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Periodicals

Computational Immunology Meets Bioinformatics: The Use of Prediction Tools for Molecular Binding in the Simulation of the Immune System

We present a new approach to the study of the immune system that combines techniques of systems biology with information provided by data-driven prediction methods. To this end, we have extended an agent-based simulator of the immune response, C-ImmSim, such that it represents pathogens, as well as lymphocytes receptors, by means of their amino acid sequences and makes use of bioinformatics methods for T and B cell epitope prediction. This is a key step for the simulation of the immune response, because it determines immunogenicity. The binding of the epitope, which is the immunogenic part of an invading pathogen, together with activation and cooperation from T helper cells, is required to trigger an immune response in the affected host. To determine a pathogen's epitopes, we use existing prediction methods. In addition, we propose a novel method, which uses Miyazawa and Jernigan protein-protein potential measurements, for assessing molecular binding in the context of immune complexes. We benchmark the resulting model by simulating a classical immunization experiment that reproduces the development of immune memory. We also investigate the role of major histocompatibility complex (MHC) haplotype heterozygosity and homozygosity with respect to the influenza virus and show that there is an advantage to heterozygosity. Finally, we investigate the emergence of one or more dominating clones of lymphocytes in the situation of chronic exposure to the same immunogenic molecule and show that high affinity clones proliferate more than any other. These results show that the simulator produces dynamics that are stable and consistent with basic immunological knowledge. We believe that the combination of genomic information and simulation of the dynamics of the immune system, in one single tool, can offer new perspectives for a better understanding of the immune system.

Architecture & Planning• 2010• Public Library of Science
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Periodicals

Neuropixels 2.0: A miniaturized high-density probe for stable, long-term brain recordings

Measuring the dynamics of neural processing across time scales requires following the spiking of thousands of individual neurons over milliseconds and months. To address this need, we introduce the Neuropixels 2.0 probe together with newly designed analysis algorithms. The probe has more than 5000 sites and is miniaturized to facilitate chronic implants in small mammals and recording during unrestrained behavior. High-quality recordings over long time scales were reliably obtained in mice and rats in six laboratories. Improved site density and arrangement combined with newly created data processing methods enable automatic post hoc correction for brain movements, allowing recording from the same neurons for more than 2 months. These probes and algorithms enable stable recordings from thousands of sites during free behavior, even in small animals such as mice.

Architecture & Planning• 2021• American Association for the Advancement of Science
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Cognitive load theory, educational research, and instructional design: some food for thought

Cognitive load is a theoretical notion with an increasingly central role in the educational research literature. The basic idea of cognitive load theory is that cognitive capacity in working memory is limited, so that if a learning task requires too much capacity, learning will be hampered. The recommended remedy is to design instructional systems that optimize the use of working memory capacity and avoid cognitive overload. Cognitive load theory has advanced educational research considerably and has been used to explain a large set of experimental findings. This article sets out to explore the open questions and the boundaries of cognitive load theory by identifying a number of problematic conceptual, methodological and application-related issues. It concludes by presenting a research agenda for future studies of cognitive load.

Architecture & Planning• 2009• Springer Science+Business Media
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Periodicals

A vision-based formation control framework

We describe a framework for cooperative control of a group of nonholonomic mobile robots that allows us to build complex systems from simple controllers and estimators. The resultant modular approach is attractive because of the potential for reusability. Our approach to composition also guarantees stability and convergence in a wide range of tasks. There are two key features in our approach: 1) a paradigm for switching between simple decentralized controllers that allows for changes in formation; 2) the use of information from a single type of sensor, an omnidirectional camera, for all our controllers. We describe estimators that abstract the sensory information at different levels, enabling both decentralized and centralized cooperative control. Our results include numerical simulations and experiments using a testbed consisting of three nonholonomic robots.

Architecture & Planning• 2002• Institute of Electrical and Electronics Engineers
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Periodicals

YOLO-v1 to YOLO-v8, the Rise of YOLO and Its Complementary Nature toward Digital Manufacturing and Industrial Defect Detection

Since its inception in 2015, the YOLO (You Only Look Once) variant of object detectors has rapidly grown, with the latest release of YOLO-v8 in January 2023. YOLO variants are underpinned by the principle of real-time and high-classification performance, based on limited but efficient computational parameters. This principle has been found within the DNA of all YOLO variants with increasing intensity, as the variants evolve addressing the requirements of automated quality inspection within the industrial surface defect detection domain, such as the need for fast detection, high accuracy, and deployment onto constrained edge devices. This paper is the first to provide an in-depth review of the YOLO evolution from the original YOLO to the recent release (YOLO-v8) from the perspective of industrial manufacturing. The review explores the key architectural advancements proposed at each iteration, followed by examples of industrial deployment for surface defect detection endorsing its compatibility with industrial requirements.

Architecture & Planning• 2023• Multidisciplinary Digital Publishing Institute
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Periodicals

A Unified Framework of Five Principles for AI in Society

Artificial Intelligence (AI) is already having a major impact on society. As a result, many organizations have launched a wide range of initiatives to establish ethical principles for the adoption of socially beneficial AI. Unfortunately, the sheer volume of proposed principles threatens to overwhelm and confuse. How might this problem of ‘principle proliferation’ be solved? In this paper, we report the results of a fine-grained analysis of several of the highest-profile sets of ethical principles for AI. We assess whether these principles converge upon a set of agreed-upon principles, or diverge, with significant disagreement over what constitutes ‘ethical AI.’ Our analysis finds a high degree of overlap among the sets of principles we analyze. We then identify an overarching framework consisting of five core principles for ethical AI. Four of them are core principles commonly used in bioethics: beneficence, non-maleficence, autonomy, and justice. On the basis of our comparative analysis, we argue that a new principle is needed in addition: explicability, understood as incorporating both the epistemological sense of intelligibility (as an answer to the question ‘how does it work?’) and in the ethical sense of accountability (as an answer to the question: ‘who is responsible for the way it works?’). In the ensuing discussion, we note the limitations and assess the implications of this ethical framework for future efforts to create laws, rules, technical standards, and best practices for ethical AI in a wide range of contexts.

Architecture & Planning• 2019• The MIT Press
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Periodicals

Application of Spectroscopic Methods for Structural Analysis of Chitin and Chitosan

Chitin, the second most important natural polymer in the world, and its N-deacetylated derivative chitosan, have been identified as versatile biopolymers for a broad range of applications in medicine, agriculture and the food industry. Two of the main reasons for this are firstly the unique chemical, physicochemical and biological properties of chitin and chitosan, and secondly the unlimited supply of raw materials for their production. These polymers exhibit widely differing physicochemical properties depending on the chitin source and the conditions of chitosan production. The presence of reactive functional groups as well as the polysaccharide nature of these biopolymers enables them to undergo diverse chemical modifications. A complete chemical and physicochemical characterization of chitin, chitosan and their derivatives is not possible without using spectroscopic techniques. This review focuses on the application of spectroscopic methods for the structural analysis of these compounds.

Architecture & Planning• 2010• Multidisciplinary Digital Publishing Institute
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Periodicals

Modeling and control of formations of nonholonomic mobile robots

This paper addresses the control of a team of nonholonomic mobile robots navigating in a terrain with obstacles while maintaining a desired formation and changing formations when required, using graph theory. We model the team as a triple, (g, r, H), consisting of a group element g that describes the gross position of the lead robot, a set of shape variables r that describe the relative positions of robots, and a control graph H that describes the behaviors of the robots in the formation. Our framework enables the representation and enumeration of possible control graphs and the coordination of transitions between any two formations.

Architecture & Planning• 2001• Institute of Electrical and Electronics Engineers
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Periodicals

A Review on UAV-Based Applications for Precision Agriculture

Emerging technologies such as Internet of Things (IoT) can provide significant potential in Smart Farming and Precision Agriculture applications, enabling the acquisition of real-time environmental data. IoT devices such as Unmanned Aerial Vehicles (UAVs) can be exploited in a variety of applications related to crops management, by capturing high spatial and temporal resolution images. These technologies are expected to revolutionize agriculture, enabling decision-making in days instead of weeks, promising significant reduction in cost and increase in the yield. Such decisions enable the effective application of farm inputs, supporting the four pillars of precision agriculture, i.e., apply the right practice, at the right place, at the right time and with the right quantity. However, the actual proliferation and exploitation of UAVs in Smart Farming has not been as robust as expected mainly due to the challenges confronted when selecting and deploying the relevant technologies, including the data acquisition and image processing methods. The main problem is that still there is no standardized workflow for the use of UAVs in such applications, as it is a relatively new area. In this article, we review the most recent applications of UAVs for Precision Agriculture. We discuss the most common applications, the types of UAVs exploited and then we focus on the data acquisition methods and technologies, appointing the benefits and drawbacks of each one. We also point out the most popular processing methods of aerial imagery and discuss the outcomes of each method and the potential applications of each one in the farming operations.

Architecture & Planning• 2019• Multidisciplinary Digital Publishing Institute
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Periodicals

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

In the quest to reconstruct the Tree of Life, researchers have increasingly turned to phylogenomics, the inference of phylogenetic relationships using genome-scale data (Box 1). Mesmerized by the sustained increase in sequencing throughput, many phylogeneticists entertained the hope that the incongruence frequently observed in studies using single or a few genes [1] would come to an end with the generation of large multigene datasets. Yet, as so often happens, reality has turned out to be far more complex, as three recent large-scale analyses, one published in PLoS Biology [2–4], make clear. The studies, which deal with the early diversification of animals, produced highly incongruent (Box 2) findings despite the use of considerable sequence data (see Figure 1). Clearly, merely adding more sequences is not enough to resolve the inconsistencies. Here, taking these three studies as a case in point, we discuss pitfalls that the simple addition of sequences cannot avoid, and show how the observed incongruence can be largely overcome and how improved bioinformatics methods can help reveal the full potential of phylogenomics.

Architecture & Planning• 2011• Public Library of Science
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Periodicals

State of the Art in Research on Microgrids: A Review

The significant benefits associated with microgrids have led to vast efforts to expand their penetration in electric power systems. Although their deployment is rapidly growing, there are still many challenges to efficiently design, control, and operate microgrids when connected to the grid, and also when in islanded mode, where extensive research activities are underway to tackle these issues. It is necessary to have an across-the-board view of the microgrid integration in power systems. This paper presents a review of issues concerning microgrids and provides an account of research in areas related to microgrids, including distributed generation, microgrid value propositions, applications of power electronics, economic issues, microgrid operation and control, microgrid clusters, and protection and communications issues.

Architecture & Planning• 2015• Institute of Electrical and Electronics Engineers
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Periodicals

A survey of software refactoring

We provide an extensive overview of existing research in the field of software refactoring. This research is compared and discussed based on a number of different criteria: the refactoring activities that are supported, the specific techniques and formalisms that are used for supporting these activities, the types of software artifacts that are being refactored, the important issues that need to be taken into account when building refactoring tool support, and the effect of refactoring on the software process. A running example is used to explain and illustrate the main concepts.

Architecture & Planning• 2004• IEEE Computer Society
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Periodicals

The Emerging Structure of International Politics

During the Cold War, the bipolar structure of international system and the nuclear weaponry available to some states combined to perpetuate a troubled peace. As the bipolar era draws to a close, one has to question the likely structural changes in prospect. Following the dissolution of the Soviet Union, bipolarity endures, albeit in an altered state, because Russia stil takes care of itself and no great powers have emerged yet. With the waning of Russian power, the United States is no longer held in check by any other country. Balance of power theory leads one to assume that other powers, alone or in concert, will bring American power into balance. Considering the likely changes in the structure of international system, one can presuppose that three political units may rise to great-power rank: Germany or a West European state, Japan and China. Despite all the progress achieved by these countries, for some years to come, the United States will be the leading country economically as well as militarily

Architecture & Planning• 1993• The MIT Press
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Periodicals

From the Phenomenology to the Mechanisms of Consciousness: Integrated Information Theory 3.0

This paper presents Integrated Information Theory (IIT) of consciousness 3.0, which incorporates several advances over previous formulations. IIT starts from phenomenological axioms: information says that each experience is specific--it is what it is by how it differs from alternative experiences; integration says that it is unified--irreducible to non-interdependent components; exclusion says that it has unique borders and a particular spatio-temporal grain. These axioms are formalized into postulates that prescribe how physical mechanisms, such as neurons or logic gates, must be configured to generate experience (phenomenology). The postulates are used to define intrinsic information as "differences that make a difference" within a system, and integrated information as information specified by a whole that cannot be reduced to that specified by its parts. By applying the postulates both at the level of individual mechanisms and at the level of systems of mechanisms, IIT arrives at an identity: an experience is a maximally irreducible conceptual structure (MICS, a constellation of concepts in qualia space), and the set of elements that generates it constitutes a complex. According to IIT, a MICS specifies the quality of an experience and integrated information ΦMax its quantity. From the theory follow several results, including: a system of mechanisms may condense into a major complex and non-overlapping minor complexes; the concepts that specify the quality of an experience are always about the complex itself and relate only indirectly to the external environment; anatomical connectivity influences complexes and associated MICS; a complex can generate a MICS even if its elements are inactive; simple systems can be minimally conscious; complicated systems can be unconscious; there can be true "zombies"--unconscious feed-forward systems that are functionally equivalent to conscious complexes.

Architecture & Planning• 2014• Public Library of Science
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Periodicals

A Vision of IoT: Applications, Challenges, and Opportunities With China Perspective

Internet of Things (IoT), which will create a huge network of billions or trillions of “Things” communicating with one another, are facing many technical and application challenges. This paper introduces the status of IoT development in China, including policies, R&D plans, applications, and standardization. With China's perspective, this paper depicts such challenges on technologies, applications, and standardization, and also proposes an open and general IoT architecture consisting of three platforms to meet the architecture challenge. Finally, this paper discusses the opportunity and prospect of IoT.

Architecture & Planning• 2014• Institute of Electrical and Electronics Engineers
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Active Inference: A Process Theory

This article describes a process theory based on active inference and belief propagation. Starting from the premise that all neuronal processing (and action selection) can be explained by maximizing Bayesian model evidence-or minimizing variational free energy-we ask whether neuronal responses can be described as a gradient descent on variational free energy. Using a standard (Markov decision process) generative model, we derive the neuronal dynamics implicit in this description and reproduce a remarkable range of well-characterized neuronal phenomena. These include repetition suppression, mismatch negativity, violation responses, place-cell activity, phase precession, theta sequences, theta-gamma coupling, evidence accumulation, race-to-bound dynamics, and transfer of dopamine responses. Furthermore, the (approximately Bayes' optimal) behavior prescribed by these dynamics has a degree of face validity, providing a formal explanation for reward seeking, context learning, and epistemic foraging. Technically, the fact that a gradient descent appears to be a valid description of neuronal activity means that variational free energy is a Lyapunov function for neuronal dynamics, which therefore conform to Hamilton's principle of least action.

Architecture & Planning• 2016• The MIT Press
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The Musicality of Non-Musicians: An Index for Assessing Musical Sophistication in the General Population

Musical skills and expertise vary greatly in Western societies. Individuals can differ in their repertoire of musical behaviours as well as in the level of skill they display for any single musical behaviour. The types of musical behaviours we refer to here are broad, ranging from performance on an instrument and listening expertise, to the ability to employ music in functional settings or to communicate about music. In this paper, we first describe the concept of 'musical sophistication' which can be used to describe the multi-faceted nature of musical expertise. Next, we develop a novel measurement instrument, the Goldsmiths Musical Sophistication Index (Gold-MSI) to assess self-reported musical skills and behaviours on multiple dimensions in the general population using a large Internet sample (n = 147,636). Thirdly, we report results from several lab studies, demonstrating that the Gold-MSI possesses good psychometric properties, and that self-reported musical sophistication is associated with performance on two listening tasks. Finally, we identify occupation, occupational status, age, gender, and wealth as the main socio-demographic factors associated with musical sophistication. Results are discussed in terms of theoretical accounts of implicit and statistical music learning and with regard to social conditions of sophisticated musical engagement.

Architecture & Planning• 2014• Public Library of Science
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