Cybernetic modeling of adaptive prediction of environmental changes by microorganisms

Microorganisms exhibit varied regulatory strategies such as direct regulation, symmetric anticipatory regulation, asymmetric anticipatory regulation, etc. Current mathematical modeling frameworks for the growth of microorganisms either do not incorporate regulation or assume that the microorganisms utilize the direct regulation strategy. In the present study, we extend the cybernetic modeling framework to account for asymmetric anticipatory regulation strategy. The extended model accurately captures various experimental observations. We use the developed model to explore the fitness advantage provided by the asymmetric anticipatory regulation strategy and observe that the optimal extent of asymmetric regulation depends on the selective pressure that the microorganisms experience. We also explore the importance of timing the response in anticipatory regulation and find that there is an optimal time, dependent on the extent of asymmetric regulation, at which microorganisms should respond anticipatorily to maximize their fitness. We then discuss the advantages offered by the cybernetic modeling framework over other modeling frameworks in modeling the asymmetric anticipatory regulation strategy. (C) 2013 Published by Elsevier Inc.

Fault Tolerance on Large Scale Systems using Adaptive Process Replication

Exascale systems of the future are predicted to have mean time between failures (MTBF) of less than one hour. At such low MTBFs, employing periodic checkpointing alone will result in low efficiency because of the high number of application failures resulting in large amount of lost work due to rollbacks. In such scenarios, it is highly necessary to have proactive fault tolerance mechanisms that can help avoid significant number of failures. In this work, we have developed a mechanism for proactive fault tolerance using partial replication of a set of application processes. Our fault tolerance framework adaptively changes the set of replicated processes periodically based on failure predictions to avoid failures. We have developed an MPI prototype implementation, PAREP-MPI that allows changing the replica set. We have shown that our strategy involving adaptive process replication significantly outperforms existing mechanisms providing up to 20 percent improvement in application efficiency even for exascale systems.

A new adaptive marine policy toolbox to support ecosystem-based approach to management

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Adaptive agent-based manufacturing control and its application to flow shop routing control

The manufacturing industry is currently facing unprecedented challenges from changes and disturbances. The sources of these changes and disturbances are of different scope and magnitude. They can be of a commercial nature, or linked to fast product development and design, or purely operational (e.g. rush order, machine breakdown, material shortage etc.). In order to meet these requirements it is increasingly important that a production operation be flexible and is able to adapt to new and more suitable ways of operating. This paper focuses on a new strategy for enabling manufacturing control systems to adapt to changing conditions both in terms of product variation and production system upgrades. The approach proposed is based on two key concepts: (1) An autonomous and distributed approach to manufacturing control based on multi-agent methods in which so called operational agents represent the key physical and logical elements in the production environment to be controlled - for example, products and machines and the control strategies that drive them and (2) An adaptation mechanism based around the evolutionary concept of replicator dynamics which updates the behaviour of newly formed operational agents based on historical performance records in order to be better suited to the production environment. An application of this approach for route selection of similar products in manufacturing flow shops is developed and is illustrated in this paper using an example based on the control of an automobile paint shop.

Applications in adaptive cluster sampling of Gulf of Alaska rockfish

Adaptive cluster sampling (ACS) has been the subject of many publications about sampling aggregated populations. Choosing the criterion value that invokes ACS remains problematic. We address this problem using data from a June 1999 ACS survey for rockfish, specifically for Pacific ocean perch (Sebastes alutus), and for shortraker (S. borealis) and rougheye (S. aleutianus) rockfish combined. Our hypotheses were that ACS would outperform simple random sampling (SRS) for S. alutus and would be more applicable for S. alutus than for S. borealis and S. aleutianus combined because populations of S. alutus are thought to be more aggregated. Three alternatives for choosing a criterion value were investigated. We chose the strategy that yielded the lowest criterion value and simulated the higher criterion values with the data after the survey. Systematic random sampling was conducted across the whole area to determine the lowest criterion value, and then a new systematic random sample was taken with adaptive sampling around each tow that exceeded the fixed criterion value. ACS yielded gains in precision (SE) over SRS. Bootstrapping showed that the distribution of an ACS estimator is approximately normal, whereas the SRS sampling distribution is skewed and bimodal. Simulation showed that a higher criterion value results in substantially less adaptive sampling with little tradeoff in precision. When time-efficiency was examined, ACS quickly added more samples, but sampling edge units caused this efficiency to be lessened, and the gain in efficiency did not measurably affect our conclusions. ACS for S. alutus should be incorporated with a fixed criterion value equal to the top quartile of previously collected survey data. The second hypothesis was confirmed because ACS did not prove to be more effective for S. borealis-S. aleutianus. Overall, our ACS results were not as optimistic as those previously published in the literature, and indicate the need for further study of this sampling method.

Adaptive evolution of primate TRIM5 alpha, a gene restricting HIV-1 infection

Recent studies showed that nonhuman primate TRIM5 alpha can efficiently block HIV-1 infection in human cell lines. It can also restrict other retroviruses, therefore, suggested as a general defender against retrovirus infection. Here, we present an evolutionary analysis of TRIM5 alpha in primates. Our results demonstrated that TRIM5a has been evolving rapidly in primates, which is likely caused by Darwinian positive selection. The SPRY domain of TRM5 alpha, which may be responsible for recognition of incoming viral capsids showed higher nonsynonymous/synonymous substitution ratios than the non-SPRY domain, indicating that the adaptive evolution of TRIM5a ill primates might be an innate strategy developed in defending retrovirus infection during primate evolution. In addition, the comparative protein sequence analysis suggested that the amino acid substitution pattern at a single site (344R/Q/P) located in the SPRY domain may explain the differences in Susceptibilities of HIV-1 infection in diverse primate species. (c) 2005 Elsevier B.V. All rights reserved.

Dynamic technology leadership: The adaptive role of the CTO

OVERVIEW: The importance of the chief technology officer role is widely accepted, particularly in today's turbulent, global conditions. However, not enough is known about the key activities of CTOs or the factors that influence their priorities. Thirty in-depth interviews conducted with the CTOs in global firms identified key activities: aligning technology and corporate strategy and business models, determining technology entry and exit points, and preparing business cases to secure funding for technology development. The research also showed that priority areas for CTOs are related to technology transition points-major contextual and business discontinuities that impact the focus of the CTO. We conclude that the determination of priorities at these technology transition points is highly idiosyncratic and closely related to whether the CTO functions more or less strategically.

Finding resonance: Adaptive frequency oscillators for dynamic legged locomotion

There is much to gain from providing walking machines with passive dynamics, e.g. by including compliant elements in the structure. These elements can offer interesting properties such as self-stabilization, energy efficiency and simplified control. However, there is still no general design strategy for such robots and their controllers. In particular, the calibration of control parameters is often complicated because of the highly nonlinear behavior of the interactions between passive components and the environment. In this article, we propose an approach in which the calibration of a key parameter of a walking controller, namely its intrinsic frequency, is done automatically. The approach uses adaptive frequency oscillators to automatically tune the intrinsic frequency of the oscillators to the resonant frequency of a compliant quadruped robot The tuning goes beyond simple synchronization and the learned frequency stays in the controller when the robot is put to halt. The controller is model free, robust and simple. Results are presented illustrating how the controller can robustly tune itself to the robot, as well as readapt when the mass of the robot is changed. We also provide an analysis of the convergence of the frequency adaptation for a linearized plant, and show how that analysis is useful for determining which type of sensory feedback must be used for stable convergence. This approach is expected to explain some aspects of developmental processes in biological and artificial adaptive systems that "develop" through the embodied system-environment interactions. © 2006 IEEE.

Adaptive Neural Networks for Control of Movement Trajectories Invariant under Speed and Force Rescaling

This article describes two neural network modules that form part of an emerging theory of how adaptive control of goal-directed sensory-motor skills is achieved by humans and other animals. The Vector-Integration-To-Endpoint (VITE) model suggests how synchronous multi-joint trajectories are generated and performed at variable speeds. The Factorization-of-LEngth-and-TEnsion (FLETE) model suggests how outflow movement commands from a VITE model may be performed at variable force levels without a loss of positional accuracy. The invariance of positional control under speed and force rescaling sheds new light upon a familiar strategy of motor skill development: Skill learning begins with performance at low speed and low limb compliance and proceeds to higher speeds and compliances. The VITE model helps to explain many neural and behavioral data about trajectory formation, including data about neural coding within the posterior parietal cortex, motor cortex, and globus pallidus, and behavioral properties such as Woodworth's Law, Fitts Law, peak acceleration as a function of movement amplitude and duration, isotonic arm movement properties before and after arm-deafferentation, central error correction properties of isometric contractions, motor priming without overt action, velocity amplification during target switching, velocity profile invariance across different movement distances, changes in velocity profile asymmetry across different movement durations, staggered onset times for controlling linear trajectories with synchronous offset times, changes in the ratio of maximum to average velocity during discrete versus serial movements, and shared properties of arm and speech articulator movements. The FLETE model provides new insights into how spina-muscular circuits process variable forces without a loss of positional control. These results explicate the size principle of motor neuron recruitment, descending co-contractive compliance signals, Renshaw cells, Ia interneurons, fast automatic reactive control by ascending feedback from muscle spindles, slow adaptive predictive control via cerebellar learning using muscle spindle error signals to train adaptive movement gains, fractured somatotopy in the opponent organization of cerebellar learning, adaptive compensation for variable moment-arms, and force feedback from Golgi tendon organs. More generally, the models provide a computational rationale for the use of nonspecific control signals in volitional control, or "acts of will", and of efference copies and opponent processing in both reactive and adaptive motor control tasks.

Adaptive Mixture Modelling Metropolis Methods for Bayesian Analysis of Non-linear State-Space Models.

We describe a strategy for Markov chain Monte Carlo analysis of non-linear, non-Gaussian state-space models involving batch analysis for inference on dynamic, latent state variables and fixed model parameters. The key innovation is a Metropolis-Hastings method for the time series of state variables based on sequential approximation of filtering and smoothing densities using normal mixtures. These mixtures are propagated through the non-linearities using an accurate, local mixture approximation method, and we use a regenerating procedure to deal with potential degeneracy of mixture components. This provides accurate, direct approximations to sequential filtering and retrospective smoothing distributions, and hence a useful construction of global Metropolis proposal distributions for simulation of posteriors for the set of states. This analysis is embedded within a Gibbs sampler to include uncertain fixed parameters. We give an example motivated by an application in systems biology. Supplemental materials provide an example based on a stochastic volatility model as well as MATLAB code.

The adaptive significance and prevalence of courtship feeding in Hawaiian swordtail crickets

Males of many insect species feed their partner during courtship and mating. Studies of male nutrient donation in various systems have established that nuptial feeding has evolved mostly through sexual selection. Although there is extensive diversity in form, the function of nuptial gifts is typically limited to either facilitating copulation or increasing ejaculate transfer, depending on the time at which the gift is consumed by females. Unlike other insects, the Hawaiian swordtail cricket Laupala (Gryllidae: Trigonidiinae) exhibits serial transfer of nuptial gifts. Males transfer multiple spermless 'micro' spermatophores over several hours before mating at the end of the day (i.e. before the transfer of a single sperm-containing 'macro' spermatophore). By experimental manipulation of male microspermatophore donation, I tested several hypotheses pertaining to the adaptive significance of nuptial gifts in this system. I found that microspermatophore transfer improves insemination, by causing the female reproductive tract to take in more sperm. This result reveals a previously undocumented function for premating nuptial gift donation among insects. Enhanced sperm transfer due to microspermatophore donation may represent male manipulation or an internal mechanism of post-copulatory choice by females. I also performed experimental manipulation of male photoperiod to investigate how time and gender influence nuptial gift production and mating behavior. I found that the timing of mating is limited in males but not females and that the time of pair formation has consequences for the degree of nuptial gift donation, which suggests that both mating timing and microspermatophore number is important for male reproductive success. Finally, I observed the mating behavior of several trigonidiine taxa for a comparative analysis of sexual behavior and found that other genera also utilize spermless microspermatophores, which suggests that microspermatophore donation may be a common nuptial gift strategy among swordtail crickets. The elaborate nuptial feeding behavior of Hawaiian swordtail crickets prior to mating represents a newly discovered strategy to increase male insemination success rather than mating success. Based on this unexpected result, it is worth exploring whether courtship behaviors in other cricket or insect mating systems have also evolved to increase sperm uptake.

Adaptive intervention design in mobile health: Intervention design and development in the Cell Phone Intervention for You trial.

BACKGROUND/AIMS: The obesity epidemic has spread to young adults, and obesity is a significant risk factor for cardiovascular disease. The prominence and increasing functionality of mobile phones may provide an opportunity to deliver longitudinal and scalable weight management interventions in young adults. The aim of this article is to describe the design and development of the intervention tested in the Cell Phone Intervention for You study and to highlight the importance of adaptive intervention design that made it possible. The Cell Phone Intervention for You study was a National Heart, Lung, and Blood Institute-sponsored, controlled, 24-month randomized clinical trial comparing two active interventions to a usual-care control group. Participants were 365 overweight or obese (body mass index≥25 kg/m2) young adults. METHODS: Both active interventions were designed based on social cognitive theory and incorporated techniques for behavioral self-management and motivational enhancement. Initial intervention development occurred during a 1-year formative phase utilizing focus groups and iterative, participatory design. During the intervention testing, adaptive intervention design, where an intervention is updated or extended throughout a trial while assuring the delivery of exactly the same intervention to each cohort, was employed. The adaptive intervention design strategy distributed technical work and allowed introduction of novel components in phases intended to help promote and sustain participant engagement. Adaptive intervention design was made possible by exploiting the mobile phone's remote data capabilities so that adoption of particular application components could be continuously monitored and components subsequently added or updated remotely. RESULTS: The cell phone intervention was delivered almost entirely via cell phone and was always-present, proactive, and interactive-providing passive and active reminders, frequent opportunities for knowledge dissemination, and multiple tools for self-tracking and receiving tailored feedback. The intervention changed over 2 years to promote and sustain engagement. The personal coaching intervention, alternatively, was primarily personal coaching with trained coaches based on a proven intervention, enhanced with a mobile application, but where all interactions with the technology were participant-initiated. CONCLUSION: The complexity and length of the technology-based randomized clinical trial created challenges in engagement and technology adaptation, which were generally discovered using novel remote monitoring technology and addressed using the adaptive intervention design. Investigators should plan to develop tools and procedures that explicitly support continuous remote monitoring of interventions to support adaptive intervention design in long-term, technology-based studies, as well as developing the interventions themselves.

ALES: a multi-mission adaptive sub-waveform retracker for coastal and open ocean altimetry

Satellite altimetry has revolutionized our understanding of ocean dynamics thanks to frequent sampling and global coverage. Nevertheless, coastal data have been flagged as unreliable due to land and calm water interference in the altimeter and radiometer footprint and uncertainty in the modelling of high-frequency tidal and atmospheric forcing. Our study addresses the first issue, i.e. altimeter footprint contamination, via retracking, presenting ALES, the Adaptive Leading Edge Subwaveform retracker. ALES is potentially applicable to all the pulse-limited altimetry missions and its aim is to retrack both open ocean and coastal data with the same accuracy using just one algorithm. ALES selects part of each returned echo and models it with a classic ”open ocean” Brown functional form, by means of least square estimation whose convergence is found through the Nelder-Mead nonlinear optimization technique. By avoiding echoes from bright targets along the trailing edge, it is capable of retrieving more coastal waveforms than the standard processing. By adapting the width of the estimation window according to the significant wave height, it aims at maintaining the accuracy of the standard processing in both the open ocean and the coastal strip. This innovative retracker is validated against tide gauges in the Adriatic Sea and in the Greater Agulhas System for three different missions: Envisat, Jason-1 and Jason-2. Considerations of noise and biases provide a further verification of the strategy. The results show that ALES is able to provide more reliable 20-Hz data for all three missions in areas where even 1-Hz averages are flagged as unreliable in standard products. Application of the ALES retracker led to roughly a half of the analysed tracks showing a marked improvement in correlation with the tide gauge records, with the rms difference being reduced by a factor of 1.5 for Jason-1 and Jason-2 and over 4 for Envisat in the Adriatic Sea (at the closest point to the tide gauge).

The role of economics in ecosystem based management: The case of the EU Marine Strategy Framework Directive, First lessons learnt and way forward

The EU Marine Strategy Framework Directive (MSFD) sets out a plan of action relating to marine environmental policy and in particular to achieving ‘good environmental status’ (GES) in European marine waters by 2020. Article 8.1 (c) of the Directive calls for ‘an economic and social analysis of the use of those waters and of the cost of degradation of the marine environment’. The MSFD is ‘informed’ by the Ecosystem Approach to management, with GES interpreted in terms of ecosystem functioning and services provision. Implementation of the Ecosystem Approach is expected to be by adaptive management policy and practice. The initial socio-economic assessment was made by maritime EU Member States between 2011 and 2012, with future updates to be made on a regular basis. For the majority of Member States, this assessment has led to an exercise combining an analysis of maritime activities both at national and coastal zone scales, and an analysis of the non-market value of marine waters. In this paper we examine the approaches taken in more detail, outline the main challenges facing the Member States in assessing the economic value of achieving GES as outlined in the Directive and make recommendations for the theoretically sound and practically useful completion of the required follow-up economic assessments specified in the MSFD.

The role of economics in ecosystem based management: The case of the EU Marine Strategy Framework Directive, First lessons learnt and way forward

The EU Marine Strategy Framework Directive (MSFD) sets out a plan of action relating to marine environmental policy and in particular to achieving ‘good environmental status’ (GES) in European marine waters by 2020. Article 8.1 (c) of the Directive calls for ‘an economic and social analysis of the use of those waters and of the cost of degradation of the marine environment’. The MSFD is ‘informed’ by the Ecosystem Approach to management, with GES interpreted in terms of ecosystem functioning and services provision. Implementation of the Ecosystem Approach is expected to be by adaptive management policy and practice. The initial socio-economic assessment was made by maritime EU Member States between 2011 and 2012, with future updates to be made on a regular basis. For the majority of Member States, this assessment has led to an exercise combining an analysis of maritime activities both at national and coastal zone scales, and an analysis of the non-market value of marine waters. In this paper we examine the approaches taken in more detail, outline the main challenges facing the Member States in assessing the economic value of achieving GES as outlined in the Directive and make recommendations for the theoretically sound and practically useful completion of the required follow-up economic assessments specified in the MSFD.