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3. Principles and Practices Fostering Inclusive Excellence: Lessons from the Howard Hughes Medical Institute's Capstone Institutions

Author

DiBartolo, Patricia Marten, Smith College (Author), Gregg-Jolly, Leslie, Grinnell College (Author), Gross, Deborah, Carleton College (Author), Iverson, Ellen, Carleton College (Author), Manduca, Cathryn A., Carleton College (Author), Cooke, David B., Carleton College (Author), Davis, Gregory K., Bryn Mawr College (Author), Davidson, Cameron, Carleton College (Author), Hertz, Paul E., Barnard College (Author), Hibbard, Lisa, Spelman College (Author), Ireland, Shubha K., Xavier University of Louisiana (Author), Mader, Catherine, Hope College (Author), Pai, Aditi, Spelman College (Author), Raps, Shirley, Hunter College (Author), Siwicki, Kathleen, Swarthmore College (Author), DiBartolo, Patricia Marten, Smith College (Author), Gregg-Jolly, Leslie, Grinnell College (Author), Gross, Deborah, Carleton College (Author), Iverson, Ellen, Carleton College (Author), Manduca, Cathryn A., Carleton College (Author), Cooke, David B., Carleton College (Author), Davis, Gregory K., Bryn Mawr College (Author), Davidson, Cameron, Carleton College (Author), Hertz, Paul E., Barnard College (Author), Hibbard, Lisa, Spelman College (Author), Ireland, Shubha K., Xavier University of Louisiana (Author), Mader, Catherine, Hope College (Author), Pai, Aditi, Spelman College (Author), Raps, Shirley, Hunter College (Author), and Siwicki, Kathleen, Swarthmore College (Author)

Abstract

Best-practices pedagogy in science, technology, engineering, and mathematics (STEM) aims for inclusive excellence that fosters student persistence. This paper describes principles of inclusivity across 11 primarily undergraduate institutions designated as Capstone Awardees in Howard Hughes Medical Institutes (HHMI) 2012 competition. The Capstones represent a range of institutional missions, student profiles, and geographical locations. Each successfully directed activities toward persistence of STEM students, especially those from traditionally underrepresented groups, through a set of common elements: mentoring programs to build community; research experiences to strengthen scientific skill/ identity; attention to quantitative skills; and outreach/bridge programs to broaden the student pool. This paper grounds these program elements in learning theory, emphasizing their essential principles with examples of how they were implemented within institutional contexts. We also describe common assessment approaches that in many cases informed programming and created traction for stakeholder buy-in. The lessons learned from our shared experiences in pursuit of inclusive excellence, including the resources housed on our companion website, can inform others efforts to increase access to and persistence in STEM in higher education. KEYWORDS: STEM education program, Howard Hughes Medical Institutes Capstone Institutions

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7. Tri-Co LIASE: Cross- and Intra-Institutional Collaboration to Build and Sustain Student-Focused Embedded Study in Asia

Author

Tania Johnson, David Eldridge, David Foreman, Sharon Bain, Haili Kong, Henry Luce Foundation, Freeman Foundation, Mertz Gilmore Foundation, Elizabeth Economy, Swarthmore College Class of 1984, and Tsuyoshi and My Phuong Mitarai, Swarthmore College Class of 1998

Subjects
Fine Arts, curriculum, administration, Asian studies, environment, collaboration, interdisciplinarity, Reciprocity (social psychology), Strategic partnership, Political science, 0502 economics and business, ComputingMilieux_COMPUTERSANDEDUCATION, asian studies, Curriculum, business.industry, Language and Literature, 05 social sciences, 050301 education, General Medicine, Public relations, business, 0503 education, 050203 business & management
Abstract

In this paper, Swarthmore College and Bryn Mawr College faculty and administrators share reflections on the Luce Initiative on Asian Studies and the Environment (LIASE) grants from the Henry Luce Foundation for the enhancement of curriculum on Asia and the environment and the cultivation of collaborations between US and Asian institutions. Supported by LIASE exploration grants in 2013 and a LIASE implementation grant awarded to the Tri-College Consortium of Bryn Mawr, Haverford, and Swarthmore Colleges in 2015, curricular innovations included the creation of courses with travel components and the introduction of topics on Asia and the environment across disciplines. Topics of discussion include fostering curricular innovation and interdisciplinarity across academic divisions; building effective and sustainable collaborations with local institutions in Asia; forging strategic partnerships with administrators in grants, advancement, and finance; leveraging institutional relationships to secure funding to pilot and sustain initiatives; and the importance of reciprocity in building long-term, cross-cultural exchanges.

Published
2021
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8. Schur's Lemma for Coupled Reducibility and Coupled Normality

Author

Dana Lahat, Christian Jutten, Helene Shapiro, Signal et Communications (IRIT-SC), Institut de recherche en informatique de Toulouse (IRIT), Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées, GIPSA - Vision and Brain Signal Processing (GIPSA-VIBS), Département Images et Signal (GIPSA-DIS), Grenoble Images Parole Signal Automatique (GIPSA-lab ), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut Polytechnique de Grenoble - Grenoble Institute of Technology-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 Polytechnique de Grenoble - Grenoble Institute of Technology-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Grenoble Images Parole Signal Automatique (GIPSA-lab ), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut Polytechnique de Grenoble - Grenoble Institute of Technology-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 Polytechnique de Grenoble - Grenoble Institute of Technology-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 ), Department of Mathematics and Statistics, Swarthmore College, Swarthmore College, European Project: 320684,EC:FP7:ERC,ERC-2012-ADG_20120216,CHESS(2013), European Project: 681839,H2020,ERC-2015-CoG,FACTORY(2016), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Toulouse Mind & Brain Institut (TMBI), Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université Toulouse Capitole (UT Capitole), and Université de Toulouse (UT)

Subjects
joint independent subspace analysis (JISA), Mathematics::Number Theory, High Energy Physics::Lattice, media_common.quotation_subject, Schur's lemma, coupled reducibility, Normal matrix, Combinatorics, Schur's Lemma, FOS: Mathematics, normal matrices, Normality, Mathematics, media_common, Condensed Matter::Quantum Gases, [MATH.MATH-RT]Mathematics [math]/Representation Theory [math.RT], [MATH.MATH-RA]Mathematics [math]/Rings and Algebras [math.RA], coupled normality, Mathematics - Rings and Algebras, 15A04, 15A21, 15A24, 15A99, 20C99, Indexed family, Sylvester equation, Rings and Algebras (math.RA), Index set, coupled decomposition, High Energy Physics::Experiment, independent component analysis (ICA), Analysis
Abstract

Let $\mathcal A = \{A_{ij} \}_{i, j \in \mathcal I}$, where $\mathcal I$ is an index set, be a doubly indexed family of matrices, where $A_{ij}$ is $n_i \times n_j$. For each $i \in \mathcal I$, let $\mathcal V_i$ be an $n_i$-dimensional vector space. We say $\mathcal A$ is reducible in the coupled sense if there exist subspaces, $\mathcal U_i \subseteq \mathcal V_i$, with $\mathcal U_i \neq \{0\}$ for at least one $i \in \mathcal I$, and $\mathcal U_i \neq \mathcal V_i$ for at least one $i$, such that $A_{ij} (\mathcal U_j) \subseteq \mathcal U_i$ for all $i, j$. Let $\mathcal B = \{B_{ij} \}_{i, j \in \mathcal I}$ also be a doubly indexed family of matrices, where $B_{ij}$ is $m_i \times m_j$. For each $i \in \mathcal I$, let $X_i$ be a matrix of size $n_i \times m_i$. Suppose $A_{ij} X_j = X_i B_{ij}$ for all~$i, j$. We prove versions of Schur's Lemma for $\mathcal A, \mathcal B$ satisfying coupled irreducibility conditions. We also consider a refinement of Schur's Lemma for sets of normal matrices and prove corresponding versions for $\mathcal A, \mathcal B$ satisfying coupled normality and coupled irreducibility conditions., 35 pages. Second version corrects some typos in the original submission and makes some changes in MSC classification numbers

Published
2018
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10. Powers of sequences and convergence of ergodic averages

Author

Nikos Frantzikinakis, Emmanuel Lesigne, Michael C. R. Johnson, Máté Wierdl, Department of Mathematics and Statistics, University of Victoria [Canada] (UVIC), Department of Mathematics and Statistics, Swarthmore College, Swarthmore College, Laboratoire de Mathématiques et Physique Théorique (LMPT), Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Université de Tours

Subjects
Mathematics::Dynamical Systems, Measurable function, General Mathematics, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], Dynamical Systems (math.DS), 01 natural sciences, law.invention, Combinatorics, AMS. Primary: 37A30, Secondary: 28D05, 11L15, law, 0103 physical sciences, FOS: Mathematics, Ergodic theory, Mathematics - Dynamical Systems, 0101 mathematics, 37A30 (Primary), 28D05 (Secondary), 11L15, Mathematics, Pointwise convergence, Discrete mathematics, Mathematics::Combinatorics, multiple ergodic averages, Applied Mathematics, 010102 general mathematics, 16. Peace & justice, ergodic theorems, Invertible matrix, Bounded function, Norm (mathematics), 010307 mathematical physics, ergodic averages
Abstract

A sequence $(s_n)$ of integers is good for the mean ergodic theorem if for each invertible measure preserving system $(X,\mathcal{B},\mu,T)$ and any bounded measurable function $f$, the averages $ \frac1N \sum_{n=1}^N f(T^{s_n}x)$ converge in the $L^2$ norm. We construct a sequence $(s_n)$ that is good for the mean ergodic theorem, but the sequence $(s_n^2)$ is not. Furthermore, we show that for any set of bad exponents $B$, there is a sequence $(s_n)$ where $(s_n^k)$ is good for the mean ergodic theorem exactly when $k$ is not in $B$. We then extend this result to multiple ergodic averages. We also prove a similar result for pointwise convergence of single ergodic averages., Comment: After a few minor corrections, to appear in Ergodic Theory and Dynamical Systems

Published
2009
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12. Blending Quadruplexes and Bordeaux: A Grand Cru!

Author

Liliya A. Yatsunyk, Dipankar Sen, David Monchaud, Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore College, Institut de Chimie Moléculaire de l'Université de Bourgogne [Dijon] (ICMUB), Université de Bourgogne (UB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Conception, synthèse et vectorisation de biomolécules. (CSVB), Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris], Simon Fraser University (SFU.ca), Institut de Chimie Moléculaire de l'Université de Bourgogne [Dijon] ( ICMUB ), Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS ), Department of Molecular Biology and Biochemistry, Simon Fraser University, Institut Curie-Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5), and Institut Curie [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)

Subjects
0301 basic medicine, Pharmacology, Clinical Biochemistry, Media studies, Cru, Nanotechnology, Biology, Biochemistry, [ CHIM ] Chemical Sciences, 03 medical and health sciences, 030104 developmental biology, Quadruplex nucleic acids, Drug Discovery, Molecular Medicine, [CHIM]Chemical Sciences, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience; The Fifth International Meeting on Quadruplex Nucleic Acids took place in Bordeaux, France. Over the course of three intense days in May 2015, the quadruplex community had an opportunity to share exciting developments in the field, especially key insights into emerging biological roles that these structures, considered for decades to be nothing more but in vitro curiosity, are playing.

Published
2016
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15. Identification of Tah11/Sid2 as the ortholog of the replication licensing factor Cdt1 in Saccharomyces cerevisiae

Author

Stephen A. Green, Etienne Schwob, Aaron Bensimon, Elizabeth A. Vallen, Alain Devault, Tina Yuan, Institut de Génétique Moléculaire de Montpellier (IGMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Swarthmore College, Stabilité des génomes, Institut Pasteur [Paris], This work was supported by grants to E.S. from CNRS (Physique et Chimie du Vivant) and Association pour la Recherche sur le Cancer (ARC 9064) as well as by grants from U.S. Public Health Service Grant GM-54300-01 and Swarthmore College Faculty Research Funds to E.A.V., We are grateful to J. Diffley for sharing data prior to publication and to P. Pasero for help with DNA combing and chromatin-binding assays. We thank F. Cross and M.-A. Bjornsti for helpful discussions, L. Dirick and P. Pasero for critical reading of the manuscript, C.X. Muñoz, J. Tashjian, and G. Rivnak for technical assistance, E. Vives for α factor synthesis, as well as K. Nasmyth, D. Koshland, and M. Longtine for strains or plasmids., Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris] (IP)

Subjects
DNA Replication, Saccharomyces cerevisiae Proteins, Transcription, Genetic, Chromosomal Proteins, Non-Histone, Molecular Sequence Data, Cell Cycle Proteins, Replication Origin, Eukaryotic DNA replication, Saccharomyces cerevisiae, Biology, Pre-replication complex, Origin of replication, General Biochemistry, Genetics and Molecular Biology, Fungal Proteins, DNA replication factor CDT1, 03 medical and health sciences, 0302 clinical medicine, Replication factor C, Control of chromosome duplication, Gene Expression Regulation, Fungal, Animals, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, 030304 developmental biology, Genetics, 0303 health sciences, Sequence Homology, Amino Acid, Agricultural and Biological Sciences(all), Biochemistry, Genetics and Molecular Biology(all), Chromatin, DNA-Binding Proteins, Licensing factor, Mutation, embryonic structures, biology.protein, Origin recognition complex, General Agricultural and Biological Sciences, Protein Kinases, 030217 neurology & neurosurgery
Abstract

Faithful duplication of the genetic material requires that replication origins fire only once per cell cycle. Central to this control is the tightly regulated formation of prereplicative complexes (preRCs) at future origins of DNA replication [1]. In all eukaryotes studied, this entails loading by Cdc6 of the Mcm2-7 helicase next to the origin recognition complex (ORC) [2]. More recently, another factor, named Cdt1, was shown to be essential for Mcm loading in fission yeast and Xenopus[3–5] as well as for DNA replication in Drosophila and humans [6, 7]. Surprisingly, no Cdt1 homolog was found in budding yeast, despite the conserved nature of origin licensing. Here we identify Tah11/Sid2, previously isolated through interactions with topoisomerase and Cdk inhibitor mutants [8, 9], as an ortholog of Cdt1. We show that sid2 mutants lose minichromosomes in an ARS number-dependent manner, consistent with ScCdt1/Sid2 being involved in origin licensing. Accordingly, cells partially depleted of Cdt1 replicate DNA from fewer origins, whereas fully depleted cells fail to load Mcm2 on chromatin and fail to initiate but not elongate DNA synthesis. We conclude that origin licensing depends in S. cerevisiae as in other eukaryotes on both Cdc6 and Cdt1.

Published
2002
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18. Early dark energy is not excluded by current large-scale structure data

Author

José Luis Bernal, Tristan L. Smith, Kimberly K. Boddy, Riccardo Murgia, Marc Kamionkowski, Vivian Poulin, Swarthmore College, Laboratoire Univers et Particules de Montpellier (LUPM), Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Johns Hopkins University (JHU), University of Texas at Austin [Austin], and TLS is supported by NSF Grant No. 2009377, NASA Grant No. 80NSSC18K0728,and the Research Corporation. This work was supported at Johns Hopkins by NSF Grant No. 1818899 and the Simons Foundation. JLB is supported by the Allan C. and Dorothy H. Davis Fellowship.

Subjects
Cosmology and Nongalactic Astrophysics (astro-ph.CO), satellite: Planck, constraint, Cosmic microwave background, FOS: Physical sciences, Context (language use), Astrophysics::Cosmology and Extragalactic Astrophysics, Astrophysics, Parameter space, 01 natural sciences, symbols.namesake, High Energy Physics - Phenomenology (hep-ph), effective field theory, cosmological model: parameter space, 0103 physical sciences, supernova, Effective field theory, energy: density, structure, Planck, 010306 general physics, dark energy, Physics, Hubble constant, 010308 nuclear & particles physics, redshift: high, resolution, tension, galaxy: power spectrum, Galaxy, High Energy Physics - Phenomenology, symbols, Dark energy, galaxy: cluster, [PHYS.ASTR]Physics [physics]/Astrophysics [astro-ph], Astrophysics - Cosmology and Nongalactic Astrophysics, Hubble's law, cosmic background radiation: anisotropy
Abstract

We revisit the impact of early dark energy (EDE) on galaxy clustering using BOSS galaxy power spectra, analyzed using the effective field theory (EFT) of large-scale structure (LSS), and anisotropies of the cosmic microwave background (CMB) from Planck. Recent studies found that these data place stringent constraints on the maximum abundance of EDE allowed in the Universe. We argue here that their conclusions are a consequence of their choice of priors on the EDE parameter space, rather than any disagreement between the data and the model. For example, when considering EFT-LSS, CMB, and high-redshift supernovae data we find the EDE and $\Lambda$CDM models can provide statistically indistinguishable fits ($\Delta \chi^2 = 0.12$) with a relatively large value for the maximum fraction of energy density in the EDE ($f_{\rm ede} = 0.09$) and Hubble constant ($H_0 = 71$ km/s/Mpc) in the EDE model. Moreover, we demonstrate that the constraining power added from the inclusion of EFT-LSS traces to the potential tension between the power-spectrum amplitudes $A_s$ derived from BOSS and from Planck that arises even within the context of $\Lambda$CDM. Until this is better understood, caution should be used when interpreting EFT-BOSS+Planck constraints to models beyond $\Lambda$CDM. These findings suggest that EDE still provides a potential resolution to the Hubble tension and that it is worthwhile to test the predictions of EDE with future data-sets and further study its theoretical possibilities., Comment: 8 pages, 3 figures, comments welcome

Published
2021
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25. Quadruplexes in ‘Dicty’: crystal structure of a four-quartet G-quadruplex formed by G-rich motif found in the Dictyostelium discoideum genome

Author

Aurore Guédin, Liliya A. Yatsunyk, Samir Armane, Linda Yingqi Lin, Jean-Louis Mergny, Stéphane Thore, Laurent Lacroix, Acides Nucléiques : Régulations Naturelle et Artificielle (ARNA), Université de Bordeaux (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Swarthmore College, SOGIP (ERC 249236)/Laboratoire d'Anthropologie des Institutions et des Organisations Sociales (IIAC-LAIOS), Institut interdisciplinaire d'anthropologie du contemporain (IIAC), École des hautes études en sciences sociales (EHESS)-Centre National de la Recherche Scientifique (CNRS)-École des hautes études en sciences sociales (EHESS)-Centre National de la Recherche Scientifique (CNRS), Institute of Biophysics of the Czech Academy of Sciences (IBP / CAS), and Czech Academy of Sciences [Prague] (CAS)

Subjects
Models, Molecular, 0301 basic medicine, Stereochemistry, Base pair, In silico, Crystallography, X-Ray, 010402 general chemistry, G-quadruplex, Antiparallel (biochemistry), 01 natural sciences, Genome, Dictyostelium discoideum, 03 medical and health sciences, chemistry.chemical_compound, Structural Biology, Genetics, Dictyostelium, Promoter Regions, Genetic, Nuclear Magnetic Resonance, Biomolecular, ComputingMilieux_MISCELLANEOUS, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], biology, Circular Dichroism, biology.organism_classification, 0104 chemical sciences, G-Quadruplexes, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, 030104 developmental biology, chemistry, Mutation, Nucleic Acid Conformation, Spectrophotometry, Ultraviolet, DNA
Abstract

Guanine-rich DNA has the potential to fold into non-canonical G-quadruplex (G4) structures. Analysis of the genome of the social amoeba Dictyostelium discoideum indicates a low number of sequences with G4-forming potential (249–1055). Therefore, D. discoideum is a perfect model organism to investigate the relationship between the presence of G4s and their biological functions. As a first step in this investigation, we crystallized the dGGGGGAGGGGTACAGGGGTACAGGGG sequence from the putative promoter region of two divergent genes in D. discoideum. According to the crystal structure, this sequence folds into a four-quartet intramolecular antiparallel G4 with two lateral and one diagonal loops. The G-quadruplex core is further stabilized by a G-C Watson–Crick base pair and a A–T–A triad and displays high thermal stability (Tm > 90°C at 100 mM KCl). Biophysical characterization of the native sequence and loop mutants suggests that the DNA adopts the same structure in solution and in crystalline form, and that loop interactions are important for the G4 stability but not for its folding. Four-tetrad G4 structures are sparse. Thus, our work advances understanding of the structural diversity of G-quadruplexes and yields coordinates for in silico drug screening programs and G4 predictive tools.

Published
2018
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28. ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates

Author

Hiroki Nishida, Magali Naville, Paul Simion, Christelle Dantec, Wendy Reeves, Bradley Davidson, Rémi Dumollard, Justine Dardaillon, Takeshi A. Onuma, Kai Wang, Kazuhiro R. Nitta, Jean-Nicolas Volff, Joseph F. Ryan, Patrick Lemaire, Emmanuel Faure, Lydia Besnardeau, Michael Veeman, Marie Fagotto, Alexandra Louis, Hugues Roest Crollius, Delphine Dauga, Marion Gueroult-Bellone, Melissa B. DeBiasse, Shigeki Fujiwara, Emmanuel J. P. Douzery, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre de recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Bioself Communication [Marseille], Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Image & Interaction (ICAR), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Osaka University [Osaka], University of Florida [Gainesville] (UF), Institut de biologie de l'ENS Paris (IBENS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Institut de Biologie du Développement de Marseille (IBDM), Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Centre National de la Recherche Scientifique (CNRS), Institut de Génomique Fonctionnelle de Lyon (IGFL), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie du Développement de Villefranche sur mer (LBDV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Kansas State University, University of Chinese Academy of Sciences [Beijing] (UCAS), Université de Montpellier (UM), Kochi University of Technology (KUT), DYnamique et Organisation des GENomes - Equipe de l'IBENS (DYOGEN), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, Swarthmore College, ANR-16-CE92-0019,EVOBOOSTER,Impact des éléments transposables sur les réseaux de régulation génique : application aux voies biologiques à évolution rapide chez les poissons(2016), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), ROEST CROLLIUS, Hugues, Centre de recherche en Biologie Cellulaire (CRBM), Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), University of Florida [Gainesville], École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU)-Collège de France (CdF)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV]Life Sciences [q-bio], RNA-Seq, Genomics, Computational biology, Biology, Genome, Synteny, Evolution, Molecular, 03 medical and health sciences, User-Computer Interface, 0302 clinical medicine, biology.animal, Cephalochordata, Databases, Genetic, Gene Order, [SDV.BDD] Life Sciences [q-bio]/Development Biology, Genetics, Computer Graphics, Database Issue, Animals, Computer Simulation, Urochordata, Gene, [SDV.BDD]Life Sciences [q-bio]/Development Biology, In Situ Hybridization, Phylogeny, 030304 developmental biology, 0303 health sciences, Internet, Deuterostome, Binding Sites, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Gene Expression Profiling, Vertebrate, food and beverages, Molecular Sequence Annotation, biology.organism_classification, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Gene expression profiling, [SDV] Life Sciences [q-bio], Vertebrates, Programming Languages, 030217 neurology & neurosurgery, Software, Echinodermata
Abstract

ANISEED (https://www.aniseed.cnrs.fr) is the main model organism database for the worldwide community of scientists working on tunicates, the vertebrate sister-group. Information provided for each species includes functionally-annotated gene and transcript models with orthology relationships within tunicates, and with echinoderms, cephalochordates and vertebrates. Beyond genes the system describes other genetic elements, including repeated elements and cis-regulatory modules. Gene expression profiles for several thousand genes are formalized in both wild-type and experimentally-manipulated conditions, using formal anatomical ontologies. These data can be explored through three complementary types of browsers, each offering a different view-point. A developmental browser summarizes the information in a gene- or territory-centric manner. Advanced genomic browsers integrate the genetic features surrounding genes or gene sets within a species. A Genomicus synteny browser explores the conservation of local gene order across deuterostome. This new release covers an extended taxonomic range of 14 species, including for the first time a non-ascidian species, the appendicularian Oikopleura dioica. Functional annotations, provided for each species, were enhanced through a combination of manual curation of gene models and the development of an improved orthology detection pipeline. Finally, gene expression profiles and anatomical territories can be explored in 4D online through the newly developed Morphonet morphogenetic browser.

Published
2019
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29. Jamming transition in non-spherical particle systems: pentagons versus disks

Author

Yiqiu Zhao, Cacey Stevens Bester, Hu Zheng, Yuanyuan Xu, Robert Behringer, Joshua E. S. Socolar, Jonathan Barés, Duke University [Durham], Moyens expérimentaux (Servex), Laboratoire de Mécanique et Génie Civil (LMGC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Tongji University, Swarthmore College, and Johns Hopkins University (JHU)

Subjects
photoelasticity, Coordination number, pentagon, 0211 other engineering and technologies, FOS: Physical sciences, General Physics and Astronomy, Uniaxial compression, Jamming, 02 engineering and technology, Condensed Matter - Soft Condensed Matter, Atomic packing factor, Granular material, 01 natural sciences, Molecular physics, 0103 physical sciences, granular matter, General Materials Science, [PHYS.COND.CM-SM]Physics [physics]/Condensed Matter [cond-mat]/Statistical Mechanics [cond-mat.stat-mech], 010306 general physics, Condensed Matter - Statistical Mechanics, 021101 geological & geomatics engineering, Particle system, Physics, Condensed Matter - Materials Science, Statistical Mechanics (cond-mat.stat-mech), Materials Science (cond-mat.mtrl-sci), Condensed Matter::Soft Condensed Matter, Mechanics of Materials, Soft Condensed Matter (cond-mat.soft), Voronoi diagram, [PHYS.COND.CM-SCM]Physics [physics]/Condensed Matter [cond-mat]/Soft Condensed Matter [cond-mat.soft], Quasistatic process
Abstract

We investigate the jamming transition in a quasi-2D granular material composed of regular pentagons or disks subjected to quasistatic uniaxial compression. We report six major findings based on experiments with monodisperse photoelastic particles with static friction coefficient $$\mu \approx 1$$. (1) For both pentagons and disks, the onset of rigidity occurs when the average coordination number of non-rattlers, $$Z_{nr}$$, reaches 3, and the dependence of $$Z_{nr}$$ on the packing fraction $$\phi$$ changes again when $$Z_{nr}$$ reaches 4. (2) Though the packing fractions $$\phi _{c1}$$ and $$\phi _{c2}$$ at these transitions differ from run to run, for both shapes the data from all runs with different initial configurations collapses when plotted as a function of the non-rattler fraction. (3) The averaged values of $$\phi _{c1}$$ and $$\phi _{c2}$$ for pentagons are around $$1\%$$ smaller than those for disks. (4) Both jammed pentagons and disks show Gamma distribution of the Voronoi cell area with same parameters. (5) The jammed pentagons have similar translational order for particle centers but slightly less orientational order for contacting pairs compared to jammed disks. (6) For jammed pentagons, the angle between edges at a face-to-vertex contact point shows a uniform distribution and the size of a cluster connected by face-to-face contacts shows a power-law distribution.

Published
2019
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32. Pharmacological or genetic targeting of Transient Receptor Potential (TRP) channels can disrupt the planarian escape response

Author

Ziad Sabry, Danielle Ireland, Eva-Maria S. Collins, Alicia Ho, Olivier Cochet-Escartin, Christina Rabeler, Swarthmore College, University of California [San Diego] (UC San Diego), University of California, Biophysique (BIOPHYSIQUE), Institut Lumière Matière [Villeurbanne] (ILM), 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), Division of Biological Sciences [San Diego], and University of California-University of California

Subjects
Nociception, Physiology, [SDV]Life Sciences [q-bio], Flatworms, Biochemistry, TRPV, Ion Channels, Database and Informatics Methods, Transient receptor potential channel, [SPI]Engineering Sciences [physics], RNA interference, Transient Receptor Potential Channels, 0302 clinical medicine, Escape Reaction, Isothiocyanates, Medicine and Health Sciences, Annelids, [PHYS]Physics [physics], 0303 health sciences, Gene knockdown, Multidisciplinary, biology, Chemistry, Physics, Eukaryota, Drugs, food and beverages, Endocannabinoid system, Cell biology, Nucleic acids, Electrophysiology, Genetic interference, Planarian, Physical Sciences, Medicine, Epigenetics, Genetic Oscillators, Cellular Structures and Organelles, Sequence Analysis, Research Article, Bioinformatics, Science, Biophysics, Neurophysiology, Escape response, Research and Analysis Methods, 03 medical and health sciences, Schmidtea mediterranea, Leeches, Genetics, Noxious stimulus, Animals, [CHIM]Chemical Sciences, Cilia, 030304 developmental biology, Pharmacology, Cannabinoids, Organisms, Biology and Life Sciences, Proteins, Planarians, Cell Biology, Hydrogen Peroxide, biology.organism_classification, Invertebrates, RNA, Gene expression, Sequence Alignment, 030217 neurology & neurosurgery, Neuroscience
Abstract

In response to noxious stimuli, planarians cease their typical ciliary gliding and exhibit an oscillatory type of locomotion called scrunching. We have previously characterized the biomechanics of scrunching and shown that it is induced by specific stimuli, such as amputation, noxious heat, and extreme pH. Because these specific inducers are known to activate Transient Receptor Potential (TRP) channels in other systems, we hypothesized that TRP channels control scrunching. We found that chemicals known to activate TRPA1 (allyl isothiocyanate (AITC) and hydrogen peroxide) and TRPV (capsaicin and anandamide) in other systems induce scrunching in the planarian species Dugesia japonica and, except for anandamide, in Schmidtea mediterranea. To confirm that these responses were specific to either TRPA1 or TRPV, respectively, we tried to block scrunching using selective TRPA1 or TRPV antagonists and RNA interference (RNAi) mediated knockdown. Unexpectedly, co-treatment with a mammalian TRPA1 antagonist, HC-030031, enhanced AITC-induced scrunching by decreasing the latency time, suggesting an agonistic relationship in planarians. We further confirmed that TRPA1 in both species is necessary for AITC-induced scrunching using RNAi. Conversely, while co-treatment of a mammalian TRPV antagonist, SB-366791, also enhanced capsaicin-induced reactions in D. japonica, combined knockdown of two previously identified D. japonica TRPV genes (DjTRPVa and DjTRPVb) did not inhibit capsaicin-induced scrunching. Surprisingly, RNAi of either DjTRPAa or DjTRPVa/DjTRPVb disrupted scrunching induced by the endocannabinoid and TRPV agonist, anandamide. Overall, our results show that although scrunching induction can involve different initial pathways for sensing stimuli, this behavior’s signature dynamical features are independent of the inducer, implying that scrunching is a stereotypical planarian escape behavior in response to various noxious stimuli that converge on a single downstream pathway. Understanding which aspects of nociception are conserved or not across different organisms can provide insight into the underlying regulatory mechanisms to better understand pain sensation.

Published
2019
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33. Analysis of a Vector-Borne Diseases Model with a Two-Lag Delay Differential Equation

Author

Qaddura, Yusuf, Mavinga, Nsoki, and Swarthmore College

Subjects
delay differential equations, epidemiology, vector-borne diseases, linearization, transcendental equations, stability, 34K20, 34K28, 92D25, 92D30, Mathematics
Abstract

We are concerned with the stability analysis of equilibrium solutions for a two-lag delay differential equation which models the spread of vector-borne diseases, where the lags are incubation periods in humans and vectors. We show that there are some values of transmission and recovery rates for which the disease dies out and others for which the disease spreads into an endemic. The proofs of the main stability results are based on the linearization method and the analysis of roots of transcendental equations. We then simulate numerical solutions using MATLAB. We observe that the solution could possess chaotic and sometimes unbounded behaviors.

Published
2018

35. Planet Formation Imager (PFI): science vision and key requirements

Author

Ridgway Steve, Regaly Zsolt, Kral Quentin, Gandhi Poshak, Packham Chris, Tristram Konrad R. W., Baruteau Clement, Tuthill Peter, Mordasini Chris, Matter Alexis, A. Pierens, Duchene Gaspard, Olofsson Johan, Ilee John, Bitsch Bertram, Wittkowski Markus, Pinte Christophe, Meru Farzana, Armitage Phil, Chiavassa Andrea, Berger Jean-Philippe, Millour Florentin, Buscher David, Rosotti Giovanni P., Zhao Ming, Pott Joerg-Uwe, Wolf Sebastian, ten Brummelaar Theo, Bayo Amelia, Labadie Lucas, Morlok Andreas, Millan-Gabet Rafael, Kishimoto Makoto, Gallenne Alexandre, Ciardi David, Turner Neal, Gonzalez Jean-Francois, Vasisht Gautam, Monnier John D., Zhu Zhaohuan, Weigelt Gerd, Quiroga-Nunez Luis Henry, Kratter Kaitlin, Ramos Almeida Cristina, Juhasz Attila, Kley Wilhelm, Smith Michael, Espaillat Catherine, Alonso Herrero Almudena, Paladini Claudia, Pope Benjamin, Bate Matthew R., de Wit Willem-Jan, Harries Tim J., Lacour Sylvestre, Boyajian Tabetha, Petrov Romain, Paardekooper Sijme-Jan, Laughlin Greg, Nelson Richard P., Hoenig Sebastian, Pepper Joshua, Stassun Keivan, Jensen Eric L. N., Bonsor Amy, Kraus Stefan, Haniff Chris, Reynold Mark, Panic Olja, Sean N. Raymond, Masset Frederic, van Belle Gerard, Morbidelli Alessandro, Kane Stephen R., Ireland Michael J., Surdej Jean, Oudmaijer Rene, Benisty Myriam, Micromotive GmbH, Mainz, Germany, Université Paris Diderot - Paris 7 (UPD7), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Université libre de Bruxelles (ULB), The Breakthrough Breast Cancer Research Centre, Institute of cancer research, Institut de Biologie du Développement de Marseille (IBDM), Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Centre National de la Recherche Scientifique (CNRS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), foreign laboratories (FL), CERN [Genève], Laboratoire de Cosmologie, Astrophysique Stellaire & Solaire, de Planétologie et de Mécanique des Fluides (CASSIOPEE), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de la Côte d'Azur, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Department of Materials Science and Engineering, Institute of Ceramics and Glass-Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Pontifical Catholic University of Paraná (PUCPR), Pontifical Catholic University of Paraná, UNESCO Chinese Center of Marine Biotechnology, Ocean University of China, Laboratoire d'études spatiales et d'instrumentation en astrophysique (LESIA), 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 Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), 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]), École Supérieure Polytechnique de Dakar (ESP), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), ECLIPSE 2016, Laboratoire d'Astrophysique de Bordeaux [Pessac] (LAB), Université de Bordeaux (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), The Samuel Roberts Noble Foundation, Max-Planck-Institut für Radioastronomie (MPIFR), LT2C, Laboratoire Telecom Claude Chappe (LT2C), Université Jean Monnet [Saint-Étienne] (UJM)-Ecole d'ingenieurs Telecom Saint Etienne-Université Jean Monnet [Saint-Étienne] (UJM)-Ecole d'ingenieurs Telecom Saint Etienne, NASA ExoPlanet Science Institute (NExScI), California Institute of Technology (CALTECH), Universidad de Concepción [Chile], European Southern Observatory (ESO), Department of Physics, Durham University, Durham University, GRI-CEL, National Optical Astronomy Observatory (NOAO), Sydney Institute for Astronomy (SIfA), The University of Sydney, Institut de recherche en astrophysique et planétologie (IRAP), Institut national des sciences de l'Univers (INSU - CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Lund Observatory, Lund University [Lund], Malbet, Fabien, Creech-Eakman, Michelle J., Tuthill, Peter G., University of Exeter, Department of Astronomy, University of Michigan, Australian National University (ANU), University of California [Berkeley] (UC Berkeley), University of California (UC), Boston University [Boston] (BU), University of Southampton, Institute of Astronomy [Cambridge], University of Cambridge [UK] (CAM), University of Bern, Instituto de Fisica y Astronomia [Valparaiso], Universidad de Valparaiso [Chile], Vanderbilt University [Nashville], Jet Propulsion Laboratory, California Institute of Technology (JPL), Centre de Recherche Astrophysique de Lyon (CRAL), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Observatoire de la Côte d'Azur (OCA), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Astrophysical Sciences, Princeton University, Konkoly Observatory, Research Center for Astronomy and Earth Sciences, University of Kiel, Pennsylvania State University, Department of Astronomy & Astrophysics, Institut für Planetologie [Münster], Westfälische Wilhelms-Universität Münster = University of Münster (WWU), San Francisco State University (SFSU), University of Arizona, Yale University [New Haven], Lehigh University [Bethlehem], Université de Bordeaux (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Universität zu Köln = University of Cologne, Queen Mary University of London (QMUL), Georgia State University, Atlanta, Georgia State University, University System of Georgia (USG)-University System of Georgia (USG), University of Leeds, University of Tübingen, University of Oxford, Swarthmore College, University of Kent, Sterrewacht Leiden, Universiteit Leiden, Joint Institute for VLBI ERIC, Dwingeloo (JIVE), European Southern Observatory [Santiago] (ESO), Instituto de Astrofisica de Canarias (IAC), University of Cantabria, Santander, University of Madrid, The University of Texas at San Antonio (UTSA), Kyoto Sangyo University, Max Planck Institute for Astronomy (MPIA), University of Liege, Liege, Belgium, Observatoire de Paris, Université Paris sciences et lettres (PSL), Lowell Observatory [Flagstaff], JILA, NIST, and Department of Physics, University of Colorado, Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Institut de Planétologie et d'Astrophysique de Grenoble (IPAG ), Observatoire des Sciences de l'Univers de Grenoble (OSUG), Université Joseph Fourier - Grenoble 1 (UJF)-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 Joseph Fourier - Grenoble 1 (UJF)-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)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS), Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM), Institut de Mathématiques de Toulouse UMR5219 (IMT), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées (INSA), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Université Libre de Bruxelles [Bruxelles] (ULB), Aix Marseille Université (AMU)-Collège de France (CdF)-Centre National de la Recherche Scientifique (CNRS), Université Côte d'Azur (UCA), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de la Côte d'Azur, Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Institute of Ceramics and Glass-Friedrich Alexander University [Erlangen-Nürnberg], Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), 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), École Supérieure Polytechnique - Université Cheikh Anta DIOP de Dakar (ESP - UCAD), Laboratoire d'Astrophysique de Grenoble (LAOG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Samuel Roberts Noble Foundation, Inc., National Optical Astronomical Observatory (NOAO), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Université Nice Sophia Antipolis (1965 - 2019) (UNS), Friedrich-Alexander Universität Erlangen-Nürnberg (FAU)-Institute of Ceramics and Glass, Pontifícia Universidade Católica do Paraná (PUCPR), Université Jean Monnet - Saint-Étienne (UJM)-Ecole d'ingenieurs Telecom Saint Etienne-Université Jean Monnet - Saint-Étienne (UJM)-Ecole d'ingenieurs Telecom Saint Etienne, Universidad de Concepción - University of Concepcion [Chile], Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA), COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de la Côte d'Azur, Université Côte d'Azur (UCA)-COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Université Fédérale Toulouse Midi-Pyrénées-Centre National d'Études Spatiales [Toulouse] (CNES)-Météo France-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Université Fédérale Toulouse Midi-Pyrénées-Centre National d'Études Spatiales [Toulouse] (CNES)-Météo France-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)

Subjects
Computer science, [SDU.ASTR.EP]Sciences of the Universe [physics]/Astrophysics [astro-ph]/Earth and Planetary Astrophysics [astro-ph.EP], FOS: Physical sciences, 01 natural sciences, Astrobiology, 010309 optics, Planet, extrasolar planets, 0103 physical sciences, planet formation, Instrumentation and Methods for Astrophysics (astro-ph.IM), 010303 astronomy & astrophysics, high angular resolution imaging, Earth and Planetary Astrophysics (astro-ph.EP), protoplanetary disks, Planetary system, interferometry, Exoplanet, 13. Climate action, Hill sphere, Systems architecture, Key (cryptography), Astrophysics::Earth and Planetary Astrophysics, Protoplanet, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Earth and Planetary Astrophysics
Abstract

The Planet Formation Imager (PFI) project aims to provide a strong scientific vision for ground-based optical astronomy beyond the upcoming generation of Extremely Large Telescopes. We make the case that a breakthrough in angular resolution imaging capabilities is required in order to unravel the processes involved in planet formation. PFI will be optimised to provide a complete census of the protoplanet population at all stellocentric radii and over the age range from 0.1 to about 100 Myr. Within this age period, planetary systems undergo dramatic changes and the final architecture of planetary systems is determined. Our goal is to study the planetary birth on the natural spatial scale where the material is assembled, which is the "Hill Sphere" of the forming planet, and to characterise the protoplanetary cores by measuring their masses and physical properties. Our science working group has investigated the observational characteristics of these young protoplanets as well as the migration mechanisms that might alter the system architecture. We simulated the imprints that the planets leave in the disk and study how PFI could revolutionise areas ranging from exoplanet to extragalactic science. In this contribution we outline the key science drivers of PFI and discuss the requirements that will guide the technology choices, the site selection, and potential science/technology tradeoffs., Comment: 13 pages, 5 figures, Proceedings of SPIE 2016

Published
2016
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36. Numerical Solutions of American Options with Dividends Using Finite Difference Methods

Author

Mavinga, Nsoki, Zhang, Chi, and Swarthmore College Summer Research Fellowship

Subjects
Mathematics, Economics, Partial Differential Equations, 91G60, 91G80
Abstract

We study the Black-Scholes model for American options with dividends. We cast the problem as a free-boundary problem for heat equations and use transformations to rewrite the problem in linear complementarity form. We use explicit and implicit finite difference methods to obtain numerical solutions. We implement and test the methods on a particular example in MATLAB. The effects of dividend payments on option pricing are also considered.

Published
2015

37. Detection of 610-MHz radio emission from hot magnetic stars

Author

Jon O. Sundqvist, David H. Cohen, Véronique Petit, Jason Grunhut, Divya Oberoi, Mary E. Oksala, Poonam Chandra, Alexandre David-Uraz, Gregg A. Wade, Asif ud-Doula, Royal Military College of Canada, Department of Physics, Ludwig-Maximilians-Universität München (LMU), European Southern Observatory (ESO), Pennsylvania State University (Penn State), Penn State System, Sources de l'Avance, Swarthmore College, Laboratoire d'études spatiales et d'instrumentation en astrophysique (LESIA), 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 Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Department of Physics and Astronomy, University of Delaware, and University of Delaware [Newark]

Subjects
Astrophysics::High Energy Astrophysical Phenomena, K-type main-sequence star, Astrophysics::Cosmology and Extragalactic Astrophysics, Astrophysics, 01 natural sciences, 0103 physical sciences, Astrophysics::Solar and Stellar Astrophysics, 010303 astronomy & astrophysics, Astrophysics::Galaxy Astrophysics, ComputingMilieux_MISCELLANEOUS, Physics, [PHYS]Physics [physics], Giant Metrewave Radio Telescope, Spiral galaxy, 010308 nuclear & particles physics, Stellar collision, Flare star, Astronomy, Astronomy and Astrophysics, T Tauri star, Stars, 13. Climate action, Space and Planetary Science, Stellar mass loss, Astrophysics::Earth and Planetary Astrophysics, [PHYS.ASTR]Physics [physics]/Astrophysics [astro-ph]
Abstract

We have carried out a study of radio emission from a small sample of magnetic O- and Btype stars using the Giant Metrewave Radio Telescope, with the goal of investigating their magnetospheres at low frequencies. These are the lowest frequency radio measurements ever obtained of hot magnetic stars. The observations were taken at random rotational phases in the 1390 and the 610 MHz bands. Out of the 8 stars, we detect five B-type stars in both the 1390 and the 610 MHz bands. The O-type stars were observed only in the 1390 MHz band, and no detections were obtained. We explain this result as a consequence of free-free absorption by the free-flowing stellar wind exterior to the c losed magnetosphere. We also study the variability of individual stars. One star - HD 1338 80 - exhibits remarkably strong and rapid variability of its low frequency flux density. We discu ss the possibility of this emission being coherent emission as reported for CU Vir by Trigilio et al. (2000).

Published
2015
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38. Guided assembly of tetramolecular G-quadruplexes

Author

Olivier Piétrement, Jean-Louis Mergny, Jean-Pierre Aimé, Daniel Renčiuk, Phong Tran, Hiroshi Sugiyama, Liliya A. Yatsunyk, Delphine Albrecht, Jean-Michel Arbona, Swarthmore College, Université de Reims Champagne-Ardenne (URCA), Institut de biochimie et génétique cellulaires (IBGC), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique de l'ENS Lyon (Phys-ENS), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Centre de physique moléculaire optique et hertzienne (CPMOH), Université Sciences et Technologies - Bordeaux 1 (UB)-Centre National de la Recherche Scientifique (CNRS), Institut Européen de Chimie et Biologie (IECB), Université de Bordeaux (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Lyon (ENS Lyon)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, and Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1

Subjects
Guanine, Macromolecular Substances, Surface Properties, Stacking, Molecular Conformation, General Physics and Astronomy, Nanotechnology, 010402 general chemistry, G-quadruplex, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, Materials Testing, heterocyclic compounds, General Materials Science, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Chemistry, General Engineering, DNA, 0104 chemical sciences, G-Quadruplexes, Template, Nucleic acid, Chemical stability, Crystallization, Biosensor
Abstract

Nucleic acids are finding applications in nanotechnology as nanomaterials, mechanical devices, templates, and biosensors. G-quadruplex DNA, formed by π-π stacking of guanine (G) quartets, is an attractive alternative to regular B-DNA because of the kinetic and thermodynamic stability of quadruplexes. However, they suffer from a fatal flaw: the rules of recognition, i.e., the formation of a G-quartet in which four identical bases are paired, prevent the controlled assembly between different strands, leading to complex mixtures. In this report, we present the solution to this recognition problem. The proposed design combines two DNA elements: parallel-stranded duplexes and a quadruplex core. Parallel-stranded duplexes direct controlled assembly of the quadruplex core, and their strands present convenient points of attachments for potential modifiers. The exceptional stability of the quadruplex core provides integrity to the entire structure, which could be used as a building block for nucleic acid-based nanomaterials. As a proof of principle for the design's versatility, we assembled quadruplex-based 1D structures and visualized them using atomic force and transmission electron microscopy. Our findings pave the way to broader utilization of G-quadruplex DNA in structural DNA nanomaterials.

Published
2013
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39. DNA quadruplexes for bio- and nanotechnologies

Author

Phong Tran, Amandine Renaud de la Faverie, Jean-Louis Mergny, Aurore Guédin, Nicole M. Smith, Liliya A. Yatsunyk, Anne Bourdoncle, Daniel Renčiuk, Julien Gros, Institut Européen de Chimie et Biologie (IECB), Université de Bordeaux (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Swarthmore College, Acides Nucléiques : Régulations Naturelle et Artificielle (ARNA), Institut de Recherche Interdisciplinaire en Sciences Sociales (IRISSO), Institut National de la Recherche Agronomique (INRA)-Université Paris Dauphine-PSL, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Régulation et dynamique des génomes, and Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
chemistry.chemical_compound, chemistry, Nanotechnology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, DNA, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2011
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40. Discovery of a magnetic field in the O9 sub-giant star HD 57682 by the MiMeS collaboration

Author

Grunhut, J. H., Wade, G. A., Marcolino, W. L. F., Petit, V., Henrichs, H. F., Cohen, D. H., Alecian, E., Bohlender, D., Bouret, J. -C., Kochukhov, O., Neiner, C., St-Louis, N., Townsend, R. H. D., Collaboration, the MiMeS, Department of Physics, Engineering Physics and Astronomy, Queen's University, Department of Physics, Royal Military College of Canada, Laboratoire d'Astrophysique de Marseille (LAM), Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS), Département de Physique, Université de Montréal, Astronomical Institute Anton Pannekoek, University of Amsterdam, Department of Physics and Astronomy, Swarthmore College, Laboratoire d'études spatiales et d'instrumentation en astrophysique (LESIA), 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 Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Pôle Astronomie du LESIA, 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)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, National Research Council of Canada (NRC), Uppsala University, Galaxies, Etoiles, Physique, Instrumentation (GEPI), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Physique stellaire et galactique, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), University of Wisconsin-Madison, and High Energy Astrophys. & Astropart. Phys (API, FNWI)

Subjects
Magnetism, stars: early type, Star (game theory), FOS: Physical sciences, Context (language use), Field strength, Astrophysics, Astrophysics::Cosmology and Extragalactic Astrophysics, stars: individual: HD 57682, 01 natural sciences, Spectral line, outflows, stars: rotation, 0103 physical sciences, stars: magnetic fields, Astrophysics::Solar and Stellar Astrophysics, Absorption (logic), 010303 astronomy & astrophysics, Solar and Stellar Astrophysics (astro-ph.SR), Astrophysics::Galaxy Astrophysics, Physics, 010308 nuclear & particles physics, Astronomy and Astrophysics, Giant star, Astrophysics - Solar and Stellar Astrophysics, Space and Planetary Science, stars: winds, Astrophysics::Earth and Planetary Astrophysics, [PHYS.ASTR]Physics [physics]/Astrophysics [astro-ph], Magnetic dipole
Abstract

We report the detection of a strong, organised magnetic field in the O9IV star HD 57682, using spectropolarimetric observations obtained with ESPaDOnS at the 3.6-m Canada-France-Hawaii Telescope within the context of the Magnetism in Massive Stars (MiMeS) Large Program. From the fitting of our spectra using NLTE model atmospheres we determined that HD 57682 is a $17^{+19}_{-9}$ M$_{\odot}$ star with a radius of $7.0^{+2.4}_{-1.8}$ R$_\odot$, and a relatively low mass-loss rate of $1.4^{+3.1}_{-0.95}\times10^{-9}$ M$_{\odot}$ yr$^{-1}$. The photospheric absorption lines are narrow, and we use the Fourier transform technique to infer $v\sin i=15\pm3$ km s$^{-1}$. This $v\sin i$ implies a maximum rotational period of 31.5 d, a value qualitatively consistent with the observed variability of the optical absorption and emission lines, as well as the Stokes $V$ profiles and longitudinal field. Using a Bayesian analysis of the velocity-resolved Stokes $V$ profiles to infer the magnetic field characteristics, we tentatively derive a dipole field strength of $1680^{+134}_{-356}$ G. The derived field strength and wind characteristics imply a wind that is strongly confined by the magnetic field., Comment: 6 pages, 5 figures. Accepted for publication in MNRAS Letters

Published
2009
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42. Model-Based Inference of Electrode Distance and Neuronal Density from Measured Detection Thresholds in Cochlear Implant Listeners.

Author

Perkel DJ, Giardina CK, Goldwyn JH, and Arenberg JG

Abstract

Purpose: Cochlear implants (CI) are a highly successful neural prosthesis that can restore hearing in individuals with sensorineural hearing loss. However, the extent of hearing restoration varies widely. Two major factors likely contribute to poor performance: (1) the distances between electrodes and surviving spiral ganglion neurons and (2) the density of those neurons. Reprogramming the CI at a poor electrode-neuron interface, using focused tripolar stimulation or remapping the electrodes, would benefit from understanding the cause of the poor interface., Methods: We used a cochlear model with simplified geometry and neuronal composition to investigate how the interface affects stimulation thresholds. We then inverted the model to infer electrode distance and neuronal density from monopolar and tripolar threshold values obtained behaviorally. We validated this inverted model for known scenarios of electrode distance and neuronal density. Finally, we assessed the model using data from 18 CI users whose electrode distances were measured from CT imaging., Results: The inverted model accurately inferred electrode distance and neuronal density for known scenarios. It also reliably reproduced behavioral monopolar and tripolar threshold profiles for CI users, with mean prediction errors within 1 dB for 17/18 subjects. Fits of electrode distance were more variable; accuracy depended on the assumed value of temporal bone resistivity. Twelve subjects had minimum distance error (0.31 mm) using low resistivity (70 Ω-cm) while the others had better fits (0.30 mm) with higher resistivity (250 Ω-cm)., Conclusion: This inverted model shows promise as a simple, practical tool to better assess and understand the electrode-neuron interface., Competing Interests: Declarations. Competing Interests: The authors declare no competing interests., (© 2025. The Author(s) under exclusive licence to Association for Research in Otolaryngology.)

Published
2025
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43. The Anlagen of Evo-devo in Fritz Müller's FürDarwin (1864).

Author

Gilbert SF and Steinert B

Abstract

FüR DARWIN: written in the early 1860s by the German zoologist and Darwinist Fritz Müller, articulates many of the concepts foundational to the contemporary field of evolutionary developmental biology, or evo-devo. Working on the Brazilian coast offered him refuge from both religious conservatism and the "great market" of Prussian academic science. Here, Müller studied the developmental stages of crustacea and used these meticulous observations to critique the extant literature on classification. In so doing, he both provided evidence for Darwin's theory, and extended it to larval forms. In this essay, we situate Für Darwin, published in English as Facts and Arguments for Darwin in 1869, within the landscape of nineteenth century biology. We propose that Für Darwin is a remarkably prophetic text in the history of developmental biology given its sharp insight into the relationship between development and evolution (ontogeny and phylogeny), its many contributions to crustacean biology, and Müller's deep appreciation of the danger of scientific dogma., (Copyright © 2025. Published by Elsevier Inc.)

Published
2025
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44. Validation of non-invasive methods for the measurement of gonadal and inter-renal steroid hormones in a desert-adapted amphibian ( Scaphiopus couchii ).

Author

Baugh AT, Cho C, Onyango-Opiyo A, Rodner SA, Mieth S, Oakes D, and Halstead L

Abstract

For aquatic and semi-aquatic vertebrates like amphibians, it is possible to estimate excreted hormone levels using non-invasive methods such as waterborne and salivary sampling. These techniques allow monitoring of endocrine activity over varying, repeated and simultaneous integration periods while minimizing handling-related stress that can 'contaminate' hormone estimates, including estimates of baseline glucocorticoids. Here we have validated the extraction and quantification of three steroid hormones (corticosterone, CORT; 17-b estradiol, E 2 ; testosterone, TST) in Couch's spadefoots ( Scaphiopus couchii )-a desert-adapted anuran of special interest for physiology, evolution and conservation-using non-invasive waterborne and minimally invasive salivary hormone methods. We combined extraction and enzyme immunoassay methods to conduct conventional technical validations of parallelism, recovery and time-course. Next, we carried out biological validations by testing the correlation between excreted and circulating concentrations and conducting pharmacological challenges. We found that all three hormones can be precisely estimated from 60-min water baths, exhibit robust parallelism, and have high recoveries. Further, we demonstrated that secretory responses to pharmacological challenges can be detected in waterborne CORT in male and female frogs; in TST and E 2 in male frogs, but not consistently for TST or E 2 in female frogs. Lastly, plasma hormone concentrations were consistently correlated with their waterborne complements for CORT (both sexes), as well as TST and E 2 in males (but not females). Plasma CORT was also positively correlated with salivary CORT. Together, our findings suggest that sampling waterborne and salivary hormones offers a minimally invasive method that field endocrinologists and conservation physiologists can use to obtain biologically informative endocrine estimates from desert-adapted amphibians., Competing Interests: We have no conflicts of interest to declare., (© The Author(s) 2025. Published by Oxford University Press and the Society for Experimental Biology.)

Published
2025
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45. Regeneration in planarians modifies behavioral switching.

Author

Tellakula NS, Collins ES, and Kristan WB Jr

Abstract

The planarian Dugesia japonica responds differently to localized stimuli: anterior regions turn, middle regions elongate, and posterior regions contract. If cut into several pieces, each piece immediately produces the same three responses. Over several days, each piece regenerates all transected body parts. This study tested how the pieces coordinate behavioral responses during regeneration. We first determined the locations of the turning/elongation and elongation/contraction behavioral switches. Immediately, all transections moved both switching sites away from the cut sites so that the worm pieces produced the same three responses as intact worms. During regeneration, the sites of behavioral switching moved progressively closer to the transection (now regeneration) sites. These results show that the immediate effects of transection (likely physiological) are coordinated with the addition of regenerating tissue (anatomical) to maintain as normal an animal as possible. Other animals that regenerate body parts, such as amphibians and reptiles, may use similar coordination mechanisms., Competing Interests: The authors declare no competing interests., (© 2025 The Authors. Published by Elsevier Inc.)

Published
2025
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46. Large Bias in Matching Small Horizontal and Vertical Extents Separated in Depth in the Real World Is Similar for Upright and Supine Observers.

Author

Durgin FH, Kwok CS, Becker KM, and Phyu YM

Abstract

The apparent sizes of horizontal and vertical lines show an anisotropy known as the horizontal vertical illusion (HVI) wherein vertical lines appear to be longer than their horizontal counterparts. Whereas a typical HVI comparing vertical and horizontal lines in a plane produces a 5-10% illusion, a much larger-scale illusion (15-25%) is often found for large objects in the real world, and this has been related to differential angular exaggerations in perceived elevation (vertical) and azimuthal (horizontal) direction. Recently supine observers in virtual environments were found to show larger exaggerations in perceived azimuth than upright observers. Here, 48 participants were tested in both supine and upright postures in an outdoor environment while matching fairly small physical extents in the real world. They adjusted the magnitude of the horizontal extent to perceptually match fairly small vertical poles (0.7-1.3 m tall) that were either presented at the same viewing distance as the matching extent or in a different depth plane, so that size at a distance had to be compared. Supine observers viewed the scene, as though upright, through a large mirror mounted overhead at 45° that was adjusted to approximate their normal eye height. When the matcher extent was at a different distance than the pole, horizontal extent matches typically exceeded the actual pole height by about 15% or more, whether the viewer was upright or supine. The average overestimation was only about 10% when the matching extent was at the same distance. Despite the similarity in performance across different postures for spatial matching, supine observers gave much higher explicit estimates of azimuthal direction than upright observers. However, although the observation of exaggeration in perceived azimuth for supine observers was replicated in a second study with 24 additional participants using a mirror with a smaller (more normal) aspect ratio, the magnitude of the exaggeration seemed to be greatly reduced when the field of view of the apparatus had a more typical aspect ratio. This suggests that the unusually large exaggeration of azimuth found in a previous report with supine observers may have been caused by the unusually large aspect ratio of the viewing apparatus used.

Published
2025
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47. Conformation and Membrane Topology of the N-Terminal Ectodomain of Influenza A M2 Protein.

Author

Roeke KC and Howard KP

Abstract

The N-terminal ectodomain of the influenza A M2 protein is a target for universal influenza vaccine development and novel antiviral strategies. Despite the significance of this domain, it is poorly understood and most structural studies of the M2 protein have disregarded the N-terminal ectodomain in their analyses. Here, we report conformational properties and describe insights into the membrane topology of sites along the N-terminal ectodomain. Full-length M2 protein is embedded in lipid bilayer nanodiscs and studied using site-directed spin labeling electron paramagnetic resonance spectroscopy. Results are consistent with a turn in the middle of the ectodomain that changes in proximity to the membrane surface upon the addition of cholesterol or the antiviral drug rimantadine. Similarly to other domains of M2 protein, lineshape analysis suggests that the N-terminal ectodomain can adopt multiple conformations.

Published
2025
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48. The RNA chaperone protein ProQ is a pleiotropic regulator in enteropathogenic Escherichia coli.

Author

Mihaita A, Robinson A, Costello E, Marino M, Mrozek Z, Long L, Fogarty A, Egan M, and Bhatt S

Subjects
Virulence genetics, Molecular Chaperones genetics, Molecular Chaperones metabolism, Phosphoproteins metabolism, Phosphoproteins genetics, Genomic Islands genetics, Escherichia coli Infections microbiology, Humans, Biofilms growth & development, Gene Deletion, RNA-Binding Proteins metabolism, RNA-Binding Proteins genetics, Operon, Enteropathogenic Escherichia coli genetics, Enteropathogenic Escherichia coli metabolism, Gene Expression Regulation, Bacterial, Escherichia coli Proteins genetics, Escherichia coli Proteins metabolism, Trans-Activators genetics, Trans-Activators metabolism
Abstract

Enteropathogenic Escherichia coli (EPEC) is a gastrointestinal pathogen that affects individuals of all age groups, with infections ranging from subclinical colonization to acute or persistent diarrhea. The bacterium's ability to cause diarrhea depends on the locus of enterocyte effacement (LEE) pathogenicity island. Although regulation of the LEE has been systematically characterized, until the last decade, studies mainly focused on its transcriptional control. Posttranscriptional regulation of the LEE continues to be an underappreciated and understudied area of gene regulation. In the past few years, multiple reports have shed light on the roles of RNA-binding proteins, such as Hfq and CsrA, that modulate virulence in EPEC. This study was undertaken to explore the role of another RNA chaperone protein, ProQ, in the pathophysiology of EPEC. Our results suggest that deletion of proQ globally derepresses gene expression from the LEE in lysogeny broth (LB) suggesting that ProQ is a negative regulator of the LEE. Further interrogation revealed that ProQ exerts its effect by downregulating the expression of PerC - a prominent transcriptional activator of the LEE-encoded master regulator ler, which, in turn leads to the observed repression from the other LEE operons. Furthermore, ProQ appears to moonlight as it affects other physiological processes including type IV pili biogenesis, flagellar-dependent motility, biofilm formation, tryptophan metabolism, and antibiotic resistance. Our study provides the very first evidence to implicate ProQ as a pleiotropic regulator in EPEC., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier Ltd.)

Published
2025
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49. Ischemia/Reperfusion Injury Enhances Accumulation of Perfluoropropane Droplets.

Author

Chen C, Li S, Matsunaga TO, Pacella JJ, Everbach EC, Xie F, Porter TR, Villanueva FS, and Chen X

Subjects
Animals, Rats, Male, Contrast Media pharmacokinetics, Rats, Sprague-Dawley, Disease Models, Animal, Microbubbles, Ultrasonography methods, Fluorocarbons pharmacokinetics, Reperfusion Injury diagnostic imaging
Abstract

Objective: Perfluoropropane droplets (PD) are nanometer-sized particles that can be formulated from commercially available contrast agents. The preferential retention of PDs in diseased microvascular beds can be detected by ultrasound imaging techniques after acoustic activation and offers an opportunity for the detection of such processes as scar formation or inflammation. We hypothesized that in the presence of ischemia/reperfusion (I/R) injury, retention of intravenously injected PDs would be enhanced., Methods: Using an established intravital microscopy model of rat cremaster microcirculation, we determined the retention and subsequent acoustic activation behavior of PDs in exteriorized rat cremaster tissue. DiI-labeled droplets (200 µL) were administered intravenously. Acoustic activation was achieved with a clinical ultrasound system at two ultrasound frequencies (1.5 and 7 MHz)., Results: Fluorescent microbubbles could be detected in the microvasculature after intravenous injection of PDs and subsequent acoustic activation. Increased retention of PDs was observed in the I/R group compared with control group with both ultrasound frequencies (p < 0.05). Using higher-resolution microscopy, we found evidence that some droplets extravasate to the outside of the endothelial border or are potentially engulfed by leukocytes., Conclusion: Our data indicate that targeted imaging of the developing scar zones might be possible with ultrasound activation of intravenously injected PDs, and a method of targeting therapies to these same regions could be developed., Competing Interests: Conflict of interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this manuscript., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Published
2025
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50. Distinguishing classes of neuroactive drugs based on computational physicochemical properties and experimental phenotypic profiling in planarians.

Author

Ireland D, Rabeler C, Rao S, Richardson RJ, and Collins ES

Subjects
Animals, Drug Discovery methods, High-Throughput Screening Assays methods, Phenotype, Cheminformatics methods, Behavior, Animal drug effects, Machine Learning, Planarians drug effects, Planarians physiology
Abstract

Mental illnesses put a tremendous burden on afflicted individuals and society. Identification of novel drugs to treat such conditions is intrinsically challenging due to the complexity of neuropsychiatric diseases and the need for a systems-level understanding that goes beyond single molecule-target interactions. Thus far, drug discovery approaches focused on target-based in silico or in vitro high-throughput screening (HTS) have had limited success because they cannot capture pathway interactions or predict how a compound will affect the whole organism. Organismal behavioral testing is needed to fill the gap, but mammalian studies are too time-consuming and cost-prohibitive for the early stages of drug discovery. Behavioral medium-throughput screening (MTS) in small organisms promises to address this need and complement in silico and in vitro HTS to improve the discovery of novel neuroactive compounds. Here, we used cheminformatics and MTS in the freshwater planarian Dugesia japonica-an invertebrate system used for neurotoxicant testing-to evaluate the extent to which complementary insight could be gained from the two data streams. In this pilot study, our goal was to classify 19 neuroactive compounds into their functional categories: antipsychotics, anxiolytics, and antidepressants. Drug classification was performed with the same computational methods, using either physicochemical descriptors or planarian behavioral profiling. As it was not obvious a priori which classification method was most suited to this task, we compared the performance of four classification approaches. We used principal coordinate analysis or uniform manifold approximation and projection, each coupled with linear discriminant analysis, and two types of machine learning models-artificial neural net ensembles and support vector machines. Classification based on physicochemical properties had comparable accuracy to classification based on planarian profiling, especially with the machine learning models that all had accuracies of 90-100%. Planarian behavioral MTS correctly identified drugs with multiple therapeutic uses, thus yielding additional information compared to cheminformatics. Given that planarian behavioral MTS is an inexpensive true 3R (refine, reduce, replace) alternative to vertebrate testing and requires zero a priori knowledge about a chemical, it is a promising experimental system to complement in silico cheminformatics to identify new drug candidates., Competing Interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: E-MC is the founder of Inveritek, LLC, which offers planarian HTS commercially. RJR currently serves as a member of the advisory board of NeuroX1, a startup biotechnology company that is developing a software platform for the discovery and development of drugs for neurodegenerative diseases. The remaining authors declare no conflict of interest. This does not alter our adherence to PLOS ONE policies on sharing data and materials., (Copyright: © 2025 Ireland 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
2025
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