study of Gaussian analogues of the classical tent spaces T 1,q of Coifman–Meyer–Stein. AU - Jan Maas AU - van Neerven, Jan M AU - Portal, Pierre ID - 2128 IS - 2 JF - Arkiv för Matematik TI - Whitney coverings and the tent spaces T 1,q (γ) for the Gaussian measure VL - 50 ER - TY - JOUR AB - We show that the electric dipole-dipole interaction between a pair of polar molecules undergoes an all-out transformation when superimposed by a far-off-resonant optical field. The combined interaction potential becomes tunable by variation of wavelength, polarisation and intensity of the optical field and its dependence on the intermolecular separation exhibits a crossover from an inverse-power to an oscillating behaviour. The ability thereby offered to control molecular interactions opens up avenues toward the creation and manipulation of novel phases of ultracold polar gases among whose characteristics is a long-range entanglement of the dipoles' mutual orientation. We devised an accurate analytic model of such optical-field-dressed dipole-dipole interaction potentials, which enables a straightforward access to the optical-field parameters required for the design of intermolecular interactions in the laboratory. AU - Mikhail Lemeshko AU - Friedrich, Břetislav ID - 2203 IS - 15-16 JF - Molecular Physics TI - Interaction between polar molecules subject to a far-off-resonant optical field: Entangled dipoles up- or down-holding each other VL - 110 ER - TY - JOUR AB - We study the growth dynamics of ordered structures of strongly interacting polar molecules in optical lattices. Using a dipole blockade of microwave excitations, we map the system onto an interacting spin-1/2 model possessing ground states with crystalline order, and describe a way to prepare these states by nonadiabatically driving the transitions between molecular rotational levels. The proposed technique bypasses the need to cross a phase transition and allows for the creation of ordered domains of considerably larger size compared to approaches relying on adiabatic preparation. AU - Lemeshko, Mikhail AU - Krems, Roman AU - Weimer, Hendrik ID - 2201 IS - 3 JF - Physical Review Letters TI - Nonadiabatic preparation of spin crystals with ultracold polar molecules VL - 109 ER - TY - JOUR AB - We propose a method for sensitive parallel detection of low-frequency electromagnetic fields based on the fine structure interactions in paramagnetic polar molecules. Compared to the recently implemented scheme employing ultracold 87Rb atoms by Böhi, the technique based on molecules offers a 100-fold higher sensitivity, the possibility to measure both the electric and magnetic field components, and a probe of a wide range of frequencies from the dc limit to the THz regime. AU - Alyabyshev, Sergey V AU - Mikhail Lemeshko AU - Krems, Roman V ID - 2202 IS - 1 JF - Physical Review A - Atomic, Molecular, and Optical Physics TI - Sensitive imaging of electromagnetic fields with paramagnetic polar molecules VL - 86 ER - TY - JOUR AB - Nestin-cre transgenic mice have been widely used to direct recombination to neural stem cells (NSCs) and intermediate neural progenitor cells (NPCs). Here we report that a readily utilized, and the only commercially available, Nestin-cre line is insufficient for directing recombination in early embryonic NSCs and NPCs. Analysis of recombination efficiency in multiple cre-dependent reporters and a genetic mosaic line revealed consistent temporal and spatial patterns of recombination in NSCs and NPCs. For comparison we utilized a knock-in Emx1cre line and found robust recombination in NSCs and NPCs in ventricular and subventricular zones of the cerebral cortices as early as embryonic day 12.5. In addition we found that the rate of Nestin-cre driven recombination only reaches sufficiently high levels in NSCs and NPCs during late embryonic and early postnatal periods. These findings are important when commercially available cre lines are considered for directing recombination to embryonic NSCs and NPCs. AU - Liang, Huixuan AU - Hippenmeyer, Simon AU - Ghashghaei, H. ID - 2263 IS - 12 JF - Biology open TI - A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors VL - 1 ER - TY - CONF AB - Capturing real-world objects with laser-scanning technology has become an everyday task. Recently, the acquisition of dynamic scenes at interactive frame rates has become feasible. A high-quality visualization of the resulting point cloud stream would require a per-frame reconstruction of object surfaces. Unfortunately, reconstruction computations are still too time-consuming to be applied interactively. In this paper we present a local surface reconstruction and visualization technique that provides interactive feedback for reasonably sized point clouds, while achieving high image quality. Our method is performed entirely on the GPU and in screen pace, exploiting the efficiency of the common rasterization pipeline. The approach is very general, as no assumption is made about point connectivity or sampling density. This naturally allows combining the outputs of multiple scanners in a single visualization, which is useful for many virtual and augmented reality applications. AU - Preiner, Reinhold AU - Jeschke, Stefan AU - Wimmer, Michael ID - 2267 TI - Auto splats: Dynamic point cloud visualization on the GPU ER - TY - JOUR AB - Mosaic Analysis with Double Markers (MADM) is a method for generating genetically mosaic mice, in which sibling mutant and wild-type cells are labeled with different fluorescent markers. It is a powerful tool that enables analysis of gene function at the single cell level in vivo. It requires transgenic cassettes to be located between the centromere and the mutation in the gene of interest on the same chromosome. Here we compare procedures for introduction of MADM cassettes into new loci in the mouse genome, and describe new approaches for expanding the utility of MADM. We show that: 1) Targeted homologous recombination outperforms random transgenesis in generation of reliably expressed MADM cassettes, 2) MADM cassettes in new genomic loci need to be validated for biallelic and ubiquitous expression, 3) Recombination between MADM cassettes on different chromosomes can be used to study reciprocal chromosomal deletions/duplications, and 4) MADM can be modified to permit transgene expression by combining it with a binary expression system. The advances described in this study expand current, and enable new and more versatile applications of MADM. AU - Tasic, Bosiljka AU - Miyamichi, Kazunari AU - Simon Hippenmeyer AU - Dani, Vardhan S. AU - Zeng, H. AU - Joo, William AU - Zong, Hui AU - Chen-Tsai, Yanru AU - Luo, Liqun ID - 2262 IS - 3 JF - PLoS One TI - Extensions of MADM (Mosaic Analysis with Double Markers) in Mice VL - 7 ER - TY - CONF AB - This paper presents an analytic formulation for anti-aliased sampling of 2D polygons and 3D polyhedra. Our framework allows the exact evaluation of the convolution integral with a linear function defined on the polytopes. The filter is a spherically symmetric polynomial of any order, supporting approximations to refined variants such as the Mitchell-Netravali filter family. This enables high-quality rasterization of triangles and tetrahedra with linearly interpolated vertex values to regular and non-regular grids. A closed form solution of the convolution is presented and an efficient implementation on the GPU using DirectX and CUDA C is described. AU - Thomas Auzinger AU - Guthe, Michael AU - Stefan Jeschke ID - 2268 IS - 121 TI - Analytic anti-aliasing of linear functions on polytopes VL - 31 ER - TY - JOUR AB - We introduce propagation models (PMs), a formalism able to express several kinds of equations that describe the behavior of biochemical reaction networks. Furthermore, we introduce the propagation abstract data type (PADT), which separates concerns regarding different numerical algorithms for the transient analysis of biochemical reaction networks from concerns regarding their implementation, thus allowing for portable and efficient solutions. The state of a propagation abstract data type is given by a vector that assigns mass values to a set of nodes, and its (next) operator propagates mass values through this set of nodes. We propose an approximate implementation of the (next) operator, based on threshold abstraction, which propagates only "significant" mass values and thus achieves a compromise between efficiency and accuracy. Finally, we give three use cases for propagation models: the chemical master equation (CME), the reaction rate equation (RRE), and a hybrid method that combines these two equations. These three applications use propagation models in order to propagate probabilities and/or expected values and variances of the model's variables. AU - Henzinger, Thomas A AU - Mateescu, Maria ID - 2302 IS - 2 JF - IEEE ACM Transactions on Computational Biology and Bioinformatics TI - The propagation approach for computing biochemical reaction networks VL - 10 ER - TY - JOUR AB - The translation of "next-generation" sequencing directly to the clinic is still being assessed but has the potential for genetic diseases to reduce costs, advance accuracy, and point to unsuspected yet treatable conditions. To study its capability in the clinic, we performed whole-exome sequencing in 118 probands with a diagnosis of a pediatric-onset neurodevelopmental disease in which most known causes had been excluded. Twenty-two genes not previously identified as disease-causing were identified in this study (19% of cohort), further establishing exome sequencing as a useful tool for gene discovery. New genes identified included EXOC8 in Joubert syndrome and GFM2 in a patient with microcephaly, simplified gyral pattern, and insulin-dependent diabetes. Exome sequencing uncovered 10 probands (8% of cohort) with mutations in genes known to cause a disease different from the initial diagnosis. Upon further medical evaluation, these mutations were found to account for each proband's disease, leading to a change in diagnosis, some of which led to changes in patient management. Our data provide proof of principle that genomic strategies are useful in clarifying diagnosis in a proportion of patients with neurodevelopmental disorders. AU - Dixon-Salazar, Tracy J AU - Silhavy, Jennifer L AU - Udpa, Nitin AU - Schroth, Jana AU - Bielas, Stephanie L AU - Schaffer, Ashleigh E AU - Olvera, Jesus AU - Bafna, Vineet K AU - Zaki, Maha S AU - Abdel-Salam, Ghada M AU - Mansour, Lobna A AU - Selim, Laila A AU - Abdel-Hadi, Sawsan S AU - Marzouki, Naima AU - Ben-Omran, Tawfeg I AU - Al-Saana, Nouriya A AU - Sönmez, Fatma M AU - Celep, Figen AU - Azam, Matloob AU - Hill, Kiley J AU - Collazo, Adrienne AU - Fenstermaker, Ali G AU - Gaia Novarino AU - Akizu, Naiara AU - Garimella, Kiran V AU - Sougnez, Carrie L AU - Russ, Carsten AU - Gabriel, Stacey B AU - Gleeson, Joseph G ID - 2313 IS - 138 JF - Science Translational Medicine TI - Exome sequencing can improve diagnosis and alter patient management VL - 4 ER -