logic

Summary

Summary: The science that investigates the principles governing correct or reliable inference and deals with the canons and criteria of validity in thought and demonstration. This system of reasoning is applicable to any branch of knowledge or study. (Random House Unabridged Dictionary, 2d ed & Sippl, Computer Dictionary, 4th ed)

Top Publications

  1. Rodriguez Paton A, Sainz de Murieta I, Sosík P. DNA strand displacement system running logic programs. Biosystems. 2014;115:5-12 pubmed publisher
    ..The model allows to run logic programs composed of Horn clauses by cascading resolution steps...
  2. Sell A, Tooby J, Cosmides L. Formidability and the logic of human anger. Proc Natl Acad Sci U S A. 2009;106:15073-8 pubmed publisher
    ..stronger men favored greater use of military force in international conflicts provides evidence that the internal logic of the anger program reflects the ancestral payoffs characteristic of a small-scale social world rather than ..
  3. Griffiths T, Tenenbaum J. Theory-based causal induction. Psychol Rev. 2009;116:661-716 pubmed publisher
  4. Kronemeijer A, Gili E, Shahid M, Rivnay J, Salleo A, Heeney M, et al. A selenophene-based low-bandgap donor-acceptor polymer leading to fast ambipolar logic. Adv Mater. 2012;24:1558-65 pubmed publisher
    Fast ambipolar CMOS-like logic is demonstrated using a new selenophene-based donor-acceptor polymer semiconductor. The polymer exhibits saturation hole and electron mobilities of 0.46 cm(2) /Vs and 0.84 cm(2) /Vs...
  5. Arellano G, Argil J, Azpeitia E, Benítez M, Carrillo M, Góngora P, et al. "Antelope": a hybrid-logic model checker for branching-time Boolean GRN analysis. BMC Bioinformatics. 2011;12:490 pubmed publisher
    ..We have developed Antelope ("Analysis of Networks through TEmporal-LOgic sPEcifications", http://turing.iimas.unam...
  6. Ikeda M, Tanida T, Yoshii T, Kurotani K, Onogi S, Urayama K, et al. Installing logic-gate responses to a variety of biological substances in supramolecular hydrogel-enzyme hybrids. Nat Chem. 2014;6:511-8 pubmed publisher
    ..Furthermore, we built Boolean logic gates (OR and AND) into the hydrogel-enzyme hybrid materials, which were able to sense simultaneously plural ..
  7. Konry T, Walt D. Intelligent medical diagnostics via molecular logic. J Am Chem Soc. 2009;131:13232-3 pubmed publisher
    In this communication, we describe the integration of microarray sensor technology with logic capability for screening combinations of proteins and DNA in a biological sample...
  8. Ramscar M, Dye M, Klein J. Children value informativity over logic in word learning. Psychol Sci. 2013;24:1017-23 pubmed publisher
    ..Adults adopted a markedly different and likely suboptimal strategy. These results suggest one explanation for why early word learning can appear baffling: Adult intuitions may be a poor source of insight into how children learn. ..
  9. Goñi Moreno A, Amos M. A reconfigurable NAND/NOR genetic logic gate. BMC Syst Biol. 2012;6:126 pubmed publisher
    Engineering genetic Boolean logic circuits is a major research theme of synthetic biology...
  10. Li T, Zhang L, Ai J, Dong S, Wang E. Ion-tuned DNA/Ag fluorescent nanoclusters as versatile logic device. ACS Nano. 2011;5:6334-8 pubmed publisher
    A novel kind of versatile logic device has been constructed utilizing ion-tuned DNA/Ag fluorescent nanoclusters, with K(+) and H(+) as two inputs...

Detail Information

Publications62

  1. Rodriguez Paton A, Sainz de Murieta I, Sosík P. DNA strand displacement system running logic programs. Biosystems. 2014;115:5-12 pubmed publisher
    ..The model allows to run logic programs composed of Horn clauses by cascading resolution steps...
  2. Sell A, Tooby J, Cosmides L. Formidability and the logic of human anger. Proc Natl Acad Sci U S A. 2009;106:15073-8 pubmed publisher
    ..stronger men favored greater use of military force in international conflicts provides evidence that the internal logic of the anger program reflects the ancestral payoffs characteristic of a small-scale social world rather than ..
  3. Griffiths T, Tenenbaum J. Theory-based causal induction. Psychol Rev. 2009;116:661-716 pubmed publisher
  4. Kronemeijer A, Gili E, Shahid M, Rivnay J, Salleo A, Heeney M, et al. A selenophene-based low-bandgap donor-acceptor polymer leading to fast ambipolar logic. Adv Mater. 2012;24:1558-65 pubmed publisher
    Fast ambipolar CMOS-like logic is demonstrated using a new selenophene-based donor-acceptor polymer semiconductor. The polymer exhibits saturation hole and electron mobilities of 0.46 cm(2) /Vs and 0.84 cm(2) /Vs...
  5. Arellano G, Argil J, Azpeitia E, Benítez M, Carrillo M, Góngora P, et al. "Antelope": a hybrid-logic model checker for branching-time Boolean GRN analysis. BMC Bioinformatics. 2011;12:490 pubmed publisher
    ..We have developed Antelope ("Analysis of Networks through TEmporal-LOgic sPEcifications", http://turing.iimas.unam...
  6. Ikeda M, Tanida T, Yoshii T, Kurotani K, Onogi S, Urayama K, et al. Installing logic-gate responses to a variety of biological substances in supramolecular hydrogel-enzyme hybrids. Nat Chem. 2014;6:511-8 pubmed publisher
    ..Furthermore, we built Boolean logic gates (OR and AND) into the hydrogel-enzyme hybrid materials, which were able to sense simultaneously plural ..
  7. Konry T, Walt D. Intelligent medical diagnostics via molecular logic. J Am Chem Soc. 2009;131:13232-3 pubmed publisher
    In this communication, we describe the integration of microarray sensor technology with logic capability for screening combinations of proteins and DNA in a biological sample...
  8. Ramscar M, Dye M, Klein J. Children value informativity over logic in word learning. Psychol Sci. 2013;24:1017-23 pubmed publisher
    ..Adults adopted a markedly different and likely suboptimal strategy. These results suggest one explanation for why early word learning can appear baffling: Adult intuitions may be a poor source of insight into how children learn. ..
  9. Goñi Moreno A, Amos M. A reconfigurable NAND/NOR genetic logic gate. BMC Syst Biol. 2012;6:126 pubmed publisher
    Engineering genetic Boolean logic circuits is a major research theme of synthetic biology...
  10. Li T, Zhang L, Ai J, Dong S, Wang E. Ion-tuned DNA/Ag fluorescent nanoclusters as versatile logic device. ACS Nano. 2011;5:6334-8 pubmed publisher
    A novel kind of versatile logic device has been constructed utilizing ion-tuned DNA/Ag fluorescent nanoclusters, with K(+) and H(+) as two inputs...
  11. Amir L, Tam T, Pita M, Meijler M, Alfonta L, Katz E. Biofuel cell controlled by enzyme logic systems. J Am Chem Soc. 2009;131:826-32 pubmed publisher
    An enzyme-based biofuel cell with a pH-switchable oxygen electrode, controlled by enzyme logic operations processing in situ biochemical input signals, has been developed...
  12. Umesono Y, Tasaki J, Nishimura Y, Hrouda M, Kawaguchi E, Yazawa S, et al. The molecular logic for planarian regeneration along the anterior-posterior axis. Nature. 2013;500:73-6 pubmed publisher
    ..Thus, we have confirmed the broad outline of Morgan's hypothesis, and refined it on the basis of our proposed default property of planarian stem cells. ..
  13. Wang B, Buck M. Customizing cell signaling using engineered genetic logic circuits. Trends Microbiol. 2012;20:376-84 pubmed publisher
    ..Here, we summarize the current state-of-the-art of engineering synthetic genetic logic circuits to customize cellular signaling behaviors, and discuss their promising applications in biocomputing, ..
  14. Silva Rocha R, De Lorenzo V. Implementing an OR-NOT (ORN) logic gate with components of the SOS regulatory network of Escherichia coli. Mol Biosyst. 2011;7:2389-96 pubmed publisher
    Whether biological or electronic, man-engineered computation is based on logic circuits assembled with binary gates that are interconnected to perform Boolean operations...
  15. Katsos N, Roqueta C, Estevan R, Cummins C. Are children with Specific Language Impairment competent with the pragmatics and logic of quantification?. Cognition. 2011;119:43-57 pubmed publisher
    ..The implications of these findings for SLI, linguistic theory, and clinical practice are discussed. ..
  16. Shamim M, Enam S, Qidwai U. Fuzzy Logic in neurosurgery: predicting poor outcomes after lumbar disk surgery in 501 consecutive patients. Surg Neurol. 2009;72:565-72; discussion 572 pubmed publisher
    ..We have used Fuzzy Logic-based fuzzy inference system (FIS) for identifying patients unlikely to improve after disk surgery and explored ..
  17. Gaber R, Lebar T, Majerle A, Ster B, Dobnikar A, Bencina M, et al. Designable DNA-binding domains enable construction of logic circuits in mammalian cells. Nat Chem Biol. 2014;10:203-8 pubmed publisher
    Electronic computer circuits consisting of a large number of connected logic gates of the same type, such as NOR, can be easily fabricated and can implement any logic function...
  18. Sprinzak E, Cokus S, Yeates T, Eisenberg D, Pellegrini M. Detecting coordinated regulation of multi-protein complexes using logic analysis of gene expression. BMC Syst Biol. 2009;3:115 pubmed publisher
    ..We detect coordinated regulation of multiple protein complexes using logic analysis of gene expression data...
  19. Cui J, Deluca T, Jung J, Wall D. Phylogenetically informed logic relationships improve detection of biological network organization. BMC Bioinformatics. 2011;12:476 pubmed publisher
    ..Here we search for logic relationships involving three genes, and explore its potential application in gene network analyses...
  20. Chen S, Guo Z, Zhu S, Shi W, Zhu W. A multiaddressable photochromic bisthienylethene with sequence-dependent responses: construction of an INHIBIT logic gate and a keypad lock. ACS Appl Mater Interfaces. 2013;5:5623-9 pubmed publisher
    ..Furthermore, an INHIBIT logic gate and a keypad lock with three inputs are constructed with the unimolecular platform by employing an absorption ..
  21. Piran R, Halperin E, Guttmann Raviv N, Keinan E, Reshef R. Algorithm of myogenic differentiation in higher-order organisms. Development. 2009;136:3831-40 pubmed publisher
    ..Specifically, we applied the ?ukasiewicz logic to a diffusible protein system that leads to myogenesis...
  22. Yu W, Li Z, Zhou H, Chen Y, Wang Y, Huang Y, et al. Vertically stacked multi-heterostructures of layered materials for logic transistors and complementary inverters. Nat Mater. 2013;12:246-52 pubmed publisher
    ..interest for future electronics, but the absence of a bandgap limits its direct applicability in transistors and logic devices...
  23. Pasotti L, Quattrocelli M, Galli D, De Angelis M, Magni P. Multiplexing and demultiplexing logic functions for computing signal processing tasks in synthetic biology. Biotechnol J. 2011;6:784-95 pubmed publisher
    ..Herein, two modular biological systems that could mimic multiplexing and demultiplexing logic functions are proposed and discussed...
  24. Scott D, Das U, Tang Y, Roy S. Mechanistic logic underlying the axonal transport of cytosolic proteins. Neuron. 2011;70:441-54 pubmed publisher
    ..We propose a model where cytosolic proteins are transported by dynamically assembling into multiprotein complexes that are directly/indirectly conveyed by motors. ..
  25. Friedrich R, Friederici A. Mathematical logic in the human brain: syntax. PLoS ONE. 2009;4:e5599 pubmed publisher
    ..This seems to imply that despite structural analogies of common and current formal languages, at the neural level, mathematics and natural language are processed differently, in principal. ..
  26. Bernardes J, Carbone A, Zaverucha G. A discriminative method for family-based protein remote homology detection that combines inductive logic programming and propositional models. BMC Bioinformatics. 2011;12:83 pubmed publisher
    ..From this, Inductive Logic Programming (ILP) finds the most frequent patterns (motifs) and uses them to train propositional models, such as ..
  27. Liu X, Aizen R, Freeman R, Yehezkeli O, Willner I. Multiplexed aptasensors and amplified DNA sensors using functionalized graphene oxide: application for logic gate operations. ACS Nano. 2012;6:3553-63 pubmed publisher
    ..detection of DNA, aptamer-substrate complexes, and for the integration of predesigned DNA constructs that activate logic gate operations...
  28. Zhou J, Arugula M, Halámek J, Pita M, Katz E. Enzyme-based NAND and NOR logic gates with modular design. J Phys Chem B. 2009;113:16065-70 pubmed publisher
    The logic gates NAND/NOR were mimicked by enzyme biocatalyzed reactions activated by sucrose, maltose and phosphate...
  29. Zhou M, Du Y, Chen C, Li B, Wen D, Dong S, et al. Aptamer-controlled biofuel cells in logic systems and used as self-powered and intelligent logic aptasensors. J Am Chem Soc. 2010;132:2172-4 pubmed publisher
    This communication demonstrates for the first time the controlled power release of biofuel cells (BFCs) by aptamer logic systems processed according to the Boolean logic operations "programmed" into the biocomputing systems...
  30. Ausländer S, Ausländer D, Müller M, Wieland M, Fussenegger M. Programmable single-cell mammalian biocomputers. Nature. 2012;487:123-7 pubmed publisher
    ..designer networks that execute input-triggered genetic instructions with precision, robustness and computational logic reminiscent of electronic circuits...
  31. Guziolowski C, Videla S, Eduati F, Thiele S, Cokelaer T, Siegel A, et al. Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming. Bioinformatics. 2013;29:2320-6 pubmed publisher
    b>Logic modeling is a useful tool to study signal transduction across multiple pathways. Logic models can be generated by training a network containing the prior knowledge to phospho-proteomics data...
  32. Daisley J, Vallortigara G, Regolin L. Logic in an asymmetrical (social) brain: Transitive inference in the young domestic chick. Soc Neurosci. 2010;5:309-19 pubmed publisher
    ..Results demonstrate that chicks with lateralized brain hemispheres show greater inference, and this is under right hemisphere control: the brain hemisphere that is dominant in social interactions. ..
  33. Regot S, Macia J, Conde N, Furukawa K, Kjellén J, Peeters T, et al. Distributed biological computation with multicellular engineered networks. Nature. 2011;469:207-11 pubmed publisher
    ..design of electronic circuits, are limited by the difficulties arising from wiring the basic computational units (logic gates) through the appropriate connections, each one to be implemented by a different molecule...
  34. Moon T, Lou C, Tamsir A, Stanton B, Voigt C. Genetic programs constructed from layered logic gates in single cells. Nature. 2012;491:249-53 pubmed publisher
    ..These programs consist of integrated genetic circuits that individually implement operations ranging from digital logic to dynamic circuits, and they have been used in various cellular engineering applications, including the ..
  35. Privman V, Halámek J, Arugula M, Melnikov D, Bocharova V, Katz E. Biochemical filter with sigmoidal response: increasing the complexity of biomolecular logic. J Phys Chem B. 2010;114:14103-9 pubmed publisher
    ..process is reported and analyzed as a promising network component for increasing the complexity of biomolecular logic systems. Key challenge in biochemical logic research has been achieving scalability for complex network designs...
  36. Choi J, Lee J, Shin T, Song H, Kim E, Cheon J. Self-confirming "AND" logic nanoparticles for fault-free MRI. J Am Chem Soc. 2010;132:11015-7 pubmed publisher
    ..not only possesses superior MR contrast effects but also has the unique capability of displaying "AND" logic signals in both the T1 and T2 modes...
  37. Terfve C, Cokelaer T, Henriques D, MacNamara A, Gonçalves E, Morris M, et al. CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms. BMC Syst Biol. 2012;6:133 pubmed publisher
    ..Here we present CellNOptR, an open-source R software package for building predictive logic models of signaling networks by training networks derived from prior knowledge to signaling (typically ..
  38. Orbach R, Remacle F, Levine R, Willner I. Logic reversibility and thermodynamic irreversibility demonstrated by DNAzyme-based Toffoli and Fredkin logic gates. Proc Natl Acad Sci U S A. 2012;109:21228-33 pubmed publisher
    The Toffoli and Fredkin gates were suggested as a means to exhibit logic reversibility and thereby reduce energy dissipation associated with logic operations in dense computing circuits...
  39. Sternberg M, Tamaddoni Nezhad A, Lesk V, Kay E, Hitchen P, Cootes A, et al. Gene function hypotheses for the Campylobacter jejuni glycome generated by a logic-based approach. J Mol Biol. 2013;425:186-97 pubmed publisher
    ..Here, we demonstrate the power of a logic-based machine learning approach to propose hypotheses for gene function integrating information from two diverse ..
  40. Monti M, Osherson D. Logic, language and the brain. Brain Res. 2012;1428:33-42 pubmed publisher
    ..These representations are then manipulated by mental operations that are not based on the neural mechanisms of natural language. This article is part of a Special Issue entitled "The Cognitive Neuroscience". ..
  41. Ran T, Kaplan S, Shapiro E. Molecular implementation of simple logic programs. Nat Nanotechnol. 2009;4:642-8 pubmed publisher
    ..Biomolecular implementations of finite automata and logic gates have already been developed...
  42. Chuang C, Lin C, Chang Y, Jennawasin T, Chen P. Design of synthetic biological logic circuits based on evolutionary algorithm. IET Syst Biol. 2013;7:89-105 pubmed publisher
    The construction of an artificial biological logic circuit using systematic strategy is recognised as one of the most important topics for the development of synthetic biology...
  43. Valencia Palomo G, Rossiter J. Programmable logic controller implementation of an auto-tuned predictive control based on minimal plant information. ISA Trans. 2011;50:92-100 pubmed publisher
    ..Hence, it describes how the constrained control algorithm is embedded in an industrial programmable logic controller (PLC) using the IEC 61131-3 programming standard...
  44. Brousselle A, Champagne F. Program theory evaluation: Logic analysis. Eval Program Plann. 2011;34:69-78 pubmed publisher
    ..This article describes a particular type of program theory evaluation-logic analysis-that allows us to test the plausibility of a program's theory using scientific knowledge...
  45. Xia F, Zuo X, Yang R, White R, Xiao Y, Kang D, et al. Label-free, dual-analyte electrochemical biosensors: a new class of molecular-electronic logic gates. J Am Chem Soc. 2010;132:8557-9 pubmed publisher
    An "XOR" gate built using label-free, dual-analyte electrochemical sensors and the activation of this logic gate via changing concentrations of cocaine and the relevant cDNA as inputs are described.
  46. Guerra D, Bulsara A, Ditto W, Sinha S, Murali K, Mohanty P. A noise-assisted reprogrammable nanomechanical logic gate. Nano Lett. 2010;10:1168-71 pubmed publisher
    We present a nanomechanical device, operating as a reprogrammable logic gate, and performing fundamental logic functions such as AND/OR and NAND/NOR. The logic function can be programmed (e.g...
  47. Miyamoto T, Razavi S, DeRose R, Inoue T. Synthesizing biomolecule-based Boolean logic gates. ACS Synth Biol. 2013;2:72-82 pubmed
    ..The main components of a computing device consist of an arithmetic logic unit, the control unit, memory, and the input and output devices...
  48. Morris M, Saez Rodriguez J, Sorger P, Lauffenburger D. Logic-based models for the analysis of cell signaling networks. Biochemistry. 2010;49:3216-24 pubmed publisher
    ..Here we review recent advances in applying logic-based modeling to mammalian cell biology...
  49. MacPhee M. Developing a practice-academic partnership logic model. Nurs Outlook. 2009;57:143-7 pubmed publisher
    This article will describe a testable logic model for practice-academic partnerships. The model can be used to build collaborative practice capacity between academic and practice partners...
  50. Borresen J, Lynch S. Oscillatory threshold logic. PLoS ONE. 2012;7:e48498 pubmed publisher
    ..Here, we demonstrate how coupled threshold oscillators may be used to perform binary logic in a manner entirely consistent with modern computer architectures...
  51. Acerbi A, Ghirlanda S, Enquist M. The logic of fashion cycles. PLoS ONE. 2012;7:e32541 pubmed publisher
    ..We also establish that alternative theories, that fashions result from individuals signaling their social status, or from individuals randomly copying each other, do not satisfactorily reproduce these empirical observations. ..
  52. Hayes H, Parchman M, Howard R. A logic model framework for evaluation and planning in a primary care practice-based research network (PBRN). J Am Board Fam Med. 2011;24:576-82 pubmed publisher
    ..The purpose of this article is to describe the development of a logic model and how the framework has been used for planning and evaluation in a primary care PBRN...
  53. Steinhauer K, Drury J, Portner P, Walenski M, Ullman M. Syntax, concepts, and logic in the temporal dynamics of language comprehension: evidence from event-related potentials. Neuropsychologia. 2010;48:1525-42 pubmed publisher
    b>Logic has been intertwined with the study of language and meaning since antiquity, and such connections persist in present day research in linguistic theory (formal semantics) and cognitive psychology (e.g., studies of human reasoning)...
  54. Ma D, Kwan M, Chan D, Lee P, Yang H, Ma V, et al. Crystal violet as a fluorescent switch-on probe for i-motif: label-free DNA-based logic gate. Analyst. 2011;136:2692-6 pubmed publisher
    ..This interaction has been exploited to develop a label-free DNA-based "OR" logic gate for potassium and hydrogen ions.
  55. Tamsir A, Tabor J, Voigt C. Robust multicellular computing using genetically encoded NOR gates and chemical 'wires'. Nature. 2011;469:212-5 pubmed publisher
    ..We construct a simple NOR logic gate in Escherichia coli by arranging two tandem promoters that function as inputs to drive the transcription of a ..
  56. Sakhanenko N, Galas D. Markov logic networks in the analysis of genetic data. J Comput Biol. 2010;17:1491-508 pubmed publisher
    ..We chose to use the most general such approach, Markov Logic Networks (MLNs), for combining deterministic knowledge with statistical analysis...
  57. Govaerts P, Vaerenberg B, De Ceulaer G, Daemers K, De Beukelaer C, Schauwers K. Development of a software tool using deterministic logic for the optimization of cochlear implant processor programming. Otol Neurotol. 2010;31:908-18 pubmed publisher
    ..An intelligent agent, Fitting to Outcomes eXpert, was developed to optimize and automate Cochlear implant (CI) programming. The current article describes the rationale, development, and features of this tool...
  58. Helikar T, Kowal B, Madrahimov A, Shrestha M, Pedersen J, Limbu K, et al. Bio-logic builder: a non-technical tool for building dynamical, qualitative models. PLoS ONE. 2012;7:e46417 pubmed publisher
    ..To help address this issue, we have developed a web-based tool, Bio-Logic Builder, that enables laboratory scientists to define mathematical representations (based on a discrete formalism) ..
  59. Fino E, Packer A, Yuste R. The logic of inhibitory connectivity in the neocortex. Neuroscientist. 2013;19:228-37 pubmed publisher
    ..In a last section, the authors describe briefly the link between dense inhibitory networks and different interneuron functions described in the neocortex. ..
  60. Bonnet J, Yin P, Ortiz M, Subsoontorn P, Endy D. Amplifying genetic logic gates. Science. 2013;340:599-603 pubmed publisher
    ..Researchers have also engineered synthetic genetic logic to realize simpler, independent control of biological processes...
  61. Dutkowski J, Ideker T. Protein networks as logic functions in development and cancer. PLoS Comput Biol. 2011;7:e1002180 pubmed publisher
    ..For each case we apply a new method, called Network-Guided Forests, to identify predictive modules together with logic functions which tie the activity of each module to the activity of its component genes...
  62. Seelig G, Soloveichik D, Zhang D, Winfree E. Enzyme-free nucleic acid logic circuits. Science. 2006;314:1585-8 pubmed
    ..To systematically create complex yet reliable circuits, electrical engineers use digital logic, wherein gates and subcircuits are composed modularly and signal restoration prevents signal degradation...