Results for 'protein complexes'

951 found
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  1. The representation of protein complexes in the Protein Ontology.Carol Bult, Harold Drabkin, Alexei Evsikov, Darren Natale, Cecilia Arighi, Natalia Roberts, Alan Ruttenberg, Peter D’Eustachio, Barry Smith, Judith Blake & Cathy Wu - 2011 - BMC Bioinformatics 12 (371):1-11.
    Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants (...)
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  2. Toll-like receptor signaling in vertebrates: Testing the integration of protein, complex, and pathway data in the Protein Ontology framework.Cecilia Arighi, Veronica Shamovsky, Anna Maria Masci, Alan Ruttenberg, Barry Smith, Darren Natale, Cathy Wu & Peter D’Eustachio - 2015 - PLoS ONE 10 (4):e0122978.
    The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology (...)
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  3. The Protein Ontology: A structured representation of protein forms and complexes.Darren Natale, Cecilia N. Arighi, Winona C. Barker, Judith A. Blake, Carol J. Bult, Michael Caudy, Harold J. Drabkin, Peter D’Eustachio, Alexei V. Evsikov, Hongzhan Huang, Jules Nchoutmboube, Natalia V. Roberts, Barry Smith, Jian Zhang & Cathy H. Wu - 2011 - Nucleic Acids Research 39 (1):D539-D545.
    The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as (...)
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  4. Protein Ontology: A controlled structured network of protein entities.A. Natale Darren, N. Arighi Cecilia, A. Blake Judith, J. Bult Carol, R. Christie Karen, Cowart Julie, D’Eustachio Peter, D. Diehl Alexander, J. Drabkin Harold, Helfer Olivia, Barry Smith & Others - 2013 - Nucleic Acids Research 42 (1):D415-21..
    The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene (...)
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  5. Protein-centric connection of biomedical knowledge: Protein Ontology research and annotation tools.Cecilia N. Arighi, Darren A. Natale, Judith A. Blake, Carol J. Bult, Michael Caudy, Alexander D. Diehl, Harold J. Drabkin, Peter D'Eustachio, Alexei Evsikov, Hongzhan Huang, Barry Smith & Others - 2011 - In Landgrebe Jobst & Smith Barry (eds.), Proceedings of the 2nd International Conference on Biomedical Ontology. CEUR, vol. 833. pp. 285-287.
    The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and (...)
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  6. Quantum transport and utilization of free energy in protein α-helices.Danko D. Georgiev & James F. Glazebrook - 2020 - Advances in Quantum Chemistry 82:253-300.
    The essential biological processes that sustain life are catalyzed by protein nano-engines, which maintain living systems in far-from-equilibrium ordered states. To investigate energetic processes in proteins, we have analyzed the system of generalized Davydov equations that govern the quantum dynamics of multiple amide I exciton quanta propagating along the hydrogen-bonded peptide groups in α-helices. Computational simulations have confirmed the generation of moving Davydov solitons by applied pulses of amide I energy for protein α-helices of varying length. The stability (...)
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  7. Framework for a protein ontology.Darren A. Natale, Cecilia N. Arighi, Winona Barker, Judith Blake, Ti-Cheng Chang, Zhangzhi Hu, Hongfang Liu, Barry Smith & Cathy H. Wu - 2007 - BMC Bioinformatics 8 (Suppl 9):S1.
    Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a (...) Ontology (PRO) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)
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  8. Protein Ontology: Enhancing and scaling up the representation of protein entities.Darren A. Natale, Cecilia N. Arighi, Judith A. Blake, Jonathan Bona, Chuming Chen, Sheng-Chih Chen, Karen R. Christie, Julie Cowart, Peter D'Eustachio, Alexander D. Diehl, Harold J. Drabkin, William D. Duncan, Hongzhan Huang, Jia Ren, Karen Ross & Alan Ruttenberg - 2017 - Nucleic Acids Research 45 (D1):D339-D346.
    The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and (...)
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  9. Thermal stability of solitons in protein α-helices.Danko D. Georgiev & James F. Glazebrook - 2022 - Chaos, Solitons and Fractals 155:111644.
    Protein α-helices provide an ordered biological environment that is conducive to soliton-assisted energy transport. The nonlinear interaction between amide I excitons and phonon deformations induced in the hydrogen-bonded lattice of peptide groups leads to self-trapping of the amide I energy, thereby creating a localized quasiparticle (soliton) that persists at zero temperature. The presence of thermal noise, however, could destabilize the protein soliton and dissipate its energy within a finite lifetime. In this work, we have computationally solved the system (...)
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  10. On the Limits of Causal Modeling: Spatially-Structurally Complex Biological Phenomena.Marie I. Kaiser - 2016 - Philosophy of Science 83 (5):921-933.
    This paper examines the adequacy of causal graph theory as a tool for modeling biological phenomena and formalizing biological explanations. I point out that the causal graph approach reaches it limits when it comes to modeling biological phenomena that involve complex spatial and structural relations. Using a case study from molecular biology, DNA-binding and -recognition of proteins, I argue that causal graph models fail to adequately represent and explain causal phenomena in this field. The inadequacy of these models is due (...)
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  11. Quantum tunneling of three-spine solitons through excentric barriers.Danko D. Georgiev & James F. Glazebrook - 2022 - Physics Letters A 448:128319.
    Macromolecular protein complexes catalyze essential physiological processes that sustain life. Various interactions between protein subunits could increase the effective mass of certain peptide groups, thereby compartmentalizing protein α-helices. Here, we study the differential effects of applied massive barriers upon the soliton-assisted energy transport within proteins. We demonstrate that excentric barriers, localized onto a single spine in the protein α-helix, reflect or trap three-spine solitons as effectively as concentric barriers with comparable total mass. Furthermore, wider (...) solitons, whose energy is lower, require heavier massive barriers for soliton reflection or trapping. Regulation of energy transport, delivery and utilization at protein active sites could thus be achieved through control of the soliton width, or of the effective mass of the protein subunits. (shrink)
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  12. Remarks on the Geometry of Complex Systems and Self-Organization.Luciano Boi - 2012 - In Vincenzo Fano, Enrico Giannetto, Giulia Giannini & Pierluigi Graziani (eds.), Complessità e Riduzionismo. ISONOMIA - Epistemologica Series Editor. pp. 28-43.
    Let us start by some general definitions of the concept of complexity. We take a complex system to be one composed by a large number of parts, and whose properties are not fully explained by an understanding of its components parts. Studies of complex systems recognized the importance of “wholeness”, defined as problems of organization (and of regulation), phenomena non resolvable into local events, dynamics interactions in the difference of behaviour of parts when isolated or in higher configuration, etc., in (...)
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  13. Is the Cell Really a Machine?Daniel J. Nicholson - 2019 - Journal of Theoretical Biology 477:108–126.
    It has become customary to conceptualize the living cell as an intricate piece of machinery, different to a man-made machine only in terms of its superior complexity. This familiar understanding grounds the conviction that a cell's organization can be explained reductionistically, as well as the idea that its molecular pathways can be construed as deterministic circuits. The machine conception of the cell owes a great deal of its success to the methods traditionally used in molecular biology. However, the recent introduction (...)
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  14. That is life: communicating RNA networks from viruses and cells in continuous interaction.Guenther Witzany - 2019 - Annals of the New York Academy of Sciences:1-16.
    All the conserved detailed results of evolution stored in DNA must be read, transcribed, and translated via an RNAmediated process. This is required for the development and growth of each individual cell. Thus, all known living organisms fundamentally depend on these RNA-mediated processes. In most cases, they are interconnected with other RNAs and their associated protein complexes and function in a strictly coordinated hierarchy of temporal and spatial steps (i.e., an RNA network). Clearly, all cellular life as we (...)
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  15.  98
    Crick's Adaptor Hypothesis and the Discovery of Transfer RNA: Experiment Surpassing Theoretical Prediction.Michael Fry - 2022 - Philosophy, Theory, and Practice in Biology 14 (11):1-31.
    Historically, hypotheses failed in most cases to correctly forecast the workings of complex biological systems. Francis Crick’s adaptor hypothesis, however, stands out as an exceptional case of a confirmed abstract prediction. This hypothesis presciently anticipated the existence of RNA adaptors that function as bridges between amino acids and the chemically different nucleic acid template for proteins. Crick conjectured that the adaptors are enzymatically charged with cognate amino acids, they bind to complementary protein-coding nucleic acid, and their liberated amino acids (...)
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  16. Two Dogmas of Biology.Leonore Fleming - 2017 - Philosophy, Theory, and Practice in Biology 9 (2).
    The problem with reductionism in biology is not the reduction, but the implicit attitude of determinism that usually accompanies it. Methodological reductionism is supported by deterministic beliefs, but making such a connection is problematic when it is based on an idea of determinism as fixed predictability. Conflating determinism with predictability gives rise to inaccurate models that overlook the dynamic complexity of our world, as well as ignore our epistemic limitations when we try to model it. Furthermore, the assumption of a (...)
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  17. (1 other version)The gene as the unit of selection: a case of evolutive delusion.Armando Aranda-Anzaldo - 1997 - Ludus Vitalis 5 (9):91-120.
    The unit of selection is the concept of that ‘something’ to which biologists refer when they speak of an adaptation as being ‘for the good of’ something. Darwin identified the organism as the unit of selection because for him the ‘struggle for existence’ was an issue among individuals. Later on it was suggested that, in order to understand the evolution of social behavior, it is necessary to argue that groups, and not individuals, are the units of selection. The last addition (...)
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  18. The Evolution of Consciousness & Subjectivity in a Biological Framework for The Universe.Ronald Williams - manuscript
    This paper explores the evolution of consciousness and subjectivity through a biological framework for understanding the universe. It posits that functional patterns in biological systems mirror cosmic mathematical principles, defining our objective reality. Similar to wave and Fibonacci patterns in different physical phenomena, biological patterns are intrinsic to all things and can be quantified using Dedre Gentner’s approach to analogy. For example, Earth’s ocean currents and the melting and freezing of Antarctica resemble the circulatory system and heart, while the production (...)
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  19. A New method for Analysis of Biomolecules Using the BSM-SG Atomic Models.Stoyan Sarg Sargoytchev - 2017 - J. Biom Biostat 8 (2):1000339.
    Biomolecules and particularly proteins and DNA exhibit some mysterious features that cannot find satisfactory explanation by quantum mechanical modes of atoms. One of them, known as a Levinthal’s paradox, is the ability to preserve their complex three-dimensional structure in appropriate environments. Another one is that they possess some unknown energy mechanism. The Basic Structures of Matter Supergravitation Unified Theory (BSM-SG) allows uncovering the real physical structures of the elementary particles and their spatial arrangement in atomic nuclei. The resulting physical models (...)
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  20. Biometaphysics.Barry Smith - 2009 - In Robin Le Poidevin, Simons Peter, McGonigal Andrew & Ross P. Cameron (eds.), The Routledge Companion to Metaphysics. New York: Routledge. pp. 537-544.
    While Darwin is commonly supposed to have demonstrated the inapplicability of the Aristotelian ontology of species to biological science, recent developments, especially in the wake of the Human Genome Project, have given rise to a new golden age of classification in which ontological ideas -- as for example in the Gene Ontology, the Cell Ontology, the Protein Ontology, and so forth -- are once again playing an important role. In regard to species, on the other hand, matters are more (...)
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  21. MAPK cascades and major abiotic stresses.Khaled Moustafa - 2014 - Plant Cell Reports 33.
    Plants have evolved with complex signaling circuits that operate under multiple conditions and govern numerous cellular functions. Stress signaling in plant cells is a sophisticated network composed of interacting proteins organized into tiered cascades where the function of a molecule is dependent on the interaction and the activation of another. In a linear scheme, the receptors of cell surface sense the stimuli and convey stress signals through specific pathways and downstream phosphorylation events controlled by mitogen-activated protein (MAP) kinases and (...)
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  22. Messy Chemical Kinds.Joyce C. Havstad - 2018 - British Journal for the Philosophy of Science 69 (3):719-743.
    Following Kripke and Putnam, the received view of chemical kinds has been a microstructuralist one. To be a microstructuralist about chemical kinds is to think that membership in said kinds is conferred by microstructural properties. Recently, the received microstructuralist view has been elaborated and defended, but it has also been attacked on the basis of complexities, both chemical and ontological. Here, I look at which complexities really challenge the microstructuralist view; at how the view itself might be made more complicated (...)
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  23. Defining Generative Artificial Intelligence: An Attempt to Resolve the Confusion about Diffusion.Raphael Ronge, Markus Maier & Benjamin Rathgeber - manuscript
    The concept of Generative Artificial Intelligence (GenAI) is ubiquitous in the public and semi-technical domain, yet rarely defined precisely. We clarify main concepts that are usually discussed in connection to GenAI and argue that one ought to distinguish between the technical and the public discourse. In order to show its complex development and associated conceptual ambiguities, we offer a historical-systematic reconstruction of GenAI and explicitly discuss two exemplary cases: the generative status of the Large Language Model BERT and the differences (...)
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  24. Macromolecular Pluralism.Matthew H. Slater - 2009 - Philosophy of Science 76 (5):851-863.
    Different chemical species are often cited as paradigm examples of structurally delimited natural kinds. While classificatory monism may thus seem plausible for simple molecules, it looks less attractive for complex biological macromolecules. I focus on the case of proteins that are most plausibly individuated by their functions. Is there a single, objective count of proteins? I argue that the vagaries of function individuation infect protein classification. We should be pluralists about macromolecular classification.
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  25. Understanding Biology in the Age of Artificial Intelligence.Adham El Shazly, Elsa Lawerence, Srijit Seal, Chaitanya Joshi, Matthew Greening, Pietro Lio, Shantung Singh, Andreas Bender & Pietro Sormanni - manuscript
    Modern life sciences research is increasingly relying on artificial intelligence (AI) approaches to model biological systems, primarily centered around the use of machine learning (ML) models. Although ML is undeniably useful for identifying patterns in large, complex data sets, its widespread application in biological sciences represents a significant deviation from traditional methods of scientific inquiry. As such, the interplay between these models and scientific understanding in biology is a topic with important implications for the future of scientific research, yet it (...)
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  26. Computational capacity of pyramidal neurons in the cerebral cortex.Danko D. Georgiev, Stefan K. Kolev, Eliahu Cohen & James F. Glazebrook - 2020 - Brain Research 1748:147069.
    The electric activities of cortical pyramidal neurons are supported by structurally stable, morphologically complex axo-dendritic trees. Anatomical differences between axons and dendrites in regard to their length or caliber reflect the underlying functional specializations, for input or output of neural information, respectively. For a proper assessment of the computational capacity of pyramidal neurons, we have analyzed an extensive dataset of three-dimensional digital reconstructions from the NeuroMorphoOrg database, and quantified basic dendritic or axonal morphometric measures in different regions and layers of (...)
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  27. Genome Informatics: The Role of DNA in Cellular Computations.James A. Shapiro - 2006 - Biological Theory 1 (3):288-301.
    Cells are cognitive entities possessing great computational power. DNA serves as a multivalent information storage medium for these computations at various time scales. Information is stored in sequences, epigenetic modifications, and rapidly changing nucleoprotein complexes. Because DNA must operate through complexes formed with other molecules in the cell, genome functions are inherently interactive and involve two-way communication with various cellular compartments. Both coding sequences and repetitive sequences contribute to the hierarchical systemic organization of the genome. By virtue of (...)
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  28. A new framework for host-pathogen interaction research.Hong Yu, Li Li, Anthony Huffman, John Beverley, Junguk Hur, Eric Merrell, Hsin-hui Huang, Yang Wang, Yingtong Liu, Edison Ong, Liang Cheng, Tao Zeng, Jingsong Zhang, Pengpai Li, Zhiping Liu, Zhigang Wang, Xiangyan Zhang, Xianwei Ye, Samuel K. Handelman, Jonathan Sexton, Kathryn Eaton, Gerry Higgins, Gilbert S. Omenn, Brian Athey, Barry Smith, Luonan Chen & Yongqun He - 2022 - Frontiers in Immunology 13.
    COVID-19 often manifests with different outcomes in different patients, highlighting the complexity of the host-pathogen interactions involved in manifestations of the disease at the molecular and cellular levels. In this paper, we propose a set of postulates and a framework for systematically understanding complex molecular host-pathogen interaction networks. Specifically, we first propose four host-pathogen interaction (HPI) postulates as the basis for understanding molecular and cellular host-pathogen interactions and their relations to disease outcomes. These four postulates cover the evolutionary dispositions involved (...)
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  29. The Origin of Consciousness.Ronald Williams - forthcoming - Biologicaluniverse.Org.
    This paper explores the evolution of consciousness and subjectivity through a biological framework for understanding the universe. It posits that functional patterns in biological systems mirror cosmic mathematical principles, defining our objective reality. Similar to wave and Fibonacci patterns in different physical phenomena, biological patterns are intrinsic to all things and can be quantified using Dedre Gentner’s approach to analogy. For example, Earth’s ocean currents and the melting and freezing of Antarctica resemble the circulatory system and heart, while the production (...)
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  30. Energy in the Universe and its Syntropic Forms of Existence According to the BSM - Superg ravitation Unified Theory.Stoyan Sarg Sargoytchev - 2013 - Syntropy 2013 (2).
    According to the BSM- Supergravitation Unified Theory (BSM-SG), the energy is indispensable feature of matter, while the matter possesses hierarchical levels of organization from a simple to complex forms, with appearance of fields at some levels. Therefore, the energy also follows these levels. At the fundamental level, where the primary energy source exists, the matter is in its primordial form, where two super-dense fundamental particles (FP) exist in a classical pure empty space (not a physical vacuum). They are associated with (...)
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  31. Probable role of ablation of cerebral ganglia and injection of its extracts on o:n ratio of Lamellidens corrianis during summer season.N. G. Shinde - 2020 - Internat Ional Journal of Applied Research 6 (6):391-394.
    Amongst invertebrates, molluscs show great variability in their nervous system ranging from primitive arrangement in Chitons to the complex mass of fused ganglia forming the ‘brain’ of cephalopods. Most of the effector organs used for pharmacological or physiological experiments. The neurosecretory cells (NSCs) with their combination of neuronal and glandular capabilities are perfectly suited to translate a neuronal input into the hormonal output best suited to long-term process. In this capacity, the NSCs may produce hormones, which act directly upon the (...)
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  32. VO: Vaccine Ontology.Yongqun He, Lindsay Cowell, Alexander D. Diehl, H. L. Mobley, Bjoern Peters, Alan Ruttenberg, Richard H. Scheuermann, Ryan R. Brinkman, Melanie Courtot, Chris Mungall, Barry Smith & Others - 2009 - In Barry Smith (ed.), ICBO 2009: Proceedings of the First International Conference on Biomedical Ontology. Buffalo: NCOR.
    Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced (...)
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  33. A Scientifically Acceptable Mechanism for the Reincarnation Process of the Self.Adrian Klein - 2022 - Cunoașterea Științifică 1 (2):71-80.
    We propose a novel paradigmatic approach to sentient reality as a whole, with specific application to Information-guided DNA dynamics, leading to a triadic genomic configuration , which accommodates besides the parental hereditar legacy, a transcendental originating highly complex guiding matrix able to control the specific way the protein-synthesis is performed. The Self’s own “Soul Genome”, transcending the zero point energy interdimensional barrier, couples to the zygote’s quantum-governed energetic configuration by way of resonant bands of subtle energy superposition effects at (...)
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  34. A framework for philosophical biology.Sepehr Ehsani - manuscript
    Advances in biology, at least over the past two centuries, have mostly relied on theories that were subsequently revised, expanded or eventually refuted using experimental and other means. The field of theoretical biology used to primarily provide a basis, similar to theoretical physics in the physical sciences, to rationally examine the frameworks within which biological experiments were carried out and to shed light on overlooked gaps in understanding. Today, however, theoretical biology has generally become synonymous with computational and mathematical biology. (...)
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  35. The Origin of Cellular Life and Biosemiotics.Attila Grandpierre - 2013 - Biosemiotics (3):1-15.
    Recent successes of systems biology clarified that biological functionality is multilevel. We point out that this fact makes it necessary to revise popular views about macromolecular functions and distinguish between local, physico-chemical and global, biological functions. Our analysis shows that physico-chemical functions are merely tools of biological functionality. This result sheds new light on the origin of cellular life, indicating that in evolutionary history, assignment of biological functions to cellular ingredients plays a crucial role. In this wider picture, even if (...)
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  36. Genetics, Epigenetics, Paragenetics: Getting Closer to Life.Bhakti Madhava Puri - 2014 - The Harmonizer.
    Gregor Mendel (1822-1884) was the first to explain that certain 'traits' were inherited in plants from one generation to the next. These would later become known as genes. Frederich Miescher in 1869 analyzed a substance from the nucleus of cells, which he therefore called nuclein. Further study of nuclein revealed that it contained elements like hydrogen, oxygen, nitrogen and phosphorous, with a specific ratio of nitrogen to phosphorous. Then in 1878 Albrecht Kossel determined that nuclein contained nucleic acid, from which (...)
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  37. Two genetic codes: Repetitive syntax for active non-coding RNAs; non-repetitive syntax for the DNA archives.Witzany Guenther - 2017 - Communicative and Integrative Biology 10 (2):e1297352-1 - e1297352-12.
    Current knowledge of the RNA world indicates 2 different genetic codes being present throughout the living world. In contrast to non-coding RNAs that are built of repetitive nucleotide syntax, the sequences that serve as templates for proteins share—as main characteristics—a non-repetitive syntax. Whereas non-coding RNAs build groups that serve as regulatory tools in nearly all genetic processes, the coding sections represent the evolutionarily successful function of the genetic information storage medium. This indicates that the differences in their syntax structure are (...)
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  38. Analytic philosophy for biomedical research: the imperative of applying yesterday's timeless messages to today's impasses.Sepehr Ehsani - 2020 - In Patrick Glauner & Philipp Plugmann (eds.), Innovative Technologies for Market Leadership: Investing in the Future. Springer. pp. 167-200.
    The mantra that "the best way to predict the future is to invent it" (attributed to the computer scientist Alan Kay) exemplifies some of the expectations from the technical and innovative sides of biomedical research at present. However, for technical advancements to make real impacts both on patient health and genuine scientific understanding, quite a number of lingering challenges facing the entire spectrum from protein biology all the way to randomized controlled trials should start to be overcome. The proposal (...)
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  39. TGF-beta signaling proteins and the Protein Ontology.Arighi Cecilia, Liu Hongfang, Natale Darren, Barker Winona, Drabkin Harold, Blake Judith, Barry Smith & Wu Cathy - 2009 - BMC Bioinformatics 10 (Suppl 5):S3.
    The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides (...)
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  40.  54
    Is Complexity Important for Philosophy of Mind?Kristina Šekrst & Sandro Skansi - manuscript
    Computational complexity has often been ignored in the philosophy of mind, in philosophical artificial intelligence studies. The purpose of this paper is threefold. First and foremost, to show the importance of complexity rather than computability in philosophical and AI problems. Second, to rephrase the notion of computability in terms of solvability, i.e., treating computability as non-sufficient for establishing intelligence. The Church-Turing thesis is therefore revisited and rephrased in order to capture the ontological background of spatial and temporal complexity. Third, to (...)
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  41. A framework for protein classification.Anand Kumar & Barry Smith - 2003 - In Anand Kumar & Barry Smith (eds.), Proceedings of the 2003 German Conference on Bioinformatics, Vol. II. pp. 55-57.
    It is widely understood that protein functions can be exhaustively described in terms of no single parameter, whether this be amino acid sequence or the three-dimensional structure of the underlying protein molecule. This means that a number of different attributes must be used to create an ontology of protein functions. Certainly much of the required information is already stored in databases such as Swiss-Prot, Protein Data Bank, SCOP and MIPS. But the latter have been developed for (...)
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  42. Where Do You Get Your Protein? Or: Biochemical Realization.Tuomas E. Tahko - 2020 - British Journal for the Philosophy of Science 71 (3):799-825.
    Biochemical kinds such as proteins pose interesting problems for philosophers of science, as they can be studied from the points of view of both biology and chemistry. The relationship between the biological functions of biochemical kinds and the microstructures that they are related to is the key question. This leads us to a more general discussion about ontological reductionism, microstructuralism, and multiple realization at the biology-chemistry interface. On the face of it, biochemical kinds seem to pose a challenge for ontological (...)
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  43. Universal Complexity in Action: Active Condensed Matter, Integral Medicine, Causal Economics and Sustainable Governance.Andrei P. Kirilyuk - manuscript
    We review the recently proposed universal concept of dynamic complexity and its new mathematics based on the unreduced interaction problem solution. We then consider its progress-bringing applications at various levels of complex world dynamics, including complex-dynamical nanometal physics and living condensed matter, unreduced nanobiosystem dynamics and the integral medicine concept, causally complete management of complex economical and social dynamics, and the ensuing concept of truly sustainable world governance.
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  44. Complexity and Emergence.Avijit Lahiri - 2024 - Bengaluru: Avijit Lahiri.
    This monograph focuses on two major themes of current interest---those of complexity and emergence. Neither of the two concepts is, in the very nature of things, precisely defined or easily comprehended. Complexity is all around us while the sciences often analyze entities and events by making simplifications. But the fault lines in the latter get exposed over larger spans of space and time. Complexity entails emergence that involves discontinuity and novelty in the evolution of complex systems, based on the appearance (...)
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  45. Complexics as a meta-transdisciplinary field.Albert Bastardas-Boada - 2019 - Congrès Mondial Pour la Pensée Complexe. Les Défis D’Un Monde Globalisé. (Paris, 8-9 Décembre. UNESCO).
    ‘Complexics’ denotes the meta-transdisciplinary field specifically concerned with giving us suitable cognitive tools to understand the world’s complexity. Additionally, the use of the adjective ‘complexical’ would avoid the common confusion caused by the adjective ‘complex’, which belongs to everyday usage and already has its own connotations of complication and confusion. Thus, ‘complexical’ thinking and ‘complexical’ perspective would provide clearer terms, be freer of confusion, and refer more precisely to epistemic elements in contrast to the ‘complexity’ typical of many phenomena of (...)
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  46. The complex nonlinear thinking: Edgar Morin's demand of a reform of thinking and the contribution of synergetics.Helena Knyazeva - 2004 - World Futures 60 (5 & 6):389 – 405.
    Main principles of the complex nonlinear thinking which are based on the notions of the modern theory of evolution and self-organization of complex systems called also synergetics are under discussion in this article. The principles are transdisciplinary, holistic, and oriented to a human being. The notions of system complexity, nonlinearity of evolution, creative chaos, space-time definiteness of structure-attractors of evolution, resonant influences, nonlinear and soft management are here of great importance. In this connection, a prominent contribution made to system analysis (...)
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  47. Model for DNA and Protein Interactions and the Function of the Operator.Alfred Gierer - 1966 - Nature 212:1480-1481.
    The short paper introduces the concept of possible branches of double-stranded DNA (later sometimes called palindromes): Certain sequences of nucleotides may be followed, after a short unpaired stretch, by a complementary sequence in reversed order, such that each DNA strand can fold back on itself, and the DNA assumes a cruciform or tree-like structure. This is postulated to interact with regulatory proteins. -/- .
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  48. Complexity Perspectives on Language, Communication and Society.Albert Bastardas-Boada & Àngels Massip-Bonet (eds.) - 2013 - Berlin: Springer.
    The “language-communication-society” triangle defies traditional scientific approaches. Rather, it is a phenomenon that calls for an integration of complex, transdisciplinary perspectives, if we are to make any progress in understanding how it works. The highly diverse agents in play are not merely cognitive and/or cultural, but also emotional and behavioural in their specificity. Indeed, the effort may require building a theoretical and methodological body of knowledge that can effectively convey the characteristic properties of phenomena in human terms. New complexity approaches (...)
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  49. SNARE proteins as molecular masters of interneuronal communication.Danko D. Georgiev & James F. Glazebrook - 2010 - Biomedical Reviews 21:17-23.
    In the beginning of the 20th century the groundbreaking work of Ramon y Cajal firmly established the neuron doctrine, according to which neurons are the basic structural and functional units of the nervous system. Von Weldeyer coined the term “neuron” in 1891, but the huge leap forward in neuroscience was due to Cajal’s meticulous microscopic observations of brain sections stained with an improved version of Golgi’s la reazione nera (black reaction). The latter improvement of Golgi’s technique made it possible to (...)
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  50. (1 other version)Complex demonstratives, hidden arguments, and presupposition.Ethan Nowak - 2019 - Synthese (4):1-36.
    Standard semantic theories predict that non-deictic readings for complex demonstratives should be much more widely available than they in fact are. If such readings are the result of a lexical ambiguity, as Kaplan (1977) and others suggest, we should expect them to be available wherever a definite description can be used. The same prediction follows from ‘hidden argument’ theories like the ones described by King (2001) and Elbourne (2005). Wolter (2006), however, has shown that complex demonstratives admit non-deictic interpretations only (...)
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