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  • 1
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    Analysis of the Opsin Repertoire in the Tardigrade Hypsibius dujardini Provides Insights into the Evolution of Opsin Genes in Panarthropoda (2014)
    Oxford University Press
    Details
    Publication Date: 2014-09-24
    Description: Screening of a deeply sequenced transcriptome using Illumina sequencing as well as the genome of the tardigrade Hypsibius dujardini revealed a set of five opsin genes. To clarify the phylogenetic position of these genes and to elucidate the evolutionary history of opsins in Panarthropoda (Onychophora + Tardigrada + Arthropoda), we reconstructed the phylogeny of broadly sampled metazoan opsin genes using maximum likelihood and Bayesian inference methods in conjunction with carefully selected substitution models. According to our findings, the opsin repertoire of H. dujardini comprises representatives of all three major bilaterian opsin clades, including one r-opsin, three c-opsins, and a Group 4 opsin (neuropsin/opsin-5). The identification of the tardigrade ortholog of neuropsin/opsin-5 is the first record of this opsin type in a protostome, but our screening of available metazoan genomes revealed that it is also present in other protostomes. Our opsin phylogeny further suggests that two r-opsins, including an "arthropsin," were present in the last common ancestor of Panarthropoda. Although both r-opsin lineages were retained in Onychophora and Arthropoda, the arthropsin was lost in Tardigrada. The single (most likely visual) r-opsin found in H. dujardini supports the hypothesis of monochromatic vision in the panarthropod ancestor, whereas two duplications of the ancestral panarthropod c-opsin have led to three c-opsins in tardigrades. Although the early-branching nodes are unstable within the metazoans, our findings suggest that the last common ancestor of Bilateria possessed six opsins: Two r-opsins, one c-opsin, and three Group 4 opsins, one of which (Go opsin) was lost in the ecdysozoan lineage.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Formation of giant planets by fragmentation of protoplanetary disks (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-12-03
    Description: The evolution of gravitationally unstable protoplanetary gaseous disks has been studied with the use of three-dimensional smoothed particle hydrodynamics simulations with unprecedented resolution. We have considered disks with initial masses and temperature profiles consistent with those inferred for the protosolar nebula and for other protoplanetary disks. We show that long-lasting, self-gravitating protoplanets arise after a few disk orbital periods if cooling is efficient enough to maintain the temperature close to 50 K. The resulting bodies have masses and orbital eccentricities similar to those of detected extrasolar planets.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mayer, Lucio -- Quinn, Thomas -- Wadsley, James -- Stadel, Joachim -- New York, N.Y. -- Science. 2002 Nov 29;298(5599):1756-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Astronomy, University of Washington, Seattle, WA 98195, USA. lucio@physik.unizh.ch〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12459581" target="_blank"〉PubMed〈/a〉
    Keywords: Computer Simulation ; *Evolution, Planetary ; Gases ; Gravitation ; Hydrogen ; Jupiter ; *Planets
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Rapid formation of supermassive black hole binaries in galaxy mergers with gas (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-06-09
    Description: Supermassive black holes (SMBHs) are a ubiquitous component of the nuclei of galaxies. It is normally assumed that after the merger of two massive galaxies, a SMBH binary will form, shrink because of stellar or gas dynamical processes, and ultimately coalesce by emitting a burst of gravitational waves. However, so far it has not been possible to show how two SMBHs bind during a galaxy merger with gas because of the difficulty of modeling a wide range of spatial scales. Here we report hydrodynamical simulations that track the formation of a SMBH binary down to scales of a few light years after the collision between two spiral galaxies. A massive, turbulent, nuclear gaseous disk arises as a result of the galaxy merger. The black holes form an eccentric binary in the disk in less than 1 million years as a result of the gravitational drag from the gas rather than from the stars.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mayer, L -- Kazantzidis, S -- Madau, P -- Colpi, M -- Quinn, T -- Wadsley, J -- New York, N.Y. -- Science. 2007 Jun 29;316(5833):1874-7. Epub 2007 Jun 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Theoretical Physics, University of Zurich, Winterthurestrasse 190, CH-8057 Zurich, Switzerland. lucio@phys.ethz.ch〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17556550" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    Ecology. Grass trumps trees with fire (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-10-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mayer, Audrey L -- Khalyani, Azad Henareh -- New York, N.Y. -- Science. 2011 Oct 14;334(6053):188-9. doi: 10.1126/science.1213908.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA. almayer@mtu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21998379" target="_blank"〉PubMed〈/a〉
    Keywords: *Ecosystem ; *Trees ; *Tropical Climate
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Ecology. Importing timber, exporting ecological impact (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-04-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mayer, Audrey L -- Kauppi, Pekka E -- Angelstam, Per K -- Zhang, Yu -- Tikka, Paivi M -- New York, N.Y. -- Science. 2005 Apr 15;308(5720):359-60.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉U.S. Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory; Cincinnati, OH 45268, USA. mayer.audrey@epa.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15831743" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biodiversity ; China ; *Commerce ; *Conservation of Natural Resources ; *Ecosystem ; Finland ; Internationality ; Russia ; *Trees ; *Wood
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    Mucus enhances gut homeostasis and oral tolerance by delivering immunoregulatory signals (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-09-28
    Description: A dense mucus layer in the large intestine prevents inflammation by shielding the underlying epithelium from luminal bacteria and food antigens. This mucus barrier is organized around the hyperglycosylated mucin MUC2. Here we show that the small intestine has a porous mucus layer, which permitted the uptake of MUC2 by antigen-sampling dendritic cells (DCs). Glycans associated with MUC2 imprinted DCs with anti-inflammatory properties by assembling a galectin-3-Dectin-1-FcgammaRIIB receptor complex that activated beta-catenin. This transcription factor interfered with DC expression of inflammatory but not tolerogenic cytokines by inhibiting gene transcription through nuclear factor kappaB. MUC2 induced additional conditioning signals in intestinal epithelial cells. Thus, mucus does not merely form a nonspecific physical barrier, but also constrains the immunogenicity of gut antigens by delivering tolerogenic signals.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4005805/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4005805/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shan, Meimei -- Gentile, Maurizio -- Yeiser, John R -- Walland, A Cooper -- Bornstein, Victor U -- Chen, Kang -- He, Bing -- Cassis, Linda -- Bigas, Anna -- Cols, Montserrat -- Comerma, Laura -- Huang, Bihui -- Blander, J Magarian -- Xiong, Huabao -- Mayer, Lloyd -- Berin, Cecilia -- Augenlicht, Leonard H -- Velcich, Anna -- Cerutti, Andrea -- AI073899/AI/NIAID NIH HHS/ -- AI095245/AI/NIAID NIH HHS/ -- AI57653/AI/NIAID NIH HHS/ -- AI61093/AI/NIAID NIH HHS/ -- AI74378/AI/NIAID NIH HHS/ -- AI95613/AI/NIAID NIH HHS/ -- AI96187/AI/NIAID NIH HHS/ -- DK072201/DK/NIDDK NIH HHS/ -- P01 AI061093/AI/NIAID NIH HHS/ -- P01 DK072201/DK/NIDDK NIH HHS/ -- P60 DK020541/DK/NIDDK NIH HHS/ -- R01 AI057653/AI/NIAID NIH HHS/ -- R01 AI093577/AI/NIAID NIH HHS/ -- U01 AI095613/AI/NIAID NIH HHS/ -- U19 AI096187/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2013 Oct 25;342(6157):447-53. doi: 10.1126/science.1237910. Epub 2013 Sep 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medicine, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24072822" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cells, Cultured ; Dendritic Cells/immunology ; Galectin 3/genetics/metabolism ; Glycosylation ; *Homeostasis ; Humans ; Immune Tolerance/genetics/*immunology ; Inflammation/immunology ; Intestinal Mucosa/immunology ; Intestine, Small/*immunology ; Lectins, C-Type/genetics/metabolism ; Mice ; Mice, Inbred C57BL ; Mice, Mutant Strains ; Mouth/*immunology ; Mucin-2/genetics/physiology ; Mucus/*immunology ; NF-kappa B/metabolism ; Receptors, IgG/genetics/metabolism ; Transcription, Genetic ; beta Catenin/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    Excepftonally strong near-bottom flows on the continental rise of nova scotia (1981)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1981-08-21
    Description: Recent current velocity measurements across the lower continental rise of Nova Scotia show a deep equatorwardflow with speeds (maximum, 73 centimeters per second) among the highest recorded for the deep sea. Silicate measurements indicate that this flow usually consists of southern-source (Antarctic) bottom water. These measurements confirm the existence of a second and deeper western boundary flow that was earlier inferredfrom geological observations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Richardson, M J -- Wimbush, M -- Mayer, L -- New York, N.Y. -- Science. 1981 Aug 21;213(4510):887-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17775272" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 8
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    Immunoregulatory lymphokines of T hybridomas from AIDS patients: constitutive and inducible suppressor factors (1984)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1984-07-06
    Description: Supernatants derived from peripheral blood mononuclear cell cultures of certain patients with the acquired immunodeficiency syndrome (AIDS) or its prodromes have the capacity to block T cell-dependent immune reactivity in vitro. T cells derived from a patient positive for antibody to the lymphadenopathy associated virus ( LAV ), and elaborating high titers of these soluble suppressor factors, were fused to a mutagenized clone of the human T lymphoblastoid cell line KE37 . Molecules capable of profoundly depressing T cell-dependent polyclonal antibody production and DNA synthetic responses, either directly or after incubation with normal adherent cells, were isolated from stable hybrid clones.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Laurence, J -- Mayer, L -- CA 35018-01/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 1984 Jul 6;225(4657):66-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6328662" target="_blank"〉PubMed〈/a〉
    Keywords: Acquired Immunodeficiency Syndrome/*immunology ; Animals ; Humans ; Hybridomas/*immunology ; Lymphokines/*immunology ; Mice ; Mice, Inbred BALB C ; Monocytes/immunology ; Retroviridae/immunology ; Retroviridae Infections/immunology ; T-Lymphocytes/*immunology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 9
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    [Working Life] A scientist on any schedule (2017)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2017-01-27
    Description: Author: Audrey L. Mayer
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
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    Predicting dark matter halo formation in N-body simulations with deep regression networks (2020)
    Oxford University Press
    Details
    Publication Date: 2020-07-07
    Description: Dark matter haloes play a fundamental role in cosmological structure formation. The most common approach to model their assembly mechanisms is through N-body simulations. In this work, we present an innovative pathway to predict dark matter halo formation from the initial density field using a Deep Learning algorithm. We implement and train a Deep Convolutional Neural Network to solve the task of retrieving Lagrangian patches from which dark matter haloes will condense. The volumetric multilabel classification task is turned into a regression problem by means of the Euclidean distance transformation. The network is complemented by an adaptive version of the watershed algorithm to form the entire protohalo identification pipeline. We show that splitting the segmentation problem into two distinct subtasks allows for training smaller and faster networks, while the predictive power of the pipeline remains the same. The model is trained on synthetic data derived from a single full N-body simulation and achieves deviations of ∼10 per cent when reconstructing the dark matter halo mass function at z = 0. This approach represents a promising framework for learning highly non-linear relations in the primordial density field. As a practical application, our method can be used to produce mock dark matter halo catalogues directly from the initial conditions of N-body simulations.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
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