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Special Protein Molecules Computational Identification

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ISBN: 9783038970439 9783038970446 Year: Pages: VIII, 296 Language: english
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Medical technology
Added to DOAB on : 2018-08-09 12:10:11
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It is time consuming and costly to detect new molecules of some special proteins. These special proteins include cytokines, enzymes, cell-penetrating peptides, anticancer peptides, cancer lectins, G-protein-coupled receptors, etc. Researchers often employ computer programs to list some candidates, and to validate the candidates with molecular experiments. These computer programs are key to possible savings on wet experiment costs. Software results with high false positive will lead to high costs in the validation process.In this Special Issue, we focus on these computer program approaches and algorithms. Some "golden features" from protein primary sequences have been proposed for these problems, such as Chou’s PseAAC (pseudo amino acid composition). PseAAC has been tried on nearly all kinds of protein identification, together with SVM (support vector machines, a type of classifier). However, I prefer special features, and classification methods should be proposed for special protein molecules. "Golden features" cannot work well on all kinds of proteins. I hope that submissions will focus on a type of special protein molecule, collect related data sets, obtain better prediction performance (especially low false positives), and develop user-friendly software tools or web servers.

Time and Causality

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889192526 Year: Pages: 118 DOI: 10.3389/978-2-88919-252-6 Language: English
Publisher: Frontiers Media SA
Subject: Psychology --- Science (General)
Added to DOAB on : 2015-11-16 15:44:59
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The problem of how humans and other intelligent systems construct causal representations from non-causal perceptual evidence has occupied scholars in cognitive science for many decades. Most contemporary approaches agree with David Hume that patterns of covariation between two events of interest are the critical input to the causal induction engine, irrespective of whether this induction is believed to be grounded in the formation of associations (Shanks & Dickinson, 1987), rule-based evaluation (White, 2004), appraisal of causal powers (Cheng, 1997), or construction of Bayesian Causal Networks (Pearl, 2000). Recent research, however, has repeatedly demonstrated that an exclusive focus on covariation while neglecting contiguity (another of Hume's cues) results in ecologically invalid models of causal inference. Temporal spacing, order, variability, predictability, and patterning all have profound influence on the type of causal representation that is constructed. The influence of time upon causal representations could be seen as a bottom-up constraint (though current bottom-up models cannot account for the full spectrum of effects). However, causal representations in turn also constrain the perception of time: Put simply, two causally related events appear closer in subjective time than two (equidistant) unrelated events. This reversal of Hume's conjecture, referred to as Causal Binding (Buehner & Humphreys, 2009) is a top-down constraint, and suggests that our representations of time and causality are mutually influencing one another. At present, the theoretical implications of this phenomenon are not yet fully understood. Some accounts link it exclusively to human motor planning (appealing to mechanisms of cross-modal temporal adaptation, or forward learning models of motor control). However, recent demonstrations of causal binding in the absence of human action, and analogous binding effects in the visual spatial domain, challenge such accounts in favour of Bayesian Evidence Integration. This Research Topic reviews and further explores the nature of the mutual influence between time and causality, how causal knowledge is constructed in the context of time, and how it in turn shapes and alters our perception of time. We draw together literatures from the perception and cognitive science, as well as experimental and theoretical papers. Contributions investigate the neural bases of binding and causal learning/perception, methodological advances, and functional implications of causal learning and perception in real time.

How Humans Recognize Objects: Segmentation, Categorization and Individual Identification

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889199402 Year: Pages: 265 DOI: 10.3389/978-2-88919-940-2 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Psychology
Added to DOAB on : 2016-01-19 14:05:46
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Human beings experience a world of objects: bounded entities that occupy space and persist through time. Our actions are directed toward objects, and our language describes objects. We categorize objects into kinds that have different typical properties and behaviors. We regard some kinds of objects – each other, for example – as animate agents capable of independent experience and action, while we regard other kinds of objects as inert. We re-identify objects, immediately and without conscious deliberation, after days or even years of non-observation, and often following changes in the features, locations, or contexts of the objects being re-identified. Comparative, developmental and adult observations using a variety of approaches and methods have yielded a detailed understanding of object detection and recognition by the visual system and an advancing understanding of haptic and auditory information processing. Many fundamental questions, however, remain unanswered. What, for example, physically constitutes an “object”? How do specific, classically-characterizable object boundaries emerge from the physical dynamics described by quantum theory, and can this emergence process be described independently of any assumptions regarding the perceptual capabilities of observers? How are visual motion and feature information combined to create object information? How are the object trajectories that indicate persistence to human observers implemented, and how are these trajectory representations bound to feature representations? How, for example, are point-light walkers recognized as single objects? How are conflicts between trajectory-driven and feature-driven identifications of objects resolved, for example in multiple-object tracking situations? Are there separate “what” and “where” processing streams for haptic and auditory perception? Are there haptic and/or auditory equivalents of the visual object file? Are there equivalents of the visual object token? How are object-identification conflicts between different perceptual systems resolved? Is the common assumption that “persistent object” is a fundamental innate category justified? How does the ability to identify and categorize objects relate to the ability to name and describe them using language? How are features that an individual object had in the past but does not have currently represented? How are categorical constraints on how objects move or act represented, and how do such constraints influence categorization and the re-identification of individuals? How do human beings re-identify objects, including each other, as persistent individuals across changes in location, context and features, even after gaps in observation lasting months or years? How do human capabilities for object categorization and re-identification over time relate to those of other species, and how do human infants develop these capabilities? What can modeling approaches such as cognitive robotics tell us about the answers to these questions? Primary research reports, reviews, and hypothesis and theory papers addressing questions relevant to the understanding of perceptual object segmentation, categorization and individual identification at any scale and from any experimental or modeling perspective are solicited for this Research Topic. Papers that review particular sets of issues from multiple disciplinary perspectives or that advance integrative hypotheses or models that take data from multiple experimental approaches into account are especially encouraged.

At The Top of the Interneuronal Pyramid - Calretinin Expressing Cortical Interneurons

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889197088 Year: Pages: 102 DOI: 10.3389/978-2-88919-708-8 Language: English
Publisher: Frontiers Media SA
Subject: Neurology --- Science (General)
Added to DOAB on : 2016-04-07 11:22:02
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It is in general well appreciated that the cortical interneurons play various important roles in cortical neuronal networks both in normal and pathological states. Based on connectivity pattern, developmental, morphological and electrophysiological properties, distinct subgroups of GABAergic interneurons can be differentiated in the neocortex as well as in the hippocampal formation. In this E-Book, we are focusing our attention on inhibitory interneurons expressing calcium-binding protein calretinin (CR). The aim of the E-Book is to consolidate the knowledge about this interneuronal population and to inspire further research on the function and malfunction of these neurons, which – functionally – seem to stand "at the top of the pyramid" of cortical interneuronal types.

Dynamics of cyclic nucleotide signaling in neurons

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889196463 Year: Pages: 92 DOI: 10.3389/978-2-88919-646-3 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Neurology
Added to DOAB on : 2016-08-16 10:34:25
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Cyclic nucleotides control a number of neuronal properties including neuronal differentiation, pathfinding, regulation of excitability and synaptic transmission, and control of gene expression. Signaling events mediated by cAMP or cGMP are transient and take place within the complex 3-dimensional structure of the neuronal cell. Signaling events happen on the time scale of seconds to minutes and the biological significance of the temporal dimension remains poorly understood. Structural features of neurons (dendritic spines and branches, cell body, nucleus, axon…) as well as AKAPs and other scaffolding proteins that keep signaling enzymes together and form "signaling microdomains", are critical spatial determinants of signal integration. Finally, the types of enzymes involved in signal integration, which are expressed as a number of different types and splice variants, yield another dimension that determines signal integration properties. Biosensor imaging provides direct temporal and spatial measurement of intracellular signals. This novel approach, together with more conventional methods such as biochemistry, electrophysiology, and modeling, now provide a better understanding of the spatial and temporal features of cyclic nucleotide signal integration in living neurons. This topic aims at providing a better understanding of how neurons are "making sense" of cyclic nucleotide signaling in living neurons.

Regulation of Chemokine- Receptor Interactions and Functions

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ISBN: 9783038427285 9783038427278 Year: Pages: 228 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Biochemistry
Added to DOAB on : 2018-03-26 15:44:06
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A hallmark of inflammation is the accumulation of leukocytes, which can serve to remove pathogens and necrotic tissue, but may also damage healthy tissue and exacerbate the inflammatory response. Our understanding of leukocyte recruitment in inflammation was revolutionized in the late 1980s by the discovery of chemokines (chemotactic cytokines), a family of small, secreted proteins that induce migration of selective subsets of leukocytes. Shortly afterwards, chemokines were found to exert their functions through the now familiar chemokine receptors, members of the G protein-coupled receptor superfamily. As their physiological and pathological functions were elucidated, chemokine receptors have become popular targets for drug development in inflammatory diseases as well as cancer metastasis and HIV infection. Extensive research has revealed that the functions of chemokines and their receptors are regulated at numerous levels, including: genetic mutations/polymorphisms; control of expression levels; ligand internalization via functional or decoy receptors; intrinsic selectivity of chemokine-receptor binding; hetero- or homo-oligomerization of chemokines or of receptors; alternative signalling pathways; interaction of chemokines with glycosaminoglycans; post-translational modifications; and binding to pathogen-derived inhibitors. This Special Issue of IJMS focused on the natural and pharmacological mechanisms by which the activities of chemokines and their receptors can be regulated.

Is Conflict Adaptation an Illusion?

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889194957 Year: Pages: 164 DOI: 10.3389/978-2-88919-495-7 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Psychology
Added to DOAB on : 2015-11-16 15:44:59
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Conflict adaptation theory is one of the most popular theories in cognitive psychology. The theory argues that participants strategically modulate attention away from distracting stimulus features in response to conflict. Although results with proportion congruent, sequential congruency, and similar paradigms seem consistent with the conflict adaptation view, some researchers have expressed scepticism. The paradigms used in the study of conflict adaptation require the manipulation of stimulus frequencies, sequential dependencies, time-on-task regularities, and various other task regularities that introduce the potential for learning of conflict-unrelated information. This results in the unintentional confounding of measures of conflict adaptation with simpler learning and memory biases. There are also alternative accounts which propose that attentional adaptation does occur, but via different mechanisms, such as valence, expectancy, or effort. A significant (and often heated) debate remains surrounding the question of whether conflict adaptation exists independent of these alternative mechanisms of action. The aim of this Research Topic is to provide a forum for current directions in this area, considering perspectives from all sides of the debate.

Perception-Cognition Interface and Cross-Modal Experiences: Insights into Unified Consciousness

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889450718 Year: Pages: 135 DOI: 10.3389/978-2-88945-071-8 Language: English
Publisher: Frontiers Media SA
Subject: Psychology --- Science (General)
Added to DOAB on : 2017-07-06 13:27:36
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The present Research Topic explores closely related aspects of mental functioning, namely an interplay between perception and cognition, interactions among various sensory modalities, and finally, more or less unified conscious experiences arising in the context of these relations. Contributions emphasize a high flexibility observed in perception and may be seen as potential challenges to the traditional modular architecture of perceptual systems. Although the articles describe different phenomena, they follow one common theme - to investigate broadly understood unified experience - by studying either perception-cognition integration or the integration between sensory modalities. These integrative processes may well apply to subpersonal unconscious representations. However, the aim here is to approach phenomenal experience and thus a straightforward way of thinking about it is in terms of conscious perception. Putting together scientific and philosophical concerns, this special issue encourages extending the study of perceptual experience beyond the single sense perception to advance our understanding of the complex interdependencies between different sensory modalities, other mental domains, and various kinds of unifying relations within conscious experience. It exhibits a remarkable need to study these phenomena in tangent, and so, the authors examine a variety of ways in which our perceptual experiences may be cross-modal or multisensory, integrated, embodied, synesthetic, cognitively penetrated, or otherwise affected by top-down influences. The Research Topic comprises theoretical and empirical contributions of such fields as philosophy of mind, cognitive science, psychology, and neuroscience in the form of hypothesis and theory articles, original research articles, opinion papers, reviews, and commentaries.The present Research Topic explores closely related aspects of mental functioning, namely an interplay between perception and cognition, interactions among various sensory modalities, and finally, more or less unified conscious experiences arising in the context of these relations. Contributions emphasize a high flexibility observed in perception and may be seen as potential challenges to the traditional modular architecture of perceptual systems. Although the articles describe different phenomena, they follow one common theme - to investigate broadly understood unified experience - by studying either perception-cognition integration or the integration between sensory modalities. These integrative processes may well apply to subpersonal unconscious representations. However, the aim here is to approach phenomenal experience and thus a straightforward way of thinking about it is in terms of conscious perception. Putting together scientific and philosophical concerns, this special issue encourages extending the study of perceptual experience beyond the single sense perception to advance our understanding of the complex interdependencies between different sensory modalities, other mental domains, and various kinds of unifying relations within conscious experience. It exhibits a remarkable need to study these phenomena in tangent, and so, the authors examine a variety of ways in which our perceptual experiences may be cross-modal or multisensory, integrated, embodied, synesthetic, cognitively penetrated, or otherwise affected by top-down influences. The Research Topic comprises theoretical and empirical contributions of such fields as philosophy of mind, cognitive science, psychology, and neuroscience in the form of hypothesis and theory articles, original research articles, opinion papers, reviews, and commentaries.

Grammatical theory: From transformational grammar to constraint-based approaches

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Book Series: Textbooks in Language Sciences ISBN: 9783944675213 9783946234296 9783946234401 9783946234302 9783946234418 Year: Pages: 831 DOI: 10.26530/OAPEN_611693 Language: English
Publisher: Language Science Press
Subject: Linguistics
Added to DOAB on : 2016-07-13 11:01:16
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"This book introduces formal grammar theories that play a role in current linguistic theorizing (Phrase Structure Grammar, Transformational Grammar/Government & Binding, Generalized Phrase Structure Grammar, Lexical Functional Grammar, Categorial Grammar, Head-​Driven Phrase Structure Grammar, Construction Grammar, Tree Adjoining Grammar). The key assumptions are explained and it is shown how the respective theory treats arguments and adjuncts, the active/passive alternation, local reorderings, verb placement, and fronting of constituents over long distances. The analyses are explained with German as the object language. The second part of the book compares these approaches with respect to their predictions regarding language acquisition and psycholinguistic plausibility. The nativism hypothesis, which assumes that humans posses genetically determined innate language-specific knowledge, is critically examined and alternative models of language acquisition are discussed. The second part then addresses controversial issues of current theory building such as the question of flat or binary branching structures being more appropriate, the question whether constructions should be treated on the phrasal or the lexical level, and the question whether abstract, non-visible entities should play a role in syntactic analyses. It is shown that the analyses suggested in the respective frameworks are often translatable into each other. The book closes with a chapter showing how properties common to all languages or to certain classes of languages can be captured. The book is a translation of the German book Grammatiktheorie, which was published by Stauffenburg in 2010. "

Metal Metabolism in Animals

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ISBN: 9783038428435 9783038428442 Year: Pages: X, 356 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Biology
Added to DOAB on : 2018-04-20 14:25:48
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Through evolution of life, animals have adapted to the ubiquitous presence of metals in the biosphere. They utilize the more frequent ones as essential constituents of their biochemical machinery. In fact, about 40% of all proteins present in animal cells are so-called metalloproteins. On the other hand, animals have invented regulatory and detoxifying mechanisms to protect themselves from critical concentrations of both essential and non-essential metal concentrations. Metallomics is a modern approach applying cellular, biochemical, molecular and analytical methods to investigate the relationships of metals in their cellular context. The present edition contains a number of original articles and reviews dealing with various aspects of metallomics in animals, published as Special Issues of the International Journal of Molecular Sciences in 2016 and 2017. The book addresses subjects such as metal definition in biology, metabolism of metals in invertebrate and vertebrate animals, metal detoxification and regulation strategies, supplementation of essential trace elements, metal behavior in pregnancy and embryonic development, as well as metal toxicology and emerging medical implications.

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