Results for 'Histone code'

975 found
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  1.  34
    Is the “Histone Code” an Organic Code?Stefan Kühn & Jan-Hendrik S. Hofmeyr - 2014 - Biosemiotics 7 (2):203-222.
    Post-translational histone modifications and their biological effects have been described as a ‘histone code’. Independently, Barbieri used the term ‘organic code’ to describe biological codes in addition to the genetic code. He also provided the defining criteria for an organic code, but to date the histone code has not been tested against these criteria. This paper therefore investigates whether the histone code is a bona fide organic code. After introducing (...)
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  2.  18
    Nutrient Sensing by Histone Marks: Reading the Metabolic Histone Code Using Tracing, Omics, and Modeling.Scott E. Campit, Alia Meliki, Neil A. Youngson & Sriram Chandrasekaran - 2020 - Bioessays 42 (9):2000083.
    Several metabolites serve as substrates for histone modifications and communicate changes in the metabolic environment to the epigenome. Technologies such as metabolomics and proteomics have allowed us to reconstruct the interactions between metabolic pathways and histones. These technologies have shed light on how nutrient availability can have a dramatic effect on various histone modifications. This metabolism–epigenome cross talk plays a fundamental role in development, immune function, and diseases like cancer. Yet, major challenges remain in understanding the interactions between (...)
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  3.  48
    Do protein motifs read the histone code?Xavier de la Cruz, Sergio Lois, Sara Sánchez-Molina & Marian A. Martínez-Balbás - 2005 - Bioessays 27 (2):164-175.
  4.  49
    Histone acetylation and an epigenetic code.Bryan M. Turner - 2000 - Bioessays 22 (9):836-845.
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  5.  12
    Code Biology: A New Science of Life.Marcello Barbieri - 2015 - Cham: Imprint: Springer.
    The genetic code appeared on Earth at the origin of life, and the codes of culture arrived almost four billion years later. For a long time it has been assumed that these are the only codes that exist in Nature, and if that were true we would have to conclude that codes are extraordinary exceptions that appeared only at the beginning and at the end of the history of life. In reality, various other organic codes have been discovered in (...)
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  6.  28
    Combinations of Histone Modifications for Pattern Genes.Xiang-Jun Cui & Chen-Xia Shi - 2016 - Acta Biotheoretica 64 (2):121-132.
    Histone post-translational modifications play important roles in transcriptional regulation. It is known that multiple histone modifications can act in a combinatorial manner. In this study, we investigated the effects of multiple histone modifications on expression levels of five gene categories in coding regions. The combinatorial patterns of modifications for the five gene categories were also studied in the regions. Our results indicated that the differences in the expression levels between any two gene categories were significant. There were (...)
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  7.  89
    Organic codes.Marcello Barbieri - 2002 - Sign Systems Studies 30 (2):743-753.
    Coding characteristics have been discovered not only in protein synthesis, but also in various other natural processes, thus showing that the genetic code is not an isolated case in the organic world. Other examples are the sequence codes, the adhesion code, the signal transduction codes, the splicing codes, the sugar code, the histone code, and probably more. These discoveries however have not had a significant impact because of the widespread belief that organic codes are not (...)
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  8.  16
    “Direct” and “Indirect” Effects of Histone Modifications: Modulation of Sterical Bulk as a Novel Source of Functionality.Wladyslaw A. Krajewski - 2020 - Bioessays 42 (1):1900136.
    The chromatin‐regulatory principles of histone post‐translational modifications (PTMs) are discussed with a focus on the potential alterations in chromatin functional state due to steric and mechanical constraints imposed by bulky histone modifications such as ubiquitin and SUMO. In the classical view, PTMs operate as recruitment platforms for histone “readers,” and as determinants of chromatin array compaction. Alterations of histone charges by “small” chemical modifications (e.g., acetylation, phosphorylation) could regulate nucleosome spontaneous dynamics without globally affecting nucleosome structure. (...)
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  9.  31
    Biological Codes: A Field Guide for Code Hunters.Robert Prinz - 2024 - Biological Theory 19 (2):120-136.
    This article presents an update on known and unknown biological codes. While the genetic code has been recognized as a code for decades, most other codes were hidden in the shadow of this hallmark discovery. It was the dawn of the new millennium when the histone language and code were proclaimed in the years 2000 and 2001, respectively, marking the start of an explosion in the number of published codes across all biological disciplines since then. Actually, (...)
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  10.  25
    Regulation of Gene Expression and Replication Initiation by Non‐Coding Transcription: A Model Based on Reshaping Nucleosome‐Depleted Regions.Julien Soudet & Françoise Stutz - 2019 - Bioessays 41 (11):1900043.
    RNA polymerase II (RNAP II) non‐coding transcription is now known to cover almost the entire eukaryotic genome, a phenomenon referred to as pervasive transcription. As a consequence, regions previously thought to be non‐transcribed are subject to the passage of RNAP II and its associated proteins for histone modification. This is the case for the nucleosome‐depleted regions (NDRs), which provide key sites of entry into the chromatin for proteins required for the initiation of coding gene transcription and DNA replication. In (...)
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  11.  33
    Recorded Versus Organic Memory: Interaction of Two Worlds as Demonstrated by the Chromatin Dynamics.Anton Markoš & Jana Švorcová - 2009 - Biosemiotics 2 (2):131-149.
    The “histone code” conjecture of gene regulation is our point of departure for analyzing the interplay between the (quasi)digital script in nucleic acids and proteins on the one hand and the body on the other, between the recorded and organic memory. We argue that the cell’s ability to encode its states into strings of “characters” dramatically enhances the capacity of encoding its experience (organic memory). Finally, we present our concept of interaction between the natural (bodily) world, and the (...)
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  12.  62
    Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms.John S. Mattick - 2003 - Bioessays 25 (10):930-939.
    The central dogma of biology holds that genetic information normally flows from DNA to RNA to protein. As a consequence it has been generally assumed that genes generally code for proteins, and that proteins fulfil not only most structural and catalytic but also most regulatory functions, in all cells, from microbes to mammals. However, the latter may not be the case in complex organisms. A number of startling observations about the extent of non-protein-coding RNA (ncRNA) transcription in the higher (...)
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  13.  30
    Integrating DNA methylation dynamics into a framework for understanding epigenetic codes.Keith E. Szulwach & Peng Jin - 2014 - Bioessays 36 (1):107-117.
    Genomic function is dictated by a combination of DNA sequence and the molecular mechanisms controlling access to genetic information. Access to DNA can be determined by the interpretation of covalent modifications that influence the packaging of DNA into chromatin, including DNA methylation and histone modifications. These modifications are believed to be forms of “epigenetic codes” that exist in discernable combinations that reflect cellular phenotype. Although DNA methylation is known to play important roles in gene regulation and genomic function, its (...)
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  14.  19
    DNA G‐Quadruplexes (G4s) Modulate Epigenetic (Re)Programming and Chromatin Remodeling.Anna Varizhuk, Ekaterina Isaakova & Galina Pozmogova - 2019 - Bioessays 41 (9):1900091.
    Here, the emerging data on DNA G‐quadruplexes (G4s) as epigenetic modulators are reviewed and integrated. This concept has appeared and evolved substantially in recent years. First, persistent G4s (e.g., those stabilized by exogenous ligands) were linked to the loss of the histone code. More recently, transient G4s (i.e., those formed upon replication or transcription and unfolded rapidly by helicases) were implicated in CpG island methylation maintenance and de novo CpG methylation control. The most recent data indicate that there (...)
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  15.  11
    The interaction between enhancer variants and environmental factors as an overlooked aetiological paradigm in human complex disease.Sarah Robert & Alvaro Rada-Iglesias - 2023 - Bioessays 45 (10):2300038.
    The interactions between genetic and environmental risk factors contribute to the aetiology of complex human diseases. Genome‐wide association studies (GWAS) have revealed that most of the genetic variants associated with complex diseases are located in the non‐coding part of the genome, preferentially within enhancers. Enhancers are distal cis‐regulatory elements composed of clusters of transcription factors binding sites that positively regulate the expression of their target genes. The generation of genome‐wide maps for histone marks (e.g., H3K27ac), chromatin accessibility and transcription (...)
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  16.  26
    A paternal environmental legacy: Evidence for epigenetic inheritance through the male germ line.Adelheid Soubry, Cathrine Hoyo, Randy L. Jirtle & Susan K. Murphy - 2014 - Bioessays 36 (4):359-371.
    Literature on maternal exposures and the risk of epigenetic changes or diseases in the offspring is growing. Paternal contributions are often not considered. However, some animal and epidemiologic studies on various contaminants, nutrition, and lifestyle‐related conditions suggest a paternal influence on the offspring's future health. The phenotypic outcomes may have been attributed to DNA damage or mutations, but increasing evidence shows that the inheritance of environmentally induced functional changes of the genome, and related disorders, are (also) driven by epigenetic components. (...)
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  17.  10
    Broad H3K4me3 domains: Maintaining cellular identity and their implication in super‐enhancer hijacking.Daniel Kent, Letizia Marchetti, Aneta Mikulasova, Lisa J. Russell & Daniel Rico - 2023 - Bioessays 45 (10):2200239.
    The human and mouse genomes are complex from a genomic standpoint. Each cell has the same genomic sequence, yet a wide array of cell types exists due to the presence of a plethora of regulatory elements in the non‐coding genome. Recent advances in epigenomic profiling have uncovered non‐coding gene proximal promoters and distal enhancers of transcription genome‐wide. Extension of promoter‐associated H3K4me3 histone mark across the gene body, known as a broad H3K4me3 domain (H3K4me3‐BD), is a signature of constitutive expression (...)
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  18.  14
    The logic of protein post‐translational modifications (PTMs): Chemistry, mechanisms and evolution of protein regulation through covalent attachments.Marcin J. Suskiewicz - 2024 - Bioessays 46 (3):2300178.
    Protein post‐translational modifications (PTMs) play a crucial role in all cellular functions by regulating protein activity, interactions and half‐life. Despite the enormous diversity of modifications, various PTM systems show parallels in their chemical and catalytic underpinnings. Here, focussing on modifications that involve the addition of new elements to amino‐acid sidechains, I describe historical milestones and fundamental concepts that support the current understanding of PTMs. The historical survey covers selected key research programmes, including the study of protein phosphorylation as a regulatory (...)
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  19.  25
    From correlation to causation: The new frontier of transgenerational epigenetic inheritance.Mohd Hafiz Rothi & Eric Lieberman Greer - 2023 - Bioessays 45 (1):2200118.
    While heredity is predominantly controlled by what deoxyribonucleic acid (DNA) sequences are passed from parents to their offspring, a small but growing number of traits have been shown to be regulated in part by the non‐genetic inheritance of information. Transgenerational epigenetic inheritance is defined as heritable information passed from parents to their offspring without changing the DNA sequence. Work of the past seven decades has transitioned what was previously viewed as rare phenomenology, into well‐established paradigms by which numerous traits can (...)
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  20.  75
    RNA regulation of epigenetic processes.John S. Mattick, Paulo P. Amaral, Marcel E. Dinger, Tim R. Mercer & Mark F. Mehler - 2009 - Bioessays 31 (1):51-59.
    There is increasing evidence that dynamic changes to chromatin, chromosomes and nuclear architecture are regulated by RNA signalling. Although the precise molecular mechanisms are not well understood, they appear to involve the differential recruitment of a hierarchy of generic chromatin modifying complexes and DNA methyltransferases to specific loci by RNAs during differentiation and development. A significant fraction of the genome-wide transcription of non-protein coding RNAs may be involved in this process, comprising a previously hidden layer of intermediary genetic information that (...)
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  21. Lorraine Code.Lorraine Code - 1998 - In Linda Alcoff (ed.), Epistemology: the big questions. Malden, Mass.: Blackwell. pp. 124.
  22. Epistemic responsibility.Lorraine Code - 1987 - Hanover, N.H.: Published for Brown University Press by University Press of New England.
    Having adequate knowledge of the world is not just a matter of survival but also one of obligation. This obligation to "know well" is what philosophers have termed "epistemic responsibility." In this innovative and eclectic study, Lorraine Code explores the possibilities inherent in this concept as a basis for understanding human attempts to know and understand the world and for discerning the nature of intellectual virtue. By focusing on the idea that knowing is a creative process guided by imperatives (...)
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  23.  54
    (1 other version)Feminist Interpretations of Hans-Georg Gadamer.Lorraine Code (ed.) - 2003 - Pennsylvania State University Press.
    Fifteen essays examine the work of German philosopher Hans Georg Gadamer to provide feminist interpretations of his views on science, language, history, ...
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  24. What Can She Know?: Feminist Theory and the Construction of Knowledge.Lorraine Code - 1991 - Ithaca: Cornell University Press.
    In this lively and accessible book Lorraine Code addresses one of the most controversial questions in contemporary theory of knowledge, a question of fundamental concern for feminist theory as well: Is the sex of the knower epistemologically significant? Responding in the affirmative, Code offers a radical alterantive to mainstream philosophy's terms for what counts as knowledge and how it is to be evaluated. Code first reviews the literature of established epistemologies and unmasks the prevailing assumption in Anglo-American (...)
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  25. The perversion of autonomy and the subjection of women: discourses of social advocacy at century's end.Lorraine Code - 2000 - In Catriona Mackenzie & Natalie Stoljar (eds.), Relational Autonomy: Feminist Perspectives on Autonomy, Agency, and the Social Self. New York: Oxford University Press.
  26. Introduction: Why feminists do not read Gadamer.Lorraine Code - 2003 - In Feminist Interpretations of Hans-Georg Gadamer. Pennsylvania State University Press. pp. 1--36.
     
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  27. What Can She Know? Feminist Theory and the Construction of Knowledge.Lorraine Code, Sandra Harding & Susan Hekman - 1993 - Hypatia 8 (3):202-210.
    Feminist epistemologists who attempt to refigure epistemology must wrestle with a number of dualisms. This essay examines the ways Lorraine Code, Sandra Harding, and Susan Hekman reconceptualize the relationship between self/other, nature/culture, and subject/object as they struggle to reformulate objectivity and knowledge.
     
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  28.  57
    Protestant Tradition in Literature.Joseph B. Code - 1938 - Thought: Fordham University Quarterly 13 (1):111-136.
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  29. Credibility: A double standard.Lorraine Code - 1988 - In Christine Overall, Sheila Mullett & Lorraine Code (eds.), Feminist Perspectives: Philosophical Essays on Method and Morals. University of Toronto Press. pp. 64--88.
     
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  30. Toward a 'responsibilist' epistemology.Lorraine Code - 1984 - Philosophy and Phenomenological Research 45 (1):29-50.
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  31. The Power Of Ignorance.Lorraine Code - 2004 - Philosophical Papers 33 (3):291-308.
    Abstract Taking my point of entry from George Eliot's reference to ?the power of Ignorance?, I analyse some manifestations of that power as she portrays it in the life of a young woman of affluence, in her novel Daniel Deronda. Comparing and contrasting this kind of ignorance with James Mill's avowed ignorance of local tradition and custom in his History of British India, I consider how ignorance can foster immoral beliefs which, in turn, contribute to social-political arrangements of dominance and (...)
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  32.  26
    Bodies, Minds, and Souls: On Putting Life Back into Nature.Murray Code - 2006 - Process Studies 35 (2):230-269.
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  33.  20
    Rhetorical Spaces: Essays on Gendered Locations.Lorraine Code - 1995 - Mind 108 (429):157-159.
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  34. Aristotle's response to Quine's objections to modal logic.Alan Code - 1976 - Journal of Philosophical Logic 5 (2):159 - 186.
  35. The Limits of Mathematics.Lisp Source Code - unknown
    In a remarkable development, I have constructed a new definition for a self-delimiting universal Turing machine (UTM) that is easy to program and runs very quickly. This provides a new foundation for algorithmic information theory (AIT), which is the theory of the size in bits of programs for selfdelimiting UTM's. Previously, AIT had an abstract mathematical quality. Now it is possible to write down executable programs that embody the constructions in the proofs of theorems. So AIT goes from dealing with (...)
     
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  36.  16
    Interpreting 'The Raw Universe': Meaning and Metaphysical Imaginaries.Murray Code - 1999 - Transactions of the Charles S. Peirce Society 35 (4):698 - 722.
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  37.  16
    Morality and Conflict Stuart Hampshire Cambridge, MA: Harvard University Press, 1983. Pp. vii, 175. $17.50.Lorraine Code - 1986 - Dialogue 25 (4):773-.
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  38. Nursing analysis.Oaths Codes - 1994 - Health Care Analysis 2:326-335.
     
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  39.  11
    Perestroika in Christendom.Moral Code - 2005 - In Nicholas Capaldi (ed.), Business and religion: a clash of civilizations? Salem, MA: M & M Scrivener Press. pp. 144.
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  40. Virtue, reason and wisdom.Lorraine Code - 2014 - In S. van Hooft, N. Athanassoulis, J. Kawall, J. Oakley & L. van Zyl (eds.), The handbook of virtue ethics. Durham: Acumen Publishing.
     
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  41. Ecological Thinking: The Politics of Epistemic Location.Lorraine Code - 2006 - New York, US: OUP Usa.
    Arguing that ecological thinking can animate an epistemology capable of addressing feminist, multicultural, and other post-colonial concerns, this book critiques the instrumental rationality, hyperbolized autonomy, abstract individualism, and exploitation of people and places that western epistemologies of mastery have legitimated. It proposes a politics of epistemic location, sensitive to the interplay of particularity and diversity, and focused on responsible epistemic practices. Starting from an epistemological approach implicit in Rachel Carson’s scientific projects, the book draws, constructively and critically, on ecological theory (...)
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  42. Rhetorical Spaces: Essays on Gendered Locations.Lorraine Code - 1995 - New York: Routledge.
    The arguments in this book are informed at once by the moral-political implications of how knowledge is produced and circulated and by issues of gendered subjectivity. In their critical dimension, these lucid essays engage with the incapacity of the philosophical mainstream's dominant epistemologies to offer regulative principles that guide people in the epistemic projects that figure centrally in their lives. In its constructive dimension, ____Rhetorical__ ____Spaces__ focuses on developing productive, case-by-case analyses of knowing other people in situations where social-political inequalities (...)
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  43.  26
    Thinking Ecologically, Knowing Responsibly.Lorraine Code - 2020 - Environmental Philosophy 17 (1):19-37.
    This essay extends my engagements with questions of epistemic agency and the politics of epistemic location, in Epistemic Responsibility and in Ecological Thinking to consider how questions of understanding and of certainty play diversely into human and other ecological circumstances. In so doing, it opens lines of inquiry not immediately available in standard western-northern approaches to epistemology with their concentration on medium-sized physical objects in their presupposed neutrality and replicability. Working from a tacit assumption that knowing and knowers are always (...)
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  44.  41
    Women Philosophers: Genre and the Boundaries of Philosophy (review).Lorraine Code - 2005 - Journal of the History of Philosophy 43 (2):215-216.
    In lieu of an abstract, here is a brief excerpt of the content:Reviewed by:Women Philosophers: Genre and the Boundaries of PhilosophyLorraine CodeCatherine Villanueva Gardner. Women Philosophers: Genre and the Boundaries of Philosophy. Boulder, CO: Westview, 2003. Pp. xv + 198. Paper, $22.00.In a tradition which "trains us to read purely for content" (xii), Catherine Gardner wonders how to read the philosophy of five women who write in "non-standard philosophical forms" (xiii): Mechthild of Magdeburg's poetry, Christine de Pisan's allegory, Catharine Macaulay's (...)
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  45. What is it to be an individual?Alan Code - 1978 - Journal of Philosophy 75 (11):647-648.
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  46.  22
    EPISTEMOLOGY: Voice and Voicelessness: A Modest Proposal?Lorraine Code - 1997 - In Janet A. Kourany (ed.), Philosophy in a Feminist Voice: Critiques and Reconstructions. Princeton University Press. pp. 204-230.
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  47. Feminists and pragmatists: A radical future?Lorraine Code - 1998 - Radical Philosophy 87.
     
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  48. Gc I 5.Alan Code - 2004 - In Frans A. J. de Haas & Jaap Mansfeld (eds.), Aristotle On generation and corruption, book 1: Symposium Aristotelicum. New York: Clarendon Press.
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  49.  30
    How Right Was Samuel Butler About Evolution? Part II: Why Evolution is Really a Problem for the Humanities.Murray Code - 2014 - Cosmos and History 10 (2):92-120.
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  50. Patriarchy.Lorraine Code - 2000 - In Encyclopedia of feminist theories. New York: Routledge. pp. 378--379.
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