[{"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"2076","publist_id":"4962","author":[{"full_name":"Beatriz Vicoso","orcid":"0000-0002-4579-8306","last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Emerson, Jr J.","last_name":"Emerson","first_name":"Jr"},{"full_name":"Zektser, Yulia","last_name":"Zektser","first_name":"Yulia"},{"first_name":"Shivani","last_name":"Mahajan","full_name":"Mahajan, Shivani"},{"first_name":"Doris","last_name":"Bachtrog","full_name":"Bachtrog, Doris"}],"title":"Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation","date_updated":"2021-01-12T06:55:09Z","citation":{"chicago":"Vicoso, Beatriz, Jr Emerson, Yulia Zektser, Shivani Mahajan, and Doris Bachtrog. “Comparative Sex Chromosome Genomics in Snakes: Differentiation Evolutionary Strata and Lack of Global Dosage Compensation.” PLoS Biology. Public Library of Science, 2013. https://doi.org/10.1371/journal.pbio.1001643.","ista":"Vicoso B, Emerson J, Zektser Y, Mahajan S, Bachtrog D. 2013. Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation. PLoS Biology. 11(8).","mla":"Vicoso, Beatriz, et al. “Comparative Sex Chromosome Genomics in Snakes: Differentiation Evolutionary Strata and Lack of Global Dosage Compensation.” PLoS Biology, vol. 11, no. 8, Public Library of Science, 2013, doi:10.1371/journal.pbio.1001643.","ama":"Vicoso B, Emerson J, Zektser Y, Mahajan S, Bachtrog D. Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation. PLoS Biology. 2013;11(8). doi:10.1371/journal.pbio.1001643","apa":"Vicoso, B., Emerson, J., Zektser, Y., Mahajan, S., & Bachtrog, D. (2013). Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1001643","short":"B. Vicoso, J. Emerson, Y. Zektser, S. Mahajan, D. Bachtrog, PLoS Biology 11 (2013).","ieee":"B. Vicoso, J. Emerson, Y. Zektser, S. Mahajan, and D. Bachtrog, “Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation,” PLoS Biology, vol. 11, no. 8. Public Library of Science, 2013."},"extern":1,"publisher":"Public Library of Science","quality_controlled":0,"month":"08","intvolume":" 11","abstract":[{"text":"Snakes exhibit genetic sex determination, with female heterogametic sex chromosomes (ZZ males, ZW females). Extensive cytogenetic work has suggested that the level of sex chromosome heteromorphism varies among species, with Boidae having entirely homomorphic sex chromosomes, Viperidae having completely heteromorphic sex chromosomes, and Colubridae showing partial differentiation. Here, we take a genomic approach to compare sex chromosome differentiation in these three snake families. We identify homomorphic sex chromosomes in boas (Boidae), but completely heteromorphic sex chromosomes in both garter snakes (Colubridae) and pygmy rattlesnake (Viperidae). Detection of W-linked gametologs enables us to establish the presence of evolutionary strata on garter and pygmy rattlesnake sex chromosomes where recombination was abolished at different time points. Sequence analysis shows that all strata are shared between pygmy rattlesnake and garter snake, i.e., recombination was abolished between the sex chromosomes before the two lineages diverged. The sex-biased transmission of the Z and its hemizygosity in females can impact patterns of molecular evolution, and we show that rates of evolution for Z-linked genes are increased relative to their pseudoautosomal homologs, both at synonymous and amino acid sites (even after controlling for mutational biases). This demonstrates that mutation rates are male-biased in snakes (male-driven evolution), but also supports faster-Z evolution due to differential selective effects on the Z. Finally, we perform a transcriptome analysis in boa and pygmy rattlesnake to establish baseline levels of sex-biased expression in homomorphic sex chromosomes, and show that heteromorphic ZW chromosomes in rattlesnakes lack chromosome-wide dosage compensation. Our study provides the first full scale overview of the evolution of snake sex chromosomes at the genomic level, thus greatly expanding our knowledge of reptilian and vertebrate sex chromosomes evolution.\n","lang":"eng"}],"acknowledgement":"Funded by NIH grants (R01GM076007 and R01GM093182) and a Packard Fellowship to DB.","doi":"10.1371/journal.pbio.1001643","date_published":"2013-08-27T00:00:00Z","issue":"8","volume":11,"date_created":"2018-12-11T11:55:34Z","publication_status":"published","year":"2013","day":"27","publication":"PLoS Biology"},{"title":"Computational design of mechanical characters","publist_id":"4927","author":[{"first_name":"Stelian","last_name":"Coros","full_name":"Coros, Stelian"},{"first_name":"Bernhard","full_name":"Thomaszewski, Bernhard","last_name":"Thomaszewski"},{"first_name":"Gioacchino","full_name":"Noris, Gioacchino","last_name":"Noris"},{"full_name":"Sueda, Shinjiro","last_name":"Sueda","first_name":"Shinjiro"},{"first_name":"Moira","last_name":"Forberg","full_name":"Forberg, Moira"},{"first_name":"Robert","last_name":"Sumner","full_name":"Sumner, Robert W"},{"full_name":"Matusik, Wojciech","last_name":"Matusik","first_name":"Wojciech"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","orcid":"0000-0001-6511-9385","full_name":"Bernd Bickel","last_name":"Bickel"}],"extern":1,"date_updated":"2021-01-12T06:55:21Z","citation":{"ieee":"S. Coros et al., “Computational design of mechanical characters,” ACM Transactions on Graphics, vol. 32, no. 4. ACM, 2013.","short":"S. Coros, B. Thomaszewski, G. Noris, S. Sueda, M. Forberg, R. Sumner, W. Matusik, B. Bickel, ACM Transactions on Graphics 32 (2013).","apa":"Coros, S., Thomaszewski, B., Noris, G., Sueda, S., Forberg, M., Sumner, R., … Bickel, B. (2013). Computational design of mechanical characters. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2461912.2461953","ama":"Coros S, Thomaszewski B, Noris G, et al. Computational design of mechanical characters. ACM Transactions on Graphics. 2013;32(4). doi:10.1145/2461912.2461953","mla":"Coros, Stelian, et al. “Computational Design of Mechanical Characters.” ACM Transactions on Graphics, vol. 32, no. 4, ACM, 2013, doi:10.1145/2461912.2461953.","ista":"Coros S, Thomaszewski B, Noris G, Sueda S, Forberg M, Sumner R, Matusik W, Bickel B. 2013. Computational design of mechanical characters. ACM Transactions on Graphics. 32(4).","chicago":"Coros, Stelian, Bernhard Thomaszewski, Gioacchino Noris, Shinjiro Sueda, Moira Forberg, Robert Sumner, Wojciech Matusik, and Bernd Bickel. “Computational Design of Mechanical Characters.” ACM Transactions on Graphics. ACM, 2013. https://doi.org/10.1145/2461912.2461953."},"status":"public","type":"journal_article","_id":"2108","volume":32,"issue":"4","date_published":"2013-07-01T00:00:00Z","doi":"10.1145/2461912.2461953","date_created":"2018-12-11T11:55:46Z","day":"01","publication":"ACM Transactions on Graphics","year":"2013","publication_status":"published","month":"07","intvolume":" 32","quality_controlled":0,"publisher":"ACM","abstract":[{"text":"We present an interactive design system that allows non-expert users to create animated mechanical characters. Given an articulated character as input, the user iteratively creates an animation by sketching motion curves indicating how different parts of the character should move. For each motion curve, our framework creates an optimized mechanism that reproduces it as closely as possible. The resulting mechanisms are attached to the character and then connected to each other using gear trains, which are created in a semi-automated fashion. The mechanical assemblies generated with our system can be driven with a single input driver, such as a hand-operated crank or an electric motor, and they can be fabricated using rapid prototyping devices. We demonstrate the versatility of our approach by designing a wide range of mechanical characters, several of which we manufactured using 3D printing. While our pipeline is designed for characters driven by planar mechanisms, significant parts of it extend directly to non-planar mechanisms, allowing us to create characters with compelling 3D motions. ","lang":"eng"}]},{"extern":1,"date_updated":"2021-01-12T06:55:22Z","citation":{"chicago":"Papas, Marios, Christian Regg, Wojciech Jarosz, Bernd Bickel, Philip Jackson, Wojciech Matusik, Steve Marschner, and Markus Groß. “Fabricating Translucent Materials Using Continuous Pigment Mixtures.” ACM Transactions on Graphics. ACM, 2013. https://doi.org/10.1145/2461912.2461974.","ista":"Papas M, Regg C, Jarosz W, Bickel B, Jackson P, Matusik W, Marschner S, Groß M. 2013. Fabricating translucent materials using continuous pigment mixtures. ACM Transactions on Graphics. 32(4).","mla":"Papas, Marios, et al. “Fabricating Translucent Materials Using Continuous Pigment Mixtures.” ACM Transactions on Graphics, vol. 32, no. 4, ACM, 2013, doi:10.1145/2461912.2461974.","apa":"Papas, M., Regg, C., Jarosz, W., Bickel, B., Jackson, P., Matusik, W., … Groß, M. (2013). Fabricating translucent materials using continuous pigment mixtures. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2461912.2461974","ama":"Papas M, Regg C, Jarosz W, et al. Fabricating translucent materials using continuous pigment mixtures. ACM Transactions on Graphics. 2013;32(4). doi:10.1145/2461912.2461974","short":"M. Papas, C. Regg, W. Jarosz, B. Bickel, P. Jackson, W. Matusik, S. Marschner, M. Groß, ACM Transactions on Graphics 32 (2013).","ieee":"M. Papas et al., “Fabricating translucent materials using continuous pigment mixtures,” ACM Transactions on Graphics, vol. 32, no. 4. ACM, 2013."},"title":"Fabricating translucent materials using continuous pigment mixtures","publist_id":"4925","author":[{"first_name":"Marios","last_name":"Papas","full_name":"Papas, Marios"},{"first_name":"Christian","last_name":"Regg","full_name":"Regg, Christian"},{"full_name":"Jarosz, Wojciech","last_name":"Jarosz","first_name":"Wojciech"},{"last_name":"Bickel","full_name":"Bernd Bickel","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"},{"first_name":"Philip","last_name":"Jackson","full_name":"Jackson, Philip V"},{"last_name":"Matusik","full_name":"Matusik, Wojciech","first_name":"Wojciech"},{"first_name":"Steve","last_name":"Marschner","full_name":"Marschner, Steve"},{"first_name":"Markus","full_name":"Groß, Markus S","last_name":"Groß"}],"_id":"2110","status":"public","type":"journal_article","day":"01","publication":"ACM Transactions on Graphics","year":"2013","publication_status":"published","date_published":"2013-07-01T00:00:00Z","issue":"4","volume":32,"doi":"10.1145/2461912.2461974","date_created":"2018-12-11T11:55:46Z","abstract":[{"text":"We present a method for practical physical reproduction and design of homogeneous materials with desired subsurface scattering. Our process uses a collection of different pigments that can be suspended in a clear base material. Our goal is to determine pigment concentrations that best reproduce the appearance and subsurface scattering of a given target material. In order to achieve this task we first fabricate a collection of material samples composed of known mixtures of the available pigments with the base material. We then acquire their reflectance profiles using a custom-built measurement device. We use the same device to measure the reflectance profile of a target material. Based on the database of mappings from pigment concentrations to reflectance profiles, we use an optimization process to compute the concentration of pigments to best replicate the target material appearance. We demonstrate the practicality of our method by reproducing a variety of different translucent materials. We also present a tool that allows the user to explore the range of achievable appearances for a given set of pigments. ","lang":"eng"}],"month":"07","intvolume":" 32","quality_controlled":0,"publisher":"ACM"},{"_id":"2111","status":"public","type":"journal_article","extern":1,"citation":{"chicago":"Bermano, Amit, Philipp Bruschweiler, Anselm Grundhöfer, Daisuke Iwai, Bernd Bickel, and Markus Groß. “Augmenting Physical Avatars Using Projector-Based Illumination.” ACM Transactions on Graphics. ACM, 2013. https://doi.org/10.1145/2508363.2508416.","ista":"Bermano A, Bruschweiler P, Grundhöfer A, Iwai D, Bickel B, Groß M. 2013. Augmenting physical avatars using projector-based illumination. ACM Transactions on Graphics. 32(6).","mla":"Bermano, Amit, et al. “Augmenting Physical Avatars Using Projector-Based Illumination.” ACM Transactions on Graphics, vol. 32, no. 6, ACM, 2013, doi:10.1145/2508363.2508416.","apa":"Bermano, A., Bruschweiler, P., Grundhöfer, A., Iwai, D., Bickel, B., & Groß, M. (2013). Augmenting physical avatars using projector-based illumination. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2508363.2508416","ama":"Bermano A, Bruschweiler P, Grundhöfer A, Iwai D, Bickel B, Groß M. Augmenting physical avatars using projector-based illumination. ACM Transactions on Graphics. 2013;32(6). doi:10.1145/2508363.2508416","short":"A. Bermano, P. Bruschweiler, A. Grundhöfer, D. Iwai, B. Bickel, M. Groß, ACM Transactions on Graphics 32 (2013).","ieee":"A. Bermano, P. Bruschweiler, A. Grundhöfer, D. Iwai, B. Bickel, and M. Groß, “Augmenting physical avatars using projector-based illumination,” ACM Transactions on Graphics, vol. 32, no. 6. ACM, 2013."},"date_updated":"2021-01-12T06:55:23Z","title":"Augmenting physical avatars using projector-based illumination","publist_id":"4922","author":[{"full_name":"Bermano, Amit H","last_name":"Bermano","first_name":"Amit"},{"last_name":"Bruschweiler","full_name":"Bruschweiler, Philipp","first_name":"Philipp"},{"full_name":"Grundhöfer, Anselm","last_name":"Grundhöfer","first_name":"Anselm"},{"full_name":"Iwai, Daisuke","last_name":"Iwai","first_name":"Daisuke"},{"last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bernd Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Markus","full_name":"Groß, Markus S","last_name":"Groß"}],"abstract":[{"lang":"eng","text":"Animated animatronic figures are a unique way to give physical presence to a character. However, their movement and expressions are often limited due to mechanical constraints. In this paper, we propose a complete process for augmenting physical avatars using projector-based illumination, significantly increasing their expressiveness. Given an input animation, the system decomposes the motion into low-frequency motion that can be physically reproduced by the animatronic head and high-frequency details that are added using projected shading. At the core is a spatio-temporal optimization process that compresses the motion in gradient space, ensuring faithful motion replay while respecting the physical limitations of the system. We also propose a complete multi-camera and projection system, including a novel defocused projection and subsurface scattering compensation scheme. The result of our system is a highly expressive physical avatar that features facial details and motion otherwise unattainable due to physical constraints."}],"month":"11","intvolume":" 32","quality_controlled":0,"publisher":"ACM","day":"01","publication":"ACM Transactions on Graphics","year":"2013","publication_status":"published","date_published":"2013-11-01T00:00:00Z","doi":"10.1145/2508363.2508416","volume":32,"issue":"6","date_created":"2018-12-11T11:55:47Z"},{"type":"journal_article","status":"public","_id":"2109","publist_id":"4924","author":[{"full_name":"Hildebrand, Kristian","last_name":"Hildebrand","first_name":"Kristian"},{"orcid":"0000-0001-6511-9385","full_name":"Bernd Bickel","last_name":"Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Alexa, Marc","last_name":"Alexa","first_name":"Marc"}],"title":"Orthogonal slicing for additive manufacturing","citation":{"chicago":"Hildebrand, Kristian, Bernd Bickel, and Marc Alexa. “Orthogonal Slicing for Additive Manufacturing.” Computers and Graphics (Pergamon). Elsevier, 2013. https://doi.org/10.1016/j.cag.2013.05.011.","ista":"Hildebrand K, Bickel B, Alexa M. 2013. Orthogonal slicing for additive manufacturing. Computers and Graphics (Pergamon). 37(6), 669–675.","mla":"Hildebrand, Kristian, et al. “Orthogonal Slicing for Additive Manufacturing.” Computers and Graphics (Pergamon), vol. 37, no. 6, Elsevier, 2013, pp. 669–75, doi:10.1016/j.cag.2013.05.011.","ieee":"K. Hildebrand, B. Bickel, and M. Alexa, “Orthogonal slicing for additive manufacturing,” Computers and Graphics (Pergamon), vol. 37, no. 6. Elsevier, pp. 669–675, 2013.","short":"K. Hildebrand, B. Bickel, M. Alexa, Computers and Graphics (Pergamon) 37 (2013) 669–675.","ama":"Hildebrand K, Bickel B, Alexa M. Orthogonal slicing for additive manufacturing. Computers and Graphics (Pergamon). 2013;37(6):669-675. doi:10.1016/j.cag.2013.05.011","apa":"Hildebrand, K., Bickel, B., & Alexa, M. (2013). Orthogonal slicing for additive manufacturing. Computers and Graphics (Pergamon). Elsevier. https://doi.org/10.1016/j.cag.2013.05.011"},"date_updated":"2021-01-12T06:55:22Z","extern":1,"publisher":"Elsevier","quality_controlled":0,"intvolume":" 37","month":"10","abstract":[{"lang":"eng","text":"Most additive manufacturing technologies work by layering, i.e. slicing the shape and then generating each slice independently. This introduces an anisotropy into the process, often as different accuracies in the tangential and normal directions, but also in terms of other parameters such as build speed or tensile strength and strain. We model this as an anisotropic cubic element. Our approach then finds a compromise between modeling each part of the shape individually in the best possible direction and using one direction for the whole shape part. In particular, we compute an orthogonal basis and consider only the three basis vectors as slice normals (i.e. fabrication directions). Then we optimize a decomposition of the shape along this basis so that each part can be consistently sliced along one of the basis vectors. In simulation, we show that this approach is superior to slicing the whole shape in one direction, only. It also has clear benefits if the shape is larger than the build volume of the available equipment."}],"page":"669 - 675","date_created":"2018-12-11T11:55:46Z","issue":"6","volume":37,"date_published":"2013-10-01T00:00:00Z","doi":"10.1016/j.cag.2013.05.011","publication_status":"published","year":"2013","publication":"Computers and Graphics (Pergamon)","day":"01"}]