Results for 'loop extrusion'

424 found
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  1.  1
    Chromatin Architecture in the Fly: Living Without CTCF/Cohesin Loop Extrusion?Nicholas E. Matthews & Rob White - 2019 - Bioessays 41 (9):1900048.
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  2.  6
    Are SMC Complexes Loop Extruding Factors? Linking Theory With Fact.Jonathan Baxter, Antony W. Oliver & Stephanie A. Schalbetter - 2019 - Bioessays 41 (1):1800182.
    The extreme length of chromosomal DNA requires organizing mechanisms to both promote functional genetic interactions and ensure faithful chromosome segregation when cells divide. Microscopy and genome‐wide contact frequency analyses indicate that intra‐chromosomal looping of DNA is a primary pathway of chromosomal organization during all stages of the cell cycle. DNA loop extrusion has emerged as a unifying model for how chromosome loops are formed in cis in different genomic contexts and cell cycle stages. The highly conserved family of (...)
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  3.  20
    Combing Chromosomal DNA Mediated by the SMC Complex: Structure and Mechanisms.Katsuhiko Kamada & Daniela Barillà - 2018 - Bioessays 40 (2):1700166.
    Genome maintenance requires various nucleoid-associated factors in prokaryotes. Among them, the SMC protein has been thought to play a static role in the organization and segregation of the chromosome during cell division. However, recent studies have shown that the bacterial SMC is required to align left and right arms of the emerging chromosome and that the protein dynamically travels from origin to Ter region. A rod form of the SMC complex mediates DNA bridging and has been recognized as a machinery (...)
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  4.  8
    Envoys of a Human God: The Jesuit Mission to Christian Ethiopia, 1557‐1632 . By Andreu Martinez d'Alòs‐Moner. Pp. 419, Leiden/Boston, Brill, 2015, $203.00. [REVIEW]Jan Loop - 2017 - Heythrop Journal 58 (3):459-461.
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  5. Interpretation of Probabilities, 243-244 Big Bang, 82, 101 Block Universe, 112, 114,252 Bohm's Theory, 51-53.I. V. Loop - 2002 - In T. Placek & J. Butterfield (eds.), Non-Locality and Modality. Kluwer Academic Publishers. pp. 343.
     
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  6.  74
    Loop Analysis and Qualitative Modeling: Limitations and Merits. [REVIEW]James Justus - 2006 - Biology and Philosophy 21 (5):647-666.
    Richard Levins has advocated the scientific merits of qualitative modeling throughout his career. He believed an excessive and uncritical focus on emulating the models used by physicists and maximizing quantitative precision was hindering biological theorizing in particular. Greater emphasis on qualitative properties of modeled systems would help counteract this tendency, and Levins subsequently developed one method of qualitative modeling, loop analysis, to study a wide variety of biological phenomena. Qualitative modeling has been criticized for being conceptually and methodologically problematic. (...)
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  7.  65
    Loop Quantum Ontology: Spin-Networks and Spacetime.Joshua Norton - unknown
    The ontological issues at stake given the theory of loop quantum gravity include the status of spacetime, the nature and reality of spin-networks, the relationship of classical spacetime to issues of causation and the status of the abstract-concrete distinction. I this paper I argue that, while spacetime seems to disappear, the spirit of substantival spacetime lives on under certain interpretations of the theory. Moreover, in order for there to be physical spin-networks, and not merely mathematical artifacts, I argue that (...)
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  8.  41
    A Loop-Free Decision Procedure for Modal Propositional Logics K4, S4 and S.Dorota Leszczyńska-Jasion - 2009 - Journal of Philosophical Logic 38 (2):151 - 177.
    The aim of this paper is to present a loop-free decision procedure for modal propositional logics K4, S4 and S5. We prove that the procedure terminates and that it is sound and complete. The procedure is based on the method of Socratic proofs for modal logics, which is grounded in the logic of questions IEL.
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  9.  26
    Quaternion-Loop Quantum Gravity.M. D. Maia, S. S. E. Almeida Silva & F. S. Carvalho - 2009 - Foundations of Physics 39 (11):1273-1279.
    It is shown that the Riemannian curvature of the 3-dimensional hypersurfaces in space-time, described by the Wilson loop integral, can be represented by a quaternion quantum operator induced by the SU(2) gauge potential, thus providing a justification for quaternion quantum gravity at the Tev energy scale.
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  10.  4
    Looping in on Ndc80–How Does a Protein Loop at the Kinetochore Control Chromosome Segregation?Jakob Nilsson - 2012 - Bioessays 34 (12):1070-1077.
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  11.  21
    Hydra Regeneration: Closing the Loop with Mechanical Processes in Morphogenesis.Erez Braun & Kinneret Keren - 2018 - Bioessays 40 (7):1700204.
  12.  36
    Closed-Loop Theory and Long-Term Retention.Jack A. Adams, Philip H. Marshall & Norman W. Bray - 1971 - Journal of Experimental Psychology 90 (2):242-250.
  13. Enaction-Based Artificial Intelligence: Toward Co-Evolution with Humans in the Loop[REVIEW]Pierre De Loor, Kristen Manac’H. & Jacques Tisseau - 2009 - Minds and Machines 19 (3):319-343.
    This article deals with the links between the enaction paradigm and artificial intelligence. Enaction is considered a metaphor for artificial intelligence, as a number of the notions which it deals with are deemed incompatible with the phenomenal field of the virtual. After explaining this stance, we shall review previous works regarding this issue in terms of artificial life and robotics. We shall focus on the lack of recognition of co-evolution at the heart of these approaches. We propose to explicitly integrate (...)
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  14.  4
    Mechanisms of Control in Motor Performance: Closed-Loop Vs Motor Programming Control.Eric A. Roy & Ronald G. Marteniuk - 1974 - Journal of Experimental Psychology 103 (5):985.
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  15. Putting the Trolley in Order: Experimental Philosophy and the Loop Case.S. Matthew Liao, Alex Wiegmann, Joshua Alexander & Gerard Vong - 2012 - Philosophical Psychology 25 (5):661-671.
    In recent years, a number of philosophers have conducted empirical studies that survey people's intuitions about various subject matters in philosophy. Some have found that intuitions vary accordingly to seemingly irrelevant facts: facts about who is considering the hypothetical case, the presence or absence of certain kinds of content, or the context in which the hypothetical case is being considered. Our research applies this experimental philosophical methodology to Judith Jarvis Thomson's famous Loop Case, which she used to call into (...)
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  16.  25
    Loop Quantum Gravity: A New Threat to Humeanism? Part I: The Problem of Spacetime.Vera Matarese - 2019 - Foundations of Physics 49 (3):232-259.
    In this paper, I discuss whether the results of loop quantum gravity constitute a fatal blow to Humeanism. There is at least a prima facie reason for believing so: while Humeanism regards spatiotemporal relations as fundamental, LQG describes the fundamental layer of our reality in terms of spin networks, which are not in spacetime. However, the question should be tackled more carefully. After explaining the importance of the debate on the tenability of Humeanism in light of LQG, and having (...)
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  17. The Loop Case and Kamm’s Doctrine of Triple Effect.S. Matthew Liao - 2009 - Philosophical Studies 146 (2):223-231.
    Judith Jarvis Thomson's Loop Case is particularly significant in normative ethics because it questions the validity of the intuitively plausible Doctrine of Double Effect, according to which there is a significant difference between harm that is intended and harm that is merely foreseen and not intended. Recently, Frances Kamm has argued that what she calls the Doctrine of Triple Effect, which draws a distinction between acting because-of and acting in-order-to, can account for our judgment about the Loop Case. (...)
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  18.  17
    Tutoring in Adult-Child Interaction: On the Loop of the Tutor’s Action Modification and the Recipient’s Gaze. [REVIEW]Karola Pitsch, Anna-Lisa Vollmer, Katharina J. Rohlfing, Jannik Fritsch & Britta Wrede - 2014 - Interaction Studies 15 (1):55-98.
    Research of tutoring in parent-infant interaction has shown that tutors – when presenting some action – modify both their verbal and manual performance for the learner (‘motherese’, ‘motionese’). Investigating the sources and effects of the tutors’ action modifications, we suggest an interactional account of ‘motionese’. Using video-data from a semi-experimental study in which parents taught their 8- to 11-month old infants how to nest a set of differently sized cups, we found that the tutors’ action modifications (in particular: high arches) (...)
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  19. Logic, Self-Awareness and Self-Improvement: The Metacognitive Loop Andthe Problem of Brittleness.Michael Anderson - manuscript
    This essay describes a general approach to building perturbation-tolerant autonomous systems, based on the conviction that artificial agents should be able to notice when something is amiss, assess the anomaly, and guide a solution into place. This basic strategy of self-guided learning is termed the metacognitive loop; it involves the system monitoring, reasoning about, and, when necessary, altering its own decision-making components. This paper (a) argues that equipping agents with a metacognitive loop can help to overcome the brittleness (...)
     
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  20.  22
    Three Kinds of Agency and Closed Loop Neural Devices.Joseph M. Vukov - 2017 - American Journal of Bioethics Neuroscience 8 (2):90-91.
    Goering and colleagues (2017) acknowledge closed-loop neural devices have the potential to undermine agency. Indeed, the authors observe that “the agent using the device may . . . sometimes doubt whether she is the author of her action, given that the device may operate in ways that are not transparent to her” (65). Still, the authors ultimately argue that closed-loop neural devices may be construed as supporting agency, especially when we view agency from a relational perspective. The reason? (...)
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  21.  29
    Allegorical Materialism: Face-Fragments, Affects of Truth and Loop-Politics in Benjamin and Badiou.Marios Constantinou - 2011 - Angelaki 16 (1):63-78.
    This essay stages a dialectical confrontation between Adorno–Horkheimer on one hand and Benjamin–Badiou on the other against the background of the former's reductive portrait of Ulysses in Dialectic of the Enlightenment, which depicts him as a proto-bourgeois archetype of profit-seeking and acquisitive ethos. In sharp contrast, Walter Benjamin's allegorical materialism foregrounds, by dialectical illumination, hieroglyphic traces of Homeric virtues. These, I argue, are sustained and further amplified by Alain Badiou's topological ethics and loop-politics.
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  22. The Metacognitive Loop I: Enhancing Reinforcement Learning with Metacognitive Monitoring and Control for Improved Perturbation Tolerance||.Michael Anderson - manuscript
    Maintaining adequate performance in dynamic and uncertain settings has been a perennial stumbling block for intelligent systems. Nevertheless, any system intended for real-world deployment must be able to accommodate unexpected change—that is, it must be perturbation tolerant. We have found that metacognitive monitoring and control—the ability of a system to self-monitor its own decision-making processes and ongoing performance, and to make targeted changes to its beliefs and action-determining components—can play an important role in helping intelligent systems cope with the perturbations (...)
     
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  23.  53
    The Mood-Emotion Loop.Muk Yan Wong - 2016 - Philosophical Studies 173 (11):3061-3080.
    This paper aims to clarify and reformulate the conceptual relationship between emotions and moods in light of recent researches in philosophy and cognitive psychology. I argue that the mechanism of mood may produces cognitive biases that affect the appraisals involved in emotions, whereas the mechanism of emotion may produce physiological and behavioral responses that affect the energy level being monitored by mood. These two distinct mechanisms can affect each other repeatedly and continuously, which form the mood-emotion loop. I argue (...)
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  24.  69
    The Abductive Loop: Tracking Irrational Sets.Tom Addis, Jan Townsend Addis, Dave Billinge, David Gooding & Bart-Floris Visscher - 2008 - Foundations of Science 13 (1):5-16.
    We argue from the Church-Turing thesis (Kleene Mathematical logic. New York: Wiley 1967) that a program can be considered as equivalent to a formal language similar to predicate calculus where predicates can be taken as functions. We can relate such a calculus to Wittgenstein’s first major work, the Tractatus, and use the Tractatus and its theses as a model of the formal classical definition of a computer program. However, Wittgenstein found flaws in his initial great work and he explored these (...)
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  25.  12
    A Moral Experience Feedback Loop: Modeling a System of Moral Self-Cultivation in Everyday Life.Stephen A. Sherblom - 2015 - Journal of Moral Education 44 (3):364-381.
    This systems thinking model illustrates a common feedback loop by which people engage the moral world and continually reshape their moral sensibility. The model highlights seven processes that collectively form this feedback loop: beginning with one’s current moral sensibility which shapes processes of perception, deliberation, decision-making, embodying action, reflection on self-evaluation and other’s responses, and consolidation into one’s moral sensibility of the lessons learned. Improvements on previous models of moral engagement include recognizing moral sensibility as the grounding for (...)
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  26.  73
    Qualitative Scientific Modeling and Loop Analysis.James Justus - 2004 - Philosophy of Science 72 (5):1272-1286.
    Loop analysis is a method of qualitative modeling anticipated by Sewall Wright and systematically developed by Richard Levins. In Levins’ (1966) distinctions between modeling strategies, loop analysis sacrifices precision for generality and realism. Besides criticizing the clarity of these distinctions, Orzack and Sober (1993) argued qualitative modeling is conceptually and methodologically problematic. Loop analysis of the stability of ecological communities shows this criticism is unjustified. It presupposes an overly narrow view of qualitative modeling and underestimates the broad (...)
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  27.  69
    Towards Closed Loop Information: Predictive Information.B. Porr, A. Egerton & F. Wörgötter - 2006 - Constructivist Foundations 1 (2):83-90.
    Motivation: Classical definitions of information, such as the Shannon information, are designed for open loop systems because they define information on a channel which has an input and an output. The main motivation of this paper is to present a closed loop information measure which is compatible with constructivist thinking. Design: Our information measure for a closed loop system reflects how additional sensor inputs are utilised to establish additional sensor-motor loops during learning. Our information measure is based (...)
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  28.  4
    A Loop-Free Decision Procedure for Modal Propositional Logics K4, S4 and S5.Dorota Leszczyńska-Jasion - 2009 - Journal of Philosophical Logic 38 (2):151-177.
    The aim of this paper is to present a loop-free decision procedure for modal propositional logics K4, S4 and S5. We prove that the procedure terminates and that it is sound and complete. The procedure is based on the method of Socratic proofs for modal logics, which is grounded in the logic of questions IEL.
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  29.  56
    Extended Scale Relativity, P-Loop Harmonic Oscillator, and Logarithmic Corrections to the Black Hole Entropy.Carlos Castro & Alex Granik - 2003 - Foundations of Physics 33 (3):445-466.
    An extended scale relativity theory, actively developed by one of the authors, incorporates Nottale's scale relativity principle where the Planck scale is the minimum impassible invariant scale in Nature, and the use of polyvector-valued coordinates in C-spaces (Clifford manifolds) where all lengths, areas, volumes⋅ are treated on equal footing. We study the generalization of the ordinary point-particle quantum mechanical oscillator to the p-loop (a closed p-brane) case in C-spaces. Its solution exhibits some novel features: an emergence of two explicit (...)
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  30.  8
    Is Knowledge of Physical Reality Still Kantian? Some Remarks About the Transcendental Character of Loop Quantum Gravity.Luigi Laino - 2018 - Foundations of Physics 48 (7):783-802.
    In the following paper, the author will try to test the meaning of the transcendental approach in respect of the inner changes implied by the idea of quantum gravity. He will firstly describe the basic methodological Kant’s aim, viz. the grounding of a meta-science of physics as the a priori corpus of physical knowledge. After that, he will take into account the problematic physical and philosophical relationship between the theory of relativity and the quantum mechanics; in showing how the elementary (...)
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  31.  14
    The Perceptual Loop Theory Not Disconfirmed: A Reply to MacKay.Willem J. M. Levelt - 1992 - Consciousness and Cognition 1 (3):226-230.
    In his paper, MacKay reviews his Node Structure theory of error detection, but precedes it with a critical discussion of the Perceptual Loop theory of self-monitoring proposed in Levelt . The present commentary is concerned with this latter critique and shows that there are more than casual problems with MacKay's argumentation.
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  32.  27
    Quantum General Invariance and Loop Gravity.D. C. Salisbury - 2001 - Foundations of Physics 31 (7):1105-1118.
    A quantum physical projector is proposed for generally covariant theories which are derivable from a Lagrangian. The projector is the quantum analogue of the integral over the generators of finite one-parameter subgroups of the gauge symmetry transformations which are connected to the identity. Gauge variables are retained in this formalism, thus permitting the construction of spacetime area and volume operators in a tentative spacetime loop formulation of quantum general relativity.
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  33.  45
    Triple-Loop Learning as Foundation for Profound Change, Individual Cultivation, and Radical Innovation. Construction Processes Beyond Scientific and Rational Knowledge.Markus F. Peschl - 2007 - Constructivist Foundations 2 (2/3):136-145.
    Purpose: Ernst von Glasersfeld’s question concerning the relationship between scientific/ rational knowledge and the domain of wisdom and how these forms of knowledge come about is the starting point. This article aims at developing an epistemological as well as methodological framework that is capable of explaining how profound change can be brought about in various contexts, such as in individual cultivation, in organizations, in processes of radical innovation, etc. This framework is based on the triple-loop learning strategy and the (...)
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  34.  15
    Interpolation in Loop-Free Logic.Kenneth A. Bowen - 1980 - Studia Logica 39 (2-3):297 - 310.
    Model-theoretic methods are used to extend Craig's Interpolation Theorem to the loop-free portion of Pratt's dynamic logic of programs with simple assignments.
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  35.  21
    Elementary Functions and LOOP Programs.Zlatan Damnjanovic - 1994 - Notre Dame Journal of Formal Logic 35 (4):496-522.
    We study a hierarchy of Kalmàr elementary functions on integers based on a classification of LOOP programs of limited complexity, namely those in which the depth of nestings of LOOP commands does not exceed two. It is proved that -place functions in can be enumerated by a single function in , and that the resulting hierarchy of elementary predicates (i.e., functions with 0,1-values) is proper in that there are predicates that are not in . Along the way the (...)
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  36.  20
    Periodic Solutions of Piecewise Affine Gene Network Models with Non Uniform Decay Rates: The Case of a Negative Feedback Loop.Etienne Farcot & Jean-Luc Gouzé - 2009 - Acta Biotheoretica 57 (4):429-455.
    This paper concerns periodic solutions of a class of equations that model gene regulatory networks. Unlike the vast majority of previous studies, it is not assumed that all decay rates are identical. To handle this more general situation, we rely on monotonicity properties of these systems. Under an alternative assumption, it is shown that a classical fixed point theorem for monotone, concave operators can be applied to these systems. The required assumption is expressed in geometrical terms as an alignment condition (...)
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  37. The Notion of Loop in the Study of Consciousness.Roberto Cordeschi, Guglielmo Tamburrini & Giuseppe Trautteur - 1999 - In Proceedings of the International School of Biocybernetics. World Scientific.
    The notion of loop seems to be ubiquitous in the study of organisms, the human mind and symbolic systems. With the possible exception of quantum-mechanical approaches, the treatments of consciousness we are acquainted with crucially appeal to the concept of loop. The uses of loops in this context fall within two broad classes. In the first one, loops are used to express the control of the organism’s interaction with the environment; in the second one, they are used to (...)
     
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  38. Open-Closed-Loop PD Iterative Learning Control with a Variable Forgetting Factor for a Two-Wheeled Self-Balancing Mobile Robot.Jian Dong, Bin He, Chenghong Zhang & Gang Li - 2019 - Complexity 2019:1-11.
    A novel iterative learning control algorithm for a two-wheeled self-balancing mobile robot with time-varying, nonlinear, and strong-coupling dynamics properties is presented to resolve the trajectory tracking problem in this research. A kinematics model and dynamic model of a two-wheeled self-balancing mobile robot are deduced in this paper, and the combination of an open-closed-loop PD-ILC law and a variable forgetting factor is presented. The open-closed-loop PD-ILC algorithm adopts current and past learning items to drive the state variables and input (...)
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  39.  10
    Staying in the Loop: Relational Agency and Identity in Next-Generation DBS for Psychiatry.Sara Goering, Eran Klein, Darin D. Dougherty & Alik S. Widge - 2017 - American Journal of Bioethics Neuroscience 8 (2):59-70.
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  40.  28
    The Effects of Closed-Loop Medical Devices on the Autonomy and Accountability of Persons and Systems.Philipp Kellmeyer, Thomas Cochrane, Oliver Müller, Christine Mitchell, Tonio Ball, Joseph J. Fins & Nikola Biller-Andorno - 2016 - Cambridge Quarterly of Healthcare Ethics 25 (4):623-633.
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  41.  6
    The Effects of Closed-Loop Brain Implants on Autonomy and Deliberation: What Are the Risks of Being Kept in the Loop?Frederic Gilbert, Terence O’Brien & Mark Cook - 2018 - Cambridge Quarterly of Healthcare Ethics 27 (2):316-325.
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  42. Symbolic Reasoning in Spiking Neurons: A Model of the Cortex/Basal Ganglia/Thalamus Loop.Terrence C. Stewart, Xuan Choo & Chris Eliasmith - 2010 - In S. Ohlsson & R. Catrambone (eds.), Proceedings of the 32nd Annual Conference of the Cognitive Science Society. Cognitive Science Society. pp. 1100--1105.
  43.  4
    Neural Network-Based State Estimation for a Closed-Loop Control Strategy Applied to a Fed-Batch Bioreactor.Santiago Rómoli, Mario Serrano, Francisco Rossomando, Jorge Vega, Oscar Ortiz & Gustavo Scaglia - 2017 - Complexity 2017:1-16.
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  44.  13
    Research on the Complexity and Chaos Control About a Closed-Loop Supply Chain with Dual-Channel Recycling and Uncertain Consumer Perception.Junhai Ma, Hao Ren, Miao Yu & Meihong Zhu - 2018 - Complexity 2018:1-13.
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  45.  12
    The Phonological Loop as a Language Learning Device.Alan Baddeley, Susan Gathercole & Costanza Papagno - 1998 - Psychological Review 105 (1):158-173.
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  46.  4
    Memory for Serial Order: A Network Model of the Phonological Loop and its Timing.Neil Burgess & Graham J. Hitch - 1999 - Psychological Review 106 (3):551-581.
  47.  1
    Robust Fractional-Order PID Controller Tuning Based on Bode’s Optimal Loop Shaping.Lu Liu & Shuo Zhang - 2018 - Complexity 2018:1-14.
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  48. Perception, Imagery, and the Sensorimotor Loop.Rick Grush - 1998 - In F. Esken & F.-D. Heckman (eds.), A Consciousness Reader. Schoeningh Verlag.
    I have argued elsewhere that imagery and represention are best explained as the result of operations of neurally implemented emulators of an agent's body and environment. In this article I extend the theory of emulation to address perceptual processing as well. The key notion will be that of an emulator of an agent's egocentric behavioral space. This emulator, when run off-line, produces mental imagery, including transformations such as visual image rotations. However, while on-line, it is used to process information from (...)
     
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  49.  17
    Society-in-the-Loop: Programming the Algorithmic Social Contract.Iyad Rahwan - 2018 - Ethics and Information Technology 20 (1):5-14.
  50.  19
    Closed-Loop Targeted Memory Reactivation During Sleep Improves Spatial Navigation.Renee E. Shimizu, Patrick M. Connolly, Nicola Cellini, Diana M. Armstrong, Lexus T. Hernandez, Rolando Estrada, Mario Aguilar, Michael P. Weisend, Sara C. Mednick & Stephen B. Simons - 2018 - Frontiers in Human Neuroscience 12.
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