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3. Author Correction: Comparative and demographic analysis of orang-utan genomes

Author

Devin P. Locke, LaDeana W. Hillier, Wesley C. Warren, Kim C. Worley, Lynne V. Nazareth, Donna M. Muzny, Shiaw-Pyng Yang, Zhengyuan Wang, Asif T. Chinwalla, Pat Minx, Makedonka Mitreva, Lisa Cook, Kim D. Delehaunty, Catrina Fronick, Heather Schmidt, Lucinda A. Fulton, Robert S. Fulton, Joanne O. Nelson, Vincent Magrini, Craig Pohl, Tina A. Graves, Chris Markovic, Andy Cree, Huyen H. Dinh, Jennifer Hume, Christie L. Kovar, Gerald R. Fowler, Gerton Lunter, Stephen Meader, Andreas Heger, Chris P. Ponting, Tomas Marques-Bonet, Can Alkan, Lin Chen, Ze Cheng, Jeffrey M. Kidd, Evan E. Eichler, Simon White, Stephen Searle, Albert J. Vilella, Yuan Chen, Paul Flicek, Jian Ma, Brian Raney, Bernard Suh, Richard Burhans, Javier Herrero, David Haussler, Rui Faria, Olga Fernando, Fleur Darré, Domènec Farré, Elodie Gazave, Meritxell Oliva, Arcadi Navarro, Roberta Roberto, Oronzo Capozzi, Nicoletta Archidiacono, Giuliano Della Valle, Stefania Purgato, Mariano Rocchi, Miriam K. Konkel, Jerilyn A. Walker, Brygg Ullmer, Mark A. Batzer, Arian F. A. Smit, Robert Hubley, Claudio Casola, Daniel R. Schrider, Matthew W. Hahn, Victor Quesada, Xose S. Puente, Gonzalo R. Ordoñez, Carlos López-Otín, Tomas Vinar, Brona Brejova, Aakrosh Ratan, Robert S. Harris, Webb Miller, Carolin Kosiol, Heather A. Lawson, Vikas Taliwal, André L. Martins, Adam Siepel, Arindam RoyChoudhury, Xin Ma, Jeremiah Degenhardt, Carlos D. Bustamante, Ryan N. Gutenkunst, Thomas Mailund, Julien Y. Dutheil, Asger Hobolth, Mikkel H. Schierup, Oliver A. Ryder, Yuko Yoshinaga, Pieter J. de Jong, George M. Weinstock, Jeffrey Rogers, Elaine R. Mardis, Richard A. Gibbs, and Richard K. Wilson

Subjects
Multidisciplinary
Published
2022
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5. Comparative and demographic analysis of orang-utan genomes

Author

Matthew W. Hahn, Andreas Heger, Carolin Kosiol, Lisa Cook, Arindam RoyChoudhury, Arcadi Navarro, Catrina Fronick, Lin Chen, Devin P. Locke, Oliver A. Ryder, Olga Fernando, Tomas Vinar, Adam Siepel, Jian Ma, Jeremiah D. Degenhardt, Giuliano Della Valle, Brona Brejova, Oronzo Capozzi, Christie Kovar, Nicoletta Archidiacono, Lucinda Fulton, Jerilyn A. Walker, Albert J. Vilella, Domènec Farré, Julien Y. Dutheil, Xose S. Puente, Mikkel H. Schierup, Carlos Bustamante, George M. Weinstock, Lynne V. Nazareth, Can Alkan, Robert S. Fulton, Brian J. Raney, Mark A. Batzer, Tina Graves, Stephen M. J. Searle, Miriam K. Konkel, Yuko Yoshinaga, Donna M. Muzny, Mariano Rocchi, Carlos López-Otín, Bernard B. Suh, Thomas Mailund, Gonzalo R. Ordóñez, Robert Hubley, Claudio Casola, Huyen Dinh, Rui Faria, Joanne O. Nelson, Tomas Marques-Bonet, Vincent Magrini, Chris Markovic, Makedonka Mitreva, Zhengyuan Wang, Elaine R. Mardis, Arian F.A. Smit, Asger Hobolth, Javier Herrero, David Haussler, Pieter J. de Jong, Kim C. Worley, Heather Schmidt, Ryan N. Gutenkunst, Webb Miller, Yuan Chen, Richard Burhans, Gerton Lunter, Simon D. M. White, André L. Martins, Richard A. Gibbs, Wesley C. Warren, Richard K. Wilson, Patrick Minx, Elodie Gazave, Xin Ma, Daniel R. Schrider, Chris P. Ponting, Roberta Roberto, Shiaw-Pyng Yang, Víctor Quesada, Stefania Purgato, Evan E. Eichler, Andy Cree, Brygg Ullmer, Jeffrey Rogers, Fleur Darré, Robert S. Harris, Vikas Taliwal, Jeffrey M. Kidd, Craig Pohl, Aakrosh Ratan, Paul Flicek, Meritxell Oliva, Kim D. Delehaunty, LaDeana W. Hillier, Jennifer Hume, Stephen Meader, Ze Cheng, Asif T. Chinwalla, Heather A. Lawson, Gerald R. Fowler, National Human Genome Research Institute (US), National Institutes of Health (US), National Science Foundation (US), David and Lucile Packard Foundation, Cornell University, Medical Research Council (UK), European Commission, Ministerio de Ciencia e Innovación (España), Fundación Botín, Instituto Nacional de Bioinformática (España), Fundação para a Ciência e a Tecnologia (Portugal), Locke, Devin P, Hillier, Ladeana W., Warren, Wesley C., Worley, Kim C., Nazareth, Lynne V., Muzny, Donna M., Yang, Shiaw-Pyng, Wang, Zhengyuan, Chinwalla, Asif T., Minx, Pat, Mitreva, Makedonka, Cook, Lisa, Delehaunty, Kim D., Fronick, Catrina, Schmidt, Heather, Fulton, Lucinda A., Fulton, Robert S., Nelson, Joanne O., Magrini, Vincent, Pohl, Craig, Graves, Tina A., Markovic, Chri, Cree, Andy, Dinh, Huyen H., Hume, Jennifer, Kovar, Christie L., Fowler, Gerald R., Lunter, Gerton, Meader, Stephen, Heger, Andrea, Ponting, Chris P., Marques-Bonet, Toma, Alkan, Can, Chen, Lin, Cheng, Ze, Kidd, Jeffrey M., Eichler, Evan E., White, Simon, Searle, Stephen, Vilella, Albert J., Chen, Yuan, Flicek, Paul, Ma, Jian, Raney, Brian, Suh, Bernard, Burhans, Richard, Herrero, Javier, Haussler, David, Faria, Rui, Fernando, Olga, Darré, Fleur, Farré, Doménec, Gazave, Elodie, Oliva, Meritxell, Navarro, Arcadi, Roberto, Roberta, Capozzi, Oronzo, Archidiacono, Nicoletta, Della Valle, Giuliano, Purgato, Stefania, Rocchi, Mariano, Konkel, Miriam K., Walker, Jerilyn A., Ullmer, Brygg, Batzer, Mark A., Smit, Arian F. A., Hubley, Robert, Casola, Claudio, Schrider, Daniel R., Hahn, Matthew W., Quesada, Victor, Puente, Xose S., Ordõez, Gonzalo R., Ĺpez-Otín, Carlo, Vinar, Toma, Brejova, Brona, Ratan, Aakrosh, Harris, Robert S., Miller, Webb, Kosiol, Carolin, Lawson, Heather A., Taliwal, Vika, Martins, André L., Siepel, Adam, Roychoudhury, Arindam, Ma, Xin, Degenhardt, Jeremiah, Bustamante, Carlos D., Gutenkunst, Ryan N., Mailund, Thoma, Dutheil, Julien Y., Hobolth, Asger, Schierup, Mikkel H., Ryder, Oliver A., Yoshinaga, Yuko, De Jong, Pieter J., Weinstock, George M., Rogers, Jeffrey, Mardis, Elaine R., Gibbs, Richard A., and Wilson, Richard K.

Subjects
Male, Pongo abelii, Genetic Speciation, Population, Population Dynamics, Centromere, Zoology, Biology, Southeast asian, Chromosome, Genome, Chromosomes, Article, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, Pongo pygmaeus, Effective population size, Cerebrosides, Species Specificity, Animals, Humans, education, Phylogeny, 030304 developmental biology, Comparative genomics, Cerebroside, Gene Rearrangement, Population Density, 0303 health sciences, education.field_of_study, Population Dynamic, Multidisciplinary, Animal, Medicine (all), Genetic Variation, Gene rearrangement, 3. Good health, Genetics, Population, Evolutionary biology, Female, Pongo pygmaeu, 030217 neurology & neurosurgery, Human
Abstract

5 páginas, 5 figuras, 2 tablas.-- This paper is distributed under the terms of the Creative Commons Attribution-Non-Commercial-Share Alike Licence, and is freely available to all readers atwww.nature.com/nature.-- et al., ‘Orang-utan’ is derived from a Malay term meaning ‘man of the forest’ and aptly describes the southeast Asian great apes native to Sumatra and Borneo. The orang-utan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orang-utan draft genome assembly and short read sequence data from five Sumatran and five Bornean orang-utan genomes. Our analyses reveal that, compared to other primates, the orang-utan genome has many unique features. Structural evolution of the orang-utan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe a primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orang-utan genome structure. Orang-utans have extremely low energy usage for a eutherian mammal1, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400,000 years ago, is more recent than most previous studies and underscores the complexity of the orang-utan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (Ne) expanded exponentially relative to the ancestral Ne after the split, while Bornean Ne declined over the same period. Overall, the resources and analyses presented here offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts., The orang-utan genome project was funded by the National Human Genome Research Institute (NHGRI), including grantsU54HG003079 (R.K.W.) and U54 HG003273 (R.A.G), with further support from National Institutes of Health R01 GM59290 (M.A.B.), PO1 AG022064 (M.A.B.), HG002385 (E.E.E.) and HG002238 (W.M.), National Science Foundation DBI-0644111 (A.S. and B.B.), David and Lucile Packard Foundation(A.S., V.T. and T.V.),CornellUniversity Provost’s Fellowship (A.L.M.), UK Medical Research Council (C.P.P., G.L., S.M. and A.H.), Marie Curie Fellowship (T.M.-B.), Ministerio de Ciencia e Innovación-Spain (MCI-Spain) and Fundación M. Botín (V.Q., X.S.P., G.R.O. and C.L.-O.), MCI-Spain BFU2006-15413-C02-01 and BFU2009-13409-C02-02 (A.N.), Spanish National Institute for Bioinformatics (INAB) and Fundação para a Ciência e a Tecnologia (Portugal), SFRH/BPD/26384/2006(R.F.) and SFRH/BD/15856/2005 (O.F.), PRIN and CEGBA (M.R., N.A. and G.D.V.), and the Commission of the European Communities IRG-224885 (T.V.), IRG-231025 (B.B.).

Published
2011
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6. 61.2: Eye Movements During Visual and Auditory Task Performance

Author

Karl Van Orden, Shawn Wing, Erik Viirre, Vikas Taliwal, Julie Kwak, Bradley Chase, and Christopher Pribe

Subjects
Visual search, Elementary cognitive task, medicine.medical_specialty, business.industry, Eye movement, Workload, Audiology, Saccadic masking, Task (project management), Gaze-contingency paradigm, medicine, Eye tracking, Computer vision, Artificial intelligence, Psychology, business
Abstract

The primary focus of this research effort was the tracking of eye movements during complex cognitive tasks. 8 volunteers performed a visual tracking task alone and a combination of the visual task and the auditory Paced Serial Addition Task (PASAT). Results showed a reduction in range on the order of 50% for eye movements and an increase in variability of vergence eye movements during the dual task. This change can be characterized as visual tunneling.

Published
2004
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7. A nonlinear filter bank model for the auditory periphery

Author

Laurel H. Carney and Vikas Taliwal

Subjects
Physics, Acoustics and Ultrasonics, Low-pass filter, Acoustics, Bandwidth (signal processing), Feedback loop, medicine.anatomical_structure, Arts and Humanities (miscellaneous), Band-pass filter, Nonlinear filter, medicine, Hair cell, Gammatone filter, Sound pressure
Abstract

The intrinsically nonlinear character of auditory processing has long been the bane of linear models for the auditory periphery. A previous computational model [Carney, J. Acoust. Soc. Am. 93, 401–417 (1993)] for single auditory nerve fibers contained a feedback mechanism to vary the bandwidth of a narrow‐band gammatone filter as a function of sound pressure level. That model simulated the compressive nonlinearity, including aspects of temporal and average discharge rate characteristics of low‐frequency auditory nerve fiber responses. The proposed model extends the previous work; its architecture is motivated by the most recent empirical evidence on outer hair cell (OHC) physiology. The nonlinear narrow‐band gammatone filter is replaced with a broad second‐order bandpass filter [G. von Bekesy, J. Acoust. Soc. Am. 21, 245–254 (1949)] inside a feedback loop. The feedback path consists of a nonlinearity representing OHC transduction, followed by a lowpass filter for the cell membrane, and finally a nonlinearity representing OHC motility. A bank of such models allows representation of spatio‐temporal discharge patterns across populations of auditory nerve fibers. [Work supported by The Whitaker Foundation and NIDCD.]

Published
1993
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