OFMTutor: An operator function model intelligent tutoring system

NASA Technical Reports Server (NTRS)

Jones, Patricia M.

1989-01-01

The design, implementation, and evaluation of an Operator Function Model intelligent tutoring system (OFMTutor) is presented. OFMTutor is intended to provide intelligent tutoring in the context of complex dynamic systems for which an operator function model (OFM) can be constructed. The human operator's role in such complex, dynamic, and highly automated systems is that of a supervisory controller whose primary responsibilities are routine monitoring and fine-tuning of system parameters and occasional compensation for system abnormalities. The automated systems must support the human operator. One potentially useful form of support is the use of intelligent tutoring systems to teach the operator about the system and how to function within that system. Previous research on intelligent tutoring systems (ITS) is considered. The proposed design for OFMTutor is presented, and an experimental evaluation is described.

Intelligent building system for airport

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ancevic, M.

1997-11-01

The Munich airport uses a state-of-the-art intelligent building management system to control systems such as HVAC, runway lights, baggage handling, etc. Planning the new Munich II international airport provided a unique opportunity to use the latest state-of-the-art technical systems, while integrating their control through a single intelligent building management system. Opened in 1992, the airport is Germany`s second-largest airport after Frankfurt. The airport is staffed by 16,000 employees and can handle 17 million passengers a year. The sprawling site encompasses more than 120 buildings. The airport`s distributed control system is specifically designed to optimize the complex`s unique range of functions,more » while providing a high degree of comfort, convenience and safety for airport visitors. With the capacity to control 200,000 points, this system controls more than 112,000 points and integrates 13 major subsystems from nine different vendors. It provides convenient, accessible control of everything including the complex`s power plant, HVAC Control, the terminal`s people-moving functions, interior lighting controls, runway lights, baggage forwarding systems, elevators, and boarding bridges. The airport was named 1993 intelligent building of the year by the Intelligent Buildings Institute Foundation. Its building management system is a striking example of the degree to which a building complex`s functions can be integrated for greater operational control and efficiency.« less

A Case Study on the Application of a Structured Experimental Method for Optimal Parameter Design of a Complex Control System

NASA Technical Reports Server (NTRS)

Torres-Pomales, Wilfredo

2015-01-01

This report documents a case study on the application of Reliability Engineering techniques to achieve an optimal balance between performance and robustness by tuning the functional parameters of a complex non-linear control system. For complex systems with intricate and non-linear patterns of interaction between system components, analytical derivation of a mathematical model of system performance and robustness in terms of functional parameters may not be feasible or cost-effective. The demonstrated approach is simple, structured, effective, repeatable, and cost and time efficient. This general approach is suitable for a wide range of systems.

Identity effects dominate the impacts of multiple species extinctions on the functioning of complex food webs.

PubMed

Harvey, Eric; Séguin, Annie; Nozais, Christian; Archambault, Philippe; Gravel, Dominique

2013-01-01

Understanding the impacts of species extinctions on the functioning of food webs is a challenging task because of the complexity of ecological interactions. We report the impacts of experimental species extinctions on the functioning of two food webs of freshwater and marine systems. We used a linear model to partition the variance among the multiple components of the diversity effect (linear group richness, nonlinear group richness, and identity). The identity of each functional group was the best explaining variable of ecosystem functioning for both systems. We assessed the contribution of each functional group in multifunctional space and found that, although the effect of functional group varied across ecosystem functions, some functional groups shared common effects on functions. This study is the first experimental demonstration that functional identity dominates the effects of extinctions on ecosystem functioning, suggesting that generalizations are possible despite the inherent complexity of interactions.

Contribution to the meaning and understanding of anticipatory systems

NASA Astrophysics Data System (ADS)

Kljajić, Miroljub

2001-06-01

The present article discusses the cybernetic method in the modelling and understanding of complex systems from the epistemological, semantic as well as psychological point of view. Biological and organisational systems are the most important among complex systems. According to Rosen [1] anticipatory systems is another name for complex systems because, in a way, they function to anticipate the future state in order to preserve its structure and functioning. This paper demonstrates a strong analogy between Rosen's modified definition of anticipatory systems [2] and decision-making through simulation in organisational systems. The possible meaning of several models modified in the anticipatory mode will also be discussed as for example: a) The modified Verhaulst Model and its anticipatory modification in the case of the description of human behavior, b) The Prey-Predator Model, and c) The Evans Market Model under different conditions of the demand and supply function.

Development of structural model of adaptive training complex in ergatic systems for professional use

NASA Astrophysics Data System (ADS)

Obukhov, A. D.; Dedov, D. L.; Arkhipov, A. E.

2018-03-01

The article considers the structural model of the adaptive training complex (ATC), which reflects the interrelations between the hardware, software and mathematical model of ATC and describes the processes in this subject area. The description of the main components of software and hardware complex, their interaction and functioning within the common system are given. Also the article scrutinizers a brief description of mathematical models of personnel activity, a technical system and influences, the interactions of which formalize the regularities of ATC functioning. The studies of main objects of training complexes and connections between them will make it possible to realize practical implementation of ATC in ergatic systems for professional use.

Diffusion Geometry Unravels the Emergence of Functional Clusters in Collective Phenomena.

PubMed

De Domenico, Manlio

2017-04-21

Collective phenomena emerge from the interaction of natural or artificial units with a complex organization. The interplay between structural patterns and dynamics might induce functional clusters that, in general, are different from topological ones. In biological systems, like the human brain, the overall functionality is often favored by the interplay between connectivity and synchronization dynamics, with functional clusters that do not coincide with anatomical modules in most cases. In social, sociotechnical, and engineering systems, the quest for consensus favors the emergence of clusters. Despite the unquestionable evidence for mesoscale organization of many complex systems and the heterogeneity of their interconnectivity, a way to predict and identify the emergence of functional modules in collective phenomena continues to elude us. Here, we propose an approach based on random walk dynamics to define the diffusion distance between any pair of units in a networked system. Such a metric allows us to exploit the underlying diffusion geometry to provide a unifying framework for the intimate relationship between metastable synchronization, consensus, and random search dynamics in complex networks, pinpointing the functional mesoscale organization of synthetic and biological systems.

Diffusion Geometry Unravels the Emergence of Functional Clusters in Collective Phenomena

NASA Astrophysics Data System (ADS)

De Domenico, Manlio

2017-04-01

Collective phenomena emerge from the interaction of natural or artificial units with a complex organization. The interplay between structural patterns and dynamics might induce functional clusters that, in general, are different from topological ones. In biological systems, like the human brain, the overall functionality is often favored by the interplay between connectivity and synchronization dynamics, with functional clusters that do not coincide with anatomical modules in most cases. In social, sociotechnical, and engineering systems, the quest for consensus favors the emergence of clusters. Despite the unquestionable evidence for mesoscale organization of many complex systems and the heterogeneity of their interconnectivity, a way to predict and identify the emergence of functional modules in collective phenomena continues to elude us. Here, we propose an approach based on random walk dynamics to define the diffusion distance between any pair of units in a networked system. Such a metric allows us to exploit the underlying diffusion geometry to provide a unifying framework for the intimate relationship between metastable synchronization, consensus, and random search dynamics in complex networks, pinpointing the functional mesoscale organization of synthetic and biological systems.

Complexity VIII. Ontology of closure in complex systems: The C* hypothesis and the O° notation

NASA Astrophysics Data System (ADS)

Chandler, Jerry LR

1999-03-01

Closure is a common characteristic of mathematical, natural and socio-cultural systems. Whether one is describing a graph, a molecule, a cell, a human, or a nation state, closure is implicitly understood. An objective of this paper is to continue a construction of a systematic framework for closure which is sufficient for future quantitative transdisciplinary investigations. A further objective is to extend the Birkhoff-von Neumann criterion for quantum systems to complex natural objects. The C* hypothesis is being constructed to be consistent with algebraic category theory (Ehresmann and Vanbremeersch, 1987, 1997, Chandler, 1990, 1991, Chandler, Ehresmann and Vanbremeersch, 1996). Five aspects of closure will be used to construct a framework for categories of complex systems: 1. Truth functions in mathematics and the natural sciences 2. Systematic descriptions in the mks and O° notations 3. Organizational structures in hierarchical scientific languages 4. Transitive organizational pathways in the causal structures of complex behaviors 5. Composing additive, multiplicative and exponential operations in complex systems Truth functions can be formal or objective or subjective, depending on the complexity of the system and on our capability to represent the fine structure of the system symbolically, observationally or descriptively. "Complete" material representations of the fine structure of a system may allow truth functions to be created over sets of one to one correspondences. Less complete descriptions can support less stringent truth functions based on coherence or subjective judgments. The role of human values in creating and perpetuating truth functions can be placed in context of the degree of fine structure in the system's description. The organization of complex systems are hypothesized to be categorizable into degrees relative to one another, thereby creating an ordering relationship. This ordering relationship is denoted by the symbols: O°1, O°2,O°3... For example, for material systems, an ordering relation such as particles, atoms, molecules, cells, tissues, organs, individuals and social groups might be assigned to classify observations for medical purposes. The C* hypothesis asserts that any complex system can be described in terms of four enumerable concepts: closure, conformation, concatenation and cyclicity. Mappings between objects are constructed within a notation for organization. Causality is organized within C* as pathways of relationships in time. The notation of organizational degrees is used to distinguish a directionality for causality: 1. bottom-up (energy flows) 2. top-down (control processes or dominating variables), 3. outside — inward (ecoment on organism) and 4. inside — outward (organism on ecoment). Closures are asserted to emerge from evolutionary cooperation. It is asserted that truth functions emerged from the necessity of an organism to identify ecoments where life can prosper. For example, basic truth functions of mathematics (operations of addition, multiplication and exponentiation) are made operationally consistent within the biochemical operations of sustaining exponential cellular growth. These fundamental mathematical functions can provide a logical basis (in conjunction with conservation rules) for a construction of complex material categories at higher degrees of organization. It is remarked that these simple functions suggests a biochemical origin for the intuitionistic philosophy of mathematics. The emergence and success of mathematics is conjectured to result from the need to acquire a consistent basis for communication among individuals seeking to cooperate socially. This suggests a cultural closure over a collection of individual closures.

[Age factor in a complex evaluation of health of air staff].

PubMed

Ushakov, I B; Batishcheva, G A; Chernov, Iu N; Khomenko, M N; Soldatov, S K

2010-03-01

Was elaborated program of a complex of estimation of health condition of air staff with determination of capability of early diagnostic of functional tension of physiological systems. According to this system there were observed 73 airmen using a complex of tests (estimation of level of pectoral control, of personal and reactive anxiety, vegetal regulation etc.). Was detected, that length of service and sympato-adrenaline activeness with vicarious decrease of adrenoreactiveness are in direct proportion. Were marked the most informative indexes of estimation of functional tension of psycho-physiological functions, vegetative regulation and cardiovascular system. Was shown that the elaborated system of individual estimation of health of air staff permits diagnose prenosological conditions and determine indexes for rehabilitation treatment.

Development of a structured approach for decomposition of complex systems on a functional basis

NASA Astrophysics Data System (ADS)

Yildirim, Unal; Felician Campean, I.

2014-07-01

The purpose of this paper is to present the System State Flow Diagram (SSFD) as a structured and coherent methodology to decompose a complex system on a solution- independent functional basis. The paper starts by reviewing common function modelling frameworks in literature and discusses practical requirements of the SSFD in the context of the current literature and current approaches in industry. The proposed methodology is illustrated through the analysis of a case study: design analysis of a generic Bread Toasting System (BTS).

A Framework for Understanding the Characteristics of Complexity in Biology

ERIC Educational Resources Information Center

Dauer, Joseph; Dauer, Jenny

2016-01-01

Understanding the functioning of natural systems is not easy, although there is general agreement that understanding complex systems is an important goal for science education. Defining what makes a natural system complex will assist in identifying gaps in research on student reasoning about systems. The goal of this commentary is to propose a…

47 CFR 25.103 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-10-01

...) Communication-satellite earth station complex. The term communication-satellite earth station complex includes transmitters, receivers, and communications antennas at the earth station site together with the... communication to terrestrial distribution system(s). (e) Communication-satellite earth station complex functions...

47 CFR 25.103 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-10-01

...) Communication-satellite earth station complex. The term communication-satellite earth station complex includes transmitters, receivers, and communications antennas at the earth station site together with the... communication to terrestrial distribution system(s). (e) Communication-satellite earth station complex functions...

Environmental Systems Microbiology of Contaminated Environments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sayler, Gary; Hazen, Terry C.

Environmental Systems Microbiology is well positioned to move forward in dynamic complex system analysis probing new questions and developing new insight into the function, robustness and resilience in response to anthropogenic perturbations. Recent studies have demonstrated that natural bacterial communities can be used as quantitative biosensors in both groundwater and deep ocean water, predicting oil concentration from the Gulf of Mexico Deep Water Horizon spill and from groundwater at nuclear production waste sites (16, 17, 25). Since the first demonstration of catabolic gene expression in soil remediation (34) it has been clear that extension beyond organismal abundance to process andmore » function of microbial communities as a whole using the whole suite of omic tools available to the post genomic era. Metatranscriptomics have been highlighted as a prime vehicle for understanding responses to environmental drivers (35) in complex systems and with rapidly developing metabolomics, full functional understanding of complex community biogeochemical cycling is an achievable goal. Perhaps more exciting is the dynamic nature of these systems and their complex adaptive strategies that may lead to new control paradigms and emergence of new states and function in the course of a changing environment.« less

Structural and functional networks in complex systems with delay.

PubMed

Eguíluz, Víctor M; Pérez, Toni; Borge-Holthoefer, Javier; Arenas, Alex

2011-05-01

Functional networks of complex systems are obtained from the analysis of the temporal activity of their components, and are often used to infer their unknown underlying connectivity. We obtain the equations relating topology and function in a system of diffusively delay-coupled elements in complex networks. We solve exactly the resulting equations in motifs (directed structures of three nodes) and in directed networks. The mean-field solution for directed uncorrelated networks shows that the clusterization of the activity is dominated by the in-degree of the nodes, and that the locking frequency decreases with increasing average degree. We find that the exponent of a power law degree distribution of the structural topology γ is related to the exponent of the associated functional network as α=(2-γ)(-1) for γ<2. © 2011 American Physical Society

Promoting Complex Systems Learning through the Use of Conceptual Representations in Hypermedia

ERIC Educational Resources Information Center

Liu, Lei; Hmelo-Silver, Cindy E.

2009-01-01

Studying complex systems is increasingly important in many science domains. Many features of complex systems make it difficult for students to develop deep understanding. Our previous research indicated that a function-centered conceptual representation is part of the disciplinary toolbox of biologists, suggesting that it is an appropriate…

Lasercom system architecture with reduced complexity

NASA Technical Reports Server (NTRS)

Lesh, James R. (Inventor); Chen, Chien-Chung (Inventor); Ansari, Homayoon (Inventor)

1994-01-01

Spatial acquisition and precision beam pointing functions are critical to spaceborne laser communication systems. In the present invention, a single high bandwidth CCD detector is used to perform both spatial acquisition and tracking functions. Compared to previous lasercom hardware design, the array tracking concept offers reduced system complexity by reducing the number of optical elements in the design. Specifically, the design requires only one detector and one beam steering mechanism. It also provides the means to optically close the point-ahead control loop. The technology required for high bandwidth array tracking was examined and shown to be consistent with current state of the art. The single detector design can lead to a significantly reduced system complexity and a lower system cost.

LaserCom System Architecture With Reduced Complexity

NASA Technical Reports Server (NTRS)

Lesh, James R. (Inventor); Chen, Chien-Chung (Inventor); Ansari, Homa-Yoon (Inventor)

1996-01-01

Spatial acquisition and precision beam pointing functions are critical to spaceborne laser communication systems. In the present invention a single high bandwidth CCD detector is used to perform both spatial acquisition and tracking functions. Compared to previous lasercom hardware design, the array tracking concept offers reduced system complexity by reducing the number of optical elements in the design. Specifically, the design requires only one detector and one beam steering mechanism. It also provides means to optically close the point-ahead control loop. The technology required for high bandwidth array tracking was examined and shown to be consistent with current state of the art. The single detector design can lead to a significantly reduced system complexity and a lower system cost.

Computer simulation of functioning of elements of security systems

NASA Astrophysics Data System (ADS)

Godovykh, A. V.; Stepanov, B. P.; Sheveleva, A. A.

2017-01-01

The article is devoted to issues of development of the informational complex for simulation of functioning of the security system elements. The complex is described from the point of view of main objectives, a design concept and an interrelation of main elements. The proposed conception of the computer simulation provides an opportunity to simulate processes of security system work for training security staff during normal and emergency operation.

A system of three-dimensional complex variables

NASA Technical Reports Server (NTRS)

Martin, E. Dale

1986-01-01

Some results of a new theory of multidimensional complex variables are reported, including analytic functions of a three-dimensional (3-D) complex variable. Three-dimensional complex numbers are defined, including vector properties and rules of multiplication. The necessary conditions for a function of a 3-D variable to be analytic are given and shown to be analogous to the 2-D Cauchy-Riemann equations. A simple example also demonstrates the analogy between the newly defined 3-D complex velocity and 3-D complex potential and the corresponding ordinary complex velocity and complex potential in two dimensions.

78 FR 28906 - Self-Regulatory Organizations; Chicago Board Options Exchange, Incorporated; Notice of Filing and...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-16

... every executed contract for complex orders routed to CBOE through their system. The purpose of this... that offer complex order execution systems in order for the Participant to qualify to participate in... complex order execution systems as of May 6, 2013. \\4\\ SR-CBOE-2013-032, pp. 5-7. The primary functional...

Computational complexity of Boolean functions

NASA Astrophysics Data System (ADS)

Korshunov, Aleksei D.

2012-02-01

Boolean functions are among the fundamental objects of discrete mathematics, especially in those of its subdisciplines which fall under mathematical logic and mathematical cybernetics. The language of Boolean functions is convenient for describing the operation of many discrete systems such as contact networks, Boolean circuits, branching programs, and some others. An important parameter of discrete systems of this kind is their complexity. This characteristic has been actively investigated starting from Shannon's works. There is a large body of scientific literature presenting many fundamental results. The purpose of this survey is to give an account of the main results over the last sixty years related to the complexity of computation (realization) of Boolean functions by contact networks, Boolean circuits, and Boolean circuits without branching. Bibliography: 165 titles.

An integrative model of evolutionary covariance: a symposium on body shape in fishes.

PubMed

Walker, Jeffrey A

2010-12-01

A major direction of current and future biological research is to understand how multiple, interacting functional systems coordinate in producing a body that works. This understanding is complicated by the fact that organisms need to work well in multiple environments, with both predictable and unpredictable environmental perturbations. Furthermore, organismal design reflects a history of past environments and not a plan for future environments. How complex, interacting functional systems evolve, then, is a truly grand challenge. In accepting the challenge, an integrative model of evolutionary covariance is developed. The model combines quantitative genetics, functional morphology/physiology, and functional ecology. The model is used to convene scientists ranging from geneticists, to physiologists, to ecologists, to engineers to facilitate the emergence of body shape in fishes as a model system for understanding how complex, interacting functional systems develop and evolve. Body shape of fish is a complex morphology that (1) results from many developmental paths and (2) functions in many different behaviors. Understanding the coordination and evolution of the many paths from genes to body shape, body shape to function, and function to a working fish body in a dynamic environment is now possible given new technologies from genetics to engineering and new theoretical models that integrate the different levels of biological organization (from genes to ecology).

Connectivity in the human brain dissociates entropy and complexity of auditory inputs☆

PubMed Central

Nastase, Samuel A.; Iacovella, Vittorio; Davis, Ben; Hasson, Uri

2015-01-01

Complex systems are described according to two central dimensions: (a) the randomness of their output, quantified via entropy; and (b) their complexity, which reflects the organization of a system's generators. Whereas some approaches hold that complexity can be reduced to uncertainty or entropy, an axiom of complexity science is that signals with very high or very low entropy are generated by relatively non-complex systems, while complex systems typically generate outputs with entropy peaking between these two extremes. In understanding their environment, individuals would benefit from coding for both input entropy and complexity; entropy indexes uncertainty and can inform probabilistic coding strategies, whereas complexity reflects a concise and abstract representation of the underlying environmental configuration, which can serve independent purposes, e.g., as a template for generalization and rapid comparisons between environments. Using functional neuroimaging, we demonstrate that, in response to passively processed auditory inputs, functional integration patterns in the human brain track both the entropy and complexity of the auditory signal. Connectivity between several brain regions scaled monotonically with input entropy, suggesting sensitivity to uncertainty, whereas connectivity between other regions tracked entropy in a convex manner consistent with sensitivity to input complexity. These findings suggest that the human brain simultaneously tracks the uncertainty of sensory data and effectively models their environmental generators. PMID:25536493

Rapamycin-induced oligomer formation system of FRB-FKBP fusion proteins.

PubMed

Inobe, Tomonao; Nukina, Nobuyuki

2016-07-01

Most proteins form larger protein complexes and perform multiple functions in the cell. Thus, artificial regulation of protein complex formation controls the cellular functions that involve protein complexes. Although several artificial dimerization systems have already been used for numerous applications in biomedical research, cellular protein complexes form not only simple dimers but also larger oligomers. In this study, we showed that fusion proteins comprising the induced heterodimer formation proteins FRB and FKBP formed various oligomers upon addition of rapamycin. By adjusting the configuration of fusion proteins, we succeeded in generating an inducible tetramer formation system. Proteins of interest also formed tetramers by fusing to the inducible tetramer formation system, which exhibits its utility in a broad range of biological applications. Copyright © 2015 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

The Generalization of Mutual Information as the Information between a Set of Variables: The Information Correlation Function Hierarchy and the Information Structure of Multi-Agent Systems

NASA Technical Reports Server (NTRS)

Wolf, David R.

2004-01-01

The topic of this paper is a hierarchy of information-like functions, here named the information correlation functions, where each function of the hierarchy may be thought of as the information between the variables it depends upon. The information correlation functions are particularly suited to the description of the emergence of complex behaviors due to many- body or many-agent processes. They are particularly well suited to the quantification of the decomposition of the information carried among a set of variables or agents, and its subsets. In more graphical language, they provide the information theoretic basis for understanding the synergistic and non-synergistic components of a system, and as such should serve as a forceful toolkit for the analysis of the complexity structure of complex many agent systems. The information correlation functions are the natural generalization to an arbitrary number of sets of variables of the sequence starting with the entropy function (one set of variables) and the mutual information function (two sets). We start by describing the traditional measures of information (entropy) and mutual information.

Quantitative detection of pathogens in centrifugal microfluidic disks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koh, Chung-Yan; Schaff, Ulrich Y.; Sommer, Gregory Jon

A system and methods for detection of a nucleic acid including forming a plurality of nucleic acid detection complexes are described, each of the complexes including a nucleic acid analyte, a detection agent and a functionalized probe. The method further including binding the nucleic acid detection complexes to a plurality of functionalized particles in a fluid sample and separating the functionalized particles having the nucleic acid detection complexes bound thereto from the fluid sample using a density media. The nucleic acid analyte is detected by detecting the detection agent.

Complex adaptive behavior and dexterous action

PubMed Central

Harrison, Steven J.; Stergiou, Nicholas

2016-01-01

Dexterous action, as conceptualized by Bernstein in his influential ecological analysis of human behavior, is revealed in the ability to flexibly generate behaviors that are adaptively tailored to the demands of the context in which they are embedded. Conceived as complex adaptive behavior, dexterity depends upon the qualities of robustness and degeneracy, and is supported by the functional complexity of the agent-environment system. Using Bernstein’s and Gibson’s ecological analyses of behavior situated in natural environments as conceptual touchstones, we consider the hypothesis that complex adaptive behavior capitalizes upon general principles of self-organization. Here, we outline a perspective in which the complex interactivity of nervous-system, body, and environment is revealed as an essential resource for adaptive behavior. From this perspective, we consider the implications for interpreting the functionality and dysfunctionality of human behavior. This paper demonstrates that, optimal variability, the topic of this special issue, is a logical consequence of interpreting the functionality of human behavior as complex adaptive behavior. PMID:26375932

Understanding health system reform - a complex adaptive systems perspective.

PubMed

Sturmberg, Joachim P; O'Halloran, Di M; Martin, Carmel M

2012-02-01

Everyone wants a sustainable well-functioning health system. However, this notion has different meaning to policy makers and funders compared to clinicians and patients. The former perceive public policy and economic constraints, the latter clinical or patient-centred strategies as the means to achieving a desired outcome. Theoretical development and critical analysis of a complex health system model. We introduce the concept of the health care vortex as a metaphor by which to understand the complex adaptive nature of health systems, and the degree to which their behaviour is predetermined by their 'shared values' or attractors. We contrast the likely functions and outcomes of a health system with a people-centred attractor and one with a financial attractor. This analysis suggests a shift in the system's attractor is fundamental to progress health reform thinking. © 2012 Blackwell Publishing Ltd.

A Tricky Trait: Applying the Fruits of the "Function Debate" in the Philosophy of Biology to the "Venom Debate" in the Science of Toxinology.

PubMed

Jackson, Timothy N W; Fry, Bryan G

2016-09-07

The "function debate" in the philosophy of biology and the "venom debate" in the science of toxinology are conceptually related. Venom systems are complex multifunctional traits that have evolved independently numerous times throughout the animal kingdom. No single concept of function, amongst those popularly defended, appears adequate to describe these systems in all their evolutionary contexts and extant variations. As such, a pluralistic view of function, previously defended by some philosophers of biology, is most appropriate. Venom systems, like many other functional traits, exist in nature as points on a continuum and the boundaries between "venomous" and "non-venomous" species may not always be clearly defined. This paper includes a brief overview of the concept of function, followed by in-depth discussion of its application to venom systems. A sound understanding of function may aid in moving the venom debate forward. Similarly, consideration of a complex functional trait such as venom may be of interest to philosophers of biology.

Free Energy Calculations of Crystalline Hard Sphere Complexes Using Density Functional Theory

DOE PAGES

Gunawardana, K. G.S.H.; Song, Xueyu

2014-12-22

Recently developed fundamental measure density functional theory (FMT) is used to study binary hard sphere (HS) complexes in crystalline phases. By comparing the excess free energy, pressure and phase diagram, we show that the fundamental measure functional yields good agreements to the available simulation results of AB, AB 2 and AB 13 crystals. Additionally, we use this functional to study the HS models of five binary crystals, Cu 5Zr(C15 b), Cu 51Zr 14(β), Cu 10Zr 7(φ), CuZr(B2) and CuZr 2 (C11 b), which are observed in the Cu-Zr system. The FMT functional gives well behaved minimum for most of themore » hard sphere crystal complexes in the two dimensional Gaussian space, namely a crystalline phase. However, the current version of FMT functional (white Bear) fails to give a stable minimum for the structure Cu 10Zr 7(φ). We argue that the observed solid phases for the HS models of the Cu-Zr system are true thermodynamic stable phases and can be used as a reference system in perturbation calculations.« less

History, anatomical nomenclature, comparative anatomy and functions of the hippocampal formation.

PubMed

El-Falougy, H; Benuska, J

2006-01-01

The complex structures in the cerebral hemispheres is included under one term, the limbic system. Our conception of this system and its special functions rises from the comparative neuroanatomical and neurophysiological studies. The components of the limbic system are the hippocampus, gyrus parahippocampalis, gyrus dentatus, gyrus cinguli, corpus amygdaloideum, nuclei anteriores thalami, hypothalamus and gyrus paraterminalis Because of its unique macroscopic and microscopic structure, the hippocampus is a conspicuous part of the limbic system. During phylogenetic development, the hippocampus developed from a simple cortical plate in amphibians into complex three-dimensional convoluted structure in mammals. In the last few decades, structures of the limbic system were extensively studied. Attention was directed to the physiological functions and pathological changes of the hippocampus. Experimental studies proved that the hippocampus has a very important role in the process of learning and memory. Another important functions of the hippocampus as a part of the limbic system is its role in regulation of sexual and emotional behaviour. The term "hippocampal formation" is defined as the complex of six structures: gyrus dentatus, hippocampus proprius, subiculum proprium, presubiculum, parasubiculum and area entorhinalis In this work we attempt to present a brief review of knowledge about the hippocampus from the point of view of history, anatomical nomenclature, comparative anatomy and functions (Tab. 1, Fig. 2, Ref. 33).

Systems approach provides management control of complex programs

NASA Technical Reports Server (NTRS)

Dudek, E. F., Jr.; Mc Carthy, J. F., Jr.

1970-01-01

Integrated program management process provides management visual assistance through three interrelated charts - system model that identifies each function to be performed, matrix that identifies personnel responsibilities for these functions, process chart that breaks down the functions into discrete tasks.

Confluence and convergence: team effectiveness in complex systems.

PubMed

Porter-OʼGrady, Tim

2015-01-01

Complex adaptive systems require nursing leadership to rethink organizational work and the viability and effectiveness of teams. Much of emergent thinking about complexity and systems and organizations alter the understanding of the nature and function of teamwork and the configuration and leadership of team effort. Reflecting on basic concepts of complexity and their application to team formation, dynamics, and outcomes lays an important foundation for effectively guiding the strategic activity of systems through the focused tactical action of teams. Basic principles of complexity, their impact on teams, and the fundamental elements of team effectiveness are explored.

Epigenomics and the concept of degeneracy in biological systems

PubMed Central

Mason, Paul H.; Barron, Andrew B.

2014-01-01

Researchers in the field of epigenomics are developing more nuanced understandings of biological complexity, and exploring the multiple pathways that lead to phenotypic expression. The concept of degeneracy—referring to the multiple pathways that a system recruits to achieve functional plasticity—is an important conceptual accompaniment to the growing body of knowledge in epigenomics. Distinct from degradation, redundancy and dilapidation; degeneracy refers to the plasticity of traits whose function overlaps in some environments, but diverges in others. While a redundant system is composed of repeated identical elements performing the same function, a degenerate system is composed of different elements performing similar or overlapping functions. Here, we describe the degenerate structure of gene regulatory systems from the basic genetic code to flexible epigenomic modifications, and discuss how these structural features have contributed to organism complexity, robustness, plasticity and evolvability. PMID:24335757

Cross-functional systems

NASA Technical Reports Server (NTRS)

Lee, Mark

1991-01-01

Many companies, including Xerox and Texas Instruments, are using cross functional systems to deal with the increasingly complex and competitive business environment. However, few firms within the aerospace industry appear to be aware of the significant benefits that cross functional systems can provide. Those benefits are examined and a flexible methodology is discussed that companies can use to identify and develop cross functional systems that will help improve organizational performance. In addition, some of the managerial issues are addressed that cross functional systems may raise and specific examples are used to explore networking's contributions to cross functional systems.

Method and apparatus for transfer function simulator for testing complex systems

NASA Technical Reports Server (NTRS)

Kavaya, M. J. (Inventor)

1985-01-01

A method and apparatus for testing the operation of a complex stabilization circuit in a closed loop system is presented. The method is comprised of a programmed analog or digital computing system for implementing the transfer function of a load thereby providing a predictable load. The digital computing system employs a table stored in a microprocessor in which precomputed values of the load transfer function are stored for values of input signal from the stabilization circuit over the range of interest. This technique may be used not only for isolating faults in the stabilization circuit, but also for analyzing a fault in a faulty load by so varying parameters of the computing system as to simulate operation of the actual load with the fault.

Atomic switch networks—nanoarchitectonic design of a complex system for natural computing

NASA Astrophysics Data System (ADS)

Demis, E. C.; Aguilera, R.; Sillin, H. O.; Scharnhorst, K.; Sandouk, E. J.; Aono, M.; Stieg, A. Z.; Gimzewski, J. K.

2015-05-01

Self-organized complex systems are ubiquitous in nature, and the structural complexity of these natural systems can be used as a model to design new classes of functional nanotechnology based on highly interconnected networks of interacting units. Conventional fabrication methods for electronic computing devices are subject to known scaling limits, confining the diversity of possible architectures. This work explores methods of fabricating a self-organized complex device known as an atomic switch network and discusses its potential utility in computing. Through a merger of top-down and bottom-up techniques guided by mathematical and nanoarchitectonic design principles, we have produced functional devices comprising nanoscale elements whose intrinsic nonlinear dynamics and memorization capabilities produce robust patterns of distributed activity and a capacity for nonlinear transformation of input signals when configured in the appropriate network architecture. Their operational characteristics represent a unique potential for hardware implementation of natural computation, specifically in the area of reservoir computing—a burgeoning field that investigates the computational aptitude of complex biologically inspired systems.

Atomic switch networks-nanoarchitectonic design of a complex system for natural computing.

PubMed

Demis, E C; Aguilera, R; Sillin, H O; Scharnhorst, K; Sandouk, E J; Aono, M; Stieg, A Z; Gimzewski, J K

2015-05-22

Self-organized complex systems are ubiquitous in nature, and the structural complexity of these natural systems can be used as a model to design new classes of functional nanotechnology based on highly interconnected networks of interacting units. Conventional fabrication methods for electronic computing devices are subject to known scaling limits, confining the diversity of possible architectures. This work explores methods of fabricating a self-organized complex device known as an atomic switch network and discusses its potential utility in computing. Through a merger of top-down and bottom-up techniques guided by mathematical and nanoarchitectonic design principles, we have produced functional devices comprising nanoscale elements whose intrinsic nonlinear dynamics and memorization capabilities produce robust patterns of distributed activity and a capacity for nonlinear transformation of input signals when configured in the appropriate network architecture. Their operational characteristics represent a unique potential for hardware implementation of natural computation, specifically in the area of reservoir computing-a burgeoning field that investigates the computational aptitude of complex biologically inspired systems.

Inhomogeneous point-process entropy: An instantaneous measure of complexity in discrete systems

NASA Astrophysics Data System (ADS)

Valenza, Gaetano; Citi, Luca; Scilingo, Enzo Pasquale; Barbieri, Riccardo

2014-05-01

Measures of entropy have been widely used to characterize complexity, particularly in physiological dynamical systems modeled in discrete time. Current approaches associate these measures to finite single values within an observation window, thus not being able to characterize the system evolution at each moment in time. Here, we propose a new definition of approximate and sample entropy based on the inhomogeneous point-process theory. The discrete time series is modeled through probability density functions, which characterize and predict the time until the next event occurs as a function of the past history. Laguerre expansions of the Wiener-Volterra autoregressive terms account for the long-term nonlinear information. As the proposed measures of entropy are instantaneously defined through probability functions, the novel indices are able to provide instantaneous tracking of the system complexity. The new measures are tested on synthetic data, as well as on real data gathered from heartbeat dynamics of healthy subjects and patients with cardiac heart failure and gait recordings from short walks of young and elderly subjects. Results show that instantaneous complexity is able to effectively track the system dynamics and is not affected by statistical noise properties.

Cognitive engineering models in space systems

NASA Technical Reports Server (NTRS)

Mitchell, Christine M.

1992-01-01

NASA space systems, including mission operations on the ground and in space, are complex, dynamic, predominantly automated systems in which the human operator is a supervisory controller. The human operator monitors and fine-tunes computer-based control systems and is responsible for ensuring safe and efficient system operation. In such systems, the potential consequences of human mistakes and errors may be very large, and low probability of such events is likely. Thus, models of cognitive functions in complex systems are needed to describe human performance and form the theoretical basis of operator workstation design, including displays, controls, and decision support aids. The operator function model represents normative operator behavior-expected operator activities given current system state. The extension of the theoretical structure of the operator function model and its application to NASA Johnson mission operations and space station applications is discussed.

Representing Operational Modes for Situation Awareness

NASA Astrophysics Data System (ADS)

Kirchhübel, Denis; Lind, Morten; Ravn, Ole

2017-01-01

Operating complex plants is an increasingly demanding task for human operators. Diagnosis of and reaction to on-line events requires the interpretation of real time data. Vast amounts of sensor data as well as operational knowledge about the state and design of the plant are necessary to deduct reasonable reactions to abnormal situations. Intelligent computational support tools can make the operator’s task easier, but they require knowledge about the overall system in form of some model. While tools used for fault-tolerant control design based on physical principles and relations are valuable tools for designing robust systems, the models become too complex when considering the interactions on a plant-wide level. The alarm systems meant to support human operators in the diagnosis of the plant-wide situation on the other hand fail regularly in situations where these interactions of systems lead to many related alarms overloading the operator with alarm floods. Functional modelling can provide a middle way to reduce the complexity of plant-wide models by abstracting from physical details to more general functions and behaviours. Based on functional models the propagation of failures through the interconnected systems can be inferred and alarm floods can potentially be reduced to their root-cause. However, the desired behaviour of a complex system changes due to operating procedures that require more than one physical and functional configuration. In this paper a consistent representation of possible configurations is deduced from the analysis of an exemplary start-up procedure by functional models. The proposed interpretation of the modelling concepts simplifies the functional modelling of distinct modes. The analysis further reveals relevant links between the quantitative sensor data and the qualitative perspective of the diagnostics tool based on functional models. This will form the basis for the ongoing development of a novel real-time diagnostics system based on the on-line adaptation of the underlying MFM model.

Analysis of undergraduate students' conceptual models of a complex biological system across a diverse body of learners

NASA Astrophysics Data System (ADS)

Dirnbeck, Matthew R.

Biological systems pose a challenge both for learners and teachers because they are complex systems mediated by feedback loops; networks of cause-effect relationships; and non-linear, hierarchical, and emergent properties. Teachers and scientists routinely use models to communicate ideas about complex systems. Model-based pedagogies engage students in model construction as a means of practicing higher-order reasoning skills. One such modeling paradigm describes systems in terms of their structures, behaviors, and functions (SBF). The SBF framework is a simple modeling language that has been used to teach about complex biological systems. Here, we used student-generated SBF models to assess students' causal reasoning in the context of a novel biological problem on an exam. We compared students' performance on the modeling problem, their performance on a set of knowledge/comprehension questions, and their performance on a set of scientific reasoning questions. We found that students who performed well on knowledge and understanding questions also constructed more networked, higher quality models. Previous studies have shown that learners' mental maps increase in complexity with increased expertise. We wanted to investigate if biology students with varying levels of training in biology showed a similar pattern when constructing system models. In a pilot study, we administered the same modeling problem to two additional groups of students: 1) an animal physiology course for students pursuing a major in biology (n=37) and 2) an exercise physiology course for non-majors (n=27). We found that there was no significant difference in model organization across the three student populations, but there was a significant difference in the ability to represent function between the three populations. Between the three groups the non-majors had the lowest function scores, the introductory majors had the middle function scores, and the upper division majors had the highest function scores.

Using a biased qubit to probe complex systems

NASA Astrophysics Data System (ADS)

Pollock, Felix A.; Checińska, Agata; Pascazio, Saverio; Modi, Kavan

2016-09-01

Complex mesoscopic systems play increasingly important roles in modern science, from understanding biological functions at the molecular level to designing solid-state information processing devices. The operation of these systems typically depends on their energetic structure, yet probing their energy landscape can be extremely challenging; they have many degrees of freedom, which may be hard to isolate and measure independently. Here, we show that a qubit (a two-level quantum system) with a biased energy splitting can directly probe the spectral properties of a complex system, without knowledge of how they couple. Our work is based on the completely positive and trace-preserving map formalism, which treats any unknown dynamics as a "black-box" process. This black box contains information about the system with which the probe interacts, which we access by measuring the survival probability of the initial state of the probe as function of the energy splitting and the process time. Fourier transforming the results yields the energy spectrum of the complex system. Without making assumptions about the strength or form of its coupling, our probe could determine aspects of a complex molecule's energy landscape as well as, in many cases, test for coherent superposition of its energy eigenstates.

Delay-dependent dynamical analysis of complex-valued memristive neural networks: Continuous-time and discrete-time cases.

PubMed

Wang, Jinling; Jiang, Haijun; Ma, Tianlong; Hu, Cheng

2018-05-01

This paper considers the delay-dependent stability of memristive complex-valued neural networks (MCVNNs). A novel linear mapping function is presented to transform the complex-valued system into the real-valued system. Under such mapping function, both continuous-time and discrete-time MCVNNs are analyzed in this paper. Firstly, when activation functions are continuous but not Lipschitz continuous, an extended matrix inequality is proved to ensure the stability of continuous-time MCVNNs. Furthermore, if activation functions are discontinuous, a discontinuous adaptive controller is designed to acquire its stability by applying Lyapunov-Krasovskii functionals. Secondly, compared with techniques in continuous-time MCVNNs, the Halanay-type inequality and comparison principle are firstly used to exploit the dynamical behaviors of discrete-time MCVNNs. Finally, the effectiveness of theoretical results is illustrated through numerical examples. Copyright © 2018 Elsevier Ltd. All rights reserved.

Connectivity in the human brain dissociates entropy and complexity of auditory inputs.

PubMed

Nastase, Samuel A; Iacovella, Vittorio; Davis, Ben; Hasson, Uri

2015-03-01

Complex systems are described according to two central dimensions: (a) the randomness of their output, quantified via entropy; and (b) their complexity, which reflects the organization of a system's generators. Whereas some approaches hold that complexity can be reduced to uncertainty or entropy, an axiom of complexity science is that signals with very high or very low entropy are generated by relatively non-complex systems, while complex systems typically generate outputs with entropy peaking between these two extremes. In understanding their environment, individuals would benefit from coding for both input entropy and complexity; entropy indexes uncertainty and can inform probabilistic coding strategies, whereas complexity reflects a concise and abstract representation of the underlying environmental configuration, which can serve independent purposes, e.g., as a template for generalization and rapid comparisons between environments. Using functional neuroimaging, we demonstrate that, in response to passively processed auditory inputs, functional integration patterns in the human brain track both the entropy and complexity of the auditory signal. Connectivity between several brain regions scaled monotonically with input entropy, suggesting sensitivity to uncertainty, whereas connectivity between other regions tracked entropy in a convex manner consistent with sensitivity to input complexity. These findings suggest that the human brain simultaneously tracks the uncertainty of sensory data and effectively models their environmental generators. Copyright © 2014. Published by Elsevier Inc.

Detecting resting-state functional connectivity in the language system using functional near-infrared spectroscopy

NASA Astrophysics Data System (ADS)

Zhang, Yu-Jin; Lu, Chun-Ming; Biswal, Bharat B.; Zang, Yu-Feng; Peng, Dan-Lin; Zhu, Chao-Zhe

2010-07-01

Functional connectivity has become one of the important approaches to understanding the functional organization of the human brain. Recently, functional near-infrared spectroscopy (fNIRS) was demonstrated as a feasible method to study resting-state functional connectivity (RSFC) in the sensory and motor systems. However, whether such fNIRS-based RSFC can be revealed in high-level and complex functional systems remains unknown. In the present study, the feasibility of such an approach is tested on the language system, of which the neural substrates have been well documented in the literature. After determination of a seed channel by a language localizer task, the correlation strength between the low frequency fluctuations of the fNIRS signal at the seed channel and those at all other channels is used to evaluate the language system RSFC. Our results show a significant RSFC between the left inferior frontal cortex and superior temporal cortex, components both associated with dominant language regions. Moreover, the RSFC map demonstrates left lateralization of the language system. In conclusion, the present study successfully utilized fNIRS-based RSFC to study a complex and high-level neural system, and provides further evidence for the validity of the fNIRS-based RSFC approach.

Towards a comprehensive understanding of emerging dynamics and function of pancreatic islets: A complex network approach. Comment on "Network science of biological systems at different scales: A review" by Gosak et al.

NASA Astrophysics Data System (ADS)

Loppini, Alessandro

2018-03-01

Complex network theory represents a comprehensive mathematical framework to investigate biological systems, ranging from sub-cellular and cellular scales up to large-scale networks describing species interactions and ecological systems. In their exhaustive and comprehensive work [1], Gosak et al. discuss several scenarios in which the network approach was able to uncover general properties and underlying mechanisms of cells organization and regulation, tissue functions and cell/tissue failure in pathology, by the study of chemical reaction networks, structural networks and functional connectivities.

Environmental Complexity and Central Nervous System Development and Function

ERIC Educational Resources Information Center

Lewis, Mark H.

2004-01-01

Environmental restriction or deprivation early in development can induce social, cognitive, affective, and motor abnormalities similar to those associated with autism. Conversely, rearing animals in larger, more complex environments results in enhanced brain structure and function, including increased brain weight, dendritic branching,…

Getting to the core of cadherin complex function in Caenorhabditis elegans.

PubMed

Hardin, Jeff

2015-01-01

The classic cadherin-catenin complex (CCC) mediates cell-cell adhesion in metazoans. Although substantial insights have been gained by studying the CCC in vertebrate tissue culture, analyzing requirements for and regulation of the CCC in vertebrates remains challenging. Caenorhabditis elegans is a powerful system for connecting the molecular details of CCC function with functional requirements in a living organism. Recent data, using an "angstroms to embryos" approach, have elucidated functions for key residues, conserved across all metazoans, that mediate cadherin/β-catenin binding. Other recent work reveals a novel, potentially ancestral, role for the C. elegans p120ctn homologue in regulating polarization of blastomeres in the early embryo via Cdc42 and the partitioning-defective (PAR)/atypical protein kinase C (aPKC) complex. Finally, recent work suggests that the CCC is trafficked to the cell surface via the clathrin adaptor protein complex 1 (AP-1) in surprising ways. These studies continue to underscore the value of C. elegans as a model system for identifying conserved molecular mechanisms involving the CCC.

Design for an aging brain.

PubMed

Thaler, David S

2002-01-01

Vaillancourt and Newell (Neurobiol. of Aging 2001) show that although many aging systems decrease in complexity as anticipated by Lipsitz and Goldberger (JAMA 1992), other aging systems increase in complexity. Vaillancourt and Newell explain the discrepancy by proposing that systems with a point attractor decrease in complexity with age, whereas those with an oscillating attractor increase in complexity with age. Vaillancourt and Newell are certainly correct that no one direction fits all results. Aging and death sometimes follow from a system being too simple, or, too complex. A perspective, based on the work of W. Ross Ashby (1956 and http://pespmc1.vub.ac.be/ASHBBOOK.html) is used in this commentary to consider why some systems become apparently more simple and others more complex as they age. In this Ashby-inspired view the measured complexity of a system's Responses to Disturbances is proportional to the ratio D/R, where D and R are sets containing the variety of possible disturbances and responses. The model expands on Ashby's by proposing that D consists of two components, Dp and Du. Dp consists of disturbances that are a function of the system's perception. Responses to Dp are often anticipatory and the response itself dominates the outcome. Du are disturbances that are unavoidable. Outcomes decrease or increase in measured entropy as a function of changes in (Dp + Du)/R. The variety of elements in both Dp and R decrease with age. When D/R decreases with age, the system shows less complexity. Conversely when D/R increases with Age, the results become more entropic.

Thermodynamic holography.

PubMed

Wei, Bo-Bo; Jiang, Zhan-Feng; Liu, Ren-Bao

2015-10-19

The holographic principle states that the information about a volume of a system is encoded on the boundary surface of the volume. Holography appears in many branches of physics, such as optics, electromagnetism, many-body physics, quantum gravity, and string theory. Here we show that holography is also an underlying principle in thermodynamics, a most important foundation of physics. The thermodynamics of a system is fully determined by its partition function. We prove that the partition function of a finite but arbitrarily large system is an analytic function on the complex plane of physical parameters, and therefore the partition function in a region on the complex plane is uniquely determined by its values along the boundary. The thermodynamic holography has applications in studying thermodynamics of nano-scale systems (such as molecule engines, nano-generators and macromolecules) and provides a new approach to many-body physics.

Modelling and prediction for chaotic fir laser attractor using rational function neural network.

PubMed

Cho, S

2001-02-01

Many real-world systems such as irregular ECG signal, volatility of currency exchange rate and heated fluid reaction exhibit highly complex nonlinear characteristic known as chaos. These chaotic systems cannot be retreated satisfactorily using linear system theory due to its high dimensionality and irregularity. This research focuses on prediction and modelling of chaotic FIR (Far InfraRed) laser system for which the underlying equations are not given. This paper proposed a method for prediction and modelling a chaotic FIR laser time series using rational function neural network. Three network architectures, TDNN (Time Delayed Neural Network), RBF (radial basis function) network and the RF (rational function) network, are also presented. Comparisons between these networks performance show the improvements introduced by the RF network in terms of a decrement in network complexity and better ability of predictability.

A complex network-based importance measure for mechatronics systems

NASA Astrophysics Data System (ADS)

Wang, Yanhui; Bi, Lifeng; Lin, Shuai; Li, Man; Shi, Hao

2017-01-01

In view of the negative impact of functional dependency, this paper attempts to provide an alternative importance measure called Improved-PageRank (IPR) for measuring the importance of components in mechatronics systems. IPR is a meaningful extension of the centrality measures in complex network, which considers usage reliability of components and functional dependency between components to increase importance measures usefulness. Our work makes two important contributions. First, this paper integrates the literature of mechatronic architecture and complex networks theory to define component network. Second, based on the notion of component network, a meaningful IPR is brought into the identifying of important components. In addition, the IPR component importance measures, and an algorithm to perform stochastic ordering of components due to the time-varying nature of usage reliability of components and functional dependency between components, are illustrated with a component network of bogie system that consists of 27 components.

Fitness landscapes, heuristics and technological paradigms: A critique on random search models in evolutionary economics

NASA Astrophysics Data System (ADS)

Frenken, Koen

2001-06-01

The biological evolution of complex organisms, in which the functioning of genes is interdependent, has been analyzed as "hill-climbing" on NK fitness landscapes through random mutation and natural selection. In evolutionary economics, NK fitness landscapes have been used to simulate the evolution of complex technological systems containing elements that are interdependent in their functioning. In these models, economic agents randomly search for new technological design by trial-and-error and run the risk of ending up in sub-optimal solutions due to interdependencies between the elements in a complex system. These models of random search are legitimate for reasons of modeling simplicity, but remain limited as these models ignore the fact that agents can apply heuristics. A specific heuristic is one that sequentially optimises functions according to their ranking by users of the system. To model this heuristic, a generalized NK-model is developed. In this model, core elements that influence many functions can be distinguished from peripheral elements that affect few functions. The concept of paradigmatic search can then be analytically defined as search that leaves core elements in tact while concentrating on improving functions by mutation of peripheral elements.

A Tricky Trait: Applying the Fruits of the “Function Debate” in the Philosophy of Biology to the “Venom Debate” in the Science of Toxinology

PubMed Central

Jackson, Timothy N. W.; Fry, Bryan G.

2016-01-01

The “function debate” in the philosophy of biology and the “venom debate” in the science of toxinology are conceptually related. Venom systems are complex multifunctional traits that have evolved independently numerous times throughout the animal kingdom. No single concept of function, amongst those popularly defended, appears adequate to describe these systems in all their evolutionary contexts and extant variations. As such, a pluralistic view of function, previously defended by some philosophers of biology, is most appropriate. Venom systems, like many other functional traits, exist in nature as points on a continuum and the boundaries between “venomous” and “non-venomous” species may not always be clearly defined. This paper includes a brief overview of the concept of function, followed by in-depth discussion of its application to venom systems. A sound understanding of function may aid in moving the venom debate forward. Similarly, consideration of a complex functional trait such as venom may be of interest to philosophers of biology. PMID:27618098

Unified functional network and nonlinear time series analysis for complex systems science: The pyunicorn package

NASA Astrophysics Data System (ADS)

Donges, Jonathan; Heitzig, Jobst; Beronov, Boyan; Wiedermann, Marc; Runge, Jakob; Feng, Qing Yi; Tupikina, Liubov; Stolbova, Veronika; Donner, Reik; Marwan, Norbert; Dijkstra, Henk; Kurths, Jürgen

2016-04-01

We introduce the pyunicorn (Pythonic unified complex network and recurrence analysis toolbox) open source software package for applying and combining modern methods of data analysis and modeling from complex network theory and nonlinear time series analysis. pyunicorn is a fully object-oriented and easily parallelizable package written in the language Python. It allows for the construction of functional networks such as climate networks in climatology or functional brain networks in neuroscience representing the structure of statistical interrelationships in large data sets of time series and, subsequently, investigating this structure using advanced methods of complex network theory such as measures and models for spatial networks, networks of interacting networks, node-weighted statistics, or network surrogates. Additionally, pyunicorn provides insights into the nonlinear dynamics of complex systems as recorded in uni- and multivariate time series from a non-traditional perspective by means of recurrence quantification analysis, recurrence networks, visibility graphs, and construction of surrogate time series. The range of possible applications of the library is outlined, drawing on several examples mainly from the field of climatology. pyunicorn is available online at https://github.com/pik-copan/pyunicorn. Reference: J.F. Donges, J. Heitzig, B. Beronov, M. Wiedermann, J. Runge, Q.-Y. Feng, L. Tupikina, V. Stolbova, R.V. Donner, N. Marwan, H.A. Dijkstra, and J. Kurths, Unified functional network and nonlinear time series analysis for complex systems science: The pyunicorn package, Chaos 25, 113101 (2015), DOI: 10.1063/1.4934554, Preprint: arxiv.org:1507.01571 [physics.data-an].

Risk Modeling of Interdependent Complex Systems of Systems: Theory and Practice.

PubMed

Haimes, Yacov Y

2018-01-01

The emergence of the complexity characterizing our systems of systems (SoS) requires a reevaluation of the way we model, assess, manage, communicate, and analyze the risk thereto. Current models for risk analysis of emergent complex SoS are insufficient because too often they rely on the same risk functions and models used for single systems. These models commonly fail to incorporate the complexity derived from the networks of interdependencies and interconnectedness (I-I) characterizing SoS. There is a need to reevaluate currently practiced risk analysis to respond to this reality by examining, and thus comprehending, what makes emergent SoS complex. The key to evaluating the risk to SoS lies in understanding the genesis of characterizing I-I of systems manifested through shared states and other essential entities within and among the systems that constitute SoS. The term "essential entities" includes shared decisions, resources, functions, policies, decisionmakers, stakeholders, organizational setups, and others. This undertaking can be accomplished by building on state-space theory, which is fundamental to systems engineering and process control. This article presents a theoretical and analytical framework for modeling the risk to SoS with two case studies performed with the MITRE Corporation and demonstrates the pivotal contributions made by shared states and other essential entities to modeling and analysis of the risk to complex SoS. A third case study highlights the multifarious representations of SoS, which require harmonizing the risk analysis process currently applied to single systems when applied to complex SoS. © 2017 Society for Risk Analysis.

Analysis of space vehicle structures using the transfer-function concept

NASA Technical Reports Server (NTRS)

Heer, E.; Trubert, M. R.

1969-01-01

Analysis of large complex systems is accomplished by dividing it into suitable subsystems and determining the individual dynamical and vibrational responses. Frequency transfer functions then determine the vibrational response of the whole system.

Density functional study of the electronic structure of dye-functionalized fullerenes and their model donor-acceptor complexes containing P3HT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baruah, Tunna; Garnica, Amanda; Paggen, Marina

2016-04-14

We study the electronic structure of C{sub 60} fullerenes functionalized with a thiophene-diketo-pyrrolopyrrole-thiophene based chromophore using density functional theory combined with large polarized basis sets. As the attached chromophore has electron donor character, the functionalization of the fullerene leads to a donor-acceptor (DA) system. We examine in detail the effect of the linker and the addition site on the electronic structure of the functionalized fullerenes. We further study the electronic structure of these DA complexes with a focus on the charge transfer excitations. Finally, we examine the interface of the functionalized fullerenes with the widely used poly(3-hexylthiophene-2,5-diyl) (P3HT) donor. Ourmore » results show that all functionalized fullerenes with an exception of the C{sub 60}-pyrrolidine [6,6], where the pyrrolidine is attached at a [6,6] site, have larger electron affinities relative to the pristine C{sub 60} fullerene. We also estimate the quasi-particle gap, lowest charge transfer excitation energy, and the exciton binding energies of the functionalized fullerene-P3MT model systems. Results show that the exciton binding energies in these model complexes are slightly smaller compared to a similarly prepared phenyl-C{sub 61}-butyric acid methyl ester (PCBM)-P3MT complex.« less

How a submarine returns to periscope depth: analysing complex socio-technical systems using Cognitive Work Analysis.

PubMed

Stanton, Neville A; Bessell, Kevin

2014-01-01

This paper presents the application of Cognitive Work Analysis to the description of the functions, situations, activities, decisions, strategies, and competencies of a Trafalgar class submarine when performing the function of returning to periscope depth. All five phases of Cognitive Work Analysis are presented, namely: Work Domain Analysis, Control Task Analysis, Strategies Analysis, Social Organisation and Cooperation Analysis, and Worker Competencies Analysis. Complex socio-technical systems are difficult to analyse but Cognitive Work Analysis offers an integrated way of analysing complex systems with the core of functional means-ends analysis underlying all of the other representations. The joined-up analysis offers a coherent framework for understanding how socio-technical systems work. Data were collected through observation and interviews at different sites across the UK. The resultant representations present a statement of how the work domain and current activities are configured in this complex socio-technical system. This is intended to provide a baseline, from which all future conceptions of the domain may be compared. The strength of the analysis is in the multiple representations from which the constraints acting on the work may be analysed. Future research needs to challenge the assumptions behind these constraints in order to develop new ways of working. Copyright © 2013 Elsevier Ltd and The Ergonomics Society. All rights reserved.

Toward a multiscale modeling framework for understanding serotonergic function

PubMed Central

Wong-Lin, KongFatt; Wang, Da-Hui; Moustafa, Ahmed A; Cohen, Jeremiah Y; Nakamura, Kae

2017-01-01

Despite its importance in regulating emotion and mental wellbeing, the complex structure and function of the serotonergic system present formidable challenges toward understanding its mechanisms. In this paper, we review studies investigating the interactions between serotonergic and related brain systems and their behavior at multiple scales, with a focus on biologically-based computational modeling. We first discuss serotonergic intracellular signaling and neuronal excitability, followed by neuronal circuit and systems levels. At each level of organization, we will discuss the experimental work accompanied by related computational modeling work. We then suggest that a multiscale modeling approach that integrates the various levels of neurobiological organization could potentially transform the way we understand the complex functions associated with serotonin. PMID:28417684

Carbohydrase Systems of Saccharophagus degradans Degrading Marine Complex Polysaccharides

PubMed Central

Hutcheson, Steven W.; Zhang, Haitao; Suvorov, Maxim

2011-01-01

Saccharophagus degradans 2–40 is a γ-subgroup proteobacterium capable of using many of the complex polysaccharides found in the marine environment for growth. To utilize these complex polysaccharides, this bacterium produces a plethora of carbohydrases dedicated to the processing of a carbohydrate class. Aiding in the identification of the contributing genes and enzymes is the known genome sequence for this bacterium. This review catalogs the genes and enzymes of the S. degradans genome that are likely to function in the systems for the utilization of agar, alginate, α- and β-glucans, chitin, mannans, pectins, and xylans and discusses the cell biology and genetics of each system as it functions to transfer carbon back to the bacterium. PMID:21731555

Social complexity as a proximate and ultimate factor in communicative complexity

PubMed Central

Freeberg, Todd M.; Dunbar, Robin I. M.; Ord, Terry J.

2012-01-01

The ‘social complexity hypothesis’ for communication posits that groups with complex social systems require more complex communicative systems to regulate interactions and relations among group members. Complex social systems, compared with simple social systems, are those in which individuals frequently interact in many different contexts with many different individuals, and often repeatedly interact with many of the same individuals in networks over time. Complex communicative systems, compared with simple communicative systems, are those that contain a large number of structurally and functionally distinct elements or possess a high amount of bits of information. Here, we describe some of the historical arguments that led to the social complexity hypothesis, and review evidence in support of the hypothesis. We discuss social complexity as a driver of communication and possible causal factor in human language origins. Finally, we discuss some of the key current limitations to the social complexity hypothesis—the lack of tests against alternative hypotheses for communicative complexity and evidence corroborating the hypothesis from modalities other than the vocal signalling channel. PMID:22641818

Functional role of the MrpA- and MrpD-homologous protein subunits in enzyme complexes evolutionary related to respiratory chain complex I.

PubMed

Moparthi, Vamsi K; Kumar, Brijesh; Al-Eryani, Yusra; Sperling, Eva; Górecki, Kamil; Drakenberg, Torbjörn; Hägerhäll, Cecilia

2014-01-01

NADH:quinone oxidoreductase or complex I is a large membrane bound enzyme complex that has evolved from the combination of smaller functional building blocks. Intermediate size enzyme complexes exist in nature that comprise some, but not all of the protein subunits in full size 14-subunit complex I. The membrane spanning complex I subunits NuoL, NuoM and NuoN are homologous to each other and to two proteins from one particular class of Na(+)/H(+) antiporters, denoted MrpA and MrpD. In complex I, these ion transporter protein subunits are prime candidates for harboring important parts of the proton pumping machinery. Using a model system, consisting of Bacillus subtilis MrpA and MrpD deletion strains and a low copy expression plasmid, it was recently demonstrated that NuoN can rescue the strain deleted for MrpD but not that deleted for MrpA, whereas the opposite tendency was seen for NuoL. This demonstrated that the MrpA-type and MrpD-type proteins have unique functional specializations. In this work, the corresponding antiporter-like protein subunits from the smaller enzymes evolutionarily related to complex I were tested in the same model system. The subunits from 11-subunit complex I from Bacillus cereus behaved essentially as those from full size complex I, corroborating that this enzyme should be regarded as a bona fide complex I. The hydrogenase-3 and hydrogenase-4 antiporter-like proteins on the other hand, could substitute equally well for MrpA or MrpD at pH7.4, suggesting that these enzymes have intermediate forms of the antiporter-like proteins, which seemingly lack the functional specificity. © 2013. Published by Elsevier B.V. All rights reserved.

A Model-based Framework for Risk Assessment in Human-Computer Controlled Systems

NASA Technical Reports Server (NTRS)

Hatanaka, Iwao

2000-01-01

The rapid growth of computer technology and innovation has played a significant role in the rise of computer automation of human tasks in modem production systems across all industries. Although the rationale for automation has been to eliminate "human error" or to relieve humans from manual repetitive tasks, various computer-related hazards and accidents have emerged as a direct result of increased system complexity attributed to computer automation. The risk assessment techniques utilized for electromechanical systems are not suitable for today's software-intensive systems or complex human-computer controlled systems. This thesis will propose a new systemic model-based framework for analyzing risk in safety-critical systems where both computers and humans are controlling safety-critical functions. A new systems accident model will be developed based upon modem systems theory and human cognitive processes to better characterize system accidents, the role of human operators, and the influence of software in its direct control of significant system functions. Better risk assessments will then be achievable through the application of this new framework to complex human-computer controlled systems.

Safety Metrics for Human-Computer Controlled Systems

NASA Technical Reports Server (NTRS)

Leveson, Nancy G; Hatanaka, Iwao

2000-01-01

The rapid growth of computer technology and innovation has played a significant role in the rise of computer automation of human tasks in modem production systems across all industries. Although the rationale for automation has been to eliminate "human error" or to relieve humans from manual repetitive tasks, various computer-related hazards and accidents have emerged as a direct result of increased system complexity attributed to computer automation. The risk assessment techniques utilized for electromechanical systems are not suitable for today's software-intensive systems or complex human-computer controlled systems.This thesis will propose a new systemic model-based framework for analyzing risk in safety-critical systems where both computers and humans are controlling safety-critical functions. A new systems accident model will be developed based upon modem systems theory and human cognitive processes to better characterize system accidents, the role of human operators, and the influence of software in its direct control of significant system functions Better risk assessments will then be achievable through the application of this new framework to complex human-computer controlled systems.

Using evaluation to adapt health information outreach to the complex environments of community-based organizations.

PubMed

Olney, Cynthia A

2005-10-01

After arguing that most community-based organizations (CBOs) function as complex adaptive systems, this white paper describes the evaluation goals, questions, indicators, and methods most important at different stages of community-based health information outreach. This paper presents the basic characteristics of complex adaptive systems and argues that the typical CBO can be considered this type of system. It then presents evaluation as a tool for helping outreach teams adapt their outreach efforts to the CBO environment and thus maximize success. Finally, it describes the goals, questions, indicators, and methods most important or helpful at each stage of evaluation (community assessment, needs assessment and planning, process evaluation, and outcomes assessment). Literature from complex adaptive systems as applied to health care, business, and evaluation settings is presented. Evaluation models and applications, particularly those based on participatory approaches, are presented as methods for maximizing the effectiveness of evaluation in dynamic CBO environments. If one accepts that CBOs function as complex adaptive systems-characterized by dynamic relationships among many agents, influences, and forces-then effective evaluation at the stages of community assessment, needs assessment and planning, process evaluation, and outcomes assessment is critical to outreach success.

To the systematization of failure analysis for perturbed systems (in German)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haller, U.

1974-01-01

The paper investigates the reliable functioning of complex technical systems. Of main importance is the question of how the functioning of technical systems which may fail or whose design still has some faults can be determined in the very earliest planning stages. The present paper is to develop a functioning schedule and to look for possible methods of systematic failure analysis of systems with stochastic failures. (RW/AK)

Hedgehog signaling mediates adaptive variation in a dynamic functional system in the cichlid feeding apparatus.

PubMed

Hu, Yinan; Albertson, R Craig

2014-06-10

Adaptive variation in the craniofacial skeleton is a key component of resource specialization and habitat divergence in vertebrates, but the proximate genetic mechanisms that underlie complex patterns of craniofacial variation are largely unknown. Here we demonstrate that the Hedgehog (Hh) signaling pathway mediates widespread variation across a complex functional system that affects the kinematics of lower jaw depression--the opercular four-bar linkage apparatus--among Lake Malawi cichlids. By using a combined quantitative trait locus mapping and population genetics approach, we show that allelic variation in the Hh receptor, ptch1, affects the development of distinct bony elements in the head that represent two of three movable links in this functional system. The evolutionarily derived allele is found in species that feed from the water column, and is associated with shifts in anatomy that translate to a four-bar system capable of faster jaw rotation. Alternatively, the ancestral allele is found in species that feed on attached algae, and is associated with the development of a four-bar system that predicts slower jaw movement. Experimental manipulation of the Hh pathway during cichlid development recapitulates functionally salient natural variation in craniofacial geometry. In all, these results significantly extend our understanding of the mechanisms that fine-tune the craniofacial skeletal complex during adaptation to new foraging niches.

Managing the Process of Protection Level Assessment of the Complex Organization and Technical Industrial Enterprises

NASA Astrophysics Data System (ADS)

Gorlov, A. P.; Averchenkov, V. I.; Rytov, M. Yu; Eryomenko, V. T.

2017-01-01

The article is concerned with mathematical simulation of protection level assessment of complex organizational and technical systems of industrial enterprises by creating automated system, which main functions are: information security (IS) audit, forming of the enterprise threats model, recommendations concerning creation of the information protection system, a set of organizational-administrative documentation.

Large-scale systems: Complexity, stability, reliability

NASA Technical Reports Server (NTRS)

Siljak, D. D.

1975-01-01

After showing that a complex dynamic system with a competitive structure has highly reliable stability, a class of noncompetitive dynamic systems for which competitive models can be constructed is defined. It is shown that such a construction is possible in the context of the hierarchic stability analysis. The scheme is based on the comparison principle and vector Liapunov functions.

The use of a mercury biosensor to evaluate the bioavailability of mercury-thiol complexes and mechanisms of mercury uptake in bacteria

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ndu, Udonna; Barkay, Tamar; Mason, Robert P.

We discuss as mercury (Hg) biosensors are sensitive to only intracellular Hg, they are useful in the investigation of Hg uptake mechanisms and the effects of speciation on Hg bioavailability to microbes. In this study, bacterial biosensors were used to evaluate the roles that several transporters such as the glutathione, cystine/cysteine, and Mer transporters play in the uptake of Hg from Hg-thiol complexes by comparing uptake rates in strains with functioning transport systems to strains where these transporters had been knocked out by deletion of key genes. The Hg uptake into the biosensors was quantified based on the intracellular conversionmore » of inorganic mercury (Hg(II)) to elemental mercury (Hg(0)) by the enzyme MerA. It was found that uptake of Hg from Hg-cysteine (Hg(CYS) 2) and Hg-glutathione (Hg(GSH) 2) complexes occurred at the same rate as that of inorganic complexes of Hg(II) into Escherichia coli strains with and without intact Mer transport systems. However, higher rates of Hg uptake were observed in the strain with a functioning Mer transport system. These results demonstrate that thiol-bound Hg is bioavailable to E. coli and that this bioavailability is higher in Hg-resistant bacteria with a complete Mer system than in non-resistant strains. No difference in the uptake rate of Hg from Hg(GSH) 2 was observed in E. coli strains with or without functioning glutathione transport systems. There was also no difference in uptake rates between a wildtype Bacillus subtilis strain with a functioning cystine/cysteine transport system, and a mutant strain where this transport system had been knocked out. These results cast doubt on the viability of the hypothesis that the entire Hg-thiol complex is taken up into the cell by a thiol transporter. It is more likely that the Hg in the Hg-thiol complex is transferred to a transport protein on the cell membrane and is subsequently internalized.« less

The use of a mercury biosensor to evaluate the bioavailability of mercury-thiol complexes and mechanisms of mercury uptake in bacteria

DOE PAGES

Ndu, Udonna; Barkay, Tamar; Mason, Robert P.; ...

2015-09-15

We discuss as mercury (Hg) biosensors are sensitive to only intracellular Hg, they are useful in the investigation of Hg uptake mechanisms and the effects of speciation on Hg bioavailability to microbes. In this study, bacterial biosensors were used to evaluate the roles that several transporters such as the glutathione, cystine/cysteine, and Mer transporters play in the uptake of Hg from Hg-thiol complexes by comparing uptake rates in strains with functioning transport systems to strains where these transporters had been knocked out by deletion of key genes. The Hg uptake into the biosensors was quantified based on the intracellular conversionmore » of inorganic mercury (Hg(II)) to elemental mercury (Hg(0)) by the enzyme MerA. It was found that uptake of Hg from Hg-cysteine (Hg(CYS) 2) and Hg-glutathione (Hg(GSH) 2) complexes occurred at the same rate as that of inorganic complexes of Hg(II) into Escherichia coli strains with and without intact Mer transport systems. However, higher rates of Hg uptake were observed in the strain with a functioning Mer transport system. These results demonstrate that thiol-bound Hg is bioavailable to E. coli and that this bioavailability is higher in Hg-resistant bacteria with a complete Mer system than in non-resistant strains. No difference in the uptake rate of Hg from Hg(GSH) 2 was observed in E. coli strains with or without functioning glutathione transport systems. There was also no difference in uptake rates between a wildtype Bacillus subtilis strain with a functioning cystine/cysteine transport system, and a mutant strain where this transport system had been knocked out. These results cast doubt on the viability of the hypothesis that the entire Hg-thiol complex is taken up into the cell by a thiol transporter. It is more likely that the Hg in the Hg-thiol complex is transferred to a transport protein on the cell membrane and is subsequently internalized.« less

Designing To Learn about Complex Systems.

ERIC Educational Resources Information Center

Hmelo, Cindy E.; Holton, Douglas L.; Kolodner, Janet L.

2000-01-01

Indicates the presence of complex structural, behavioral, and functional relations to understanding. Reports on a design experiment in which 6th grade children learned about the human respiratory system by designing artificial lungs and building partial working models. Makes suggestions for successful learning from design activities. (Contains 44…

Computer-Assisted Monitoring Of A Complex System

NASA Technical Reports Server (NTRS)

Beil, Bob J.; Mickelson, Eric M.; Sterritt, John M.; Costantino, Rob W.; Houvener, Bob C.; Super, Mike A.

1995-01-01

Propulsion System Advisor (PSA) computer-based system assists engineers and technicians in analyzing masses of sensory data indicative of operating conditions of space shuttle propulsion system during pre-launch and launch activities. Designed solely for monitoring; does not perform any control functions. Although PSA developed for highly specialized application, serves as prototype of noncontrolling, computer-based subsystems for monitoring other complex systems like electric-power-distribution networks and factories.

Unified functional network and nonlinear time series analysis for complex systems science: The pyunicorn package

NASA Astrophysics Data System (ADS)

Donges, Jonathan F.; Heitzig, Jobst; Beronov, Boyan; Wiedermann, Marc; Runge, Jakob; Feng, Qing Yi; Tupikina, Liubov; Stolbova, Veronika; Donner, Reik V.; Marwan, Norbert; Dijkstra, Henk A.; Kurths, Jürgen

2015-11-01

We introduce the pyunicorn (Pythonic unified complex network and recurrence analysis toolbox) open source software package for applying and combining modern methods of data analysis and modeling from complex network theory and nonlinear time series analysis. pyunicorn is a fully object-oriented and easily parallelizable package written in the language Python. It allows for the construction of functional networks such as climate networks in climatology or functional brain networks in neuroscience representing the structure of statistical interrelationships in large data sets of time series and, subsequently, investigating this structure using advanced methods of complex network theory such as measures and models for spatial networks, networks of interacting networks, node-weighted statistics, or network surrogates. Additionally, pyunicorn provides insights into the nonlinear dynamics of complex systems as recorded in uni- and multivariate time series from a non-traditional perspective by means of recurrence quantification analysis, recurrence networks, visibility graphs, and construction of surrogate time series. The range of possible applications of the library is outlined, drawing on several examples mainly from the field of climatology.

The Effect of Functional Flow Diagrams on Apprentice Aircraft Mechanics' Technical System Understanding.

ERIC Educational Resources Information Center

Johnson, Scott D.; Satchwell, Richard E.

1993-01-01

Describes an experimental study that tested the impact of a conceptual illustration on college students' understanding of the structure, function, and behavior of complex technical systems. The use of functional flow diagrams in aircraft mechanics' training is explained, a concept map analysis is discussed, and implications for technical training…

To Use or Not to Use--ERP Resistance Is the Question: The Roles of Tacit Knowledge and Complexity

ERIC Educational Resources Information Center

Freeze, Ronald D.; Schmidt, Pamela J.

2015-01-01

Enterprise Resource Planning (ERP) systems in business environments demand multidisciplinary understanding and collaboration between functional departments. The traditional educational paradigm isolates the learning of each functional discipline as if business people operated in functional isolation. ERP system value can only be realized by…

Late Stage Azidation of Complex Molecules

PubMed Central

2016-01-01

Selective functionalization of complex scaffolds is a promising approach to alter the pharmacological profiles of natural products and their derivatives. We report the site-selective azidation of benzylic and aliphatic C–H bonds in complex molecules catalyzed by the combination of Fe(OAc)2 and a PyBox ligand. The same system also catalyzes the trifluoromethyl azidation of olefins to form derivatives of natural products containing both fluorine atoms and azides. In general, both reactions tolerate a wide range of functional groups and occur with predictable regioselectivity. Azides obtained by functionalization of C–H and C=C bonds were converted to the corresponding amines, amides, and triazoles, thus providing a wide variety of nitrogen-containing complex molecules. PMID:27800554

Mathematical Methods for Optical Physics and Engineering

NASA Astrophysics Data System (ADS)

Gbur, Gregory J.

2011-01-01

1. Vector algebra; 2. Vector calculus; 3. Vector calculus in curvilinear coordinate systems; 4. Matrices and linear algebra; 5. Advanced matrix techniques and tensors; 6. Distributions; 7. Infinite series; 8. Fourier series; 9. Complex analysis; 10. Advanced complex analysis; 11. Fourier transforms; 12. Other integral transforms; 13. Discrete transforms; 14. Ordinary differential equations; 15. Partial differential equations; 16. Bessel functions; 17. Legendre functions and spherical harmonics; 18. Orthogonal functions; 19. Green's functions; 20. The calculus of variations; 21. Asymptotic techniques; Appendices; References; Index.

Towards Engineering Biological Systems in a Broader Context.

PubMed

Venturelli, Ophelia S; Egbert, Robert G; Arkin, Adam P

2016-02-27

Significant advances have been made in synthetic biology to program information processing capabilities in cells. While these designs can function predictably in controlled laboratory environments, the reliability of these devices in complex, temporally changing environments has not yet been characterized. As human society faces global challenges in agriculture, human health and energy, synthetic biology should develop predictive design principles for biological systems operating in complex environments. Natural biological systems have evolved mechanisms to overcome innumerable and diverse environmental challenges. Evolutionary design rules should be extracted and adapted to engineer stable and predictable ecological function. We highlight examples of natural biological responses spanning the cellular, population and microbial community levels that show promise in synthetic biology contexts. We argue that synthetic circuits embedded in host organisms or designed ecologies informed by suitable measurement of biotic and abiotic environmental parameters could be used as engineering substrates to achieve target functions in complex environments. Successful implementation of these methods will broaden the context in which synthetic biological systems can be applied to solve important problems. Copyright © 2015 Elsevier Ltd. All rights reserved.

Graphical Environment Tools for Application to Gamma-Ray Energy Tracking Arrays

DOE Office of Scientific and Technical Information (OSTI.GOV)

Todd, Richard A.; Radford, David C.

2013-12-30

Highly segmented, position-sensitive germanium detector systems are being developed for nuclear physics research where traditional electronic signal processing with mixed analog and digital function blocks would be enormously complex and costly. Future systems will be constructed using pipelined processing of high-speed digitized signals as is done in the telecommunications industry. Techniques which provide rapid algorithm and system development for future systems are desirable. This project has used digital signal processing concepts and existing graphical system design tools to develop a set of re-usable modular functions and libraries targeted for the nuclear physics community. Researchers working with complex nuclear detector arraysmore » such as the Gamma-Ray Energy Tracking Array (GRETA) have been able to construct advanced data processing algorithms for implementation in field programmable gate arrays (FPGAs) through application of these library functions using intuitive graphical interfaces.« less

Modeling microbial community structure and functional diversity across time and space.

PubMed

Larsen, Peter E; Gibbons, Sean M; Gilbert, Jack A

2012-07-01

Microbial communities exhibit exquisitely complex structure. Many aspects of this complexity, from the number of species to the total number of interactions, are currently very difficult to examine directly. However, extraordinary efforts are being made to make these systems accessible to scientific investigation. While recent advances in high-throughput sequencing technologies have improved accessibility to the taxonomic and functional diversity of complex communities, monitoring the dynamics of these systems over time and space - using appropriate experimental design - is still expensive. Fortunately, modeling can be used as a lens to focus low-resolution observations of community dynamics to enable mathematical abstractions of functional and taxonomic dynamics across space and time. Here, we review the approaches for modeling bacterial diversity at both the very large and the very small scales at which microbial systems interact with their environments. We show that modeling can help to connect biogeochemical processes to specific microbial metabolic pathways. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Exact exchange and Wilson-Levy correlation: a pragmatic device for studying complex weakly-bonded systems.

PubMed

Walsh, T R

2005-02-07

The Wilson-Levy (WL) correlation functional is used together with Hartree-Fock (HF) theory to evaluate interaction energies at intermediate separations (i.e. around equilibrium separation) for several weakly-bonded systems. The HF+WL approach reproduces binding trends for all complexes studied: selected rare-gas dimers, isomers of the methane dimer, benzene dimer and naphthalene dimer, and base-pair stacking structures for pyrimidine, cytosine, uracil and guanine dimers. These HF+WL data are contrasted against results obtained from some popular functionals (including B3LYP and PBE), as well as two newly-developed functionals, X3LYP and xPBE. The utility of HF+WL, with reference to exact-exchange (EXX) density-functional theory, is discussed in terms of a suggested EXXWL exchange-correlation functional.

The multi-replication protein A (RPA) system--a new perspective.

PubMed

Sakaguchi, Kengo; Ishibashi, Toyotaka; Uchiyama, Yukinobu; Iwabata, Kazuki

2009-02-01

Replication protein A (RPA) complex has been shown, using both in vivo and in vitro approaches, to be required for most aspects of eukaryotic DNA metabolism: replication, repair, telomere maintenance and homologous recombination. Here, we review recent data concerning the function and biological importance of the multi-RPA complex. There are distinct complexes of RPA found in the biological kingdoms, although for a long time only one type of RPA complex was believed to be present in eukaryotes. Each complex probably serves a different role. In higher plants, three distinct large and medium subunits are present, but only one species of the smallest subunit. Each of these protein subunits forms stable complexes with their respective partners. They are paralogs as complex. Humans possess two paralogs and one analog of RPA. The multi-RPA system can be regarded as universal in eukaryotes. Among eukaryotic kingdoms, paralogs, orthologs, analogs and heterologs of many DNA synthesis-related factors, including RPA, are ubiquitous. Convergent evolution seems to be ubiquitous in these processes. Using recent findings, we review the composition and biological functions of RPA complexes.

Cellulosome-based, Clostridium-derived multi-functional enzyme complexes for advanced biotechnology tool development: advances and applications.

PubMed

Hyeon, Jeong Eun; Jeon, Sang Duck; Han, Sung Ok

2013-11-01

The cellulosome is one of nature's most elegant and elaborate nanomachines and a key biological and biotechnological macromolecule that can be used as a multi-functional protein complex tool. Each protein module in the cellulosome system is potentially useful in an advanced biotechnology application. The high-affinity interactions between the cohesin and dockerin domains can be used in protein-based biosensors to improve both sensitivity and selectivity. The scaffolding protein includes a carbohydrate-binding module (CBM) that attaches strongly to cellulose substrates and facilitates the purification of proteins fused with the dockerin module through a one-step CBM purification method. Although the surface layer homology (SLH) domain of CbpA is not present in other strains, replacement of the cell surface anchoring domain allows a foreign protein to be displayed on the surface of other strains. The development of a hydrolysis enzyme complex is a useful strategy for consolidated bioprocessing (CBP), enabling microorganisms with biomass hydrolysis activity. Thus, the development of various configurations of multi-functional protein complexes for use as tools in whole-cell biocatalyst systems has drawn considerable attention as an attractive strategy for bioprocess applications. This review provides a detailed summary of the current achievements in Clostridium-derived multi-functional complex development and the impact of these complexes in various areas of biotechnology. Copyright © 2013 Elsevier Inc. All rights reserved.

Editorial [Special issue on software defined networks and infrastructures, network function virtualisation, autonomous systems and network management

DOE PAGES

Biswas, Amitava; Liu, Chen; Monga, Inder; ...

2016-01-01

For last few years, there has been a tremendous growth in data traffic due to high adoption rate of mobile devices and cloud computing. Internet of things (IoT) will stimulate even further growth. This is increasing scale and complexity of telecom/internet service provider (SP) and enterprise data centre (DC) compute and network infrastructures. As a result, managing these large network-compute converged infrastructures is becoming complex and cumbersome. To cope up, network and DC operators are trying to automate network and system operations, administrations and management (OAM) functions. OAM includes all non-functional mechanisms which keep the network running.

The State of the Field: Qualitative Analyses of Text Complexity

ERIC Educational Resources Information Center

Pearson, P. David; Hiebert, Elfrieda H.

2014-01-01

The purpose of this article is to understand the function, logic, and impact of qualitative systems for analyzing text complexity, focusing on their benefits and imperfections. We identified two primary functions for their use: (a) to match texts to reader ability so that readers read books that are within their grasp, and (b) to unearth, and then…

Deconstructing the core dynamics from a complex time-lagged regulatory biological circuit.

PubMed

Eriksson, O; Brinne, B; Zhou, Y; Björkegren, J; Tegnér, J

2009-03-01

Complex regulatory dynamics is ubiquitous in molecular networks composed of genes and proteins. Recent progress in computational biology and its application to molecular data generate a growing number of complex networks. Yet, it has been difficult to understand the governing principles of these networks beyond graphical analysis or extensive numerical simulations. Here the authors exploit several simplifying biological circumstances which thereby enable to directly detect the underlying dynamical regularities driving periodic oscillations in a dynamical nonlinear computational model of a protein-protein network. System analysis is performed using the cell cycle, a mathematically well-described complex regulatory circuit driven by external signals. By introducing an explicit time delay and using a 'tearing-and-zooming' approach the authors reduce the system to a piecewise linear system with two variables that capture the dynamics of this complex network. A key step in the analysis is the identification of functional subsystems by identifying the relations between state-variables within the model. These functional subsystems are referred to as dynamical modules operating as sensitive switches in the original complex model. By using reduced mathematical representations of the subsystems the authors derive explicit conditions on how the cell cycle dynamics depends on system parameters, and can, for the first time, analyse and prove global conditions for system stability. The approach which includes utilising biological simplifying conditions, identification of dynamical modules and mathematical reduction of the model complexity may be applicable to other well-characterised biological regulatory circuits. [Includes supplementary material].

Ferrocene-containing non-interlocked molecular machines.

PubMed

Scottwell, Synøve Ø; Crowley, James D

2016-02-11

Ferrocene is the prototypical organometallic sandwich complex and despite over 60 years passing since the discovery and elucidation of ferrocene's structure, research into ferrocene-containing compounds continues to grow as potential new applications in catalysis, biology and the material sciences are found. Ferrocene is chemically robust and readily functionalized which enables its facile incorporation into more complex molecular systems. This coupled with ferrocene's reversible redox properties and ability function as a "molecular ball bearing" has led to the use of ferrocene as a component in wide range of interlocked and non-interlocked synthetic molecular machine systems. This review will focus on the exploitation of ferrocene (and related sandwich complexes) for the development of non-interlocked synthetic molecular machines.

Grafting of [(64)Cu]-TPPF20 porphyrin complex on Functionalized nano-porous MCM-41 silica as a potential cancer imaging agent.

PubMed

Fazaeli, Yousef; Feizi, Shahzad; Jalilian, Amir R; Hejrani, Ali

2016-06-01

Mesoporous silica, MCM-41, functionalized with 3-aminopropyltriethoxysilane (APTES) was investigated as a potential drug delivery system, using [(64)Cu]-5, 10, 15, 20-tetrakis penta fluorophenyl porphyrin complex. [(64)Cu]-TPPF20 complex was grafted on functionalized MCM-41. The product was characterized by paper chromatography, FTIR spectroscopy, low angle X-ray diffraction, CHN and TGA/DTA analyses and atomic force microscopy. The biological evaluations of the grafted complex, [(64)Cu]-TPPF20@NH2-MCM-41, were done in Fibrosarcoma tumor-bearing Sprague-Dawley rats using scarification studies and Sopha DST-XL Dual-Head SPECT system. The actual loading amount of aminopropyl groups was found about 1.6mmol per gram of final silica. The specific activity of the final compound was found to be 3Ci/g. Amine functionalized MCM-41 was found to be a good platform for theranostic radiopharmaceuticals such as copper-64 complexes. Considering the accumulation of the tracer in tumor cells, fast wash-out from normal tissues, the short half-life copper-64 and less imposed radiation doses to patients, [(64)Cu]-TPPF20@NH2-MCM-41 can potentially be a suitable candidate for tumor imaging applications and future PET studies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Dynamics of mononuclear phagocyte system Fc receptor function in systemic lupus erythematosus. Relation to disease activity and circulating immune complexes.

PubMed Central

Kimberly, R P; Parris, T M; Inman, R D; McDougal, J S

1983-01-01

Seventeen pairs of longitudinal studies of mononuclear phagocyte system (MPS) Fc receptor function in 15 patients with systemic lupus were performed to explore the dynamic range of Fc receptor dysfunction in lupus and to establish the relationships between MPS function, clinical disease activity and circulating immune complexes (CIC). Fc receptor function was measured by the clearance of IgG sensitized autologous erythrocytes. At the time of first study the degree of MPS dysfunction was correlated with both clinical activity (P less than 0.05) and CIC (P less than 0.05). At follow-up patients with a change in clinical status show significantly larger changes in clearance function compared to clinically stable patients (206 min vs 7 min; P less than 0.001). MPS function changed concordantly with a change in clinical status in all cases (P = 0.002). Longitudinal assessments did not demonstrate concordance of changes in MPS function and CIC, measured by three different assays. The MPS Fc receptor defect in systemic lupus is dynamic and closely associated with disease activity. The lack of concordance of the defect with changes in CIC suggests that either CIC does not adequately reflect receptor site saturation or that other factors may also contribute to the magnitude of MPS dysfunction. PMID:6839542

Telerobot operator control station requirements

NASA Technical Reports Server (NTRS)

Kan, Edwin P.

1988-01-01

The operator control station of a telerobot system has unique functional and human factors requirements. It has to satisfy the needs of a truly interactive and user-friendly complex system, a telerobot system being a hybrid between a teleoperated and an autonomous system. These functional, hardware and software requirements are discussed, with explicit reference to the design objectives and constraints of the JPL/NASA Telerobot Demonstrator System.

The Capabilities of Chaos and Complexity

PubMed Central

Abel, David L.

2009-01-01

To what degree could chaos and complexity have organized a Peptide or RNA World of crude yet necessarily integrated protometabolism? How far could such protolife evolve in the absence of a heritable linear digital symbol system that could mutate, instruct, regulate, optimize and maintain metabolic homeostasis? To address these questions, chaos, complexity, self-ordered states, and organization must all be carefully defined and distinguished. In addition their cause-and-effect relationships and mechanisms of action must be delineated. Are there any formal (non physical, abstract, conceptual, algorithmic) components to chaos, complexity, self-ordering and organization, or are they entirely physicodynamic (physical, mass/energy interaction alone)? Chaos and complexity can produce some fascinating self-ordered phenomena. But can spontaneous chaos and complexity steer events and processes toward pragmatic benefit, select function over non function, optimize algorithms, integrate circuits, produce computational halting, organize processes into formal systems, control and regulate existing systems toward greater efficiency? The question is pursued of whether there might be some yet-to-be discovered new law of biology that will elucidate the derivation of prescriptive information and control. “System” will be rigorously defined. Can a low-informational rapid succession of Prigogine’s dissipative structures self-order into bona fide organization? PMID:19333445

The New Kid on the Block: A Specialized Secretion System during Bacterial Sporulation.

PubMed

Morlot, Cécile; Rodrigues, Christopher D A

2018-02-02

The transport of proteins across the bacterial cell envelope is mediated by protein complexes called specialized secretion systems. These nanomachines exist in both Gram-positive and Gram-negative bacteria and have been categorized into different types based on their structural components and function. Interestingly, multiple studies suggest the existence of a protein complex in endospore-forming bacteria that appears to be a new type of specialized secretion system. This protein complex is called the SpoIIIA-SpoIIQ complex and is an exception to the categorical norm since it appears to be a hybrid composed of different parts from well-defined specialized secretion systems. Here we summarize and discuss the current understanding of this complex and its potential role as a specialized secretion system. Copyright © 2018 Elsevier Ltd. All rights reserved.

Shannon entropy in the research on stationary regimes and the evolution of complexity

NASA Astrophysics Data System (ADS)

Eskov, V. M.; Eskov, V. V.; Vochmina, Yu. V.; Gorbunov, D. V.; Ilyashenko, L. K.

2017-05-01

The questions of the identification of complex biological systems (complexity) as special self-organizing systems or systems of the third type first defined by W. Weaver in 1948 continue to be of interest. No reports on the evaluation of entropy for systems of the third type were found among the publications currently available to the authors. The present study addresses the parameters of muscle biopotentials recorded using surface interference electromyography and presents the results of calculation of the Shannon entropy, autocorrelation functions, and statistical distribution functions for electromyograms of subjects in different physiological states (rest and tension of muscles). The results do not allow for statistically reliable discrimination between the functional states of muscles. However, the data obtained by calculating electromyogram quasiatttractor parameters and matrices of paired comparisons of electromyogram samples (calculation of the number k of "coinciding" pairs among the electromyogram samples) provide an integral characteristic that allows the identification of substantial differences between the state of rest and the different states of functional activity. Modifications and implementation of new methods in combination with the novel methods of the theory of chaos and self-organization are obviously essential. The stochastic approach paradigm is not applicable to systems of the third type due to continuous and chaotic changes of the parameters of the state vector x( t) of an organism or the contrasting constancy of these parameters (in the case of entropy).

Intertextuality for Handling Complex Environmental Issues

ERIC Educational Resources Information Center

Byhring, Anne Kristine; Knain, Erik

2016-01-01

Nowhere is the need for handling complexity more pertinent than in addressing environmental issues. Our study explores students' situated constructs of complexity in unfolding discourses on socio-scientific issues. Students' dialogues in two group-work episodes are analysed in detail, with tools from Systemic Functional Linguistics. We identify…

Measurement and simulation of the relatively competitive advantages and weaknesses between economies based on bipartite graph theory.

PubMed

Guan, Jun; Xu, Xiaoyu; Wu, Shan; Xing, Lizhi

2018-01-01

The input-output table is very comprehensive and detailed in describing the national economic systems with abundant economic relationships, which contain supply and demand information among various industrial sectors. The complex network, a theory, and method for measuring the structure of a complex system can depict the structural characteristics of the internal structure of the researched object by measuring the structural indicators of the social and economic systems, revealing the complex relationships between the inner hierarchies and the external economic functions. In this paper, functions of industrial sectors on the global value chain are to be distinguished with bipartite graph theory, and inter-sector competitive relationships are to be extracted through resource allocation process. Furthermore, quantitative analysis indices will be proposed under the perspective of a complex network, which will be used to bring about simulations on the variation tendencies of economies' status in different situations of commercial intercourses. Finally, a new econophysics analytical framework of international trade is to be established.

Measurement and simulation of the relatively competitive advantages and weaknesses between economies based on bipartite graph theory

PubMed Central

Guan, Jun; Xu, Xiaoyu; Wu, Shan

2018-01-01

The input-output table is very comprehensive and detailed in describing the national economic systems with abundant economic relationships, which contain supply and demand information among various industrial sectors. The complex network, a theory, and method for measuring the structure of a complex system can depict the structural characteristics of the internal structure of the researched object by measuring the structural indicators of the social and economic systems, revealing the complex relationships between the inner hierarchies and the external economic functions. In this paper, functions of industrial sectors on the global value chain are to be distinguished with bipartite graph theory, and inter-sector competitive relationships are to be extracted through resource allocation process. Furthermore, quantitative analysis indices will be proposed under the perspective of a complex network, which will be used to bring about simulations on the variation tendencies of economies’ status in different situations of commercial intercourses. Finally, a new econophysics analytical framework of international trade is to be established. PMID:29813083

Biomimicry Promotes the Efficiency of a 10-Step Sequential Enzymatic Reaction on Nanoparticles, Converting Glucose to Lactate.

PubMed

Mukai, Chinatsu; Gao, Lizeng; Nelson, Jacquelyn L; Lata, James P; Cohen, Roy; Wu, Lauren; Hinchman, Meleana M; Bergkvist, Magnus; Sherwood, Robert W; Zhang, Sheng; Travis, Alexander J

2017-01-02

For nanobiotechnology to achieve its potential, complex organic-inorganic systems must grow to utilize the sequential functions of multiple biological components. Critical challenges exist: immobilizing enzymes can block substrate-binding sites or prohibit conformational changes, substrate composition can interfere with activity, and multistep reactions risk diffusion of intermediates. As a result, the most complex tethered reaction reported involves only 3 enzymes. Inspired by the oriented immobilization of glycolytic enzymes on the fibrous sheath of mammalian sperm, here we show a complex reaction of 10 enzymes tethered to nanoparticles. Although individual enzyme efficiency was higher in solution, the efficacy of the 10-step pathway measured by conversion of glucose to lactate was significantly higher when tethered. To our knowledge, this is the most complex organic-inorganic system described, and it shows that tethered, multi-step biological pathways can be reconstituted in hybrid systems to carry out functions such as energy production or delivery of molecular cargo. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Biomimicry promotes the efficiency of a 10-step sequential enzymatic reaction on nanoparticles, converting glucose to lactate

PubMed Central

Mukai, Chinatsu; Gao, Lizeng; Nelson, Jacquelyn L.; Lata, James P.; Cohen, Roy; Wu, Lauren; Hinchman, Meleana M.; Bergkvist, Magnus; Sherwood, Robert W.; Zhang, Sheng; Travis, Alexander J.

2016-01-01

For nanobiotechnology to achieve its potential, complex organic-inorganic systems must grow to utilize the sequential functions of multiple biological components. Critical challenges exist: immobilizing enzymes can block substrate-binding sites or prohibit conformational changes, substrate composition can interfere with activity, and multistep reactions risk diffusion of intermediates. As a result, the most complex tethered reaction reported involves only 3 enzymes. Inspired by the oriented immobilization of glycolytic enzymes on the fibrous sheath of mammalian sperm, here we show a complex reaction of 10 enzymes tethered to nanoparticles. Although individual enzyme efficiency was higher in solution, the efficacy of the 10-step pathway measured by conversion of glucose to lactate was significantly higher when tethered. To our knowledge, this is the most complex organic-inorganic system described, and it shows that tethered, multi-step biological pathways can be reconstituted in hybrid systems to carry out functions such as energy production or delivery of molecular cargo. PMID:27901298

On a useful functional representation of control system structure

NASA Technical Reports Server (NTRS)

Malchow, Harvey L.

1988-01-01

An alternative structure for control systems is proposed. The structure is represented by a three-element block diagram and three functional definitions. It is argued that the three functional elements form a canonical set. The set includes the functions description, estimation and control. General overlay of the structure on parallel state and nested-state control systems is discussed. Breakdown of two real nested-state control systems into the proposed functional format is displayed. Application of the process to the mapping of complex control systems R and D efforts is explained with the Mars Rover Sample and Return mission as an example. A previous application of this basic functional structure to Space Station performance requirements organization is discussed.

Nickel(0)-Catalyzed Inert C-O Bond Functionalization: Organo Rare-Earth Metal Complex as the Coupling Partner.

PubMed

Yan, Xiangqian; Yang, Fanzhi; Cai, Guilong; Meng, Qingwei; Li, Xiaofang

2018-02-02

An organo rare-earth metal complex has been employed as a highly efficient nucleophile in Ni(0)-catalyzed C-O bond functionalization. The optimized catalytic system which consists of Ni(cod) 2 , PCy 3 , and t-BuONa could smoothly convert 1 equiv of naphthyl ethers to alkylated naphthalene analogues with 0.4 equiv of Ln(CH 2 SiMe 3 ) 3 (THF) 2 , delivering good to excellent yields. The reaction system could also activate the ArCH 2 -O bond with mild base.

Detailed requirements document for the integrated structural analysis system, phase B

NASA Technical Reports Server (NTRS)

Rainey, J. A.

1976-01-01

The requirements are defined for a software system entitled integrated Structural Analysis System (ISAS) Phase B which is being developed to provide the user with a tool by which a complete and detailed analysis of a complex structural system can be performed. This software system will allow for automated interface with numerous structural analysis batch programs and for user interaction in the creation, selection, and validation of data. This system will include modifications to the 4 functions developed for ISAS, and the development of 25 new functions. The new functions are described.

SU-E-T-76: A Software System to Monitor VMAT Plan Complexity in a Large Radiotherapy Centre

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arumugam, S; Xing, A; Ingham Institute, Sydney, NSW

2015-06-15

Purpose: To develop a system that analyses and reports the complexity of Volumetric Modulated Arc Therapy (VMAT) plans to aid in the decision making for streamlining patient specific dosimetric quality assurance (QA) tests. Methods: A software system, Delcheck, was developed in-house to calculate VMAT plan and delivery complexity using the treatment delivery file. Delcheck has the functionality to calculate multiple plan complexity metrics including the Li-Xing Modulation Index (LI-MI), multiplicative combination of Leaf Travel and Modulation Complexity Score (LTMCSv), Monitor Units per prescribed dose (MU/D) and the delivery complexity index (MIt) that incorporates the modulation of dose rate, leaf speedmore » and gantry speed. Delcheck includes database functionality to store and compare plan metrics for a specified treatment site. The overall plan and delivery complexity is assessed based on the 95% conformance limit of the complexity metrics as Similar, More or Less complex. The functionality of the software was tested using 42 prostate conventional, 10 prostate SBRT and 15 prostate bed VMAT plans generated for an Elekta linear accelerator. Results: The mean(σ) of LI-MI for conventional, SBRT and prostate bed plans were 1690(486), 3215.4(1294) and 3258(982) respectively. The LTMCSv of the studied categories were 0.334(0.05), 0.325(0.07) and 0.3112(0.09). The MU/D of the studied categories were 2.4(0.4), 2.7(0.7) and 2.5(0.5). The MIt of the studied categories were 21.6(3.4), 18.2(3.0) and 35.9(6.6). The values of the complexity metrics show that LI-MI appeared to resolve the plan complexity better than LTMCSv and MU/D. The MIt value increased as the delivery complexity increased. Conclusion: The developed software was shown to be working as expected. In studied treatment categories Prostate bed plans are more complex in both plan and delivery and SBRT is more complex in plan and less complex in delivery as demonstrated by LI-MI and MIt. This project was funded through a Cancer Council NSW Project Grant (RG14-11)« less

Cardiac mitochondrial matrix and respiratory complex protein phosphorylation

PubMed Central

Covian, Raul

2012-01-01

It has become appreciated over the last several years that protein phosphorylation within the cardiac mitochondrial matrix and respiratory complexes is extensive. Given the importance of oxidative phosphorylation and the balance of energy metabolism in the heart, the potential regulatory effect of these classical signaling events on mitochondrial function is of interest. However, the functional impact of protein phosphorylation and the kinase/phosphatase system responsible for it are relatively unknown. Exceptions include the well-characterized pyruvate dehydrogenase and branched chain α-ketoacid dehydrogenase regulatory system. The first task of this review is to update the current status of protein phosphorylation detection primarily in the matrix and evaluate evidence linking these events with enzymatic function or protein processing. To manage the scope of this effort, we have focused on the pathways involved in energy metabolism. The high sensitivity of modern methods of detecting protein phosphorylation and the low specificity of many kinases suggests that detection of protein phosphorylation sites without information on the mole fraction of phosphorylation is difficult to interpret, especially in metabolic enzymes, and is likely irrelevant to function. However, several systems including protein translocation, adenine nucleotide translocase, cytochrome c, and complex IV protein phosphorylation have been well correlated with enzymatic function along with the classical dehydrogenase systems. The second task is to review the current understanding of the kinase/phosphatase system within the matrix. Though it is clear that protein phosphorylation occurs within the matrix, based on 32P incorporation and quantitative mass spectrometry measures, the kinase/phosphatase system responsible for this process is ill-defined. An argument is presented that remnants of the much more labile bacterial protein phosphoryl transfer system may be present in the matrix and that the evaluation of this possibility will require the application of approaches developed for bacterial cell signaling to the mitochondria. PMID:22886415

Designing for adaptation to novelty and change: functional information, emergent feature graphics, and higher-level control.

PubMed

Hajdukiewicz, John R; Vicente, Kim J

2002-01-01

Ecological interface design (EID) is a theoretical framework that aims to support worker adaptation to change and novelty in complex systems. Previous evaluations of EID have emphasized representativeness to enhance generalizability of results to operational settings. The research presented here is complementary, emphasizing experimental control to enhance theory building. Two experiments were conducted to test the impact of functional information and emergent feature graphics on adaptation to novelty and change in a thermal-hydraulic process control microworld. Presenting functional information in an interface using emergent features encouraged experienced participants to become perceptually coupled to the interface and thereby to exhibit higher-level control and more successful adaptation to unanticipated events. The absence of functional information or of emergent features generally led to lower-level control and less success at adaptation, the exception being a minority of participants who compensated by relying on analytical reasoning. These findings may have practical implications for shaping coordination in complex systems and fundamental implications for the development of a general unified theory of coordination for the technical, human, and social sciences. Actual or potential applications of this research include the design of human-computer interfaces that improve safety in complex sociotechnical systems.

Design for testability and diagnosis at the system-level

NASA Technical Reports Server (NTRS)

Simpson, William R.; Sheppard, John W.

1993-01-01

The growing complexity of full-scale systems has surpassed the capabilities of most simulation software to provide detailed models or gate-level failure analyses. The process of system-level diagnosis approaches the fault-isolation problem in a manner that differs significantly from the traditional and exhaustive failure mode search. System-level diagnosis is based on a functional representation of the system. For example, one can exercise one portion of a radar algorithm (the Fast Fourier Transform (FFT) function) by injecting several standard input patterns and comparing the results to standardized output results. An anomalous output would point to one of several items (including the FFT circuit) without specifying the gate or failure mode. For system-level repair, identifying an anomalous chip is sufficient. We describe here an information theoretic and dependency modeling approach that discards much of the detailed physical knowledge about the system and analyzes its information flow and functional interrelationships. The approach relies on group and flow associations and, as such, is hierarchical. Its hierarchical nature allows the approach to be applicable to any level of complexity and to any repair level. This approach has been incorporated in a product called STAMP (System Testability and Maintenance Program) which was developed and refined through more than 10 years of field-level applications to complex system diagnosis. The results have been outstanding, even spectacular in some cases. In this paper we describe system-level testability, system-level diagnoses, and the STAMP analysis approach, as well as a few STAMP applications.

A toolbox for discrete modelling of cell signalling dynamics.

PubMed

Paterson, Yasmin Z; Shorthouse, David; Pleijzier, Markus W; Piterman, Nir; Bendtsen, Claus; Hall, Benjamin A; Fisher, Jasmin

2018-06-18

In an age where the volume of data regarding biological systems exceeds our ability to analyse it, many researchers are looking towards systems biology and computational modelling to help unravel the complexities of gene and protein regulatory networks. In particular, the use of discrete modelling allows generation of signalling networks in the absence of full quantitative descriptions of systems, which are necessary for ordinary differential equation (ODE) models. In order to make such techniques more accessible to mainstream researchers, tools such as the BioModelAnalyzer (BMA) have been developed to provide a user-friendly graphical interface for discrete modelling of biological systems. Here we use the BMA to build a library of discrete target functions of known canonical molecular interactions, translated from ordinary differential equations (ODEs). We then show that these BMA target functions can be used to reconstruct complex networks, which can correctly predict many known genetic perturbations. This new library supports the accessibility ethos behind the creation of BMA, providing a toolbox for the construction of complex cell signalling models without the need for extensive experience in computer programming or mathematical modelling, and allows for construction and simulation of complex biological systems with only small amounts of quantitative data.

Adaptative synchronization in multi-output fractional-order complex dynamical networks and secure communications

NASA Astrophysics Data System (ADS)

Mata-Machuca, Juan L.; Aguilar-López, Ricardo

2018-01-01

This work deals with the adaptative synchronization of complex dynamical networks with fractional-order nodes and its application in secure communications employing chaotic parameter modulation. The complex network is composed of multiple fractional-order systems with mismatch parameters and the coupling functions are given to realize the network synchronization. We introduce a fractional algebraic synchronizability condition (FASC) and a fractional algebraic identifiability condition (FAIC) which are used to know if the synchronization and parameters estimation problems can be solved. To overcome these problems, an adaptative synchronization methodology is designed; the strategy consists in proposing multiple receiver systems which tend to follow asymptotically the uncertain transmitters systems. The coupling functions and parameters of the receiver systems are adjusted continually according to a convenient sigmoid-like adaptative controller (SLAC), until the measurable output errors converge to zero, hence, synchronization between transmitter and receivers is achieved and message signals are recovered. Indeed, the stability analysis of the synchronization error is based on the fractional Lyapunov direct method. Finally, numerical results corroborate the satisfactory performance of the proposed scheme by means of the synchronization of a complex network consisting of several fractional-order unified chaotic systems.

Applications of systems approaches in the study of rheumatic diseases.

PubMed

Kim, Ki-Jo; Lee, Saseong; Kim, Wan-Uk

2015-03-01

The complex interaction of molecules within a biological system constitutes a functional module. These modules are then acted upon by both internal and external factors, such as genetic and environmental stresses, which under certain conditions can manifest as complex disease phenotypes. Recent advances in high-throughput biological analyses, in combination with improved computational methods for data enrichment, functional annotation, and network visualization, have enabled a much deeper understanding of the mechanisms underlying important biological processes by identifying functional modules that are temporally and spatially perturbed in the context of disease development. Systems biology approaches such as these have produced compelling observations that would be impossible to replicate using classical methodologies, with greater insights expected as both the technology and methods improve in the coming years. Here, we examine the use of systems biology and network analysis in the study of a wide range of rheumatic diseases to better understand the underlying molecular and clinical features.

Whole-cell biocomputing

NASA Technical Reports Server (NTRS)

Simpson, M. L.; Sayler, G. S.; Fleming, J. T.; Applegate, B.

2001-01-01

The ability to manipulate systems on the molecular scale naturally leads to speculation about the rational design of molecular-scale machines. Cells might be the ultimate molecular-scale machines and our ability to engineer them is relatively advanced when compared with our ability to control the synthesis and direct the assembly of man-made materials. Indeed, engineered whole cells deployed in biosensors can be considered one of the practical successes of molecular-scale devices. However, these devices explore only a small portion of cellular functionality. Individual cells or self-organized groups of cells perform extremely complex functions that include sensing, communication, navigation, cooperation and even fabrication of synthetic nanoscopic materials. In natural systems, these capabilities are controlled by complex genetic regulatory circuits, which are only partially understood and not readily accessible for use in engineered systems. Here, we focus on efforts to mimic the functionality of man-made information-processing systems within whole cells.

Video Views and Reviews: Neurulation and the Fashioning of the Vertebrate Central Nervous System

ERIC Educational Resources Information Center

Watters, Christopher

2006-01-01

The central nervous system (CNS) is the first adult organ system to appear during vertebrate development, and the process of its emergence is commonly called neurulation. Such biological "urgency" is perhaps not surprising given the structural and functional complexity of the CNS and the importance of neural function to adaptive behavior and…

Health worker posting and transfer at primary level in Tamil Nadu: Governance of a complex health system function

PubMed Central

Garimella, Surekha; Sheikh, Kabir

2016-01-01

Background: Posting and transfer (PT) of health personnel – placing the right health workers in the right place at the right time – is a core function of any large-scale health service. In the context of government health services, this may be seen as a simple process of bureaucratic governance and implementation of the rule of law. However the literature from India and comparable low and middle-income country health systems suggests that in reality PT is a contested domain, driven by varied expressions of private and public interest throughout the chain of implementation. Objective: To investigate policymaking for PT in the government health sector and implementation of policies as experienced by different health system actors and stakeholders at primary health care level. Methodology: We undertook an empirical case study of a PT reform policy at primary health care level in Tamil Nadu State, to understand how different groups of health systems actors experience PT. In-depth qualitative methods were undertaken to study processes of implementation of PT policies enacted through ‘counselling’ of health workers (individualized consultations to determine postings and transfers). Results: PT emerges as a complex phenomenon, shaped partially by the laws of the state and partially as a parallel system of norms and incentives requiring consideration and coordination of the interests of different groups. Micro-practices of governance represent homegrown coping mechanisms of health administrators that reconcile public and private interests and sustain basic health system functions. Beyond a functional perspective of PT, it also reflects justice and fairness as it plays out in the health system. It signifies how well a system treats its employees, and by inference, is an index of the overall health of the system. Conclusions: For a complex governance function such as PT, the roles of private actors and private interests are not easily separable from the public, but rather are intertwined within the complexities of delivery of a public service. This complexity blurs conventional boundaries of private and public ownership and behaviour, and raises critical questions for the interpretation of coordinated governance. Hence, the imperative of enforcing rules may need to be complemented with bottom-up policy approaches, including treating PT not merely as system dysfunction, but also as a potential instrument of governance innovations, procedural justice and the accountability of health services to communities they seek to serve. PMID:28217602

FIGENIX: Intelligent automation of genomic annotation: expertise integration in a new software platform

PubMed Central

Gouret, Philippe; Vitiello, Vérane; Balandraud, Nathalie; Gilles, André; Pontarotti, Pierre; Danchin, Etienne GJ

2005-01-01

Background Two of the main objectives of the genomic and post-genomic era are to structurally and functionally annotate genomes which consists of detecting genes' position and structure, and inferring their function (as well as of other features of genomes). Structural and functional annotation both require the complex chaining of numerous different software, algorithms and methods under the supervision of a biologist. The automation of these pipelines is necessary to manage huge amounts of data released by sequencing projects. Several pipelines already automate some of these complex chaining but still necessitate an important contribution of biologists for supervising and controlling the results at various steps. Results Here we propose an innovative automated platform, FIGENIX, which includes an expert system capable to substitute to human expertise at several key steps. FIGENIX currently automates complex pipelines of structural and functional annotation under the supervision of the expert system (which allows for example to make key decisions, check intermediate results or refine the dataset). The quality of the results produced by FIGENIX is comparable to those obtained by expert biologists with a drastic gain in terms of time costs and avoidance of errors due to the human manipulation of data. Conclusion The core engine and expert system of the FIGENIX platform currently handle complex annotation processes of broad interest for the genomic community. They could be easily adapted to new, or more specialized pipelines, such as for example the annotation of miRNAs, the classification of complex multigenic families, annotation of regulatory elements and other genomic features of interest. PMID:16083500

The genotype-phenotype map of an evolving digital organism.

PubMed

Fortuna, Miguel A; Zaman, Luis; Ofria, Charles; Wagner, Andreas

2017-02-01

To understand how evolving systems bring forth novel and useful phenotypes, it is essential to understand the relationship between genotypic and phenotypic change. Artificial evolving systems can help us understand whether the genotype-phenotype maps of natural evolving systems are highly unusual, and it may help create evolvable artificial systems. Here we characterize the genotype-phenotype map of digital organisms in Avida, a platform for digital evolution. We consider digital organisms from a vast space of 10141 genotypes (instruction sequences), which can form 512 different phenotypes. These phenotypes are distinguished by different Boolean logic functions they can compute, as well as by the complexity of these functions. We observe several properties with parallels in natural systems, such as connected genotype networks and asymmetric phenotypic transitions. The likely common cause is robustness to genotypic change. We describe an intriguing tension between phenotypic complexity and evolvability that may have implications for biological evolution. On the one hand, genotypic change is more likely to yield novel phenotypes in more complex organisms. On the other hand, the total number of novel phenotypes reachable through genotypic change is highest for organisms with simple phenotypes. Artificial evolving systems can help us study aspects of biological evolvability that are not accessible in vastly more complex natural systems. They can also help identify properties, such as robustness, that are required for both human-designed artificial systems and synthetic biological systems to be evolvable.

The genotype-phenotype map of an evolving digital organism

PubMed Central

Zaman, Luis; Wagner, Andreas

2017-01-01

To understand how evolving systems bring forth novel and useful phenotypes, it is essential to understand the relationship between genotypic and phenotypic change. Artificial evolving systems can help us understand whether the genotype-phenotype maps of natural evolving systems are highly unusual, and it may help create evolvable artificial systems. Here we characterize the genotype-phenotype map of digital organisms in Avida, a platform for digital evolution. We consider digital organisms from a vast space of 10141 genotypes (instruction sequences), which can form 512 different phenotypes. These phenotypes are distinguished by different Boolean logic functions they can compute, as well as by the complexity of these functions. We observe several properties with parallels in natural systems, such as connected genotype networks and asymmetric phenotypic transitions. The likely common cause is robustness to genotypic change. We describe an intriguing tension between phenotypic complexity and evolvability that may have implications for biological evolution. On the one hand, genotypic change is more likely to yield novel phenotypes in more complex organisms. On the other hand, the total number of novel phenotypes reachable through genotypic change is highest for organisms with simple phenotypes. Artificial evolving systems can help us study aspects of biological evolvability that are not accessible in vastly more complex natural systems. They can also help identify properties, such as robustness, that are required for both human-designed artificial systems and synthetic biological systems to be evolvable. PMID:28241039

Transporters, channels, or simple diffusion? Dogmas, atypical roles and complexity in transport systems.

PubMed

Conde, Artur; Diallinas, George; Chaumont, François; Chaves, Manuela; Gerós, Hernâni

2010-06-01

The recent breakthrough discoveries of transport systems assigned with atypical functions provide evidence for complexity in membrane transport biochemistry. Some channels are far from being simple pores creating hydrophilic passages for solutes and can, unexpectedly, act as enzymes, or mediate high-affinity uptake, and some transporters are surprisingly able to function as sensors, channels or even enzymes. Furthermore, numerous transport studies have demonstrated complex multiphasic uptake kinetics for organic and mineral nutrients. The biphasic kinetics of glucose uptake in Saccharomyces cerevisiae, a result of several genetically distinct uptake systems operating simultaneously, is a classical example that is a subject of continuous debate. In contrast, some transporters display biphasic kinetics, being bona fidae dual-affinity transporters, their kinetic properties often modulated by post-translational regulation. Also, aquaporins have recently been reported to exhibit diverse transport properties and can behave as highly adapted, multifunctional channels, transporting solutes such as CO(2), hydrogen peroxide, urea, ammonia, glycerol, polyols, carbamides, purines and pyrimidines, metalloids, glycine, and lactic acid, rather than being simple water pores. The present review provides an overview on some atypical functions displayed by transporter proteins and discusses how this novel knowledge on cellular uptake systems may be related to complex multiphasic uptake kinetics often seen in a wide variety of living organisms and the intriguing diffusive uptake of sugars and other solutes. Copyright 2009 Elsevier Ltd. All rights reserved.

Genes of the major histocompatibility complex highlight interactions of the innate and adaptive immune system

PubMed Central

Lukasch, Barbara; Westerdahl, Helena; Strandh, Maria; Winkler, Hans; Moodley, Yoshan; Knauer, Felix

2017-01-01

Background A well-functioning immune defence is crucial for fitness, but our knowledge about the immune system and its complex interactions is still limited. Major histocompatibility complex (MHC) molecules are involved in T-cell mediated adaptive immune responses, but MHC is also highly upregulated during the initial innate immune response. The aim of our study was therefore to determine to what extent the highly polymorphic MHC is involved in interactions of the innate and adaptive immune defence and if specific functional MHC alleles (FA) or heterozygosity at the MHC are more important. Methods To do this we used captive house sparrows (Passer domesticus) to survey MHC diversity and immune function controlling for several environmental factors. MHC class I alleles were identified using parallel amplicon sequencing and to mirror immune function, several immunological tests that correspond to the innate and adaptive immunity were conducted. Results Our results reveal that MHC was linked to all immune tests, highlighting its importance for the immune defence. While all innate responses were associated with one single FA, adaptive responses (cell-mediated and humoral) were associated with several different alleles. Discussion We found that repeated injections of an antibody in nestlings and adults were linked to different FA and hence might affect different areas of the immune system. Also, individuals with a higher number of different FA produced a smaller secondary response, indicating a disadvantage of having numerous MHC alleles. These results demonstrate the complexity of the immune system in relation to the MHC and lay the foundation for other studies to further investigate this topic. PMID:28875066

Genes of the major histocompatibility complex highlight interactions of the innate and adaptive immune system.

PubMed

Lukasch, Barbara; Westerdahl, Helena; Strandh, Maria; Winkler, Hans; Moodley, Yoshan; Knauer, Felix; Hoi, Herbert

2017-01-01

A well-functioning immune defence is crucial for fitness, but our knowledge about the immune system and its complex interactions is still limited. Major histocompatibility complex (MHC) molecules are involved in T-cell mediated adaptive immune responses, but MHC is also highly upregulated during the initial innate immune response. The aim of our study was therefore to determine to what extent the highly polymorphic MHC is involved in interactions of the innate and adaptive immune defence and if specific functional MHC alleles (FA) or heterozygosity at the MHC are more important. To do this we used captive house sparrows ( Passer domesticus ) to survey MHC diversity and immune function controlling for several environmental factors. MHC class I alleles were identified using parallel amplicon sequencing and to mirror immune function, several immunological tests that correspond to the innate and adaptive immunity were conducted. Our results reveal that MHC was linked to all immune tests, highlighting its importance for the immune defence. While all innate responses were associated with one single FA, adaptive responses (cell-mediated and humoral) were associated with several different alleles. We found that repeated injections of an antibody in nestlings and adults were linked to different FA and hence might affect different areas of the immune system. Also, individuals with a higher number of different FA produced a smaller secondary response, indicating a disadvantage of having numerous MHC alleles. These results demonstrate the complexity of the immune system in relation to the MHC and lay the foundation for other studies to further investigate this topic.

Inclusive Education as Complex Process and Challenge for School System

ERIC Educational Resources Information Center

Al-Khamisy, Danuta

2015-01-01

Education may be considered as a number of processes, actions and effects affecting human being, as the state or level of the results of these processes or as the modification of the functions, institutions and social practices roles, which in the result of inclusion become new, integrated system. Thus this is very complex process. Nowadays the…

Emerging themes in the ecology and management of North American forests

Treesearch

Terry L. Sharik; William Adair; Fred A. Baker; Michael Battaglia; Emily J. Comfort; Anthony W. D' Amato; Craig Delong; R. Justin DeRose; Mark J. Ducey; Mark Harmon; Louise Levy; Jesse A. Logan; Joseph O' Brien; Brian J. Palik; Scott D. Roberts; Paul C. Rogers; Douglas J. Shinneman; Thomas Spies; Sarah L. Taylor; Christopher Woodall; Andrew Youngblood

2010-01-01

Forests are extremely complex systems that respond to an overwhelming number of biological and environmental factors, which can act singularly and in concert with each other, as exemplified by Puettmann et al. [1]. The complexity of forest systems presents an enormous challenge for forest researchers who try to deepen their understanding of the structure and function...

Heterarchies: Reconciling Networks and Hierarchies.

PubMed

Cumming, Graeme S

2016-08-01

Social-ecological systems research suffers from a disconnect between hierarchical (top-down or bottom-up) and network (peer-to-peer) analyses. The concept of the heterarchy unifies these perspectives in a single framework. Here, I review the history and application of 'heterarchy' in neuroscience, ecology, archaeology, multiagent control systems, business and organisational studies, and politics. Recognising complex system architecture as a continuum along vertical and lateral axes ('flat versus hierarchical' and 'individual versus networked') suggests four basic types of heterarchy: reticulated, polycentric, pyramidal, and individualistic. Each has different implications for system functioning and resilience. Systems can also shift predictably and abruptly between architectures. Heterarchies suggest new ways of contextualising and generalising from case studies and new methods for analysing complex structure-function relations. Copyright © 2016 Elsevier Ltd. All rights reserved.

Serotonin: Modulator of a Drive to Withdraw

ERIC Educational Resources Information Center

Tops, Mattie; Russo, Sascha; Boksem, Maarten A. S.; Tucker, Don M.

2009-01-01

Serotonin is a fundamental neuromodulator in both vertebrate and invertebrate nervous systems, with a suspected role in many human mental disorders. Yet, because of the complexity of serotonergic function, researchers have been unable to agree on a general theory. One function suggested for serotonin systems is the avoidance of threat. We propose…

Public Relations Roles and Systems Theory: Functional and Historicist Causal Models.

ERIC Educational Resources Information Center

Broom, Glen M.

The effectiveness of an organizations's adaptive behavior depends on the extent to which public relations concerns are considered in goal setting and program planning. The following five open systems propositions, based on a "functional" paradigm, address the complex relationship between public relations and organizational intelligence and do not…

Validation of inertial measurement units with an optoelectronic system for whole-body motion analysis.

PubMed

Robert-Lachaine, Xavier; Mecheri, Hakim; Larue, Christian; Plamondon, André

2017-04-01

The potential of inertial measurement units (IMUs) for ergonomics applications appears promising. However, previous IMUs validation studies have been incomplete regarding aspects of joints analysed, complexity of movements and duration of trials. The objective was to determine the technological error and biomechanical model differences between IMUs and an optoelectronic system and evaluate the effect of task complexity and duration. Whole-body kinematics from 12 participants was recorded simultaneously with a full-body Xsens system where an Optotrak cluster was fixed on every IMU. Short functional movements and long manual material handling tasks were performed and joint angles were compared between the two systems. The differences attributed to the biomechanical model showed significantly greater (P ≤ .001) RMSE than the technological error. RMSE was systematically higher (P ≤ .001) for the long complex task with a mean on all joints of 2.8° compared to 1.2° during short functional movements. Definition of local coordinate systems based on anatomical landmarks or single posture was the most influent difference between the two systems. Additionally, IMUs accuracy was affected by the complexity and duration of the tasks. Nevertheless, technological error remained under 5° RMSE during handling tasks, which shows potential to track workers during their daily labour.

A Synthetic Biology Framework for Programming Eukaryotic Transcription Functions

PubMed Central

Khalil, Ahmad S.; Lu, Timothy K.; Bashor, Caleb J.; Ramirez, Cherie L.; Pyenson, Nora C.; Joung, J. Keith; Collins, James J.

2013-01-01

SUMMARY Eukaryotic transcription factors (TFs) perform complex and combinatorial functions within transcriptional networks. Here, we present a synthetic framework for systematically constructing eukaryotic transcription functions using artificial zinc fingers, modular DNA-binding domains found within many eukaryotic TFs. Utilizing this platform, we construct a library of orthogonal synthetic transcription factors (sTFs) and use these to wire synthetic transcriptional circuits in yeast. We engineer complex functions, such as tunable output strength and transcriptional cooperativity, by rationally adjusting a decomposed set of key component properties, e.g., DNA specificity, affinity, promoter design, protein-protein interactions. We show that subtle perturbations to these properties can transform an individual sTF between distinct roles (activator, cooperative factor, inhibitory factor) within a transcriptional complex, thus drastically altering the signal processing behavior of multi-input systems. This platform provides new genetic components for synthetic biology and enables bottom-up approaches to understanding the design principles of eukaryotic transcriptional complexes and networks. PMID:22863014

Reliability analysis in interdependent smart grid systems

NASA Astrophysics Data System (ADS)

Peng, Hao; Kan, Zhe; Zhao, Dandan; Han, Jianmin; Lu, Jianfeng; Hu, Zhaolong

2018-06-01

Complex network theory is a useful way to study many real complex systems. In this paper, a reliability analysis model based on complex network theory is introduced in interdependent smart grid systems. In this paper, we focus on understanding the structure of smart grid systems and studying the underlying network model, their interactions, and relationships and how cascading failures occur in the interdependent smart grid systems. We propose a practical model for interdependent smart grid systems using complex theory. Besides, based on percolation theory, we also study the effect of cascading failures effect and reveal detailed mathematical analysis of failure propagation in such systems. We analyze the reliability of our proposed model caused by random attacks or failures by calculating the size of giant functioning components in interdependent smart grid systems. Our simulation results also show that there exists a threshold for the proportion of faulty nodes, beyond which the smart grid systems collapse. Also we determine the critical values for different system parameters. In this way, the reliability analysis model based on complex network theory can be effectively utilized for anti-attack and protection purposes in interdependent smart grid systems.

The sleeping brain as a complex system.

PubMed

Olbrich, Eckehard; Achermann, Peter; Wennekers, Thomas

2011-10-13

'Complexity science' is a rapidly developing research direction with applications in a multitude of fields that study complex systems consisting of a number of nonlinear elements with interesting dynamics and mutual interactions. This Theme Issue 'The complexity of sleep' aims at fostering the application of complexity science to sleep research, because the brain in its different sleep stages adopts different global states that express distinct activity patterns in large and complex networks of neural circuits. This introduction discusses the contributions collected in the present Theme Issue. We highlight the potential and challenges of a complex systems approach to develop an understanding of the brain in general and the sleeping brain in particular. Basically, we focus on two topics: the complex networks approach to understand the changes in the functional connectivity of the brain during sleep, and the complex dynamics of sleep, including sleep regulation. We hope that this Theme Issue will stimulate and intensify the interdisciplinary communication to advance our understanding of the complex dynamics of the brain that underlies sleep and consciousness.

Wigner distribution functions for complex dynamical systems: the emergence of the Wigner-Boltzmann equation.

PubMed

Sels, Dries; Brosens, Fons

2013-10-01

The equation of motion for the reduced Wigner function of a system coupled to an external quantum system is presented for the specific case when the external quantum system can be modeled as a set of harmonic oscillators. The result is derived from the Wigner function formulation of the Feynman-Vernon influence functional theory. It is shown how the true self-energy for the equation of motion is connected with the influence functional for the path integral. Explicit expressions are derived in terms of the bare Wigner propagator. Finally, we show under which approximations the resulting equation of motion reduces to the Wigner-Boltzmann equation.

Structural Behavioral Study on the General Aviation Network Based on Complex Network

NASA Astrophysics Data System (ADS)

Zhang, Liang; Lu, Na

2017-12-01

The general aviation system is an open and dissipative system with complex structures and behavioral features. This paper has established the system model and network model for general aviation. We have analyzed integral attributes and individual attributes by applying the complex network theory and concluded that the general aviation network has influential enterprise factors and node relations. We have checked whether the network has small world effect, scale-free property and network centrality property which a complex network should have by applying degree distribution of functions and proved that the general aviation network system is a complex network. Therefore, we propose to achieve the evolution process of the general aviation industrial chain to collaborative innovation cluster of advanced-form industries by strengthening network multiplication effect, stimulating innovation performance and spanning the structural hole path.

Landscape approach to the formation of the ecological frame of Moscow

NASA Astrophysics Data System (ADS)

Nizovtsev, Vyacheslav; Natalia, Erman

2015-04-01

The territory of Moscow, in particular in its former borders, is distinct for its strong transformation of the natural properties of virtually all types of landscape complexes. The modern landscape structure is characterized by fragmentation of natural land cover. Natural and quasinatural (natural and anthropogenic) landscape complexes with preserved natural structure are represented by isolated areas and occupy small areas. During recent years landscape diversity in general and biodiversity in particular have been rapidly declining, and many of the natural landscape complexes are under ever-increasing degradation. Ecological balance is broken, and preserved natural landscapes are not able to maintain it. Effective territorial organization of Moscow and the rational use of its territory are impossible without taking into account the natural component of the city as well as the properties and potential of the landscape complexes that integrate all natural features in specific areas. The formation of the ecological framework of the city is particularly important. It should be a single system of interrelated and complementary components that make up a single environmental space: habitat-forming cores (junctions), ecological corridors and elements of environmental infrastructure. Systemic unity of the environmental framework can support the territorial ecological compensation where a break of the ecological functions of one part of the system is compensated by maintaining or restoring them in another part and contribute to the polarization of incompatible types of land use. Habitat-forming cores should include as mandatory parts all the specifically protected natural areas (SPNAs), particularly valuable landscape complexes, as well as preserved adjacent forest areas. Their most important function should be to maintain resources and area reproducing abilities of landscapes, landscape diversity and biodiversity. Ecological corridors which perform environmental and operating transit functions should include unified landscape systems of river valleys, their hollow-beam upstreams and drained lows. The most important elements of environmental infrastructure include the most valuable forest and wetland complexes, springs and other landscape and aquatic complexes, cultural and historical landscape complexes, landscape complexes with high concentration of cultural heritage sites, sites of natural and green areas with great potential of natural and recreational resources, natural and recreational parks, natural monuments. They can serve as centers of landscape and biological diversity and perform partial transit (migration) and buffer functions. The territory of the ecological framework can be used for strictly regulated or limited recreation (tourism, short leisure). The adjacent natural and green spaces and natural parks may play a buffer role for the SPNAs and valuable landscape complexes. The spatial pattern of the landscape complexes of Moscow allows to create a single ecological framework based on the landscape, distinct for its interrelated and complementary components. Its basis may be consisted of uniform landscape complexes of valley outwash plains and river valleys, their hollow-beam upstreams and drained lows which perform system forming, environmental and transit functions. In the plan river valleys and small erosional forms are as if enclosed in the gullies and constitute single paradynamic systems unified by lateral flows. Therefore not only the edges of river valleys, but also the rear seams of the valley outwash plains should become important natural boundaries, limiting urban development of the area. Their most important functional feature is that they serve as local collectors and surface water runoff channels. These landscape complexes are distinct for most dynamic natural processes and thus negative exogenous processes. The authors have drawn indigenous (conditionally restored) and modern landscapes of Moscow on a scale of 1: 50,000 and on their basis an ecological framework map of Moscow. These maps are an important natural basis for the analysis of conditions and identification of limiting factors of the urban development of the big city.

Spectral simplicity of apparent complexity. II. Exact complexities and complexity spectra

NASA Astrophysics Data System (ADS)

Riechers, Paul M.; Crutchfield, James P.

2018-03-01

The meromorphic functional calculus developed in Part I overcomes the nondiagonalizability of linear operators that arises often in the temporal evolution of complex systems and is generic to the metadynamics of predicting their behavior. Using the resulting spectral decomposition, we derive closed-form expressions for correlation functions, finite-length Shannon entropy-rate approximates, asymptotic entropy rate, excess entropy, transient information, transient and asymptotic state uncertainties, and synchronization information of stochastic processes generated by finite-state hidden Markov models. This introduces analytical tractability to investigating information processing in discrete-event stochastic processes, symbolic dynamics, and chaotic dynamical systems. Comparisons reveal mathematical similarities between complexity measures originally thought to capture distinct informational and computational properties. We also introduce a new kind of spectral analysis via coronal spectrograms and the frequency-dependent spectra of past-future mutual information. We analyze a number of examples to illustrate the methods, emphasizing processes with multivariate dependencies beyond pairwise correlation. This includes spectral decomposition calculations for one representative example in full detail.

Reliability Standards of Complex Engineering Systems

NASA Astrophysics Data System (ADS)

Galperin, E. M.; Zayko, V. A.; Gorshkalev, P. A.

2017-11-01

Production and manufacture play an important role in today’s modern society. Industrial production is nowadays characterized by increased and complex communications between its parts. The problem of preventing accidents in a large industrial enterprise becomes especially relevant. In these circumstances, the reliability of enterprise functioning is of particular importance. Potential damage caused by an accident at such enterprise may lead to substantial material losses and, in some cases, can even cause a loss of human lives. That is why industrial enterprise functioning reliability is immensely important. In terms of their reliability, industrial facilities (objects) are divided into simple and complex. Simple objects are characterized by only two conditions: operable and non-operable. A complex object exists in more than two conditions. The main characteristic here is the stability of its operation. This paper develops the reliability indicator combining the set theory methodology and a state space method. Both are widely used to analyze dynamically developing probability processes. The research also introduces a set of reliability indicators for complex technical systems.

Three faces of entropy for complex systems: Information, thermodynamics, and the maximum entropy principle

NASA Astrophysics Data System (ADS)

Thurner, Stefan; Corominas-Murtra, Bernat; Hanel, Rudolf

2017-09-01

There are at least three distinct ways to conceptualize entropy: entropy as an extensive thermodynamic quantity of physical systems (Clausius, Boltzmann, Gibbs), entropy as a measure for information production of ergodic sources (Shannon), and entropy as a means for statistical inference on multinomial processes (Jaynes maximum entropy principle). Even though these notions represent fundamentally different concepts, the functional form of the entropy for thermodynamic systems in equilibrium, for ergodic sources in information theory, and for independent sampling processes in statistical systems, is degenerate, H (p ) =-∑ipilogpi . For many complex systems, which are typically history-dependent, nonergodic, and nonmultinomial, this is no longer the case. Here we show that for such processes, the three entropy concepts lead to different functional forms of entropy, which we will refer to as SEXT for extensive entropy, SIT for the source information rate in information theory, and SMEP for the entropy functional that appears in the so-called maximum entropy principle, which characterizes the most likely observable distribution functions of a system. We explicitly compute these three entropy functionals for three concrete examples: for Pólya urn processes, which are simple self-reinforcing processes, for sample-space-reducing (SSR) processes, which are simple history dependent processes that are associated with power-law statistics, and finally for multinomial mixture processes.

Self-assembled peptide nanostructures for functional materials

NASA Astrophysics Data System (ADS)

Sardan Ekiz, Melis; Cinar, Goksu; Aref Khalily, Mohammad; Guler, Mustafa O.

2016-10-01

Nature is an important inspirational source for scientists, and presents complex and elegant examples of adaptive and intelligent systems created by self-assembly. Significant effort has been devoted to understanding these sophisticated systems. The self-assembly process enables us to create supramolecular nanostructures with high order and complexity, and peptide-based self-assembling building blocks can serve as suitable platforms to construct nanostructures showing diverse features and applications. In this review, peptide-based supramolecular assemblies will be discussed in terms of their synthesis, design, characterization and application. Peptide nanostructures are categorized based on their chemical and physical properties and will be examined by rationalizing the influence of peptide design on the resulting morphology and the methods employed to characterize these high order complex systems. Moreover, the application of self-assembled peptide nanomaterials as functional materials in information technologies and environmental sciences will be reviewed by providing examples from recently published high-impact studies.

Activity Diagrams for DEVS Models: A Case Study Modeling Health Care Behavior

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ozmen, Ozgur; Nutaro, James J

Discrete Event Systems Specification (DEVS) is a widely used formalism for modeling and simulation of discrete and continuous systems. While DEVS provides a sound mathematical representation of discrete systems, its practical use can suffer when models become complex. Five main functions, which construct the core of atomic modules in DEVS, can realize the behaviors that modelers want to represent. The integration of these functions is handled by the simulation routine, however modelers can implement each function in various ways. Therefore, there is a need for graphical representations of complex models to simplify their implementation and facilitate their reproduction. In thismore » work, we illustrate the use of activity diagrams for this purpose in the context of a health care behavior model, which is developed with an agent-based modeling paradigm.« less

Mapping complex traits as a dynamic system

PubMed Central

Sun, Lidan; Wu, Rongling

2017-01-01

Despite increasing emphasis on the genetic study of quantitative traits, we are still far from being able to chart a clear picture of their genetic architecture, given an inherent complexity involved in trait formation. A competing theory for studying such complex traits has emerged by viewing their phenotypic formation as a “system” in which a high-dimensional group of interconnected components act and interact across different levels of biological organization from molecules through cells to whole organisms. This system is initiated by a machinery of DNA sequences that regulate a cascade of biochemical pathways to synthesize endophenotypes and further assemble these endophenotypes toward the end-point phenotype in virtue of various developmental changes. This review focuses on a conceptual framework for genetic mapping of complex traits by which to delineate the underlying components, interactions and mechanisms that govern the system according to biological principles and understand how these components function synergistically under the control of quantitative trait loci (QTLs) to comprise a unified whole. This framework is built by a system of differential equations that quantifies how alterations of different components lead to the global change of trait development and function, and provides a quantitative and testable platform for assessing the multiscale interplay between QTLs and development. The method will enable geneticists to shed light on the genetic complexity of any biological system and predict, alter or engineer its physiological and pathological states. PMID:25772476

Normal people working in normal organizations with normal equipment: system safety and cognition in a mid-air collision.

PubMed

de Carvalho, Paulo Victor Rodrigues; Gomes, José Orlando; Huber, Gilbert Jacob; Vidal, Mario Cesar

2009-05-01

A fundamental challenge in improving the safety of complex systems is to understand how accidents emerge in normal working situations, with equipment functioning normally in normally structured organizations. We present a field study of the en route mid-air collision between a commercial carrier and an executive jet, in the clear afternoon Amazon sky in which 154 people lost their lives, that illustrates one response to this challenge. Our focus was on how and why the several safety barriers of a well structured air traffic system melted down enabling the occurrence of this tragedy, without any catastrophic component failure, and in a situation where everything was functioning normally. We identify strong consistencies and feedbacks regarding factors of system day-to-day functioning that made monitoring and awareness difficult, and the cognitive strategies that operators have developed to deal with overall system behavior. These findings emphasize the active problem-solving behavior needed in air traffic control work, and highlight how the day-to-day functioning of the system can jeopardize such behavior. An immediate consequence is that safety managers and engineers should review their traditional safety approach and accident models based on equipment failure probability, linear combinations of failures, rules and procedures, and human errors, to deal with complex patterns of coincidence possibilities, unexpected links, resonance among system functions and activities, and system cognition.

Thiol/disulfide redox states in signaling and sensing

PubMed Central

Go, Young-Mi; Jones, Dean P.

2015-01-01

Rapid advances in redox systems biology are creating new opportunities to understand complexities of human disease and contributions of environmental exposures. New understanding of thiol-disulfide systems have occurred during the past decade as a consequence of the discoveries that thiol and disulfide systems are maintained in kinetically controlled steady-states displaced from thermodynamic equilibrium, that a widely distributed family of NADPH oxidases produces oxidants that function in cell signaling, and that a family of peroxiredoxins utilize thioredoxin as a reductant to complement the well-studied glutathione antioxidant system for peroxide elimination and redox regulation. This review focuses on thiol/disulfide redox state in biologic systems and the knowledge base available to support development of integrated redox systems biology models to better understand the function and dysfunction of thiol-disulfide redox systems. In particular, central principles have emerged concerning redox compartmentalization and utility of thiol/disulfide redox measures as indicators of physiologic function. Advances in redox proteomics show that, in addition to functioning in protein active sites and cell signaling, cysteine residues also serve as redox sensors to integrate biologic functions. These advances provide a framework for translation of redox systems biology concepts to practical use in understanding and treating human disease. Biological responses to cadmium, a widespread environmental agent, are used to illustrate the utility of these advances to the understanding of complex pleiotropic toxicities. PMID:23356510

Functional safety for the Advanced Technology Solar Telescope

NASA Astrophysics Data System (ADS)

Bulau, Scott; Williams, Timothy R.

2012-09-01

Since inception, the Advanced Technology Solar Telescope (ATST) has planned to implement a facility-wide functional safety system to protect personnel from harm and prevent damage to the facility or environment. The ATST will deploy an integrated safety-related control system (SRCS) to achieve functional safety throughout the facility rather than relying on individual facility subsystems to provide safety functions on an ad hoc basis. The Global Interlock System (GIS) is an independent, distributed, facility-wide, safety-related control system, comprised of commercial off-the-shelf (COTS) programmable controllers that monitor, evaluate, and control hazardous energy and conditions throughout the facility that arise during operation and maintenance. The GIS has been designed to utilize recent advances in technology for functional safety plus revised national and international standards that allow for a distributed architecture using programmable controllers over a local area network instead of traditional hard-wired safety functions, while providing an equivalent or even greater level of safety. Programmable controllers provide an ideal platform for controlling the often complex interrelationships between subsystems in a modern astronomical facility, such as the ATST. A large, complex hard-wired relay control system is no longer needed. This type of system also offers greater flexibility during development and integration in addition to providing for expanded capability into the future. The GIS features fault detection, self-diagnostics, and redundant communications that will lead to decreased maintenance time and increased availability of the facility.

Drug Release Kinetics and Transport Mechanisms of Non-degradable and Degradable Polymeric Delivery Systems

PubMed Central

Fu, Yao; Kao, Weiyuan John

2010-01-01

Importance of the field The advancement in material design and engineering has led to the rapid development of novel materials with increasing complexity and functions. Both non-degradable and degradable polymers have found wide applications in the controlled delivery field. Studies on drug release kinetics provide important information into the function of material systems. To elucidate the detailed transport mechanism and the structure-function relationship of a material system, it is critical to bridge the gap between the macroscopic data and the transport behavior at the molecular level. Areas covered in this review The structure and function information of selected non-degradable and degradable polymers have been collected and summarized from literatures published after 1990s. The release kinetics of selected drug compounds from various material systems will be discussed in case studies. Recent progresses in the mathematical models based on different transport mechanisms will be highlighted. What the reader will gain This article aims to provide an overview of structure-function relationships of selected non-degradable and degradable polymers as drug delivery matrices. Take home message Understanding the structure-function relationship of the material system is key to the successful design of a delivery system for a particular application. Moreover, developing complex polymeric matrices requires more robust mathematical models to elucidate the solute transport mechanisms. PMID:20331353

Service quality and maturity of health care organizations through the lens of Complexity Leadership Theory.

PubMed

Horvat, Ana; Filipovic, Jovan

2018-02-01

This research focuses on Complexity Leadership Theory and the relationship between leadership-examined through the lens of Complexity Leadership Theory-and organizational maturity as an indicator of the performance of health organizations. The research adopts a perspective that conceptualizes organizations as complex adaptive systems and draws upon a survey of opinion of 189 managers working in Serbian health organizations. As the results indicate a dependency between functions of leadership and levels of the maturity of health organizations, we propose a model that connects the two. The study broadens our understanding of the implications of complexity thinking and its reflection on leadership functions and overall organizational performance. The correlations between leadership functions and maturity could have practical applications in policy processing, thus improving the quality of outcomes and the overall level of service quality. © 2017 John Wiley & Sons, Ltd.

Adaptive control for a class of nonlinear complex dynamical systems with uncertain complex parameters and perturbations

PubMed Central

Liu, Jian; Liu, Kexin; Liu, Shutang

2017-01-01

In this paper, adaptive control is extended from real space to complex space, resulting in a new control scheme for a class of n-dimensional time-dependent strict-feedback complex-variable chaotic (hyperchaotic) systems (CVCSs) in the presence of uncertain complex parameters and perturbations, which has not been previously reported in the literature. In detail, we have developed a unified framework for designing the adaptive complex scalar controller to ensure this type of CVCSs asymptotically stable and for selecting complex update laws to estimate unknown complex parameters. In particular, combining Lyapunov functions dependent on complex-valued vectors and back-stepping technique, sufficient criteria on stabilization of CVCSs are derived in the sense of Wirtinger calculus in complex space. Finally, numerical simulation is presented to validate our theoretical results. PMID:28467431

Adaptive control for a class of nonlinear complex dynamical systems with uncertain complex parameters and perturbations.

PubMed

Liu, Jian; Liu, Kexin; Liu, Shutang

2017-01-01

In this paper, adaptive control is extended from real space to complex space, resulting in a new control scheme for a class of n-dimensional time-dependent strict-feedback complex-variable chaotic (hyperchaotic) systems (CVCSs) in the presence of uncertain complex parameters and perturbations, which has not been previously reported in the literature. In detail, we have developed a unified framework for designing the adaptive complex scalar controller to ensure this type of CVCSs asymptotically stable and for selecting complex update laws to estimate unknown complex parameters. In particular, combining Lyapunov functions dependent on complex-valued vectors and back-stepping technique, sufficient criteria on stabilization of CVCSs are derived in the sense of Wirtinger calculus in complex space. Finally, numerical simulation is presented to validate our theoretical results.

Complex Networks - A Key to Understanding Brain Function

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sporns, Olaf

2008-01-23

The brain is a complex network of neurons, engaging in spontaneous and evoked activity that is thought to be the main substrate of mental life.  How this complex system works together to process information and generate coherent cognitive states, even consciousness, is not yet well understood.  In my talk I will review recent studies that have revealed characteristic structural and functional attributes of brain networks, and discuss efforts to build computational models of the brain that are informed by our growing knowledge of brain anatomy and physiology.

Complex Networks - A Key to Understanding Brain Function

ScienceCinema

Sporns, Olaf

2017-12-22

The brain is a complex network of neurons, engaging in spontaneous and evoked activity that is thought to be the main substrate of mental life.  How this complex system works together to process information and generate coherent cognitive states, even consciousness, is not yet well understood.  In my talk I will review recent studies that have revealed characteristic structural and functional attributes of brain networks, and discuss efforts to build computational models of the brain that are informed by our growing knowledge of brain anatomy and physiology.

Experiences on developing digital down conversion algorithms using Xilinx system generator

NASA Astrophysics Data System (ADS)

Xu, Chengfa; Yuan, Yuan; Zhao, Lizhi

2013-07-01

The Digital Down Conversion (DDC) algorithm is a classical signal processing method which is widely used in radar and communication systems. In this paper, the DDC function is implemented by Xilinx System Generator tool on FPGA. System Generator is an FPGA design tool provided by Xilinx Inc and MathWorks Inc. It is very convenient for programmers to manipulate the design and debug the function, especially for the complex algorithm. Through the developing process of DDC function based on System Generator, the results show that System Generator is a very fast and efficient tool for FPGA design.

Recording information on protein complexes in an information management system

PubMed Central

Savitsky, Marc; Diprose, Jonathan M.; Morris, Chris; Griffiths, Susanne L.; Daniel, Edward; Lin, Bill; Daenke, Susan; Bishop, Benjamin; Siebold, Christian; Wilson, Keith S.; Blake, Richard; Stuart, David I.; Esnouf, Robert M.

2011-01-01

The Protein Information Management System (PiMS) is a laboratory information management system (LIMS) designed for use with the production of proteins in a research environment. The software is distributed under the CCP4 licence, and so is available free of charge to academic laboratories. Like most LIMS, the underlying PiMS data model originally had no support for protein–protein complexes. To support the SPINE2-Complexes project the developers have extended PiMS to meet these requirements. The modifications to PiMS, described here, include data model changes, additional protocols, some user interface changes and functionality to detect when an experiment may have formed a complex. Example data are shown for the production of a crystal of a protein complex. Integration with SPINE2-Complexes Target Tracker application is also described. PMID:21605682

Recording information on protein complexes in an information management system.

PubMed

Savitsky, Marc; Diprose, Jonathan M; Morris, Chris; Griffiths, Susanne L; Daniel, Edward; Lin, Bill; Daenke, Susan; Bishop, Benjamin; Siebold, Christian; Wilson, Keith S; Blake, Richard; Stuart, David I; Esnouf, Robert M

2011-08-01

The Protein Information Management System (PiMS) is a laboratory information management system (LIMS) designed for use with the production of proteins in a research environment. The software is distributed under the CCP4 licence, and so is available free of charge to academic laboratories. Like most LIMS, the underlying PiMS data model originally had no support for protein-protein complexes. To support the SPINE2-Complexes project the developers have extended PiMS to meet these requirements. The modifications to PiMS, described here, include data model changes, additional protocols, some user interface changes and functionality to detect when an experiment may have formed a complex. Example data are shown for the production of a crystal of a protein complex. Integration with SPINE2-Complexes Target Tracker application is also described. Copyright © 2011 Elsevier Inc. All rights reserved.

Paucity of attractors in nonlinear systems driven with complex signals.

PubMed

Pethel, Shawn D; Blakely, Jonathan N

2011-04-01

We study the probability of multistability in a quadratic map driven repeatedly by a random signal of length N, where N is taken as a measure of the signal complexity. We first establish analytically that the number of coexisting attractors is bounded above by N. We then numerically estimate the probability p of a randomly chosen signal resulting in a multistable response as a function of N. Interestingly, with increasing drive signal complexity the system exhibits a paucity of attractors. That is, almost any drive signal beyond a certain complexity level will result in a single attractor response (p=0). This mechanism may play a role in allowing sensitive multistable systems to respond consistently to external influences.

Test procedures and performance measures sensitive to automobile steering dynamics. [considering operator/vehicle responses

NASA Technical Reports Server (NTRS)

Klein, R. H.; Mcruer, D. T.; Weir, D.

1975-01-01

A maneuver complex and related performance measures used to evaluate driver/vehicle system responses as effected by variations in the directional response characteristics of passenger cars are described. The complex consists of normal and emergency maneuvers (including random and discrete disturbances) which, taken as a whole, represent all classes of steering functions and all modes of driver response behavior. Measures of driver/vehicle system response and performance in regulation tasks included direct describing function measurements and rms yaw velocity. In transient maneuvers, measures such as steering activity and cone strikes were used.

Systems Proteomics for Translational Network Medicine

PubMed Central

Arrell, D. Kent; Terzic, Andre

2012-01-01

Universal principles underlying network science, and their ever-increasing applications in biomedicine, underscore the unprecedented capacity of systems biology based strategies to synthesize and resolve massive high throughput generated datasets. Enabling previously unattainable comprehension of biological complexity, systems approaches have accelerated progress in elucidating disease prediction, progression, and outcome. Applied to the spectrum of states spanning health and disease, network proteomics establishes a collation, integration, and prioritization algorithm to guide mapping and decoding of proteome landscapes from large-scale raw data. Providing unparalleled deconvolution of protein lists into global interactomes, integrative systems proteomics enables objective, multi-modal interpretation at molecular, pathway, and network scales, merging individual molecular components, their plurality of interactions, and functional contributions for systems comprehension. As such, network systems approaches are increasingly exploited for objective interpretation of cardiovascular proteomics studies. Here, we highlight network systems proteomic analysis pipelines for integration and biological interpretation through protein cartography, ontological categorization, pathway and functional enrichment and complex network analysis. PMID:22896016

Discovering Link Communities in Complex Networks by an Integer Programming Model and a Genetic Algorithm

PubMed Central

Li, Zhenping; Zhang, Xiang-Sun; Wang, Rui-Sheng; Liu, Hongwei; Zhang, Shihua

2013-01-01

Identification of communities in complex networks is an important topic and issue in many fields such as sociology, biology, and computer science. Communities are often defined as groups of related nodes or links that correspond to functional subunits in the corresponding complex systems. While most conventional approaches have focused on discovering communities of nodes, some recent studies start partitioning links to find overlapping communities straightforwardly. In this paper, we propose a new quantity function for link community identification in complex networks. Based on this quantity function we formulate the link community partition problem into an integer programming model which allows us to partition a complex network into overlapping communities. We further propose a genetic algorithm for link community detection which can partition a network into overlapping communities without knowing the number of communities. We test our model and algorithm on both artificial networks and real-world networks. The results demonstrate that the model and algorithm are efficient in detecting overlapping community structure in complex networks. PMID:24386268

Quasi-projective synchronization of fractional-order complex-valued recurrent neural networks.

PubMed

Yang, Shuai; Yu, Juan; Hu, Cheng; Jiang, Haijun

2018-08-01

In this paper, without separating the complex-valued neural networks into two real-valued systems, the quasi-projective synchronization of fractional-order complex-valued neural networks is investigated. First, two new fractional-order inequalities are established by using the theory of complex functions, Laplace transform and Mittag-Leffler functions, which generalize traditional inequalities with the first-order derivative in the real domain. Additionally, different from hybrid control schemes given in the previous work concerning the projective synchronization, a simple and linear control strategy is designed in this paper and several criteria are derived to ensure quasi-projective synchronization of the complex-valued neural networks with fractional-order based on the established fractional-order inequalities and the theory of complex functions. Moreover, the error bounds of quasi-projective synchronization are estimated. Especially, some conditions are also presented for the Mittag-Leffler synchronization of the addressed neural networks. Finally, some numerical examples with simulations are provided to show the effectiveness of the derived theoretical results. Copyright © 2018 Elsevier Ltd. All rights reserved.

Flood vulnerability evaluation in complex urban areas

NASA Astrophysics Data System (ADS)

Giosa, L.; Pascale, S.; Sdao, F.; Sole, A.; Cantisani, A.

2009-04-01

This paper deals the conception, the development and the subsequent validation of an integrated numerical model for the assessment of systemic vulnerability in complex and urbanized areas, subject to flood risk. The proposed methodology is based on the application of the concept of "systemic vulnerability", the model is a mathematician-decisional model action to estimate the vulnerability of complex a territorial system during a flood event. The model uses a group of "pressure pointers" in order to define, qualitatively and quantitatively, the influence exercised on the territorial system from factors like as those physicists, social, economic, etc.. The model evaluates the exposure to the flood risk of the elements that belong to a system. The proposed model, which is based on the studies of Tamura et al., 2000; Minciardi et al., 2004; Pascale et al., 2008; considers the vulnerability not as a characteristic of a particular element at risk, but as a peculiarity of a complex territorial system, in which the different elements are reciprocally linked in a functional way. The proposed model points out the elements with the major functional lost and that make the whole system critical. This characteristic makes the proposed model able to support a correct territorial planning and a suitable management of the emergency following natural disasters such as floods. The proposed approach was tested on the study area in the city of Potenza, southern Italy.

Optimizing Nutrient Uptake in Biological Transport Networks

NASA Astrophysics Data System (ADS)

Ronellenfitsch, Henrik; Katifori, Eleni

2013-03-01

Many biological systems employ complex networks of vascular tubes to facilitate transport of solute nutrients, examples include the vascular system of plants (phloem), some fungi, and the slime-mold Physarum. It is believed that such networks are optimized through evolution for carrying out their designated task. We propose a set of hydrodynamic governing equations for solute transport in a complex network, and obtain the optimal network architecture for various classes of optimizing functionals. We finally discuss the topological properties and statistical mechanics of the resulting complex networks, and examine correspondence of the obtained networks to those found in actual biological systems.

Functional toxicology: tools to advance the future of toxicity testing

PubMed Central

Gaytán, Brandon D.; Vulpe, Chris D.

2014-01-01

The increased presence of chemical contaminants in the environment is an undeniable concern to human health and ecosystems. Historically, by relying heavily upon costly and laborious animal-based toxicity assays, the field of toxicology has often neglected examinations of the cellular and molecular mechanisms of toxicity for the majority of compounds—information that, if available, would strengthen risk assessment analyses. Functional toxicology, where cells or organisms with gene deletions or depleted proteins are used to assess genetic requirements for chemical tolerance, can advance the field of toxicity testing by contributing data regarding chemical mechanisms of toxicity. Functional toxicology can be accomplished using available genetic tools in yeasts, other fungi and bacteria, and eukaryotes of increased complexity, including zebrafish, fruit flies, rodents, and human cell lines. Underscored is the value of using less complex systems such as yeasts to direct further studies in more complex systems such as human cell lines. Functional techniques can yield (1) novel insights into chemical toxicity; (2) pathways and mechanisms deserving of further study; and (3) candidate human toxicant susceptibility or resistance genes. PMID:24847352

Towards systemic theories in biological psychiatry.

PubMed

Bender, W; Albus, M; Möller, H-J; Tretter, F

2006-02-01

Although still rather controversial, empirical data on the neurobiology of schizophrenia have reached a degree of complexity that makes it hard to obtain a coherent picture of the malfunctions of the brain in schizophrenia. Theoretical neuropsychiatry should therefore use the tools of theoretical sciences like cybernetics, informatics, computational neuroscience or systems science. The methodology of systems science permits the modeling of complex dynamic nonlinear systems. Such procedures might help us to understand brain functions and the disorders and actions of psychiatric drugs better.

Initial flight qualification and operational maintenance of X-29A flight software

NASA Technical Reports Server (NTRS)

Earls, Michael R.; Sitz, Joel R.

1989-01-01

A discussion is presented of some significant aspects of the initial flight qualification and operational maintenance of the flight control system softward for the X-29A technology demonstrator. Flight qualification and maintenance of complex, embedded flight control system software poses unique problems. The X-29A technology demonstrator aircraft has a digital flight control system which incorporates functions generally considered too complex for analog systems. Organizational responsibilities, software assurance issues, tools, and facilities are discussed.

A biomimetic colorimetric logic gate system based on multi-functional peptide-mediated gold nanoparticle assembly

NASA Astrophysics Data System (ADS)

Li, Yong; Li, Wang; He, Kai-Yu; Li, Pei; Huang, Yan; Nie, Zhou; Yao, Shou-Zhuo

2016-04-01

In natural biological systems, proteins exploit various functional peptide motifs to exert target response and activity switch, providing a functional and logic basis for complex cellular activities. Building biomimetic peptide-based bio-logic systems is highly intriguing but remains relatively unexplored due to limited logic recognition elements and complex signal outputs. In this proof-of-principle work, we attempted to address these problems by utilizing multi-functional peptide probes and the peptide-mediated nanoparticle assembly system. Here, the rationally designed peptide probes function as the dual-target responsive element specifically responsive to metal ions and enzymes as well as the mediator regulating the assembly of gold nanoparticles (AuNPs). Taking advantage of Zn2+ ions and chymotrypsin as the model inputs of metal ions and enzymes, respectively, we constructed the peptide logic system computed by the multi-functional peptide probes and outputted by the readable colour change of AuNPs. In this way, the representative binary basic logic gates (AND, OR, INHIBIT, NAND, IMPLICATION) have been achieved by delicately coding the peptide sequence, demonstrating the versatility of our logic system. Additionally, we demonstrated that the three-input combinational logic gate (INHIBIT-OR) could also be successfully integrated and applied as a multi-tasking biosensor for colorimetric detection of dual targets. This nanoparticle-based peptide logic system presents a valid strategy to illustrate peptide information processing and provides a practical platform for executing peptide computing or peptide-related multiplexing sensing, implying that the controllable nanomaterial assembly is a promising and potent methodology for the advancement of biomimetic bio-logic computation.In natural biological systems, proteins exploit various functional peptide motifs to exert target response and activity switch, providing a functional and logic basis for complex cellular activities. Building biomimetic peptide-based bio-logic systems is highly intriguing but remains relatively unexplored due to limited logic recognition elements and complex signal outputs. In this proof-of-principle work, we attempted to address these problems by utilizing multi-functional peptide probes and the peptide-mediated nanoparticle assembly system. Here, the rationally designed peptide probes function as the dual-target responsive element specifically responsive to metal ions and enzymes as well as the mediator regulating the assembly of gold nanoparticles (AuNPs). Taking advantage of Zn2+ ions and chymotrypsin as the model inputs of metal ions and enzymes, respectively, we constructed the peptide logic system computed by the multi-functional peptide probes and outputted by the readable colour change of AuNPs. In this way, the representative binary basic logic gates (AND, OR, INHIBIT, NAND, IMPLICATION) have been achieved by delicately coding the peptide sequence, demonstrating the versatility of our logic system. Additionally, we demonstrated that the three-input combinational logic gate (INHIBIT-OR) could also be successfully integrated and applied as a multi-tasking biosensor for colorimetric detection of dual targets. This nanoparticle-based peptide logic system presents a valid strategy to illustrate peptide information processing and provides a practical platform for executing peptide computing or peptide-related multiplexing sensing, implying that the controllable nanomaterial assembly is a promising and potent methodology for the advancement of biomimetic bio-logic computation. Electronic supplementary information (ESI) available: Additional figures (Tables S1-S3 and Fig. S1-S6). See DOI: 10.1039/c6nr01072e

The fractal geometry of Hartree-Fock

NASA Astrophysics Data System (ADS)

Theel, Friethjof; Karamatskou, Antonia; Santra, Robin

2017-12-01

The Hartree-Fock method is an important approximation for the ground-state electronic wave function of atoms and molecules so that its usage is widespread in computational chemistry and physics. The Hartree-Fock method is an iterative procedure in which the electronic wave functions of the occupied orbitals are determined. The set of functions found in one step builds the basis for the next iteration step. In this work, we interpret the Hartree-Fock method as a dynamical system since dynamical systems are iterations where iteration steps represent the time development of the system, as encountered in the theory of fractals. The focus is put on the convergence behavior of the dynamical system as a function of a suitable control parameter. In our case, a complex parameter λ controls the strength of the electron-electron interaction. An investigation of the convergence behavior depending on the parameter λ is performed for helium, neon, and argon. We observe fractal structures in the complex λ-plane, which resemble the well-known Mandelbrot set, determine their fractal dimension, and find that with increasing nuclear charge, the fragmentation increases as well.

Systems science and obesity policy: a novel framework for analyzing and rethinking population-level planning.

PubMed

Johnston, Lee M; Matteson, Carrie L; Finegood, Diane T

2014-07-01

We demonstrate the use of a systems-based framework to assess solutions to complex health problems such as obesity. We coded 12 documents published between 2004 and 2013 aimed at influencing obesity planning for complex systems design (9 reports from US and Canadian governmental or health authorities, 1 Cochrane review, and 2 Institute of Medicine reports). We sorted data using the intervention-level framework (ILF), a novel solutions-oriented approach to complex problems. An in-depth comparison of 3 documents provides further insight into complexity and systems design in obesity policy. The majority of strategies focused mainly on changing the determinants of energy imbalance (food intake and physical activity). ILF analysis brings to the surface actions aimed at higher levels of system function and points to a need for more innovative policy design. Although many policymakers acknowledge obesity as a complex problem, many strategies stem from the paradigm of individual choice and are limited in scope. The ILF provides a template to encourage natural systems thinking and more strategic policy design grounded in complexity science.

The Network Organization of Cancer-associated Protein Complexes in Human Tissues

PubMed Central

Zhao, Jing; Lee, Sang Hoon; Huss, Mikael; Holme, Petter

2013-01-01

Differential gene expression profiles for detecting disease genes have been studied intensively in systems biology. However, it is known that various biological functions achieved by proteins follow from the ability of the protein to form complexes by physically binding to each other. In other words, the functional units are often protein complexes rather than individual proteins. Thus, we seek to replace the perspective of disease-related genes by disease-related complexes, exemplifying with data on 39 human solid tissue cancers and their original normal tissues. To obtain the differential abundance levels of protein complexes, we apply an optimization algorithm to genome-wide differential expression data. From the differential abundance of complexes, we extract tissue- and cancer-selective complexes, and investigate their relevance to cancer. The method is supported by a clustering tendency of bipartite cancer-complex relationships, as well as a more concrete and realistic approach to disease-related proteomics. PMID:23567845

Decay of Complex-Time Determinantal and Pfaffian Correlation Functionals in Lattices

NASA Astrophysics Data System (ADS)

Aza, N. J. B.; Bru, J.-B.; de Siqueira Pedra, W.

2018-04-01

We supplement the determinantal and Pfaffian bounds of Sims and Warzel (Commun Math Phys 347:903-931, 2016) for many-body localization of quasi-free fermions, by considering the high dimensional case and complex-time correlations. Our proof uses the analyticity of correlation functions via the Hadamard three-line theorem. We show that the dynamical localization for the one-particle system yields the dynamical localization for the many-point fermionic correlation functions, with respect to the Hausdorff distance in the determinantal case. In Sims and Warzel (2016), a stronger notion of decay for many-particle configurations was used but only at dimension one and for real times. Considering determinantal and Pfaffian correlation functionals for complex times is important in the study of weakly interacting fermions.

Decay of Complex-Time Determinantal and Pfaffian Correlation Functionals in Lattices

NASA Astrophysics Data System (ADS)

Aza, N. J. B.; Bru, J.-B.; de Siqueira Pedra, W.

2018-06-01

We supplement the determinantal and Pfaffian bounds of Sims and Warzel (Commun Math Phys 347:903-931, 2016) for many-body localization of quasi-free fermions, by considering the high dimensional case and complex-time correlations. Our proof uses the analyticity of correlation functions via the Hadamard three-line theorem. We show that the dynamical localization for the one-particle system yields the dynamical localization for the many-point fermionic correlation functions, with respect to the Hausdorff distance in the determinantal case. In Sims and Warzel (2016), a stronger notion of decay for many-particle configurations was used but only at dimension one and for real times. Considering determinantal and Pfaffian correlation functionals for complex times is important in the study of weakly interacting fermions.

Characterization and 454 pyrosequencing of Major Histocompatibility Complex class I genes in the great tit reveal complexity in a passerine system

PubMed Central

2012-01-01

Background The critical role of Major Histocompatibility Complex (Mhc) genes in disease resistance and their highly polymorphic nature make them exceptional candidates for studies investigating genetic effects on survival, mate choice and conservation. Species that harbor many Mhc loci and high allelic diversity are particularly intriguing as they are potentially under strong selection and studies of such species provide valuable information as to the mechanisms maintaining Mhc diversity. However comprehensive genotyping of complex multilocus systems has been a major challenge to date with the result that little is known about the consequences of this complexity in terms of fitness effects and disease resistance. Results In this study, we genotyped the Mhc class I exon 3 of the great tit (Parus major) from two nest-box breeding populations near Oxford, UK that have been monitored for decades. Characterization of Mhc class I exon 3 was adopted and bidirectional sequencing was carried using the 454 sequencing platform. Full analysis of sequences through a stepwise variant validation procedure allowed reliable typing of more than 800 great tits based on 214,357 reads; from duplicates we estimated the repeatability of typing as 0.94. A total of 862 alleles were detected, and the presence of at least 16 functional loci was shown - the highest number characterized in a wild bird species. Finally, the functional alleles were grouped into 17 supertypes based on their antigen binding affinities. Conclusions We found extreme complexity at the Mhc class I of the great tit both in terms of allelic diversity and gene number. The presence of many functional loci was shown, together with a pseudogene family and putatively non-functional alleles; there was clear evidence that functional alleles were under strong balancing selection. This study is the first step towards an in-depth analysis of this gene complex in this species, which will help understanding how parasite-mediated and sexual selection shape and maintain host genetic variation in nature. We believe that study systems like ours can make important contributions to the field of evolutionary biology and emphasize the necessity of integrating long-term field-based studies with detailed genetic analysis to unravel complex evolutionary processes. PMID:22587557

Noncovalent Interactions of DNA Bases with Naphthalene and Graphene.

PubMed

Cho, Yeonchoo; Min, Seung Kyu; Yun, Jeonghun; Kim, Woo Youn; Tkatchenko, Alexandre; Kim, Kwang S

2013-04-09

The complexes of a DNA base bound to graphitic systems are studied. Considering naphthalene as the simplest graphitic system, DNA base-naphthalene complexes are scrutinized at high levels of ab initio theory including coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)] at the complete basis set (CBS) limit. The stacked configurations are the most stable, where the CCSD(T)/CBS binding energies of guanine, adenine, thymine, and cytosine are 9.31, 8.48, 8.53, 7.30 kcal/mol, respectively. The energy components are investigated using symmetry-adapted perturbation theory based on density functional theory including the dispersion energy. We compared the CCSD(T)/CBS results with several density functional methods applicable to periodic systems. Considering accuracy and availability, the optB86b nonlocal functional and the Tkatchenko-Scheffler functional are used to study the binding energies of nucleobases on graphene. The predicted values are 18-24 kcal/mol, though many-body effects on screening and energy need to be further considered.

Functionalization of Platinum Complexes for Biomedical Applications.

PubMed

Wang, Xiaoyong; Wang, Xiaohui; Guo, Zijian

2015-09-15

Platinum-based anticancer drugs are the mainstay of chemotherapy regimens in clinic. Nevertheless, the efficacy of platinum drugs is badly affected by serious systemic toxicities and drug resistance, and the pharmacokinetics of most platinum drugs is largely unknown. In recent years, a keen interest in functionalizing platinum complexes with bioactive molecules, targeting groups, photosensitizers, fluorophores, or nanomaterials has been sparked among chemical and biomedical researchers. The motivation for functionalization comes from some of the following demands: to improve the tumor selectivity or minimize the systemic toxicity of the drugs, to enhance the cellular accumulation of the drugs, to overcome the tumor resistance to the drugs, to visualize the drug molecules in vitro or in vivo, to achieve a synergistic anticancer effect between different therapeutic modalities, or to add extra functionality to the drugs. In this Account, we present different strategies being used for functionalizing platinum complexes, including conjugation with bisphosphonates, peptides, receptor-specific ligands, polymers, nanoparticles, magnetic resonance imaging contrast agents, metal chelators, or photosensitizers. Among them, bisphosphonates, peptides, and receptor-specific ligands are used for actively targeted drug delivery, polymers and nanoparticles are for passively targeted drug delivery, magnetic resonance imaging contrast agents are for theranostic purposes, metal chelators are for the treatment or prevention of Alzheimer's disease (AD), and photosensitizers are for photodynamic therapy of cancers. The rationales behind these designs are explained and justified at the molecular or cellular level, associating with the requirements for diagnosis, therapy, and visualization of biological processes. To illustrate the wide range of opportunities and challenges that are emerging in this realm, representative examples of targeted drug delivery systems, anticancer conjugates, anticancer theranostic agents, and anti-AD compounds relevant to functionalized platinum complexes are provided. All the examples exhibit new potential of platinum complexes for future applications in biomedical areas. The emphases of this Account are placed on the functionalization for targeted drug delivery and theranostic agents. In the end, a general assessment of various strategies has been made according to their major shortcomings and defects. The original information in this Account comes entirely from literature appearing since 2010.

Implementation of Complexity Analyzing Based on Additional Effect

NASA Astrophysics Data System (ADS)

Zhang, Peng; Li, Na; Liang, Yanhong; Liu, Fang

According to the Complexity Theory, there is complexity in the system when the functional requirement is not be satisfied. There are several study performances for Complexity Theory based on Axiomatic Design. However, they focus on reducing the complexity in their study and no one focus on method of analyzing the complexity in the system. Therefore, this paper put forth a method of analyzing the complexity which is sought to make up the deficiency of the researches. In order to discussing the method of analyzing the complexity based on additional effect, this paper put forth two concepts which are ideal effect and additional effect. The method of analyzing complexity based on additional effect combines Complexity Theory with Theory of Inventive Problem Solving (TRIZ). It is helpful for designers to analyze the complexity by using additional effect. A case study shows the application of the process.

Complex ambulatory settings demand scheduling systems.

PubMed

Ross, K M

1998-01-01

Practice management systems are becoming more and more complex, as they are asked to integrate all aspects of patient and resource management. Although patient scheduling is a standard expectation in any ambulatory environment, facilities and equipment resource scheduling are additional functionalities of scheduling systems. Because these functions were not typically managed in manual patient scheduling, often the result was resource mismanagement, along with a potential negative impact on utilization, patient flow and provider productivity. As ambulatory organizations have become more seasoned users of practice management software, the value of resource scheduling has become apparent. Appointment scheduling within a fully integrated practice management system is recognized as an enhancement of scheduling itself and provides additional tools to manage other information needs. Scheduling, as one component of patient information management, provides additional tools in these areas.

RATANA MEEKHAM, AN ELECTRICAL INTEGRATION TECHNICIAN FOR QUALIS CORP. OF HUNTSVILLE, ALABAMA, HELPS TEST AVIONICS -- COMPLEX VEHICLE SYSTEMS ENABLING NAVIGATION, COMMUNICATIONS AND OTHER FUNCTIONS CRITICAL TO HUMAN SPACEFLIGHT

NASA Image and Video Library

2015-01-08

RATANA MEEKHAM, AN ELECTRICAL INTEGRATION TECHNICIAN FOR QUALIS CORP. OF HUNTSVILLE, ALABAMA, HELPS TEST AVIONICS -- COMPLEX VEHICLE SYSTEMS ENABLING NAVIGATION, COMMUNICATIONS AND OTHER FUNCTIONS CRITICAL TO HUMAN SPACEFLIGHT -- FOR THE SPACE LAUNCH SYSTEM PROGRAM AT NASA’S MARSHALL SPACE FLIGHT CENTER IN HUNTSVILLE, ALABAMA. HER WORK SUPPORTS THE NASA ENGINEERING & SCIENCE SERVICES AND SKILLS AUGMENTATION CONTRACT LED BY JACOBS ENGINEERING OF HUNTSVILLE. MEEKHAM WORKS FULL-TIME AT MARSHALL WHILE FINISHING HER ASSOCIATE'S DEGREE IN MACHINE TOOL TECHNOLOGY AT CALHOUN COMMUNITY COLLEGE IN DECATUR, ALABAMA. THE SPACE LAUNCH SYSTEM, NASA’S NEXT HEAVY-LIFT LAUNCH VEHICLE, IS THE WORLD’S MOST POWERFUL ROCKET, SET TO FLY ITS FIRST UNCREWED LUNAR ORBITAL MISSION IN 2018. ITS FIRST.

Complex Physical, Biophysical and Econophysical Systems

NASA Astrophysics Data System (ADS)

Dewar, Robert L.; Detering, Frank

1. Introduction to complex and econophysics systems: a navigation map / T. Aste and T. Di Matteo -- 2. An introduction to fractional diffusion / B. I. Henry, T.A.M. Langlands and P. Straka -- 3. Space plasmas and fusion plasmas as complex systems / R. O. Dendy -- 4. Bayesian data analysis / M. S. Wheatland -- 5. Inverse problems and complexity in earth system science / I. G. Enting -- 6. Applied fluid chaos: designing advection with periodically reoriented flows for micro to geophysical mixing and transport enhancement / G. Metcalfe -- 7. Approaches to modelling the dynamical activity of brain function based on the electroencephalogram / D. T. J. Liley and F. Frascoli -- 8. Jaynes' maximum entropy principle, Riemannian metrics and generalised least action bound / R. K. Niven and B. Andresen -- 9. Complexity, post-genomic biology and gene expression programs / R. B. H. Williams and O. J.-H. Luo -- 10. Tutorials on agent-based modelling with NetLogo and network analysis with Pajek / M. J. Berryman and S. D. Angus.

Native structure of a type IV secretion system core complex essential for Legionella pathogenesis.

PubMed

Kubori, Tomoko; Koike, Masafumi; Bui, Xuan Thanh; Higaki, Saori; Aizawa, Shin-Ichi; Nagai, Hiroki

2014-08-12

Bacterial type IV secretion systems are evolutionarily related to conjugation systems and play a pivotal role in infection by delivering numerous virulence factors into host cells. Using transmission electron microscopy, we report the native molecular structure of the core complex of the Dot/Icm type IV secretion system encoded by Legionella pneumophila, an intracellular human pathogen. The biochemically isolated core complex, composed of at least five proteins--DotC, DotD, DotF, DotG, and DotH--has a ring-shaped structure. Intriguingly, morphologically distinct premature complexes are formed in the absence of DotG or DotF. Our data suggest that DotG forms a central channel spanning inner and outer membranes. DotF, a component dispensable for type IV secretion, plays a role in efficient embedment of DotG into the functional core complex. These results highlight a common scheme for the biogenesis of transport machinery.

A novel grid multiwing chaotic system with only non-hyperbolic equilibria

NASA Astrophysics Data System (ADS)

Zhang, Sen; Zeng, Yicheng; Li, Zhijun; Wang, Mengjiao; Xiong, Le

2018-05-01

The structure of the chaotic attractor of a system is mainly determined by the nonlinear functions in system equations. By using a new saw-tooth wave function and a new stair function, a novel complex grid multiwing chaotic system which belongs to non-Shil'nikov chaotic system with non-hyperbolic equilibrium points is proposed in this paper. It is particularly interesting that the complex grid multiwing attractors are generated by increasing the number of non-hyperbolic equilibrium points, which are different from the traditional methods of realising multiwing attractors by adding the index-2 saddle-focus equilibrium points in double-wing chaotic systems. The basic dynamical properties of the new system, such as dissipativity, phase portraits, the stability of the equilibria, the time-domain waveform, power spectrum, bifurcation diagram, Lyapunov exponents, and so on, are investigated by theoretical analysis and numerical simulations. Furthermore, the corresponding electronic circuit is designed and simulated on the Multisim platform. The Multisim simulation results and the hardware experimental results are in good agreement with the numerical simulations of the same system on Matlab platform, which verify the feasibility of this new grid multiwing chaotic system.

A systems approach to animal communication

PubMed Central

Barron, Andrew B.; Balakrishnan, Christopher N.; Hauber, Mark E.; Hoke, Kim L.

2016-01-01

Why animal communication displays are so complex and how they have evolved are active foci of research with a long and rich history. Progress towards an evolutionary analysis of signal complexity, however, has been constrained by a lack of hypotheses to explain similarities and/or differences in signalling systems across taxa. To address this, we advocate incorporating a systems approach into studies of animal communication—an approach that includes comprehensive experimental designs and data collection in combination with the implementation of systems concepts and tools. A systems approach evaluates overall display architecture, including how components interact to alter function, and how function varies in different states of the system. We provide a brief overview of the current state of the field, including a focus on select studies that highlight the dynamic nature of animal signalling. We then introduce core concepts from systems biology (redundancy, degeneracy, pluripotentiality, and modularity) and discuss their relationships with system properties (e.g. robustness, flexibility, evolvability). We translate systems concepts into an animal communication framework and accentuate their utility through a case study. Finally, we demonstrate how consideration of the system-level organization of animal communication poses new practical research questions that will aid our understanding of how and why animal displays are so complex. PMID:26936240

A systems approach to animal communication.

PubMed

Hebets, Eileen A; Barron, Andrew B; Balakrishnan, Christopher N; Hauber, Mark E; Mason, Paul H; Hoke, Kim L

2016-03-16

Why animal communication displays are so complex and how they have evolved are active foci of research with a long and rich history. Progress towards an evolutionary analysis of signal complexity, however, has been constrained by a lack of hypotheses to explain similarities and/or differences in signalling systems across taxa. To address this, we advocate incorporating a systems approach into studies of animal communication--an approach that includes comprehensive experimental designs and data collection in combination with the implementation of systems concepts and tools. A systems approach evaluates overall display architecture, including how components interact to alter function, and how function varies in different states of the system. We provide a brief overview of the current state of the field, including a focus on select studies that highlight the dynamic nature of animal signalling. We then introduce core concepts from systems biology (redundancy, degeneracy, pluripotentiality, and modularity) and discuss their relationships with system properties (e.g. robustness, flexibility, evolvability). We translate systems concepts into an animal communication framework and accentuate their utility through a case study. Finally, we demonstrate how consideration of the system-level organization of animal communication poses new practical research questions that will aid our understanding of how and why animal displays are so complex. © 2016 The Author(s).

Magnetic Exchange Couplings from Semilocal Functionals Evaluated Nonself-Consistently on Hybrid Densities: Insights on Relative Importance of Exchange, Correlation, and Delocalization.

PubMed

Phillips, Jordan J; Peralta, Juan E

2012-09-11

Semilocal functionals generally yield poor magnetic exchange couplings for transition-metal complexes, typically overpredicting in magnitude the experimental values. Here we show that semilocal functionals evaluated nonself-consistently on densities from hybrid functionals can yield magnetic exchange couplings that are greatly improved with respect to their self-consistent semilocal values. Furthermore, when semilocal functionals are evaluated nonself-consistently on densities from a "half-and-half" hybrid, their errors with respect to experimental values can actually be lower than those from self-consistent calculations with standard hybrid functionals such as PBEh or TPSSh. This illustrates that despite their notoriously poor performance for exchange couplings, for many systems semilocal functionals are capable of delivering accurate relative energies for magnetic states provided that their electron delocalization error is corrected. However, while self-consistent calculations with hybrids uniformly improve results for all complexes, evaluating nonself-consistently with semilocal functionals does not give a balanced improvement for both ferro- and antiferromagnetically coupled complexes, indicating that there is more at play with the overestimation problem than simply the delocalization error. Additionally, we show that for some systems the conventional wisdom of choice of exchange functional mattering more than correlation does not hold. This combined with results from the nonself-consistent calculations provide insight on clarifying the relative roles of exchange, correlation, and delocalization in calculating magnetic exchange coupling parameters in Kohn-Sham Density Functional Theory.

The difficulties of using MACSYMA and the function of user aids

NASA Technical Reports Server (NTRS)

Genesereth, M. R.

1977-01-01

The size and complexity of the MACSYMA system may create learning difficulties for users. Deficiency in understanding the system leads to resource knowledge difficulties. A communication factor arises from a difference between the primitive objects, actions, and relations of a user's problem and those provided by the system. The functions of various user aids in handling each of these difficulties are discussed.

Rewiring cells: synthetic biology as a tool to interrogate the organizational principles of living systems.

PubMed

Bashor, Caleb J; Horwitz, Andrew A; Peisajovich, Sergio G; Lim, Wendell A

2010-01-01

The living cell is an incredibly complex entity, and the goal of predictively and quantitatively understanding its function is one of the next great challenges in biology. Much of what we know about the cell concerns its constituent parts, but to a great extent we have yet to decode how these parts are organized to yield complex physiological function. Classically, we have learned about the organization of cellular networks by disrupting them through genetic or chemical means. The emerging discipline of synthetic biology offers an additional, powerful approach to study systems. By rearranging the parts that comprise existing networks, we can gain valuable insight into the hierarchical logic of the networks and identify the modular building blocks that evolution uses to generate innovative function. In addition, by building minimal toy networks, one can systematically explore the relationship between network structure and function. Here, we outline recent work that uses synthetic biology approaches to investigate the organization and function of cellular networks, and describe a vision for a synthetic biology toolkit that could be used to interrogate the design principles of diverse systems.

Sensorimotor restriction affects complex movement topography and reachable space in the rat motor cortex.

PubMed

Budri, Mirco; Lodi, Enrico; Franchi, Gianfranco

2014-01-01

Long-duration intracortical microstimulation (ICMS) studies with 500 ms of current pulses suggest that the forelimb area of the motor cortex is organized into several spatially distinct functional zones that organize movements into complex sequences. Here we studied how sensorimotor restriction modifies the extent of functional zones, complex movements, and reachable space representation in the rat forelimb M1. Sensorimotor restriction was achieved by means of whole-forelimb casting of 30 days duration. Long-duration ICMS was carried out 12 h and 14 days after cast removal. Evoked movements were measured using a high-resolution 3D optical system. Long-term cast caused: (i) a reduction in the number of sites where complex forelimb movement could be evoked; (ii) a shrinkage of functional zones but no change in their center of gravity; (iii) a reduction in movement with proximal/distal coactivation; (iv) a reduction in maximal velocity, trajectory and vector length of movement, but no changes in latency or duration; (v) a large restriction of reachable space. Fourteen days of forelimb freedom after casting caused: (i) a recovery of the number of sites where complex forelimb movement could be evoked; (ii) a recovery of functional zone extent and movement with proximal/distal coactivation; (iii) an increase in movement kinematics, but only partial restoration of control rat values; (iv) a slight increase in reachability parameters, but these remained far below baseline values. We pose the hypothesis that specific aspects of complex movement may be stored within parallel motor cortex re-entrant systems.

Sensorimotor restriction affects complex movement topography and reachable space in the rat motor cortex

PubMed Central

Budri, Mirco; Lodi, Enrico; Franchi, Gianfranco

2014-01-01

Long-duration intracortical microstimulation (ICMS) studies with 500 ms of current pulses suggest that the forelimb area of the motor cortex is organized into several spatially distinct functional zones that organize movements into complex sequences. Here we studied how sensorimotor restriction modifies the extent of functional zones, complex movements, and reachable space representation in the rat forelimb M1. Sensorimotor restriction was achieved by means of whole-forelimb casting of 30 days duration. Long-duration ICMS was carried out 12 h and 14 days after cast removal. Evoked movements were measured using a high-resolution 3D optical system. Long-term cast caused: (i) a reduction in the number of sites where complex forelimb movement could be evoked; (ii) a shrinkage of functional zones but no change in their center of gravity; (iii) a reduction in movement with proximal/distal coactivation; (iv) a reduction in maximal velocity, trajectory and vector length of movement, but no changes in latency or duration; (v) a large restriction of reachable space. Fourteen days of forelimb freedom after casting caused: (i) a recovery of the number of sites where complex forelimb movement could be evoked; (ii) a recovery of functional zone extent and movement with proximal/distal coactivation; (iii) an increase in movement kinematics, but only partial restoration of control rat values; (iv) a slight increase in reachability parameters, but these remained far below baseline values. We pose the hypothesis that specific aspects of complex movement may be stored within parallel motor cortex re-entrant systems. PMID:25565987

Reference Avionics Architecture for Lunar Surface Systems

NASA Technical Reports Server (NTRS)

Somervill, Kevin M.; Lapin, Jonathan C.; Schmidt, Oron L.

2010-01-01

Developing and delivering infrastructure capable of supporting long-term manned operations to the lunar surface has been a primary objective of the Constellation Program in the Exploration Systems Mission Directorate. Several concepts have been developed related to development and deployment lunar exploration vehicles and assets that provide critical functionality such as transportation, habitation, and communication, to name a few. Together, these systems perform complex safety-critical functions, largely dependent on avionics for control and behavior of system functions. These functions are implemented using interchangeable, modular avionics designed for lunar transit and lunar surface deployment. Systems are optimized towards reuse and commonality of form and interface and can be configured via software or component integration for special purpose applications. There are two core concepts in the reference avionics architecture described in this report. The first concept uses distributed, smart systems to manage complexity, simplify integration, and facilitate commonality. The second core concept is to employ extensive commonality between elements and subsystems. These two concepts are used in the context of developing reference designs for many lunar surface exploration vehicles and elements. These concepts are repeated constantly as architectural patterns in a conceptual architectural framework. This report describes the use of these architectural patterns in a reference avionics architecture for Lunar surface systems elements.

Double Wigner distribution function of a first-order optical system with a hard-edge aperture.

PubMed

Pan, Weiqing

2008-01-01

The effect of an apertured optical system on Wigner distribution can be expressed as a superposition integral of the input Wigner distribution function and the double Wigner distribution function of the apertured optical system. By introducing a hard aperture function into a finite sum of complex Gaussian functions, the double Wigner distribution functions of a first-order optical system with a hard aperture outside and inside it are derived. As an example of application, the analytical expressions of the Wigner distribution for a Gaussian beam passing through a spatial filtering optical system with an internal hard aperture are obtained. The analytical results are also compared with the numerical integral results, and they show that the analytical results are proper and ascendant.

Transfer function of analog fiber-optic systems driven by Fabry-Perot lasers: comment

NASA Astrophysics Data System (ADS)

Gyula, Veszely

2006-10-01

A bad notation makes difficult the understanding of the paper of Capmany et al. [J. Opt. Soc. Am. B22, 2099 (2005)]. The reason is that the real time function and the complex time function run into one another.

Petri net-based dependability modeling methodology for reconfigurable field programmable gate arrays

NASA Astrophysics Data System (ADS)

Graczyk, Rafał; Orleański, Piotr; Poźniak, Krzysztof

2015-09-01

Dependability modeling is an important issue for aerospace and space equipment designers. From system level perspective, one has to choose from multitude of possible architectures, redundancy levels, component combinations in a way to meet desired properties and dependability and finally fit within required cost and time budgets. Modeling of such systems is getting harder as its levels of complexity grow together with demand for more functional and flexible, yet more available systems that govern more and more crucial parts of our civilization's infrastructure (aerospace transport systems, telecommunications, exploration probes). In this article promising method of modeling complex systems using Petri networks is introduced in context of qualitative and quantitative dependability analysis. This method, although with some limitation and drawback offer still convenient visual formal method of describing system behavior on different levels (functional, timing, random events) and offers straight correspondence to underlying mathematical engine, perfect for simulations and engineering support.

Pseudosatellite technologies based on the use of functionally stable complexes of remote-piloted aircrafts

NASA Astrophysics Data System (ADS)

Mashkov, O. A.; Samborskiy, I. I.

2009-10-01

A bundle of papers dealing with functionally stable systems requires the necessity of analyzing of obtained results and their understanding in a general context of cybernetic's development and applications. Description of this field of science, main results and perspectives of the new theory of functionally stability of dynamical systems concerning the problem of remote-piloted aircrafts engineering using pseudosatellite technologies are proposed in the paper.

Signal transduction in a covalent post-assembly modification cascade

NASA Astrophysics Data System (ADS)

Pilgrim, Ben S.; Roberts, Derrick A.; Lohr, Thorsten G.; Ronson, Tanya K.; Nitschke, Jonathan R.

2017-12-01

Natural reaction cascades control the movement of biomolecules between cellular compartments. Inspired by these systems, we report a synthetic reaction cascade employing post-assembly modification reactions to direct the partitioning of supramolecular complexes between phases. The system is composed of a self-assembled tetrazine-edged FeII8L12 cube and a maleimide-functionalized FeII4L6 tetrahedron. Norbornadiene (NBD) functions as the stimulus that triggers the cascade, beginning with the inverse-electron-demand Diels-Alder reaction of NBD with the tetrazine moieties of the cube. This reaction generates cyclopentadiene as a transient by-product, acting as a relay signal that subsequently undergoes a Diels-Alder reaction with the maleimide-functionalized tetrahedron. Cyclooctyne can selectively inhibit the cascade by outcompeting NBD as the initial trigger. Initiating the cascade with 2-octadecyl NBD leads to selective alkylation of the tetrahedron upon cascade completion. The increased lipophilicity of the C18-tagged tetrahedron drives this complex into a non-polar phase, allowing its isolation from the initially inseparable mixture of complexes.

Functional network organization of the human brain

PubMed Central

Power, Jonathan D; Cohen, Alexander L; Nelson, Steven M; Wig, Gagan S; Barnes, Kelly Anne; Church, Jessica A; Vogel, Alecia C; Laumann, Timothy O; Miezin, Fran M; Schlaggar, Bradley L; Petersen, Steven E

2011-01-01

Summary Real-world complex systems may be mathematically modeled as graphs, revealing properties of the system. Here we study graphs of functional brain organization in healthy adults using resting state functional connectivity MRI. We propose two novel brain-wide graphs, one of 264 putative functional areas, the other a modification of voxelwise networks that eliminates potentially artificial short-distance relationships. These graphs contain many subgraphs in good agreement with known functional brain systems. Other subgraphs lack established functional identities; we suggest possible functional characteristics for these subgraphs. Further, graph measures of the areal network indicate that the default mode subgraph shares network properties with sensory and motor subgraphs: it is internally integrated but isolated from other subgraphs, much like a “processing” system. The modified voxelwise graph also reveals spatial motifs in the patterning of systems across the cortex. PMID:22099467

A broadband variable-temperature test system for complex permittivity measurements of solid and powder materials

NASA Astrophysics Data System (ADS)

Zhang, Yunpeng; Li, En; Zhang, Jing; Yu, Chengyong; Zheng, Hu; Guo, Gaofeng

2018-02-01

A microwave test system to measure the complex permittivity of solid and powder materials as a function of temperature has been developed. The system is based on a TM0n0 multi-mode cylindrical cavity with a slotting structure, which provides purer test modes compared to a traditional cavity. To ensure the safety, effectiveness, and longevity, heating and testing are carried out separately and the sample can move between two functional areas through an Alundum tube. Induction heating and a pneumatic platform are employed to, respectively, shorten the heating and cooling time of the sample. The single trigger function of the vector network analyzer is added to test software to suppress the drift of the resonance peak during testing. Complex permittivity is calculated by the rigorous field theoretical solution considering multilayer media loading. The variation of the cavity equivalent radius caused by the sample insertion holes is discussed in detail, and its influence to the test result is analyzed. The calibration method for the complex permittivity of the Alundum tube and quartz vial (for loading powder sample), which vary with the temperature, is given. The feasibility of the system has been verified by measuring different samples in a wide range of relative permittivity and loss tangent, and variable-temperature test results of fused quartz and SiO2 powder up to 1500 °C are compared with published data. The results indicate that the presented system is reliable and accurate. The stability of the system is verified by repeated and long-term tests, and error analysis is presented to estimate the error incurred due to the uncertainties in different error sources.

Patients with Parkinson's disease learn to control complex systems-an indication for intact implicit cognitive skill learning.

PubMed

Witt, Karsten; Daniels, Christine; Daniel, Victoria; Schmitt-Eliassen, Julia; Volkmann, Jens; Deuschl, Günther

2006-01-01

Implicit memory and learning mechanisms are composed of multiple processes and systems. Previous studies demonstrated a basal ganglia involvement in purely cognitive tasks that form stimulus response habits by reinforcement learning such as implicit classification learning. We will test the basal ganglia influence on two cognitive implicit tasks previously described by Berry and Broadbent, the sugar production task and the personal interaction task. Furthermore, we will investigate the relationship between certain aspects of an executive dysfunction and implicit learning. To this end, we have tested 22 Parkinsonian patients and 22 age-matched controls on two implicit cognitive tasks, in which participants learned to control a complex system. They interacted with the system by choosing an input value and obtaining an output that was related in a complex manner to the input. The objective was to reach and maintain a specific target value across trials (dynamic system learning). The two tasks followed the same underlying complex rule but had different surface appearances. Subsequently, participants performed an executive test battery including the Stroop test, verbal fluency and the Wisconsin card sorting test (WCST). The results demonstrate intact implicit learning in patients, despite an executive dysfunction in the Parkinsonian group. They lead to the conclusion that the basal ganglia system affected in Parkinson's disease does not contribute to the implicit acquisition of a new cognitive skill. Furthermore, the Parkinsonian patients were able to reach a specific goal in an implicit learning context despite impaired goal directed behaviour in the WCST, a classic test of executive functions. These results demonstrate a functional independence of implicit cognitive skill learning and certain aspects of executive functions.

Embracing Complexity beyond Systems Medicine: A New Approach to Chronic Immune Disorders

PubMed Central

te Velde, Anje A.; Bezema, Tjitske; van Kampen, Antoine H. C.; Kraneveld, Aletta D.; 't Hart, Bert A.; van Middendorp, Henriët; Hack, Erik C.; van Montfrans, Joris M.; Belzer, Clara; Jans-Beken, Lilian; Pieters, Raymond H.; Knipping, Karen; Huber, Machteld; Boots, Annemieke M. H.; Garssen, Johan; Radstake, Tim R.; Evers, Andrea W. M.; Prakken, Berent J.; Joosten, Irma

2016-01-01

In order to combat chronic immune disorders (CIDs), it is an absolute necessity to understand the bigger picture, one that goes beyond insights at a one-disease, molecular, cellular, and static level. To unravel this bigger picture we advocate an integral, cross-disciplinary approach capable of embracing the complexity of the field. This paper discusses the current knowledge on common pathways in CIDs including general psychosocial and lifestyle factors associated with immune functioning. We demonstrate the lack of more in-depth psychosocial and lifestyle factors in current research cohorts and most importantly the need for an all-encompassing analysis of these factors. The second part of the paper discusses the challenges of understanding immune system dynamics and effectively integrating all key perspectives on immune functioning, including the patient’s perspective itself. This paper suggests the use of techniques from complex systems science in describing and simulating healthy or deviating behavior of the immune system in its biopsychosocial surroundings. The patient’s perspective data are suggested to be generated by using specific narrative techniques. We conclude that to gain more insight into the behavior of the whole system and to acquire new ways of combatting CIDs, we need to construct and apply new techniques in the field of computational and complexity science, to an even wider variety of dynamic data than used in today’s systems medicine. PMID:28018353

On the recognition of complex structures: Computer software using artificial intelligence applied to pattern recognition

NASA Technical Reports Server (NTRS)

Yakimovsky, Y.

1974-01-01

An approach to simultaneous interpretation of objects in complex structures so as to maximize a combined utility function is presented. Results of the application of a computer software system to assign meaning to regions in a segmented image based on the principles described in this paper and on a special interactive sequential classification learning system, which is referenced, are demonstrated.

Low-complexity camera digital signal imaging for video document projection system

NASA Astrophysics Data System (ADS)

Hsia, Shih-Chang; Tsai, Po-Shien

2011-04-01

We present high-performance and low-complexity algorithms for real-time camera imaging applications. The main functions of the proposed camera digital signal processing (DSP) involve color interpolation, white balance, adaptive binary processing, auto gain control, and edge and color enhancement for video projection systems. A series of simulations demonstrate that the proposed method can achieve good image quality while keeping computation cost and memory requirements low. On the basis of the proposed algorithms, the cost-effective hardware core is developed using Verilog HDL. The prototype chip has been verified with one low-cost programmable device. The real-time camera system can achieve 1270 × 792 resolution with the combination of extra components and can demonstrate each DSP function.

Chronobiology of the neuroimmunoendocrine system and aging.

PubMed

Mate, Ianire; Madrid, Juan Antonio; De la Fuente, Mónica

2014-01-01

The health maintenance depends on the preservation of the homeostatic systems, such as nervous, endocrine and immune system, and a proper communication between them. In this regard, the circadian system, which promotes a better physiological system functions and thus well being, could be considered part of that homeostatic complex, since the neuroimmunoendocrine system possesses circadian patterns in most variables, as well as circannual or seasonal variations. With aging, an impairment of the homeostatic systems occurs and an alteration of circadian system regulation has been demonstrated. In the immune system, several function parameters, which are good markers of health and of the rate of aging, change not only with age (immunosenescence) but also throughout the day and year. Indeed, with advancing age there is a modification of immune cell circadian function especially in lymphocytes. Moreover, immune functions at early afternoon correspond to more aged values than at morning, especially in mature subjects (60-79 years of age). In addition, these mature men and women showed a significant impaired immune cell function, which is especially remarkable in the winter. It is noteworthy the role of immunomodulatory hormones, such as melatonin, in the regulation of biological rhythms and their involvement in the aging process. Furthermore, the evidence of a neuroimmune regulation of the circadian system and its disturbance with aging, highlights the importance of proinflammatory cytokines in this complex cross-talk. The biological rhythms disruption with age and some diseases (jet lag, cancer and seasonal affective disorder), could contribute increasing the immune system impairment and consequently the loss of health.

Mode Transitions in Glass Cockpit Aircraft: Results of a Field Study

NASA Technical Reports Server (NTRS)

Degani, Asaf; Kirlik, Alex; Shafto, Michael (Technical Monitor)

1995-01-01

One consequence of increased levels of automation in complex control systems is the presence of modes. A mode is a particular configuration of a control system that defines how human command inputs are interpreted. In complex systems, modes also often determine a specific allocation of control authority between the human and automated systems. Even in simple static devices (e.g., electronic watches, word processors), the presence of modes has been found to cause problems in either-the acquisition or production of skilled performance. Many of these problems arise due to the fact that the selection of a mode causes device behavior to be mediated by hidden internal state information. For these simple systems, many of these interaction problems can be solved by the design of appropriate feedback to communicate internal state information to the human operator. In complex dynamic systems, however, the design issues associated with modes seem to trancend the problem of merely communicating internal state information via displayed feedback. In complex supervisory control systems (e.g., aircraft, spacecraft, military command and control), a key function of modes is the selection of a particular configuration of control authority between the human operator and automated control systems. One mode may result in full manual control, another may result in a mix of manual and automatic control, while a third may result in full automatic control over the entire system. The human operator selects an appropriate mode as a function of current goals, operating conditions, and operating procedures. Thus, the operator is put in a position of essentially trying to control two coupled dynamic systems: the target system itself, and also a highly complex suite of automation controlling the target system. From a historical perspective, it should probably not come as a surprise that very little information is available to guide the design of mode-oriented control systems. The topic of function allocation (i.e., the proper division of control authority among human and computer) has a long history in human-machine systems research. Although this research has produced some relevant guidelines, a design approach capable of defining appropriate allocations of control function between the human and automation is not yet available. As a result, the function allocation decision itself has been allocated to the operator, to be performed in real-time, in the operation of mode-oriented control systems. A variety of documented aircraft accidents and incidents suggest that the real-time selection and monitoring of control modes is a weak link in the effective operation of complex supervisory control systems. Research in human-machine systems and human-computer interaction has barely scraped the surface of the problem of understanding how operators manage this task.The purpose of this paper is to present the results of a field study which examined how operators manage mode selection in a complex supervisory control system. Data on mode engagements using the Boeing B757/767 auto-flight system were collected during approach and descent into four major airports in the East Coast of the United States. Protocols documenting mode selection, automatic mode changes, pilot actions, quantitative records of flight-path variables, and verbal reports during and after mode engagements were collected by an observer from the jumpseat. Observations were conducted on two typical trips between three airports. Each trip was be replicated 11 times, which yielded a total of 22 trips and 66 legs on which data were collected. All data collected concerned the same flight numbers, and therefore, the same time of day, same type of aircraft, and identical operational environments (e.g., ATC facilities, weather patterns, traffic flow etc.)

Technological integration and hyperconnectivity: Tools for promoting extreme human lifespans

NASA Astrophysics Data System (ADS)

Kyriazis, Marios

2015-07-01

Artificial, neurobiological, and social networks are three distinct complex adaptive systems (CAS), each containing discrete processing units (nodes, neurons, and humans respectively). Despite the apparent differences, these three networks are bound by common underlying principles which describe the behaviour of the system in terms of the connections of its components, and its emergent properties. The longevity (long-term retention and functionality) of the components of each of these systems is also defined by common principles. Here, I will examine some properties of the longevity and function of the components of artificial and neurobiological systems, and generalise these to the longevity and function of the components of social CAS. In other words, I will show that principles governing the long-term functionality of computer nodes and of neurons, may be extrapolated to the study of the long-term functionality of humans (or more precisely, of the noemes, an abstract combination of existence and digital fame). The study of these phenomena can provide useful insights regarding practical ways that can be used in order to maximize human longevity. The basic law governing these behaviours is the Law of Requisite Usefulness, which states that the length of retention of an agent within a CAS is proportional to the contribution of the agent to the overall adaptability of the system. Key Words: Complex Adaptive Systems, Hyper-connectivity, Human Longevity, Adaptability and Evolution, Noeme

Statistical Techniques Complement UML When Developing Domain Models of Complex Dynamical Biosystems.

PubMed

Williams, Richard A; Timmis, Jon; Qwarnstrom, Eva E

2016-01-01

Computational modelling and simulation is increasingly being used to complement traditional wet-lab techniques when investigating the mechanistic behaviours of complex biological systems. In order to ensure computational models are fit for purpose, it is essential that the abstracted view of biology captured in the computational model, is clearly and unambiguously defined within a conceptual model of the biological domain (a domain model), that acts to accurately represent the biological system and to document the functional requirements for the resultant computational model. We present a domain model of the IL-1 stimulated NF-κB signalling pathway, which unambiguously defines the spatial, temporal and stochastic requirements for our future computational model. Through the development of this model, we observe that, in isolation, UML is not sufficient for the purpose of creating a domain model, and that a number of descriptive and multivariate statistical techniques provide complementary perspectives, in particular when modelling the heterogeneity of dynamics at the single-cell level. We believe this approach of using UML to define the structure and interactions within a complex system, along with statistics to define the stochastic and dynamic nature of complex systems, is crucial for ensuring that conceptual models of complex dynamical biosystems, which are developed using UML, are fit for purpose, and unambiguously define the functional requirements for the resultant computational model.

Statistical Techniques Complement UML When Developing Domain Models of Complex Dynamical Biosystems

PubMed Central

Timmis, Jon; Qwarnstrom, Eva E.

2016-01-01

Computational modelling and simulation is increasingly being used to complement traditional wet-lab techniques when investigating the mechanistic behaviours of complex biological systems. In order to ensure computational models are fit for purpose, it is essential that the abstracted view of biology captured in the computational model, is clearly and unambiguously defined within a conceptual model of the biological domain (a domain model), that acts to accurately represent the biological system and to document the functional requirements for the resultant computational model. We present a domain model of the IL-1 stimulated NF-κB signalling pathway, which unambiguously defines the spatial, temporal and stochastic requirements for our future computational model. Through the development of this model, we observe that, in isolation, UML is not sufficient for the purpose of creating a domain model, and that a number of descriptive and multivariate statistical techniques provide complementary perspectives, in particular when modelling the heterogeneity of dynamics at the single-cell level. We believe this approach of using UML to define the structure and interactions within a complex system, along with statistics to define the stochastic and dynamic nature of complex systems, is crucial for ensuring that conceptual models of complex dynamical biosystems, which are developed using UML, are fit for purpose, and unambiguously define the functional requirements for the resultant computational model. PMID:27571414

Wigner distribution function of Hermite-cosine-Gaussian beams through an apertured optical system.

PubMed

Sun, Dong; Zhao, Daomu

2005-08-01

By introducing the hard-aperture function into a finite sum of complex Gaussian functions, the approximate analytical expressions of the Wigner distribution function for Hermite-cosine-Gaussian beams passing through an apertured paraxial ABCD optical system are obtained. The analytical results are compared with the numerically integrated ones, and the absolute errors are also given. It is shown that the analytical results are proper and that the calculation speed for them is much faster than for the numerical results.

Frustration across the periodic table: heterolytic cleavage of dihydrogen by metal complexes.

PubMed

Bullock, R Morris; Chambers, Geoffrey M

2017-08-28

This perspective examines frustrated Lewis pairs (FLPs) in the context of heterolytic cleavage of H 2 by transition metal complexes, with an emphasis on molecular complexes bearing an intramolecular Lewis base. FLPs have traditionally been associated with main group compounds, yet many reactions of transition metal complexes support a broader classification of FLPs that includes certain types of transition metal complexes with reactivity resembling main group-based FLPs. This article surveys transition metal complexes that heterolytically cleave H 2 , which vary in the degree that the Lewis pairs within these systems interact. Many of the examples include complexes bearing a pendant amine functioning as the base with the metal functioning as the hydride acceptor. Consideration of transition metal compounds in the context of FLPs can inspire new innovations and improvements in transition metal catalysis.This article is part of the themed issue 'Frustrated Lewis pair chemistry'. © 2017 The Author(s).

Engineering complex orthopaedic tissues via strategic biomimicry.

PubMed

Qu, Dovina; Mosher, Christopher Z; Boushell, Margaret K; Lu, Helen H

2015-03-01

The primary current challenge in regenerative engineering resides in the simultaneous formation of more than one type of tissue, as well as their functional assembly into complex tissues or organ systems. Tissue-tissue synchrony is especially important in the musculoskeletal system, wherein overall organ function is enabled by the seamless integration of bone with soft tissues such as ligament, tendon, or cartilage, as well as the integration of muscle with tendon. Therefore, in lieu of a traditional single-tissue system (e.g., bone, ligament), composite tissue scaffold designs for the regeneration of functional connective tissue units (e.g., bone-ligament-bone) are being actively investigated. Closely related is the effort to re-establish tissue-tissue interfaces, which is essential for joining these tissue building blocks and facilitating host integration. Much of the research at the forefront of the field has centered on bioinspired stratified or gradient scaffold designs which aim to recapitulate the structural and compositional inhomogeneity inherent across distinct tissue regions. As such, given the complexity of these musculoskeletal tissue units, the key question is how to identify the most relevant parameters for recapitulating the native structure-function relationships in the scaffold design. Therefore, the focus of this review, in addition to presenting the state-of-the-art in complex scaffold design, is to explore how strategic biomimicry can be applied in engineering tissue connectivity. The objective of strategic biomimicry is to avoid over-engineering by establishing what needs to be learned from nature and defining the essential matrix characteristics that must be reproduced in scaffold design. Application of this engineering strategy for the regeneration of the most common musculoskeletal tissue units (e.g., bone-ligament-bone, muscle-tendon-bone, cartilage-bone) will be discussed in this review. It is anticipated that these exciting efforts will enable integrative and functional repair of soft tissue injuries, and moreover, lay the foundation for the development of composite tissue systems and ultimately, total limb or joint regeneration.

Engineering Complex Orthopaedic Tissues via Strategic Biomimicry

PubMed Central

Qu, Dovina; Mosher, Christopher Z.; Boushell, Margaret K.; Lu, Helen H.

2014-01-01

The primary current challenge in regenerative engineering resides in the simultaneous formation of more than one type of tissue, as well as their functional assembly into complex tissues or organ systems. Tissue-tissue synchrony is especially important in the musculoskeletal system, whereby overall organ function is enabled by the seamless integration of bone with soft tissues such as ligament, tendon, or cartilage, as well as the integration of muscle with tendon. Therefore, in lieu of a traditional single-tissue system (e.g. bone, ligament), composite tissue scaffold designs for the regeneration of functional connective tissue units (e.g. bone-ligament-bone) are being actively investigated. Closely related is the effort to re-establish tissue-tissue interfaces, which is essential for joining these tissue building blocks and facilitating host integration. Much of the research at the forefront of the field has centered on bioinspired stratified or gradient scaffold designs which aim to recapitulate the structural and compositional inhomogeneity inherent across distinct tissue regions. As such, given the complexity of these musculoskeletal tissue units, the key question is how to identify the most relevant parameters for recapitulating the native structure-function relationships in the scaffold design. Therefore, the focus of this review, in addition to presenting the state-of-the-art in complex scaffold design, is to explore how strategic biomimicry can be applied in engineering tissue connectivity. The objective of strategic biomimicry is to avoid over-engineering by establishing what needs to be learned from nature and defining the essential matrix characteristics that must be reproduced in scaffold design. Application of this engineering strategy for the regeneration of the most common musculoskeletal tissue units (e.g. bone-ligament-bone, muscle-tendon-bone, cartilage-bone) will be discussed in this review. It is anticipated that these exciting efforts will enable integrative and functional repair of soft tissue injuries, and moreover, lay the foundation for the development of composite tissue systems and ultimately, total limb or joint regeneration. PMID:25465616

Designing novel cellulase systems through agent-based modeling and global sensitivity analysis.

PubMed

Apte, Advait A; Senger, Ryan S; Fong, Stephen S

2014-01-01

Experimental techniques allow engineering of biological systems to modify functionality; however, there still remains a need to develop tools to prioritize targets for modification. In this study, agent-based modeling (ABM) was used to build stochastic models of complexed and non-complexed cellulose hydrolysis, including enzymatic mechanisms for endoglucanase, exoglucanase, and β-glucosidase activity. Modeling results were consistent with experimental observations of higher efficiency in complexed systems than non-complexed systems and established relationships between specific cellulolytic mechanisms and overall efficiency. Global sensitivity analysis (GSA) of model results identified key parameters for improving overall cellulose hydrolysis efficiency including: (1) the cellulase half-life, (2) the exoglucanase activity, and (3) the cellulase composition. Overall, the following parameters were found to significantly influence cellulose consumption in a consolidated bioprocess (CBP): (1) the glucose uptake rate of the culture, (2) the bacterial cell concentration, and (3) the nature of the cellulase enzyme system (complexed or non-complexed). Broadly, these results demonstrate the utility of combining modeling and sensitivity analysis to identify key parameters and/or targets for experimental improvement.

Complex systems dynamics in aging: new evidence, continuing questions.

PubMed

Cohen, Alan A

2016-02-01

There have long been suggestions that aging is tightly linked to the complex dynamics of the physiological systems that maintain homeostasis, and in particular to dysregulation of regulatory networks of molecules. This review synthesizes recent work that is starting to provide evidence for the importance of such complex systems dynamics in aging. There is now clear evidence that physiological dysregulation--the gradual breakdown in the capacity of complex regulatory networks to maintain homeostasis--is an emergent property of these regulatory networks, and that it plays an important role in aging. It can be measured simply using small numbers of biomarkers. Additionally, there are indications of the importance during aging of emergent physiological processes, functional processes that cannot be easily understood through clear metabolic pathways, but can nonetheless be precisely quantified and studied. The overall role of such complex systems dynamics in aging remains an important open question, and to understand it future studies will need to distinguish and integrate related aspects of aging research, including multi-factorial theories of aging, systems biology, bioinformatics, network approaches, robustness, and loss of complexity.

Designing novel cellulase systems through agent-based modeling and global sensitivity analysis

PubMed Central

Apte, Advait A; Senger, Ryan S; Fong, Stephen S

2014-01-01

Experimental techniques allow engineering of biological systems to modify functionality; however, there still remains a need to develop tools to prioritize targets for modification. In this study, agent-based modeling (ABM) was used to build stochastic models of complexed and non-complexed cellulose hydrolysis, including enzymatic mechanisms for endoglucanase, exoglucanase, and β-glucosidase activity. Modeling results were consistent with experimental observations of higher efficiency in complexed systems than non-complexed systems and established relationships between specific cellulolytic mechanisms and overall efficiency. Global sensitivity analysis (GSA) of model results identified key parameters for improving overall cellulose hydrolysis efficiency including: (1) the cellulase half-life, (2) the exoglucanase activity, and (3) the cellulase composition. Overall, the following parameters were found to significantly influence cellulose consumption in a consolidated bioprocess (CBP): (1) the glucose uptake rate of the culture, (2) the bacterial cell concentration, and (3) the nature of the cellulase enzyme system (complexed or non-complexed). Broadly, these results demonstrate the utility of combining modeling and sensitivity analysis to identify key parameters and/or targets for experimental improvement. PMID:24830736

Toolsets Maintain Health of Complex Systems

NASA Technical Reports Server (NTRS)

2010-01-01

First featured in Spinoff 2001, Qualtech Systems Inc. (QSI), of Wethersfield, Connecticut, adapted its Testability, Engineering, and Maintenance System (TEAMS) toolset under Small Business Innovation Research (SBIR) contracts from Ames Research Center to strengthen NASA's systems health management approach for its large, complex, and interconnected systems. Today, six NASA field centers utilize the TEAMS toolset, including TEAMS-Designer, TEAMS-RT, TEAMATE, and TEAMS-RDS. TEAMS is also being used on industrial systems that generate power, carry data, refine chemicals, perform medical functions, and produce semiconductor wafers. QSI finds TEAMS can lower costs by decreasing problems requiring service by 30 to 50 percent.

Protein-Protein Interactions of Azurin Complex by Coarse-Grained Simulations with a Gō-Like Model

NASA Astrophysics Data System (ADS)

Rusmerryani, Micke; Takasu, Masako; Kawaguchi, Kazutomo; Saito, Hiroaki; Nagao, Hidemi

Proteins usually perform their biological functions by forming a complex with other proteins. It is very important to study the protein-protein interactions since these interactions are crucial in many processes of a living organism. In this study, we develop a coarse grained model to simulate protein complex in liquid system. We carry out molecular dynamics simulations with topology-based potential interactions to simulate dynamical properties of Pseudomonas Aeruginosa azurin complex systems. Azurin is known to play an essential role as an anticancer agent and bind many important intracellular molecules. Some physical properties are monitored during simulation time to get a better understanding of the influence of protein-protein interactions to the azurin complex dynamics. These studies will provide valuable insights for further investigation on protein-protein interactions in more realistic system.

Maximizing photovoltaic power generation of a space-dart configured satellite

NASA Astrophysics Data System (ADS)

Lee, Dae Young; Cutler, James W.; Mancewicz, Joe; Ridley, Aaron J.

2015-06-01

Many small satellites are power constrained due to their minimal solar panel area and the eclipse environment of low-Earth orbit. As with larger satellites, these small satellites, including CubeSats, use deployable power arrays to increase power production. This presents a design opportunity to develop various objective functions related to energy management and methods for optimizing these functions over a satellite design. A novel power generation model was created, and a simulation system was developed to evaluate various objective functions describing energy management for complex satellite designs. The model uses a spacecraft-body-fixed spherical coordinate system to analyze the complex geometry of a satellite's self-induced shadowing with computation provided by the Open Graphics Library. As an example design problem, a CubeSat configured as a space-dart with four deployable panels is optimized. Due to the fast computation speed of the solution, an exhaustive search over the design space is used to find the solar panel deployment angles which maximize total power generation. Simulation results are presented for a variety of orbit scenarios. The method is extendable to a variety of complex satellite geometries and power generation systems.

Dynamics and computation in functional shifts

NASA Astrophysics Data System (ADS)

Namikawa, Jun; Hashimoto, Takashi

2004-07-01

We introduce a new type of shift dynamics as an extended model of symbolic dynamics, and investigate the characteristics of shift spaces from the viewpoints of both dynamics and computation. This shift dynamics is called a functional shift, which is defined by a set of bi-infinite sequences of some functions on a set of symbols. To analyse the complexity of functional shifts, we measure them in terms of topological entropy, and locate their languages in the Chomsky hierarchy. Through this study, we argue that considering functional shifts from the viewpoints of both dynamics and computation gives us opposite results about the complexity of systems. We also describe a new class of shift spaces whose languages are not recursively enumerable.

Cadherins and Their Partners in the Nematode Worm Caenorhabditis elegans

PubMed Central

Hardin, Jeff; Lynch, Allison; Loveless, Timothy; Pettitt, Jonathan

2018-01-01

The extreme simplicity of Caenorhabditis elegans makes it an ideal system to study the basic principles of cadherin function at the level of single cells within the physiologically relevant context of a developing animal. The genetic tractability of C. elegans also means that components of cadherin complexes can be identified through genetic modifier screens, allowing a comprehensive in vivo characterization of the macromolecular assemblies involved in cadherin function during tissue formation and maintenance in C. elegans. This work shows that a single cadherin system, the classical cadherin–catenin complex, is essential for diverse morphogenetic events during embryogenesis through its interactions with a range of mostly conserved proteins that act to modulate its function. The role of other members of the cadherin family in C. elegans, including members of the Fat-like, Flamingo/CELSR and calsyntenin families is less well characterized, but they have clear roles in neuronal development and function. PMID:23481198

Kondo effect and enhanced magnetic properties in gadolinium functionalized carbon nanotube supramolecular complex.

PubMed

Ncube, S; Coleman, C; Strydom, A; Flahaut, E; de Sousa, A; Bhattacharyya, S

2018-05-23

We report on the enhancement of magnetic properties of multiwalled carbon nanotubes (MWNTs) functionalized with a gadolinium based supramolecular complex. By employing a newly developed synthesis technique we find that the functionalization method of the nanocomposite enhances the strength of magnetic interaction leading to a large effective moment of 15.79 µ B and non-superparamagnetic behaviour unlike what has been previously reported. Saturating resistance at low temperatures is fitted with the numerical renormalization group formula verifying the Kondo effect for magnetic impurities on a metallic electron system. Magnetoresistance shows devices fabricated from aligned gadolinium functionalized MWNTs (Gd-Fctn-MWNTs) exhibit spin-valve switching behaviour of up to 8%. This study highlights the possibility of enhancing magnetic interactions in carbon systems through chemical modification, moreover we demonstrate the rich physics that might be useful for developing spin based quantum computing elements based on one-dimensional (1D) channels.

Clinical decision making-a functional medicine perspective.

PubMed

Pizzorno, Joseph E

2012-09-01

As 21st century health care moves from a disease-based approach to a more patient-centric system that can address biochemical individuality to improve health and function, clinical decision making becomes more complex. Accentuating the problem is the lack of a clear standard for this more complex functional medicine approach. While there is relatively broad agreement in Western medicine for what constitutes competent assessment of disease and identification of related treatment approaches, the complex functional medicine model posits multiple and individualized diagnostic and therapeutic approaches, most or many of which have reasonable underlying science and principles, but which have not been rigorously tested in a research or clinical setting. This has led to non-rigorous thinking and sometimes to uncritical acceptance of both poorly documented diagnostic procedures and ineffective therapies, resulting in less than optimal clinical care.

Clinical Decision Making—A Functional Medicine Perspective

PubMed Central

2012-01-01

As 21st century health care moves from a disease-based approach to a more patient-centric system that can address biochemical individuality to improve health and function, clinical decision making becomes more complex. Accentuating the problem is the lack of a clear standard for this more complex functional medicine approach. While there is relatively broad agreement in Western medicine for what constitutes competent assessment of disease and identification of related treatment approaches, the complex functional medicine model posits multiple and individualized diagnostic and therapeutic approaches, most or many of which have reasonable underlying science and principles, but which have not been rigorously tested in a research or clinical setting. This has led to non-rigorous thinking and sometimes to uncritical acceptance of both poorly documented diagnostic procedures and ineffective therapies, resulting in less than optimal clinical care. PMID:24278827

Reflecting on complexity of biological systems: Kant and beyond?

PubMed

Van de Vijver, Gertrudis; Van Speybroeck, Linda; Vandevyvere, Windy

2003-01-01

Living organisms are currently most often seen as complex dynamical systems that develop and evolve in relation to complex environments. Reflections on the meaning of the complex dynamical nature of living systems show an overwhelming multiplicity in approaches, descriptions, definitions and methodologies. Instead of sustaining an epistemic pluralism, which often functions as a philosophical armistice in which tolerance and so-called neutrality discharge proponents of the burden to clarify the sources and conditions of agreement and disagreement, this paper aims at analysing: (i) what has been Kant's original conceptualisation of living organisms as natural purposes; (ii) how the current perspectives are to be related to Kant's viewpoint; (iii) what are the main trends in current complexity thinking. One of the basic ideas is that the attention for structure and its epistemological consequences witness to a great extent of Kant's viewpoint, and that the idea of organisational stratification today constitutes a different breeding ground within which complexity issues are raised. The various approaches of complexity in biological systems are captured in terms of two different styles, universalism and (weak and strong) constructivism, between which hybrid forms exist.

Midbond basis functions for weakly bound complexes

NASA Astrophysics Data System (ADS)

Shaw, Robert A.; Hill, J. Grant

2018-06-01

Weakly bound systems present a difficult problem for conventional atom-centred basis sets due to large separations, necessitating the use of large, computationally expensive bases. This can be remedied by placing a small number of functions in the region between molecules in the complex. We present compact sets of optimised midbond functions for a range of complexes involving noble gases, alkali metals and small molecules for use in high accuracy coupled -cluster calculations, along with a more robust procedure for their optimisation. It is shown that excellent results are possible with double-zeta quality orbital basis sets when a few midbond functions are added, improving both the interaction energy and the equilibrium bond lengths of a series of noble gas dimers by 47% and 8%, respectively. When used in conjunction with explicitly correlated methods, near complete basis set limit accuracy is readily achievable at a fraction of the cost that using a large basis would entail. General purpose auxiliary sets are developed to allow explicitly correlated midbond function studies to be carried out, making it feasible to perform very high accuracy calculations on weakly bound complexes.

A system architecture for a planetary rover

NASA Technical Reports Server (NTRS)

Smith, D. B.; Matijevic, J. R.

1989-01-01

Each planetary mission requires a complex space vehicle which integrates several functions to accomplish the mission and science objectives. A Mars Rover is one of these vehicles, and extends the normal spacecraft functionality with two additional functions: surface mobility and sample acquisition. All functions are assembled into a hierarchical and structured format to understand the complexities of interactions between functions during different mission times. It can graphically show data flow between functions, and most importantly, the necessary control flow to avoid unambiguous results. Diagrams are presented organizing the functions into a structured, block format where each block represents a major function at the system level. As such, there are six blocks representing telecomm, power, thermal, science, mobility and sampling under a supervisory block called Data Management/Executive. Each block is a simple collection of state machines arranged into a hierarchical order very close to the NASREM model for Telerobotics. Each layer within a block represents a level of control for a set of state machines that do the three primary interface functions: command, telemetry, and fault protection. This latter function is expanded to include automatic reactions to the environment as well as internal faults. Lastly, diagrams are presented that trace the system operations involved in moving from site to site after site selection. The diagrams clearly illustrate both the data and control flows. They also illustrate inter-block data transfers and a hierarchical approach to fault protection. This systems architecture can be used to determine functional requirements, interface specifications and be used as a mechanism for grouping subsystems (i.e., collecting groups of machines, or blocks consistent with good and testable implementations).

Application of advanced multidisciplinary analysis and optimization methods to vehicle design synthesis

NASA Technical Reports Server (NTRS)

Consoli, Robert David; Sobieszczanski-Sobieski, Jaroslaw

1990-01-01

Advanced multidisciplinary analysis and optimization methods, namely system sensitivity analysis and non-hierarchical system decomposition, are applied to reduce the cost and improve the visibility of an automated vehicle design synthesis process. This process is inherently complex due to the large number of functional disciplines and associated interdisciplinary couplings. Recent developments in system sensitivity analysis as applied to complex non-hierarchic multidisciplinary design optimization problems enable the decomposition of these complex interactions into sub-processes that can be evaluated in parallel. The application of these techniques results in significant cost, accuracy, and visibility benefits for the entire design synthesis process.

High dimensional model representation method for fuzzy structural dynamics

NASA Astrophysics Data System (ADS)

Adhikari, S.; Chowdhury, R.; Friswell, M. I.

2011-03-01

Uncertainty propagation in multi-parameter complex structures possess significant computational challenges. This paper investigates the possibility of using the High Dimensional Model Representation (HDMR) approach when uncertain system parameters are modeled using fuzzy variables. In particular, the application of HDMR is proposed for fuzzy finite element analysis of linear dynamical systems. The HDMR expansion is an efficient formulation for high-dimensional mapping in complex systems if the higher order variable correlations are weak, thereby permitting the input-output relationship behavior to be captured by the terms of low-order. The computational effort to determine the expansion functions using the α-cut method scales polynomically with the number of variables rather than exponentially. This logic is based on the fundamental assumption underlying the HDMR representation that only low-order correlations among the input variables are likely to have significant impacts upon the outputs for most high-dimensional complex systems. The proposed method is first illustrated for multi-parameter nonlinear mathematical test functions with fuzzy variables. The method is then integrated with a commercial finite element software (ADINA). Modal analysis of a simplified aircraft wing with fuzzy parameters has been used to illustrate the generality of the proposed approach. In the numerical examples, triangular membership functions have been used and the results have been validated against direct Monte Carlo simulations. It is shown that using the proposed HDMR approach, the number of finite element function calls can be reduced without significantly compromising the accuracy.

From isolated light-harvesting complexes to the thylakoid membrane: a single-molecule perspective

NASA Astrophysics Data System (ADS)

Gruber, J. Michael; Malý, Pavel; Krüger, Tjaart P. J.; Grondelle, Rienk van

2018-01-01

The conversion of solar radiation to chemical energy in plants and green algae takes place in the thylakoid membrane. This amphiphilic environment hosts a complex arrangement of light-harvesting pigment-protein complexes that absorb light and transfer the excitation energy to photochemically active reaction centers. This efficient light-harvesting capacity is moreover tightly regulated by a photoprotective mechanism called non-photochemical quenching to avoid the stress-induced destruction of the catalytic reaction center. In this review we provide an overview of single-molecule fluorescence measurements on plant light-harvesting complexes (LHCs) of varying sizes with the aim of bridging the gap between the smallest isolated complexes, which have been well-characterized, and the native photosystem. The smallest complexes contain only a small number (10-20) of interacting chlorophylls, while the native photosystem contains dozens of protein subunits and many hundreds of connected pigments. We discuss the functional significance of conformational dynamics, the lipid environment, and the structural arrangement of this fascinating nano-machinery. The described experimental results can be utilized to build mathematical-physical models in a bottom-up approach, which can then be tested on larger in vivo systems. The results also clearly showcase the general property of biological systems to utilize the same system properties for different purposes. In this case it is the regulated conformational flexibility that allows LHCs to switch between efficient light-harvesting and a photoprotective function.

Protein Folding and Self-Organized Criticality

NASA Astrophysics Data System (ADS)

Bajracharya, Arun; Murray, Joelle

Proteins are known to fold into tertiary structures that determine their functionality in living organisms. However, the complex dynamics of protein folding and the way they consistently fold into the same structures is not fully understood. Self-organized criticality (SOC) has provided a framework for understanding complex systems in various systems (earthquakes, forest fires, financial markets, and epidemics) through scale invariance and the associated power law behavior. In this research, we use a simple hydrophobic-polar lattice-bound computational model to investigate self-organized criticality as a possible mechanism for generating complexity in protein folding.

Cyclic Peptide-Polymer Nanotubes as Efficient and Highly Potent Drug Delivery Systems for Organometallic Anticancer Complexes.

PubMed

Larnaudie, Sophie C; Brendel, Johannes C; Romero-Canelón, Isolda; Sanchez-Cano, Carlos; Catrouillet, Sylvain; Sanchis, Joaquin; Coverdale, James P C; Song, Ji-Inn; Habtemariam, Abraha; Sadler, Peter J; Jolliffe, Katrina A; Perrier, Sébastien

2018-01-08

Functional drug carrier systems have potential for increasing solubility and potency of drugs while reducing side effects. Complex polymeric materials, particularly anisotropic structures, are especially attractive due to their long circulation times. Here, we have conjugated cyclic peptides to the biocompatible polymer poly(2-hydroxypropyl methacrylamide) (pHPMA). The resulting conjugates were functionalized with organoiridium anticancer complexes. Small angle neutron scattering and static light scattering confirmed their self-assembly and elongated cylindrical shape. Drug-loaded nanotubes exhibited more potent antiproliferative activity toward human cancer cells than either free drug or the drug-loaded polymers, while the nanotubes themselves were nontoxic. Cellular accumulation studies revealed that the increased potency of the conjugate appears to be related to a more efficient mode of action rather than a higher cellular accumulation of iridium.

Does human cognition allow Human Factors (HF) certification of advanced aircrew systems?

NASA Technical Reports Server (NTRS)

Macleod, Iain S.; Taylor, Robert M.

1994-01-01

This paper has examined the requirements of HF specification and certification within advanced or complex aircrew systems. It suggests reasons for current inadequacies in the use of HF in the design process, giving some examples in support, and suggesting an avenue towards the improvement of the HF certification process. The importance of human cognition to the operation and performance of advanced aircrew systems has been stressed. Many of the shortfalls of advanced aircrew systems must be attributed to over automated designs that show little consideration on either the mental limits or the cognitive capabilities of the human system component. Traditional approaches to system design and HF certification are set within an over physicalistic foundation. Also, traditionally it was assumed that physicalistic system functions could be attributed to either the human or the machine on a one to one basis. Moreover, any problems associated with the parallel needs, or promoting human understanding alongside system operation and direction, were generally equated in reality by the natural flexibility and adaptability of human skills. The consideration of the human component of a complex system is seen as being primarily based on manifestations of human behavior to the almost total exclusion of any appreciation of unobservable human mental and cognitive processes. The argument of this paper is that the considered functionality of any complex human-machine system must contain functions that are purely human and purely cognitive. Human-machine system reliability ultimately depends on human reliability and dependability and, therefore, on the form and frequency of cognitive processes that have to be conducted to support system performance. The greater the demand placed by an advanced aircraft system on the human component's basic knowledge processes or cognition, rather than on skill, the more insiduous the effects the human may have on that system. This paper discusses one example of an attempt to devise an improved method of specificaiton and certification with relation to the advanced aircrew system, that of the RN Merlin helicopter. The method is realized to have limitations in practice, these mainly associated with the late production of the system specification in relation to the system development process. The need for a careful appreciation of the capabilities and support needs of human cognition within the design process of a complex man machine system has been argued, especially with relation to the concept of system functionality. Unlike the physicalistic Fitts list, a new classification of system functionality is proposed, namely: (1) equipment - system equipment related; (2) cognitive - human cognition related; and (3) associated - necessary combinatin of equipment and cognitive. This paper has not proposed a method for a fuller consideration of cognition within systems design, but has suggested the need for such a method and indicated an avenue towards its development. Finally, the HF certification of advanced aircrew systems is seen as only being possible in a qualified sense until the important functions of human cognition are considered within the system design process. (This paper contains the opinions of its authors and does not necessarily refledt the standpoint of their respective organizations).

Method for Evaluating Information to Solve Problems of Control, Monitoring and Diagnostics

NASA Astrophysics Data System (ADS)

Vasil'ev, V. A.; Dobrynina, N. V.

2017-06-01

The article describes a method for evaluating information to solve problems of control, monitoring and diagnostics. It is necessary for reducing the dimensionality of informational indicators of situations, bringing them to relative units, for calculating generalized information indicators on their basis, ranking them by characteristic levels, for calculating the efficiency criterion of a system functioning in real time. The design of information evaluation system has been developed on its basis that allows analyzing, processing and assessing information about the object. Such object can be a complex technical, economic and social system. The method and the based system thereof can find a wide application in the field of analysis, processing and evaluation of information on the functioning of the systems, regardless of their purpose, goals, tasks and complexity. For example, they can be used to assess the innovation capacities of industrial enterprises and management decisions.

Introduction to the magnet and vacuum systems of an electron storage ring

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weng, W.T.

An accelerator or storage ring complex is a concerted interplay of various functional systems. For the convenience of discussion we can divide it into the following systems: injector, magnet, RF, vacuum, instrumentation and control. In addition, the conventional construction of the building and radiation safety consideration are also needed and finally the beam lines, detector, data acquisition and analysis set-ups for research programs. Dr. L. Teng has given a comprehensive review of the whole complex and the operation of such a facility. I concentrate on the description of magnet and vacuum systems. Only the general function of each system andmore » the basic design concepts will be introduced, no detailed engineering practice will be given which will be best done after a machine design is produced. For further understanding and references a table of bibliography is provided at the end of the paper.« less

A mechanism producing power law etc. distributions

NASA Astrophysics Data System (ADS)

Li, Heling; Shen, Hongjun; Yang, Bin

2017-07-01

Power law distribution is playing an increasingly important role in the complex system study. Based on the insolvability of complex systems, the idea of incomplete statistics is utilized and expanded, three different exponential factors are introduced in equations about the normalization condition, statistical average and Shannon entropy, with probability distribution function deduced about exponential function, power function and the product form between power function and exponential function derived from Shannon entropy and maximal entropy principle. So it is shown that maximum entropy principle can totally replace equal probability hypothesis. Owing to the fact that power and probability distribution in the product form between power function and exponential function, which cannot be derived via equal probability hypothesis, can be derived by the aid of maximal entropy principle, it also can be concluded that maximal entropy principle is a basic principle which embodies concepts more extensively and reveals basic principles on motion laws of objects more fundamentally. At the same time, this principle also reveals the intrinsic link between Nature and different objects in human society and principles complied by all.

Functional specifications for a radioactive waste decision support system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Westrom, G.B.; Kurrasch, E.R.; Carlton, R.E.

1989-09-01

It is generally recognized that decisions relative to the treatment, handling, transportation and disposal of low-level wastes produced in nuclear power plants involve a complex array of many inter-related elements or considerations. Complex decision processes can be aided through the use of computer-based expert systems which are based on the knowledge of experts and the inferencing of that knowledge to provide advice to an end-user. To determine the feasibility of developing and applying an expert system in nuclear plant low level waste operations, a Functional Specification for a Radwaste Decision Support System (RDSS) was developed. All areas of radwaste management,more » from the point of waste generation to the disposition of the waste in the final disposal location were considered for inclusion within the scope of the RDSS. 27 figs., 8 tabs.« less

Anion-induced reconstitution of a self-assembling system to express a chloride-binding Co10L15 pentagonal prism.

PubMed

Riddell, Imogen A; Smulders, Maarten M J; Clegg, Jack K; Hristova, Yana R; Breiner, Boris; Thoburn, John D; Nitschke, Jonathan R

2012-09-01

Biochemical systems are adaptable, capable of reconstitution at all levels to achieve the functions associated with life. Synthetic chemical systems are more limited in their ability to reorganize to achieve new functions; they can reconfigure to bind an added substrate (template effect) or one binding event may modulate a receptor's affinity for a second substrate (allosteric effect). Here we describe a synthetic chemical system that is capable of structural reconstitution on receipt of one anionic signal (perchlorate) to create a tight binding pocket for another anion (chloride). The complex, barrel-like structure of the chloride receptor is templated by five perchlorate anions. This second-order templation phenomenon allows chemical networks to be envisaged that express more complex responses to chemical signals than is currently feasible.

Experimental analysis of bidirectional reflectance distribution function cross section conversion term in direction cosine space.

PubMed

Butler, Samuel D; Nauyoks, Stephen E; Marciniak, Michael A

2015-06-01

Of the many classes of bidirectional reflectance distribution function (BRDF) models, two popular classes of models are the microfacet model and the linear systems diffraction model. The microfacet model has the benefit of speed and simplicity, as it uses geometric optics approximations, while linear systems theory uses a diffraction approach to compute the BRDF, at the expense of greater computational complexity. In this Letter, nongrazing BRDF measurements of rough and polished surface-reflecting materials at multiple incident angles are scaled by the microfacet cross section conversion term, but in the linear systems direction cosine space, resulting in great alignment of BRDF data at various incident angles in this space. This results in a predictive BRDF model for surface-reflecting materials at nongrazing angles, while avoiding some of the computational complexities in the linear systems diffraction model.

Is Model-Based Development a Favorable Approach for Complex and Safety-Critical Computer Systems on Commercial Aircraft?

NASA Technical Reports Server (NTRS)

Torres-Pomales, Wilfredo

2014-01-01

A system is safety-critical if its failure can endanger human life or cause significant damage to property or the environment. State-of-the-art computer systems on commercial aircraft are highly complex, software-intensive, functionally integrated, and network-centric systems of systems. Ensuring that such systems are safe and comply with existing safety regulations is costly and time-consuming as the level of rigor in the development process, especially the validation and verification activities, is determined by considerations of system complexity and safety criticality. A significant degree of care and deep insight into the operational principles of these systems is required to ensure adequate coverage of all design implications relevant to system safety. Model-based development methodologies, methods, tools, and techniques facilitate collaboration and enable the use of common design artifacts among groups dealing with different aspects of the development of a system. This paper examines the application of model-based development to complex and safety-critical aircraft computer systems. Benefits and detriments are identified and an overall assessment of the approach is given.

Self-organization of network dynamics into local quantized states

DOE PAGES

Nicolaides, Christos; Juanes, Ruben; Cueto-Felgueroso, Luis

2016-02-17

Self-organization and pattern formation in network-organized systems emerges from the collective activation and interaction of many interconnected units. A striking feature of these non-equilibrium structures is that they are often localized and robust: only a small subset of the nodes, or cell assembly, is activated. Understanding the role of cell assemblies as basic functional units in neural networks and socio-technical systems emerges as a fundamental challenge in network theory. A key open question is how these elementary building blocks emerge, and how they operate, linking structure and function in complex networks. Here we show that a network analogue of themore » Swift-Hohenberg continuum model—a minimal-ingredients model of nodal activation and interaction within a complex network—is able to produce a complex suite of localized patterns. Thus, the spontaneous formation of robust operational cell assemblies in complex networks can be explained as the result of self-organization, even in the absence of synaptic reinforcements.« less

Self-organization of network dynamics into local quantized states.

PubMed

Nicolaides, Christos; Juanes, Ruben; Cueto-Felgueroso, Luis

2016-02-17

Self-organization and pattern formation in network-organized systems emerges from the collective activation and interaction of many interconnected units. A striking feature of these non-equilibrium structures is that they are often localized and robust: only a small subset of the nodes, or cell assembly, is activated. Understanding the role of cell assemblies as basic functional units in neural networks and socio-technical systems emerges as a fundamental challenge in network theory. A key open question is how these elementary building blocks emerge, and how they operate, linking structure and function in complex networks. Here we show that a network analogue of the Swift-Hohenberg continuum model-a minimal-ingredients model of nodal activation and interaction within a complex network-is able to produce a complex suite of localized patterns. Hence, the spontaneous formation of robust operational cell assemblies in complex networks can be explained as the result of self-organization, even in the absence of synaptic reinforcements.

Self-organization of network dynamics into local quantized states

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nicolaides, Christos; Juanes, Ruben; Cueto-Felgueroso, Luis

Self-organization and pattern formation in network-organized systems emerges from the collective activation and interaction of many interconnected units. A striking feature of these non-equilibrium structures is that they are often localized and robust: only a small subset of the nodes, or cell assembly, is activated. Understanding the role of cell assemblies as basic functional units in neural networks and socio-technical systems emerges as a fundamental challenge in network theory. A key open question is how these elementary building blocks emerge, and how they operate, linking structure and function in complex networks. Here we show that a network analogue of themore » Swift-Hohenberg continuum model—a minimal-ingredients model of nodal activation and interaction within a complex network—is able to produce a complex suite of localized patterns. Thus, the spontaneous formation of robust operational cell assemblies in complex networks can be explained as the result of self-organization, even in the absence of synaptic reinforcements.« less

DNA Origami Scaffolds as Templates for Functional Tetrameric Kir3 K+ Channels.

PubMed

Kurokawa, Tatsuki; Kiyonaka, Shigeki; Nakata, Eiji; Endo, Masayuki; Koyama, Shohei; Mori, Emiko; Tran, Nam Ha; Dinh, Huyen; Suzuki, Yuki; Hidaka, Kumi; Kawata, Masaaki; Sato, Chikara; Sugiyama, Hiroshi; Morii, Takashi; Mori, Yasuo

2018-03-01

In native systems, scaffolding proteins play important roles in assembling proteins into complexes to transduce signals. This concept is yet to be applied to the assembly of functional transmembrane protein complexes in artificial systems. To address this issue, DNA origami has the potential to serve as scaffolds that arrange proteins at specific positions in complexes. Herein, we report that Kir3 K + channel proteins are assembled through zinc-finger protein (ZFP)-adaptors at specific locations on DNA origami scaffolds. Specific binding of the ZFP-fused Kir3 channels and ZFP-based adaptors on DNA origami were confirmed by atomic force microscopy and gel electrophoresis. Furthermore, the DNA origami with ZFP binding sites nearly tripled the K + channel current activity elicited by heterotetrameric Kir3 channels in HEK293T cells. Thus, our method provides a useful template to control the oligomerization states of membrane protein complexes in vitro and in living cells. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure and function of the C-terminal domain of MrpA in the Bacillus subtilis Mrp-antiporter complex--the evolutionary progenitor of the long horizontal helix in complex I.

PubMed

Virzintiene, Egle; Moparthi, Vamsi K; Al-Eryani, Yusra; Shumbe, Leonard; Górecki, Kamil; Hägerhäll, Cecilia

2013-10-11

MrpA and MrpD are homologous to NuoL, NuoM and NuoN in complex I over the first 14 transmembrane helices. In this work, the C-terminal domain of MrpA, outside this conserved area, was investigated. The transmembrane orientation was found to correspond to that of NuoJ in complex I. We have previously demonstrated that the subunit NuoK is homologous to MrpC. The function of the MrpA C-terminus was tested by expression in a previously used Bacillus subtilis model system. At neutral pH, the truncated MrpA still worked, but at pH 8.4, where Mrp-complex formation is needed for function, the C-terminal domain of MrpA was absolutely required. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

[Complex surgical procedures in orthopedics and trauma surgery. A contribution to the proposal procedure for the DRG system in 2009].

PubMed

Flohé, S; Nabring, J; Luetkes, P; Nast-Kolb, D; Windolf, J

2008-10-01

Since the DRG system was introduced in 2003/2004 the system for remuneration has been continually modified in conjunction with input from specialized medical associations. As part of this development of the payment system, the criteria for classification of a diagnosis-related group were further expanded and new functions were added. This contribution addresses the importance of the complex surgical procedures as criteria for subdivision of the DRG case-based lump sums in orthopedics and trauma surgery.

Exploiting the locality of periodic subsystem density-functional theory: efficient sampling of the Brillouin zone.

PubMed

Genova, Alessandro; Pavanello, Michele

2015-12-16

In order to approximately satisfy the Bloch theorem, simulations of complex materials involving periodic systems are made n(k) times more complex by the need to sample the first Brillouin zone at n(k) points. By combining ideas from Kohn-Sham density-functional theory (DFT) and orbital-free DFT, for which no sampling is needed due to the absence of waves, subsystem DFT offers an interesting middle ground capable of sizable theoretical speedups against Kohn-Sham DFT. By splitting the supersystem into interacting subsystems, and mapping their quantum problem onto separate auxiliary Kohn-Sham systems, subsystem DFT allows an optimal topical sampling of the Brillouin zone. We elucidate this concept with two proof of principle simulations: a water bilayer on Pt[1 1 1]; and a complex system relevant to catalysis-a thiophene molecule physisorbed on a molybdenum sulfide monolayer deposited on top of an α-alumina support. For the latter system, a speedup of 300% is achieved against the subsystem DTF reference by using an optimized Brillouin zone sampling (600% against KS-DFT).

A biomimetic colorimetric logic gate system based on multi-functional peptide-mediated gold nanoparticle assembly.

PubMed

Li, Yong; Li, Wang; He, Kai-Yu; Li, Pei; Huang, Yan; Nie, Zhou; Yao, Shou-Zhuo

2016-04-28

In natural biological systems, proteins exploit various functional peptide motifs to exert target response and activity switch, providing a functional and logic basis for complex cellular activities. Building biomimetic peptide-based bio-logic systems is highly intriguing but remains relatively unexplored due to limited logic recognition elements and complex signal outputs. In this proof-of-principle work, we attempted to address these problems by utilizing multi-functional peptide probes and the peptide-mediated nanoparticle assembly system. Here, the rationally designed peptide probes function as the dual-target responsive element specifically responsive to metal ions and enzymes as well as the mediator regulating the assembly of gold nanoparticles (AuNPs). Taking advantage of Zn2+ ions and chymotrypsin as the model inputs of metal ions and enzymes, respectively, we constructed the peptide logic system computed by the multi-functional peptide probes and outputted by the readable colour change of AuNPs. In this way, the representative binary basic logic gates (AND, OR, INHIBIT, NAND, IMPLICATION) have been achieved by delicately coding the peptide sequence, demonstrating the versatility of our logic system. Additionally, we demonstrated that the three-input combinational logic gate (INHIBIT-OR) could also be successfully integrated and applied as a multi-tasking biosensor for colorimetric detection of dual targets. This nanoparticle-based peptide logic system presents a valid strategy to illustrate peptide information processing and provides a practical platform for executing peptide computing or peptide-related multiplexing sensing, implying that the controllable nanomaterial assembly is a promising and potent methodology for the advancement of biomimetic bio-logic computation.

Risk of Impaired Control of Spacecraft/Associated Systems and Decreased Mobility Due to Vestibular/Sensorimotor Alterations Associated with Space flight

NASA Technical Reports Server (NTRS)

Bloomberg, Jacob J.; Reschke, Millard F.; Clement, Gilles R.; Mulavara, Ajitkumar P.; Taylor, Laura C..

2015-01-01

Control of vehicles and other complex systems is a high-level integrative function of the central nervous system (CNS). It requires well-functioning subsystem performance, including good visual acuity, eye-hand coordination, spatial and geographic orientation perception, and cognitive function. Evidence from space flight research demonstrates that the function of each of these subsystems is altered by removing gravity, a fundamental orientation reference, which is sensed by vestibular, proprioceptive, and haptic receptors and used by the CNS for spatial orientation, posture, navigation, and coordination of movements. The available evidence also shows that the degree of alteration of each subsystem depends on a number of crew- and mission-related factors. There is only limited operational evidence that these alterations cause functional impacts on mission-critical vehicle (or complex system) control capabilities. Furthermore, while much of the operational performance data collected during space flight has not been available for independent analysis, those that have been reviewed are somewhat equivocal owing to uncontrolled (and/or unmeasured) environmental and/or engineering factors. Whether this can be improved by further analysis of previously inaccessible operational data or by development of new operational research protocols remains to be seen. The true operational risks will be estimable only after we have filled the knowledge gaps and when we can accurately assess integrated performance in off-nominal operational settings (Paloski et al. 2008). Thus, our current understanding of the Risk of Impaired Control of Spacecraft/Associated Systems and Decreased Mobility Due to Vestibular/Sensorimotor Alterations Associated with Space flight is limited primarily to extrapolation of scientific research findings, and, since there are limited ground-based analogs of the sensorimotor and vestibular changes associated with space flight, observation of their functional impacts is limited to studies performed in the space flight environment. Fortunately, many sensorimotor and vestibular experiments have been performed during and/or after space flight missions since 1959 (Reschke et al. 2007). While not all of these experiments were directly relevant to the question of vehicle/complex system control, most provide insight into changes in aspects of sensorimotor control that might bear on the physiological subsystems underlying this high-level integrated function.

Methods of information geometry in computational system biology (consistency between chemical and biological evolution).

PubMed

Astakhov, Vadim

2009-01-01

Interest in simulation of large-scale metabolic networks, species development, and genesis of various diseases requires new simulation techniques to accommodate the high complexity of realistic biological networks. Information geometry and topological formalisms are proposed to analyze information processes. We analyze the complexity of large-scale biological networks as well as transition of the system functionality due to modification in the system architecture, system environment, and system components. The dynamic core model is developed. The term dynamic core is used to define a set of causally related network functions. Delocalization of dynamic core model provides a mathematical formalism to analyze migration of specific functions in biosystems which undergo structure transition induced by the environment. The term delocalization is used to describe these processes of migration. We constructed a holographic model with self-poetic dynamic cores which preserves functional properties under those transitions. Topological constraints such as Ricci flow and Pfaff dimension were found for statistical manifolds which represent biological networks. These constraints can provide insight on processes of degeneration and recovery which take place in large-scale networks. We would like to suggest that therapies which are able to effectively implement estimated constraints, will successfully adjust biological systems and recover altered functionality. Also, we mathematically formulate the hypothesis that there is a direct consistency between biological and chemical evolution. Any set of causal relations within a biological network has its dual reimplementation in the chemistry of the system environment.

Transfer functions for protein signal transduction: application to a model of striatal neural plasticity.

PubMed

Scheler, Gabriele

2013-01-01

We present a novel formulation for biochemical reaction networks in the context of protein signal transduction. The model consists of input-output transfer functions, which are derived from differential equations, using stable equilibria. We select a set of "source" species, which are interpreted as input signals. Signals are transmitted to all other species in the system (the "target" species) with a specific delay and with a specific transmission strength. The delay is computed as the maximal reaction time until a stable equilibrium for the target species is reached, in the context of all other reactions in the system. The transmission strength is the concentration change of the target species. The computed input-output transfer functions can be stored in a matrix, fitted with parameters, and even recalled to build dynamical models on the basis of state changes. By separating the temporal and the magnitudinal domain we can greatly simplify the computational model, circumventing typical problems of complex dynamical systems. The transfer function transformation of biochemical reaction systems can be applied to mass-action kinetic models of signal transduction. The paper shows that this approach yields significant novel insights while remaining a fully testable and executable dynamical model for signal transduction. In particular we can deconstruct the complex system into local transfer functions between individual species. As an example, we examine modularity and signal integration using a published model of striatal neural plasticity. The modularizations that emerge correspond to a known biological distinction between calcium-dependent and cAMP-dependent pathways. Remarkably, we found that overall interconnectedness depends on the magnitude of inputs, with higher connectivity at low input concentrations and significant modularization at moderate to high input concentrations. This general result, which directly follows from the properties of individual transfer functions, contradicts notions of ubiquitous complexity by showing input-dependent signal transmission inactivation.

Functional microporous materials of metal carboxylate: Gas-occlusion properties and catalytic activities

NASA Astrophysics Data System (ADS)

Mori, Wasuke; Sato, Tomohiko; Ohmura, Tesushi; Nozaki Kato, Chika; Takei, Tohru

2005-08-01

Copper(II) terephthalate is the first transition metal complex found capable of adsorbing gases. This complex has opened the new field of adsorbent complex chemistry. It is recognized as the lead complex in the construction of microporous complexes. This specific system has been expanded to a systematic series of derivatives of other isomorphous transition metals, molybdenum(II), ruthenium(II, III), and rhodium(II). These complexes with open frameworks are widely recognized as very useful materials for applications to catalysis, separation at molecular level, and gas storage.

Launching AI in NASA ground systems

NASA Technical Reports Server (NTRS)

Perkins, Dorothy C.; Truszkowski, Walter F.

1990-01-01

This paper will discuss recent operational successes in implementing expert systems to support the complex functions of NASA mission control systems at the Goddard Space Flight Center, including fault detection and diagnosis for real time and engineering analysis functions in the Cosmic Background Explorer and Gamma Ray Observatory missions and automation of resource planning and scheduling functions for various missions. It will also discuss ongoing developments and prototypes that will lead to increasingly sophisticated applications of artificial intelligence. These include the use of neural networks to perform telemetry monitoring functions, the implementation of generic expert system shells that can be customized to telemetry handling functions specific to NASA control centers, the applications of AI in training and user support, the long-term potential of implementing systems based around distributed, cooperative problem solving, and the use of AI to control and assist system development activities.

Spectroscopic studies of Np(V) complexation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stout, B.E.

The complexation of Np(V) with aliphatic (oxalic, malonic, succinic, glutaric, and maleic) and aromatic (phthalic, pyromellitic, hemimellitic, trimellitic, and mellitic) polycarboxylic acids was studied by spectrophotometry at 1 M ionic strength (NaClO{sub 4}) and 23 C. For the aliphatic systems, the stability of the neptunyl complexes was found to decrease as the carbon chain length of the ligand increased which was attributed to an entropy effect. In polycarboxylate systems, the stability constant decreased in the order hemimellitate > mellitate > pyromellitate > trimellitate, phthalate. With the exception of hemimellitate, this trend follows the order of decreasing basicity of the ligand.more » After correction of the stability constant for statistical effects, the stability of the mellitate, pyromellitate, trimellitate, and phthalate complexes were approximately the same. The unexpected strength the hemimellitate complexation was attributed to an increase in electron density at the binding site from the non-chelating carboxylate group through induction. The complexation of phthalate, trimellitate and hemimellitate and mellitate were studied as a function of pH. Trimellitate and mellitate were found to form ML as well as ML complexes while for phthalate and hemimellitate only ML species were observed. The stability constants of the cation-cation complexes Np(V)-U(VI) and Np(V)-Np(V), measured at 6 M ionic strength (HClO{sub 4}) and 25 C, were found to be 2.45 {+-} 0.05 and 1.41 {+-} 0.14, respectively. The change in enthalpy for the Np(V)-U(VI) system as determined by the measurement of the stability constant as function of temperature was -14.3 {+-} 1.6 kJ/mol.« less

Effective control of complex turbulent dynamical systems through statistical functionals.

PubMed

Majda, Andrew J; Qi, Di

2017-05-30

Turbulent dynamical systems characterized by both a high-dimensional phase space and a large number of instabilities are ubiquitous among complex systems in science and engineering, including climate, material, and neural science. Control of these complex systems is a grand challenge, for example, in mitigating the effects of climate change or safe design of technology with fully developed shear turbulence. Control of flows in the transition to turbulence, where there is a small dimension of instabilities about a basic mean state, is an important and successful discipline. In complex turbulent dynamical systems, it is impossible to track and control the large dimension of instabilities, which strongly interact and exchange energy, and new control strategies are needed. The goal of this paper is to propose an effective statistical control strategy for complex turbulent dynamical systems based on a recent statistical energy principle and statistical linear response theory. We illustrate the potential practical efficiency and verify this effective statistical control strategy on the 40D Lorenz 1996 model in forcing regimes with various types of fully turbulent dynamics with nearly one-half of the phase space unstable.

Systems Integration Challenges for a National Space Launch System

NASA Technical Reports Server (NTRS)

May, Todd A.

2011-01-01

System Integration was refined through the complexity and early failures experienced in rocket flight. System Integration encompasses many different viewpoints of the system development. System Integration must ensure consistency in development and operations activities. Human Space Flight tends toward large, complex systems. Understanding the system fs operational and use context is the guiding principle for System Integration: (1) Sizeable costs can be driven into systems by not fully understanding context (2). Adhering to the system context throughout the system fs life cycle is essential to maintaining efficient System Integration. System Integration exists within the System Architecture. Beautiful systems are simple in use and operation -- Block upgrades facilitate manageable steps in functionality evolution. Effective System Integration requires a stable system concept. Communication is essential to system simplicity

Functional Assembly of Soluble and Membrane Recombinant Proteins of Mammalian NADPH Oxidase Complex.

PubMed

Souabni, Hajer; Ezzine, Aymen; Bizouarn, Tania; Baciou, Laura

2017-01-01

Activation of phagocyte cells from an innate immune system is associated with a massive consumption of molecular oxygen to generate highly reactive oxygen species (ROS) as microbial weapons. This is achieved by a multiprotein complex, the so-called NADPH oxidase. The activity of phagocyte NADPH oxidase relies on an assembly of more than five proteins, among them the membrane heterodimer named flavocytochrome b 558 (Cytb 558 ), constituted by the tight association of the gp91 phox (also named Nox2) and p22 phox proteins. The Cytb 558 is the membrane catalytic core of the NADPH oxidase complex, through which the reducing equivalent provided by NADPH is transferred via the associated prosthetic groups (one flavin and two hemes) to reduce dioxygen into superoxide anion. The other major proteins (p47 phox , p67 phox , p40 phox , Rac) requisite for the complex activity are cytosolic proteins. Thus, the NADPH oxidase functioning relies on a synergic multi-partner assembly that in vivo can be hardly studied at the molecular level due to the cell complexity. Thus, a cell-free assay method has been developed to study the NADPH oxidase activity that allows measuring and eventually quantifying the ROS generation based on optical techniques following reduction of cytochrome c. This setup is a valuable tool for the identification of protein interactions, of crucial components and additives for a functional enzyme. Recently, this method was improved by the engineering and the production of a complete recombinant NADPH oxidase complex using the combination of purified proteins expressed in bacterial and yeast host cells. The reconstitution into artificial membrane leads to a fully controllable system that permits fine functional studies.

State analysis requirements database for engineering complex embedded systems

NASA Technical Reports Server (NTRS)

Bennett, Matthew B.; Rasmussen, Robert D.; Ingham, Michel D.

2004-01-01

It has become clear that spacecraft system complexity is reaching a threshold where customary methods of control are no longer affordable or sufficiently reliable. At the heart of this problem are the conventional approaches to systems and software engineering based on subsystem-level functional decomposition, which fail to scale in the tangled web of interactions typically encountered in complex spacecraft designs. Furthermore, there is a fundamental gap between the requirements on software specified by systems engineers and the implementation of these requirements by software engineers. Software engineers must perform the translation of requirements into software code, hoping to accurately capture the systems engineer's understanding of the system behavior, which is not always explicitly specified. This gap opens up the possibility for misinterpretation of the systems engineer's intent, potentially leading to software errors. This problem is addressed by a systems engineering tool called the State Analysis Database, which provides a tool for capturing system and software requirements in the form of explicit models. This paper describes how requirements for complex aerospace systems can be developed using the State Analysis Database.

Drosophila-Cdh1 (Rap/Fzr) a regulatory subunit of APC/C is required for synaptic morphology, synaptic transmission and locomotion.

PubMed

Wise, Alexandria; Schatoff, Emma; Flores, Julian; Hua, Shao-Ying; Ueda, Atsushi; Wu, Chun-Fang; Venkatesh, Tadmiri

2013-11-01

The assembly of functional synapses requires the orchestration of the synthesis and degradation of a multitude of proteins. Protein degradation and modification by the conserved ubiquitination pathway has emerged as a key cellular regulatory mechanism during nervous system development and function (Kwabe and Brose, 2011). The anaphase promoting complex/cyclosome (APC/C) is a multi-subunit ubiquitin ligase complex primarily characterized for its role in the regulation of mitosis (Peters, 2002). In recent years, a role for APC/C in nervous system development and function has been rapidly emerging (Stegmuller and Bonni, 2005; Li et al., 2008). In the mammalian central nervous system the activator subunit, APC/C-Cdh1, has been shown to be a regulator of axon growth and dendrite morphogenesis (Konishi et al., 2004). In the Drosophila peripheral nervous system (PNS), APC2, a ligase subunit of the APC/C complex has been shown to regulate synaptic bouton size and activity (van Roessel et al., 2004). To investigate the role of APC/C-Cdh1 at the synapse we examined loss-of-function mutants of Rap/Fzr (Retina aberrant in pattern/Fizzy related), a Drosophila homolog of the mammalian Cdh1 during the development of the larval neuromuscular junction in Drosophila. Our cell biological, ultrastructural, electrophysiological, and behavioral data showed that rap/fzr loss-of-function mutations lead to changes in synaptic structure and function as well as locomotion defects. Data presented here show changes in size and morphology of synaptic boutons, and, muscle tissue organization. Electrophysiological experiments show that loss-of-function mutants exhibit increased frequency of spontaneous miniature synaptic potentials, indicating a higher rate of spontaneous synaptic vesicle fusion events. In addition, larval locomotion and peristaltic movement were also impaired. These findings suggest a role for Drosophila APC/C-Cdh1 mediated ubiquitination in regulating synaptic morphology, function and integrity of muscle structure in the peripheral nervous system. Copyright © 2013 ISDN. Published by Elsevier Ltd. All rights reserved.

Synthetic biology: insights into biological computation.

PubMed

Manzoni, Romilde; Urrios, Arturo; Velazquez-Garcia, Silvia; de Nadal, Eulàlia; Posas, Francesc

2016-04-18

Organisms have evolved a broad array of complex signaling mechanisms that allow them to survive in a wide range of environmental conditions. They are able to sense external inputs and produce an output response by computing the information. Synthetic biology attempts to rationally engineer biological systems in order to perform desired functions. Our increasing understanding of biological systems guides this rational design, while the huge background in electronics for building circuits defines the methodology. In this context, biocomputation is the branch of synthetic biology aimed at implementing artificial computational devices using engineered biological motifs as building blocks. Biocomputational devices are defined as biological systems that are able to integrate inputs and return outputs following pre-determined rules. Over the last decade the number of available synthetic engineered devices has increased exponentially; simple and complex circuits have been built in bacteria, yeast and mammalian cells. These devices can manage and store information, take decisions based on past and present inputs, and even convert a transient signal into a sustained response. The field is experiencing a fast growth and every day it is easier to implement more complex biological functions. This is mainly due to advances in in vitro DNA synthesis, new genome editing tools, novel molecular cloning techniques, continuously growing part libraries as well as other technological advances. This allows that digital computation can now be engineered and implemented in biological systems. Simple logic gates can be implemented and connected to perform novel desired functions or to better understand and redesign biological processes. Synthetic biological digital circuits could lead to new therapeutic approaches, as well as new and efficient ways to produce complex molecules such as antibiotics, bioplastics or biofuels. Biological computation not only provides possible biomedical and biotechnological applications, but also affords a greater understanding of biological systems.

Advances in cardiovascular fluid mechanics: bench to bedside.

PubMed

Dasi, Lakshmi P; Sucosky, Philippe; de Zelicourt, Diane; Sundareswaran, Kartik; Jimenez, Jorge; Yoganathan, Ajit P

2009-04-01

This paper presents recent advances in cardiovascular fluid mechanics that define the current state of the art. These studies include complex multimodal investigations with advanced measurement and simulation techniques. We first discuss the complex flows within the total cavopulmonary connection in Fontan patients. We emphasize the quantification of energy losses by studying the importance of caval offsets as well as the differences among various Fontan surgical protocols. In our studies of the fluid mechanics of prosthetic heart valves, we reveal for the first time the full three-dimensional complexity of flow fields in the vicinity of bileaflet and trileaflet valves and the microscopic hinge flow dynamics. We also present results of these valves functioning in a patient-specific native aorta geometry. Our in vitro mitral valve studies show the complex mechanism of the native mitral valve apparatus. We demonstrate that the different components of the mitral valve have independent and synergistically complex functions that allow the valve to operate efficiently. We also show how valve mechanics change under pathological and repair conditions associated with enlarged ventricles. Finally, our ex vivo studies on the interactions between the aortic valve and its surrounding hemodynamic environment are aimed at providing insights into normal valve function and valve pathology. We describe the development of organ- and tissue-culture systems and the biological response of the tissue subjected to their respective simulated mechanical environment. The studies noted above have enhanced our understanding of the complex fluid mechanics associated with the cardiovascular system and have led to new translational technologies.

Formulation and stabilization of nano-/microdispersion systems using naturally occurring edible polyelectrolytes by electrostatic deposition and complexation.

PubMed

Kuroiwa, Takashi; Kobayashi, Isao; Chuah, Ai Mey; Nakajima, Mitsutoshi; Ichikawa, Sosaku

2015-12-01

This review paper presents an overview of the formulation and functionalization of nano-/microdispersion systems composed of edible materials. We first summarized general aspects on the stability of colloidal systems and the roles of natural polyelectrolytes such as proteins and ionic polysaccharides for the formation and stabilization of colloidal systems. Then we introduced our research topics on (1) stabilization of emulsions by the electrostatic deposition using natural polyelectrolytes and (2) formulation of stable nanodispersion systems by complexation of natural polyelectrolytes. In both cases, the preparation procedures were relatively simple, without high energy input or harmful chemical addition. The properties of the nano-/microdispersion systems, such as particle size, surface charge and dispersion stability were significantly affected by the concerned materials and preparation conditions, including the type and concentration of used natural polyelectrolytes. These dispersion systems would be useful for developing novel foods having high functionality and good stability. Copyright © 2015 Elsevier B.V. All rights reserved.

On the sensitivity of complex, internally coupled systems

NASA Technical Reports Server (NTRS)

Sobieszczanskisobieski, Jaroslaw

1988-01-01

A method is presented for computing sensitivity derivatives with respect to independent (input) variables for complex, internally coupled systems, while avoiding the cost and inaccuracy of finite differencing performed on the entire system analysis. The method entails two alternative algorithms: the first is based on the classical implicit function theorem formulated on residuals of governing equations, and the second develops the system sensitivity equations in a new form using the partial (local) sensitivity derivatives of the output with respect to the input of each part of the system. A few application examples are presented to illustrate the discussion.

Advances and Computational Tools towards Predictable Design in Biological Engineering

PubMed Central

2014-01-01

The design process of complex systems in all the fields of engineering requires a set of quantitatively characterized components and a method to predict the output of systems composed by such elements. This strategy relies on the modularity of the used components or the prediction of their context-dependent behaviour, when parts functioning depends on the specific context. Mathematical models usually support the whole process by guiding the selection of parts and by predicting the output of interconnected systems. Such bottom-up design process cannot be trivially adopted for biological systems engineering, since parts function is hard to predict when components are reused in different contexts. This issue and the intrinsic complexity of living systems limit the capability of synthetic biologists to predict the quantitative behaviour of biological systems. The high potential of synthetic biology strongly depends on the capability of mastering this issue. This review discusses the predictability issues of basic biological parts (promoters, ribosome binding sites, coding sequences, transcriptional terminators, and plasmids) when used to engineer simple and complex gene expression systems in Escherichia coli. A comparison between bottom-up and trial-and-error approaches is performed for all the discussed elements and mathematical models supporting the prediction of parts behaviour are illustrated. PMID:25161694

Grandmother Support, Family Functioning, and Parenting Stress in Families with a Child with a Disability

ERIC Educational Resources Information Center

Tumbarello, Natasha

2010-01-01

This study examined the relationship among grandparent support, family functioning, and parental stress on families with children with and without disabilities between the ages of 2 and 12 years. Families are viewed as an ever-changing complex system with reciprocal interactions. One possible stressor on the family system is the birth of a child…

Thermal Environment for Classrooms. Central System Approach to Air Conditioning.

ERIC Educational Resources Information Center

Triechler, Walter W.

This speech compares the air conditioning requirements of high-rise office buildings with those of large centralized school complexes. A description of one particular air conditioning system provides information about the system's arrangement, functions, performance efficiency, and cost effectiveness. (MLF)

Assessment of Ab Initio and Density Functional Theory Methods for the Excitations of Donor-Acceptor Complexes: The Case of the Benzene-Tetracyanoethylene Model.

PubMed

Xu, Peng; Zhang, Cai-Rong; Wang, Wei; Gong, Ji-Jun; Liu, Zi-Jiang; Chen, Hong-Shan

2018-04-10

The understanding of the excited-state properties of electron donors, acceptors and their interfaces in organic optoelectronic devices is a fundamental issue for their performance optimization. In order to obtain a balanced description of the different excitation types for electron-donor-acceptor systems, including the singlet charge transfer (CT), local excitations, and triplet excited states, several ab initio and density functional theory (DFT) methods for excited-state calculations were evaluated based upon the selected model system of benzene-tetracyanoethylene (B-TCNE) complexes. On the basis of benchmark calculations of the equation-of-motion coupled-cluster with single and double excitations method, the arithmetic mean of the absolute errors and standard errors of the electronic excitation energies for the different computational methods suggest that the M11 functional in DFT is superior to the other tested DFT functionals, and time-dependent DFT (TDDFT) with the Tamm-Dancoff approximation improves the accuracy of the calculated excitation energies relative to that of the full TDDFT. The performance of the M11 functional underlines the importance of kinetic energy density, spin-density gradient, and range separation in the development of novel DFT functionals. According to the TDDFT results, the performances of the different TDDFT methods on the CT properties of the B-TCNE complexes were also analyzed.

Uncertainties in building a strategic defense.

PubMed

Zraket, C A

1987-03-27

Building a strategic defense against nuclear ballistic missiles involves complex and uncertain functional, spatial, and temporal relations. Such a defensive system would evolve and grow over decades. It is too complex, dynamic, and interactive to be fully understood initially by design, analysis, and experiments. Uncertainties exist in the formulation of requirements and in the research and design of a defense architecture that can be implemented incrementally and be fully tested to operate reliably. The analysis and measurement of system survivability, performance, and cost-effectiveness are critical to this process. Similar complexities exist for an adversary's system that would suppress or use countermeasures against a missile defense. Problems and opportunities posed by these relations are described, with emphasis on the unique characteristics and vulnerabilities of space-based systems.

A systems biology approach to studying Tai Chi, physiological complexity and healthy aging: design and rationale of a pragmatic randomized controlled trial.

PubMed

Wayne, Peter M; Manor, Brad; Novak, Vera; Costa, Madelena D; Hausdorff, Jeffrey M; Goldberger, Ary L; Ahn, Andrew C; Yeh, Gloria Y; Peng, C-K; Lough, Matthew; Davis, Roger B; Quilty, Mary T; Lipsitz, Lewis A

2013-01-01

Aging is typically associated with progressive multi-system impairment that leads to decreased physical and cognitive function and reduced adaptability to stress. Due to its capacity to characterize complex dynamics within and between physiological systems, the emerging field of complex systems biology and its array of quantitative tools show great promise for improving our understanding of aging, monitoring senescence, and providing biomarkers for evaluating novel interventions, including promising mind-body exercises, that treat age-related disease and promote healthy aging. An ongoing, two-arm randomized clinical trial is evaluating the potential of Tai Chi mind-body exercise to attenuate age-related loss of complexity. A total of 60 Tai Chi-naïve healthy older adults (aged 50-79) are being randomized to either six months of Tai Chi training (n=30), or to a waitlist control receiving unaltered usual medical care (n=30). Our primary outcomes are complexity-based measures of heart rate, standing postural sway and gait stride interval dynamics assessed at 3 and 6months. Multiscale entropy and detrended fluctuation analysis are used as entropy- and fractal-based measures of complexity, respectively. Secondary outcomes include measures of physical and psychological function and tests of physiological adaptability also assessed at 3 and 6months. Results of this study may lead to novel biomarkers that help us monitor and understand the physiological processes of aging and explore the potential benefits of Tai Chi and related mind-body exercises for healthy aging. Copyright © 2012 Elsevier Inc. All rights reserved.

Synchronization in complex networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arenas, A.; Diaz-Guilera, A.; Moreno, Y.

Synchronization processes in populations of locally interacting elements are in the focus of intense research in physical, biological, chemical, technological and social systems. The many efforts devoted to understand synchronization phenomena in natural systems take now advantage of the recent theory of complex networks. In this review, we report the advances in the comprehension of synchronization phenomena when oscillating elements are constrained to interact in a complex network topology. We also overview the new emergent features coming out from the interplay between the structure and the function of the underlying pattern of connections. Extensive numerical work as well as analyticalmore » approaches to the problem are presented. Finally, we review several applications of synchronization in complex networks to different disciplines: biological systems and neuroscience, engineering and computer science, and economy and social sciences.« less

Reconstruction of Complex Directional Networks with Group Lasso Nonlinear Conditional Granger Causality.

PubMed

Yang, Guanxue; Wang, Lin; Wang, Xiaofan

2017-06-07

Reconstruction of networks underlying complex systems is one of the most crucial problems in many areas of engineering and science. In this paper, rather than identifying parameters of complex systems governed by pre-defined models or taking some polynomial and rational functions as a prior information for subsequent model selection, we put forward a general framework for nonlinear causal network reconstruction from time-series with limited observations. With obtaining multi-source datasets based on the data-fusion strategy, we propose a novel method to handle nonlinearity and directionality of complex networked systems, namely group lasso nonlinear conditional granger causality. Specially, our method can exploit different sets of radial basis functions to approximate the nonlinear interactions between each pair of nodes and integrate sparsity into grouped variables selection. The performance characteristic of our approach is firstly assessed with two types of simulated datasets from nonlinear vector autoregressive model and nonlinear dynamic models, and then verified based on the benchmark datasets from DREAM3 Challenge4. Effects of data size and noise intensity are also discussed. All of the results demonstrate that the proposed method performs better in terms of higher area under precision-recall curve.

The general theory of the Quasi-reproducible experiments: How to describe the measured data of complex systems?

NASA Astrophysics Data System (ADS)

Nigmatullin, Raoul R.; Maione, Guido; Lino, Paolo; Saponaro, Fabrizio; Zhang, Wei

2017-01-01

In this paper, we suggest a general theory that enables to describe experiments associated with reproducible or quasi-reproducible data reflecting the dynamical and self-similar properties of a wide class of complex systems. Under complex system we understand a system when the model based on microscopic principles and suppositions about the nature of the matter is absent. This microscopic model is usually determined as ;the best fit" model. The behavior of the complex system relatively to a control variable (time, frequency, wavelength, etc.) can be described in terms of the so-called intermediate model (IM). One can prove that the fitting parameters of the IM are associated with the amplitude-frequency response of the segment of the Prony series. The segment of the Prony series including the set of the decomposition coefficients and the set of the exponential functions (with k = 1,2,…,K) is limited by the final mode K. The exponential functions of this decomposition depend on time and are found by the original algorithm described in the paper. This approach serves as a logical continuation of the results obtained earlier in paper [Nigmatullin RR, W. Zhang and Striccoli D. General theory of experiment containing reproducible data: The reduction to an ideal experiment. Commun Nonlinear Sci Numer Simul, 27, (2015), pp 175-192] for reproducible experiments and includes the previous results as a partial case. In this paper, we consider a more complex case when the available data can create short samplings or exhibit some instability during the process of measurements. We give some justified evidences and conditions proving the validity of this theory for the description of a wide class of complex systems in terms of the reduced set of the fitting parameters belonging to the segment of the Prony series. The elimination of uncontrollable factors expressed in the form of the apparatus function is discussed. To illustrate how to apply the theory and take advantage of its benefits, we consider the experimental data associated with typical working conditions of the injection system in a common rail diesel engine. In particular, the flow rate of the injected fuel is considered at different reference rail pressures. The measured data are treated by the proposed algorithm to verify the adherence to the proposed general theory. The obtained results demonstrate the undoubted effectiveness of the proposed theory.

A finite element formulation for scattering from electrically large 2-dimensional structures

NASA Technical Reports Server (NTRS)

Ross, Daniel C.; Volakis, John L.

1992-01-01

A finite element formulation is given using the scattered field approach with a fictitious material absorber to truncate the mesh. The formulation includes the use of arbitrary approximation functions so that more accurate results can be achieved without any modification to the software. Additionally, non-polynomial approximation functions can be used, including complex approximation functions. The banded system that results is solved with an efficient sparse/banded iterative scheme and as a consequence, large structures can be analyzed. Results are given for simple cases to verify the formulation and also for large, complex geometries.

Finite-time synchronization of complex networks with non-identical nodes and impulsive disturbances

NASA Astrophysics Data System (ADS)

Zhang, Wanli; Li, Chuandong; He, Xing; Li, Hongfei

2018-01-01

This paper investigates the finite-time synchronization of complex networks (CNs) with non-identical nodes and impulsive disturbances. By utilizing stability theories, new 1-norm-based analytical techniques and suitable comparison, systems, several sufficient conditions are obtained to realize the synchronization goal in finite time. State feedback controllers with and without the sign function are designed. Results show that the controllers with sign function can reduce the conservativeness of control gains and the controllers without sign function can overcome the chattering phenomenon. Numerical simulations are offered to verify the effectiveness of the theoretical analysis.

Specification and Design of Electrical Flight System Architectures with SysML

NASA Technical Reports Server (NTRS)

McKelvin, Mark L., Jr.; Jimenez, Alejandro

2012-01-01

Modern space flight systems are required to perform more complex functions than previous generations to support space missions. This demand is driving the trend to deploy more electronics to realize system functionality. The traditional approach for the specification, design, and deployment of electrical system architectures in space flight systems includes the use of informal definitions and descriptions that are often embedded within loosely coupled but highly interdependent design documents. Traditional methods become inefficient to cope with increasing system complexity, evolving requirements, and the ability to meet project budget and time constraints. Thus, there is a need for more rigorous methods to capture the relevant information about the electrical system architecture as the design evolves. In this work, we propose a model-centric approach to support the specification and design of electrical flight system architectures using the System Modeling Language (SysML). In our approach, we develop a domain specific language for specifying electrical system architectures, and we propose a design flow for the specification and design of electrical interfaces. Our approach is applied to a practical flight system.

Propagation of various dark hollow beams through an apertured paraxial ABCD optical system

NASA Astrophysics Data System (ADS)

Cai, Yangjian; Ge, Di

2006-08-01

Propagation of a dark hollow beam (DHB) of circular, elliptical or rectangular symmetry through an apertured paraxial ABCD optical system is investigated. Approximate analytical formulas for various DHBs propagating through an apertured paraxial optical system are derived by expanding the hard-aperture function into a finite sum of complex Gaussian functions in terms of a tensor method. Some numerical results are given. Our formulas provide a convenient way for studying the propagation of various DHBs through an apertured paraxial optical system.

Hydrogen exchange differences between chemoreceptor signaling complexes localize to functionally important subdomains.

PubMed

Koshy, Seena S; Li, Xuni; Eyles, Stephen J; Weis, Robert M; Thompson, Lynmarie K

2014-12-16

The goal of understanding mechanisms of transmembrane signaling, one of many key life processes mediated by membrane proteins, has motivated numerous studies of bacterial chemotaxis receptors. Ligand binding to the receptor causes a piston motion of an α helix in the periplasmic and transmembrane domains, but it is unclear how the signal is then propagated through the cytoplasmic domain to control the activity of the associated kinase CheA. Recent proposals suggest that signaling in the cytoplasmic domain involves opposing changes in dynamics in different subdomains. However, it has been difficult to measure dynamics within the functional system, consisting of extended arrays of receptor complexes with two other proteins, CheA and CheW. We have combined hydrogen exchange mass spectrometry with vesicle template assembly of functional complexes of the receptor cytoplasmic domain to reveal that there are significant signaling-associated changes in exchange, and these changes localize to key regions of the receptor involved in the excitation and adaptation responses. The methylation subdomain exhibits complex changes that include slower hydrogen exchange in complexes in a kinase-activating state, which may be partially consistent with proposals that this subdomain is stabilized in this state. The signaling subdomain exhibits significant protection from hydrogen exchange in complexes in a kinase-activating state, suggesting a tighter and/or larger interaction interface with CheA and CheW in this state. These first measurements of the stability of protein subdomains within functional signaling complexes demonstrate the promise of this approach for measuring functionally important protein dynamics within the various physiologically relevant states of multiprotein complexes.

Hydrogen Exchange Differences between Chemoreceptor Signaling Complexes Localize to Functionally Important Subdomains

PubMed Central

2015-01-01

The goal of understanding mechanisms of transmembrane signaling, one of many key life processes mediated by membrane proteins, has motivated numerous studies of bacterial chemotaxis receptors. Ligand binding to the receptor causes a piston motion of an α helix in the periplasmic and transmembrane domains, but it is unclear how the signal is then propagated through the cytoplasmic domain to control the activity of the associated kinase CheA. Recent proposals suggest that signaling in the cytoplasmic domain involves opposing changes in dynamics in different subdomains. However, it has been difficult to measure dynamics within the functional system, consisting of extended arrays of receptor complexes with two other proteins, CheA and CheW. We have combined hydrogen exchange mass spectrometry with vesicle template assembly of functional complexes of the receptor cytoplasmic domain to reveal that there are significant signaling-associated changes in exchange, and these changes localize to key regions of the receptor involved in the excitation and adaptation responses. The methylation subdomain exhibits complex changes that include slower hydrogen exchange in complexes in a kinase-activating state, which may be partially consistent with proposals that this subdomain is stabilized in this state. The signaling subdomain exhibits significant protection from hydrogen exchange in complexes in a kinase-activating state, suggesting a tighter and/or larger interaction interface with CheA and CheW in this state. These first measurements of the stability of protein subdomains within functional signaling complexes demonstrate the promise of this approach for measuring functionally important protein dynamics within the various physiologically relevant states of multiprotein complexes. PMID:25420045

Revisiting the Quantum Brain Hypothesis: Toward Quantum (Neuro)biology?

PubMed

Jedlicka, Peter

2017-01-01

The nervous system is a non-linear dynamical complex system with many feedback loops. A conventional wisdom is that in the brain the quantum fluctuations are self-averaging and thus functionally negligible. However, this intuition might be misleading in the case of non-linear complex systems. Because of an extreme sensitivity to initial conditions, in complex systems the microscopic fluctuations may be amplified and thereby affect the system's behavior. In this way quantum dynamics might influence neuronal computations. Accumulating evidence in non-neuronal systems indicates that biological evolution is able to exploit quantum stochasticity. The recent rise of quantum biology as an emerging field at the border between quantum physics and the life sciences suggests that quantum events could play a non-trivial role also in neuronal cells. Direct experimental evidence for this is still missing but future research should address the possibility that quantum events contribute to an extremely high complexity, variability and computational power of neuronal dynamics.

Assembly and activation of neurotrophic factor receptor complexes.

PubMed

Simi, Anastasia; Ibáñez, Carlos F

2010-04-01

Neurotrophic factors play important roles in the development and function of both neuronal and glial elements of the central and peripheral nervous systems. Their functional diversity is in part based on their ability to interact with alternative complexes of receptor molecules. This review focuses on our current understanding of the mechanisms that govern the assembly and activation of neurotrophic factor receptor complexes. The realization that many, if not the majority, of these complexes exist in a preassembled form at the plasma membrane has forced the revision of classical ligand-mediated oligomerization models, and led to the discovery of novel mechanisms of receptor activation and generation of signaling diversity which are likely to be shared by many different classes of receptors.

Quantification of Degeneracy in Biological Systems for Characterization of Functional Interactions Between Modules

PubMed Central

Li, Yao; Dwivedi, Gaurav; Huang, Wen; Yi, Yingfei

2012-01-01

There is an evolutionary advantage in having multiple components with overlapping functionality (i.e degeneracy) in organisms. While theoretical considerations of degeneracy have been well established in neural networks using information theory, the same concepts have not been developed for differential systems, which form the basis of many biochemical reaction network descriptions in systems biology. Here we establish mathematical definitions of degeneracy, complexity and robustness that allow for the quantification of these properties in a system. By exciting a dynamical system with noise, the mutual information associated with a selected observable output and the interacting subspaces of input components can be used to define both complexity and degeneracy. The calculation of degeneracy in a biological network is a useful metric for evaluating features such as the sensitivity of a biological network to environmental evolutionary pressure. Using a two-receptor signal transduction network, we find that redundant components will not yield high degeneracy whereas compensatory mechanisms established by pathway crosstalk will. This form of analysis permits interrogation of large-scale differential systems for non-identical, functionally equivalent features that have evolved to maintain homeostasis during disruption of individual components. PMID:22619750

Adaptive identifier for uncertain complex nonlinear systems based on continuous neural networks.

PubMed

Alfaro-Ponce, Mariel; Cruz, Amadeo Argüelles; Chairez, Isaac

2014-03-01

This paper presents the design of a complex-valued differential neural network identifier for uncertain nonlinear systems defined in the complex domain. This design includes the construction of an adaptive algorithm to adjust the parameters included in the identifier. The algorithm is obtained based on a special class of controlled Lyapunov functions. The quality of the identification process is characterized using the practical stability framework. Indeed, the region where the identification error converges is derived by the same Lyapunov method. This zone is defined by the power of uncertainties and perturbations affecting the complex-valued uncertain dynamics. Moreover, this convergence zone is reduced to its lowest possible value using ideas related to the so-called ellipsoid methodology. Two simple but informative numerical examples are developed to show how the identifier proposed in this paper can be used to approximate uncertain nonlinear systems valued in the complex domain.

Gels of sodium alginate‒chitosan interpolyelectrolyte complexes

NASA Astrophysics Data System (ADS)

Brovko, O. S.; Palamarchuk, I. A.; Val'chuk, N. A.; Chukhchin, D. G.; Bogolitsyn, K. G.; Boitsova, T. A.

2017-08-01

Aspects of the formation of gels of interpolyelectrolyte complexes (IPECs) based on sodium alginate (NaAlg) and chitosan are studied. The effect the conditions of synthesis and complex composition have on the morphological structure and functional properties of these complexes is examined. It is established that complexation in this system proceeds according to a mechanism of electrostatic interaction between the oppositely charged carboxylic groups of the L-hyaluronic acid pyranose cycles of NaAlg proximal polymer chains and chitosan's amino groups, along with a multitude of hydrogen bonds and dispersion forces. We show that the mechanism of IPEC formation is strongly influenced by the conformational state of a lyophilizing component that is present in the system in excess. The inner surfaces of cryogels based on NaAlg‒chitosan IPECs is found to be strongly influenced by the degree of conversion between the parental polyelectrolytes. The most developed mesoporous structure is obtained when a denser gel forms in the system.

The evolution and regulation of the mucosal immune complexity in the basal chordate amphioxus.

PubMed

Huang, Shengfeng; Wang, Xin; Yan, Qingyu; Guo, Lei; Yuan, Shaochun; Huang, Guangrui; Huang, Huiqing; Li, Jun; Dong, Meiling; Chen, Shangwu; Xu, Anlong

2011-02-15

Both amphioxus and the sea urchin encode a complex innate immune gene repertoire in their genomes, but the composition and mechanisms of their innate immune systems, as well as the fundamental differences between two systems, remain largely unexplored. In this study, we dissect the mucosal immune complexity of amphioxus into different evolutionary-functional modes and regulatory patterns by integrating information from phylogenetic inferences, genome-wide digital expression profiles, time course expression dynamics, and functional analyses. With these rich data, we reconstruct several major immune subsystems in amphioxus and analyze their regulation during mucosal infection. These include the TNF/IL-1R network, TLR and NLR networks, complement system, apoptosis network, oxidative pathways, and other effector genes (e.g., peptidoglycan recognition proteins, Gram-negative binding proteins, and chitin-binding proteins). We show that beneath the superficial similarity to that of the sea urchin, the amphioxus innate system, despite preserving critical invertebrate components, is more similar to that of the vertebrates in terms of composition, expression regulation, and functional strategies. For example, major effectors in amphioxus gut mucous tissue are the well-developed complement and oxidative-burst systems, and the signaling network in amphioxus seems to emphasize signal transduction/modulation more than initiation. In conclusion, we suggest that the innate immune systems of amphioxus and the sea urchin are strategically different, possibly representing two successful cases among many expanded immune systems that arose at the age of the Cambrian explosion. We further suggest that the vertebrate innate immune system should be derived from one of these expanded systems, most likely from the same one that was shared by amphioxus.

Structure, Behavior, Function as a Framework For Teaching and Learning about Complexity In Ecosystems: Lessons from Middle School Classrooms (Invited)

NASA Astrophysics Data System (ADS)

Hmelo-Silver, C.; Gray, S.; Jordan, R.

2010-12-01

Complex systems surround us, and as Sabelli (2006) has argued, understanding complex systems is a critical component of science literacy. Understanding natural and designed systems are also prominent in the new draft science standards (NRC, 2010) and therefore of growing importance in the science classroom. Our work has focused on promoting an understanding of one complex natural system, aquatic ecosystems, which given current events, is fast becoming a requisite for informed decision-making as citizens (Jordan et al. 2008). Learners have difficulty understanding many concepts related to complex natural systems (e.g., Hmelo-Silver, Marathe, & Liu, 2007; Jordan, Gray, Liu, Demeter, & Hmelo-Silver, 2009). Studies of how students think about complex ecological systems (e.g; Hmelo-Silver, Marathe, & Liu, 2007; Hogan, 2000, Hogan & Fisherkeller, 1996: Covitt & Gunkel, 2008) have revealed difficulties in thinking beyond linear flow, single causality, and visible structure. Helping students to learn about ecosystems is a complex task that requires providing opportunities for students to not only engage directly with ecosystems but also with resources that provide relevant background knowledge and opportunities for learners to make their thinking visible. Both tasks can be difficult given the large spatial and temporal scales on which ecosystems operate. Additionally, visible components interact with often invisible components which can obscure ecosystem processes for students. Working in the context of aquatic ecosystems, we sought to provide learners with representations and simulations that make salient the relationship between system components. In particular, we provided learners with opportunities to experience both the micro-level and macro-level phenomena that are key to understanding ecosystems (Hmelo-Silver, Liu, Gray, & Jordan, submitted; Liu & Hmelo-Silver, 2008; Jacobson & Wilensky, 2006). To accomplish this, we needed to help learners make connections across the levels of ecosystems. A big part of this is making phenomena accessible to their experience. We accomplished through the use of physical models and computers simulations at different scale. In an effort to promote a coherent understanding in our learners, we sought to develop tools that can provide dynamic feedback that will enable them to modify, enrich, and repair their mental models as needed (e.g., Roschelle, 1996). Additionally, we also wanted to develop a conceptual representation that can be used across multiple ecosystems to prepare students to learn about new systems in the future (Bransford & Schwartz, 1999). Our approach to this has been to use the structure-behavior-function (SBF) conceptual representation (Liu & Hmelo-Silver, 2009; Vattam et al., in press). Often, learning life science is about learning the names of structures. One of our design principles is to ensure instruction emphasizes the behaviors (or mechanisms) of systems as well as the functions (the system outputs) in addition to the structures. We have used simulations to help make behaviors and functions visible and a modeling tool that supports students in thinking about the SBF conceptual representation. In this presentation, we will report on the results of classroom interventions and the lessons learned.

Symbolic Dynamics and Grammatical Complexity

NASA Astrophysics Data System (ADS)

Hao, Bai-Lin; Zheng, Wei-Mou

The following sections are included: * Formal Languages and Their Complexity * Formal Language * Chomsky Hierarchy of Grammatical Complexity * The L-System * Regular Language and Finite Automaton * Finite Automaton * Regular Language * Stefan Matrix as Transfer Function for Automaton * Beyond Regular Languages * Feigenbaum and Generalized Feigenbaum Limiting Sets * Even and Odd Fibonacci Sequences * Odd Maximal Primitive Prefixes and Kneading Map * Even Maximal Primitive Prefixes and Distinct Excluded Blocks * Summary of Results

Motor system evolution and the emergence of high cognitive functions.

PubMed

Mendoza, Germán; Merchant, Hugo

2014-11-01

In human and nonhuman primates, the cortical motor system comprises a collection of brain areas primarily related to motor control. Existing evidence suggests that no other mammalian group has the number, extension, and complexity of motor-related areas observed in the frontal lobe of primates. Such diversity is probably related to the wide behavioral flexibility that primates display. Indeed, recent comparative anatomical, psychophysical, and neurophysiological studies suggest that the evolution of the motor cortical areas closely correlates with the emergence of high cognitive abilities. Advances in understanding the cortical motor system have shown that these areas are also related to functions previously linked to higher-order associative areas. In addition, experimental observations have shown that the classical distinction between perceptual and motor functions is not strictly followed across cortical areas. In this paper, we review evidence suggesting that evolution of the motor system had a role in the shaping of different cognitive functions in primates. We argue that the increase in the complexity of the motor system has contributed to the emergence of new abilities observed in human and nonhuman primates, including the recognition and imitation of the actions of others, speech perception and production, and the execution and appreciation of the rhythmic structure of music. Copyright © 2014 Elsevier Ltd. All rights reserved.

Magnetic exchange couplings from noncollinear perturbation theory: dinuclear CuII complexes.

PubMed

Phillips, Jordan J; Peralta, Juan E

2014-08-07

To benchmark the performance of a new method based on noncollinear coupled-perturbed density functional theory [J. Chem. Phys. 138, 174115 (2013)], we calculate the magnetic exchange couplings in a series of triply bridged ferromagnetic dinuclear Cu(II) complexes that have been recently synthesized [Phys. Chem. Chem. Phys. 15, 1966 (2013)]. We find that for any basis-set the couplings from our noncollinear coupled-perturbed methodology are practically identical to those of spin-projected energy-differences when a hybrid density functional approximation is employed. This demonstrates that our methodology properly recovers a Heisenberg description for these systems, and is robust in its predictive power of magnetic couplings. Furthermore, this indicates that the failure of density functional theory to capture the subtle variation of the exchange couplings in these complexes is not simply an artifact of broken-symmetry methods, but rather a fundamental weakness of current approximate density functionals for the description of magnetic couplings.

Continually emerging mechanistic complexity of the multi-enzyme cellulosome complex.

PubMed

Smith, Steven P; Bayer, Edward A; Czjzek, Mirjam

2017-06-01

The robust plant cell wall polysaccharide-degrading properties of anaerobic bacteria are harnessed within elegant, marcomolecular assemblages called cellulosomes, in which proteins of complementary activities amass on scaffold protein networks. Research efforts have focused and continue to focus on providing detailed mechanistic insights into cellulosomal complex assembly, topology, and function. The accumulated information is expanding our fundamental understanding of the lignocellulosic biomass decomposition process and enhancing the potential of engineered cellulosomal systems for biotechnological purposes. Ongoing biochemical studies continue to reveal unexpected functional diversity within traditional cellulase families. Genomic, proteomic, and functional analyses have uncovered unanticipated cellulosomal proteins that augment the function of the native and designer cellulosomes. In addition, complementary structural and computational methods are continuing to provide much needed insights on the influence of cellulosomal interdomain linker regions on cellulosomal assembly and activity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Development of curcumin-cyclodextrin/cellulose nanocrystals complexes: New anticancer drug delivery systems.

PubMed

Ndong Ntoutoume, Gautier M A; Granet, Robert; Mbakidi, Jean Pierre; Brégier, Frédérique; Léger, David Y; Fidanzi-Dugas, Chloë; Lequart, Vincent; Joly, Nicolas; Liagre, Bertrand; Chaleix, Vincent; Sol, Vincent

2016-02-01

The synthesis of curcumin-cyclodextrin/cellulose nanocrystals (CNCx) nano complexes was performed. CNCx were functionalized by ionic association with cationic β-cyclodextrin (CD) and CD/CNCx complexes were used to encapsulate curcumin. Preliminary in vitro results showed that the resulting curcumin-CD/CNCx complexes exerted antiproliferative effect on colorectal and prostatic cancer cell lines, with IC50s lower than that of curcumin alone. Copyright © 2015 Elsevier Ltd. All rights reserved.

Renewal Processes in the Critical Brain

NASA Astrophysics Data System (ADS)

Allegrini, Paolo; Paradisi, Paolo; Menicucci, Danilo; Gemignani, Angelo

We describe herein a multidisciplinary research, as it developes and applies concepts of the theory of complexity, in turn stemming from recent advancements of statistical physics, onto cognitive neuroscience. We discuss (define) complexity, and how the human brain is a paradigm of it. We discuss how the hypothesis of brain activity dynamically behaving as a critical system is taking momentum in literature, then we focus on a feature of critical systems (hence of the brain), which is the intermittent passage between metastable states, marked by events, locally resetting the memory, but giving rise to correlation functions with infinite correlation times. The events, extracted from multi-channel ElectroEncephaloGrams, mark (are interpreted as) a birth/death process of cooperation, namely of system elements being recruited into collective states. Finally we discuss a recently discovered form of control (in the form of a new Linear Response Theory), that allows an optimized information transmission between complex systems, named Complexity Matching.

The role of TREX in gene expression and disease

PubMed Central

Heath, Catherine G.; Viphakone, Nicolas; Wilson, Stuart A.

2016-01-01

TRanscription and EXport (TREX) is a conserved multisubunit complex essential for embryogenesis, organogenesis and cellular differentiation throughout life. By linking transcription, mRNA processing and export together, it exerts a physiologically vital role in the gene expression pathway. In addition, this complex prevents DNA damage and regulates the cell cycle by ensuring optimal gene expression. As the extent of TREX activity in viral infections, amyotrophic lateral sclerosis and cancer emerges, the need for a greater understanding of TREX function becomes evident. A complete elucidation of the composition, function and interactions of the complex will provide the framework for understanding the molecular basis for a variety of diseases. This review details the known composition of TREX, how it is regulated and its cellular functions with an emphasis on mammalian systems. PMID:27679854

Guiding principles for peptide nanotechnology through directed discovery.

PubMed

Lampel, A; Ulijn, R V; Tuttle, T

2018-05-21

Life's diverse molecular functions are largely based on only a small number of highly conserved building blocks - the twenty canonical amino acids. These building blocks are chemically simple, but when they are organized in three-dimensional structures of tremendous complexity, new properties emerge. This review explores recent efforts in the directed discovery of functional nanoscale systems and materials based on these same amino acids, but that are not guided by copying or editing biological systems. The review summarises insights obtained using three complementary approaches of searching the sequence space to explore sequence-structure relationships for assembly, reactivity and complexation, namely: (i) strategic editing of short peptide sequences; (ii) computational approaches to predicting and comparing assembly behaviours; (iii) dynamic peptide libraries that explore the free energy landscape. These approaches give rise to guiding principles on controlling order/disorder, complexation and reactivity by peptide sequence design.

Modeling fluctuations in default-mode brain network using a spiking neural network.

PubMed

Yamanishi, Teruya; Liu, Jian-Qin; Nishimura, Haruhiko

2012-08-01

Recently, numerous attempts have been made to understand the dynamic behavior of complex brain systems using neural network models. The fluctuations in blood-oxygen-level-dependent (BOLD) brain signals at less than 0.1 Hz have been observed by functional magnetic resonance imaging (fMRI) for subjects in a resting state. This phenomenon is referred to as a "default-mode brain network." In this study, we model the default-mode brain network by functionally connecting neural communities composed of spiking neurons in a complex network. Through computational simulations of the model, including transmission delays and complex connectivity, the network dynamics of the neural system and its behavior are discussed. The results show that the power spectrum of the modeled fluctuations in the neuron firing patterns is consistent with the default-mode brain network's BOLD signals when transmission delays, a characteristic property of the brain, have finite values in a given range.

[System of technical facilities for equipping the anesthesiologist's work place in the operating room].

PubMed

Burlakov, R I; Iurevich, V M

1981-01-01

The authors proved the advisability of complex technical provision for certain functional cycles, or parts of medical technological process. The example given is a modification of working place for anesthesiologist at the operating theatre. Principle and additional devices included in the complex are specified.

Risk analysis with a fuzzy-logic approach of a complex installation

NASA Astrophysics Data System (ADS)

Peikert, Tim; Garbe, Heyno; Potthast, Stefan

2016-09-01

This paper introduces a procedural method based on fuzzy logic to analyze systematic the risk of an electronic system in an intentional electromagnetic environment (IEME). The method analyzes the susceptibility of a complex electronic installation with respect to intentional electromagnetic interference (IEMI). It combines the advantages of well-known techniques as fault tree analysis (FTA), electromagnetic topology (EMT) and Bayesian networks (BN) and extends the techniques with an approach to handle uncertainty. This approach uses fuzzy sets, membership functions and fuzzy logic to handle the uncertainty with probability functions and linguistic terms. The linguistic terms add to the risk analysis the knowledge from experts of the investigated system or environment.

Molecular dynamics simulations of large macromolecular complexes.

PubMed

Perilla, Juan R; Goh, Boon Chong; Cassidy, C Keith; Liu, Bo; Bernardi, Rafael C; Rudack, Till; Yu, Hang; Wu, Zhe; Schulten, Klaus

2015-04-01

Connecting dynamics to structural data from diverse experimental sources, molecular dynamics simulations permit the exploration of biological phenomena in unparalleled detail. Advances in simulations are moving the atomic resolution descriptions of biological systems into the million-to-billion atom regime, in which numerous cell functions reside. In this opinion, we review the progress, driven by large-scale molecular dynamics simulations, in the study of viruses, ribosomes, bioenergetic systems, and other diverse applications. These examples highlight the utility of molecular dynamics simulations in the critical task of relating atomic detail to the function of supramolecular complexes, a task that cannot be achieved by smaller-scale simulations or existing experimental approaches alone. Copyright © 2015 Elsevier Ltd. All rights reserved.

Energy-density field approach for low- and medium-frequency vibroacoustic analysis of complex structures using a statistical computational model

NASA Astrophysics Data System (ADS)

Kassem, M.; Soize, C.; Gagliardini, L.

2009-06-01

In this paper, an energy-density field approach applied to the vibroacoustic analysis of complex industrial structures in the low- and medium-frequency ranges is presented. This approach uses a statistical computational model. The analyzed system consists of an automotive vehicle structure coupled with its internal acoustic cavity. The objective of this paper is to make use of the statistical properties of the frequency response functions of the vibroacoustic system observed from previous experimental and numerical work. The frequency response functions are expressed in terms of a dimensionless matrix which is estimated using the proposed energy approach. Using this dimensionless matrix, a simplified vibroacoustic model is proposed.

Complexes of the ATP-dependent Lon protease and DNA aptamers with G-quadruplexes as a model for developing a nanosensor biomagnetic immunoassay system

NASA Astrophysics Data System (ADS)

Spiridonova, V. A.; Sizov, V. A.; Kuzmenko, E. O.; Melnichuk, A. V.; Oleinichenko, E. A.; Kudzhaev, A. M.; Rotanova, T. V.; Snigirev, O. V.

2017-07-01

The binding to Lon protease through biotinylated aptamers whose structures contain G-quadruplex fragments with magnetic nanoparticles (MNPs) functionalized by streptavidin was investigated. The conditions of binding of target aptamers to MNPs are met. The resulting complexes are proposed for detection of Lon protease in different biological sources and for constructing a novel biomagnetic nanosensor immunoassay system.

A Database Management System for Interlibrary Loan.

ERIC Educational Resources Information Center

Chang, Amy

1990-01-01

Discusses the increasing complexity of dealing with interlibrary loan requests and describes a database management system for interlibrary loans used at Texas Tech University. System functions are described, including file control, records maintenance, and report generation, and the impact on staff productivity is discussed. (CLB)

Representation of Complex Spectra in Auditory Cortex

DTIC Science & Technology

1997-01-01

predict the response to any broadband dynamic sound. Fourier Transform Inverse Transform ∫ [.] exp(±2πjΩx±2πjwt) 2 1 2 / 1 1 a 2 1 2 / 1 1 a...Systems Research University of Maryland Spectro-Temporal Transform Ω wx = log f t w = “ripple velocity” Ω = “ripple frequency” Fourier Transform Inverse ... Transform ∫ [.] exp(±2πjΩx±2πjwt) Real functions in the spectro-temporal domain give rise to complex conjugate symmetric functions in the Fourier

Frequency domain system identification of helicopter rotor dynamics incorporating models with time periodic coefficients

NASA Astrophysics Data System (ADS)

Hwang, Sunghwan

1997-08-01

One of the most prominent features of helicopter rotor dynamics in forward flight is the periodic coefficients in the equations of motion introduced by the rotor rotation. The frequency response characteristics of such a linear time periodic system exhibits sideband behavior, which is not the case for linear time invariant systems. Therefore, a frequency domain identification methodology for linear systems with time periodic coefficients was developed, because the linear time invariant theory cannot account for sideband behavior. The modulated complex Fourier series was introduced to eliminate the smearing effect of Fourier series expansions of exponentially modulated periodic signals. A system identification theory was then developed using modulated complex Fourier series expansion. Correlation and spectral density functions were derived using the modulated complex Fourier series expansion for linear time periodic systems. Expressions of the identified harmonic transfer function were then formulated using the spectral density functions both with and without additive noise processes at input and/or output. A procedure was developed to identify parameters of a model to match the frequency response characteristics between measured and estimated harmonic transfer functions by minimizing an objective function defined in terms of the trace of the squared frequency response error matrix. Feasibility was demonstrated by the identification of the harmonic transfer function and parameters for helicopter rigid blade flapping dynamics in forward flight. This technique is envisioned to satisfy the needs of system identification in the rotating frame, especially in the context of individual blade control. The technique was applied to the coupled flap-lag-inflow dynamics of a rigid blade excited by an active pitch link. The linear time periodic technique results were compared with the linear time invariant technique results. Also, the effect of noise processes and initial parameter guess on the identification procedure were investigated. To study the effect of elastic modes, a rigid blade with a trailing edge flap excited by a smart actuator was selected and system parameters were successfully identified, but with some expense of computational storage and time. Conclusively, the linear time periodic technique substantially improved the identified parameter accuracy compared to the linear time invariant technique. Also, the linear time periodic technique was robust to noises and initial guess of parameters. However, an elastic mode of higher frequency relative to the system pumping frequency tends to increase the computer storage requirement and computing time.

Flexible endoscopes: structure and function: the endoscopic retrograde cholangiopancreatography elevator system.

PubMed

Holland, Pat; Shoop, Nancy M

2002-01-01

Flexible endoscopes are complex medical instruments that are easily damaged. In order to maintain the flexible endoscope in optimum working condition, the user must have a thorough understanding of the structure and function of the instrument. This is the fourth in a series of articles presenting an in-depth look at the care and handling of the flexible endoscope. The first three articles discussed the air-water system, the suction channel system, and the mechanical system. This article will focus specifically on the endoscopic retrograde cholangiopancreatography elevator system.

Strategic optimisation of microgrid by evolving a unitised regenerative fuel cell system operational criterion

NASA Astrophysics Data System (ADS)

Bhansali, Gaurav; Singh, Bhanu Pratap; Kumar, Rajesh

2016-09-01

In this paper, the problem of microgrid optimisation with storage has been addressed in an unaccounted way rather than confining it to loss minimisation. Unitised regenerative fuel cell (URFC) systems have been studied and employed in microgrids to store energy and feed it back into the system when required. A value function-dependent on line losses, URFC system operational cost and stored energy at the end of the day are defined here. The function is highly complex, nonlinear and multi dimensional in nature. Therefore, heuristic optimisation techniques in combination with load flow analysis are used here to resolve the network and time domain complexity related with the problem. Particle swarm optimisation with the forward/backward sweep algorithm ensures optimal operation of microgrid thereby minimising the operational cost of the microgrid. Results are shown and are found to be consistently improving with evolution of the solution strategy.

Flight Testing the Rotor Systems Research Aircraft (RSRA)

NASA Technical Reports Server (NTRS)

Hall, G. W.; Merrill, R. K.

1983-01-01

In the late 1960s, efforts to advance the state-of-the-art in rotor systems technology indicated a significant gap existed between our ability to accurately predict the characteristics of a complex rotor system and the results obtained through flight verification. Even full scale wind tunnel efforts proved inaccurate because of the complex nature of a rotating, maneuvering rotor system. The key element missing, which prevented significant advances, was our inability to precisely measure the exact rotor state as a function of time and flight condition. Two Rotor Research Aircraft (RSRA) were designed as pure research aircraft and dedicated rotor test vehicles whose function is to fill the gap between theory, wind tunnel testing, and flight verification. The two aircraft, the development of the piloting techniques required to safely fly the compound helicopter, the government flight testing accomplished to date, and proposed future research programs.

Molecular gearing systems

DOE PAGES

Gakh, Andrei A.; Sachleben, Richard A.; Bryan, Jeff C.

1997-11-01

The race to create smaller devices is fueling much of the research in electronics. The competition has intensified with the advent of microelectromechanical systems (MEMS), in which miniaturization is already reaching the dimensional limits imposed by physics of current lithographic techniques. Also, in the realm of biochemistry, evidence is accumulating that certain enzyme complexes are capable of very sophisticated modes of motion. Complex synergistic biochemical complexes driven by sophisticated biomechanical processes are quite common. Their biochemical functions are based on the interplay of mechanical and chemical processes, including allosteric effects. In addition, the complexity of this interplay far exceeds thatmore » of typical chemical reactions. Understanding the behavior of artificial molecular devices as well as complex natural molecular biomechanical systems is difficult. Fortunately, the problem can be successfully resolved by direct molecular engineering of simple molecular systems that can mimic desired mechanical or electronic devices. These molecular systems are called technomimetics (the name is derived, by analogy, from biomimetics). Several classes of molecular systems that can mimic mechanical, electronic, or other features of macroscopic devices have been successfully synthesized by conventional chemical methods during the past two decades. In this article we discuss only one class of such model devices: molecular gearing systems.« less

Employment of sawtooth-shaped-function excitation signal and oversampling for improving resistance measurement accuracy

NASA Astrophysics Data System (ADS)

Lin, Ling; Li, Shujuan; Yan, Wenjuan; Li, Gang

2016-10-01

In order to achieve higher measurement accuracy of routine resistance without increasing the complexity and cost of the system circuit of existing methods, this paper presents a novel method that exploits a shaped-function excitation signal and oversampling technology. The excitation signal source for resistance measurement is modulated by the sawtooth-shaped-function signal, and oversampling technology is employed to increase the resolution and the accuracy of the measurement system. Compared with the traditional method of using constant amplitude excitation signal, this method can effectively enhance the measuring accuracy by almost one order of magnitude and reduce the root mean square error by 3.75 times under the same measurement conditions. The results of experiments show that the novel method can attain the aim of significantly improve the measurement accuracy of resistance on the premise of not increasing the system cost and complexity of the circuit, which is significantly valuable for applying in electronic instruments.

Forward design of a complex enzyme cascade reaction

PubMed Central

Hold, Christoph; Billerbeck, Sonja; Panke, Sven

2016-01-01

Enzymatic reaction networks are unique in that one can operate a large number of reactions under the same set of conditions concomitantly in one pot, but the nonlinear kinetics of the enzymes and the resulting system complexity have so far defeated rational design processes for the construction of such complex cascade reactions. Here we demonstrate the forward design of an in vitro 10-membered system using enzymes from highly regulated biological processes such as glycolysis. For this, we adapt the characterization of the biochemical system to the needs of classical engineering systems theory: we combine online mass spectrometry and continuous system operation to apply standard system theory input functions and to use the detailed dynamic system responses to parameterize a model of sufficient quality for forward design. This allows the facile optimization of a 10-enzyme cascade reaction for fine chemical production purposes. PMID:27677244

SEU System Analysis: Not Just the Sum of All Parts

NASA Technical Reports Server (NTRS)

Berg, Melanie D.; Label, Kenneth

2014-01-01

Single event upset (SEU) analysis of complex systems is challenging. Currently, system SEU analysis is performed by component level partitioning and then either: the most dominant SEU cross-sections (SEUs) are used in system error rate calculations; or the partition SEUs are summed to eventually obtain a system error rate. In many cases, system error rates are overestimated because these methods generally overlook system level derating factors. The problem with overestimating is that it can cause overdesign and consequently negatively affect the following: cost, schedule, functionality, and validation/verification. The scope of this presentation is to discuss the risks involved with our current scheme of SEU analysis for complex systems; and to provide alternative methods for improvement.

Functional Genomics Assistant (FUGA): a toolbox for the analysis of complex biological networks

PubMed Central

2011-01-01

Background Cellular constituents such as proteins, DNA, and RNA form a complex web of interactions that regulate biochemical homeostasis and determine the dynamic cellular response to external stimuli. It follows that detailed understanding of these patterns is critical for the assessment of fundamental processes in cell biology and pathology. Representation and analysis of cellular constituents through network principles is a promising and popular analytical avenue towards a deeper understanding of molecular mechanisms in a system-wide context. Findings We present Functional Genomics Assistant (FUGA) - an extensible and portable MATLAB toolbox for the inference of biological relationships, graph topology analysis, random network simulation, network clustering, and functional enrichment statistics. In contrast to conventional differential expression analysis of individual genes, FUGA offers a framework for the study of system-wide properties of biological networks and highlights putative molecular targets using concepts of systems biology. Conclusion FUGA offers a simple and customizable framework for network analysis in a variety of systems biology applications. It is freely available for individual or academic use at http://code.google.com/p/fuga. PMID:22035155

Forms of adsorption and transition states of oxidation of carbon monoxide by molecular oxygen and dissociation of nitrogen monooxide, catalyzed by monovalent copper

NASA Astrophysics Data System (ADS)

Ermakov, A. I.; Mashutin, V. Y.; Vishnjakov, A. V.

With the help of the results of semiempirical (parametric method 3) and ab initio (second-order Møller-Plesset [MP2] unrestricted Hartree-Fock [UHF] 6-31G**, unrestricted density functional theory [UDFT] 6-31G** Becke's three-parameter exchange functional and the gradient-corrected functional of Lee, Yang, and Paar [B3LYP] and UDFT LANL2DZ B3LYP) quantum-chemical calculations has been studied the complexation CO and NO with molecular hydroxide of copper(I). The influence of charge defects has been simulated by the calculations of anionic, neutral, and cationic systems. It is shown that CO and NO are mainly coordinated by nonoxygen atom on an atom of copper(I) hydroxide as one- and two-center forms. These forms are suitable for appearance of prereactionary complexes of catalytic oxidation CO by molecular oxygen and decomposition NO into atoms of nitrogen and oxygen. The corresponding prereactionary complexes for systems with participation of copper(II) hydroxide and copper(III) hydroxide are not revealed. The calculations predict inhibiting impact of copper(II) and copper(III) of the observed reactions. Computed stability of complexes CO and NO with copper(I) hydroxide and activation energy of catalytic conversion of monooxides essentially depend on an excessive charge of the system. Introduction of electron-donating additives into copper(I) hydroxide promotes rise of catalytic activity of copper(I) compound.

Tuberous sclerosis complex: Recent advances in manifestations and therapy.

PubMed

Wataya-Kaneda, Mari; Uemura, Motohide; Fujita, Kazutoshi; Hirata, Haruhiko; Osuga, Keigo; Kagitani-Shimono, Kuriko; Nonomura, Norio

2017-09-01

Tuberous sclerosis complex is an autosomal dominant inherited disorder characterized by generalized involvement and variable manifestations with a birth incidence of 1:6000. In a quarter of a century, significant progress in tuberous sclerosis complex has been made. Two responsible genes, TSC1 and TSC2, which encode hamartin and tuberin, respectively, were discovered in the 1990s, and their functions were elucidated in the 2000s. Hamartin-Tuberin complex is involved in the phosphoinositide 3-kinase-protein kinase B-mammalian target of rapamycin signal transduction pathway, and suppresses mammalian target of rapamycin complex 1 activity, which is a center for various functions. Constitutive activation of mammalian target of rapamycin complex 1 causes variable manifestations in tuberous sclerosis complex. Recently, genetic tests were launched to diagnose tuberous sclerosis complex, and mammalian target of rapamycin complex 1 inhibitors are being used to treat tuberous sclerosis complex patients. As a result of these advances, new diagnostic criteria have been established and an indispensable new treatment method; that is, "a cross-sectional medical examination system," a system to involve many experts for tuberous sclerosis complex diagnosis and treatments, was also created. Simultaneously, the frequency of genetic tests and advances in diagnostic technology have resulted in new views on symptoms. The numbers of tuberous sclerosis complex patients without neural symptoms are increasing, and for these patients, renal manifestations and pulmonary lymphangioleiomyomatosis have become important manifestations. New concepts of tuberous sclerosis complex-associated neuropsychiatric disorders or perivascular epithelioid cell tumors are being created. The present review contains a summary of recent advances, significant manifestations and therapy in tuberous sclerosis complex. © 2017 The Japanese Urological Association.

Conditions for Fully Autonomous Anticipation

NASA Astrophysics Data System (ADS)

Collier, John

2006-06-01

Anticipation allows a system to adapt to conditions that have not yet come to be, either externally to the system or internally. Autonomous systems actively control the conditions of their own existence so as to increase their overall viability. This paper will first give minimal necessary and sufficient conditions for autonomous anticipation, followed by a taxonomy of autonomous anticipation. In more complex systems, there can be semi-autonomous subsystems that can anticipate and adapt on their own. Such subsystems can be integrated into a system's overall autonomy, typically with greater efficiency due to modularity and specialization of function. However, it is also possible that semi-autonomous subsystems can act against the viability of the overall system, and have their own functions that conflict with overall system functions.

Endobiogeny: a global approach to systems biology (part 2 of 2).

PubMed

Lapraz, Jean-Claude; Hedayat, Kamyar M; Pauly, Patrice

2013-03-01

ENDOBIOGENY AND THE BIOLOGY OF FUNCTIONS ARE BASED ON FOUR SCIENTIFIC CONCEPTS THAT ARE KNOWN AND GENERALLY ACCEPTED: (1) human physiology is complex and multifactorial and exhibits the properties of a system; (2) the endocrine system manages metabolism, which is the basis of the continuity of life; (3) the metabolic activity managed by the endocrine system results in the output of biomarkers that reflect the functional achievement of specific aspects of metabolism; and (4) when biomarkers are related to each other in ratios, it contextualizes one type of function relative to another to which is it linked anatomically, sequentially, chronologically, biochemically, etc.

Engineering Complex Embedded Systems with State Analysis and the Mission Data System

NASA Technical Reports Server (NTRS)

Ingham, Michel D.; Rasmussen, Robert D.; Bennett, Matthew B.; Moncada, Alex C.

2004-01-01

It has become clear that spacecraft system complexity is reaching a threshold where customary methods of control are no longer affordable or sufficiently reliable. At the heart of this problem are the conventional approaches to systems and software engineering based on subsystem-level functional decomposition, which fail to scale in the tangled web of interactions typically encountered in complex spacecraft designs. Furthermore, there is a fundamental gap between the requirements on software specified by systems engineers and the implementation of these requirements by software engineers. Software engineers must perform the translation of requirements into software code, hoping to accurately capture the systems engineer's understanding of the system behavior, which is not always explicitly specified. This gap opens up the possibility for misinterpretation of the systems engineer s intent, potentially leading to software errors. This problem is addressed by a systems engineering methodology called State Analysis, which provides a process for capturing system and software requirements in the form of explicit models. This paper describes how requirements for complex aerospace systems can be developed using State Analysis and how these requirements inform the design of the system software, using representative spacecraft examples.

Long-term immunologically competent human peripheral lymphoid tissue cultures in a 3D bioreactor

PubMed Central

Kuzin, Igor; Sun, Hongliang; Moshkani, Safiekhatoon; Feng, Changyong; Mantalaris, Athanasios; Wu, JH David; Bottaro, Andrea

2011-01-01

Peripheral lymphoid organs (PLOs), the primary sites of development of adaptive immune responses, display a complex structural organization reflecting separation of cellular subsets (e.g. T and B lymphocytes) and functional compartments which is critical for immune function. The generation of in vitro culture systems capable of recapitulating salient features of PLOs for experimental, biotechnological and clinical applications would be highly desirable, but has been hampered so far by the complexity of these systems. We have previously developed a three-dimensional bioreactor system for long-term, functional culture of human bone marrow cells on macroporous microspheres in a packed-bed bioreactor with frequent medium change. Here we adapt the same system for culture of human primary cells from PLOs (tonsil) in the absence of specific exogenous growth factors or activators. Cells in this system displayed higher viability over several weeks, and maintain population diversity and cell surface markers largely comparable to primary cells. Light microscopy showed cells organizing in large diverse clusters within the scaffold pores and presence of B cell-enriched areas. Strikingly, these cultures generated a significant number of antibody-producing B cells when challenged with a panel of diverse antigens, as expected from a lymphoid tissue. Thus the three-dimensional tonsil bioreactor culture system may serve as a useful model of PLOs by recapitulating their structural organization and function ex vivo. PMID:21309085

Long-term immunologically competent human peripheral lymphoid tissue cultures in a 3D bioreactor.

PubMed

Kuzin, Igor; Sun, Hongliang; Moshkani, Safiekhatoon; Feng, Changyong; Mantalaris, Athanasios; Wu, J H David; Bottaro, Andrea

2011-06-01

Peripheral lymphoid organs (PLOs), the primary sites of development of adaptive immune responses, display a complex structural organization reflecting separation of cellular subsets (e.g., T and B lymphocytes) and functional compartments which is critical for immune function. The generation of in vitro culture systems capable of recapitulating salient features of PLOs for experimental, biotechnological, and clinical applications would be highly desirable, but has been hampered so far by the complexity of these systems. We have previously developed a three-dimensional bioreactor system for long-term, functional culture of human bone marrow cells on macroporous microspheres in a packed-bed bioreactor with frequent medium change. Here we adapt the same system for culture of human primary cells from PLOs (tonsil) in the absence of specific exogenous growth factors or activators. Cells in this system displayed higher viability over several weeks, and maintain population diversity and cell surface markers largely comparable to primary cells. Light microscopy showed cells organizing in large diverse clusters within the scaffold pores and presence of B cell-enriched areas. Strikingly, these cultures generated a significant number of antibody-producing B cells when challenged with a panel of diverse antigens, as expected from a lymphoid tissue. Thus the three-dimensional tonsil bioreactor culture system may serve as a useful model of PLOs by recapitulating their structural organization and function ex vivo. Copyright © 2011 Wiley Periodicals, Inc.

Neuroprotective Effects and Mechanisms of Curcumin-Cu(II) and -Zn(II) Complexes Systems and Their Pharmacological Implications.

PubMed

Yan, Fa-Shun; Sun, Jian-Long; Xie, Wen-Hai; Shen, Liang; Ji, Hong-Fang

2017-12-28

Alzheimer's disease (AD) is the main form of dementia and has a steadily increasing prevalence. As both oxidative stress and metal homeostasis are involved in the pathogenesis of AD, it would be interesting to develop a dual function agent, targeting the two factors. Curcumin, a natural compound isolated from the rhizome of Curcuma longa , is an antioxidant and can also chelate metal ions. Whether the complexes of curcumin with metal ions possess neuroprotective effects has not been evaluated. Therefore, the present study was designed to investigate the protective effects of the complexes of curcumin with Cu(II) or Zn(II) on hydrogen peroxide (H₂O₂)-induced injury and the underlying molecular mechanisms. The use of rat pheochromocytoma (PC12) cells, a widely used neuronal cell model system, was adopted. It was revealed that curcumin-Cu(II) complexes systems possessed enhanced O₂ ·- -scavenging activities compared to unchelated curcumin. In comparison with unchelated curcumin, the protective effects of curcumin-Cu(II) complexes systems were stronger than curcumin-Zn(II) system. Curcumin-Cu(II) or -Zn(II) complexes systems significantly enhanced the superoxide dismutase, catalase, and glutathione peroxidase activities and attenuated the increase of malondialdehyde levels and caspase-3 and caspase-9 activities, in a dose-dependent manner. The curcumin-Cu(II) complex system with a 2:1 ratio exhibited the most significant effect. Further mechanistic study demonstrated that curcumin-Cu(II) or -Zn(II) complexes systems inhibited cell apoptosis via downregulating the nuclear factor κB (NF-κB) pathway and upregulating Bcl-2/Bax pathway. In summary, the present study found that curcumin-Cu(II) or -Zn(II) complexes systems, especially the former, possess significant neuroprotective effects, which indicates the potential advantage of curcumin as a promising agent against AD and deserves further study.

CRISPR-Cas Adaptive Immune Systems of the Sulfolobales: Unravelling Their Complexity and Diversity

PubMed Central

Garrett, Roger A.; Shah, Shiraz A.; Erdmann, Susanne; Liu, Guannan; Mousaei, Marzieh; León-Sobrino, Carlos; Peng, Wenfang; Gudbergsdottir, Soley; Deng, Ling; Vestergaard, Gisle; Peng, Xu; She, Qunxin

2015-01-01

The Sulfolobales have provided good model organisms for studying CRISPR-Cas systems of the crenarchaeal kingdom of the archaea. These organisms are infected by a wide range of exceptional archaea-specific viruses and conjugative plasmids, and their CRISPR-Cas systems generally exhibit extensive structural and functional diversity. They carry large and multiple CRISPR loci and often multiple copies of diverse Type I and Type III interference modules as well as more homogeneous adaptation modules. These acidothermophilic organisms have recently provided seminal insights into both the adaptation process, the diverse modes of interference, and their modes of regulation. The functions of the adaptation and interference modules tend to be loosely coupled and the stringency of the crRNA-DNA sequence matching during DNA interference is relatively low, in contrast to some more streamlined CRISPR-Cas systems of bacteria. Despite this, there is evidence for a complex and differential regulation of expression of the diverse functional modules in response to viral infection. Recent work also supports critical roles for non-core Cas proteins, especially during Type III-directed interference, and this is consistent with these proteins tending to coevolve with core Cas proteins. Various novel aspects of CRISPR-Cas systems of the Sulfolobales are considered including an alternative spacer acquisition mechanism, reversible spacer acquisition, the formation and significance of antisense CRISPR RNAs, and a novel mechanism for avoidance of CRISPR-Cas defense. Finally, questions regarding the basis for the complexity, diversity, and apparent redundancy, of the intracellular CRISPR-Cas systems are discussed. PMID:25764276

Hydrogen exchange mass spectrometry of functional membrane-bound chemotaxis receptor complexes.

PubMed

Koshy, Seena S; Eyles, Stephen J; Weis, Robert M; Thompson, Lynmarie K

2013-12-10

The transmembrane signaling mechanism of bacterial chemotaxis receptors is thought to involve changes in receptor conformation and dynamics. The receptors function in ternary complexes with two other proteins, CheA and CheW, that form extended membrane-bound arrays. Previous studies have shown that attractant binding induces a small (∼2 Å) piston displacement of one helix of the periplasmic and transmembrane domains toward the cytoplasm, but it is not clear how this signal propagates through the cytoplasmic domain to control the kinase activity of the CheA bound at the membrane-distal tip, nearly 200 Å away. The cytoplasmic domain has been shown to be highly dynamic, which raises the question of how a small piston motion could propagate through a dynamic domain to control CheA kinase activity. To address this, we have developed a method for measuring dynamics of the receptor cytoplasmic fragment (CF) in functional complexes with CheA and CheW. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) measurements of global exchange of the CF demonstrate that the CF exhibits significantly slower exchange in functional complexes than in solution. Because the exchange rates in functional complexes are comparable to those of other proteins with similar structures, the CF appears to be a well-structured protein within these complexes, which is compatible with its role in propagating a signal that appears to be a tiny conformational change in the periplasmic and transmembrane domains of the receptor. We also demonstrate the feasibility of this protocol for local exchange measurements by incorporating a pepsin digest step to produce peptides with 87% sequence coverage and only 20% back exchange. This method extends HDX-MS to membrane-bound functional complexes without detergents that may perturb the stability or structure of the system.

Hydrogen Exchange Mass Spectrometry of Functional Membrane-bound Chemotaxis Receptor Complexes

PubMed Central

Koshy, Seena S.; Eyles, Stephen J.; Weis, Robert M.; Thompson, Lynmarie K.

2014-01-01

The transmembrane signaling mechanism of bacterial chemotaxis receptors is thought to involve changes in receptor conformation and dynamics. The receptors function in ternary complexes with two other proteins, CheA and CheW, that form extended membrane-bound arrays. Previous studies have shown that attractant binding induces a small (~2 Å) piston displacement of one helix of the periplasmic and transmembrane domains towards the cytoplasm, but it is not clear how this signal propagates through the cytoplasmic domain to control the kinase activity of the CheA bound at the membrane-distal tip, nearly 200 Å away. The cytoplasmic domain has been shown to be highly dynamic, which raises the question of how a small piston motion could propagate through a dynamic domain to control CheA kinase activity. To address this, we have developed a method for measuring dynamics of the receptor cytoplasmic fragment (CF) in functional complexes with CheA and CheW. Hydrogen exchange mass spectrometry (HDX-MS) measurements of global exchange of CF demonstrate that CF exhibits significantly slower exchange in functional complexes than in solution. Since the exchange rates in functional complexes are comparable to that of other proteins of similar structure, the CF appears to be a well-structured protein within these complexes, which is compatible with its role in propagating a signal that appears to be a tiny conformational change in the periplasmic and transmembrane domains of the receptor. We also demonstrate the feasibility of this protocol for local exchange measurements, by incorporating a pepsin digest step to produce peptides with 87% sequence coverage and only 20% back exchange. This method extends HDX-MS to membrane-bound functional complexes without detergents that may perturb the stability or structure of the system. PMID:24274333

Multiscale entropy-based methods for heart rate variability complexity analysis

NASA Astrophysics Data System (ADS)

Silva, Luiz Eduardo Virgilio; Cabella, Brenno Caetano Troca; Neves, Ubiraci Pereira da Costa; Murta Junior, Luiz Otavio

2015-03-01

Physiologic complexity is an important concept to characterize time series from biological systems, which associated to multiscale analysis can contribute to comprehension of many complex phenomena. Although multiscale entropy has been applied to physiological time series, it measures irregularity as function of scale. In this study we purpose and evaluate a set of three complexity metrics as function of time scales. Complexity metrics are derived from nonadditive entropy supported by generation of surrogate data, i.e. SDiffqmax, qmax and qzero. In order to access accuracy of proposed complexity metrics, receiver operating characteristic (ROC) curves were built and area under the curves was computed for three physiological situations. Heart rate variability (HRV) time series in normal sinus rhythm, atrial fibrillation, and congestive heart failure data set were analyzed. Results show that proposed metric for complexity is accurate and robust when compared to classic entropic irregularity metrics. Furthermore, SDiffqmax is the most accurate for lower scales, whereas qmax and qzero are the most accurate when higher time scales are considered. Multiscale complexity analysis described here showed potential to assess complex physiological time series and deserves further investigation in wide context.

Light-controlled resistors provide quadrature signal rejection for high-gain servo systems

NASA Technical Reports Server (NTRS)

Mc Cauley, D. D.

1967-01-01

Servo amplifier feedback system, in which the phase sensitive detection, low pass filtering, and multiplication functions required for quadrature rejection, are preformed by light-controlled photoresistors, eliminates complex circuitry. System increases gain, improves signal-to-noise ratio, and eliminates the necessity for compensation.

Analysis of Power Laws, Shape Collapses, and Neural Complexity: New Techniques and MATLAB Support via the NCC Toolbox.

PubMed

Marshall, Najja; Timme, Nicholas M; Bennett, Nicholas; Ripp, Monica; Lautzenhiser, Edward; Beggs, John M

2016-01-01

Neural systems include interactions that occur across many scales. Two divergent methods for characterizing such interactions have drawn on the physical analysis of critical phenomena and the mathematical study of information. Inferring criticality in neural systems has traditionally rested on fitting power laws to the property distributions of "neural avalanches" (contiguous bursts of activity), but the fractal nature of avalanche shapes has recently emerged as another signature of criticality. On the other hand, neural complexity, an information theoretic measure, has been used to capture the interplay between the functional localization of brain regions and their integration for higher cognitive functions. Unfortunately, treatments of all three methods-power-law fitting, avalanche shape collapse, and neural complexity-have suffered from shortcomings. Empirical data often contain biases that introduce deviations from true power law in the tail and head of the distribution, but deviations in the tail have often been unconsidered; avalanche shape collapse has required manual parameter tuning; and the estimation of neural complexity has relied on small data sets or statistical assumptions for the sake of computational efficiency. In this paper we present technical advancements in the analysis of criticality and complexity in neural systems. We use maximum-likelihood estimation to automatically fit power laws with left and right cutoffs, present the first automated shape collapse algorithm, and describe new techniques to account for large numbers of neural variables and small data sets in the calculation of neural complexity. In order to facilitate future research in criticality and complexity, we have made the software utilized in this analysis freely available online in the MATLAB NCC (Neural Complexity and Criticality) Toolbox.

Exact density-potential pairs from complex-shifted axisymmetric systems

NASA Astrophysics Data System (ADS)

Ciotti, Luca; Marinacci, Federico

2008-07-01

In a previous paper, the complex-shift method has been applied to self-gravitating spherical systems, producing new analytical axisymmetric density-potential pairs. We now extend the treatment to the Miyamoto-Nagai disc and the Binney logarithmic halo, and we study the resulting axisymmetric and triaxial analytical density-potential pairs; we also show how to obtain the surface density of shifted systems from the complex shift of the surface density of the parent model. In particular, the systems obtained from Miyamoto-Nagai discs can be used to describe disc galaxies with a peanut-shaped bulge or with a central triaxial bar, depending on the direction of the shift vector. By using a constructive method that can be applied to generic axisymmetric systems, we finally show that the Miyamoto-Nagai and the Satoh discs, and the Binney logarithmic halo cannot be obtained from the complex shift of any spherical parent distribution. As a by-product of this study, we also found two new generating functions in closed form for even and odd Legendre polynomials, respectively.

Revisiting the Quantum Brain Hypothesis: Toward Quantum (Neuro)biology?

PubMed Central

Jedlicka, Peter

2017-01-01

The nervous system is a non-linear dynamical complex system with many feedback loops. A conventional wisdom is that in the brain the quantum fluctuations are self-averaging and thus functionally negligible. However, this intuition might be misleading in the case of non-linear complex systems. Because of an extreme sensitivity to initial conditions, in complex systems the microscopic fluctuations may be amplified and thereby affect the system’s behavior. In this way quantum dynamics might influence neuronal computations. Accumulating evidence in non-neuronal systems indicates that biological evolution is able to exploit quantum stochasticity. The recent rise of quantum biology as an emerging field at the border between quantum physics and the life sciences suggests that quantum events could play a non-trivial role also in neuronal cells. Direct experimental evidence for this is still missing but future research should address the possibility that quantum events contribute to an extremely high complexity, variability and computational power of neuronal dynamics. PMID:29163041

Discovery of a new method for potent drug development using power function of stoichiometry ofhomomeric biocomplexes or biological nanomotors

PubMed Central

Pi, Fengmei; Vieweger, Mario; Zhao, Zhengyi; Wang, Shaoying; Guo, Peixuan

2015-01-01

Introduction Multidrug resistance and the appearance of incurable diseases inspire the quest for potent therapeutics. Areas Covered We review a new methodology in designing potent drugs by targeting multi-subunit homomeric biological motors, machines, or complexes with Z>1 and K=1, where Z is the stoichiometry of the target, and K is the number of drugged subunits required to block the function of the complex. The condition is similar to a series, electrical circuit of Christmas decorations; failure of one light bulb causes the entire lighting system to lose power. In most multisubunit, homomeric biological systems, a sequential coordination or cooperative action mechanism is utilized, thus K equals 1. Drug inhibition depends on the ratio of drugged to nondrugged complexes. When K=1, and Z>1, the inhibition effect follows a power law with respect to Z, leading to enhanced drug potency. The hypothesis that the potency of drug inhibition depends on the stoichiometry of the targeted biological complexes was recently quantified by Yang-Hui's Triangle (or binomial distribution), and proved using a highly sensitive in vitro phi29 viral DNA packaging system. Examples of targeting homomeric bio-complexes with high stoichiometry for potent drug discovery are discussed. Expert Opinion Biomotors with multiple subunits are widespread in viruses, bacteria, and cells, making this approach generally applicable in the development of inhibition drugs with high efficiency. PMID:26307193

ISYMOD: a knowledge warehouse for the identification, assembly and analysis of bacterial integrated systems.

PubMed

Chabalier, Julie; Capponi, Cécile; Quentin, Yves; Fichant, Gwennaele

2005-04-01

Complex biological functions emerge from interactions between proteins in stable supra-molecular assemblies and/or through transitory contacts. Most of the time protein partners of the assemblies are composed of one or several domains which exhibit different biochemical functions. Thus the study of cellular process requires the identification of different functional units and their integration in an interaction network; such complexes are referred to as integrated systems. In order to exploit with optimum efficiency the increased release of data, automated bioinformatics strategies are needed to identify, reconstruct and model such systems. For that purpose, we have developed a knowledge warehouse dedicated to the representation and acquisition of bacterial integrated systems involved in the exchange of the bacterial cell with its environment. ISYMOD is a knowledge warehouse that consistently integrates in the same environment the data and the methods used for their acquisition. This is achieved through the construction of (1) a domain knowledge base (DKB) devoted to the storage of the knowledge about the systems, their functional specificities, their partners and how they are related and (2) a methodological knowledge base (MKB) which depicts the task layout used to identify and reconstruct functional integrated systems. Instantiation of the DKB is obtained by solving the tasks of the MKB, whereas some tasks need instances of the DKB to be solved. AROM, an object-based knowledge representation system, has been used to design the DKB, and its task manager, AROMTasks, for developing the MKB. In this study two integrated systems, ABC transporters and two component systems, both involved in adaptation processes of a bacterial cell to its biotope, have been used to evaluate the feasibility of the approach.

Acquisition Program Lead Systems Integration/Lead Capabilities Integration Decision Support Methodology and Tool

DTIC Science & Technology

2015-04-30

from the MIT Sloan School that provide a relative complexity score for functions (Product and Context Complexity). The PMA assesses the complexity...collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources...gathering and maintaining the data needed, and completing and reviewing the collection of information. Send comments regarding this burden estimate or

Applications of fidelity measures to complex quantum systems

PubMed Central

2016-01-01

We revisit fidelity as a measure for the stability and the complexity of the quantum motion of single-and many-body systems. Within the context of cold atoms, we present an overview of applications of two fidelities, which we call static and dynamical fidelity, respectively. The static fidelity applies to quantum problems which can be diagonalized since it is defined via the eigenfunctions. In particular, we show that the static fidelity is a highly effective practical detector of avoided crossings characterizing the complexity of the systems and their evolutions. The dynamical fidelity is defined via the time-dependent wave functions. Focusing on the quantum kicked rotor system, we highlight a few practical applications of fidelity measurements in order to better understand the large variety of dynamical regimes of this paradigm of a low-dimensional system with mixed regular–chaotic phase space. PMID:27140967

Tandem Affinity Purification of Protein Complexes from Eukaryotic Cells.

PubMed

Ma, Zheng; Fung, Victor; D'Orso, Iván

2017-01-26

The purification of active protein-protein and protein-nucleic acid complexes is crucial for the characterization of enzymatic activities and de novo identification of novel subunits and post-translational modifications. Bacterial systems allow for the expression and purification of a wide variety of single polypeptides and protein complexes. However, this system does not enable the purification of protein subunits that contain post-translational modifications (e.g., phosphorylation and acetylation), and the identification of novel regulatory subunits that are only present/expressed in the eukaryotic system. Here, we provide a detailed description of a novel, robust, and efficient tandem affinity purification (TAP) method using STREP- and FLAG-tagged proteins that facilitates the purification of protein complexes with transiently or stably expressed epitope-tagged proteins from eukaryotic cells. This protocol can be applied to characterize protein complex functionality, to discover post-translational modifications on complex subunits, and to identify novel regulatory complex components by mass spectrometry. Notably, this TAP method can be applied to study protein complexes formed by eukaryotic or pathogenic (viral and bacterial) components, thus yielding a wide array of downstream experimental opportunities. We propose that researchers working with protein complexes could utilize this approach in many different ways.

Endocrine system and obesity.

PubMed

Ashburn, Doyle D; Reed, Mary Jane

2010-10-01

Obesity is associated with significant alterations in endocrine function. An association with type 2 diabetes mellitus and dyslipidemia has been well documented. This article highlights the complexities of treating endocrine system disorders in obese patients. Copyright © 2010. Published by Elsevier Inc.

Modeling Patient Treatment With Medical Records: An Abstraction Hierarchy to Understand User Competencies and Needs.

PubMed

St-Maurice, Justin D; Burns, Catherine M

2017-07-28

Health care is a complex sociotechnical system. Patient treatment is evolving and needs to incorporate the use of technology and new patient-centered treatment paradigms. Cognitive work analysis (CWA) is an effective framework for understanding complex systems, and work domain analysis (WDA) is useful for understanding complex ecologies. Although previous applications of CWA have described patient treatment, due to their scope of work patients were previously characterized as biomedical machines, rather than patient actors involved in their own care. An abstraction hierarchy that characterizes patients as beings with complex social values and priorities is needed. This can help better understand treatment in a modern approach to care. The purpose of this study was to perform a WDA to represent the treatment of patients with medical records. The methods to develop this model included the analysis of written texts and collaboration with subject matter experts. Our WDA represents the ecology through its functional purposes, abstract functions, generalized functions, physical functions, and physical forms. Compared with other work domain models, this model is able to articulate the nuanced balance between medical treatment, patient education, and limited health care resources. Concepts in the analysis were similar to the modeling choices of other WDAs but combined them in as a comprehensive, systematic, and contextual overview. The model is helpful to understand user competencies and needs. Future models could be developed to model the patient's domain and enable the exploration of the shared decision-making (SDM) paradigm. Our work domain model links treatment goals, decision-making constraints, and task workflows. This model can be used by system developers who would like to use ecological interface design (EID) to improve systems. Our hierarchy is the first in a future set that could explore new treatment paradigms. Future hierarchies could model the patient as a controller and could be useful for mobile app development. ©Justin D St-Maurice, Catherine M Burns. Originally published in JMIR Human Factors (http://humanfactors.jmir.org), 28.07.2017.

Modeling Patient Treatment With Medical Records: An Abstraction Hierarchy to Understand User Competencies and Needs

PubMed Central

2017-01-01

Background Health care is a complex sociotechnical system. Patient treatment is evolving and needs to incorporate the use of technology and new patient-centered treatment paradigms. Cognitive work analysis (CWA) is an effective framework for understanding complex systems, and work domain analysis (WDA) is useful for understanding complex ecologies. Although previous applications of CWA have described patient treatment, due to their scope of work patients were previously characterized as biomedical machines, rather than patient actors involved in their own care. Objective An abstraction hierarchy that characterizes patients as beings with complex social values and priorities is needed. This can help better understand treatment in a modern approach to care. The purpose of this study was to perform a WDA to represent the treatment of patients with medical records. Methods The methods to develop this model included the analysis of written texts and collaboration with subject matter experts. Our WDA represents the ecology through its functional purposes, abstract functions, generalized functions, physical functions, and physical forms. Results Compared with other work domain models, this model is able to articulate the nuanced balance between medical treatment, patient education, and limited health care resources. Concepts in the analysis were similar to the modeling choices of other WDAs but combined them in as a comprehensive, systematic, and contextual overview. The model is helpful to understand user competencies and needs. Future models could be developed to model the patient’s domain and enable the exploration of the shared decision-making (SDM) paradigm. Conclusion Our work domain model links treatment goals, decision-making constraints, and task workflows. This model can be used by system developers who would like to use ecological interface design (EID) to improve systems. Our hierarchy is the first in a future set that could explore new treatment paradigms. Future hierarchies could model the patient as a controller and could be useful for mobile app development. PMID:28754650

Stoichiometry for binding and transport by the twin arginine translocation system.

PubMed

Celedon, Jose M; Cline, Kenneth

2012-05-14

Twin arginine translocation (Tat) systems transport large folded proteins across sealed membranes. Tat systems accomplish this feat with three membrane components organized in two complexes. In thylakoid membranes, cpTatC and Hcf106 comprise a large receptor complex containing an estimated eight cpTatC-Hcf106 pairs. Protein transport occurs when Tha4 joins the receptor complex as an oligomer of uncertain size that is thought to form the protein-conducting structure. Here, binding analyses with intact membranes or purified complexes indicate that each receptor complex could bind eight precursor proteins. Kinetic analysis of translocation showed that each precursor-bound site was independently functional for transport, and, with sufficient Tha4, all sites were concurrently active for transport. Tha4 titration determined that ∼26 Tha4 protomers were required for transport of each OE17 (oxygen-evolving complex subunit of 17 kD) precursor protein. Our results suggest that, when fully saturated with precursor proteins and Tha4, the Tat translocase is an ∼2.2-megadalton complex that can individually transport eight precursor proteins or cooperatively transport multimeric precursors.

Thermodynamics and the evolution of a city: a tale of how Chicago came to be, from biophysical and socio-economic perspectives

EPA Science Inventory

Cities are complex organized systems, similar to biological and ecological systems in the way that they are structured and function. These systems are subject to the laws of thermodynamics and the principles of Energy Systems Theory (EST). Like other systems, cities experience l...

Microfluidic neurite guidance to study structure-function relationships in topologically-complex population-based neural networks.

PubMed

Honegger, Thibault; Thielen, Moritz I; Feizi, Soheil; Sanjana, Neville E; Voldman, Joel

2016-06-22

The central nervous system is a dense, layered, 3D interconnected network of populations of neurons, and thus recapitulating that complexity for in vitro CNS models requires methods that can create defined topologically-complex neuronal networks. Several three-dimensional patterning approaches have been developed but none have demonstrated the ability to control the connections between populations of neurons. Here we report a method using AC electrokinetic forces that can guide, accelerate, slow down and push up neurites in un-modified collagen scaffolds. We present a means to create in vitro neural networks of arbitrary complexity by using such forces to create 3D intersections of primary neuronal populations that are plated in a 2D plane. We report for the first time in vitro basic brain motifs that have been previously observed in vivo and show that their functional network is highly decorrelated to their structure. This platform can provide building blocks to reproduce in vitro the complexity of neural circuits and provide a minimalistic environment to study the structure-function relationship of the brain circuitry.

Microfluidic neurite guidance to study structure-function relationships in topologically-complex population-based neural networks

NASA Astrophysics Data System (ADS)

Honegger, Thibault; Thielen, Moritz I.; Feizi, Soheil; Sanjana, Neville E.; Voldman, Joel

2016-06-01

The central nervous system is a dense, layered, 3D interconnected network of populations of neurons, and thus recapitulating that complexity for in vitro CNS models requires methods that can create defined topologically-complex neuronal networks. Several three-dimensional patterning approaches have been developed but none have demonstrated the ability to control the connections between populations of neurons. Here we report a method using AC electrokinetic forces that can guide, accelerate, slow down and push up neurites in un-modified collagen scaffolds. We present a means to create in vitro neural networks of arbitrary complexity by using such forces to create 3D intersections of primary neuronal populations that are plated in a 2D plane. We report for the first time in vitro basic brain motifs that have been previously observed in vivo and show that their functional network is highly decorrelated to their structure. This platform can provide building blocks to reproduce in vitro the complexity of neural circuits and provide a minimalistic environment to study the structure-function relationship of the brain circuitry.

A case for Sandia investment in complex adaptive systems science and technology.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Colbaugh, Richard; Tsao, Jeffrey Yeenien; Johnson, Curtis Martin

2012-05-01

This white paper makes a case for Sandia National Laboratories investments in complex adaptive systems science and technology (S&T) -- investments that could enable higher-value-added and more-robustly-engineered solutions to challenges of importance to Sandia's national security mission and to the nation. Complex adaptive systems are ubiquitous in Sandia's national security mission areas. We often ignore the adaptive complexity of these systems by narrowing our 'aperture of concern' to systems or subsystems with a limited range of function exposed to a limited range of environments over limited periods of time. But by widening our aperture of concern we could increase ourmore » impact considerably. To do so, the science and technology of complex adaptive systems must mature considerably. Despite an explosion of interest outside of Sandia, however, that science and technology is still in its youth. What has been missing is contact with real (rather than model) systems and real domain-area detail. With its center-of-gravity as an engineering laboratory, Sandia's has made considerable progress applying existing science and technology to real complex adaptive systems. It has focused much less, however, on advancing the science and technology itself. But its close contact with real systems and real domain-area detail represents a powerful strength with which to help complex adaptive systems science and technology mature. Sandia is thus both a prime beneficiary of, as well as potentially a prime contributor to, complex adaptive systems science and technology. Building a productive program in complex adaptive systems science and technology at Sandia will not be trivial, but a credible path can be envisioned: in the short run, continue to apply existing science and technology to real domain-area complex adaptive systems; in the medium run, jump-start the creation of new science and technology capability through Sandia's Laboratory Directed Research and Development program; and in the long run, inculcate an awareness at the Department of Energy of the importance of supporting complex adaptive systems science through its Office of Science.« less

TAFII-independent activation mediated by human TBP in the presence of the positive cofactor PC4.

PubMed Central

Wu, S Y; Kershnar, E; Chiang, C M

1998-01-01

TFIID is a multiprotein complex comprised of the TATA-binding protein (TBP) and an array of TBP-associated factors (TAFIIs). Whereas TBP is sufficient for basal transcription in conjunction with other general transcription factors and RNA polymerase II, TAFIIs are additionally required for activator-dependent transcription in mammalian cell-free transcription systems. However, recent in vivo studies carried out in yeast suggest that TAFIIs are not globally required for activator function. The discrepancy between in vivo yeast studies and in vitro mammalian cell-free systems remains to be resolved. In this study, we describe a mammalian cell-free transcription system reconstituted with only recombinant proteins and epitope-tagged multiprotein complexes. Transcriptional activation can be recapitulated in this highly purified in vitro transcription system in the absence of TAFIIs. This TBP-mediated activation is not induced by human mediator, another transcriptional coactivator complex potentially implicated in activator response. In contrast, general transcription factors TFIIH and TFIIA play a significant role in TBP-mediated activation, which can be detected in vitro with Gal4 fusion proteins containing various transcriptional activation domains. Our data, therefore, suggest that TFIIH and TFIIA can mediate activator function in the absence of TAFIIs. PMID:9687514

Fluid Intelligence Predicts Novel Rule Implementation in a Distributed Frontoparietal Control Network.

PubMed

Tschentscher, Nadja; Mitchell, Daniel; Duncan, John

2017-05-03

Fluid intelligence has been associated with a distributed cognitive control or multiple-demand (MD) network, comprising regions of lateral frontal, insular, dorsomedial frontal, and parietal cortex. Human fluid intelligence is also intimately linked to task complexity, and the process of solving complex problems in a sequence of simpler, more focused parts. Here, a complex target detection task included multiple independent rules, applied one at a time in successive task epochs. Although only one rule was applied at a time, increasing task complexity (i.e., the number of rules) impaired performance in participants of lower fluid intelligence. Accompanying this loss of performance was reduced response to rule-critical events across the distributed MD network. The results link fluid intelligence and MD function to a process of attentional focus on the successive parts of complex behavior. SIGNIFICANCE STATEMENT Fluid intelligence is intimately linked to the ability to structure complex problems in a sequence of simpler, more focused parts. We examine the basis for this link in the functions of a distributed frontoparietal or multiple-demand (MD) network. With increased task complexity, participants of lower fluid intelligence showed reduced responses to task-critical events. Reduced responses in the MD system were accompanied by impaired behavioral performance. Low fluid intelligence is linked to poor foregrounding of task-critical information across a distributed MD system. Copyright © 2017 Tschentscher et al.

Selective CO2 reduction conjugated with H2O oxidation utilizing semiconductor/metal-complex hybrid photocatalysts

NASA Astrophysics Data System (ADS)

Morikawa, T.; Sato, S.; Arai, T.; Uemura, K.; Yamanaka, K. I.; Suzuki, T. M.; Kajino, T.; Motohiro, T.

2013-12-01

We developed a new hybrid photocatalyst for CO2 reduction, which is composed of a semiconductor and a metal complex. In the hybrid photocatalyst, ΔG between the position of conduction band minimum (ECBM) of the semiconductor and the CO2 reduction potential of the complex is an essential factor for realizing fast electron transfer from the conduction band of semiconductor to metal complex leading to high photocatalytic activity. On the basis of this concept, the hybrid photocatalyst InP/Ru-complex, which functions in aqueous media, was developed. The photoreduction of CO2 to formate using water as an electron donor and a proton source was successfully achieved as a Z-scheme system by functionally conjugating the InP/Ru-complex photocatalyst for CO2 reduction with a TiO2 photocatalyst for water oxidation. The conversion efficiency from solar energy to chemical energy was ca. 0.04%, which approaches that for photosynthesis in a plant. Because this system can be applied to many other inorganic semiconductors and metal-complex catalysts, the efficiency and reaction selectivity can be enhanced by optimization of the electron transfer process including the energy-band configurations, conjugation conformations, and catalyst structures. This electrical-bias-free reaction is a huge leap forward for future practical applications of artificial photosynthesis under solar irradiation to produce organic species.

Systems Genetics as a Tool to Identify Master Genetic Regulators in Complex Disease.

PubMed

Moreno-Moral, Aida; Pesce, Francesco; Behmoaras, Jacques; Petretto, Enrico

2017-01-01

Systems genetics stems from systems biology and similarly employs integrative modeling approaches to describe the perturbations and phenotypic effects observed in a complex system. However, in the case of systems genetics the main source of perturbation is naturally occurring genetic variation, which can be analyzed at the systems-level to explain the observed variation in phenotypic traits. In contrast with conventional single-variant association approaches, the success of systems genetics has been in the identification of gene networks and molecular pathways that underlie complex disease. In addition, systems genetics has proven useful in the discovery of master trans-acting genetic regulators of functional networks and pathways, which in many cases revealed unexpected gene targets for disease. Here we detail the central components of a fully integrated systems genetics approach to complex disease, starting from assessment of genetic and gene expression variation, linking DNA sequence variation to mRNA (expression QTL mapping), gene regulatory network analysis and mapping the genetic control of regulatory networks. By summarizing a few illustrative (and successful) examples, we highlight how different data-modeling strategies can be effectively integrated in a systems genetics study.

Improved multi-objective ant colony optimization algorithm and its application in complex reasoning

NASA Astrophysics Data System (ADS)

Wang, Xinqing; Zhao, Yang; Wang, Dong; Zhu, Huijie; Zhang, Qing

2013-09-01

The problem of fault reasoning has aroused great concern in scientific and engineering fields. However, fault investigation and reasoning of complex system is not a simple reasoning decision-making problem. It has become a typical multi-constraint and multi-objective reticulate optimization decision-making problem under many influencing factors and constraints. So far, little research has been carried out in this field. This paper transforms the fault reasoning problem of complex system into a paths-searching problem starting from known symptoms to fault causes. Three optimization objectives are considered simultaneously: maximum probability of average fault, maximum average importance, and minimum average complexity of test. Under the constraints of both known symptoms and the causal relationship among different components, a multi-objective optimization mathematical model is set up, taking minimizing cost of fault reasoning as the target function. Since the problem is non-deterministic polynomial-hard(NP-hard), a modified multi-objective ant colony algorithm is proposed, in which a reachability matrix is set up to constrain the feasible search nodes of the ants and a new pseudo-random-proportional rule and a pheromone adjustment mechinism are constructed to balance conflicts between the optimization objectives. At last, a Pareto optimal set is acquired. Evaluation functions based on validity and tendency of reasoning paths are defined to optimize noninferior set, through which the final fault causes can be identified according to decision-making demands, thus realize fault reasoning of the multi-constraint and multi-objective complex system. Reasoning results demonstrate that the improved multi-objective ant colony optimization(IMACO) can realize reasoning and locating fault positions precisely by solving the multi-objective fault diagnosis model, which provides a new method to solve the problem of multi-constraint and multi-objective fault diagnosis and reasoning of complex system.

Plant peptide hormone signalling.

PubMed

Motomitsu, Ayane; Sawa, Shinichiro; Ishida, Takashi

2015-01-01

The ligand-receptor-based cell-to-cell communication system is one of the most important molecular bases for the establishment of complex multicellular organisms. Plants have evolved highly complex intercellular communication systems. Historical studies have identified several molecules, designated phytohormones, that function in these processes. Recent advances in molecular biological analyses have identified phytohormone receptors and signalling mediators, and have led to the discovery of numerous peptide-based signalling molecules. Subsequent analyses have revealed the involvement in and contribution of these peptides to multiple aspects of the plant life cycle, including development and environmental responses, similar to the functions of canonical phytohormones. On the basis of this knowledge, the view that these peptide hormones are pivotal regulators in plants is becoming increasingly accepted. Peptide hormones are transcribed from the genome and translated into peptides. However, these peptides generally undergo further post-translational modifications to enable them to exert their function. Peptide hormones are expressed in and secreted from specific cells or tissues. Apoplastic peptides are perceived by specialized receptors that are located at the surface of target cells. Peptide hormone-receptor complexes activate intracellular signalling through downstream molecules, including kinases and transcription factors, which then trigger cellular events. In this chapter we provide a comprehensive summary of the biological functions of peptide hormones, focusing on how they mature and the ways in which they modulate plant functions. © 2015 Authors; published by Portland Press Limited.

Using machine-learning methods to analyze economic loss function of quality management processes

NASA Astrophysics Data System (ADS)

Dzedik, V. A.; Lontsikh, P. A.

2018-05-01

During analysis of quality management systems, their economic component is often analyzed insufficiently. To overcome this issue, it is necessary to withdraw the concept of economic loss functions from tolerance thinking and address it. Input data about economic losses in processes have a complex form, thus, using standard tools to solve this problem is complicated. Use of machine learning techniques allows one to obtain precise models of the economic loss function based on even the most complex input data. Results of such analysis contain data about the true efficiency of a process and can be used to make investment decisions.

Implementation of Arithmetic and Nonarithmetic Functions on a Label-free and DNA-based Platform

NASA Astrophysics Data System (ADS)

Wang, Kun; He, Mengqi; Wang, Jin; He, Ronghuan; Wang, Jianhua

2016-10-01

A series of complex logic gates were constructed based on graphene oxide and DNA-templated silver nanoclusters to perform both arithmetic and nonarithmetic functions. For the purpose of satisfying the requirements of progressive computational complexity and cost-effectiveness, a label-free and universal platform was developed by integration of various functions, including half adder, half subtractor, multiplexer and demultiplexer. The label-free system avoided laborious modification of biomolecules. The designed DNA-based logic gates can be implemented with readout of near-infrared fluorescence, and exhibit great potential applications in the field of bioimaging as well as disease diagnosis.

Invariant resolutions for several Fueter operators

NASA Astrophysics Data System (ADS)

Colombo, Fabrizio; Souček, Vladimir; Struppa, Daniele C.

2006-07-01

A proper generalization of complex function theory to higher dimension is Clifford analysis and an analogue of holomorphic functions of several complex variables were recently described as the space of solutions of several Dirac equations. The four-dimensional case has special features and is closely connected to functions of quaternionic variables. In this paper we present an approach to the Dolbeault sequence for several quaternionic variables based on symmetries and representation theory. In particular we prove that the resolution of the Cauchy-Fueter system obtained algebraically, via Gröbner bases techniques, is equivalent to the one obtained by R.J. Baston (J. Geom. Phys. 1992).

Complex catalysts from self-repairing ensembles to highly reactive air-based oxidation systems

Treesearch

Craig L. Hill; Laurent Delannoy; Dean C. Duncan; Ira A. Weinstock; Roman F. Renneke; Richard S. Reiner; Rajai H. Atalla; Jong Woo Han; Daniel A. Hillesheim; Rui Cao; Travis M. Anderson; Nelya M. Okun; Djamaladdin G. Musaev; Yurii V. Geletii

2007-01-01

Progress in four interrelated catalysis research efforts in our laboratory are summarized: (1) catalytic photochemical functionalization of unactivated CeH bonds by polyoxometalates (POMs); (2) self-repairing catalysts; (3) catalysts for air-based oxidations under ambient conditions; and (4) terminal oxo complexes of the late-transition metal elements and their...

Tilts, dopants, vacancies and non-stoichiometry: Understanding and designing the properties of complex solid oxide perovskites from first principles

NASA Astrophysics Data System (ADS)

Bennett, Joseph W.

Perovskite oxides of formula ABO3 have a wide range of structural, electrical and mechanical properties, making them vital materials for many applications, such as catalysis, ultrasound machines and communication devices. Perovskite solid solutions with high piezoelectric response, such as ferroelectrics, are of particular interest as they can be employed as sensors in SONAR devices. Ferroelectric materials are unique in that their chemical and electrical properties can be non-invasively and reversibly changed, by switching the bulk polarization. This makes ferroelectrics useful for applications in non-volatile random access memory (NVRAM) devices. Perovskite solid solutions with a lower piezoelectric response than ferroelectrics are important for communication technology, as they function well as electroceramic capacitors. Also of interest is how these materials act as a component in a solid oxide fuel cell, as they can function as an efficient source of energy. Altering the chemical composition of these solid oxide materials offers an opportunity to change the desired properties of the final ceramic, adding a degree of flexibility that is advantageous for a variety of applications. These solid oxides are complex, sometimes disordered systems that are a challenge to study experimentally. However, as it is their complexity which produces favorable properties, highly accurate modeling which captures the essential features of the disordered structure is necessary to explain the behavior of current materials and predict favorable compositions for new materials. Methodological improvements and faster computer speeds have made first-principles and atomistic calculations a viable tool for understanding these complex systems. Offering a combination of accuracy and computational speed, the density functional theory (DFT) approach can reveal details about the microscopic structure and interactions of complex systems. Using DFT and a combination of principles from both inorganic chemistry and materials science, I have been able to gain insights into solid oxide perovskite-based systems.

Probing the structural dynamics of the CRISPR-Cas9 RNA-guided DNA-cleavage system by coarse-grained modeling.

PubMed

Zheng, Wenjun

2017-02-01

In the adaptive immune systems of many bacteria and archaea, the Cas9 endonuclease forms a complex with specific guide/scaffold RNA to identify and cleave complementary target sequences in foreign DNA. This DNA targeting machinery has been exploited in numerous applications of genome editing and transcription control. However, the molecular mechanism of the Cas9 system is still obscure. Recently, high-resolution structures have been solved for Cas9 in different structural forms (e.g., unbound forms, RNA-bound binary complexes, and RNA-DNA-bound tertiary complexes, corresponding to an inactive state, a pre-target-bound state, and a cleavage-competent or product state), which offered key structural insights to the Cas9 mechanism. To further probe the structural dynamics of Cas9 interacting with RNA and DNA at the amino-acid level of details, we have performed systematic coarse-grained modeling using an elastic network model and related analyses. Our normal mode analysis predicted a few key modes of collective motions that capture the observed conformational changes featuring large domain motions triggered by binding of RNA and DNA. Our flexibility analysis identified specific regions with high or low flexibility that coincide with key functional sites (such as DNA/RNA-binding sites, nuclease cleavage sites, and key hinges). We also identified a small set of hotspot residues that control the energetics of functional motions, which overlap with known functional sites and offer promising targets for future mutagenesis efforts to improve the specificity of Cas9. Finally, we modeled the conformational transitions of Cas9 from the unbound form to the binary complex and then the tertiary complex, and predicted a distinct sequence of domain motions. In sum, our findings have offered rich structural and dynamic details relevant to the Cas9 machinery, and will guide future investigation and engineering of the Cas9 systems. Proteins 2017; 85:342-353. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Space and Time Partitioning with Hardware Support for Space Applications

NASA Astrophysics Data System (ADS)

Pinto, S.; Tavares, A.; Montenegro, S.

2016-08-01

Complex and critical systems like airplanes and spacecraft implement a very fast growing amount of functions. Typically, those systems were implemented with fully federated architectures, but the number and complexity of desired functions of todays systems led aerospace industry to follow another strategy. Integrated Modular Avionics (IMA) arose as an attractive approach for consolidation, by combining several applications into one single generic computing resource. Current approach goes towards higher integration provided by space and time partitioning (STP) of system virtualization. The problem is existent virtualization solutions are not ready to fully provide what the future of aerospace are demanding: performance, flexibility, safety, security while simultaneously containing Size, Weight, Power and Cost (SWaP-C).This work describes a real time hypervisor for space applications assisted by commercial off-the-shell (COTS) hardware. ARM TrustZone technology is exploited to implement a secure virtualization solution with low overhead and low memory footprint. This is demonstrated by running multiple guest partitions of RODOS operating system on a Xilinx Zynq platform.

FeP(Im)–AB Bonding Energies Evaluated with A Large Number of Density Functionals (P = porphine, Im = imidazole, AB = CO, NO, and O2)

PubMed Central

Liao, Meng-Sheng; Huang, Ming-Ju; Watts, John D.

2011-01-01

Sixty-four (64) density functionals, ranging from GGA, meta-GGA, hybrid GGA to hybrid meta-GGA, were tested to evaluate the FeP(Im)-AB bonding energies (Ebond) in the heme model complexes FeP(Im)(AB) (P = porphine, Im = imidazole, AB = CO, NO, and O2). The results indicate that an accurate prediction of Ebond for the various ligands to heme is difficult with the DFT methods; usually a functional successful for one system does not perform equally well for the other system(s). Relatively satisfactory results for the various FeP(Im)-AB bonding energies are obtained with the meta-GGA funtionals BLAP3 and Bmτ1; they yield Ebond values of ca.1.1, 1.2, and 0.4 eV for AB = CO, NO, and O2, respectively, which are in reasonable agreement with experimental data (0.78 – 0.85 eV for CO, 0.99 eV for NO, and 0.44 – 0.53 eV for O2). The other functionals show more or less deficiency for one or two of the systems. The performances of the various functionals in describing the spin-state energetics of the five-coordinate FeP(Im) complex were also examined. PMID:22228914

Enhancing the magnetic anisotropy of maghemite nanoparticles via the surface coordination of molecular complexes

NASA Astrophysics Data System (ADS)

Prado, Yoann; Daffé, Niéli; Michel, Aude; Georgelin, Thomas; Yaacoub, Nader; Grenèche, Jean-Marc; Choueikani, Fadi; Otero, Edwige; Ohresser, Philippe; Arrio, Marie-Anne; Cartier-Dit-Moulin, Christophe; Sainctavit, Philippe; Fleury, Benoit; Dupuis, Vincent; Lisnard, Laurent; Fresnais, Jérôme

2015-12-01

Superparamagnetic nanoparticles are promising objects for data storage or medical applications. In the smallest--and more attractive--systems, the properties are governed by the magnetic anisotropy. Here we report a molecule-based synthetic strategy to enhance this anisotropy in sub-10-nm nanoparticles. It consists of the fabrication of composite materials where anisotropic molecular complexes are coordinated to the surface of the nanoparticles. Reacting 5 nm γ-Fe2O3 nanoparticles with the [CoII(TPMA)Cl2] complex (TPMA: tris(2-pyridylmethyl)amine) leads to the desired composite materials and the characterization of the functionalized nanoparticles evidences the successful coordination--without nanoparticle aggregation and without complex dissociation--of the molecular complexes to the nanoparticles surface. Magnetic measurements indicate the significant enhancement of the anisotropy in the final objects. Indeed, the functionalized nanoparticles show a threefold increase of the blocking temperature and a coercive field increased by one order of magnitude.

Basal ganglia systems in ritualistic social displays: reptiles and humans; function and illness.

PubMed

Baxter, Lewis R

2003-08-01

Complex, situation-specific territorial maintenance routines are similar across living terrestrial vertebrates (=amniotes). Decades ago, Paul MacLean et al., at the Laboratory of Brain Evolution and Behavior of the National Institute of Mental Health, postulated that these are evolutionarily conserved behaviors whose expression is mediated by the similarly conserved amniote basal ganglia and related brain systems (BG systems). Therefore, they undertook studies in nonhuman primates and in small social lizards (the common green anole, Anolis carolinensis) to examine this idea. MacLean et al. also postulated that when BG systems misfunction in humans, behavioral abnormalities result, some of them under the rubric of psychiatric illnesses. Obsessive-compulsive disorder (OCD) was singled out as one likely candidate. In the last dozen years, functional brain imaging studies of OCD patients have validated the contention that this is, in fact, a condition involving dysfunctioning BG systems. Inspired by the MacLean group's original investigations, my colleagues and I have now applied related functional imaging techniques in naturalistic experiments using Anolis to better understand BG systems' roles in the mediation of complex behavioral routines in healthy amniotes. Here, I will review this functional imaging work in primates (man, and a little in monkey) and in lizards. I believe the literature not only supports MacLean et al.'s contentions about BG systems and behavior in general, but also validates Paul MacLean's life-long contention that human behavioral medicine can profit from a broad comparative approach.

Network science of biological systems at different scales: A review

NASA Astrophysics Data System (ADS)

Gosak, Marko; Markovič, Rene; Dolenšek, Jurij; Slak Rupnik, Marjan; Marhl, Marko; Stožer, Andraž; Perc, Matjaž

2018-03-01

Network science is today established as a backbone for description of structure and function of various physical, chemical, biological, technological, and social systems. Here we review recent advances in the study of complex biological systems that were inspired and enabled by methods of network science. First, we present

Advanced functional network analysis in the geosciences: The pyunicorn package

NASA Astrophysics Data System (ADS)

Donges, Jonathan F.; Heitzig, Jobst; Runge, Jakob; Schultz, Hanna C. H.; Wiedermann, Marc; Zech, Alraune; Feldhoff, Jan; Rheinwalt, Aljoscha; Kutza, Hannes; Radebach, Alexander; Marwan, Norbert; Kurths, Jürgen

2013-04-01

Functional networks are a powerful tool for analyzing large geoscientific datasets such as global fields of climate time series originating from observations or model simulations. pyunicorn (pythonic unified complex network and recurrence analysis toolbox) is an open-source, fully object-oriented and easily parallelizable package written in the language Python. It allows for constructing functional networks (aka climate networks) representing the structure of statistical interrelationships in large datasets and, subsequently, investigating this structure using advanced methods of complex network theory such as measures for networks of interacting networks, node-weighted statistics or network surrogates. Additionally, pyunicorn allows to study the complex dynamics of geoscientific systems as recorded by time series by means of recurrence networks and visibility graphs. The range of possible applications of the package is outlined drawing on several examples from climatology.

Towards a Functionally-Formed Air Traffic System-of-Systems

NASA Technical Reports Server (NTRS)

Conway, Sheila R.; Consiglio, Maria C.

2005-01-01

Incremental improvements to the national aviation infrastructure have not resulted in sufficient increases in capacity and flexibility to meet emerging demand. Unfortunately, revolutionary changes capable of substantial and rapid increases in capacity have proven elusive. Moreover, significant changes have been difficult to implement, and the operational consequences of such change, difficult to predict due to the system s complexity. Some research suggests redistributing air traffic control functions through the system, but this work has largely been dismissed out of hand, accused of being impractical. However, the case for functionally-based reorganization of form can be made from a theoretical, systems perspective. This paper investigates Air Traffic Management functions and their intrinsic biases towards centralized/distributed operations, grounded in systems engineering and information technology theories. Application of these concepts to a small airport operations design is discussed. From this groundwork, a robust, scalable system transformation plan may be made in light of uncertain demand.

Toward simulating complex systems with quantum effects

NASA Astrophysics Data System (ADS)

Kenion-Hanrath, Rachel Lynn

Quantum effects like tunneling, coherence, and zero point energy often play a significant role in phenomena on the scales of atoms and molecules. However, the exact quantum treatment of a system scales exponentially with dimensionality, making it impractical for characterizing reaction rates and mechanisms in complex systems. An ongoing effort in the field of theoretical chemistry and physics is extending scalable, classical trajectory-based simulation methods capable of capturing quantum effects to describe dynamic processes in many-body systems; in the work presented here we explore two such techniques. First, we detail an explicit electron, path integral (PI)-based simulation protocol for predicting the rate of electron transfer in condensed-phase transition metal complex systems. Using a PI representation of the transferring electron and a classical representation of the transition metal complex and solvent atoms, we compute the outer sphere free energy barrier and dynamical recrossing factor of the electron transfer rate while accounting for quantum tunneling and zero point energy effects. We are able to achieve this employing only a single set of force field parameters to describe the system rather than parameterizing along the reaction coordinate. Following our success in describing a simple model system, we discuss our next steps in extending our protocol to technologically relevant materials systems. The latter half focuses on the Mixed Quantum-Classical Initial Value Representation (MQC-IVR) of real-time correlation functions, a semiclassical method which has demonstrated its ability to "tune'' between quantum- and classical-limit correlation functions while maintaining dynamic consistency. Specifically, this is achieved through a parameter that determines the quantumness of individual degrees of freedom. Here, we derive a semiclassical correction term for the MQC-IVR to systematically characterize the error introduced by different choices of simulation parameters, and demonstrate the ability of this approach to optimize MQC-IVR simulations.

Fuzzy Integration of Support Vector Regression Models for Anticipatory Control of Complex Energy Systems

DOE PAGES

Alamaniotis, Miltiadis; Agarwal, Vivek

2014-04-01

Anticipatory control systems are a class of systems whose decisions are based on predictions for the future state of the system under monitoring. Anticipation denotes intelligence and is an inherent property of humans that make decisions by projecting in future. Likewise, artificially intelligent systems equipped with predictive functions may be utilized for anticipating future states of complex systems, and therefore facilitate automated control decisions. Anticipatory control of complex energy systems is paramount to their normal and safe operation. In this paper a new intelligent methodology integrating fuzzy inference with support vector regression is introduced. Our proposed methodology implements an anticipatorymore » system aiming at controlling energy systems in a robust way. Initially a set of support vector regressors is adopted for making predictions over critical system parameters. Furthermore, the predicted values are fed into a two stage fuzzy inference system that makes decisions regarding the state of the energy system. The inference system integrates the individual predictions into a single one at its first stage, and outputs a decision together with a certainty factor computed at its second stage. The certainty factor is an index of the significance of the decision. The proposed anticipatory control system is tested on a real world set of data obtained from a complex energy system, describing the degradation of a turbine. Results exhibit the robustness of the proposed system in controlling complex energy systems.« less

A complex guided spectral transform Lanczos method for studying quantum resonance states

DOE PAGES

Yu, Hua-Gen

2014-12-28

A complex guided spectral transform Lanczos (cGSTL) algorithm is proposed to compute both bound and resonance states including energies, widths and wavefunctions. The algorithm comprises of two layers of complex-symmetric Lanczos iterations. A short inner layer iteration produces a set of complex formally orthogonal Lanczos (cFOL) polynomials. They are used to span the guided spectral transform function determined by a retarded Green operator. An outer layer iteration is then carried out with the transform function to compute the eigen-pairs of the system. The guided spectral transform function is designed to have the same wavefunctions as the eigenstates of the originalmore » Hamiltonian in the spectral range of interest. Therefore the energies and/or widths of bound or resonance states can be easily computed with their wavefunctions or by using a root-searching method from the guided spectral transform surface. The new cGSTL algorithm is applied to bound and resonance states of HO₂, and compared to previous calculations.« less

Evolutionarily conserved mechanisms for the selection and maintenance of behavioural activity.

PubMed

Fiore, Vincenzo G; Dolan, Raymond J; Strausfeld, Nicholas J; Hirth, Frank

2015-12-19

Survival and reproduction entail the selection of adaptive behavioural repertoires. This selection manifests as phylogenetically acquired activities that depend on evolved nervous system circuitries. Lorenz and Tinbergen already postulated that heritable behaviours and their reliable performance are specified by genetically determined programs. Here we compare the functional anatomy of the insect central complex and vertebrate basal ganglia to illustrate their role in mediating selection and maintenance of adaptive behaviours. Comparative analyses reveal that central complex and basal ganglia circuitries share comparable lineage relationships within clusters of functionally integrated neurons. These clusters are specified by genetic mechanisms that link birth time and order to their neuronal identities and functions. Their subsequent connections and associated functions are characterized by similar mechanisms that implement dimensionality reduction and transition through attractor states, whereby spatially organized parallel-projecting loops integrate and convey sensorimotor representations that select and maintain behavioural activity. In both taxa, these neural systems are modulated by dopamine signalling that also mediates memory-like processes. The multiplicity of similarities between central complex and basal ganglia suggests evolutionarily conserved computational mechanisms for action selection. We speculate that these may have originated from ancestral ground pattern circuitries present in the brain of the last common ancestor of insects and vertebrates. © 2015 The Authors.

Evolutionarily conserved mechanisms for the selection and maintenance of behavioural activity

PubMed Central

Fiore, Vincenzo G.; Dolan, Raymond J.; Strausfeld, Nicholas J.; Hirth, Frank

2015-01-01

Survival and reproduction entail the selection of adaptive behavioural repertoires. This selection manifests as phylogenetically acquired activities that depend on evolved nervous system circuitries. Lorenz and Tinbergen already postulated that heritable behaviours and their reliable performance are specified by genetically determined programs. Here we compare the functional anatomy of the insect central complex and vertebrate basal ganglia to illustrate their role in mediating selection and maintenance of adaptive behaviours. Comparative analyses reveal that central complex and basal ganglia circuitries share comparable lineage relationships within clusters of functionally integrated neurons. These clusters are specified by genetic mechanisms that link birth time and order to their neuronal identities and functions. Their subsequent connections and associated functions are characterized by similar mechanisms that implement dimensionality reduction and transition through attractor states, whereby spatially organized parallel-projecting loops integrate and convey sensorimotor representations that select and maintain behavioural activity. In both taxa, these neural systems are modulated by dopamine signalling that also mediates memory-like processes. The multiplicity of similarities between central complex and basal ganglia suggests evolutionarily conserved computational mechanisms for action selection. We speculate that these may have originated from ancestral ground pattern circuitries present in the brain of the last common ancestor of insects and vertebrates. PMID:26554043

Brain evolution and development: adaptation, allometry and constraint

PubMed Central

Barton, Robert A.

2016-01-01

Phenotypic traits are products of two processes: evolution and development. But how do these processes combine to produce integrated phenotypes? Comparative studies identify consistent patterns of covariation, or allometries, between brain and body size, and between brain components, indicating the presence of significant constraints limiting independent evolution of separate parts. These constraints are poorly understood, but in principle could be either developmental or functional. The developmental constraints hypothesis suggests that individual components (brain and body size, or individual brain components) tend to evolve together because natural selection operates on relatively simple developmental mechanisms that affect the growth of all parts in a concerted manner. The functional constraints hypothesis suggests that correlated change reflects the action of selection on distributed functional systems connecting the different sub-components, predicting more complex patterns of mosaic change at the level of the functional systems and more complex genetic and developmental mechanisms. These hypotheses are not mutually exclusive but make different predictions. We review recent genetic and neurodevelopmental evidence, concluding that functional rather than developmental constraints are the main cause of the observed patterns. PMID:27629025

[Influence Mildrocard on the morfo-functional condition of cardio-respiratory system at patients with chronic heart failure with concomitant chronic obstructive pulmonary disease].

PubMed

Ignatenko, G A; Mukhin, I V; Faierman, A O; Pola, M K; Taktashov, G S; Goncharov, O M; Rybalko, G S; Volodkina, N O

2011-01-01

In paper influence of a cytoprotective drug "Mildrocard" on morfo-functional condition of cardiorespiratory system at patients with chronic heart failure with concomitant chronic obstructive pulmonary disease is estimated. It is established, that joining "Mildrocard" to complex therapy associated to pathology promotes reduction clinical display of heart failure, shows cardioprotective and pulmoprotective effects.

Improving binding mode and binding affinity predictions of docking by ligand-based search of protein conformations: evaluation in D3R grand challenge 2015

NASA Astrophysics Data System (ADS)

Xu, Xianjin; Yan, Chengfei; Zou, Xiaoqin

2017-08-01

The growing number of protein-ligand complex structures, particularly the structures of proteins co-bound with different ligands, in the Protein Data Bank helps us tackle two major challenges in molecular docking studies: the protein flexibility and the scoring function. Here, we introduced a systematic strategy by using the information embedded in the known protein-ligand complex structures to improve both binding mode and binding affinity predictions. Specifically, a ligand similarity calculation method was employed to search a receptor structure with a bound ligand sharing high similarity with the query ligand for the docking use. The strategy was applied to the two datasets (HSP90 and MAP4K4) in recent D3R Grand Challenge 2015. In addition, for the HSP90 dataset, a system-specific scoring function (ITScore2_hsp90) was generated by recalibrating our statistical potential-based scoring function (ITScore2) using the known protein-ligand complex structures and the statistical mechanics-based iterative method. For the HSP90 dataset, better performances were achieved for both binding mode and binding affinity predictions comparing with the original ITScore2 and with ensemble docking. For the MAP4K4 dataset, although there were only eight known protein-ligand complex structures, our docking strategy achieved a comparable performance with ensemble docking. Our method for receptor conformational selection and iterative method for the development of system-specific statistical potential-based scoring functions can be easily applied to other protein targets that have a number of protein-ligand complex structures available to improve predictions on binding.

Origins of Aminergic Regulation of Behavior in Complex Insect Social Systems

PubMed Central

Kamhi, J. Frances; Arganda, Sara; Moreau, Corrie S.; Traniello, James F. A.

2017-01-01

Neuromodulators are conserved across insect taxa, but how biogenic amines and their receptors in ancestral solitary forms have been co-opted to control behaviors in derived socially complex species is largely unknown. Here we explore patterns associated with the functions of octopamine (OA), serotonin (5-HT) and dopamine (DA) in solitary ancestral insects and their derived functions in eusocial ants, bees, wasps and termites. Synthesizing current findings that reveal potential ancestral roles of monoamines in insects, we identify physiological processes and conserved behaviors under aminergic control, consider how biogenic amines may have evolved to modulate complex social behavior, and present focal research areas that warrant further study. PMID:29066958

A meta-cognitive learning algorithm for a Fully Complex-valued Relaxation Network.

PubMed

Savitha, R; Suresh, S; Sundararajan, N

2012-08-01

This paper presents a meta-cognitive learning algorithm for a single hidden layer complex-valued neural network called "Meta-cognitive Fully Complex-valued Relaxation Network (McFCRN)". McFCRN has two components: a cognitive component and a meta-cognitive component. A Fully Complex-valued Relaxation Network (FCRN) with a fully complex-valued Gaussian like activation function (sech) in the hidden layer and an exponential activation function in the output layer forms the cognitive component. The meta-cognitive component contains a self-regulatory learning mechanism which controls the learning ability of FCRN by deciding what-to-learn, when-to-learn and how-to-learn from a sequence of training data. The input parameters of cognitive components are chosen randomly and the output parameters are estimated by minimizing a logarithmic error function. The problem of explicit minimization of magnitude and phase errors in the logarithmic error function is converted to system of linear equations and output parameters of FCRN are computed analytically. McFCRN starts with zero hidden neuron and builds the number of neurons required to approximate the target function. The meta-cognitive component selects the best learning strategy for FCRN to acquire the knowledge from training data and also adapts the learning strategies to implement best human learning components. Performance studies on a function approximation and real-valued classification problems show that proposed McFCRN performs better than the existing results reported in the literature. Copyright © 2012 Elsevier Ltd. All rights reserved.

Integrating technology into complex intervention trial processes: a case study.

PubMed

Drew, Cheney J G; Poile, Vincent; Trubey, Rob; Watson, Gareth; Kelson, Mark; Townson, Julia; Rosser, Anne; Hood, Kerenza; Quinn, Lori; Busse, Monica

2016-11-17

Trials of complex interventions are associated with high costs and burdens in terms of paperwork, management, data collection, validation, and intervention fidelity assessment occurring across multiple sites. Traditional data collection methods rely on paper-based forms, where processing can be time-consuming and error rates high. Electronic source data collection can potentially address many of these inefficiencies, but has not routinely been used in complex intervention trials. Here we present the use of an on-line system for managing all aspects of data handling and for the monitoring of trial processes in a multicentre trial of a complex intervention. We custom built a web-accessible software application for the delivery of ENGAGE-HD, a multicentre trial of a complex physical therapy intervention. The software incorporated functionality for participant randomisation, data collection and assessment of intervention fidelity. It was accessible to multiple users with differing levels of access depending on required usage or to maintain blinding. Each site was supplied with a 4G-enabled iPad for accessing the system. The impact of this system was quantified through review of data quality and collation of feedback from site coordinators and assessors through structured process interviews. The custom-built system was an efficient tool for collecting data and managing trial processes. Although the set-up time required was significant, using the system resulted in an overall data completion rate of 98.5% with a data query rate of 0.1%, the majority of which were resolved in under a week. Feedback from research staff indicated that the system was highly acceptable for use in a research environment. This was a reflection of the portability and accessibility of the system when using the iPad and its usefulness in aiding accurate data collection, intervention fidelity and general administration. A combination of commercially available hardware and a bespoke online database designed to support data collection, intervention fidelity and trial progress provides a viable option for streamlining trial processes in a multicentre complex intervention trial. There is scope to further extend the system to cater for larger trials and add further functionality such as automatic reporting facilities and participant management support. ISRCTN65378754 , registered on 13 March 2014.

What Is a Complex Innovation System?

PubMed Central

Katz, J. Sylvan

2016-01-01

Innovation systems are sometimes referred to as complex systems, something that is intuitively understood but poorly defined. A complex system dynamically evolves in non-linear ways giving it unique properties that distinguish it from other systems. In particular, a common signature of complex systems is scale-invariant emergent properties. A scale-invariant property can be identified because it is solely described by a power law function, f(x) = kxα, where the exponent, α, is a measure of scale-invariance. The focus of this paper is to describe and illustrate that innovation systems have properties of a complex adaptive system. In particular scale-invariant emergent properties indicative of their complex nature that can be quantified and used to inform public policy. The global research system is an example of an innovation system. Peer-reviewed publications containing knowledge are a characteristic output. Citations or references to these articles are an indirect measure of the impact the knowledge has on the research community. Peer-reviewed papers indexed in Scopus and in the Web of Science were used as data sources to produce measures of sizes and impact. These measures are used to illustrate how scale-invariant properties can be identified and quantified. It is demonstrated that the distribution of impact has a reasonable likelihood of being scale-invariant with scaling exponents that tended toward a value of less than 3.0 with the passage of time and decreasing group sizes. Scale-invariant correlations are shown between the evolution of impact and size with time and between field impact and sizes at points in time. The recursive or self-similar nature of scale-invariance suggests that any smaller innovation system within the global research system is likely to be complex with scale-invariant properties too. PMID:27258040

Bifurcation Phenomena of Opinion Dynamics in Complex Networks

NASA Astrophysics Data System (ADS)

Guo, Long; Cai, Xu

In this paper, we study the opinion dynamics of Improved Deffuant model (IDM), where the convergence parameter μ is a function of the opposite’s degree K according to the celebrity effect, in small-world network (SWN) and scale-free network (SFN). Generically, the system undergoes a phase transition from the plurality state to the polarization state and to the consensus state as the confidence parameter ɛ increasing. Furthermore, the evolution of the steady opinion s * as a function of ɛ, and the relation between the minority steady opinion s_{*}^{min} and the individual connectivity k also have been analyzed. Our present work shows the crucial role of the confidence parameter and the complex system topology in the opinion dynamics of IDM.

Complex Riccati equations as a link between different approaches for the description of dissipative and irreversible systems

NASA Astrophysics Data System (ADS)

Schuch, Dieter

2012-08-01

Quantum mechanics is essentially described in terms of complex quantities like wave functions. The interesting point is that phase and amplitude of the complex wave function are not independent of each other, but coupled by some kind of conservation law. This coupling exists in time-independent quantum mechanics and has a counterpart in its time-dependent form. It can be traced back to a reformulation of quantum mechanics in terms of nonlinear real Ermakov equations or equivalent complex nonlinear Riccati equations, where the quadratic term in the latter equation explains the origin of the phase-amplitude coupling. Since realistic physical systems are always in contact with some kind of environment this aspect is also taken into account. In this context, different approaches for describing open quantum systems, particularly effective ones, are discussed and compared. Certain kinds of nonlinear modifications of the Schrödinger equation are discussed as well as their interrelations and their relations to linear approaches via non-unitary transformations. The modifications of the aforementioned Ermakov and Riccati equations when environmental effects are included can be determined in the time-dependent case. From formal similarities conclusions can be drawn how the equations of time-independent quantum mechanics can be modified to also incluce the enviromental aspects.

Efficient Cisplatin Pro-Drug Delivery Visualized with Sub-100 nm Resolution: Interfacing Engineered Thermosensitive Magnetomicelles with a Living System

DOE PAGES

Vitol, Elina A.; Rozhkova, Elena A.; Rose, Volker; ...

2014-06-06

Temperature-responsive magnetic nanomicelles can serve as thermal energy and cargo carriers with controlled drug release functionality. In view of their potential biomedical applications, understanding the modes of interaction between nanomaterials and living systems and evaluation of efficiency of cargo delivery is of the utmost importance. In this paper, we investigate the interaction between the hybrid magnetic nanomicelles engineered for controlled platinum complex drug delivery and a biological system at three fundamental levels: subcellular compartments, a single cell and whole living animal. Nanomicelles with polymeric P(NIPAAm-co-AAm)-b-PCL core-shell were loaded with a hydrophobic Pt(IV) complex and Fe 3O 4 nanoparticles though self-assembly.more » The distribution of a platinum complex on subcellular level is visualized using hard X-ray fluorescence microscopy with unprecedented level of detail at sub-100 nm spatial resolution. We then study the cytotoxic effects of platinum complex-loaded micelles in vitro on a head and neck cancer cell culture model SQ20B. In conclusion, by employing the magnetic functionality of the micelles and additionally loading them with a near infrared fluorescent dye, we magnetically target them to a tumor site in a live animal xenografted model which allows to visualize their biodistribution in vivo.« less

Emerging Synaptic Molecules as Candidates in the Etiology of Neurological Disorders

PubMed Central

Torres, Viviana I.; Vallejo, Daniela

2017-01-01

Synapses are complex structures that allow communication between neurons in the central nervous system. Studies conducted in vertebrate and invertebrate models have contributed to the knowledge of the function of synaptic proteins. The functional synapse requires numerous protein complexes with specialized functions that are regulated in space and time to allow synaptic plasticity. However, their interplay during neuronal development, learning, and memory is poorly understood. Accumulating evidence links synapse proteins to neurodevelopmental, neuropsychiatric, and neurodegenerative diseases. In this review, we describe the way in which several proteins that participate in cell adhesion, scaffolding, exocytosis, and neurotransmitter reception from presynaptic and postsynaptic compartments, mainly from excitatory synapses, have been associated with several synaptopathies, and we relate their functions to the disease phenotype. PMID:28331639

Evaluation of exchange-correlation functionals for time-dependent density functional theory calculations on metal complexes.

PubMed

Holland, Jason P; Green, Jennifer C

2010-04-15

The electronic absorption spectra of a range of copper and zinc complexes have been simulated by using time-dependent density functional theory (TD-DFT) calculations implemented in Gaussian03. In total, 41 exchange-correlation (XC) functionals including first-, second-, and third-generation (meta-generalized gradient approximation) DFT methods were compared in their ability to predict the experimental electronic absorption spectra. Both pure and hybrid DFT methods were tested and differences between restricted and unrestricted calculations were also investigated by comparison of analogous neutral zinc(II) and copper(II) complexes. TD-DFT calculated spectra were optimized with respect to the experimental electronic absorption spectra by use of a Matlab script. Direct comparison of the performance of each XC functional was achieved both qualitatively and quantitatively by comparison of optimized half-band widths, root-mean-squared errors (RMSE), energy scaling factors (epsilon(SF)), and overall quality-of-fit (Q(F)) parameters. Hybrid DFT methods were found to outperform all pure DFT functionals with B1LYP, B97-2, B97-1, X3LYP, and B98 functionals providing the highest quantitative and qualitative accuracy in both restricted and unrestricted systems. Of the functionals tested, B1LYP gave the most accurate results with both average RMSE and overall Q(F) < 3.5% and epsilon(SF) values close to unity (>0.990) for the copper complexes. The XC functional performance in spin-restricted TD-DFT calculations on the zinc complexes was found to be slightly worse. PBE1PBE, mPW1PW91 and B1LYP gave the most accurate results with typical RMSE and Q(F) values between 5.3 and 7.3%, and epsilon(SF) around 0.930. These studies illustrate the power of modern TD-DFT calculations for exploring excited state transitions of metal complexes. 2009 Wiley Periodicals, Inc.

Drug Delivery Systems For Anti-Cancer Active Complexes of Some Coinage Metals.

PubMed

Zhang, Ming; Saint-Germain, Camille; He, Guiling; Sun, Raymond Wai-Yin

2018-02-12

Although cisplatin and a number of platinum complexes have widely been used for the treatment of neoplasia, patients receiving these treatments have frequently suffered from their severe toxic side effects, the development of resistance with consequent relapse. In the recent decades, numerous complexes of coinage metals including that of gold, copper and silver have been reported to display promising in vitro and/or in vivo anti-cancer activities as well as potent activities towards cisplatin-resistant tumors. Nevertheless, the medical development of these metal complexes has been hampered by their instability in aqueous solutions and the nonspecific binding in biological systems. One of the approaches to overcome these problems is to design and develop adequate drug delivery systems (DDSs) for the transport of these complexes. By functionalization, encapsulation or formulation of the metal complexes, several types of DDSs have been reported to improve the desired pharmacological profile of the metal complexes, improving their overall stability, bioavailability, anti-cancer activity and reducing their toxicity towards normal cells. In this review, we summarized the recent findings for different DDSs for various anti- cancer active complexes of some coinage metals. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

New approaches to the analysis of complex samples using fluorescence lifetime techniques and organized media

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hertz, P.R.

Fluorescence spectroscopy is a highly sensitive and selective tool for the analysis of complex systems. In order to investigate the efficacy of several steady state and dynamic techniques for the analysis of complex systems, this work focuses on two types of complex, multicomponent samples: petrolatums and coal liquids. It is shown in these studies dynamic, fluorescence lifetime-based measurements provide enhanced discrimination between complex petrolatum samples. Additionally, improved quantitative analysis of multicomponent systems is demonstrated via incorporation of organized media in coal liquid samples. This research provides the first systematic studies of (1) multifrequency phase-resolved fluorescence spectroscopy for dynamic fluorescence spectralmore » fingerprinting of complex samples, and (2) the incorporation of bile salt micellar media to improve accuracy and sensitivity for characterization of complex systems. In the petroleum studies, phase-resolved fluorescence spectroscopy is used to combine spectral and lifetime information through the measurement of phase-resolved fluorescence intensity. The intensity is collected as a function of excitation and emission wavelengths, angular modulation frequency, and detector phase angle. This multidimensional information enhances the ability to distinguish between complex samples with similar spectral characteristics. Examination of the eigenvalues and eigenvectors from factor analysis of phase-resolved and steady state excitation-emission matrices, using chemometric methods of data analysis, confirms that phase-resolved fluorescence techniques offer improved discrimination between complex samples as compared with conventional steady state methods.« less

Operational resilience: concepts, design and analysis

NASA Astrophysics Data System (ADS)

Ganin, Alexander A.; Massaro, Emanuele; Gutfraind, Alexander; Steen, Nicolas; Keisler, Jeffrey M.; Kott, Alexander; Mangoubi, Rami; Linkov, Igor

2016-01-01

Building resilience into today’s complex infrastructures is critical to the daily functioning of society and its ability to withstand and recover from natural disasters, epidemics, and cyber-threats. This study proposes quantitative measures that capture and implement the definition of engineering resilience advanced by the National Academy of Sciences. The approach is applicable across physical, information, and social domains. It evaluates the critical functionality, defined as a performance function of time set by the stakeholders. Critical functionality is a source of valuable information, such as the integrated system resilience over a time interval, and its robustness. The paper demonstrates the formulation on two classes of models: 1) multi-level directed acyclic graphs, and 2) interdependent coupled networks. For both models synthetic case studies are used to explore trends. For the first class, the approach is also applied to the Linux operating system. Results indicate that desired resilience and robustness levels are achievable by trading off different design parameters, such as redundancy, node recovery time, and backup supply available. The nonlinear relationship between network parameters and resilience levels confirms the utility of the proposed approach, which is of benefit to analysts and designers of complex systems and networks.

Operational resilience: concepts, design and analysis

PubMed Central

Ganin, Alexander A.; Massaro, Emanuele; Gutfraind, Alexander; Steen, Nicolas; Keisler, Jeffrey M.; Kott, Alexander; Mangoubi, Rami; Linkov, Igor

2016-01-01

Building resilience into today’s complex infrastructures is critical to the daily functioning of society and its ability to withstand and recover from natural disasters, epidemics, and cyber-threats. This study proposes quantitative measures that capture and implement the definition of engineering resilience advanced by the National Academy of Sciences. The approach is applicable across physical, information, and social domains. It evaluates the critical functionality, defined as a performance function of time set by the stakeholders. Critical functionality is a source of valuable information, such as the integrated system resilience over a time interval, and its robustness. The paper demonstrates the formulation on two classes of models: 1) multi-level directed acyclic graphs, and 2) interdependent coupled networks. For both models synthetic case studies are used to explore trends. For the first class, the approach is also applied to the Linux operating system. Results indicate that desired resilience and robustness levels are achievable by trading off different design parameters, such as redundancy, node recovery time, and backup supply available. The nonlinear relationship between network parameters and resilience levels confirms the utility of the proposed approach, which is of benefit to analysts and designers of complex systems and networks. PMID:26782180

Operational resilience: concepts, design and analysis.

PubMed

Ganin, Alexander A; Massaro, Emanuele; Gutfraind, Alexander; Steen, Nicolas; Keisler, Jeffrey M; Kott, Alexander; Mangoubi, Rami; Linkov, Igor

2016-01-19

Building resilience into today's complex infrastructures is critical to the daily functioning of society and its ability to withstand and recover from natural disasters, epidemics, and cyber-threats. This study proposes quantitative measures that capture and implement the definition of engineering resilience advanced by the National Academy of Sciences. The approach is applicable across physical, information, and social domains. It evaluates the critical functionality, defined as a performance function of time set by the stakeholders. Critical functionality is a source of valuable information, such as the integrated system resilience over a time interval, and its robustness. The paper demonstrates the formulation on two classes of models: 1) multi-level directed acyclic graphs, and 2) interdependent coupled networks. For both models synthetic case studies are used to explore trends. For the first class, the approach is also applied to the Linux operating system. Results indicate that desired resilience and robustness levels are achievable by trading off different design parameters, such as redundancy, node recovery time, and backup supply available. The nonlinear relationship between network parameters and resilience levels confirms the utility of the proposed approach, which is of benefit to analysts and designers of complex systems and networks.

Proteomics-Based Analysis of Protein Complexes in Pluripotent Stem Cells and Cancer Biology.

PubMed

Sudhir, Putty-Reddy; Chen, Chung-Hsuan

2016-03-22

A protein complex consists of two or more proteins that are linked together through protein-protein interactions. The proteins show stable/transient and direct/indirect interactions within the protein complex or between the protein complexes. Protein complexes are involved in regulation of most of the cellular processes and molecular functions. The delineation of protein complexes is important to expand our knowledge on proteins functional roles in physiological and pathological conditions. The genetic yeast-2-hybrid method has been extensively used to characterize protein-protein interactions. Alternatively, a biochemical-based affinity purification coupled with mass spectrometry (AP-MS) approach has been widely used to characterize the protein complexes. In the AP-MS method, a protein complex of a target protein of interest is purified using a specific antibody or an affinity tag (e.g., DYKDDDDK peptide (FLAG) and polyhistidine (His)) and is subsequently analyzed by means of MS. Tandem affinity purification, a two-step purification system, coupled with MS has been widely used mainly to reduce the contaminants. We review here a general principle for AP-MS-based characterization of protein complexes and we explore several protein complexes identified in pluripotent stem cell biology and cancer biology as examples.

Proteomics-Based Analysis of Protein Complexes in Pluripotent Stem Cells and Cancer Biology

PubMed Central

Sudhir, Putty-Reddy; Chen, Chung-Hsuan

2016-01-01

A protein complex consists of two or more proteins that are linked together through protein–protein interactions. The proteins show stable/transient and direct/indirect interactions within the protein complex or between the protein complexes. Protein complexes are involved in regulation of most of the cellular processes and molecular functions. The delineation of protein complexes is important to expand our knowledge on proteins functional roles in physiological and pathological conditions. The genetic yeast-2-hybrid method has been extensively used to characterize protein-protein interactions. Alternatively, a biochemical-based affinity purification coupled with mass spectrometry (AP-MS) approach has been widely used to characterize the protein complexes. In the AP-MS method, a protein complex of a target protein of interest is purified using a specific antibody or an affinity tag (e.g., DYKDDDDK peptide (FLAG) and polyhistidine (His)) and is subsequently analyzed by means of MS. Tandem affinity purification, a two-step purification system, coupled with MS has been widely used mainly to reduce the contaminants. We review here a general principle for AP-MS-based characterization of protein complexes and we explore several protein complexes identified in pluripotent stem cell biology and cancer biology as examples. PMID:27011181

A new order-theoretic characterisation of the polytime computable functions☆

PubMed Central

Avanzini, Martin; Eguchi, Naohi; Moser, Georg

2015-01-01

We propose a new order-theoretic characterisation of the class of polytime computable functions. To this avail we define the small polynomial path order (sPOP⁎ for short). This termination order entails a new syntactic method to analyse the innermost runtime complexity of term rewrite systems fully automatically: for any rewrite system compatible with sPOP⁎ that employs recursion up to depth d, the (innermost) runtime complexity is polynomially bounded of degree d. This bound is tight. Thus we obtain a direct correspondence between a syntactic (and easily verifiable) condition of a program and the asymptotic worst-case complexity of the program. PMID:26412933

The production of multiprotein complexes in insect cells using the baculovirus expression system.

PubMed

Abdulrahman, Wassim; Radu, Laura; Garzoni, Frederic; Kolesnikova, Olga; Gupta, Kapil; Osz-Papai, Judit; Berger, Imre; Poterszman, Arnaud

2015-01-01

The production of a homogeneous protein sample in sufficient quantities is an essential prerequisite not only for structural investigations but represents also a rate-limiting step for many functional studies. In the cell, a large fraction of eukaryotic proteins exists as large multicomponent assemblies with many subunits, which act in concert to catalyze specific activities. Many of these complexes cannot be obtained from endogenous source material, so recombinant expression and reconstitution are then required to overcome this bottleneck. This chapter describes current strategies and protocols for the efficient production of multiprotein complexes in large quantities and of high quality, using the baculovirus/insect cell expression system.

Riemann surfaces of complex classical trajectories and tunnelling splitting in one-dimensional systems

NASA Astrophysics Data System (ADS)

Harada, Hiromitsu; Mouchet, Amaury; Shudo, Akira

2017-10-01

The topology of complex classical paths is investigated to discuss quantum tunnelling splittings in one-dimensional systems. Here the Hamiltonian is assumed to be given as polynomial functions, so the fundamental group for the Riemann surface provides complete information on the topology of complex paths, which allows us to enumerate all the possible candidates contributing to the semiclassical sum formula for tunnelling splittings. This naturally leads to action relations among classically disjoined regions, revealing entirely non-local nature in the quantization condition. The importance of the proper treatment of Stokes phenomena is also discussed in Hamiltonians in the normal form.

Functional Entropy Variables: A New Methodology for Deriving Thermodynamically Consistent Algorithms for Complex Fluids, with Particular Reference to the Isothermal Navier-Stokes-Korteweg Equations

DTIC Science & Technology

2012-11-01

multicorrector algorithm . Predictor stage: Set Cρn+1,(0) = C ρ n, (157) Cun+1,(0) = C u n, (158) Cvn+1,(0) = C v n. (159) Multicorrector stage: Repeat the... corrector algorithm given by (157)-(178). Remark 20. We adopt the preconditioned GMRES algorithm [53] from PETSc [2] to solve the linear system given by (175...ICES REPORT 12-43 November 2012 Functional Entropy Variables: A New Methodology for Deriving Thermodynamically Consistent Algorithms for Complex

From Molecules to Life: Quantifying the Complexity of Chemical and Biological Systems in the Universe.

PubMed

Böttcher, Thomas

2018-01-01

Life is a complex phenomenon and much research has been devoted to both understanding its origins from prebiotic chemistry and discovering life beyond Earth. Yet, it has remained elusive how to quantify this complexity and how to compare chemical and biological units on one common scale. Here, a mathematical description of molecular complexity was applied allowing to quantitatively assess complexity of chemical structures. This in combination with the orthogonal measure of information complexity resulted in a two-dimensional complexity space ranging over the entire spectrum from molecules to organisms. Entities with a certain level of information complexity directly require a functionally complex mechanism for their production or replication and are hence indicative for life-like systems. In order to describe entities combining molecular and information complexity, the term biogenic unit was introduced. Exemplified biogenic unit complexities were calculated for ribozymes, protein enzymes, multimeric protein complexes, and even an entire virus particle. Complexities of prokaryotic and eukaryotic cells, as well as multicellular organisms, were estimated. Thereby distinct evolutionary stages in complexity space were identified. The here developed approach to compare the complexity of biogenic units allows for the first time to address the gradual characteristics of prebiotic and life-like systems without the need for a definition of life. This operational concept may guide our search for life in the Universe, and it may direct the investigations of prebiotic trajectories that lead towards the evolution of complexity at the origins of life.

Demonstration Advanced Avionics System (DAAS) function description

NASA Technical Reports Server (NTRS)

Bailey, A. J.; Bailey, D. G.; Gaabo, R. J.; Lahn, T. G.; Larson, J. C.; Peterson, E. M.; Schuck, J. W.; Rodgers, D. L.; Wroblewski, K. A.

1982-01-01

The Demonstration Advanced Avionics System, DAAS, is an integrated avionics system utilizing microprocessor technologies, data busing, and shared displays for demonstrating the potential of these technologies in improving the safety and utility of general aviation operations in the late 1980's and beyond. Major hardware elements of the DAAS include a functionally distributed microcomputer complex, an integrated data control center, an electronic horizontal situation indicator, and a radio adaptor unit. All processing and display resources are interconnected by an IEEE-488 bus in order to enhance the overall system effectiveness, reliability, modularity and maintainability. A detail description of the DAAS architecture, the DAAS hardware, and the DAAS functions is presented. The system is designed for installation and flight test in a NASA Cessna 402-B aircraft.

ERP (enterprise resource planning) systems can streamline healthcare business functions.

PubMed

Jenkins, E K; Christenson, E

2001-05-01

Enterprise resource planning (ERP) software applications are designed to facilitate the systemwide integration of complex processes and functions across a large enterprise consisting of many internal and external constituents. Although most currently available ERP applications generally are tailored to the needs of the manufacturing industry, many large healthcare systems are investigating these applications. Due to the significant differences between manufacturing and patient care, ERP-based systems do not easily translate to the healthcare setting. In particular, the lack of clinical standardization impedes the use of ERP systems for clinical integration. Nonetheless, an ERP-based system can help a healthcare organization integrate many functions, including patient scheduling, human resources management, workload forecasting, and management of workflow, that are not directly dependent on clinical decision making.

Complex collective dynamics of active torque-driven colloids at interfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Snezhko, Alexey

Modern self-assembly techniques aiming to produce complex structural order or functional diversity often rely on non-equilibrium conditions in the system. Light, electric, or magnetic fields are predominantly used to modify interaction profiles of colloidal particles during self-assembly or induce complex out-of-equilibrium dynamic ordering. The energy injection rate, properties of the environment are important control parameters that influence the outcome of active (dynamic) self-assembly. The current review is focused on a case of collective dynamics and self-assembly of particles with externally driven torques coupled to a liquid or solid interface. The complexity of interactions in such systems is further enriched bymore » strong hydrodynamic coupling between particles. Unconventionally ordered dynamic self-assembled patterns, spontaneous symmetry breaking phenomena, self-propulsion, and collective transport have been reported in torque-driven colloids. Some of the features of the complex collective behavior and dynamic pattern formation in those active systems have been successfully captured in simulations.« less

Transparent Information Systems through Gateways, Front Ends, Intermediaries, and Interfaces.

ERIC Educational Resources Information Center

Williams, Martha E.

1986-01-01

Provides overview of design requirements for transparent information retrieval (implies that user sees through complexity of retrieval activities sequence). Highlights include need for transparent systems; history of transparent retrieval research; information retrieval functions (automated converters, routers, selectors, evaluators/analyzers);…

Analysis of Power Laws, Shape Collapses, and Neural Complexity: New Techniques and MATLAB Support via the NCC Toolbox

PubMed Central

Marshall, Najja; Timme, Nicholas M.; Bennett, Nicholas; Ripp, Monica; Lautzenhiser, Edward; Beggs, John M.

2016-01-01

Neural systems include interactions that occur across many scales. Two divergent methods for characterizing such interactions have drawn on the physical analysis of critical phenomena and the mathematical study of information. Inferring criticality in neural systems has traditionally rested on fitting power laws to the property distributions of “neural avalanches” (contiguous bursts of activity), but the fractal nature of avalanche shapes has recently emerged as another signature of criticality. On the other hand, neural complexity, an information theoretic measure, has been used to capture the interplay between the functional localization of brain regions and their integration for higher cognitive functions. Unfortunately, treatments of all three methods—power-law fitting, avalanche shape collapse, and neural complexity—have suffered from shortcomings. Empirical data often contain biases that introduce deviations from true power law in the tail and head of the distribution, but deviations in the tail have often been unconsidered; avalanche shape collapse has required manual parameter tuning; and the estimation of neural complexity has relied on small data sets or statistical assumptions for the sake of computational efficiency. In this paper we present technical advancements in the analysis of criticality and complexity in neural systems. We use maximum-likelihood estimation to automatically fit power laws with left and right cutoffs, present the first automated shape collapse algorithm, and describe new techniques to account for large numbers of neural variables and small data sets in the calculation of neural complexity. In order to facilitate future research in criticality and complexity, we have made the software utilized in this analysis freely available online in the MATLAB NCC (Neural Complexity and Criticality) Toolbox. PMID:27445842

An integrative approach to inferring biologically meaningful gene modules.

PubMed

Cho, Ji-Hoon; Wang, Kai; Galas, David J

2011-07-26

The ability to construct biologically meaningful gene networks and modules is critical for contemporary systems biology. Though recent studies have demonstrated the power of using gene modules to shed light on the functioning of complex biological systems, most modules in these networks have shown little association with meaningful biological function. We have devised a method which directly incorporates gene ontology (GO) annotation in construction of gene modules in order to gain better functional association. We have devised a method, Semantic Similarity-Integrated approach for Modularization (SSIM) that integrates various gene-gene pairwise similarity values, including information obtained from gene expression, protein-protein interactions and GO annotations, in the construction of modules using affinity propagation clustering. We demonstrated the performance of the proposed method using data from two complex biological responses: 1. the osmotic shock response in Saccharomyces cerevisiae, and 2. the prion-induced pathogenic mouse model. In comparison with two previously reported algorithms, modules identified by SSIM showed significantly stronger association with biological functions. The incorporation of semantic similarity based on GO annotation with gene expression and protein-protein interaction data can greatly enhance the functional relevance of inferred gene modules. In addition, the SSIM approach can also reveal the hierarchical structure of gene modules to gain a broader functional view of the biological system. Hence, the proposed method can facilitate comprehensive and in-depth analysis of high throughput experimental data at the gene network level.

Emergence of complex chemistry on an organic monolayer.

PubMed

Prins, Leonard J

2015-07-21

In many origin-of-life scenarios, inorganic materials, such as FeS or mineral clays, play an important role owing to their ability to concentrate and select small organic molecules on their surface and facilitate their chemical transformations into new molecules. However, considering that life is made up of organic matter, at a certain stage during the evolution the role of the inorganic material must have been taken over by organic molecules. How this exactly happened is unclear, and, indeed, a big gap separates the rudimentary level of organization involving inorganic materials and the complex organization of cells, which are the building blocks of life. Over the past years, we have extensively studied the interaction of small molecules with monolayer-protected gold nanoparticles (Au NPs) for the purpose of developing innovative sensing and catalytic systems. During the course of these studies, we realized that the functional role of this system is very similar to that typically attributed to inorganic surfaces in the early stages of life, with the important being difference that the functional properties (molecular recognition, catalysis, signaling, adaptation) originate entirely from the organic monolayer rather than the inorganic support. This led us to the proposition that this system may serve as a model that illustrates how the important role of inorganic surfaces in dictating chemical processes in the early stages of life may have been taken over by organic matter. Here, we reframe our previously obtained results in the context of the origin-of-life question. The following functional roles of Au NPs will be discussed: the ability to concentrate small molecules and create different local populations, the ability to catalyze the chemical transformation of bound molecules, and, finally, the ability to install rudimentary signaling pathways and display primitive adaptive behavior. In particular, we will show that many of the functional properties of the system originate from two features: the presence of metal ions that are complexed in the organic monolayer and the multivalent nature of the system. Complexed metal ions play an important role in determining the affinity and selectivity of the interaction with small molecules, but serve also as regulatory elements for determining how many molecules are bound simultaneously. Importantly, neighboring metal ion complexes also create catalytic pockets in which two metal ions cooperatively catalyze the cleavage of an RNA-model compound. The multivalent nature of the system permits multiple noncovalent interactions with small molecules that enhances the affinity, but is also at the basis of simple signal transduction pathways and adaptive behavior.

Prognostics Methodology for Complex Systems

NASA Technical Reports Server (NTRS)

Gulati, Sandeep; Mackey, Ryan

2003-01-01

An automatic method to schedule maintenance and repair of complex systems is produced based on a computational structure called the Informed Maintenance Grid (IMG). This method provides solutions to the two fundamental problems in autonomic logistics: (1) unambiguous detection of deterioration or impending loss of function and (2) determination of the time remaining to perform maintenance or other corrective action based upon information from the system. The IMG provides a health determination over the medium-to-longterm operation of the system, from one or more days to years of study. The IMG is especially applicable to spacecraft and both piloted and autonomous aircraft, or industrial control processes.

Micro-electro-optical devices in a five-level polysilicon surface-micromachining technology

NASA Astrophysics Data System (ADS)

Smith, James H.; Rodgers, M. Steven; Sniegowski, Jeffry J.; Miller, Samuel L.; Hetherington, Dale L.; McWhorter, Paul J.; Warren, Mial E.

1998-09-01

We recently reported on the development of a 5-level polysilicon surface micromachine fabrication process consisting of four levels of mechanical poly plus an electrical interconnect layer and its application to complex mechanical systems. This paper describes the application of this technology to create micro-optical systems-on-a-chip. These are demonstration systems, which show that give levels of polysilicon provide greater performance, reliability, and significantly increased functionality. This new technology makes it possible to realize levels of system complexity that have so far only existed on paper, while simultaneously adding to the robustness of many of the individual subassemblies.

An evolutionary link between capsular biogenesis and surface motility in bacteria.

PubMed

Agrebi, Rym; Wartel, Morgane; Brochier-Armanet, Céline; Mignot, Tâm

2015-05-01

Studying the evolution of macromolecular assemblies is important to improve our understanding of how complex cellular structures evolved, and to identify the functional building blocks that are involved. Recent studies suggest that the macromolecular complexes that are involved in two distinct processes in Myxococcus xanthus - surface motility and sporulation - are derived from an ancestral polysaccharide capsule assembly system. In this Opinion article, we argue that the available data suggest that the motility machinery evolved from this capsule assembly system following a gene duplication event, a change in carbohydrate polymer specificity and the acquisition of additional proteins by the motility complex, all of which are key features that distinguish the motility and sporulation systems. Furthermore, the presence of intermediates of these systems in bacterial genomes suggests a testable evolutionary model for their emergence and spread.

A new method for predicting response in complex linear systems. II. [under random or deterministic steady state excitation

NASA Technical Reports Server (NTRS)

Bogdanoff, J. L.; Kayser, K.; Krieger, W.

1977-01-01

The paper describes convergence and response studies in the low frequency range of complex systems, particularly with low values of damping of different distributions, and reports on the modification of the relaxation procedure required under these conditions. A new method is presented for response estimation in complex lumped parameter linear systems under random or deterministic steady state excitation. The essence of the method is the use of relaxation procedures with a suitable error function to find the estimated response; natural frequencies and normal modes are not computed. For a 45 degree of freedom system, and two relaxation procedures, convergence studies and frequency response estimates were performed. The low frequency studies are considered in the framework of earlier studies (Kayser and Bogdanoff, 1975) involving the mid to high frequency range.

Interpreting Popov criteria in Lure´ systems with complex scaling stability analysis

NASA Astrophysics Data System (ADS)

Zhou, J.

2018-06-01

The paper presents a novel frequency-domain interpretation of Popov criteria for absolute stability in Lure´ systems by means of what we call complex scaling stability analysis. The complex scaling technique is developed for exponential/asymptotic stability in LTI feedback systems, which dispenses open-loop poles distribution, contour/locus orientation and prior frequency sweeping. Exploiting the technique for alternatively revealing positive realness of transfer functions, re-interpreting Popov criteria is explicated. More specifically, the suggested frequency-domain stability conditions are conformable both in scalar and multivariable cases, and can be implemented either graphically with locus plotting or numerically without; in particular, the latter is suitable as a design tool with auxiliary parameter freedom. The interpretation also reveals further frequency-domain facts about Lure´ systems. Numerical examples are included to illustrate the main results.

A neurobehavioral examination of individuals with high-functioning autism and Asperger's disorder using a fronto-striatal model of dysfunction.

PubMed

Rinehart, Nicole J; Bradshaw, John L; Tonge, Bruce J; Brereton, Avril V; Bellgrove, Mark A

2002-06-01

The repetitive, stereotyped, and obsessive behaviors that characterize autism may in part be attributable to disruption of the region of the fronto-striatal system, which mediates executive abilities. Neuropsychological testing has shown that children with autism exhibit set-shifting deficiencies on tests such as the Wisconsin Card Sorting task but show normal inhibitory ability on variants of the Stroop color-word test. According to Minshew and Goldstein's multiple primary deficit theory, the complexity of the executive functioning task is important in determining the performance of individuals with autism. This study employed a visual-spatial task (with a Stroop-type component) to examine the integrity of executive functioning, in particular inhibition, in autism (n = 12) and Asperger's disorder (n = 12) under increasing levels of cognitive complexity. Whereas the Asperger's disorder group performed similarly to age- and IQ-matched control participants, even at the higher levels of cognitive complexity, the high-functioning autism group displayed inhibitory deficits specifically associated with increasing cognitive load.

Ecological Understanding 1: Ways of Experiencing Photosynthesis.

ERIC Educational Resources Information Center

Carlsson, Britta

2002-01-01

Investigates 10 student teachers' understanding of the different ways in which the function of the ecosystem could be experienced. Explores the functional aspects of the ecosystem using a system approach. Concludes that the idea of transformation is crucial to more complex ways of understanding photosynthesis. (Contains 62 references.) (Author/YDS)

Functional evaluation and rehabilitation engineering.

PubMed

Aliverti, Andrea; Frigo, C; Andreoni, G; Baroni, G; Bonarini, A; Cerveri, P; Crivellini, M; Dellaca, R; Ferrigno, G; Galli, M; Pedrocchi, A; Rodano, R; Santambrogio, G C; Tognola, G; Pedotti, A

2011-01-01

Life is complex and all about movement, which allows us to interact with the environment and communicate with each other. The human nervous system is capable of performing a simultaneous and integrated control of 100-150 mechanical degrees of freedom of movement in the body via tensions generated by about 700 muscles. In its widest context, movement is carried out by a sensory motor system comprising multiple sensors (visual,auditory, and proprioceptive),multiple actuators (muscles acting on the skeletal system),and an intermediary processor that can be summarized as a multiple-input–multiple-output nonlinear dynamic time-varying control system. This grand control system is capable of responding with remarkable accuracy,speed, appropriateness,versatility, and adaptability to a wide spectrum of continuous and discrete stimuli and conditions and is certainly orders of magnitude more complex and sophisticated than the most advanced robotic systems currently available. In the last decades,a great deal of research has been carried out in the fields of functional evaluation of human performance and rehabilitation engineering. These fields combine knowledge, concepts, and methods from across many disciplines (e.g., biomechanics,neuroscience, and physiology), with the aim of developing apparatuses and methods fort he measurement and analysis of complex sensory motor performance and the ultimate goal of enhancing the execution of different tasks in both healthy people and persons with reduced capabilities from different causes (injury, disease, amputation,and neural degeneration).

Complexity: the organizing principle at the interface of biological (dis)order.

PubMed

Bhat, Ramray; Pally, Dharma

2017-07-01

The term complexity means several things to biologists.When qualifying morphological phenotype, on the one hand, it is used to signify the sheer complicatedness of living systems, especially as a result of the multicomponent aspect of biological form. On the other hand, it has been used to represent the intricate nature of the connections between constituents that make up form: a more process-based explanation. In the context of evolutionary arguments, complexity has been defined, in a quantifiable fashion, as the amount of information, an informatic template such as a sequence of nucleotides or amino acids stores about its environment. In this perspective, we begin with a brief review of the history of complexity theory. We then introduce a developmental and an evolutionary understanding of what it means for biological systems to be complex.We propose that the complexity of living systems can be understood through two interdependent structural properties: multiscalarity of interconstituent mechanisms and excitability of the biological materials. The answer to whether a system becomes more or less complex over time depends on the potential for its constituents to interact in novel ways and combinations to give rise to new structures and functions, as well as on the evolution of excitable properties that would facilitate the exploration of interconstituent organization in the context of their microenvironments and macroenvironments.

Density functional theory studies of oxygen and carbonate binding to a dicopper patellamide complex.

PubMed

Latifi, Reza; Bagherzadeh, Mojtaba; Milne, Bruce F; Jaspars, Marcel; de Visser, Sam P

2008-12-01

In this work we present results of density functional theory (DFT) calculations on dicopper patellamides and their affinity for molecular oxygen and carbonate. Patellamides are cyclic octapeptides that are produced by a cyanobacterium, and may show promise as therapeutics. Thus, carbonate binding to a dicopper patellamide center gives a stable cyclic octapeptide with a twist of almost 90 degrees . The system exists in close-lying open-shell singlet and triplet spin states with two unpaired electrons in orthogonal sigma* orbitals on each metal center. Subsequently, we replaced carbonate with dioxygen and found a stable Cu2(mu-O)2 diamond shaped patellamide core. In this structure the original dioxygen bond is significantly weakened to essentially a single bond, which should enable the system to transfer these oxygen atoms to substrates. We predicted the IR and Raman spectra of the Cu2(mu-O)2 diamond shaped patellamide structure using density functional theory and found a considerable isotope effect on the O-O stretch vibration for 16O2 versus 18O2 bound structures. Our studies reveal that carbonate forms an extremely stable complex with dicopper patellamide, but that additional molecular oxygen to this system does not give a potential oxidant. Therefore, it is more likely that carbonate prepares the system for dioxygen binding by folding it into the correct configuration followed in the proposed catalytic cycle by a protonation event preceding dioxygen binding to enable the system to reorganize to form a stable Cu2(mu-O)2-patellamide cluster. Alternatively, carbonate may act as an inhibitor that blocks the catalytic activity of the system. It is anticipated that the Cu2(mu-O)2-patellamide structure is a potential active oxidant of the dicopper patellamide complex.

The murine SNF5/INI1 chromatin remodeling factor is essential for embryonic development and tumor suppression.

PubMed

Klochendler-Yeivin, A; Fiette, L; Barra, J; Muchardt, C; Babinet, C; Yaniv, M

2000-12-01

The assembly of eukaryotic DNA into nucleosomes and derived higher order structures constitutes a barrier for transcription, replication and repair. A number of chromatin remodeling complexes, as well as histone acetylation, were shown to facilitate gene activation. To investigate the function of two closely related mammalian SWI/SNF complexes in vivo, we inactivated the murine SNF5/INI1 gene, a common subunit of these two complexes. Mice lacking SNF5 protein stop developing at the peri-implantation stage, showing that the SWI/SNF complex is essential for early development and viability of early embryonic cells. Furthermore, heterozygous mice develop nervous system and soft tissue sarcomas. In these tumors the wild-type allele was lost, providing further evidence that SNF5 functions as a tumor suppressor gene in certain cell types.

The murine SNF5/INI1 chromatin remodeling factor is essential for embryonic development and tumor suppression

PubMed Central

Klochendler-Yeivin, Agnes; Fiette, Laurence; Barra, Jaqueline; Muchardt, Christian; Babinet, Charles; Yaniv, Moshe

2000-01-01

The assembly of eukaryotic DNA into nucleosomes and derived higher order structures constitutes a barrier for transcription, replication and repair. A number of chromatin remodeling complexes, as well as histone acetylation, were shown to facilitate gene activation. To investigate the function of two closely related mammalian SWI/SNF complexes in vivo, we inactivated the murine SNF5/INI1 gene, a common subunit of these two complexes. Mice lacking SNF5 protein stop developing at the peri-implantation stage, showing that the SWI/SNF complex is essential for early development and viability of early embryonic cells. Furthermore, heterozygous mice develop nervous system and soft tissue sarcomas. In these tumors the wild-type allele was lost, providing further evidence that SNF5 functions as a tumor suppressor gene in certain cell types. PMID:11263494

A Multi-Resolution Nonlinear Mapping Technique for Design and Analysis Applications

NASA Technical Reports Server (NTRS)

Phan, Minh Q.

1998-01-01

This report describes a nonlinear mapping technique where the unknown static or dynamic system is approximated by a sum of dimensionally increasing functions (one-dimensional curves, two-dimensional surfaces, etc.). These lower dimensional functions are synthesized from a set of multi-resolution basis functions, where the resolutions specify the level of details at which the nonlinear system is approximated. The basis functions also cause the parameter estimation step to become linear. This feature is taken advantage of to derive a systematic procedure to determine and eliminate basis functions that are less significant for the particular system under identification. The number of unknown parameters that must be estimated is thus reduced and compact models obtained. The lower dimensional functions (identified curves and surfaces) permit a kind of "visualization" into the complexity of the nonlinearity itself.

A Multi-Resolution Nonlinear Mapping Technique for Design and Analysis Application

NASA Technical Reports Server (NTRS)

Phan, Minh Q.

1997-01-01

This report describes a nonlinear mapping technique where the unknown static or dynamic system is approximated by a sum of dimensionally increasing functions (one-dimensional curves, two-dimensional surfaces, etc.). These lower dimensional functions are synthesized from a set of multi-resolution basis functions, where the resolutions specify the level of details at which the nonlinear system is approximated. The basis functions also cause the parameter estimation step to become linear. This feature is taken advantage of to derive a systematic procedure to determine and eliminate basis functions that are less significant for the particular system under identification. The number of unknown parameters that must be estimated is thus reduced and compact models obtained. The lower dimensional functions (identified curves and surfaces) permit a kind of "visualization" into the complexity of the nonlinearity itself.

B cell biology: implications for treatment of systemic lupus erythematosus.

PubMed

Anolik, J H

2013-04-01

B cells are critical players in the orchestration of properly regulated immune responses, normally providing protective immunity without autoimmunity. Balance in the B cell compartment is achieved through the finely regulated participation of multiple B cell populations with different antibody-dependent and independent functions. Both types of functions allow B cells to modulate other components of the innate and adaptive immune system. Autoantibody-independent B cell functions include antigen presentation, T cell activation and polarization, and dendritic cell modulation. Several of these functions are mediated by the ability of B cells to produce immunoregulatory cytokines and chemokines and by their critical contribution to lymphoid tissue development and organization including the development of ectopic tertiary lymphoid tissue. Additionally, the functional versatility of B cells enables them to play either protective or pathogenic roles in autoimmunity. In turn, B cell dysfunction has been critically implicated in the pathophysiology of systemic lupus erythematosus (SLE), a complex disease characterized by the production of autoantibodies and heterogeneous clinical involvement. Thus, the breakdown of B cell tolerance is a defining and early event in the disease process and may occur by multiple pathways, including alterations in factors that affect B cell activation thresholds, B cell longevity, and apoptotic cell processing. Once tolerance is broken, autoantibodies contribute to autoimmunity by multiple mechanisms including immune-complex mediated Type III hypersensitivity reactions, type II antibody-dependent cytotoxicity, and by instructing innate immune cells to produce pathogenic cytokines including IFNα, TNF and IL-1. The complexity of B cell functions has been highlighted by the variable success of B cell-targeted therapies in multiple autoimmune diseases, including those conventionally viewed as T cell-mediated conditions. Given the widespread utilization of B cell depletion therapy in autoimmune diseases and the need for new therapeutic approaches in SLE, a better understanding of human B cell subsets and the balance of pathogenic and regulatory functions is of the essence.

Effect of complex aerobic physical exercise on PSD-95 in the hippocampus and on cognitive function in juvenile mice

NASA Astrophysics Data System (ADS)

Satriani, W. H.; Redjeki, S.; Kartinah, N. T.

2017-08-01

Increased neuroplasticity induced by complex aerobic physical exercise is associated with improved cognitive function in adult mice. Increased cognitive function is assumed to be based on increased synapse formation. One of the regions of the brain that is important in cognitive function is the hippocampus, which plays a role in memory formation. Post synaptic density-95 (PSD-95) is an adhesion protein of the post-synaptic density scaffolding that is essential to synaptic stabilization. As we age, the PSD-95 molecule matures the synapses needed for the formation of the basic circuitry of the nervous system in the brain. However, during the growth period, synapse elimination is higher than its formation. This study aims to determine whether complex aerobic exercise can improve cognitive function and PSD-95 levels in the hippocampus of juvenile mice during their growth stage. The mice performed complex aerobic exercise starting at five weeks of age and continuing for seven weeks with a gradual increase of 8 m/min. At eight weeks it was increased to 10 m/min. The exercise was done for five days of each week. The subjects of the study were tested for cognition one week before being sacrificed (at 12 weeks). The PSD-95 in the hippocampus was measured with ELISA. The results showed that there was a significant difference in cognitive function, where p < 0.05, between the group that was given complex aerobic exercise and a control group that did not. However, the PSD-95 levels did not differ significantly between the two groups. The results of this study indicate that early complex aerobic exercise can improve cognitive ability in adulthood but does not increase the levels of PSD-95 in adults.

Determining the folding and binding free energy of DNA-based nanodevices and nanoswitches using urea titration curves

PubMed Central

Idili, Andrea

2017-01-01

Abstract DNA nanotechnology takes advantage of the predictability of DNA interactions to build complex DNA-based functional nanoscale structures. However, when DNA functional and responsive units that are based on non-canonical DNA interactions are employed it becomes quite challenging to predict, understand and control their thermodynamics. In response to this limitation, here we demonstrate the use of isothermal urea titration experiments to estimate the free energy involved in a set of DNA-based systems ranging from unimolecular DNA-based nanoswitches to more complex DNA folds (e.g. aptamers) and nanodevices. We propose here a set of fitting equations that allow to analyze the urea titration curves of these DNA responsive units based on Watson–Crick and non-canonical interactions (stem-loop, G-quadruplex, triplex structures) and to correctly estimate their relative folding and binding free energy values under different experimental conditions. The results described herein will pave the way toward the use of urea titration experiments in the field of DNA nanotechnology to achieve easier and more reliable thermodynamic characterization of DNA-based functional responsive units. More generally, our results will be of general utility to characterize other complex supramolecular systems based on different biopolymers. PMID:28605461

Lunar Surface Scenarios: Habitation and Life Support Systems for a Pressurized Rover

NASA Technical Reports Server (NTRS)

Anderson, Molly; Hanford, Anthony; Howard, Robert; Toups, Larry

2006-01-01

Pressurized rovers will be a critical component of successful lunar exploration to enable safe investigation of sites distant from the outpost location. A pressurized rover is a complex system with the same functions as any other crewed vehicle. Designs for a pressurized rover need to take into account significant constraints, a multitude of tasks to be performed inside and out, and the complexity of life support systems to support the crew. In future studies, pressurized rovers should be given the same level of consideration as any other vehicle occupied by the crew.

An empirical comparison of a dynamic software testability metric to static cyclomatic complexity

NASA Technical Reports Server (NTRS)

Voas, Jeffrey M.; Miller, Keith W.; Payne, Jeffrey E.

1993-01-01

This paper compares the dynamic testability prediction technique termed 'sensitivity analysis' to the static testability technique termed cyclomatic complexity. The application that we chose in this empirical study is a CASE generated version of a B-737 autoland system. For the B-737 system we analyzed, we isolated those functions that we predict are more prone to hide errors during system/reliability testing. We also analyzed the code with several other well-known static metrics. This paper compares and contrasts the results of sensitivity analysis to the results of the static metrics.

Methods for evaluating information in managing the enterprise on the basis of a hybrid three-tier system

NASA Astrophysics Data System (ADS)

Vasil'ev, V. A.; Dobrynina, N. V.

2017-01-01

The article presents data on the influence of information upon the functioning of complex systems in the process of ensuring their effective management. Ways and methods for evaluating multidimensional information that reduce time and resources, improve the validity of the studied system management decisions, were proposed.

A cardiovascular system model for lower-body negative pressure response

NASA Technical Reports Server (NTRS)

Mitchell, B. A., Jr.; Giese, R. P.

1971-01-01

Mathematical models used to study complex physiological control systems are discussed. Efforts were made to modify a model of the cardiovascular system for use in studying lower body negative pressure. A computer program was written which allows orderly, straightforward expansion to include exercise, metabolism (thermal stress), respiration, and other body functions.

The Legionella pneumophila IcmS-LvgA protein complex is important for Dot/Icm-dependent intracellular growth.

PubMed

Vincent, Carr D; Vogel, Joseph P

2006-08-01

Many bacterial pathogens require a functional type IV secretion system (T4SS) for virulence. Legionella pneumophila, the causative agent of Legionnaires' disease, employs the Dot/Icm T4SS to inject a large number of protein substrates into its host, thereby altering phagosome trafficking. The L. pneumophila T4SS substrate SdeA has been shown to require the accessory factor IcmS for its export. IcmS, defined as a type IV adaptor, exists as a heterodimer with IcmW and this complex functions in a manner similar to a type III secretion chaperone. Here we report an interaction between IcmS and the previously identified virulence factor LvgA. Similar to the icmS mutant, the lvgA mutant appears to assemble a fully functional Dot/Icm complex. Both LvgA and IcmS are small, acidic proteins localized to the cytoplasm and are not exported by the Dot/Icm system, suggesting they form a novel type IV adaptor complex. Inactivation of lvgA causes a minimal defect in growth in the human monocytic cell line U937 and the environmental host Acanthamoeba castellanii. However, the lvgA mutant was severely attenuated for intracellular growth of L. pneumophila in mouse macrophages, suggesting LvgA may be a critical factor that confers host specificity.

Intramolecular Hydroamination of Unbiased and Functionalized Primary Aminoalkenes Catalyzed by a Rhodium Aminophosphine Complex

PubMed Central

Julian, Lisa D.; Hartwig, John F.

2010-01-01

We report a rhodium catalyst that exhibits high reactivity for the hydroamination of primary aminoalkenes that are unbiased toward cyclization and that possess functional groups that would not be tolerated in hydroaminations catalyzed by more electrophilic systems. This catalyst contains an unusual diaminophosphine ligand that binds to rhodium in a κ3-P,O,P mode. The reactions catalyzed by this complex typically proceed at mild temperatures (room temperature to 70 °C), occur with primary aminoalkenes lacking substituents on the alkyl chain that bias the system toward cyclization, occur with primary aminoalkenes containing chloride, ester, ether, enolizable ketone, nitrile, and unprotected alcohol functionality, and occur with primary aminoalkenes containing internal olefins. Mechanistic data imply that these reactions occur with a turnover-limiting step that is different from that of reactions catalyzed by late transition metal complexes of Pd, Pt, and Ir. This change in the turnover-limiting step and resulting high activity of the catalyst stem from favorable relative rates for protonolysis of the M-C bond to release the hydroamination product vs reversion of the aminoalkyl intermediate to regenerate the acyclic precursor. Probes for the origin of the reactivity of the rhodium complex of L1 imply that the aminophosphine groups lead to these favorable rates by effects beyond steric demands and simple electron donation to the metal center. PMID:20839807

Mitochondrial multifaceted dysfunction in schizophrenia; complex I as a possible pathological target.

PubMed

Ben-Shachar, Dorit

2017-09-01

Mitochondria are key players in various essential cellular processes beyond being the main energy supplier of the cell. Accordingly, they are involved in neuronal synaptic transmission, neuronal growth and sprouting and consequently neuronal plasticity and connectivity. In addition, mitochondria participate in the modulation of gene transcription and inflammation as well in physiological responses in health and disease. Schizophrenia is currently regarded as a neurodevelopmental disorder associated with impaired immune system, aberrant neuronal differentiation and abnormalities in various neurotransmitter systems mainly the dopaminergic, glutaminergic and GABAergic. Ample evidence has been accumulated over the last decade indicating a multifaceted dysfunction of mitochondria in schizophrenia. Indeed, mitochondrial deficit can be of relevance for the majority of the pathologies observed in this disease. In the present article, we overview specific deficits of the mitochondria in schizophrenia, with a focus on the first complex (complex I) of the mitochondrial electron transport chain (ETC). We argue that complex I, being a major factor in the regulation of mitochondrial ETC, is a possible key modulator of various functions of the mitochondria. We review biochemical, molecular, cellular and functional evidence for mitochondrial impairments and their possible convergence to impact in-vitro neuronal differentiation efficiency in schizophrenia. Mitochondrial function in schizophrenia may advance our knowledge of the disease pathophysiology and open the road for new treatment targets for the benefit of the patients. Copyright © 2016 Elsevier B.V. All rights reserved.

Design, fabrication and control of origami robots

NASA Astrophysics Data System (ADS)

Rus, Daniela; Tolley, Michael T.

2018-06-01

Origami robots are created using folding processes, which provide a simple approach to fabricating a wide range of robot morphologies. Inspired by biological systems, engineers have started to explore origami folding in combination with smart material actuators to enable intrinsic actuation as a means to decouple design from fabrication complexity. The built-in crease structure of origami bodies has the potential to yield compliance and exhibit many soft body properties. Conventional fabrication of robots is generally a bottom-up assembly process with multiple low-level steps for creating subsystems that include manual operations and often multiple iterations. By contrast, natural systems achieve elegant designs and complex functionalities using top-down parallel transformation approaches such as folding. Folding in nature creates a wide spectrum of complex morpho-functional structures such as proteins and intestines and enables the development of structures such as flowers, leaves and insect wings. Inspired by nature, engineers have started to explore folding powered by embedded smart material actuators to create origami robots. The design and fabrication of origami robots exploits top-down, parallel transformation approaches to achieve elegant designs and complex functionalities. In this Review, we first introduce the concept of origami robotics and then highlight advances in design principles, fabrication methods, actuation, smart materials and control algorithms. Applications of origami robots for a variety of devices are investigated, and future directions of the field are discussed, examining both challenges and opportunities.

Suppressor Analysis of the Fusogenic Lambda Spanins.

PubMed

Cahill, Jesse; Rajaure, Manoj; Holt, Ashley; Moreland, Russell; O'Leary, Chandler; Kulkarni, Aneesha; Sloan, Jordan; Young, Ry

2017-07-15

The final step of lysis in phage λ infections of Escherichia coli is mediated by the spanins Rz and Rz1. These proteins form a complex that bridges the cell envelope and that has been proposed to cause fusion of the inner and outer membranes. Accordingly, mutations that block spanin function are found within coiled-coil domains and the proline-rich region, motifs essential in other fusion systems. To gain insight into spanin function, pseudorevertant alleles that restored plaque formation for lysis-defective mutants of Rz and Rz1 were selected. Most second-site suppressors clustered within a coiled-coil domain of Rz near the outer leaflet of the cytoplasmic membrane and were not allele specific. Suppressors largely encoded polar insertions within the hydrophobic core of the coiled-coil interface. Such suppressor changes resulted in decreased proteolytic stability of the Rz double mutants in vivo Unlike the wild type, in which lysis occurs while the cells retain a rod shape, revertant alleles with second-site suppressor mutations supported lysis events that were preceded by spherical cell formation. This suggests that destabilization of the membrane-proximal coiled coil restores function for defective spanin alleles by increasing the conformational freedom of the complex at the cost of its normal, all-or-nothing functionality. IMPORTANCE Caudovirales encode cell envelope-spanning proteins called spanins, which are thought to fuse the inner and outer membranes during phage lysis. Recent genetic analysis identified the functional domains of the lambda spanins, which are similar to class I viral fusion proteins. While the pre- and postfusion structures of model fusion systems have been well characterized, the intermediate structure(s) formed during the fusion reaction remains elusive. Genetic analysis would be expected to identify functional connections between intermediates. Since most membrane fusion systems are not genetically tractable, only few such investigations have been reported. Here, we report a suppressor analysis of lambda spanin function. To our knowledge this is the first suppression analysis of a class I-like complex and also the first such analysis of a prokaryote membrane fusion system. Copyright © 2017 American Society for Microbiology.

A robotic system for automation of logistics functions on the Space Station

NASA Technical Reports Server (NTRS)

Martin, J. C.; Purves, R. B.; Hosier, R. N.; Krein, B. A.

1988-01-01

Spacecraft inventory management is currently performed by the crew and as systems become more complex, increased crew time will be required to perform routine logistics activities. If future spacecraft are to function effectively as research labs and production facilities, the efficient use of crew time as a limited resource for performing mission functions must be employed. The use of automation and robotics technology, such as automated warehouse and materials handling functions, can free the crew from many logistics tasks and provide more efficient use of crew time. Design criteria for a Space Station Automated Logistics Inventory Management System is focused on through the design and demonstration of a mobile two armed terrestrial robot. The system functionally represents a 0 gravity automated inventory management system and the problems associated with operating in such an environment. Features of the system include automated storage and retrieval, item recognition, two armed robotic manipulation, and software control of all inventory item transitions and queries.

Multi-level and hybrid modelling approaches for systems biology.

PubMed

Bardini, R; Politano, G; Benso, A; Di Carlo, S

2017-01-01

During the last decades, high-throughput techniques allowed for the extraction of a huge amount of data from biological systems, unveiling more of their underling complexity. Biological systems encompass a wide range of space and time scales, functioning according to flexible hierarchies of mechanisms making an intertwined and dynamic interplay of regulations. This becomes particularly evident in processes such as ontogenesis, where regulative assets change according to process context and timing, making structural phenotype and architectural complexities emerge from a single cell, through local interactions. The information collected from biological systems are naturally organized according to the functional levels composing the system itself. In systems biology, biological information often comes from overlapping but different scientific domains, each one having its own way of representing phenomena under study. That is, the different parts of the system to be modelled may be described with different formalisms. For a model to have improved accuracy and capability for making a good knowledge base, it is good to comprise different system levels, suitably handling the relative formalisms. Models which are both multi-level and hybrid satisfy both these requirements, making a very useful tool in computational systems biology. This paper reviews some of the main contributions in this field.

Mathematical and Computational Modeling in Complex Biological Systems

PubMed Central

Li, Wenyang; Zhu, Xiaoliang

2017-01-01

The biological process and molecular functions involved in the cancer progression remain difficult to understand for biologists and clinical doctors. Recent developments in high-throughput technologies urge the systems biology to achieve more precise models for complex diseases. Computational and mathematical models are gradually being used to help us understand the omics data produced by high-throughput experimental techniques. The use of computational models in systems biology allows us to explore the pathogenesis of complex diseases, improve our understanding of the latent molecular mechanisms, and promote treatment strategy optimization and new drug discovery. Currently, it is urgent to bridge the gap between the developments of high-throughput technologies and systemic modeling of the biological process in cancer research. In this review, we firstly studied several typical mathematical modeling approaches of biological systems in different scales and deeply analyzed their characteristics, advantages, applications, and limitations. Next, three potential research directions in systems modeling were summarized. To conclude, this review provides an update of important solutions using computational modeling approaches in systems biology. PMID:28386558

Mathematical and Computational Modeling in Complex Biological Systems.

PubMed

Ji, Zhiwei; Yan, Ke; Li, Wenyang; Hu, Haigen; Zhu, Xiaoliang

2017-01-01

The biological process and molecular functions involved in the cancer progression remain difficult to understand for biologists and clinical doctors. Recent developments in high-throughput technologies urge the systems biology to achieve more precise models for complex diseases. Computational and mathematical models are gradually being used to help us understand the omics data produced by high-throughput experimental techniques. The use of computational models in systems biology allows us to explore the pathogenesis of complex diseases, improve our understanding of the latent molecular mechanisms, and promote treatment strategy optimization and new drug discovery. Currently, it is urgent to bridge the gap between the developments of high-throughput technologies and systemic modeling of the biological process in cancer research. In this review, we firstly studied several typical mathematical modeling approaches of biological systems in different scales and deeply analyzed their characteristics, advantages, applications, and limitations. Next, three potential research directions in systems modeling were summarized. To conclude, this review provides an update of important solutions using computational modeling approaches in systems biology.

Multimeric complexes among ankyrin-repeat and SOCS-box protein 9 (ASB9), ElonginBC, and Cullin 5: insights into the structure and assembly of ECS-type Cullin-RING E3 ubiquitin ligases.

PubMed

Thomas, Jemima C; Matak-Vinkovic, Dijana; Van Molle, Inge; Ciulli, Alessio

2013-08-06

Proteins of the ankyrin-repeat and SOCS-box (ASB) family act as the substrate-recognition subunits of ECS-type (ElonginBC-Cullin-SOCS-box) Cullin RING E3 ubiquitin ligase (CRL) complexes that catalyze the specific polyubiquitination of cellular proteins to target them for degradation by the proteasome. Therefore, ASB multimeric complexes are involved in numerous cell processes and pathways; however, their interactions, assembly, and biological roles remain poorly understood. To enhance our understanding of ASB CRL systems, we investigated the structure, affinity, and assembly of the quaternary multisubunit complex formed by ASB9, Elongin B, Elongin C (EloBC), and Cullin 5. Here, we describe the application of several biophysical techniques including differential scanning fluorimetry, isothermal titration calorimetry (ITC), nanoelectrospray ionization, and ion-mobility mass spectrometry (IM-MS) to provide structural and thermodynamic information for a quaternary ASB CRL complex. We find that ASB9 is unstable alone but forms a stable ternary complex with EloBC that binds with high affinity to the Cullin 5 N-terminal domain (Cul5NTD) but not to Cul2NTD. The structure of the monomeric ASB9-EloBC-Cul5NTD quaternary complex is revealed by molecular modeling and is consistent with IM-MS and temperature-dependent ITC data. This is the first experimental study to validate structural information for the assembly of the quaternary N-terminal region of an ASB CRL complex. The results suggest that ASB E3 ligase complexes function and assemble in an analogous manner to that of other CRL systems and provide a platform for further molecular investigation of this important protein family. The data reported here will also be of use for the future development of chemical probes to examine the biological function and modulation of other ECS-type CRL systems.

Multimeric Complexes among Ankyrin-Repeat and SOCS-box Protein 9 (ASB9), ElonginBC, and Cullin 5: Insights into the Structure and Assembly of ECS-type Cullin-RING E3 Ubiquitin Ligases

PubMed Central

2013-01-01

Proteins of the ankyrin-repeat and SOCS-box (ASB) family act as the substrate-recognition subunits of ECS-type (ElonginBC–Cullin–SOCS-box) Cullin RING E3 ubiquitin ligase (CRL) complexes that catalyze the specific polyubiquitination of cellular proteins to target them for degradation by the proteasome. Therefore, ASB multimeric complexes are involved in numerous cell processes and pathways; however, their interactions, assembly, and biological roles remain poorly understood. To enhance our understanding of ASB CRL systems, we investigated the structure, affinity, and assembly of the quaternary multisubunit complex formed by ASB9, Elongin B, Elongin C (EloBC), and Cullin 5. Here, we describe the application of several biophysical techniques including differential scanning fluorimetry, isothermal titration calorimetry (ITC), nanoelectrospray ionization, and ion-mobility mass spectrometry (IM–MS) to provide structural and thermodynamic information for a quaternary ASB CRL complex. We find that ASB9 is unstable alone but forms a stable ternary complex with EloBC that binds with high affinity to the Cullin 5 N-terminal domain (Cul5NTD) but not to Cul2NTD. The structure of the monomeric ASB9–EloBC–Cul5NTD quaternary complex is revealed by molecular modeling and is consistent with IM–MS and temperature-dependent ITC data. This is the first experimental study to validate structural information for the assembly of the quaternary N-terminal region of an ASB CRL complex. The results suggest that ASB E3 ligase complexes function and assemble in an analogous manner to that of other CRL systems and provide a platform for further molecular investigation of this important protein family. The data reported here will also be of use for the future development of chemical probes to examine the biological function and modulation of other ECS-type CRL systems. PMID:23837592

Organization and hierarchy of the human functional brain network lead to a chain-like core.

PubMed

Mastrandrea, Rossana; Gabrielli, Andrea; Piras, Fabrizio; Spalletta, Gianfranco; Caldarelli, Guido; Gili, Tommaso

2017-07-07

The brain is a paradigmatic example of a complex system: its functionality emerges as a global property of local mesoscopic and microscopic interactions. Complex network theory allows to elicit the functional architecture of the brain in terms of links (correlations) between nodes (grey matter regions) and to extract information out of the noise. Here we present the analysis of functional magnetic resonance imaging data from forty healthy humans at rest for the investigation of the basal scaffold of the functional brain network organization. We show how brain regions tend to coordinate by forming a highly hierarchical chain-like structure of homogeneously clustered anatomical areas. A maximum spanning tree approach revealed the centrality of the occipital cortex and the peculiar aggregation of cerebellar regions to form a closed core. We also report the hierarchy of network segregation and the level of clusters integration as a function of the connectivity strength between brain regions.

Transdisciplinary Application of Cross-Scale Resilience ...

EPA Pesticide Factsheets

The cross-scale resilience model was developed in ecology to explain the emergence of resilience from the distribution of ecological functions within and across scales, and as a tool to assess resilience. We propose that the model and the underlyingdiscontinuity hypothesis are relevant to other complex adaptive systems, and can be used to identify and track changes in system parameters related to resilience. We explain the theory behind the cross-scale resilience model, review the cases where it has been applied to non-ecological systems, and discuss some examples of social-ecological, archaeological/anthropological, and economic systems where a cross-scale resilience analysis could add a quantitative dimension to our current understanding of system dynamics and resilience. We argue that the scaling and diversity parameters suitable for a resilience analysis of ecological systems are appropriate for a broad suite of systems where non-normative quantitative assessments of resilience are desired. Our planet is currently characterized by fast environmental and social change, and the cross-scale resilience model has the potential to quantify resilience across many types of complex adaptive systems. Comparative analyses of complex systems have, in fact, demonstrated commonalities among distinctly different types of systems (Schneider & Kay 1994; Holling 2001; Lansing 2003; Foster 2005; Bullmore et al. 2009). Both biological and non-biological complex systems appear t

Modeling of the Human - Operator in a Complex System Functioning Under Extreme Conditions

NASA Astrophysics Data System (ADS)

Getzov, Peter; Hubenova, Zoia; Yordanov, Dimitar; Popov, Wiliam

2013-12-01

Problems, related to the explication of sophisticated control systems of objects, operating under extreme conditions, have been examined and the impact of the effectiveness of the operator's activity on the systems as a whole. The necessity of creation of complex simulation models, reflecting operator's activity, is discussed. Organizational and technical system of an unmanned aviation complex is described as a sophisticated ergatic system. Computer realization of main subsystems of algorithmic system of the man as a controlling system is implemented and specialized software for data processing and analysis is developed. An original computer model of a Man as a tracking system has been implemented. Model of unmanned complex for operators training and formation of a mental model in emergency situation, implemented in "matlab-simulink" environment, has been synthesized. As a unit of the control loop, the pilot (operator) is simplified viewed as an autocontrol system consisting of three main interconnected subsystems: sensitive organs (perception sensors); central nervous system; executive organs (muscles of the arms, legs, back). Theoretical-data model of prediction the level of operator's information load in ergatic systems is proposed. It allows the assessment and prediction of the effectiveness of a real working operator. Simulation model of operator's activity in takeoff based on the Petri nets has been synthesized.

Preparing new nurses with complexity science and problem-based learning.

PubMed

Hodges, Helen F

2011-01-01

Successful nurses function effectively with adaptability, improvability, and interconnectedness, and can see emerging and unpredictable complex problems. Preparing new nurses for complexity requires a significant change in prevalent but dated nursing education models for rising graduates. The science of complexity coupled with problem-based learning and peer review contributes a feasible framework for a constructivist learning environment to examine real-time systems data; explore uncertainty, inherent patterns, and ambiguity; and develop skills for unstructured problem solving. This article describes a pilot study of a problem-based learning strategy guided by principles of complexity science in a community clinical nursing course. Thirty-five senior nursing students participated during a 3-year period. Assessments included peer review, a final project paper, reflection, and a satisfaction survey. Results were higher than expected levels of student satisfaction, increased breadth and analysis of complex data, acknowledgment of community as complex adaptive systems, and overall higher level thinking skills than in previous years. 2011, SLACK Incorporated.

The life of plant mitochondrial complex I.

PubMed

Braun, Hans-Peter; Binder, Stefan; Brennicke, Axel; Eubel, Holger; Fernie, Alisdair R; Finkemeier, Iris; Klodmann, Jennifer; König, Ann-Christine; Kühn, Kristina; Meyer, Etienne; Obata, Toshihiro; Schwarzländer, Markus; Takenaka, Mizuki; Zehrmann, Anja

2014-11-01

The mitochondrial NADH dehydrogenase complex (complex I) of the respiratory chain has several remarkable features in plants: (i) particularly many of its subunits are encoded by the mitochondrial genome, (ii) its mitochondrial transcripts undergo extensive maturation processes (e.g. RNA editing, trans-splicing), (iii) its assembly follows unique routes, (iv) it includes an additional functional domain which contains carbonic anhydrases and (v) it is, indirectly, involved in photosynthesis. Comprising about 50 distinct protein subunits, complex I of plants is very large. However, an even larger number of proteins are required to synthesize these subunits and assemble the enzyme complex. This review aims to follow the complete "life cycle" of plant complex I from various molecular perspectives. We provide arguments that complex I represents an ideal model system for studying the interplay of respiration and photosynthesis, the cooperation of mitochondria and the nucleus during organelle biogenesis and the evolution of the mitochondrial oxidative phosphorylation system. Copyright © 2014 Elsevier B.V. and Mitochondria Research Society. All rights reserved.

A program code generator for multiphysics biological simulation using markup languages.

PubMed

Amano, Akira; Kawabata, Masanari; Yamashita, Yoshiharu; Rusty Punzalan, Florencio; Shimayoshi, Takao; Kuwabara, Hiroaki; Kunieda, Yoshitoshi

2012-01-01

To cope with the complexity of the biological function simulation models, model representation with description language is becoming popular. However, simulation software itself becomes complex in these environment, thus, it is difficult to modify the simulation conditions, target computation resources or calculation methods. In the complex biological function simulation software, there are 1) model equations, 2) boundary conditions and 3) calculation schemes. Use of description model file is useful for first point and partly second point, however, third point is difficult to handle for various calculation schemes which is required for simulation models constructed from two or more elementary models. We introduce a simulation software generation system which use description language based description of coupling calculation scheme together with cell model description file. By using this software, we can easily generate biological simulation code with variety of coupling calculation schemes. To show the efficiency of our system, example of coupling calculation scheme with three elementary models are shown.

Computational complexities and storage requirements of some Riccati equation solvers

NASA Technical Reports Server (NTRS)

Utku, Senol; Garba, John A.; Ramesh, A. V.

1989-01-01

The linear optimal control problem of an nth-order time-invariant dynamic system with a quadratic performance functional is usually solved by the Hamilton-Jacobi approach. This leads to the solution of the differential matrix Riccati equation with a terminal condition. The bulk of the computation for the optimal control problem is related to the solution of this equation. There are various algorithms in the literature for solving the matrix Riccati equation. However, computational complexities and storage requirements as a function of numbers of state variables, control variables, and sensors are not available for all these algorithms. In this work, the computational complexities and storage requirements for some of these algorithms are given. These expressions show the immensity of the computational requirements of the algorithms in solving the Riccati equation for large-order systems such as the control of highly flexible space structures. The expressions are also needed to compute the speedup and efficiency of any implementation of these algorithms on concurrent machines.

Polynomiography and Chaos

NASA Astrophysics Data System (ADS)

Kalantari, Bahman

Polynomiography is the algorithmic visualization of iterative systems for computing roots of a complex polynomial. It is well known that iterations of a rational function in the complex plane result in chaotic behavior near its Julia set. In one scheme of computing polynomiography for a given polynomial p(z), we select an individual member from the Basic Family, an infinite fundamental family of rational iteration functions that in particular include Newton's. Polynomiography is an excellent means for observing, understanding, and comparing chaotic behavior for variety of iterative systems. Other iterative schemes in polynomiography are possible and result in chaotic behavior of different kinds. In another scheme, the Basic Family is collectively applied to p(z) and the iterates for any seed in the Voronoi cell of a root converge to that root. Polynomiography reveals chaotic behavior of another kind near the boundary of the Voronoi diagram of the roots. We also describe a novel Newton-Ellipsoid iterative system with its own chaos and exhibit images demonstrating polynomiographies of chaotic behavior of different kinds. Finally, we consider chaos for the more general case of polynomiography of complex analytic functions. On the one hand polynomiography is a powerful medium capable of demonstrating chaos in different forms, it is educationally instructive to students and researchers, also it gives rise to numerous research problems. On the other hand, it is a medium resulting in images with enormous aesthetic appeal to general audiences.

Towards the blackbox computation of magnetic exchange coupling parameters in polynuclear transition-metal complexes: theory, implementation, and application.

PubMed

Phillips, Jordan J; Peralta, Juan E

2013-05-07

We present a method for calculating magnetic coupling parameters from a single spin-configuration via analytic derivatives of the electronic energy with respect to the local spin direction. This method does not introduce new approximations beyond those found in the Heisenberg-Dirac Hamiltonian and a standard Kohn-Sham Density Functional Theory calculation, and in the limit of an ideal Heisenberg system it reproduces the coupling as determined from spin-projected energy-differences. Our method employs a generalized perturbative approach to constrained density functional theory, where exact expressions for the energy to second order in the constraints are obtained by analytic derivatives from coupled-perturbed theory. When the relative angle between magnetization vectors of metal atoms enters as a constraint, this allows us to calculate all the magnetic exchange couplings of a system from derivatives with respect to local spin directions from the high-spin configuration. Because of the favorable computational scaling of our method with respect to the number of spin-centers, as compared to the broken-symmetry energy-differences approach, this opens the possibility for the blackbox exploration of magnetic properties in large polynuclear transition-metal complexes. In this work we outline the motivation, theory, and implementation of this method, and present results for several model systems and transition-metal complexes with a variety of density functional approximations and Hartree-Fock.

Modern Perspectives on Numerical Modeling of Cardiac Pacemaker Cell

PubMed Central

Maltsev, Victor A.; Yaniv, Yael; Maltsev, Anna V.; Stern, Michael D.; Lakatta, Edward G.

2015-01-01

Cardiac pacemaking is a complex phenomenon that is still not completely understood. Together with experimental studies, numerical modeling has been traditionally used to acquire mechanistic insights in this research area. This review summarizes the present state of numerical modeling of the cardiac pacemaker, including approaches to resolve present paradoxes and controversies. Specifically we discuss the requirement for realistic modeling to consider symmetrical importance of both intracellular and cell membrane processes (within a recent “coupled-clock” theory). Promising future developments of the complex pacemaker system models include the introduction of local calcium control, mitochondria function, and biochemical regulation of protein phosphorylation and cAMP production. Modern numerical and theoretical methods such as multi-parameter sensitivity analyses within extended populations of models and bifurcation analyses are also important for the definition of the most realistic parameters that describe a robust, yet simultaneously flexible operation of the coupled-clock pacemaker cell system. The systems approach to exploring cardiac pacemaker function will guide development of new therapies, such as biological pacemakers for treating insufficient cardiac pacemaker function that becomes especially prevalent with advancing age. PMID:24748434

Complexity of heart rate fluctuations in near-term sheep and human fetuses during sleep.

PubMed

Frank, Birgit; Frasch, Martin G; Schneider, Uwe; Roedel, Marcus; Schwab, Matthias; Hoyer, Dirk

2006-10-01

We investigated how the complexity of fetal heart rate fluctuations (fHRF) is related to the sleep states in sheep and human fetuses. The complexity as a function of time scale for fetal heart rate data for 7 sheep and 27 human fetuses was estimated in rapid eye movement (REM) and non-REM sleep by means of permutation entropy and the associated Kullback-Leibler entropy. We found that in humans, fHRF complexity is higher in non-REM than REM sleep, whereas in sheep this relationship is reversed. To show this relation, choice of the appropriate time scale is crucial. In sheep fetuses, we found differences in the complexity of fHRF between REM and non-REM sleep only for larger time scales (above 2.5 s), whereas in human fetuses the complexity was clearly different between REM and non-REM sleep over the whole range of time scales. This may be due to inherent time scales of complexity, which reflect species-specific functions of the autonomic nervous system. Such differences have to be considered when animal data are translated to the human situation.

The 2-oxoacid dehydrogenase multi-enzyme complex of the archaeon Thermoplasma acidophilum - recombinant expression, assembly and characterization.

PubMed

Heath, Caroline; Posner, Mareike G; Aass, Hans C; Upadhyay, Abhishek; Scott, David J; Hough, David W; Danson, Michael J

2007-10-01

The aerobic archaea possess four closely spaced, adjacent genes that encode proteins showing significant sequence identities with the bacterial and eukaryal components comprising the 2-oxoacid dehydrogenase multi-enzyme complexes. However, catalytic activities of such complexes have never been detected in the archaea, although 2-oxoacid ferredoxin oxidoreductases that catalyze the equivalent metabolic reactions are present. In the current paper, we clone and express the four genes from the thermophilic archaeon, Thermoplasma acidophilum, and demonstrate that the recombinant enzymes are active and assemble into a large (M(r) = 5 x 10(6)) multi-enzyme complex. The post-translational incorporation of lipoic acid into the transacylase component of the complex is demonstrated, as is the assembly of this enzyme into a 24-mer core to which the other components bind to give the functional multi-enzyme system. This assembled complex is shown to catalyze the oxidative decarboxylation of branched-chain 2-oxoacids and pyruvate to their corresponding acyl-CoA derivatives. Our data constitute the first proof that the archaea possess a functional 2-oxoacid dehydrogenase complex.

Comparative density functional study of the complexes [UO2(CO3)3]4- and [(UO2)3(CO3)6]6- in aqueous solution.

PubMed

Schlosser, Florian; Moskaleva, Lyudmila V; Kremleva, Alena; Krüger, Sven; Rösch, Notker

2010-06-28

With a relativistic all-electron density functional method, we studied two anionic uranium(VI) carbonate complexes that are important for uranium speciation and transport in aqueous medium, the mononuclear tris(carbonato) complex [UO(2)(CO(3))(3)](4-) and the trinuclear hexa(carbonato) complex [(UO(2))(3)(CO(3))(6)](6-). Focusing on the structures in solution, we applied for the first time a full solvation treatment to these complexes. We approximated short-range effects by explicit aqua ligands and described long-range electrostatic interactions via a polarizable continuum model. Structures and vibrational frequencies of "gas-phase" models with explicit aqua ligands agree best with experiment. This is accidental because the continuum model of the solvent to some extent overestimates the electrostatic interactions of these highly anionic systems with the bulk solvent. The calculated free energy change when three mono-nuclear complexes associate to the trinuclear complex, agrees well with experiment and supports the formation of the latter species upon acidification of a uranyl carbonate solution.

ASSESSMENT OF NEUROTOXICITY USING ASSAYS OF NEURON-GLIA LOCALIZED PROTEINS: CHRONOLOGY AND CRITIQUE

EPA Science Inventory

The achievements in neuroscience research over recent years have greatly advanced our understanding of nervous system structure and function. et, with each increment in knowledge, we are increasingly faced with the realization of the overwhelming complexity of this organ system. ...

Spectral simplicity of apparent complexity. I. The nondiagonalizable metadynamics of prediction

NASA Astrophysics Data System (ADS)

Riechers, Paul M.; Crutchfield, James P.

2018-03-01

Virtually all questions that one can ask about the behavioral and structural complexity of a stochastic process reduce to a linear algebraic framing of a time evolution governed by an appropriate hidden-Markov process generator. Each type of question—correlation, predictability, predictive cost, observer synchronization, and the like—induces a distinct generator class. Answers are then functions of the class-appropriate transition dynamic. Unfortunately, these dynamics are generically nonnormal, nondiagonalizable, singular, and so on. Tractably analyzing these dynamics relies on adapting the recently introduced meromorphic functional calculus, which specifies the spectral decomposition of functions of nondiagonalizable linear operators, even when the function poles and zeros coincide with the operator's spectrum. Along the way, we establish special properties of the spectral projection operators that demonstrate how they capture the organization of subprocesses within a complex system. Circumventing the spurious infinities of alternative calculi, this leads in the sequel, Part II [P. M. Riechers and J. P. Crutchfield, Chaos 28, 033116 (2018)], to the first closed-form expressions for complexity measures, couched either in terms of the Drazin inverse (negative-one power of a singular operator) or the eigenvalues and projection operators of the appropriate transition dynamic.

An Overdetermined System for Improved Autocorrelation Based Spectral Moment Estimator Performance

NASA Technical Reports Server (NTRS)

Keel, Byron M.

1996-01-01

Autocorrelation based spectral moment estimators are typically derived using the Fourier transform relationship between the power spectrum and the autocorrelation function along with using either an assumed form of the autocorrelation function, e.g., Gaussian, or a generic complex form and applying properties of the characteristic function. Passarelli has used a series expansion of the general complex autocorrelation function and has expressed the coefficients in terms of central moments of the power spectrum. A truncation of this series will produce a closed system of equations which can be solved for the central moments of interest. The autocorrelation function at various lags is estimated from samples of the random process under observation. These estimates themselves are random variables and exhibit a bias and variance that is a function of the number of samples used in the estimates and the operational signal-to-noise ratio. This contributes to a degradation in performance of the moment estimators. This dissertation investigates the use autocorrelation function estimates at higher order lags to reduce the bias and standard deviation in spectral moment estimates. In particular, Passarelli's series expansion is cast in terms of an overdetermined system to form a framework under which the application of additional autocorrelation function estimates at higher order lags can be defined and assessed. The solution of the overdetermined system is the least squares solution. Furthermore, an overdetermined system can be solved for any moment or moments of interest and is not tied to a particular form of the power spectrum or corresponding autocorrelation function. As an application of this approach, autocorrelation based variance estimators are defined by a truncation of Passarelli's series expansion and applied to simulated Doppler weather radar returns which are characterized by a Gaussian shaped power spectrum. The performance of the variance estimators determined from a closed system is shown to improve through the application of additional autocorrelation lags in an overdetermined system. This improvement is greater in the narrowband spectrum region where the information is spread over more lags of the autocorrelation function. The number of lags needed in the overdetermined system is a function of the spectral width, the number of terms in the series expansion, the number of samples used in estimating the autocorrelation function, and the signal-to-noise ratio. The overdetermined system provides a robustness to the chosen variance estimator by expanding the region of spectral widths and signal-to-noise ratios over which the estimator can perform as compared to the closed system.

Anharmonic Rovibrational Partition Functions for Fluxional Species at High Temperatures via Monte Carlo Phase Space Integrals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jasper, Ahren W.; Gruey, Zackery B.; Harding, Lawrence B.

Monte Carlo phase space integration (MCPSI) is used to compute full dimensional and fully anharmonic, but classical, rovibrational partition functions for 22 small- and medium-sized molecules and radicals. Several of the species considered here feature multiple minima and low-frequency nonlocal motions, and efficiently sampling these systems is facilitated using curvilinear (stretch, bend, and torsion) coordinates. The curvilinear coordinate MCPSI method is demonstrated to be applicable to the treatment of fluxional species with complex rovibrational structures and as many as 21 fully coupled rovibrational degrees of freedom. Trends in the computed anharmonicity corrections are discussed. For many systems, rovibrational anharmonicities atmore » elevated temperatures are shown to vary consistently with the number of degrees of freedom and with temperature once rovibrational coupling and torsional anharmonicity are accounted for. Larger corrections are found for systems with complex vibrational structures, such as systems with multiple large-amplitude modes and/or multiple minima.« less

Bulk measurements of messy chemistries are needed for a theory of the origins of life

NASA Astrophysics Data System (ADS)

Guttenberg, Nicholas; Virgo, Nathaniel; Chandru, Kuhan; Scharf, Caleb; Mamajanov, Irena

2017-11-01

A feature of many of the chemical systems plausibly involved in the origins of terrestrial life is that they are complex and messy-producing a wide range of compounds via a wide range of mechanisms. However, the fundamental behaviour of such systems is currently not well understood; we do not have the tools to make statistical predictions about such complex chemical networks. This is, in part, due to a lack of quantitative data from which such a theory could be built; specifically, functional measurements of messy chemical systems. Here, we propose that the pantheon of experimental approaches to the origins of life should be expanded to include the study of `functional measurements'-the direct study of bulk properties of chemical systems and their interactions with other compounds, the formation of structures and other behaviours, even in cases where the precise composition and mechanisms are unknown. This article is part of the themed issue 'Reconceptualizing the origins of life'.

Sensorimotor Integration by Corticospinal System

PubMed Central

Moreno-López, Yunuen; Olivares-Moreno, Rafael; Cordero-Erausquin, Matilde; Rojas-Piloni, Gerardo

2016-01-01

The corticospinal (CS) tract is a complex system which targets several areas of the spinal cord. In particular, the CS descending projection plays a major role in motor command, which results from direct and indirect control of spinal cord pre-motor interneurons as well as motoneurons. But in addition, this system is also involved in a selective and complex modulation of sensory feedback. Despite recent evidence confirms that CS projections drive distinct segmental neural circuits that are part of the sensory and pre-motor pathways, little is known about the spinal networks engaged by the corticospinal tract (CST), the organization of CS projections, the intracortical microcircuitry, and the synaptic interactions in the sensorimotor cortex (SMC) that may encode different cortical outputs to the spinal cord. Here is stressed the importance of integrated approaches for the study of sensorimotor function of CS system, in order to understand the functional compartmentalization and hierarchical organization of layer 5 output neurons, who are key elements for motor control and hence, of behavior. PMID:27013985

Sensorimotor Integration by Corticospinal System.

PubMed

Moreno-López, Yunuen; Olivares-Moreno, Rafael; Cordero-Erausquin, Matilde; Rojas-Piloni, Gerardo

2016-01-01

The corticospinal (CS) tract is a complex system which targets several areas of the spinal cord. In particular, the CS descending projection plays a major role in motor command, which results from direct and indirect control of spinal cord pre-motor interneurons as well as motoneurons. But in addition, this system is also involved in a selective and complex modulation of sensory feedback. Despite recent evidence confirms that CS projections drive distinct segmental neural circuits that are part of the sensory and pre-motor pathways, little is known about the spinal networks engaged by the corticospinal tract (CST), the organization of CS projections, the intracortical microcircuitry, and the synaptic interactions in the sensorimotor cortex (SMC) that may encode different cortical outputs to the spinal cord. Here is stressed the importance of integrated approaches for the study of sensorimotor function of CS system, in order to understand the functional compartmentalization and hierarchical organization of layer 5 output neurons, who are key elements for motor control and hence, of behavior.

Synthetic biology: new engineering rules for an emerging discipline

PubMed Central

Andrianantoandro, Ernesto; Basu, Subhayu; Karig, David K; Weiss, Ron

2006-01-01

Synthetic biologists engineer complex artificial biological systems to investigate natural biological phenomena and for a variety of applications. We outline the basic features of synthetic biology as a new engineering discipline, covering examples from the latest literature and reflecting on the features that make it unique among all other existing engineering fields. We discuss methods for designing and constructing engineered cells with novel functions in a framework of an abstract hierarchy of biological devices, modules, cells, and multicellular systems. The classical engineering strategies of standardization, decoupling, and abstraction will have to be extended to take into account the inherent characteristics of biological devices and modules. To achieve predictability and reliability, strategies for engineering biology must include the notion of cellular context in the functional definition of devices and modules, use rational redesign and directed evolution for system optimization, and focus on accomplishing tasks using cell populations rather than individual cells. The discussion brings to light issues at the heart of designing complex living systems and provides a trajectory for future development. PMID:16738572

Synthetic biology: new engineering rules for an emerging discipline.

PubMed

Andrianantoandro, Ernesto; Basu, Subhayu; Karig, David K; Weiss, Ron

2006-01-01

Synthetic biologists engineer complex artificial biological systems to investigate natural biological phenomena and for a variety of applications. We outline the basic features of synthetic biology as a new engineering discipline, covering examples from the latest literature and reflecting on the features that make it unique among all other existing engineering fields. We discuss methods for designing and constructing engineered cells with novel functions in a framework of an abstract hierarchy of biological devices, modules, cells, and multicellular systems. The classical engineering strategies of standardization, decoupling, and abstraction will have to be extended to take into account the inherent characteristics of biological devices and modules. To achieve predictability and reliability, strategies for engineering biology must include the notion of cellular context in the functional definition of devices and modules, use rational redesign and directed evolution for system optimization, and focus on accomplishing tasks using cell populations rather than individual cells. The discussion brings to light issues at the heart of designing complex living systems and provides a trajectory for future development.

A digital front-end and readout microsystem for calorimetry at LHC

NASA Astrophysics Data System (ADS)

Alippi, C.; Appelquist, G.; Berglund, S.; Bohm, C.; Breveglieri, L.; Brigati, S.; Carlson, P.; Cattaneo, P.; Dadda, L.; David, J.; Del Buono, L.; Dell'Acqua, A.; Engström, M.; Fumagalli, G.; Gatti, U.; Genat, J. F.; Goggi, G.; Hansen, M.; Hentzell, H.; Höglund, I.; Inkinen, S.; Kerek, A.; Lebbolo, H.; LeDortz, O.; Lofstedt, B.; Maloberti, F.; Nayman, P.; Persson, S.-T.; Piuri, V.; Salice, F.; Sami, M.; Savoy-Navarro, A.; Stefanelli, R.; Sundblad, R.; Svensson, C.; Torelli, G.; Vanuxem, J. P.; Yamdagni, N.; Yuan, J.; Zitoun, R.

1994-04-01

A digital solution to the front-end electronics for calorimetric detectors at future supercolliders is presented. The solution is based on high speed {A}/{D} converters, a fully programmable pipeline/digital filter chain and local intelligence. Questions of error correction, fault-tolerance and system redundancy are also being considered. A system integration of a multichannel device in a multichip, Silicon-on-Silicon Microsystem hybrid, is used. This solution allows a new level of integration of complex analogue and digital functions, with an excellent flexibility in mixing technologies for the different functional blocks. It also allows a high degree of programmability at both the function and the system level, and offers the possibility of customising the microsystem with detector-specific functions.

Parameter identification for nonlinear aerodynamic systems

NASA Technical Reports Server (NTRS)

Pearson, Allan E.

1990-01-01

Parameter identification for nonlinear aerodynamic systems is examined. It is presumed that the underlying model can be arranged into an input/output (I/O) differential operator equation of a generic form. The algorithm estimation is especially efficient since the equation error can be integrated exactly given any I/O pair to obtain an algebraic function of the parameters. The algorithm for parameter identification was extended to the order determination problem for linear differential system. The degeneracy in a least squares estimate caused by feedback was addressed. A method of frequency analysis for determining the transfer function G(j omega) from transient I/O data was formulated using complex valued Fourier based modulating functions in contrast with the trigonometric modulating functions for the parameter estimation problem. A simulation result of applying the algorithm is given under noise-free conditions for a system with a low pass transfer function.

Crystallization of bi-functional ligand protein complexes.

PubMed

Antoni, Claudia; Vera, Laura; Devel, Laurent; Catalani, Maria Pia; Czarny, Bertrand; Cassar-Lajeunesse, Evelyn; Nuti, Elisa; Rossello, Armando; Dive, Vincent; Stura, Enrico Adriano

2013-06-01

Homodimerization is important in signal transduction and can play a crucial role in many other biological systems. To obtaining structural information for the design of molecules able to control the signalization pathways, the proteins involved will have to be crystallized in complex with ligands that induce dimerization. Bi-functional drugs have been generated by linking two ligands together chemically and the relative crystallizability of complexes with mono-functional and bi-functional ligands has been evaluated. There are problems associated with crystallization with such ligands, but overall, the advantages appear to be greater than the drawbacks. The study involves two matrix metalloproteinases, MMP-12 and MMP-9. Using flexible and rigid linkers we show that it is possible to control the crystal packing and that by changing the ligand-enzyme stoichiometric ratio, one can toggle between having one bi-functional ligand binding to two enzymes and having the same ligand bound to each enzyme. The nature of linker and its point of attachment on the ligand can be varied to aid crystallization, and such variations can also provide valuable structural information about the interactions made by the linker with the protein. We report here the crystallization and structure determination of seven ligand-dimerized complexes. These results suggest that the use of bi-functional drugs can be extended beyond the realm of protein dimerization to include all drug design projects. Copyright © 2013 Elsevier Inc. All rights reserved.

Glucose Modulates Respiratory Complex I Activity in Response to Acute Mitochondrial Dysfunction

PubMed Central

Cannino, Giuseppe; El-Khoury, Riyad; Pirinen, Marja; Hutz, Bettina; Rustin, Pierre; Jacobs, Howard T.; Dufour, Eric

2012-01-01

Proper coordination between glycolysis and respiration is essential, yet the regulatory mechanisms involved in sensing respiratory chain defects and modifying mitochondrial functions accordingly are unclear. To investigate the nature of this regulation, we introduced respiratory bypass enzymes into cultured human (HEK293T) cells and studied mitochondrial responses to respiratory chain inhibition. In the absence of respiratory chain inhibitors, the expression of alternative respiratory enzymes did not detectably alter cell physiology or mitochondrial function. However, in permeabilized cells NDI1 (alternative NADH dehydrogenase) bypassed complex I inhibition, whereas alternative oxidase (AOX) bypassed complex III or IV inhibition. In contrast, in intact cells the effects of the AOX bypass were suppressed by growth on glucose, whereas those produced by NDI1 were unaffected. Moreover, NDI1 abolished the glucose suppression of AOX-driven respiration, implicating complex I as the target of this regulation. Rapid Complex I down-regulation was partly released upon prolonged respiratory inhibition, suggesting that it provides an “emergency shutdown” system to regulate metabolism in response to dysfunctions of the oxidative phosphorylation. This system was independent of HIF1, mitochondrial superoxide, or ATP synthase regulation. Our findings reveal a novel pathway for adaptation to mitochondrial dysfunction and could provide new opportunities for combatting diseases. PMID:23007390

Development of functional ectopic compound eyes in scarabaeid beetles by knockdown of orthodenticle.

PubMed

Zattara, Eduardo E; Macagno, Anna L M; Busey, Hannah A; Moczek, Armin P

2017-11-07

Complex traits like limbs, brains, or eyes form through coordinated integration of diverse cell fates across developmental space and time, yet understanding how complexity and integration emerge from uniform, undifferentiated precursor tissues remains limited. Here, we use ectopic eye formation as a paradigm to investigate the emergence and integration of novel complex structures following massive ontogenetic perturbation. We show that down-regulation via RNAi of a single head patterning gene- orthodenticle -induces ectopic structures externally resembling compound eyes at the middorsal adult head of both basal and derived scarabaeid beetle species (Onthophagini and Oniticellini). Scanning electron microscopy documents ommatidial organization of these induced structures, while immunohistochemistry reveals the presence of rudimentary ommatidial lenses, crystalline cones, and associated neural-like tissue within them. Further, RNA-sequencing experiments show that after orthodenticle down-regulation, the transcriptional signature of the middorsal head-the location of ectopic eye induction-converges onto that of regular compound eyes, including up-regulation of several retina-specific genes. Finally, a light-aversion behavioral assay to assess functionality reveals that ectopic compound eyes can rescue the ability to respond to visual stimuli when wild-type eyes are surgically removed. Combined, our results show that knockdown of a single gene is sufficient for the middorsal head to acquire the competence to ectopically generate a functional compound eye-like structure. These findings highlight the buffering capacity of developmental systems, allowing massive genetic perturbations to be channeled toward orderly and functional developmental outcomes, and render ectopic eye formation a widely accessible paradigm to study the evolution of complex systems. Published under the PNAS license.

Selective CO{sub 2} reduction conjugated with H{sub 2}O oxidation utilizing semiconductor/metal-complex hybrid photocatalysts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morikawa, T., E-mail: morikawa@mosk.tytlabs.co.jp; Sato, S., E-mail: morikawa@mosk.tytlabs.co.jp; Arai, T., E-mail: morikawa@mosk.tytlabs.co.jp

2013-12-10

We developed a new hybrid photocatalyst for CO{sub 2} reduction, which is composed of a semiconductor and a metal complex. In the hybrid photocatalyst, ΔG between the position of conduction band minimum (E{sub CBM}) of the semiconductor and the CO{sub 2} reduction potential of the complex is an essential factor for realizing fast electron transfer from the conduction band of semiconductor to metal complex leading to high photocatalytic activity. On the basis of this concept, the hybrid photocatalyst InP/Ru-complex, which functions in aqueous media, was developed. The photoreduction of CO{sub 2} to formate using water as an electron donor andmore » a proton source was successfully achieved as a Z-scheme system by functionally conjugating the InP/Ru-complex photocatalyst for CO{sub 2} reduction with a TiO{sub 2} photocatalyst for water oxidation. The conversion efficiency from solar energy to chemical energy was ca. 0.04%, which approaches that for photosynthesis in a plant. Because this system can be applied to many other inorganic semiconductors and metal-complex catalysts, the efficiency and reaction selectivity can be enhanced by optimization of the electron transfer process including the energy-band configurations, conjugation conformations, and catalyst structures. This electrical-bias-free reaction is a huge leap forward for future practical applications of artificial photosynthesis under solar irradiation to produce organic species.« less

Field programmable gate array based fuzzy neural signal processing system for differential diagnosis of QRS complex tachycardia and tachyarrhythmia in noisy ECG signals.

PubMed

Chowdhury, Shubhajit Roy

2012-04-01

The paper reports of a Field Programmable Gate Array (FPGA) based embedded system for detection of QRS complex in a noisy electrocardiogram (ECG) signal and thereafter differential diagnosis of tachycardia and tachyarrhythmia. The QRS complex has been detected after application of entropy measure of fuzziness to build a detection function of ECG signal, which has been previously filtered to remove power line interference and base line wander. Using the detected QRS complexes, differential diagnosis of tachycardia and tachyarrhythmia has been performed. The entire algorithm has been realized in hardware on an FPGA. Using the standard CSE ECG database, the algorithm performed highly effectively. The performance of the algorithm in respect of QRS detection with sensitivity (Se) of 99.74% and accuracy of 99.5% is achieved when tested using single channel ECG with entropy criteria. The performance of the QRS detection system has been compared and found to be better than most of the QRS detection systems available in literature. Using the system, 200 patients have been diagnosed with an accuracy of 98.5%.

Neuronal avalanches and learning

NASA Astrophysics Data System (ADS)

de Arcangelis, Lucilla

2011-05-01

Networks of living neurons represent one of the most fascinating systems of biology. If the physical and chemical mechanisms at the basis of the functioning of a single neuron are quite well understood, the collective behaviour of a system of many neurons is an extremely intriguing subject. Crucial ingredient of this complex behaviour is the plasticity property of the network, namely the capacity to adapt and evolve depending on the level of activity. This plastic ability is believed, nowadays, to be at the basis of learning and memory in real brains. Spontaneous neuronal activity has recently shown features in common to other complex systems. Experimental data have, in fact, shown that electrical information propagates in a cortex slice via an avalanche mode. These avalanches are characterized by a power law distribution for the size and duration, features found in other problems in the context of the physics of complex systems and successful models have been developed to describe their behaviour. In this contribution we discuss a statistical mechanical model for the complex activity in a neuronal network. The model implements the main physiological properties of living neurons and is able to reproduce recent experimental results. Then, we discuss the learning abilities of this neuronal network. Learning occurs via plastic adaptation of synaptic strengths by a non-uniform negative feedback mechanism. The system is able to learn all the tested rules, in particular the exclusive OR (XOR) and a random rule with three inputs. The learning dynamics exhibits universal features as function of the strength of plastic adaptation. Any rule could be learned provided that the plastic adaptation is sufficiently slow.

Hierarchical Control Using Networks Trained with Higher-Level Forward Models

PubMed Central

Wayne, Greg; Abbott, L.F.

2015-01-01

We propose and develop a hierarchical approach to network control of complex tasks. In this approach, a low-level controller directs the activity of a “plant,” the system that performs the task. However, the low-level controller may only be able to solve fairly simple problems involving the plant. To accomplish more complex tasks, we introduce a higher-level controller that controls the lower-level controller. We use this system to direct an articulated truck to a specified location through an environment filled with static or moving obstacles. The final system consists of networks that have memorized associations between the sensory data they receive and the commands they issue. These networks are trained on a set of optimal associations that are generated by minimizing cost functions. Cost function minimization requires predicting the consequences of sequences of commands, which is achieved by constructing forward models, including a model of the lower-level controller. The forward models and cost minimization are only used during training, allowing the trained networks to respond rapidly. In general, the hierarchical approach can be extended to larger numbers of levels, dividing complex tasks into more manageable sub-tasks. The optimization procedure and the construction of the forward models and controllers can be performed in similar ways at each level of the hierarchy, which allows the system to be modified to perform other tasks, or to be extended for more complex tasks without retraining lower-levels. PMID:25058706

Impact of pentadecapeptide BPC 157 on muscle healing impaired by systemic corticosteroid application.

PubMed

Pevec, Danira; Novinscak, Tomislav; Brcic, Luka; Sipos, Kristijan; Jukic, Ivana; Staresinic, Mario; Mise, Sandro; Brcic, Iva; Kolenc, Danijela; Klicek, Robert; Banic, Tihomir; Sever, Marko; Kocijan, Ana; Berkopic, Lidija; Radic, Bozo; Buljat, Gojko; Anic, Tomislav; Zoricic, Ivan; Bojanic, Ivan; Seiwerth, Sven; Sikiric, Predrag

2010-03-01

The effect of systemic and local peptide treatment effective in muscle contusion and then on counteraction of corticosteroid-induced impairment was tested. The pentadecapeptide BPC 157, given without a carrier, improved the healing of transected quadriceps muscle. It also improved muscle healing in rats with muscle crush injury when applied systemically or locally. Importantly, it counteracted corticosteroid-impairment in tendon to bone healing. Thus BPC 157 is proposed as an effective treatment that can improve muscle healing in spite of corticosteroid treatment. After the gastrocnemius muscle complex had been injured, rats received BPC 157 (intraperitoneally or locally as a cream) and/or 6alpha-methylprednisolone (intraperitoneally) only once (immediately after injury, sacrifice at 2 h) or once daily (final dose 24 hours before sacrifice and/or assessment procedure at days 1, 2, 4, 7, and 14). Muscle healing was evaluated functionally, macroscopically, and histologically. Without therapy, crushed gastrocnemius muscle complex controls showed limited improvement. 6alpha-methylprednisolone markedly aggravated healing. In contrast, BPC 157 induced faster muscle healing and full function restoration and improved muscle healing despite systemic corticosteroid treatment when given intraperitoneally or locally and demonstrated functionally, macroscopically, and histologically at all investigated intervals. BPC 157 completely reversed systemic corticosteroid-impaired muscle healing.

Solving the quantum many-body problem with artificial neural networks

NASA Astrophysics Data System (ADS)

Carleo, Giuseppe; Troyer, Matthias

2017-02-01

The challenge posed by the many-body problem in quantum physics originates from the difficulty of describing the nontrivial correlations encoded in the exponential complexity of the many-body wave function. Here we demonstrate that systematic machine learning of the wave function can reduce this complexity to a tractable computational form for some notable cases of physical interest. We introduce a variational representation of quantum states based on artificial neural networks with a variable number of hidden neurons. A reinforcement-learning scheme we demonstrate is capable of both finding the ground state and describing the unitary time evolution of complex interacting quantum systems. Our approach achieves high accuracy in describing prototypical interacting spins models in one and two dimensions.

Dissolving variables in connectionist combinatory logic

NASA Technical Reports Server (NTRS)

Barnden, John; Srinivas, Kankanahalli

1990-01-01

A connectionist system which can represent and execute combinator expressions to elegantly solve the variable binding problem in connectionist networks is presented. This system is a graph reduction machine utilizing graph representations and traversal mechanisms similar to ones described in the BoltzCONS system of Touretzky (1986). It is shown that, as combinators eliminate variables by introducing special functions, these functions can be connectionistically implemented without reintroducing variable binding. This approach 'dissolves' an important part of the variable binding problem, in that a connectionist system still has to manipulate complex data structures, but those structures and their manipulations are rendered more uniform.

Operator function modeling: An approach to cognitive task analysis in supervisory control systems

NASA Technical Reports Server (NTRS)

Mitchell, Christine M.

1987-01-01

In a study of models of operators in complex, automated space systems, an operator function model (OFM) methodology was extended to represent cognitive as well as manual operator activities. Development continued on a software tool called OFMdraw, which facilitates construction of an OFM by permitting construction of a heterarchic network of nodes and arcs. Emphasis was placed on development of OFMspert, an expert system designed both to model human operation and to assist real human operators. The system uses a blackboard method of problem solving to make an on-line representation of operator intentions, called ACTIN (actions interpreter).

Policy experimentation and innovation as a response to complexity in China's management of health reforms.

PubMed

Husain, Lewis

2017-08-03

There are increasing criticisms of dominant models for scaling up health systems in developing countries and a recognition that approaches are needed that better take into account the complexity of health interventions. Since Reform and Opening in the late 1970s, Chinese government has managed complex, rapid and intersecting reforms across many policy areas. As with reforms in other policy areas, reform of the health system has been through a process of trial and error. There is increasing understanding of the importance of policy experimentation and innovation in many of China's reforms; this article argues that these processes have been important in rebuilding China's health system. While China's current system still has many problems, progress is being made in developing a functioning system able to ensure broad population access. The article analyses Chinese thinking on policy experimentation and innovation and their use in management of complex reforms. It argues that China's management of reform allows space for policy tailoring and innovation by sub-national governments under a broad agreement over the ends of reform, and that shared understandings of policy innovation, alongside informational infrastructures for the systemic propagation and codification of useful practices, provide a framework for managing change in complex environments and under conditions of uncertainty in which 'what works' is not knowable in advance. The article situates China's use of experimentation and innovation in management of health system reform in relation to recent literature which applies complex systems thinking to global health, and concludes that there are lessons to be learnt from China's approaches to managing complexity in development of health systems for the benefit of the poor.

Lactate oxidation coupled to energy production in mitochondria like particles from Setaria digitata, a filarial parasite.

PubMed

Sivan, V M; Raj, R K

1994-10-14

In the filarial parasite, Setaria digitata, the mitochondria like particles (MLP) show NAD reduction with sodium lactate. The MLP also reduces dye and ferricyanide with lactate. The ferricyanide reduction by lactate is found to be sensitive to the cytochrome o inhibitor orthohydroxy diphenyl (OHD) and complex I inhibitor rotenone, modulated by ADP (+) and ATP (-) and inhibited by pyruvate and oxaloacetate. MLP shows lactate oxidation sensitive to OHD, rotenone and sodium malonate. Thus, the lactate utilizing complex system, consisting of an NADH generating MLP bound lactate dehydrogenase and a lactate flavocytochrome reductase tightly linked to complex I and cytochrome o, produces ATP in functional association with fumarate reductase complex and other enzyme systems. Hence, this study provides new dimensions to the study of metabolism in filarial parasites.

JMS: An Open Source Workflow Management System and Web-Based Cluster Front-End for High Performance Computing.

PubMed

Brown, David K; Penkler, David L; Musyoka, Thommas M; Bishop, Özlem Tastan

2015-01-01

Complex computational pipelines are becoming a staple of modern scientific research. Often these pipelines are resource intensive and require days of computing time. In such cases, it makes sense to run them over high performance computing (HPC) clusters where they can take advantage of the aggregated resources of many powerful computers. In addition to this, researchers often want to integrate their workflows into their own web servers. In these cases, software is needed to manage the submission of jobs from the web interface to the cluster and then return the results once the job has finished executing. We have developed the Job Management System (JMS), a workflow management system and web interface for high performance computing (HPC). JMS provides users with a user-friendly web interface for creating complex workflows with multiple stages. It integrates this workflow functionality with the resource manager, a tool that is used to control and manage batch jobs on HPC clusters. As such, JMS combines workflow management functionality with cluster administration functionality. In addition, JMS provides developer tools including a code editor and the ability to version tools and scripts. JMS can be used by researchers from any field to build and run complex computational pipelines and provides functionality to include these pipelines in external interfaces. JMS is currently being used to house a number of bioinformatics pipelines at the Research Unit in Bioinformatics (RUBi) at Rhodes University. JMS is an open-source project and is freely available at https://github.com/RUBi-ZA/JMS.

JMS: An Open Source Workflow Management System and Web-Based Cluster Front-End for High Performance Computing

PubMed Central

Brown, David K.; Penkler, David L.; Musyoka, Thommas M.; Bishop, Özlem Tastan

2015-01-01

Complex computational pipelines are becoming a staple of modern scientific research. Often these pipelines are resource intensive and require days of computing time. In such cases, it makes sense to run them over high performance computing (HPC) clusters where they can take advantage of the aggregated resources of many powerful computers. In addition to this, researchers often want to integrate their workflows into their own web servers. In these cases, software is needed to manage the submission of jobs from the web interface to the cluster and then return the results once the job has finished executing. We have developed the Job Management System (JMS), a workflow management system and web interface for high performance computing (HPC). JMS provides users with a user-friendly web interface for creating complex workflows with multiple stages. It integrates this workflow functionality with the resource manager, a tool that is used to control and manage batch jobs on HPC clusters. As such, JMS combines workflow management functionality with cluster administration functionality. In addition, JMS provides developer tools including a code editor and the ability to version tools and scripts. JMS can be used by researchers from any field to build and run complex computational pipelines and provides functionality to include these pipelines in external interfaces. JMS is currently being used to house a number of bioinformatics pipelines at the Research Unit in Bioinformatics (RUBi) at Rhodes University. JMS is an open-source project and is freely available at https://github.com/RUBi-ZA/JMS. PMID:26280450

Regeneration in the era of functional genomics and gene network analysis.

PubMed

Smith, Joel; Morgan, Jennifer R; Zottoli, Steven J; Smith, Peter J; Buxbaum, Joseph D; Bloom, Ona E

2011-08-01

What gives an organism the ability to regrow tissues and to recover function where another organism fails is the central problem of regenerative biology. The challenge is to describe the mechanisms of regeneration at the molecular level, delivering detailed insights into the many components that are cross-regulated. In other words, a broad, yet deep dissection of the system-wide network of molecular interactions is needed. Functional genomics has been used to elucidate gene regulatory networks (GRNs) in developing tissues, which, like regeneration, are complex systems. Therefore, we reason that the GRN approach, aided by next generation technologies, can also be applied to study the molecular mechanisms underlying the complex functions of regeneration. We ask what characteristics a model system must have to support a GRN analysis. Our discussion focuses on regeneration in the central nervous system, where loss of function has particularly devastating consequences for an organism. We examine a cohort of cells conserved across all vertebrates, the reticulospinal (RS) neurons, which lend themselves well to experimental manipulations. In the lamprey, a jawless vertebrate, there are giant RS neurons whose large size and ability to regenerate make them particularly suited for a GRN analysis. Adding to their value, a distinct subset of lamprey RS neurons reproducibly fail to regenerate, presenting an opportunity for side-by-side comparison of gene networks that promote or inhibit regeneration. Thus, determining the GRN for regeneration in RS neurons will provide a mechanistic understanding of the fundamental cues that lead to success or failure to regenerate.

Multi-agent-based bio-network for systems biology: protein-protein interaction network as an example.

PubMed

Ren, Li-Hong; Ding, Yong-Sheng; Shen, Yi-Zhen; Zhang, Xiang-Feng

2008-10-01

Recently, a collective effort from multiple research areas has been made to understand biological systems at the system level. This research requires the ability to simulate particular biological systems as cells, organs, organisms, and communities. In this paper, a novel bio-network simulation platform is proposed for system biology studies by combining agent approaches. We consider a biological system as a set of active computational components interacting with each other and with an external environment. Then, we propose a bio-network platform for simulating the behaviors of biological systems and modelling them in terms of bio-entities and society-entities. As a demonstration, we discuss how a protein-protein interaction (PPI) network can be seen as a society of autonomous interactive components. From interactions among small PPI networks, a large PPI network can emerge that has a remarkable ability to accomplish a complex function or task. We also simulate the evolution of the PPI networks by using the bio-operators of the bio-entities. Based on the proposed approach, various simulators with different functions can be embedded in the simulation platform, and further research can be done from design to development, including complexity validation of the biological system.

Single cell transcriptomics to explore the immune system in health and disease†

PubMed Central

Regev, Aviv; Teichmann, Sarah A.

2017-01-01

The immune system varies in cell types, states, and locations. The complex networks, interactions and responses of immune cells produce diverse cellular ecosystems composed of multiple cell types, accompanied by genetic diversity in antigen receptors. Within this ecosystem, innate and adaptive immune cells maintain and protect tissue function, integrity and homeostasis upon changes in functional demands and diverse insults. Characterizing this inherent complexity requires studies at single-cell resolution. Recent advances such as, massively-parallel single cell RNA-Seq and sophisticated computational methods are catalysing a revolution in our understanding of immunology. Here, we provide an overview of the state of single cell genomics methods and an outlook on the use of single-cell techniques to decipher the adaptive and innate components of immunity. PMID:28983043

Neurodevelopment and executive function in autism.

PubMed

O'Hearn, Kirsten; Asato, Miya; Ordaz, Sarah; Luna, Beatriz

2008-01-01

Autism is a neurodevelopmental disorder characterized by social and communication deficits, and repetitive behavior. Studies investigating the integrity of brain systems in autism suggest a wide range of gray and white matter abnormalities that are present early in life and change with development. These abnormalities predominantly affect association areas and undermine functional integration. Executive function, which has a protracted development into adolescence and reflects the integration of complex widely distributed brain function, is also affected in autism. Evidence from studies probing response inhibition and working memory indicate impairments in these core components of executive function, as well as compensatory mechanisms that permit normative function in autism. Studies also demonstrate age-related improvements in executive function from childhood to adolescence in autism, indicating the presence of plasticity and suggesting a prolonged window for effective treatment. Despite developmental gains, mature executive functioning is limited in autism, reflecting abnormalities in wide-spread brain networks that may lead to impaired processing of complex information across all domains.

A Computerized Hospital Patient Information Management System

PubMed Central

Wig, Eldon D.

1982-01-01

The information processing needs of a hospital are many, with varying degrees of complexity. The prime concern in providing an integrated hospital information management system lies in the ability to process the data relating to the single entity for which every hospital functions - the patient. This paper examines the PRIMIS computer system developed to accommodate hospital needs with respect to a central patient registry, inpatients (i.e., Admission/Transfer/Discharge), and out-patients. Finally, the potential for expansion to permit the incorporation of more hospital functions within PRIMIS is examined.

Combined distribution functions: A powerful tool to identify cation coordination geometries in liquid systems

NASA Astrophysics Data System (ADS)

Sessa, Francesco; D'Angelo, Paola; Migliorati, Valentina

2018-01-01

In this work we have developed an analytical procedure to identify metal ion coordination geometries in liquid media based on the calculation of Combined Distribution Functions (CDFs) starting from Molecular Dynamics (MD) simulations. CDFs provide a fingerprint which can be easily and unambiguously assigned to a reference polyhedron. The CDF analysis has been tested on five systems and has proven to reliably identify the correct geometries of several ion coordination complexes. This tool is simple and general and can be efficiently applied to different MD simulations of liquid systems.

A new flow-regulating cell type in the Demosponge Tethya wilhelma - functional cellular anatomy of a leuconoid canal system.

PubMed

Hammel, Jörg U; Nickel, Michael

2014-01-01

Demosponges possess a leucon-type canal system which is characterized by a highly complex network of canal segments and choanocyte chambers. As sponges are sessile filter feeders, their aquiferous system plays an essential role in various fundamental physiological processes. Due to the morphological and architectural complexity of the canal system and the strong interdependence between flow conditions and anatomy, our understanding of fluid dynamics throughout leuconoid systems is patchy. This paper provides comprehensive morphometric data on the general architecture of the canal system, flow measurements and detailed cellular anatomical information to help fill in the gaps. We focus on the functional cellular anatomy of the aquiferous system and discuss all relevant cell types in the context of hydrodynamic and evolutionary constraints. Our analysis is based on the canal system of the tropical demosponge Tethya wilhelma, which we studied using scanning electron microscopy. We found a hitherto undescribed cell type, the reticuloapopylocyte, which is involved in flow regulation in the choanocyte chambers. It has a highly fenestrated, grid-like morphology and covers the apopylar opening. The minute opening of the reticuloapopylocyte occurs in an opened, intermediate and closed state. These states permit a gradual regulation of the total apopylar opening area. In this paper the three states are included in a theoretical study into flow conditions which aims to draw a link between functional cellular anatomy, the hydrodynamic situation and the regular body contractions seen in T. wilhelma. This provides a basis for new hypotheses regarding the function of bypass elements and the role of hydrostatic pressure in body contractions. Our study provides insights into the local and global flow conditions in the sponge canal system and thus enhances current understanding of related physiological processes.

A New Flow-Regulating Cell Type in the Demosponge Tethya wilhelma – Functional Cellular Anatomy of a Leuconoid Canal System

PubMed Central

Hammel, Jörg U.; Nickel, Michael

2014-01-01

Demosponges possess a leucon-type canal system which is characterized by a highly complex network of canal segments and choanocyte chambers. As sponges are sessile filter feeders, their aquiferous system plays an essential role in various fundamental physiological processes. Due to the morphological and architectural complexity of the canal system and the strong interdependence between flow conditions and anatomy, our understanding of fluid dynamics throughout leuconoid systems is patchy. This paper provides comprehensive morphometric data on the general architecture of the canal system, flow measurements and detailed cellular anatomical information to help fill in the gaps. We focus on the functional cellular anatomy of the aquiferous system and discuss all relevant cell types in the context of hydrodynamic and evolutionary constraints. Our analysis is based on the canal system of the tropical demosponge Tethya wilhelma, which we studied using scanning electron microscopy. We found a hitherto undescribed cell type, the reticuloapopylocyte, which is involved in flow regulation in the choanocyte chambers. It has a highly fenestrated, grid-like morphology and covers the apopylar opening. The minute opening of the reticuloapopylocyte occurs in an opened, intermediate and closed state. These states permit a gradual regulation of the total apopylar opening area. In this paper the three states are included in a theoretical study into flow conditions which aims to draw a link between functional cellular anatomy, the hydrodynamic situation and the regular body contractions seen in T. wilhelma. This provides a basis for new hypotheses regarding the function of bypass elements and the role of hydrostatic pressure in body contractions. Our study provides insights into the local and global flow conditions in the sponge canal system and thus enhances current understanding of related physiological processes. PMID:25409176

Analyzing Distributed Functions in an Integrated Hazard Analysis

NASA Technical Reports Server (NTRS)

Morris, A. Terry; Massie, Michael J.

2010-01-01

Large scale integration of today's aerospace systems is achievable through the use of distributed systems. Validating the safety of distributed systems is significantly more difficult as compared to centralized systems because of the complexity of the interactions between simultaneously active components. Integrated hazard analysis (IHA), a process used to identify unacceptable risks and to provide a means of controlling them, can be applied to either centralized or distributed systems. IHA, though, must be tailored to fit the particular system being analyzed. Distributed systems, for instance, must be analyzed for hazards in terms of the functions that rely on them. This paper will describe systems-oriented IHA techniques (as opposed to traditional failure-event or reliability techniques) that should be employed for distributed systems in aerospace environments. Special considerations will be addressed when dealing with specific distributed systems such as active thermal control, electrical power, command and data handling, and software systems (including the interaction with fault management systems). Because of the significance of second-order effects in large scale distributed systems, the paper will also describe how to analyze secondary functions to secondary functions through the use of channelization.

Music in Research and Rehabilitation of Disorders of Consciousness: Psychological and Neurophysiological Foundations.

PubMed

Kotchoubey, Boris; Pavlov, Yuri G; Kleber, Boris

2015-01-01

According to a prevailing view, the visual system works by dissecting stimuli into primitives, whereas the auditory system processes simple and complex stimuli with their corresponding features in parallel. This makes musical stimulation particularly suitable for patients with disorders of consciousness (DoC), because the processing pathways related to complex stimulus features can be preserved even when those related to simple features are no longer available. An additional factor speaking in favor of musical stimulation in DoC is the low efficiency of visual stimulation due to prevalent maladies of vision or gaze fixation in DoC patients. Hearing disorders, in contrast, are much less frequent in DoC, which allows us to use auditory stimulation at various levels of complexity. The current paper overviews empirical data concerning the four main domains of brain functioning in DoC patients that musical stimulation can address: perception (e.g., pitch, timbre, and harmony), cognition (e.g., musical syntax and meaning), emotions, and motor functions. Music can approach basic levels of patients' self-consciousness, which may even exist when all higher-level cognitions are lost, whereas music induced emotions and rhythmic stimulation can affect the dopaminergic reward-system and activity in the motor system respectively, thus serving as a starting point for rehabilitation.

Music in Research and Rehabilitation of Disorders of Consciousness: Psychological and Neurophysiological Foundations

PubMed Central

Kotchoubey, Boris; Pavlov, Yuri G.; Kleber, Boris

2015-01-01

According to a prevailing view, the visual system works by dissecting stimuli into primitives, whereas the auditory system processes simple and complex stimuli with their corresponding features in parallel. This makes musical stimulation particularly suitable for patients with disorders of consciousness (DoC), because the processing pathways related to complex stimulus features can be preserved even when those related to simple features are no longer available. An additional factor speaking in favor of musical stimulation in DoC is the low efficiency of visual stimulation due to prevalent maladies of vision or gaze fixation in DoC patients. Hearing disorders, in contrast, are much less frequent in DoC, which allows us to use auditory stimulation at various levels of complexity. The current paper overviews empirical data concerning the four main domains of brain functioning in DoC patients that musical stimulation can address: perception (e.g., pitch, timbre, and harmony), cognition (e.g., musical syntax and meaning), emotions, and motor functions. Music can approach basic levels of patients’ self-consciousness, which may even exist when all higher-level cognitions are lost, whereas music induced emotions and rhythmic stimulation can affect the dopaminergic reward-system and activity in the motor system respectively, thus serving as a starting point for rehabilitation. PMID:26640445

The interaction of insulin with phospholipids

PubMed Central

Perry, M. C.; Tampion, W.; Lucy, J. A.

1971-01-01

1. A simple two-phase chloroform–aqueous buffer system was used to investigate the interaction of insulin with phospholipids and other amphipathic substances. 2. The distribution of 125I-labelled insulin in this system was determined after incubation at 37°C. Phosphatidic acid, dicetylphosphoric acid and, to a lesser extent, phosphatidylcholine and cetyltrimethylammonium bromide solubilized 125I-labelled insulin in the chloroform phase, indicating the formation of chloroform-soluble insulin–phospholipid or insulin–amphipath complexes. Phosphatidylethanolamine, sphingomyelin, cholesterol, stearylamine and Triton X-100 were without effect. 3. Formation of insulin–phospholipid complex was confirmed by paper chromatography. 4. The two-phase system was adapted to act as a simple functional system with which to investigate possible effects of insulin on the structural and functional properties of phospholipid micelles in chloroform, by using the distribution of [14C]glucose between the two phases as a monitor of phospholipid–insulin interactions. The ability of phospholipids to solubilize [14C]glucose in chloroform increased in the order phosphatidylcholine

SE Capstone Project: Building Systems Engineering Education and Workforce Capacity

DTIC Science & Technology

2012-04-01

This project developed a system to improve fuel efficiency by means of regenerative braking . The team designed a simple system that allows "bolt-on...air traffic control, social networking, credit/debit cards, and anti-lock brakes are only a few functions enabled by complex systems of systems . We...Building Systems Engineering Education and Workforce Capacity SE Capstone Project APRIL 2012 Report Documentation Page Form ApprovedOMB No. 0704

Generalized sample entropy analysis for traffic signals based on similarity measure

NASA Astrophysics Data System (ADS)

Shang, Du; Xu, Mengjia; Shang, Pengjian

2017-05-01

Sample entropy is a prevailing method used to quantify the complexity of a time series. In this paper a modified method of generalized sample entropy and surrogate data analysis is proposed as a new measure to assess the complexity of a complex dynamical system such as traffic signals. The method based on similarity distance presents a different way of signals patterns match showing distinct behaviors of complexity. Simulations are conducted over synthetic data and traffic signals for providing the comparative study, which is provided to show the power of the new method. Compared with previous sample entropy and surrogate data analysis, the new method has two main advantages. The first one is that it overcomes the limitation about the relationship between the dimension parameter and the length of series. The second one is that the modified sample entropy functions can be used to quantitatively distinguish time series from different complex systems by the similar measure.

Grafting of a novel gold(III) complex on nanoporous MCM-41 and evaluation of its toxicity in Saccharomyces cerevisiae.

PubMed

Fazaeli, Yousef; Amini, Mostafa M; Ashourion, Hamed; Heydari, Homayoun; Majdabadi, Abbas; Jalilian, Amir Reza; Abolmaali, Shamsozoha

2011-01-01

The goal of this research was to investigate the potential of newly synthesized gold complex trichloro(2,4,6-trimethylpyridine)Au(III) as an anticancer agent. The gold(III) complex was synthesized and grafted on nanoporous silica, MCM-41, to produce AuCl(3)@PF-MCM- 41 (AuCl(3) grafted on pyridine-functionalized MCM-41). The toxicity of trichloro(2,4,6- trimethylpyridine)Au(III) and AuCl(3)@PF-MCM-41 in Saccharomyces cerevisiae (as a model system) was studied. The gold(III) complex showed a mid cytotoxic effect on yeast viability. Using the drug delivery system, nanoporous MCM-41, the gold(III) complex became a strong inhibitor for growth of yeast cells at a very low concentration. Furthermore, the animal tests revealed a high uptake of AuCl(3)@PF-MCM-41 in tumor cells. The stability of the compound was confirmed in human serum.

Mirror Me: Imitative Responses in Adults with Autism

ERIC Educational Resources Information Center

Schunke, Odette; Schöttle, Daniel; Vettorazzi, Eik; Brandt, Valerie; Kahl, Ursula; Bäumer, Tobias; Ganos, Christos; David, Nicole; Peiker, Ina; Engel, Andreas K; Brass, Marcel; Münchau, Alexander

2016-01-01

Dysfunctions of the human mirror neuron system have been postulated to underlie some deficits in autism spectrum disorders including poor imitative performance and impaired social skills. Using three reaction time experiments addressing mirror neuron system functions under simple and complex conditions, we examined 20 adult autism spectrum…

Performance of Geno-Fuzzy Model on rainfall-runoff predictions in claypan watersheds

USDA-ARS?s Scientific Manuscript database

Fuzzy logic provides a relatively simple approach to simulate complex hydrological systems while accounting for the uncertainty of environmental variables. The objective of this study was to develop a fuzzy inference system (FIS) with genetic algorithm (GA) optimization for membership functions (MF...

Library of the Future: Croydon's New Central Library Complex.

ERIC Educational Resources Information Center

Batt, Chris

1993-01-01

A new library and cultural center in Croyden (England) is described. Function-based areas include library, administration, technical services, museum and galleries, museum offices and store, cinema, tourist information center, and local government offices. Information technology systems include the library management system, office automation, and…

The conundrum of harmonizing resistance surveillance systems on a global level

USDA-ARS?s Scientific Manuscript database

Surveillance systems, particularly those involving complex data over time, provide unique challenges. They are as varied in design, intent, funding and function as the countries in which they exist. The Centers for Disease Control and Prevention define surveillance as ‘the ongoing systematic colle...

Enhancing metaproteomics-The value of models and defined environmental microbial systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Herbst, Florian-Alexander; Lünsmann, Vanessa; Kjeldal, Henrik

Metaproteomicsthe large-scale characterization of the entire protein complement of environmental microbiota at a given point in timehas provided new features to study complex microbial communities in order to unravel these black boxes. Some new technical challenges arose that were not an issue for classical proteome analytics before that could be tackled by the application of different model systems. Here, we review different current and future model systems for metaproteome analysis. We introduce model systems for clinical and biotechnological research questions including acid mine drainage, anaerobic digesters, and activated sludge, following a short introduction to microbial communities and metaproteomics. Model systemsmore » are useful to evaluate the challenges encountered within (but not limited to) metaproteomics, including species complexity and coverage, biomass availability, or reliable protein extraction. Moreover, the implementation of model systems can be considered as a step forward to better understand microbial community responses and ecological functions of single member organisms. In the future, improvements are necessary to fully explore complex environmental systems by metaproteomics.« less

Enhancing metaproteomics-The value of models and defined environmental microbial systems

DOE PAGES

Herbst, Florian-Alexander; Lünsmann, Vanessa; Kjeldal, Henrik; ...

2016-01-21

Metaproteomicsthe large-scale characterization of the entire protein complement of environmental microbiota at a given point in timehas provided new features to study complex microbial communities in order to unravel these black boxes. Some new technical challenges arose that were not an issue for classical proteome analytics before that could be tackled by the application of different model systems. Here, we review different current and future model systems for metaproteome analysis. We introduce model systems for clinical and biotechnological research questions including acid mine drainage, anaerobic digesters, and activated sludge, following a short introduction to microbial communities and metaproteomics. Model systemsmore » are useful to evaluate the challenges encountered within (but not limited to) metaproteomics, including species complexity and coverage, biomass availability, or reliable protein extraction. Moreover, the implementation of model systems can be considered as a step forward to better understand microbial community responses and ecological functions of single member organisms. In the future, improvements are necessary to fully explore complex environmental systems by metaproteomics.« less

Grounding explanations in evolving, diagnostic situations

NASA Technical Reports Server (NTRS)

Johannesen, Leila J.; Cook, Richard I.; Woods, David D.

1994-01-01

Certain fields of practice involve the management and control of complex dynamic systems. These include flight deck operations in commercial aviation, control of space systems, anesthetic management during surgery or chemical or nuclear process control. Fault diagnosis of these dynamic systems generally must occur with the monitored process on-line and in conjunction with maintaining system integrity.This research seeks to understand in more detail what it means for an intelligent system to function cooperatively, or as a 'team player' in complex, dynamic environments. The approach taken was to study human practitioners engaged in the management of a complex, dynamic process: anesthesiologists during neurosurgical operations. The investigation focused on understanding how team members cooperate in management and fault diagnosis and comparing this interaction to the situation with an Artificial Intelligence(AI) system that provides diagnoses and explanations. Of particular concern was to study the ways in which practitioners support one another in keeping aware of relevant information concerning the state of the monitored process and of the problem solving process.

Graph theoretical analysis of complex networks in the brain

PubMed Central

Stam, Cornelis J; Reijneveld, Jaap C

2007-01-01

Since the discovery of small-world and scale-free networks the study of complex systems from a network perspective has taken an enormous flight. In recent years many important properties of complex networks have been delineated. In particular, significant progress has been made in understanding the relationship between the structural properties of networks and the nature of dynamics taking place on these networks. For instance, the 'synchronizability' of complex networks of coupled oscillators can be determined by graph spectral analysis. These developments in the theory of complex networks have inspired new applications in the field of neuroscience. Graph analysis has been used in the study of models of neural networks, anatomical connectivity, and functional connectivity based upon fMRI, EEG and MEG. These studies suggest that the human brain can be modelled as a complex network, and may have a small-world structure both at the level of anatomical as well as functional connectivity. This small-world structure is hypothesized to reflect an optimal situation associated with rapid synchronization and information transfer, minimal wiring costs, as well as a balance between local processing and global integration. The topological structure of functional networks is probably restrained by genetic and anatomical factors, but can be modified during tasks. There is also increasing evidence that various types of brain disease such as Alzheimer's disease, schizophrenia, brain tumours and epilepsy may be associated with deviations of the functional network topology from the optimal small-world pattern. PMID:17908336