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  • 1
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    Balls, cups, and quasi‐potentials: quantifying stability in stochastic systems (2015)
    Wiley
    In: Ecology
    Details
    Publication Date: 2015
    Description: Abstract When a system has more than one stable state, how can the stability of these states be compared? This deceptively simple question has important consequences for ecosystems, because systems with alternative stable states can undergo dramatic regime shifts. The probability, frequency, duration, and dynamics of these shifts will all depend on the relative stability of the stable states. Unfortunately, the concept of stability” in ecology has suffered from substantial confusion and this is particularly problematic for systems where stochastic perturbations can cause shifts between coexisting alternative stable states. A useful way to visualize stable states in stochastic systems is with a ball‐in‐cup diagram, in which the state of the system is represented as the position of a ball rolling on a surface, and the random perturbations can push the ball from one basin of attraction to another. The surface is determined by a potential function, which provides a natural stability metric. However, systems amenable to this representation, called gradient systems, are quite rare. As a result, the potential function is not widely used and other approaches based on linear stability analysis have become standard. Linear stability analysis is designed for local analysis of deterministic systems and, as we show, can produce a highly misleading picture of how the system will behave under continual, stochastic perturbations. In this paper, we show how the potential function can be generalized so that it can be applied broadly, employing a concept from stochastic analysis called the quasi‐potential. Using three classic ecological models, we demonstrate that the quasi‐potential provides a useful way to quantify stability in stochastic systems. We show that the quasi‐potential framework helps clarify long‐standing confusion about stability in stochastic ecological systems, and we argue that ecologists should adopt it as a practical tool for analyzing these systems. This article is protected by copyright. All rights reserved.
    Print ISSN: 0012-9658
    Electronic ISSN: 1939-9170
    Topics: Biology
    Published by Wiley on behalf of The Ecological Society of America (ESA).
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  • 2
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    Balls, cups, and quasi-potentials: quantifying stability in stochastic systems (2016)
    Wiley
    In: Ecology
    Details
    Publication Date: 2016-02-23
    Description: When a system has more than one stable state, how can the stability of these states be compared? This deceptively simple question has important consequences for ecosystems, because systems with alternative stable states can undergo dramatic regime shifts. The probability, frequency, duration, and dynamics of these shifts will all depend on the relative stability of the stable states. Unfortunately, the concept of stability” in ecology has suffered from substantial confusion and this is particularly problematic for systems where stochastic perturbations can cause shifts between coexisting alternative stable states. A useful way to visualize stable states in stochastic systems is with a ball-in-cup diagram, in which the state of the system is represented as the position of a ball rolling on a surface, and the random perturbations can push the ball from one basin of attraction to another. The surface is determined by a potential function, which provides a natural stability metric. However, systems amenable to this representation, called gradient systems, are quite rare. As a result, the potential function is not widely used and other approaches based on linear stability analysis have become standard. Linear stability analysis is designed for local analysis of deterministic systems and, as we show, can produce a highly misleading picture of how the system will behave under continual, stochastic perturbations. In this paper, we show how the potential function can be generalized so that it can be applied broadly, employing a concept from stochastic analysis called the quasi-potential. Using three classic ecological models, we demonstrate that the quasi-potential provides a useful way to quantify stability in stochastic systems. We show that the quasi-potential framework helps clarify long-standing confusion about stability in stochastic ecological systems, and we argue that ecologists should adopt it as a practical tool for analyzing these systems. This article is protected by copyright. All rights reserved.
    Print ISSN: 0012-9658
    Electronic ISSN: 1939-9170
    Topics: Biology
    Published by Wiley on behalf of The Ecological Society of America (ESA).
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  • 3
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    Surface architecture of endospores of the Bacillus cereus/anthracis/thuringiensis family at the subnanometer scale [Microbiology] (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-09-21
    Description: Bacteria of the Bacillus cereus family form highly resistant spores, which in the case of the pathogen B. anthracis act as the agents of infection. The outermost layer, the exosporium, enveloping spores of the B. cereus family as well as a number of Clostridia, plays roles in spore adhesion, dissemination, targeting, and germination control. We have analyzed two naturally crystalline layers associated with the exosporium, one representing the “basal” layer to which the outermost spore layer (“hairy nap”) is attached, and the other likely representing a subsurface (“parasporal”) layer. We have used electron cryomicroscopy at a resolution of 0.8–0.6 nm and circular dichroism spectroscopic measurements to reveal a highly α-helical structure for both layers. The helices are assembled into 2D arrays of “cups” or “crowns.” High-resolution atomic force microscopy of the outermost layer showed that the open ends of these cups face the external environment and the highly immunogenic collagen-like fibrils of the hairy nap (BclA) are attached to this surface. Based on our findings, we present a molecular model for the spore surface and propose how this surface can act as a semipermeable barrier and a matrix for binding of molecules involved in defense, germination control, and other interactions of the spore with the environment.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 4
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    Dark Energy Survey year 1 results: Cosmological constraints from galaxy clustering and weak lensing (2018)
    American Physical Society (APS)
    Details
    Publication Date: 2018-08-28
    Description: Author(s): T. M. C. Abbott et al. (Dark Energy Survey Collaboration) Analyzing its first year of data, the Dark Energy Survey has demonstrated that weak lensing can probe cosmological parameters with a precision comparable to cosmic microwave background observations. [Phys. Rev. D 98, 043526] Published Mon Aug 27, 2018
    Keywords: Cosmology
    Print ISSN: 0556-2821
    Electronic ISSN: 1089-4918
    Topics: Physics
    Published by American Physical Society (APS)
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  • 5
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    Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-12-15
    Description: Powdery mildews are phytopathogens whose growth and reproduction are entirely dependent on living plant cells. The molecular basis of this life-style, obligate biotrophy, remains unknown. We present the genome analysis of barley powdery mildew, Blumeria graminis f.sp. hordei (Blumeria), as well as a comparison with the analysis of two powdery mildews pathogenic on dicotyledonous plants. These genomes display massive retrotransposon proliferation, genome-size expansion, and gene losses. The missing genes encode enzymes of primary and secondary metabolism, carbohydrate-active enzymes, and transporters, probably reflecting their redundancy in an exclusively biotrophic life-style. Among the 248 candidate effectors of pathogenesis identified in the Blumeria genome, very few (less than 10) define a core set conserved in all three mildews, suggesting that most effectors represent species-specific adaptations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Spanu, Pietro D -- Abbott, James C -- Amselem, Joelle -- Burgis, Timothy A -- Soanes, Darren M -- Stuber, Kurt -- Ver Loren van Themaat, Emiel -- Brown, James K M -- Butcher, Sarah A -- Gurr, Sarah J -- Lebrun, Marc-Henri -- Ridout, Christopher J -- Schulze-Lefert, Paul -- Talbot, Nicholas J -- Ahmadinejad, Nahal -- Ametz, Christian -- Barton, Geraint R -- Benjdia, Mariam -- Bidzinski, Przemyslaw -- Bindschedler, Laurence V -- Both, Maike -- Brewer, Marin T -- Cadle-Davidson, Lance -- Cadle-Davidson, Molly M -- Collemare, Jerome -- Cramer, Rainer -- Frenkel, Omer -- Godfrey, Dale -- Harriman, James -- Hoede, Claire -- King, Brian C -- Klages, Sven -- Kleemann, Jochen -- Knoll, Daniela -- Koti, Prasanna S -- Kreplak, Jonathan -- Lopez-Ruiz, Francisco J -- Lu, Xunli -- Maekawa, Takaki -- Mahanil, Siraprapa -- Micali, Cristina -- Milgroom, Michael G -- Montana, Giovanni -- Noir, Sandra -- O'Connell, Richard J -- Oberhaensli, Simone -- Parlange, Francis -- Pedersen, Carsten -- Quesneville, Hadi -- Reinhardt, Richard -- Rott, Matthias -- Sacristan, Soledad -- Schmidt, Sarah M -- Schon, Moritz -- Skamnioti, Pari -- Sommer, Hans -- Stephens, Amber -- Takahara, Hiroyuki -- Thordal-Christensen, Hans -- Vigouroux, Marielle -- Wessling, Ralf -- Wicker, Thomas -- Panstruga, Ralph -- BB/E0009831/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/E002803/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/H001948/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2010 Dec 10;330(6010):1543-6. doi: 10.1126/science.1194573.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Life Sciences, Imperial College London, London, UK. p.spanu@imperial.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21148392" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Ascomycota/*genetics/growth & development/metabolism/pathogenicity ; Carbohydrate Metabolism ; Carrier Proteins/genetics/metabolism ; Enzymes/genetics/metabolism ; Evolution, Molecular ; Fungal Proteins/chemistry/genetics/metabolism ; *Gene Deletion ; *Genes, Fungal ; *Genome, Fungal ; Hordeum/*microbiology ; Host-Pathogen Interactions/genetics ; Metabolic Networks and Pathways/genetics ; Molecular Sequence Annotation ; Plant Diseases/*microbiology ; Retroelements ; Sequence Analysis, DNA ; Species Specificity
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    Supramolecular assembly of amelogenin nanospheres into birefringent microribbons (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-03-05
    Description: Although both tooth enamel and bone are composed of organized assemblies of carbonated apatite crystals, enamel is unusual in that it does not contain collagen nor does it remodel. Self-assembly of amelogenin protein into nanospheres has been recognized as a key factor in controlling the oriented and elongated growth of carbonated apatite crystals during dental enamel biomineralization. We report the in vitro formation of birefringent microribbon structures that were generated through the supramolecular assembly of amelogenin nanospheres. These microribbons have diffraction patterns that indicate a periodic structure of crystalline units along the long axis. The growth of apatite crystals orientated along the c axis and parallel to the long axes of the microribbons was observed in vitro. The linear arrays (chains) of nanospheres observed as intermediate states before the microribbon formation give an important indication as to the function of amelogenin in controlling the oriented growth of apatite crystals during enamel mineralization.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Du, Chang -- Falini, Giuseppe -- Fermani, Simona -- Abbott, Christopher -- Moradian-Oldak, Janet -- R01 DE013414/DE/NIDCR NIH HHS/ -- R01-DE-13414/DE/NIDCR NIH HHS/ -- R21-DE-15332/DE/NIDCR NIH HHS/ -- New York, N.Y. -- Science. 2005 Mar 4;307(5714):1450-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Craniofacial Molecular Biology, School of Dentistry, University of Southern California, 2250 Alcazar Street, CSA 103, Los Angeles, CA 90033, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15746422" target="_blank"〉PubMed〈/a〉
    Keywords: *Amelogenesis ; Amelogenin ; Animals ; Birefringence ; Crystallization ; Dental Enamel Proteins/*chemistry/metabolism ; Durapatite/chemistry ; Hydrophobic and Hydrophilic Interactions ; Microscopy, Atomic Force ; Microscopy, Electron ; *Nanotubes ; Phosvitin ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry ; Swine ; X-Ray Diffraction
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 7
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    Inactivation of TNF signaling by rationally designed dominant-negative TNF variants (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-09-27
    Description: Tumor necrosis factor (TNF) is a key regulator of inflammatory responses and has been implicated in many pathological conditions. We used structure-based design to engineer variant TNF proteins that rapidly form heterotrimers with native TNF to give complexes that neither bind to nor stimulate signaling through TNF receptors. Thus, TNF is inactivated by sequestration. Dominant-negative TNFs represent a possible approach to anti-inflammatory biotherapeutics, and experiments in animal models show that the strategy can attenuate TNF-mediated pathology. Similar rational design could be used to engineer inhibitors of additional TNF superfamily cytokines as well as other multimeric ligands.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Steed, Paul M -- Tansey, Malu G -- Zalevsky, Jonathan -- Zhukovsky, Eugene A -- Desjarlais, John R -- Szymkowski, David E -- Abbott, Christina -- Carmichael, David -- Chan, Cheryl -- Cherry, Lisa -- Cheung, Peter -- Chirino, Arthur J -- Chung, Hyo H -- Doberstein, Stephen K -- Eivazi, Araz -- Filikov, Anton V -- Gao, Sarah X -- Hubert, Rene S -- Hwang, Marian -- Hyun, Linus -- Kashi, Sandhya -- Kim, Alice -- Kim, Esther -- Kung, James -- Martinez, Sabrina P -- Muchhal, Umesh S -- Nguyen, Duc-Hanh T -- O'Brien, Christopher -- O'Keefe, Donald -- Singer, Karen -- Vafa, Omid -- Vielmetter, Jost -- Yoder, Sean C -- Dahiyat, Bassil I -- New York, N.Y. -- Science. 2003 Sep 26;301(5641):1895-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Xencor, 111 West Lemon Avenue, Monrovia, CA 91016, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14512626" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Animals ; Antigens, CD/metabolism ; Apoptosis ; Arthritis, Experimental/drug therapy ; Biopolymers ; Caspases/metabolism ; Cell Line ; Cell Nucleus/metabolism ; Computer Simulation ; Disease Progression ; Enzyme-Linked Immunosorbent Assay ; Female ; Galactosamine/pharmacology ; HeLa Cells ; Humans ; Liver/drug effects ; NF-kappa B/metabolism ; Point Mutation ; *Protein Engineering ; Rats ; Receptors, Tumor Necrosis Factor/metabolism ; Receptors, Tumor Necrosis Factor, Type I ; Receptors, Tumor Necrosis Factor, Type II ; *Signal Transduction ; Transcription Factor RelA ; Transcription, Genetic ; Tumor Necrosis Factor-alpha/*antagonists & ; inhibitors/genetics/metabolism/*pharmacology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 8
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    Massless Lüscher terms and the limitations of the AdS_{3} asymptotic Bethe ansatz (2016)
    American Physical Society (APS)
    Details
    Publication Date: 2016-05-26
    Description: Author(s): Michael C. Abbott and Inês Aniceto Within the AdS/CFT framework, string theory in “integrable” curved backgrounds may also be described by Bethe ansatz equations. By carefully accounting for the “wrapping” corrections, the authors show that, in the case of a certain background ( A d S 3 × S 3 × T 4 ), Bethe ansatz description can match the string theory calculations. [Phys. Rev. D 93, 106006] Published Wed May 25, 2016
    Keywords: String Theory
    Print ISSN: 0556-2821
    Electronic ISSN: 1089-4918
    Topics: Physics
    Published by American Physical Society (APS)
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  • 9
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    Balls, cups, and quasi-potentials: quantifying stability in stochastic systems (2016)
    Wiley
    In: Ecology
    Details
    Publication Date: 2016-04-09
    Description: When a system has more than one stable state, how can the stability of these states be compared? This deceptively simple question has important consequences for ecosystems, because systems with alternative stable states can undergo dramatic regime shifts. The probability, frequency, duration, and dynamics of these shifts will all depend on the relative stability of the stable states. Unfortunately, the concept of “stability” in ecology has suffered from substantial confusion and this is particularly problematic for systems where stochastic perturbations can cause shifts between coexisting alternative stable states. A useful way to visualize stable states in stochastic systems is with a ball-in-cup-diagram, in which the state of the system is represented as the position of a ball rolling on a surface, and the random perturbations can push the ball from one basin of attraction to another. The surface is determined by a potential function, which provides a natural stability metric. Systems amenable to this representation, called gradient systems, are quite rare, however. As a result, the potential function is not widely used and other approaches based on linear stability analysis have become standard. Linear stability analysis is designed for local analysis of deterministic systems and, as we show, can produce a highly misleading picture of how the system will behave under continual, stochastic perturbations. In this paper, we show how the potential function can be generalized so that it can be applied broadly, employing a concept from stochastic analysis called the quasi-potential. Using three classic ecological models, we demonstrate that the quasi-potential provides a useful way to quantify stability in stochastic systems. We show that the quasi-potential framework helps clarify long-standing confusion about stability in stochastic ecological systems, and we argue that ecologists should adopt it as a practical tool for analyzing these systems.
    Print ISSN: 0012-9658
    Electronic ISSN: 1939-9170
    Topics: Biology
    Published by Wiley on behalf of The Ecological Society of America (ESA).
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  • 10
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    Quantum centrality testing on directed graphs via $PT$-symmetric quantum walks (2017)
    American Physical Society (APS)
    Details
    Publication Date: 2017-09-06
    Description: Author(s): J. A. Izaac, J. B. Wang, P. C. Abbott, and X. S. Ma Various quantum-walk-based algorithms have been proposed to analyze and rank the centrality of graph vertices. However, issues arise when working with directed graphs: the resulting non-Hermitian Hamiltonian leads to nonunitary dynamics, and the total probability of the quantum walker is no longer c... [Phys. Rev. A 96, 032305] Published Tue Sep 05, 2017
    Keywords: Quantum information
    Print ISSN: 1050-2947
    Electronic ISSN: 1094-1622
    Topics: Physics
    Published by American Physical Society (APS)
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