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661 results on '"Reed College"'

1. Gender and Politics in Buenos Aires

Author: Mariela Szwarcberg; Reed College, Portland, Oregon and Mariela Szwarcberg; Reed College, Portland, Oregon
Abstract: This paper examines the persistent gender gap in electoral politics at the local level in Buenos Aires, Argentina. I argue that the combination of the division of political work and existing social norms regarding the separation of domestic chores contributes to women’s political underrepresentation at the local level. Studying everyday politics in Buenos Aires, a clear division of political work between men and women was found. Only women were in charge of finding solutions to issues of domestic abuse and violence, and of taking care of children, the pregnant, and senior citizens. Using information from Buenos Aires municipalities, I document the gender gap in elected legislative and executive offices at the local level – as well as in non-elected offices within municipal cabinets. It was also found that the types of political work assigned to female activists and candidates reinforce existing stereotypes of women as mothers of the poor., Este documento examina la persistente brecha de género en la política electoral municipal en Buenos Aires, Argentina. Sostengo que la combinación de la división del trabajo político y las normas sociales existentes con respecto a la separación de las tareas domésticas contribuye a la insuficiente representación política de las mujeres a nivel local. Al estudiar la política cotidiana en Buenos Aires, encuentro una clara división del trabajo político entre hombres y mujeres: solo las mujeres se encargan de encontrar soluciones a los problemas de abuso y violencia doméstica, y de cuidar a los niños, a las mujeres embarazadas y a las personas mayores. Utilizando información de los municipios de Buenos Aires, documenté la brecha de género en las oficinas legislativas y ejecutivas elegidas a nivel local, así como en las oficinas no elegidas dentro de los gabinetes municipales. También encontré que los tipos de trabajo político asignado a mujeres activistas y candidatas refuerzan los estereotipos existentes sobre las mujeres como madres de los pobres.
Published: 2018

2. Soft-collinear supersymmetry

Author: Larkoski, Andrew [Reed College, Portland, OR (United States); Harvard Univ., Cambridge, MA (United States)]
Published: 2017
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3. Influence of crustal dust and sea spray supermicron particle concentrations and acidity on inorganic NO3− aerosol during the 2013 Southern Oxidant and Aerosol Study

Author: Fry, J. [Reed College, Portland, OR (United States)]
Published: 2015
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4. Environmental variability in aquatic ecosystems: Avenues for future multifactorial experiments

Author: Gerhard, Miriam, Koussoroplis, Apostolos‐Manuel, Raatz, Michael, Pansch, Christian, Fey, Samuel B., Vajedsamiei, Jahangir, Calderó‐Pascual, Maria, Cunillera‐Montcusí, David, Juvigny‐Khenafou, Noël P. D., Polazzo, Francesco, Thomas, Patrick K., Symons, Celia C., Beklioğlu, Meryem, Berger, Stella A., Chefaoui, Rosa M., Ger, Kemal Ali, Langenheder, Silke, Nejstgaard, Jens C., Ptacnik, Robert, Striebel, Maren, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, University of Oldenburg, Laboratoire Microorganismes : Génome et Environnement (LMGE), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), Department for Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Environmental and Marine Biology, Åbo Akademi University, Turku, Department of Biology, Reed college, Portland, OR, USA, Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), CENTRE FOR FRESHWATER AND ENVIRONMENTAL STUDIES DUNDALK INSTITUTE OF TECHNOLOGY CO LOUTH IRELAND GBR, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), AquaScale Lab, WasserCluster Lunz - Biologische Station GmbH, Lunz am See, Freshwater Ecology, Hydrology and Management (FEHM), UNIVERSITY OF KOBLENZ LANDAU INSTITUTE FOR ENVIRONMENTAL SCIENCES LANDAU DEU, Department of Ecotoxicology, IMDEA Water Institute, Alcala de Henares, Ecology and Evolutionary Biology, University of California, Irvine, Department of Biological Sciences and Centre for Ecosystem Research and Implementation, Middle East Technical University, Ankara, Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Stechlin, ESCET, Universidad Rey Juan Carlos [Madrid] (URJC), Department of Ecology, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, and Uppsala University, Department of Ecology and Genetics/Limnology, Uppsala, Sweden
Subjects: Ekologi, Ecology, [SDE.MCG]Environmental Sciences/Global Changes, Q Science (General), [SDE.BE]Environmental Sciences/Biodiversity and Ecology, QS Ecology
Abstract: International audience; The relevance of considering environmental variability for understanding and predicting biological responses to environmental changes has resulted in a recent surge in variability-focused ecological research. However, integration of findings that emerge across studies and identification of remaining knowledge gaps in aquatic ecosystems remain critical. Here, we address these aspects by: (1) summarizing relevant terms of variability research including the components (characteristics) of variability and key interactions when considering multiple environmental factors; (2) identifying conceptual frameworks for understanding the consequences of environmental variability in single and multifactorial scenarios; (3) highlighting challenges for bridging theoretical and experimental studies involving transitioning from simple to more complex scenarios; (4) proposing improved approaches to overcome current mismatches between theoretical predictions and experimental observations; and (5) providing a guide for designing integrated experiments across multiple scales, degrees of control, and complexity in light of their specific strengths and limitations.
Published: 2023
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5. Herschel Spectroscopy of Early-type Galaxies

Author: Crocker, Alison [Physics Department, Reed College, Portland, OR 97202 (United States)]
Published: 2017
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6. Automatic Test-Case Reduction in Proof Assistants: A Case Study in Coq

Author: Gross, Jason, Zimmermann, Théo, Poddar-Agrawal, Miraya, Chlipala, Adam, Computer Science and Artificial Intelligence Laboratory [Cambridge] (CSAIL), Massachusetts Institute of Technology (MIT), Machine Intelligence Research Institute (MIRI), Design, study and implementation of languages for proofs and programs (PI.R2), Centre National de la Recherche Scientifique (CNRS)-Inria de Paris, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université Paris Cité (UPCité)-Institut de Recherche en Informatique Fondamentale (IRIF (UMR_8243)), Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Institut de Recherche en Informatique Fondamentale (IRIF (UMR_8243)), Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Reed College, This work was supported in part by a Google Research Award, National Science Foundation grants CCF-1253229, CCF-1512611, and CCF-1521584, and the National Science Foundation Graduate Research Fellowship under Grant Nos. 1122374 and 1745302, and Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
Subjects: Software Engineering (cs.SE), FOS: Computer and information sciences, Computer Science - Software Engineering, [INFO.INFO-PL]Computer Science [cs]/Programming Languages [cs.PL], Automatic test-case reduction, Software and its engineering → Formal software verification, Coq, Debugging, Software and its engineering → Software evolution, [INFO.INFO-SE]Computer Science [cs]/Software Engineering [cs.SE], Bug minimizer, Software and its engineering → Compilers, Software and its engineering → Maintaining software
Abstract: As the adoption of proof assistants increases, there is a need for efficiency in identifying, documenting, and fixing compatibility issues that arise from proof-assistant evolution. We present the Coq Bug Minimizer, a tool for reproducing buggy behavior with minimal and standalone files, integrated with coqbot to trigger automatically on failures from Coq’s reverse dependency compatibility testing. Our tool eliminates the overhead of having to download, set up, compile, and then explore and understand large developments, enabling Coq developers to easily obtain modular test-case files for fast experimentation. In this paper, we describe insights about how test-case reduction is different in Coq than in traditional compilers. We expect that our insights will generalize to other proof assistants. We evaluate the Coq Bug Minimizer on over 150 compatibility testing failures. Our tool succeeds in reducing failures to smaller test cases roughly 75% of the time. The minimizer produces a fully standalone test case 89% of the time, and it is on average about one-third the size of the original test. The average reduced test case compiles in 1.25 seconds, with 75% taking under half a second., LIPIcs, Vol. 237, 13th International Conference on Interactive Theorem Proving (ITP 2022), pages 18:1-18:18
Published: 2022
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7. New solid acids in the triple-layer Dion-Jacobson layered perovskite family

Author: Kurzman, Joshua [Reed College, Department of Chemistry, 3203 SE Woodstock Blvd., Portland, OR 97202 (United States)]
Published: 2011
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8. TRIGASIM: A computer program to simulate a TRIGA Mark I Reactor

Author: Ruby, Lawrence [Reed College, Portland, OR 97202 (United States)]
Published: 1992

9. A problem in the teaching of reactor kinetics

Author: Ruby, Lawrence [Reed College, Portland, OR 97202 (United States)]
Published: 1990

10. Initial results from the New Horizons exploration of 2014 MU 69 , a small Kuiper Belt object

Author: J. Fischetti, S. Bhaskaran, Matthias Hahn, Karl Whittenburg, Derek S. Nelson, G. A. Griffith, Amanda M. Zangari, B. J. Buratti, James T. Keane, E. J. Lessac-Chenen, Ralph L. McNutt, Tiffany J. Finley, J. Scherrer, M. A. Ritterbush, M. M. Saina, G. Dunn, T. A. Hill, J. Van Eck, T. Stryk, J. M. Albers, D. C. Reuter, C. M. Dalle Ore, H. A. Elliott, D. J. Schultz, J. Andrews, Douglas P. Hamilton, M. H. Versteeg, Orkan M. Umurhan, Matthew E. Hill, Hai Nguyen, M. Simon, L. Gabasova, D. E. Jennings, D. J. Katz, J. E. Riedel, N. Behrooz, M. N. Fosbury, Henry B. Throop, A. J. Verbiscer, E. Bernardoni, Ross A. Beyer, C. Engelbrecht, Francesca Scipioni, H. L. Winters, Thomas H. Zurbuchen, Carey M. Lisse, Veronica J. Bray, M. G. Ryschkewitsch, Stuart J. Robbins, S. E. Jaskulek, M. C. Kochte, Thomas Mehoke, M. S. Lahr, M. J. Salinas, V. A. Mallder, S. P. Williams, B. H. May, D. M. Mages, C. C. Deboy, Simon B. Porter, Gerhard Kruizinga, Marc W. Buie, Jorge I. Nunez, John Hayes, Peter Kollmann, P. Dharmavaram, J. M. Moore, Darrell F. Strobel, John Stansberry, R. P. Binzel, H. M. Hart, Jillian Redfern, E. W. Stahlheber, H. K. Kang, James L. Green, Anthony F. Egan, Carly Howett, Fran Bagenal, Dale Stanbridge, Chris B. Hersman, C. L. Chavez, Debi Rose, J. Y. Pelgrift, Maria E. Banks, D. C. Schurr, Matthew R. Buckley, L. S. Turner, Ivan Linscott, Kaj E. Williams, J. Eisig, Mihaly Horanyi, Matthew Jones, Mark R. Showalter, William B. McKinnon, Leslie A. Young, E. J. Colwell, Daniel T. Britt, Kirby Runyon, David J. McComas, G. Weigle, Bernard Schmitt, Susan D. Benecchi, Alissa M. Earle, M. J. Kinczyk, Tod R. Lauer, M. R. Piquette, Lori S. Glaze, Carver J. Bierson, L. M. Burke, Brian Carcich, O. S. Custodio, A. Harch, Harold A. Weaver, Dale P. Cruikshank, Oliver L. White, L. E. Brown, William M. Grundy, G. K. Oxton, Chelsea L. Ferrell, David E. Kaufmann, Mohamed Ramy El-Maarry, K. A. Harmon, W. R. Schlei, Eric Quirico, Derek C. Richardson, J. M. Freeze, Jennifer Hanley, R. G. Shelton, Andrew J. Steffl, Mike Bird, H. W. Taylor, Harold J. Reitsema, Stamatios M. Krimigis, D. R. Boone, E. D. Fattig, A. L. Regiec, D. J. Rodgers, Jason D. Hofgartner, D. Velez, Catherine B. Olkin, Kelsi N. Singer, Brian Bauer, Carl J. Ercol, Martin Pätzold, Nicole Martin, Stewart Bushman, J. Firer, Allen W. Lunsford, R. W. Webbert, A. L. Chaikin, Alex Parker, C. A. Conrad, M. P. Conner, S. B. Cooper, Chloe B. Beddingfield, William M. Folkner, J. E. Lee, M. B. Tapley, G. R. Gladstone, D. A. Aguilar, Glen H. Fountain, Emma Birath, Rebecca Sepan, Jeremy Bauman, J. Wm. Parker, S. Weidner, J. R. Jensen, Jason C. Cook, Alan D. Howard, William M. Owen, Andrew F. Cheng, B. L. Enke, Sarah A. Hamilton, Tom Andert, K. B. Beisser, K. E. Bechtold, J. R. Wendel, Rajani D. Dhingra, Paul M. Schenk, Michael E. Summers, J. R. Spencer, D. W. Hals, Silvia Protopapa, A. C. Ocampo, Mark E. Holdridge, S. A. Stern, A. Taylor, R. M. Tedford, G. P. Keleher, Gabe Rogers, Frederic Pelletier, Jj Kavelaars, Yanping Guo, Jon Pineau, Steven J. Conard, Alice Bowman, A. Hosadurga, B. G. Williams, Michael Vincent, David Y. Kusnierkiewicz, Paul E. Rosendall, G. B. Lawrence, J. R. Stuart, M. M. Stothoff, Jr. D. S. Mehoke, Southwest Research Institute [Boulder] (SwRI), Johns Hopkins University Applied Physics Laboratory [Laurel, MD] (APL), Lowell Observatory [Flagstaff], Space Physics Research Laboratory [Ann Arbor] (SPRL), University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, SwRI Planetary Science Directorate [Boulder], Universitat de Lleida, Institut für Raumfahrttechnik, Universität der Bundeswehr München [Neubiberg], Laboratory for Atmospheric and Space Physics [Boulder] (LASP), University of Colorado [Boulder], Department of Space Studies [Boulder], Rheinische Friedrich-Wilhelms-Universität Bonn, Jet Propulsion Laboratory (JPL), NASA-California Institute of Technology (CALTECH), Institut de Planétologie et d'Astrophysique de Grenoble (IPAG), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Grenoble (OSUG ), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Institute of Hydrology, NASA Goddard Space Flight Center (GSFC), Department of Physics, Chemistry and Biology [Linköping] (IFM), Linköping University (LIU), Africa Rice Center [Bénin] (AfricaRice), Africa Rice Center [Côte d'Ivoire] (AfricaRice), Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Yonsei University, Galaxies, Etoiles, Physique, Instrumentation (GEPI), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Centre International de Hautes Etudes Agronomiques Méditerranéennes - Institut Agronomique Méditerranéen de Montpellier (CIHEAM-IAMM), Centre International de Hautes Études Agronomiques Méditerranéennes (CIHEAM), Princeton University, Reed College, Hanoi National University of Education (HNUE), Rhenish Institute for Environmental Research (RIU), University of Cologne, School of Earth, Atmospheric and Environmental Sciences [Manchester] (SEAES), University of Manchester [Manchester], ESA, Southwest Research Institute [San Antonio] (SwRI), NASA Ames Research Center (ARC), Laboratoire pour l'utilisation du rayonnement électromagnétique (LURE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-MENRT-Centre National de la Recherche Scientifique (CNRS), Lunar and Planetary Laboratory [Tucson] (LPL), University of Arizona, Johns Hopkins University (JHU), Institute of Physics of the Czech Academy of Sciences (FZU / CAS), Czech Academy of Sciences [Prague] (CAS), Laboratoire de Chimie Analytique Bio-Inorganique et Environnement (LCABIE), Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS), Department of Biochemistry, Faculty of Biology, University of Warmia and Mazury [Olsztyn], California Institute of Technology (CALTECH)-NASA, Centre National d'Études Spatiales [Toulouse] (CNES)-Observatoire des Sciences de l'Univers de Grenoble (OSUG ), Institut national des sciences de l'Univers (INSU - CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), University of Warmia and Mazury, Institut de Mécanique Céleste et de Calcul des Ephémérides (IMCCE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), inconnu temporaire UPEMLV, Inconnu, INGENIERIE (INGENIERIE), Institut de recherches sur la catalyse et l'environnement de Lyon (IRCELYON), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Génie des Procédés Plasmas et Traitement de Surface (ENSCP), PARIS, Africa Rice Center, Africa Rice Center (AfricaRice), Institut de pharmacologie moléculaire et cellulaire (IPMC), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), PSL Research University (PSL)-PSL Research University (PSL)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), PSL Research University (PSL)-PSL Research University (PSL)-Centre National de la Recherche Scientifique (CNRS), Centre National d'Études Spatiales [Toulouse] (CNES)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Grenoble (OSUG), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Institute of Physics of Academy of Sciences of Czech Republic, and Czech Academy of Sciences [Prague] (ASCR)
Subjects: Earth and Planetary Astrophysics (astro-ph.EP), Solar System, Multidisciplinary, 010504 meteorology & atmospheric sciences, Spacecraft, business.industry, [SDU.ASTR.EP]Sciences of the Universe [physics]/Astrophysics [astro-ph]/Earth and Planetary Astrophysics [astro-ph.EP], FOS: Physical sciences, Astronomy, Coma (optics), Contact binary, Albedo, 01 natural sciences, Object (philosophy), Solar wind, 13. Climate action, 0103 physical sciences, Pebble, business, 010303 astronomy & astrophysics, Geology, ComputingMilieux_MISCELLANEOUS, Astrophysics - Earth and Planetary Astrophysics, 0105 earth and related environmental sciences
Abstract: The Kuiper Belt is a distant region of the Solar System. On 1 January 2019, the New Horizons spacecraft flew close to (486958) 2014 MU69, a Cold Classical Kuiper Belt Object, a class of objects that have never been heated by the Sun and are therefore well preserved since their formation. Here we describe initial results from these encounter observations. MU69 is a bi-lobed contact binary with a flattened shape, discrete geological units, and noticeable albedo heterogeneity. However, there is little surface color and compositional heterogeneity. No evidence for satellites, ring or dust structures, gas coma, or solar wind interactions was detected. By origin MU69 appears consistent with pebble cloud collapse followed by a low velocity merger of its two lobes., 43 pages, 8 figure
Published: 2019
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11. Renormalization of a model quantum field theory

Author: Griffiths, D [Physics Department, Reed College, Portland, Oregon 97202 (United States)]
Published: 1992
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12. Dipoles at rest

Author: Griffiths, D [Department of Physics, Reed College, Portland, Oregon 97202 (United States)]
Published: 1992
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13. Baboons, like humans, solve analogy by categorical abstraction of relations

Author: Roger K. R. Thompson, Timothy M. Flemming, Joël Fagot, Laboratoire de psychologie cognitive (LPC), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Reed College, Franklin and Marshall College, ANR-10-BLAN-1908,ANAFONEX,Le rôle des fonctions exécutives dans le développement de la compréhension des analogies : une approche multi-disciplinaire(2010), European Project: 262443,EUPRIM-Net Project, and Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Adult, Male, Analogical reasoning, Abstract thinking, Analogy, Concept Formation, media_common.quotation_subject, Experimental and Cognitive Psychology, 050105 experimental psychology, Thinking, Young Adult, 03 medical and health sciences, 0302 clinical medicine, Perception, Animals, Humans, Premack's principle, 0501 psychology and cognitive sciences, Categorical variable, Problem Solving, Ecology, Evolution, Behavior and Systematics, media_common, Cognitive science, 05 social sciences, Same/different, [SDV.NEU.SC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Cognitive Sciences, Cognition, Conceptual mapping, Representation, RMTS Monkey, Homo sapiens, Papio papio, [SCCO.PSYC]Cognitive science/Psychology, Female, Psychology, 030217 neurology & neurosurgery, Cognitive psychology
Abstract: International audience; Reasoning by analogy is one of the most complex and highly adaptive cognitive processes in abstract thinking. For humans, analogical reasoning entails the judgment and conceptual mapping of relations-between-relations and is facilitated by language (Gentner in Cogn Sci 7:155-170, 1983; Premack in Thought without language, Oxford University Press, New York, 1986). Recent evidence, however, shows that monkeys like ``language-trained'' apes exhibit similar capacity to match relations-between-relations (Fagot and Thompson in Psychol Sci 22:1304-1309, 2011; Flemming et al. in J Exp Psychol: Anim Behav Process 37:353-360, 2011; Truppa et al. in Plos One 6(8):e23809, 2011). Whether this behavior is driven by the abstraction of categorical relations or alternatively by direct perception of variability (entropy) is crucial to the debate as to whether nonhuman animals are capable of analogical reasoning. In the current study, we presented baboons (Papio papio) and humans (Homo sapiens) with a computerized same/different relational-matching task that in principle could be solved by either strategy. Both baboons and humans produced markedly similar patterns of responding. Both species responded different when the perceptual variability of a stimulus array fell exactly between or even closer to that of a same display. Overall, these results demonstrate that categorical abstraction trumped perceptual properties and, like humans, Old World monkeys can solve the analogical matching task by judging the categorical abstract equivalence of same/different relations-between-relations.
Published: 2013
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14. Open-Ended Evolution: Perspectives from the OEE Workshop in York

Author: Simon McGregor, Charles Ofria, Nathaniel Virgo, Alastair Channon, Wolfgang Banzhaf, Guillaume Beslon, Michael J. Wiser, Glen E. P. Ropella, Takashi Ikegami, Steen Rasmussen, Christopher Steven Timperley, Tim Taylor, Lee Spector, Adam Stanton, Anya E. Vostinar, Mark A. Bedau, Norman H. Packard, Barry McMullin, Tom Froese, Edward B. Clark, Eran Agmon, David H. Ackley, Kenneth O. Stanley, Emily Dolson, Simon Hickinbotham, University of York [York, UK], Department of Biology, Reed college, Portland, OR, USA, Keele University [Keele], The University of New Mexico [Albuquerque], Memorial University of Newfoundland [St. John's], Artificial Evolution and Computational Biology (BEAGLE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'InfoRmatique en Image et Systèmes d'information (LIRIS), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-École Centrale de Lyon (ECL), Université de Lyon-Université Lumière - Lyon 2 (UL2)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-École Centrale de Lyon (ECL), Université de Lyon-Université Lumière - Lyon 2 (UL2), Laboratoire d'InfoRmatique en Image et Systèmes d'information (LIRIS), Michigan State University [East Lansing], Michigan State University System, National Autonomous University of Mexico (UNAM), The University of Tokyo (UTokyo), Dublin City University [Dublin] (DCU), ProtoLife, Inc., University of Southern Denmark (SDU), Earth-Life Science Institute [Tokyo] (ELSI), Tokyo Institute of Technology [Tokyo] (TITECH), Indiana University [Bloomington], Indiana University System, University of Sussex, Tempus Dictum, Inc., School of Cognitive Science [Amherst], Hampshire College [Amherst], University of Central Florida [Orlando] (UCF), European Project: 610427,EC:FP7:ICT,FP7-ICT-2013-10,EVOEVO(2013), Memorial University of Newfoundland = Université Memorial de Terre-Neuve [St. John's, Canada] (MUN), Université Lumière - Lyon 2 (UL2)-École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Lumière - Lyon 2 (UL2)-École Centrale de Lyon (ECL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM), Beslon, Guillaume, and Evolution of Evolution - EVOEVO - - EC:FP7:ICT2013-11-01 - 2016-10-31 - 610427 - VALID
Subjects: 0301 basic medicine, Ongoing evolution, Operations research, Computer science, media_common.quotation_subject, Open-ended evolution, Adaptive evolution, 02 engineering and technology, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Presentation, Open research, Artificial Intelligence, 0202 electrical engineering, electronic engineering, information engineering, Mexico, Major transitions, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], media_common, adaptive evolution, major transitions, ongoing evolution, perpetual novelty, dynamical hierarchies, Biological evolution, Dynamical hierarchies, Congresses as Topic, Biological Evolution, 030104 developmental biology, Pluralism (political theory), Perpetual novelty, 020201 artificial intelligence & image processing, Engineering ethics, Synthetic Biology, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: International audience; We describe the content and outcomes of the First Workshop on Open-Ended Evolution: Recent Progress and Future Milestones (OEE1), held during the ECAL 2015 conference at the University of York, UK, in July 2015. We briefly summarize the content of the workshopʼs talks, and identify the main themes that emerged from the open discussions. Two important conclusions from the discussions are: (1) the idea of pluralism about OEE—it seems clear that there is more than one interesting and important kind of OEE; and (2) the importance of distinguishing observable behavioral hallmarks of systems undergoing OEE from hypothesized underlying mechanisms that explain why a system exhibits those hallmarks. We summarize the different hallmarks and mechanisms discussed during the workshop, and list the specific systems that were highlighted with respect to particular hallmarks and mechanisms. We conclude by identifying some of the most important open research questions about OEE that are apparent in light of the discussions. The York workshop provides a foundation for a follow-up OEE2 workshop taking place at the ALIFE XV conference in Cancún, Mexico, in July 2016. Additional materials from the York workshop, including talk abstracts, presentation slides, and videos of each talk, are available at http://alife.org/ws/oee1.
Published: 2016
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15. Repetición, originalidad, tradición. ¿Cuál es el tiempo de la literatura actual?

Author: Premat, Julio, Shtalbi, Haki, Laboratoire d'études romanes (LER), Université Paris 8 Vincennes-Saint-Denis (UP8), and Conférence plénière organisée par Reed College (Etats-Unis)
Subjects: [SHS.LITT] Humanities and Social Sciences/Literature, [SHS.LITT]Humanities and Social Sciences/Literature, [SHS] Humanities and Social Sciences, ComputingMilieux_MISCELLANEOUS, [SHS]Humanities and Social Sciences
Abstract: International audience
Published: 2016

16. The locus of sexual selection: moving sexual selection studies into the post-genomics era

Author: Seth M. Barribeau, Andrew D. Higginson, Felix Breden, Walter Salzburger, Suzy C. P. Renn, Gerald S. Wilkinson, Patrick C. Phillips, Locke Rowe, Elena Arriero, Michael G. Ritchie, Julie Jaquiéry, Jacek Radwan, Judith E. Mank, Department of Biology, Department of Biological Sciences [Burnaby], Simon Fraser University (SFU.ca), Dept of Genetics, Evolution and Environment [London] (UCL-GEE), University College of London [London] (UCL), Centre for Biological Diversity, University of St Andrews [Scotland], School of Biological Sciences, University of Bristol [Bristol], Department of Behavioural Ecology, Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University in Poznań (UAM), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Zoological Institute, University of Basel (Unibas), Departamento de Zoologia y Antropologia Fisica, Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Institute for Integrative Biology [Zürich] (IBZ), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), University of Oregon [Eugene], Department of Biology, Reed college, Portland, OR, USA, Department of Ecology and Evolutionary Biology [Princeton], Princeton University, DEB-0952260, National Science Foundation, Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)
Subjects: 0106 biological sciences, Candidate gene, cis-regulation, Genomics, Locus (genetics), Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Sexual Behavior, Animal, reverse genetics, Animals, Selection, Genetic, transcriptome, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, resequencing, 0303 health sciences, genomewide association studies, Novelty, candidate gene, Mating Preference, Animal, Forward genetics, forward genetics, Mate choice, Evolutionary biology, Sexual selection, Trait, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Sexual selection drives fundamental evolutionary processes such as trait elaboration and speciation. Despite this importance, there are surprisingly few examples of genes unequivocally responsible for variation in sexually selected phenotypes. This lack of information inhibits our ability to predict phenotypic change due to universal behaviours, such as fighting over mates and mate choice. Here, we discuss reasons for this apparent gap and provide recommendations for how it can be overcome by adopting contemporary genomic methods, exploiting underutilized taxa that may be ideal for detecting the effects of sexual selection and adopting appropriate experimental paradigms. Identifying genes that determine variation in sexually selected traits has the potential to improve theoretical models and reveal whether the genetic changes underlying phenotypic novelty utilize common or unique molecular mechanisms. Such a genomic approach to sexual selection will help answer questions in the evolution of sexually selected phenotypes that were first asked by Darwin and can furthermore serve as a model for the application of genomics in all areas of evolutionary biology.
Published: 2015
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17. Endogenous hepadnaviruses, bornaviruses and circoviruses in snakes

Author: Clément Gilbert, Daren C. Card, Daniel Dashevsky, Sarah Schaack, Jesse M. Meik, Todd A. Castoe, Ecologie, Evolution, Symbiose (EES), Ecologie et biologie des interactions (EBI), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS)-Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Department of Biological Sciences, Tarleton State University, Stephenville, TX, USA, Department of Biology, Reed college, Portland, OR, USA, Biology Department, University of Texas at Arlington, University of Texas at Arlington [Arlington], Biosciences eastern and central Africa [Nairobi] (BeCA), International Livestock Research Institute [CGIAR, Ethiopie] (ILRI), Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), and Centre for Bioinformatics, University of Nairobi, Kenya
Subjects: 0106 biological sciences, animal structures, King cobra, Crotalus mitchellii, Genes, Viral, viruses, Molecular Sequence Data, Zoology, Biology, Hepadnaviridae, 010603 evolutionary biology, 01 natural sciences, Genome, General Biochemistry, Genetics and Molecular Biology, Evolution, Molecular, 03 medical and health sciences, Phylogenetics, Animals, Amino Acid Sequence, Virus classification, Research Articles, Phylogeny, 030304 developmental biology, General Environmental Science, Circoviridae, 0303 health sciences, General Immunology and Microbiology, Crotalus, myr, General Medicine, biology.organism_classification, Biological Evolution, Evolutionary biology, Bornaviridae, Female, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, General Agricultural and Biological Sciences, Paleovirology
Abstract: We report the discovery of endogenous viral elements (EVEs) from Hepadnaviridae, Bornaviridae and Circoviridae in the speckled rattlesnake, Crotalus mitchellii , the first viperid snake for which a draft whole genome sequence assembly is available. Analysis of the draft assembly reveals genome fragments from the three virus families were inserted into the genome of this snake over the past 50 Myr. Cross-species PCR screening of orthologous loci and computational scanning of the python and king cobra genomes reveals that circoviruses integrated most recently (within the last approx. 10 Myr), whereas bornaviruses and hepadnaviruses integrated at least approximately 13 and approximately 50 Ma, respectively. This is, to our knowledge, the first report of circo-, borna- and hepadnaviruses in snakes and the first characterization of non-retroviral EVEs in non-avian reptiles. Our study provides a window into the historical dynamics of viruses in these host lineages and shows that their evolution involved multiple host-switches between mammals and reptiles.
Published: 2014
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18. The genomic substrate for adaptive radiation in African cichlid fish

Author: Alison P. Lee, Michaelle Rakotomanga, Jeremy A. Johnson, Hidenori Nishihara, Frederick J. Tan, Jessica Alföldi, Alvin Yu Jin Ng, Naoual Azzouzi, Byrappa Venkatesh, Steve Searle, Orly Eshel, Bronwen Aken, Ted Sharpe, Thomas D. Kocher, Gideon Hulata, Filipe J. Ribeiro, Eric S. Lander, Norihiro Okada, Wilfried Haerty, Thibaut Hourlier, Natalie S. Haddad, Marcia Lara, Rosa Alcazar, Karen L. Carleton, Catherine E. Wagner, Federica Di Palma, M. Emília Santos, Masato Nikaido, Eric A. Miska, Salome Mwaiko, Axel Meyer, Frédérique Barloy-Hubler, Leslie Gaffney, Sante Gnerre, David B. Jaffe, Jason Turner-Maier, David Brawand, Oleg Simakov, Lucie Greuter, Helena D'Cotta, Milan Malinsky, Iain MacCallum, Hyun Ji Noh, Shuangye Yin, Luis Sanchez-Pulido, Jean-François Baroiller, Shaohua Fan, David J. Penman, Ryan F. Bloomquist, Ross Swofford, Matthew A. Conte, Chris P. Ponting, Chris T. Amemiya, J. Todd Streelman, Richard Guyon, Hugo F. Gante, Dariusz Przybylski, Robert M Harris, Walter Salzburger, Irene Keller, Francis Galibert, Russell D. Fernald, Aaron M. Berlin, Yang I. Li, Pamela Russell, Hans A. Hofmann, Ole Seehausen, Suzy C. P. Renn, Louise Williams, Micha Ron, Kerstin Lindblad-Toh, Zhi Wei Lim, Catherine Ozouf-Costaz, Etienne Bezault, Sarah Young, University of Oxford [Oxford], Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Centre of Ecology, Evolution and Biogeochemistry, Department of Fish Ecology and Evolution, Swiss Federal Institute for Environmental Science and Technology, Sanger Institute, Welcome Trust, Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge [UK] (CAM), Institute of Zoology, University of Bern, Université de Bern, Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, EMBL Heidelberg, Institute of Molecular and Cell Biology, Singapour, Department of Biology, Reed college, Portland, OR, USA, Stanford University, California Institute of Technology (CALTECH), Benaroya Research Institute, Virginia Mason, Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Intensification raisonnée et écologique pour une pisciculture durable (UMR INTREPID), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Georgia Institute of Technology [Atlanta], University of Maryland [College Park], University of Maryland System, The Volcani Center, University of Basel (Unibas), University of Texas at Austin [Austin], Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Tokyo Institute of Technology [Tokyo] (TITECH), Muséum national d'Histoire naturelle (MNHN), University of Stirling, Carnegie Institution for Science [Washington], Science for Life Laboratory, Uppsala University-Department of Medical Biochemistry and Microbiology, National Cheng Kung University (NCKU), The Genome Analysis Centre (TGAC), Sequencing, assembly, annotation and analysis by Broad Institute were supported by grants from the National Human Genome Research Institute (NHGRI). Genome evolution, duplication and TE analysis, ILS and ancient variant analyses were also supported by Swiss National Science Foundation grant PBLAP3-142774 awarded to D.B. and by University of Oxford Nuffield Department of Medicine Prize Studentship to Y.I.L. TE and copy number variation analyses were supported by the German Science Foundation (DFG), and advanced grant 29700 ('GenAdap') by the European Research Council (ERC). CNE analysis and zebrafish functional assays were supported by the Biomedical Research Council of A*STAR, Singapore. MicroRNA sequencing and annotation was supported by ERC Starting Grant to E.A.M., M.M. was supported by a fellowship from the Wellcome Trust. MicroRNA and target in situ hybridization was supported by grant 2R01DE019637-04 to J.T.S. Population genomics analyses were supported by Swiss National Science Foundation grants 31003A-118293 and 31003A-144046 to O.S., Massachusetts Institute of Technology. Department of Biology, Lander, Eric S., University of Oxford, Universität Bern [Bern] (UNIBE), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Carnegie Institution for Science, and Jonchère, Laurent
Subjects: Phylogénie, Astatotilapia burtoni, Polymorphisme génétique, Lineage (evolution), Évolution, Evolutionary biology, [SDV.GEN] Life Sciences [q-bio]/Genetics, Eastern, Nile tilapia, Adaptive radiation, Gene Duplication, Phylogeny, Multidisciplinary, Genome, Oreochromis niloticus, Tilapia, Cichlids, Genomics, Cichlidae, Africa, Eastern, Oreochromis, Genome evolution, Evolution, Comparative genomics, Evolutionary biology, Neolamprologus, Séquence nucléotidique, food.ingredient, Evolution, Genetic Speciation, General Science & Technology, 1.1 Normal biological development and functioning, Cours d'eau, Zoology, Biology, Evolution, Molecular, food, Genetic, Cichlid, Underpinning research, ddc:570, Genetics, Animals, 14. Life underwater, Adaptation, Polymorphism, Génie génétique, Lac, [SDV.GEN]Life Sciences [q-bio]/Genetics, Génome, Polymorphism, Genetic, Comparative genomics, Human Genome, L60 - Taxonomie et géographie animales, Molecular, L10 - Génétique et amélioration des animaux, biology.organism_classification, Genome evolution, M01 - Pêche et aquaculture - Considérations générales, MicroRNAs, Lakes, Gene Expression Regulation, Africa, DNA Transposable Elements, 570 Life sciences, biology, human activities
Abstract: CC-BY-NC-SA; International audience; Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.
Published: 2014
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19. Genomic signatures of relaxed disruptive selection associated with speciation reversal in whitefish

Author: Ole Seehausen, Alan G. Hudson, Etienne Bezault, Pascal Vonlanthen, Univ Bern, Div Aquat Ecol & Macroevolut, Inst Ecol & Evolut, CH-3012 Bern, Switzerland, EAWAG Ctr Ecol Evolut & Biogeochem, Dept Fish Ecol & Evolut, CH-6047 Kastanienbaum, Switzerland, Reed College, Dept Biol, Portland, OR 97202 USA, Institute of Zoology, University of Bern, and Université de Bern
Subjects: Sympatry, Evolutionsbiologi, Ecological speciation, Adaptive radiation, Human Activities, ComputingMilieux_MISCELLANEOUS, Genome, Natural selection, biology, Ecology, Genomics, Eutrophication, Miljövetenskap, Relaxed selection, Phenotype, Sympatric speciation, Speciation reversal, Salmonidae, Research Article, Gene Flow, Species complex, Reproductive Isolation, Genetic Speciation, [SDE.MCG]Environmental Sciences/Global Changes, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Zoologi, Animals, Humans, Selection, Genetic, Coregonus, Divergence hitchhiking, Ecosystem, Ecology, Evolution, Behavior and Systematics, Evolutionary Biology, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Disruptive selection, Speciation-with-gene-flow, Water Pollution, Heterogeneous genomic divergence, biology.organism_classification, Lakes, Evolutionary biology, 570 Life sciences, Hybridization, Genetic, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Population genomics, Zoology, Environmental Sciences
Abstract: Background: Speciation reversal: the erosion of species differentiation via an increase in introgressive hybridization due to the weakening of previously divergent selection regimes, is thought to be an important, yet poorly understood, driver of biodiversity loss. Our study system, the Alpine whitefish (Coregonus spp.) species complex is a classic example of a recent postglacial adaptive radiation: forming an array of endemic lake flocks, with the independent origination of similar ecotypes among flocks. However, many of the lakes of the Alpine radiation have been seriously impacted by anthropogenic nutrient enrichment, resulting in a collapse in neutral genetic and phenotypic differentiation within the most polluted lakes. Here we investigate the effects of eutrophication on the selective forces that have shaped this radiation, using population genomics. We studied eight sympatric species assemblages belonging to five independent parallel adaptive radiations, and one species pair in secondary contact. We used AFLP markers, and applied F-ST outlier (BAYESCAN, DFDIST) and logistic regression analyses (MATSAM), to identify candidate regions for disruptive selection in the genome and their associations with adaptive traits within each lake flock. The number of outlier and adaptive trait associated loci identified per lake were then regressed against two variables (historical phosphorus concentration and contemporary oxygen concentration) representing the strength of eutrophication. Results: Whilst we identify disruptive selection candidate regions in all lake flocks, we find similar trends, across analysis methods, towards fewer disruptive selection candidate regions and fewer adaptive trait/candidate loci associations in the more polluted lakes. Conclusions: Weakened disruptive selection and a concomitant breakdown in reproductive isolating mechanisms in more polluted lakes has lead to increased gene flow between coexisting Alpine whitefish species. We hypothesize that the resulting higher rates of interspecific recombination reduce either the number or extent of genomic islands of divergence surrounding loci evolving under disruptive natural selection. This produces the negative trend seen in the number of selection candidate loci recovered during genome scans of whitefish species flocks, with increasing levels of anthropogenic eutrophication: as the likelihood decreases that AFLP restriction sites will fall within regions of heightened genomic divergence and therefore be classified as F-ST outlier loci. This study explores for the first time the potential effects of human-mediated relaxation of disruptive selection on heterogeneous genomic divergence between coexisting species.
Published: 2013
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20. Operations of a TRIGA reactor at a small private liberal arts college

Author: Church, L [Reed College, Portland, OR (United States)]
Published: 1978

21. The cause and effect of power fluctuations near 250 kW

Author: Church, L [Reed College, Portland, OR 97202 (United States)]
Published: 1980

22. Computer-assisted documentation: One device to keep your nose above the water

Author: Church, L [Reed College, Portland, OR 97202 (United States)]
Published: 1980

23. Operating experience at the Reed College TRIGA Mark I facility

Author: Keedy, C [Reed College, Portland, OR (United States)]
Published: 1972

24. Microsatellites cross-species amplification across some african cichlids

Author: Etienne Bezault, Jean-François Baroiller, Bernard Chevassus, Xavier Rognon, Karim Gharbi, Intensification raisonnée et écologique pour une pisciculture durable (UMR INTREPID), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Department of Biology, Reed College, Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, This study was supported by grants from the CIRAD and INRA (France)., Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)
Subjects: 0106 biological sciences, food.ingredient, Article Subject, Polymorphisme génétique, [SDV]Life Sciences [q-bio], satellite, Zoology, Locus (genetics), Aquaculture, amplification, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Nile tilapia, food, Sensu, Cichlid, Sarotherodon, cichlid, Marqueur génétique, 14. Life underwater, Tilapia (genre), 030304 developmental biology, Génie génétique, 0303 health sciences, biology, Ecology, Oreochromis niloticus, Microsatellite, Tilapia, Cichlidae, L10 - Génétique et amélioration des animaux, biology.organism_classification, Oreochromis, M12 - Production de l'aquaculture, human activities, Research Article
Abstract: The transfer of the genomic resources developed in the Nile tilapia,Oreochromis niloticus, to other Tilapiinessensu latoand African cichlid would provide new possibilities to study this amazing group from genetics, ecology, evolution, aquaculture, and conservation point of view. We tested the cross-species amplification of 32O. niloticusmicrosatellite markers in a panel of 15 species from 5 different African cichlid tribes: Oreochromines (Oreochromis, Sarotherodon), Boreotilapiines (Tilapia), Chromidotilapines, Hemichromines, and Haplochromines. Amplification was successfully observed for 29 markers (91%), with a frequency of polymorphic (P95) loci per species around 70%. The mean number of alleles per locus and species was 3.2 but varied from 3.7 withinOreochromisspecies to 1.6 within the nontilapia species. The high level of cross-species amplification and polymorphism of the microsatellite markers tested in this study provides powerful tools for a wide range of molecular genetic studies within tilapia species as well as for other African cichlids.
Published: 2012
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25. Analysis of the meiotic segregation in intergeneric hybrids of tilapias

Author: Etienne Bezault, Frédéric Clota, Bernard Chevassus, Jean-François Baroiller, Xavier Rognon, Karim Gharbi, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Department of Biology, Reed College, Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, and AgroParisTech-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, Article Subject, tilapia, [SDV]Life Sciences [q-bio], Hybridation intergénérique, Évolution, Genomics, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, symbols.namesake, Meiosis, Cichlid, 030304 developmental biology, Hybrid, Génie génétique, Genetics, 0303 health sciences, Génome, biology, hybrid, Oreochromis niloticus, Microsatellite, Cichlidae, L10 - Génétique et amélioration des animaux, biology.organism_classification, meiotic segregation, Oreochromis, Ségrégation, Backcrossing, Mendelian inheritance, symbols, Sarotherodon melanotheron, M12 - Production de l'aquaculture, Méiose, Research Article
Abstract: Tilapia species exhibit a large ecological diversity and an important propensity to interspecific hybridisation. This has been shown in the wild and used in aquaculture. However, despite its important evolutionary implications, few studies have focused on the analysis of hybrid genomes and their meiotic segregation. Intergeneric hybrids betweenOreochromis niloticusandSarotherodon melanotheron, two species highly differentiated genetically, ecologically, and behaviourally, were produced experimentally. The meiotic segregation of these hybrids was analysed in reciprocal second generation hybrid (F2) and backcross families and compared to the meiosis of both parental species, using a panel of 30 microsatellite markers. Hybrid meioses showed segregation in accordance to Mendelian expectations, independent from sex and the direction of crosses. In addition, we observed a conservation of linkage associations between markers, which suggests a relatively similar genome structure between the two parental species and the apparent lack of postzygotic incompatibility, despite their important divergence. These results provide genomics insights into the relative ease of hybridisation within cichlid species when prezygotic barriers are disrupted. Overall our results support the hypothesis that hybridisation may have played an important role in the evolution and diversification of cichlids.
Published: 2012
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26. MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape

Author: Joel Franklin, Marc Delarue, Patrice Koehl, Sebastian Doniach, Reed College, University of California [Davis] (UC Davis), University of California, Stanford University, Dynamique Structurale des Macromolécules (DSM), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Funding to pay the Open Access publication charges for this article was provided by Institut Pasteur., University of California (UC), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Models, Molecular, Protein Conformation, Crossover, MESH: Amino Acid Sequence, Energy minimization, 01 natural sciences, law.invention, MESH: Protein Structure, Tertiary, MESH: Protein Conformation, Theoretical, law, Models, Cartesian coordinate system, MESH: Proteins, Statistical physics, MESH: Models, Theoretical, 0303 health sciences, 010304 chemical physics, MESH: Models, Chemical, Articles, Biological Sciences, Langevin equation, Harmonics, symbols, Thermodynamics, MESH: Thermodynamics, MESH: Models, Molecular, Algorithms, MESH: Computational Biology, Protein Structure, Lorentz transformation, Molecular Sequence Data, MESH: Algorithms, Chemical, Biology, Models, Biological, 03 medical and health sciences, symbols.namesake, MESH: Software, Linear differential equation, MESH: Computer Simulation, Information and Computing Sciences, 0103 physical sciences, Genetics, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Computer Simulation, Amino Acid Sequence, MESH: Energy Transfer, 030304 developmental biology, MESH: Molecular Sequence Data, MESH: Models, Biological, Proteins, Computational Biology, Molecular, Models, Theoretical, Biological, Protein Structure, Tertiary, Morphing, Models, Chemical, Energy Transfer, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Tertiary, Software, Environmental Sciences, Developmental Biology
Abstract: International audience; The non-linear problem of simulating the structural transition between two known forms of a macromolecule still remains a challenge in structural biology. The problem is usually addressed in an approximate way using 'morphing' techniques, which are linear interpolations of either the Cartesian or the internal coordinates between the initial and end states, followed by energy minimization. Here we describe a web tool that implements a new method to calculate the most probable trajectory that is exact for harmonic potentials; as an illustration of the method, the classical Calpha-based Elastic Network Model (ENM) is used both for the initial and the final states but other variants of the ENM are also possible. The Langevin equation under this potential is solved analytically using the Onsager and Machlup action minimization formalism on each side of the transition, thus replacing the original non-linear problem by a pair of linear differential equations joined by a non-linear boundary matching condition. The crossover between the two multidimensional energy curves around each state is found numerically using an iterative approach, producing the most probable trajectory and fully characterizing the transition state and its energy. Jobs calculating such trajectories can be submitted on-line at: http://lorentz.dynstr.pasteur.fr/joel/index.php.
Published: 2007
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27. Load data analysis workstation

Author: Smith, B [Reed College, Portland, OR (US)]
Published: 1988
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28. Behavioral determinants of energy use in small commercial buildings; Implications for energy efficiency

Author: Katzev, R [Dept. of Psychology, Reed College, Portland,OR (US)]
Published: 1988

29. Neural signatures of visual awareness independent of postperceptual processing.

Author: Cohen MA, Dembski C, Ortego K, Steinhibler C, and Pitts M
Subjects: Humans, Male, Female, Young Adult, Adult, Evoked Potentials physiology, Photic Stimulation methods, Perceptual Masking physiology, Brain physiology, Adolescent, Electroencephalography, Awareness physiology, Visual Perception physiology
Abstract: What are the neural processes associated with perceptual awareness that are distinct from preconscious sensory encoding and postperceptual processes such as reporting an experience? Using electroencephalography and a no-report visual masking paradigm, we manipulated stimulus visibility by varying the time between stimuli and masks in linear steps (17, 33, 50, 67, and 83 ms). Awareness increased nonlinearly, with stimuli never seen at the two shortest intervals, always seen at the two longest, and 50% seen at the intermediate interval. Separate report and no-report conditions were used to isolate awareness from task performance. Our results revealed a neural signal closely linked to perceptual awareness, independent of the task: a fronto-central event-related potential that we refer to as the N2 (~250 to 300 ms). Earlier event-related potential signals reflected the linear manipulation of stimulus strength, while later signals like P3b and temporal generalization of decoding were tied to task performance, appearing only in the report condition. Taken together, these findings inform current debates regarding theories of consciousness and offer new avenues for exploring the neural mechanisms supporting conscious processing., (© The Author(s) 2024. Published by Oxford University Press.)
Published: 2024
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30. Transitive inference in a clinical childhood sample with a focus on autism spectrum disorder.

Author: Kao T, Michaelcheck C, Ferrera VP, Terrace HS, and Jensen G
Subjects: Humans, Child, Male, Female, Attention Deficit Disorder with Hyperactivity, Anxiety Disorders, Reaction Time physiology, Specific Learning Disorder physiopathology, Communication Disorders, Learning physiology, Autism Spectrum Disorder physiopathology
Abstract: Transitive inference (TI) has a long history in the study of human development. There have, however, few pediatric studies that report clinical diagnoses have tested trial-and-error TI learning, in which participants infer item relations, rather than evaluate them explicitly from verbal descriptions. Children aged 8-10 underwent a battery of clinical assessments and received a range of diagnoses, potentially including autism spectrum disorder (ASD), attention-deficit hyperactive disorder (ADHD), anxiety disorders (AD), specific learning disorders (SLD), and/or communication disorders (CD). Participants also performed a trial-and-error learning task that tested for TI. Response accuracy and reaction time were assessed using a statistical model that controlled for diagnostic comorbidity at the group level. Participants in all diagnostic categories showed evidence of TI. However, a model comparison analysis suggested that those diagnosed with ASD succeeded in a qualitatively different way, responding more slowly to each choice and improving faster across trials than their non-ASD counterparts. Additionally, TI performance was not associated with IQ. Overall, our data suggest that superficially similar performance levels between ASD and non-ASD participants may have resulted from a difference in the speed-accuracy tradeoff made by each group. Our work provides a preliminary profile of the impact of various clinical diagnoses on TI performance in young children. Of these, an ASD diagnosis resulted in the largest difference in task strategy., (© 2024 International Society for Autism Research and Wiley Periodicals LLC.)
Published: 2024
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31. Effects of posttransfer feedback informativeness in a transitive inference task.

Author: Joy Y, Kao T, and Jensen G
Abstract: Transitive inference (TI), referring to one's ability to learn that if A > B and B > C, one can infer that A > C, is a form of serial learning that has been tested using a variety of experimental protocols. An element of most of these protocols is the presentation of some form of visual corrective feedback to help inform naïve participants about the nature of the task. Therefore, corrective feedback is often used as a critical tool for experimental TI. To further explore this tool, we presented varying forms/presence of visual feedback during TI performance: corrective, none, and ambiguous. Of the three conditions, presentation of the ambiguous feedback yielded the clearest disruption of TI performance, obvious in measurements of both response accuracy and reaction times. Participants appears to remain engaged with feedback was withheld entirely, but to disengage when presented with ambiguous feedback. Therefore, the choice regarding the form of feedback provided during testing may be critical for information processing of inferences., (© 2024. The Psychonomic Society, Inc.)
Published: 2024
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32. No electrophysiological evidence for semantic processing during inattentional blindness.

Author: Hutchinson BT, Jack BN, Pammer K, Canseco-Gonzalez E, and Pitts M
Subjects: Humans, Male, Female, Young Adult, Adult, Brain physiology, Attention physiology, Semantics, Electroencephalography methods, Evoked Potentials physiology
Abstract: A long-standing question concerns whether sensory input can reach semantic stages of processing in the absence of attention and awareness. Here, we examine whether the N400, an event related potential associated with semantic processing, can occur under conditions of inattentional blindness. By employing a novel three-phase inattentional blindness paradigm designed to maximise the opportunity for detecting an N400, we found no evidence for it when participants were inattentionally blind to the eliciting stimuli (related and unrelated word pairs). In contrast, participants noticed the same task-irrelevant word pairs when minimal attention was allocated to them, and a small N400 became evident. When the same stimuli were fully attended and relevant to the task, a robust N400 was observed. In addition to univariate ERP measures, multivariate decoding analyses were unable to classify related from unrelated word pairs when observers were inattentionally blind to the words, with decoding reaching above-chance levels only when the words were (at least minimally) attended. By comparison, decoding reached above-chance levels when contrasting word pairs with non-word stimuli, even when participants were inattentionally blind to these stimuli. Our results also replicated several previous studies by finding a "visual awareness negativity" (VAN) that distinguished task-irrelevant stimuli that participants noticed compared with those that were not perceived, and a P3b (or "late positivity") that was evident only when the stimuli were task relevant. Together, our findings suggest that semantic processing might require at least a minimal amount of attention., Competing Interests: Declaration of competing interest None, (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)
Published: 2024
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33. Emotion regulation elicits cross-linguistically shared and language-specific forms of linguistic distancing.

Author: Holmes KJ, Kassin L, Buchillon-Almeida D, and Canseco-Gonzalez E
Subjects: Humans, Female, Male, Adult, Emotions physiology, Young Adult, Adolescent, Multilingualism, Language, Emotional Regulation physiology, Linguistics methods
Abstract: Cognitively reappraising a stressful experience-reinterpreting the situation to blunt its emotional impact-is effective for regulating negative emotions. English speakers have been shown to engage in linguistic distancing when reappraising, spontaneously using words that are more abstract or impersonal. Across two preregistered studies (N = 299), we investigated whether such shifts in language use generalize to Spanish, a language proposed to offer unique tools for expressing psychological distance. Bilingual speakers of Spanish and English and a comparison group of English monolinguals transcribed their thoughts in each of their languages while responding naturally to negative images or reappraising them. Reappraisal shifted markers of psychological distance common to both languages (e.g., reduced use of "I"/"yo"), as well as Spanish-specific markers (e.g., greater use of "estar": "to be" for temporary states). Whether these linguistic shifts reflected successful emotion regulation depended on language experience: in exploratory analyses, the common markers were more strongly linked to reduced negative affect for late than early Spanish learners, and one Spanish-specific marker ("estar") also predicted reduced negative affect for early learners. Our findings suggest that people distance their language in both cross-linguistically shared and language-specific ways when regulating their emotions., (© 2024. The Author(s).)
Published: 2024
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34. Current and future directions in network biology.

Author: Zitnik M, Li MM, Wells A, Glass K, Morselli Gysi D, Krishnan A, Murali TM, Radivojac P, Roy S, Baudot A, Bozdag S, Chen DZ, Cowen L, Devkota K, Gitter A, Gosline SJC, Gu P, Guzzi PH, Huang H, Jiang M, Kesimoglu ZN, Koyuturk M, Ma J, Pico AR, Pržulj N, Przytycka TM, Raphael BJ, Ritz A, Sharan R, Shen Y, Singh M, Slonim DK, Tong H, Yang XH, Yoon BJ, Yu H, and Milenković T
Abstract: Summary: Network biology is an interdisciplinary field bridging computational and biological sciences that has proved pivotal in advancing the understanding of cellular functions and diseases across biological systems and scales. Although the field has been around for two decades, it remains nascent. It has witnessed rapid evolution, accompanied by emerging challenges. These stem from various factors, notably the growing complexity and volume of data together with the increased diversity of data types describing different tiers of biological organization. We discuss prevailing research directions in network biology, focusing on molecular/cellular networks but also on other biological network types such as biomedical knowledge graphs, patient similarity networks, brain networks, and social/contact networks relevant to disease spread. In more detail, we highlight areas of inference and comparison of biological networks, multimodal data integration and heterogeneous networks, higher-order network analysis, machine learning on networks, and network-based personalized medicine. Following the overview of recent breakthroughs across these five areas, we offer a perspective on future directions of network biology. Additionally, we discuss scientific communities, educational initiatives, and the importance of fostering diversity within the field. This article establishes a roadmap for an immediate and long-term vision for network biology., Availability and Implementation: Not applicable., Competing Interests: In Section 8, we rely on ISCB’s diversity statistics. These statistics are publicly available, and so there is no conflict of interest. Yet, to remedy any potential perceived conflict of interest, we declare that Predrag Radivojac is the President of ISCB and currently serves on the Board of Directors of ISCB. In addition, Tijana Milenković currently serves on the ISCB Board of Directors and the ISCB EDI Committee. The remaining authors have no conflicts of interest to declare., (© The Author(s) 2024. Published by Oxford University Press.)
Published: 2024
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35. Life Course Models of Child Maltreatment: Effects on General Psychopathology Outcomes in a Longitudinal Sample.

Author: Wong DR and Anderson KG
Abstract: The study compared life course models (LCM; accumulation, recency, and sensitive period) of child maltreatment and general psychopathology in a large, national longitudinal data set of 1354 youth ages birth-16 years (657 boys, 53.2% Black, 59.7% <$40K caregiver income). Previous research has supported the accumulation and recency models, albeit with shorter or fewer time periods of outcome measurement. We extend this work by modeling the impact of combined abuse and neglect allegations on a general psychopathology factor (dysregulation profile). Cross-sectional structural equation models were constructed using LCMs and tested across two-year periods from 4-16 years old and compared using Akaike Information Criterion weights. The recency variable generally explained the greatest proportion of variance in psychopathology. Notably, maltreatment more proximal to the time of outcome measurement had the strongest effect, suggesting that more recent maltreatment may have stronger effects on general psychopathology. These results lend support to a recency effect of maltreatment on psychopathology outcomes, although substantive overlaps with the accumulation model are noted., Competing Interests: Declaration of Conflicting InterestsThe author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.
Published: 2024
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36. ASCB statement of commitment to diversity, equity, and inclusion.

Author: Murray SA, Holzbaur ELF, Munson M, Cimini D, Lane TF, Alvania R, Applewhite DA, Chang F, Chen EH, Earnshaw WC, Evans CS, Li R, Mierzwa BE, Oliver T, Segarra VA, Skop AR, Weaver LN, Asai DJ, Boyce M, Zavala ME, Hammonds-Odie L, and Vigoreaux J
Subjects: Humans, Societies, Scientific, Cultural Diversity
Abstract: Competing Interests: Conflict of interest: The authors declare no financial conflict of interest.
Published: 2024
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37. Kuhnian Lessons for the Study of Open-Ended Evolution.

Author: Bedau MA
Subjects: Philosophy, Biological Evolution
Abstract: Kuhnian philosophy of science implies that progress in the study of open-ended evolution (OEE) would be accelerated if the OEE science community were to agree on some examples of striking success in OEE science. This article recounts the important role of scientific paradigms and scientific exemplars in creating the productivity of what Kuhn, in The Structure of Scientific Revolutions, calls "normal" science, and it describes how the study of OEE today would benefit from exhibiting more of the hallmarks of normal science. The article concludes by describing five proposed projects that would help create a consensus in the OEE community on some good examples of the scientific study of OEE., (© 2023 Massachusetts Institute of Technology.)
Published: 2024
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38. Measurement of Atmospheric Mercury: Current Limitations and Suggestions for Paths Forward.

Author: Gustin MS, Dunham-Cheatham SM, Lyman S, Horvat M, Gay DA, Gačnik J, Gratz L, Kempkes G, Khalizov A, Lin CJ, Lindberg SE, Lown L, Martin L, Mason RP, MacSween K, Vijayakumaran Nair S, Nguyen LSP, O'Neil T, Sommar J, Weiss-Penzias P, Zhang L, and Živković I
Subjects: Mercury analysis, Atmosphere chemistry, Environmental Monitoring methods, Air Pollutants analysis
Abstract: Mercury (Hg) researchers have made progress in understanding atmospheric Hg, especially with respect to oxidized Hg (Hg II ) that can represent 2 to 20% of Hg in the atmosphere. Knowledge developed over the past ∼10 years has pointed to existing challenges with current methods for measuring atmospheric Hg concentrations and the chemical composition of Hg II compounds. Because of these challenges, atmospheric Hg experts met to discuss limitations of current methods and paths to overcome them considering ongoing research. Major conclusions included that current methods to measure gaseous oxidized and particulate-bound Hg have limitations, and new methods need to be developed to make these measurements more accurate. Developing analytical methods for measurement of Hg II chemistry is challenging. While the ultimate goal is the development of ultrasensitive methods for online detection of Hg II directly from ambient air, in the meantime, new surfaces are needed on which Hg II can be quantitatively collected and from which it can be reversibly desorbed to determine Hg II chemistry. Discussion and identification of current limitations, described here, provide a basis for paths forward. Since the atmosphere is the means by which Hg is globally distributed, accurately calibrated measurements are critical to understanding the Hg biogeochemical cycle.
Published: 2024
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39. Structural basis for transcription activation through cooperative recruitment of MntR.

Author: Shi H, Fu Y, Kodyte V, Andreas A, Sachla AJ, Miller K, Shrestha R, Helmann JD, Glasfeld A, and Ahuja S
Abstract: The manganese transport regulator (MntR) from B. subtilis is a dual regulatory protein that responds to heightened Mn 2+ availability in the cell by both repressing the expression of uptake transporters and activating the expression of efflux proteins. Recent work indicates that, in its role as an activator, MntR binds several sites upstream of the genes encoding Mn 2+ exporters, leading to a cooperative response to manganese. Here, we use cryo-EM to explore the molecular basis of gene activation by MntR and report a structure of four MntR dimers bound to four 18-base pair sites across an 84-base pair regulatory region of the mneP promoter. Our structures, along with solution studies including mass photometry and in vivo transcription assays, reveal that MntR dimers employ polar and non-polar contacts to bind cooperatively to an array of low-affinity DNA-binding sites. These results reveal the molecular basis for cooperativity in the activation of manganese efflux., Competing Interests: Conflict of Interest The authors declare no relevant financial or non-financial competing interests.
Published: 2024
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40. A mathematical theory of relational generalization in transitive inference.

Author: Lippl S, Kay K, Jensen G, Ferrera VP, and Abbott LF
Subjects: Humans, Learning physiology, Cognition physiology, Models, Theoretical, Brain physiology, Generalization, Psychological physiology
Abstract: Humans and animals routinely infer relations between different items or events and generalize these relations to novel combinations of items. This allows them to respond appropriately to radically novel circumstances and is fundamental to advanced cognition. However, how learning systems (including the brain) can implement the necessary inductive biases has been unclear. We investigated transitive inference (TI), a classic relational task paradigm in which subjects must learn a relation ([Formula: see text] and [Formula: see text]) and generalize it to new combinations of items ([Formula: see text]). Through mathematical analysis, we found that a broad range of biologically relevant learning models (e.g. gradient flow or ridge regression) perform TI successfully and recapitulate signature behavioral patterns long observed in living subjects. First, we found that models with item-wise additive representations automatically encode transitive relations. Second, for more general representations, a single scalar "conjunctivity factor" determines model behavior on TI and, further, the principle of norm minimization (a standard statistical inductive bias) enables models with fixed, partly conjunctive representations to generalize transitively. Finally, neural networks in the "rich regime," which enables representation learning and improves generalization on many tasks, unexpectedly show poor generalization and anomalous behavior on TI. We find that such networks implement a form of norm minimization (over hidden weights) that yields a local encoding mechanism lacking transitivity. Our findings show how minimal statistical learning principles give rise to a classical relational inductive bias (transitivity), explain empirically observed behaviors, and establish a formal approach to understanding the neural basis of relational abstraction., Competing Interests: Competing interests statement:The authors declare no competing interest.
Published: 2024
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41. Chromic and dynamic: soft crystals of platinum(II) complexes pave the way for multi-responsive materials.

Author: Campillo-Alvarado G
Abstract: The development of smart, stimuli-responsive materials has received increased attention in the past decade for their applications as sensing technologies. This commentary discusses a timely topical review by Kato [(2024). IUCrJ, 11, 442-452] on the fabrication of multi-stimuli responsive crystals comprised of luminescent platinum(II) complexes, which exhibit intriguing chromic phenomena in response to stimuli., (open access.)
Published: 2024
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42. Adding Tools to the Behavioral Toolkit.

Author: Hackenberg TD
Published: 2024
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43. Confinement and Separation of Benzene from an Azeotropic Mixture Using a Chlorinated B←N Adduct.

Author: Jupiter IJ, Loya JD, Lutz N, Sittinger PM, Reinheimer EW, and Campillo-Alvarado G
Abstract: Separations of azeotropic mixtures are typically carried out using energy-demanding processes (e.g., distillation). Here, we report the capacity of a self-assembled chlorinated boronic ester-based adduct to confine acetonitrile and benzene in channels upon crystallization. The solvent confinement occurs via a combination of hydrogen bonding and [π···π] interactions. Quantitative separation of benzene from an azeotropic 1:1 mixture of a benzene/acetonitrile (v/v), and methanol is achieved through crystallization with the chlorinated adduct by complementary [C-H···O] and [C-H···π] interactions. Inclusion behavior is rationalized by molecular modeling and crystallographic analysis. The chlorinated boronic ester adduct shows the potential of modularity via isosteric substitution for the separation of challenging chemical mixtures (e.g., azeotropes)., Competing Interests: The authors declare no competing financial interest., (© 2024 The Authors. Published by American Chemical Society.)
Published: 2024
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44. Traceable Calibration of Atmospheric Oxidized Mercury Measurements.

Author: Elgiar TR, Lyman SN, Andron TD, Gratz L, Hallar AG, Horvat M, Vijayakumaran Nair S, O'Neil T, Volkamer R, and Živković I
Subjects: Calibration, Atmosphere chemistry, Air Pollutants analysis, Colorado, Gas Chromatography-Mass Spectrometry, Mercury analysis, Oxidation-Reduction, Environmental Monitoring methods
Abstract: Most previous measurements of oxidized mercury were collected using a method now known to be biased low. In this study, a dual-channel system with an oxidized mercury detection limit of 6-12 pg m -3 was deployed alongside a permeation tube-based automated calibrator at a mountain top site in Steamboat Springs Colorado, USA, in 2021 and 2022. Permeation tubes containing elemental mercury and mercury halides were characterized via an International System of Units (SI)-traceable gravimetric method and gas chromatography/mass spectrometry before deployment in the calibrator. The dual-channel system recovered 97 ± 4 and 100 ± 8% (±standard deviation) of injected elemental mercury and HgBr 2 , respectively. Total Hg permeation rates and Hg speciation from the gravimetric method, the chromatography system, the dual-channel system, and an independent SI-traceable measurement method performed at the Jožef Stefan Institute laboratory were all comparable within the respective uncertainties of each method. These are the first measurements of oxidized mercury at low environmental concentrations that have been verified against an SI-traceable calibration system in field conditions while sampling ambient air, and they show that accurate, routinely calibrated oxidized mercury measurements are achievable.
Published: 2024
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45. Engineering Lipophilic Aggregation of Adapalene and Adamantane-Based Cocrystals via van der Waals Forces and Hydrogen Bonding.

Author: Bicknell J, Agarwal SA, Petersen KJ, Loya JD, Lutz N, Sittinger PM, Teat SJ, Settineri NS, and Campillo-Alvarado G
Abstract: Lipophilic aggregation using adamantanes is a widely exploited molecular property in medicinal and materials chemistry. Adamantanes are traditionally installed to molecular units via covalent bonds. However, the noncovalent installation of adamantanes has been relatively underexplored and presents the potential to bring properties associated with adamantanes to molecules without affecting their intrinsic properties (e.g., pharmacophores). Here, we systematically study a series of adamantanecarboxylic acids with varying substitution levels of methyl groups and their cocrystals with bipyridines. Specifically, single-crystal X-ray diffraction shows that while the directionality of single-component adamantanes is notably sensitive to changes in methyl substitution, hydrogen-bonded cocrystals with bipyridines show consistent and robust packing due to π-stacking predominance. Our observations are supported by Hirshfeld surface and energy framework analyses. The applicability of cocrystal formation of adamantanes bearing carboxylic acids was used to generate the first cocrystals of adapalene, an adamantane-bearing retinoid used for treating acne vulgaris. We envisage our study to inspire noncovalent (i.e., cocrystal) installation of adamantanes to generate lipophilic aggregation in multicomponent systems., Competing Interests: The authors declare no competing financial interest., (© 2024 The Authors. Published by American Chemical Society.)
Published: 2024
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46. Nanoscale Dodecahedral and Fullerene-Type Organoboroxine and Borazine Cages from Planar Building Units.

Author: Sánchez M, Baltrusaitis J, Vasquez-Ríos MG, Campillo-Alvarado G, MacGillivray LR, and Höpfl H
Abstract: Boroxine- and borazine-cage analogs to C 20 , C 60 , and C 70 were calculated and compared in terms of structure, strain indicators, and physical properties relevant to nanoscale applications. The results show C 60 and C 70 type cages are less strained than the smaller congener, primarily due to minimized bending in the B-arylene-B segments. The smallest cage calculated has a diameter of 2.4 nm, which increases up to 4.9 nm by either variation of the polyhedron (C 20 < C 60 < C 70 -type cage) or organic spacer elongation between boron centers. All calculated cages are porous (apertures ranging from 0.6 to 1.9 nm). Molecular electrostatic potential and Hirshfeld population analysis revealed both nucleophilic and electrophilic sites in the interior and exterior cage surfaces. HOMO-LUMO gaps range from 3.98 to 4.89 eV and 5.10-5.18 eV for the boroxine- and borazine-cages, respectively. Our findings provide insights into the design and properties of highly porous boroxine and borazine cages for nanoscience.
Published: 2024
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47. Teaching transposon classification as a means to crowd source the curation of repeat annotation - a tardigrade perspective.

Author: Peona V, Martelossi J, Almojil D, Bocharkina J, Brännström I, Brown M, Cang A, Carrasco-Valenzuela T, DeVries J, Doellman M, Elsner D, Espíndola-Hernández P, Montoya GF, Gaspar B, Zagorski D, Hałakuc P, Ivanovska B, Laumer C, Lehmann R, Boštjančić LL, Mashoodh R, Mazzoleni S, Mouton A, Nilsson MA, Pei Y, Potente G, Provataris P, Pardos-Blas JR, Raut R, Sbaffi T, Schwarz F, Stapley J, Stevens L, Sultana N, Symonova R, Tahami MS, Urzì A, Yang H, Yusuf A, Pecoraro C, and Suh A
Abstract: Background: The advancement of sequencing technologies results in the rapid release of hundreds of new genome assemblies a year providing unprecedented resources for the study of genome evolution. Within this context, the significance of in-depth analyses of repetitive elements, transposable elements (TEs) in particular, is increasingly recognized in understanding genome evolution. Despite the plethora of available bioinformatic tools for identifying and annotating TEs, the phylogenetic distance of the target species from a curated and classified database of repetitive element sequences constrains any automated annotation effort. Moreover, manual curation of raw repeat libraries is deemed essential due to the frequent incompleteness of automatically generated consensus sequences., Results: Here, we present an example of a crowd-sourcing effort aimed at curating and annotating TE libraries of two non-model species built around a collaborative, peer-reviewed teaching process. Manual curation and classification are time-consuming processes that offer limited short-term academic rewards and are typically confined to a few research groups where methods are taught through hands-on experience. Crowd-sourcing efforts could therefore offer a significant opportunity to bridge the gap between learning the methods of curation effectively and empowering the scientific community with high-quality, reusable repeat libraries., Conclusions: The collaborative manual curation of TEs from two tardigrade species, for which there were no TE libraries available, resulted in the successful characterization of hundreds of new and diverse TEs in a reasonable time frame. Our crowd-sourcing setting can be used as a teaching reference guide for similar projects: A hidden treasure awaits discovery within non-model organisms., (© 2024. The Author(s).)
Published: 2024
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48. Autoimmune Disorders and the Eye.

Author: Thompson L, Patrianakos T, Garcia J, Wadhwa A, Yang E, Thomas C, Schneider R, Stern H, Palma C, Hill K, Barquet V, Anderson-Nelson S, McMahon K, Patel U, Ghadiali Q, Danek D, Larsen B, Wong A, Dawood S, Ludington M, Zhang G, Garakani R, Dwarakanathan S, Simotas A, Sangal K, Phelps P, Ashourian T, Darwish D, Bamba S, Zein M, Nichols J, To J, Sarmiento A, Chaudhary S, Breshears B, Nelson J, Anderson-Nelson S, and Giovingo M
Subjects: Humans, Autoimmune Diseases, Eye Diseases
Published: 2024
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49. The Imperial Politics of Time in the British History Classroom.

Author: Natarajan R
Published: 2024
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50. Emergent neural dynamics and geometry for generalization in a transitive inference task.

Author: Kay K, Biderman N, Khajeh R, Beiran M, Cueva CJ, Shohamy D, Jensen G, Wei XX, Ferrera VP, and Abbott LF
Subjects: Humans, Models, Neurological, Computational Biology, Male, Adult, Female, Young Adult, Nerve Net physiology, Task Performance and Analysis, Neural Networks, Computer, Cognition physiology, Brain physiology, Memory, Short-Term physiology
Abstract: Relational cognition-the ability to infer relationships that generalize to novel combinations of objects-is fundamental to human and animal intelligence. Despite this importance, it remains unclear how relational cognition is implemented in the brain due in part to a lack of hypotheses and predictions at the levels of collective neural activity and behavior. Here we discovered, analyzed, and experimentally tested neural networks (NNs) that perform transitive inference (TI), a classic relational task (if A > B and B > C, then A > C). We found NNs that (i) generalized perfectly, despite lacking overt transitive structure prior to training, (ii) generalized when the task required working memory (WM), a capacity thought to be essential to inference in the brain, (iii) emergently expressed behaviors long observed in living subjects, in addition to a novel order-dependent behavior, and (iv) expressed different task solutions yielding alternative behavioral and neural predictions. Further, in a large-scale experiment, we found that human subjects performing WM-based TI showed behavior inconsistent with a class of NNs that characteristically expressed an intuitive task solution. These findings provide neural insights into a classical relational ability, with wider implications for how the brain realizes relational cognition., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Kay et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
Published: 2024
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