Anticipatory Functions, Digital-Analog Forms and Biosemiotics: Integrating the Tools to Model Information and Normativity in Autonomous Biological Agents

We argue that living systems process information such that functionality emerges in them on a continuous basis. We then provide a framework that can explain and model the normativity of biological functionality. In addition we offer an explanation of the anticipatory nature of functionality within our overall approach. We adopt a Peircean approach to Biosemiotics, and a dynamical approach to Digital-Analog relations and to the interplay between different levels of functionality in autonomous systems, taking an integrative approach. We then apply the underlying biosemiotic logic to a particular biological system, giving a model of the B-Cell Receptor signaling system, in order to demonstrate how biosemiotic concepts can be used to build an account of biological information and functionality. Next we show how this framework can be used to explain and model more complex aspects of biological normativity, for example, how cross-talk between different signaling pathways can be avoided. Overall, we describe an integrated theoretical framework for the emergence of normative functions and, consequently, for the way information is transduced across several interconnected organizational levels in an autonomous system, and we demonstrate how this can be applied in real biological phenomena. Our aim is to open the way towards realistic tools for the modeling of information and normativity in autonomous biological agents.     

STACRP: a secure trusted auction oriented clustering based routing protocol for MANET

In mobile ad hoc network?(MANET) nodes have a tendency to drop others’ packet to conserve its own energy. If most of the nodes in a network start to behave in this way, either a portion of the network would be isolated or total network functionality would be hampered. This behavior is known as selfishness. Therefore, selfishness mitigation and enforcing cooperation between nodes is very important to increase the availability of nodes and overall throughput and to achieve the robustness of the network. Both credit and reputation based mechanisms are used to attract nodes to forward others’ packets. In light of this, we propose a game theoretic routing model, Secure Trusted Auction oriented Clustering based Routing Protocol (STACRP), to provide trusted framework for MANET. Two auction mechanisms procurement and Dutch are used to determine the forwarding cost-per-hop for intermediate nodes. Our model is lightweight in terms of computational and communication requirements, yet powerful in terms of flexibility in managing trust between nodes of heterogeneous deployments. It manages trust locally with minimal overhead in terms of extra messages. STACRP organizes the network into 1-hop disjoint clusters and elects the most qualified and trustworthy nodes as Clusterhead. The trust is quantified with carefully chosen parameters having deep impact on network functionality. The trust model is analyzed using Markov chain and is proven as continuous time Markov chain. The security analysis of the model is analyzed to guarantee that the proposed approach achieves a secure reliable routing solution for MANETs. The proposed model have been evaluated with a set of simulations that show STACRP detects selfish nodes and enforces cooperation between nodes and achieves better throughput and packet delivery ratio with lees routing overhead compare to AODV.     

Loss of Infectivity of HIV-1 Particles Produced by Mobile Lymphocytes

HIV-1 spreads by cell-free particles and through direct cell contacts. To discriminate between these two modes of dissemination, an assay in which the cells are cultured under shaking conditions impairing cell-to-cell transmission has been described. We addressed the impact of shaking on HIV-1 particle infectivity. Kinetics of HIV-1 infection in static or shaking conditions confirmed that HIV-1 replication is reduced in mobile lymphocyte T cells. Strikingly, the infectivity of viruses produced by mobile lymphocytes was dramatically reduced. In parallel, the amount of envelope protein present on these particles showed a continuous decrease over time. We conclude that inefficient HIV-1 replication in mobile lymphocytes in this experimental system is not only due to avoidance of viral cell-to-cell transfer but also to the loss of infectivity of the viral particles due to the alteration of the composition and functionality of the particles produced by these lymphocytes. It is important to take these observations into account when studying viral transmission under shaking conditions.     

A Consistent Framework for Assessing the Impacts from Resource Use - A focus on resource functionality (8 pp)

Background The quantification of resource depletion in Life Cycle Assessment has been the topic of much debate; to date no definitive approach for quantifying effects in this impact category has been developed. In this paper we argue that the main reason for this extensive debate is because all methods for quantifying resource depletion impacts have focussed on resource extraction. - Aim and Scope. To further the state of the debate we present a general framework for assessing the impacts of resource use across the entire suite of biotic and abiotic resources. The main aim of this framework is to define the necessary and sufficient set of information required to quantify the effects of resources use. Method logy. Our method is based on a generic concept of the quality state of resource inputs and outputs to and from a production system. Using this approach we show that it is not the extraction of materials which is of concern, but rather the dissipative use and disposal of materials. Using this as a point of departure we develop and define two key variables for use in the modelling of impacts of resource use, namely the ultimate quality limit, which is related to the functionality of the material, and backup technology. Existing methodologies for determining the effects of resource depletion are discussed in the context of this framework. Results We demonstrate the ability of the general framework to describe impacts related to all resource categories: metallic and non-metallic minerals, energy minerals, water, soil, and biotic resources (wild or domesticated plants and animals). Recommendation focus on suggestions for a functionality measure for each of these categories; and how best the two modelling variables derived can be determined.     

Secure outsourcing of modular exponentiations in cloud and cluster computing

Cloud computing and cluster computing are user-centric computing services. The shared software and hardware resources and information can be provided to the computers and other equipments according to the demands of users. A majority of services are deployed through outsourcing. Outsourcing computation allows resource-constrained clients to outsource their complex computation workloads to a powerful server which is rich of computation resources. Modular exponentiation is one of the most complex computations in public key based cryptographic schemes. It is useful to reduce the computation cost of the clients by using outsourcing computation. In this paper, we propose a novel outsourcing algorithm for modular exponentiation based on the new mathematical division under the setting of two non-colluding cloud servers. The base and the power of the outsourced data can be kept private and the efficiency is improved compared with former works.     

On clustering in database servers for supporting mobile clients

The use of mobile computers is gaining popularity. There is an increasing trend in the number of users with laptops, PDAs, and smart phones. Access to information repositories in the future will be dominated by mobile clients rather than traditional “fixed” clients. These mobile clients download information by periodically connecting to repositories of data stored in either databases or file systems. Such mobile clients constitute a new and different kind of workload and exhibit a different access pattern than seen in traditional client server systems. Though file systems have been modified to handle clients that can download information, disconnect, and later reintegrate, databases have not been redesigned to accommodate mobile clients. There is a need to support mobile clients in the context of client server databases. This paper is about organizing the database server to take into consideration the access patterns of mobile clients. We propose the concept of hoard attributes which capture these access patterns. Three different techniques for organizing data on the server based on the hoard attribute are presented. We argue that each technique is suited for a particular workload. The workload is a combination of requests from mobile clients and traditional clients. This reorganization also allows us to address issues of concurrency control, disconnection and replica control in mobile databases. We present simulation results that show the performance of server reorganization using hoard attributes. We also provide an elaborate discussion of issues resulting from this reorganization in this new paradigm taking into account both mobile and traditional clients. This revised version was published online in August 2006 with corrections to the Cover Date.     

Quantifying spatial habitat loss from hydrocarbon development through assessing habitat selection patterns of mule deer

Extraction of oil and natural gas (hydrocarbons) from shale is increasing rapidly in North America, with documented impacts to native species and ecosystems. With shale oil and gas resources on nearly every continent, this development is set to become a major driver of global land‐use change. It is increasingly critical to quantify spatial habitat loss driven by this development to implement effective mitigation strategies and develop habitat offsets. Habitat selection is a fundamental ecological process, influencing both individual fitness and population‐level distribution on the landscape. Examinations of habitat selection provide a natural means for understanding spatial impacts. We examined the impact of natural gas development on habitat selection patterns of mule deer on their winter range in Colorado. We fit resource selection functions in a Bayesian hierarchical framework, with habitat availability defined using a movement‐based modeling approach. Energy development drove considerable alterations to deer habitat selection patterns, with the most substantial impacts manifested as avoidance of well pads with active drilling to a distance of at least 800 m. Deer displayed more nuanced responses to other infrastructure, avoiding pads with active production and roads to a greater degree during the day than night. In aggregate, these responses equate to alteration of behavior by human development in over 50% of the critical winter range in our study area during the day and over 25% at night. Compared to other regions, the topographic and vegetative diversity in the study area appear to provide refugia that allow deer to behaviorally mediate some of the impacts of development. This study, and the methods we employed, provides a template for quantifying spatial take by industrial activities in natural areas and the results offer guidance for policy makers, mangers, and industry when attempting to mitigate habitat loss due to energy development.     

Bayesian Parameter Inference and Model Selection by Population Annealing in Systems Biology

Parameter inference and model selection are very important for mathematical modeling in systems biology. Bayesian statistics can be used to conduct both parameter inference and model selection. Especially, the framework named approximate Bayesian computation is often used for parameter inference and model selection in systems biology. However, Monte Carlo methods needs to be used to compute Bayesian posterior distributions. In addition, the posterior distributions of parameters are sometimes almost uniform or very similar to their prior distributions. In such cases, it is difficult to choose one specific value of parameter with high credibility as the representative value of the distribution. To overcome the problems, we introduced one of the population Monte Carlo algorithms, population annealing. Although population annealing is usually used in statistical mechanics, we showed that population annealing can be used to compute Bayesian posterior distributions in the approximate Bayesian computation framework. To deal with un-identifiability of the representative values of parameters, we proposed to run the simulations with the parameter ensemble sampled from the posterior distribution, named “posterior parameter ensemble”. We showed that population annealing is an efficient and convenient algorithm to generate posterior parameter ensemble. We also showed that the simulations with the posterior parameter ensemble can, not only reproduce the data used for parameter inference, but also capture and predict the data which was not used for parameter inference. Lastly, we introduced the marginal likelihood in the approximate Bayesian computation framework for Bayesian model selection. We showed that population annealing enables us to compute the marginal likelihood in the approximate Bayesian computation framework and conduct model selection depending on the Bayes factor.     

Optimal configuration selection for Reconfigurable Manufacturing Systems

The selection of Reconfigurable Manufacturing Systems (RMS) configurations that include arrangement of machines, equipment selection, and assignment of operations, has a significant impact on their performance. This paper reviews the relevant literature and highlights the gaps that exist in this area of research. A novel “RMS Configuration Selection Approach” is introduced. It consists of two phases; the first deals with the selection of the near-optimal alternative configurations for each possible demand scenario over the considered configuration periods. It uses a constraint satisfaction procedure and powerful meta-heuristics, real-coded Genetic Algorithms (GAs) and Tabu Search (TS), for the continuous optimization of capital cost and system availability. The second phase utilizes integer-coded GAs and TS to determine the alternatives, from those produced in the first phase, that would optimize the degree of transition smoothness over the planning horizon. It uses a stochastic model of the level of reconfiguration smoothness (RS) across all the configuration periods in the planning horizon according to the anticipated demand scenarios. This model is based on a RS metric and a reconfiguration planning procedure that guide the development of execution plans for reconfiguration. The developed approach is demonstrated and validated using a case study. It was shown that it is possible to provide the manufacturing capacity and functionality needed when needed while minimizing the reconfiguration effort. The proposed approach can provide decision support for management in selecting RMS configurations at the beginning of each configuration period.     

Bayesian mapping of genomewide interacting quantitative trait loci for ordinal traits

Development of statistical methods and software for mapping interacting QTL has been the focus of much recent research. We previously developed a Bayesian model selection framework, based on the composite model space approach, for mapping multiple epistatic QTL affecting continuous traits. In this study we extend the composite model space approach to complex ordinal traits in experimental crosses. We jointly model main and epistatic effects of QTL and environmental factors on the basis of the ordinal probit model (also called threshold model) that assumes a latent continuous trait underlies the generation of the ordinal phenotypes through a set of unknown thresholds. A data augmentation approach is developed to jointly generate the latent data and the thresholds. The proposed ordinal probit model, combined with the composite model space framework for continuous traits, offers a convenient way for genomewide interacting QTL analysis of ordinal traits. We illustrate the proposed method by detecting new QTL and epistatic effects for an ordinal trait, dead fetuses, in a F(2) intercross of mice. Utility and flexibility of the method are also demonstrated using a simulated data set. Our method has been implemented in the freely available package R/qtlbim, which greatly facilitates the general usage of the Bayesian methodology for genomewide interacting QTL analysis for continuous, binary, and ordinal traits in experimental crosses.     

Group-theoretical approaches in molecular magnetism: Metal clusters

In this article I review the application of the group-theoretical approaches to a wide area of molecular magnetism dealing with metal clusters. The following main aspects are discussed: (1) irreducible tensor operator (ITO) approach that is based on the so-called “spin-symmetry”. Use of this approach in molecular magnetism has given a revolutionary impact on the evaluation of the energy levels, thermodynamic and spectroscopic properties of high-nuclearity metal clusters. ITO approach facilitated development and applications of the isotropic and anisotropic spin-Hamiltonians and the study of the magnetic anisotropy in clusters containing orbitally degenerate metal ions; (2) group-theoretical classification (assignment) of the exchange multiplets based on both spin-symmetry and point symmetry that allows to analyze the non-Heisenberg forms of the exchange interaction and magnetic anisotropy in general terms, establishes selection rules for magnetic resonance transitions and facilitates computation of spin levels. This approach allows also to reveal the selection rules for the active Jahn–Teller coupling and to clear understand the interrelation between spin frustration and structural instabilities; (3) group-theoretical classification of the delocalized electronic and electron-vibrational states of mixed-valence compounds in terms of spin and point symmetries (including delocalization of the electronic pair) that essentially reduces the time of calculations and provides direct assess to the selection rules for different kinds of transitions. This becomes crucial in the dynamical vibronic problems inherently related to mixed-valency even for the truncated basis sets when the calculations become hardly executable not only in the case of strong vibronic coupling but even provided that the vibronic coupling is moderate. The proposed approach includes the design of the symmetry adapted vibronic basis and can enormously extend computational abilities in the dynamical problem of mixed-valency.     

Estimating impact of food choices on life expectancy: A modeling study

BackgroundInterpreting and utilizing the findings of nutritional research can be challenging to clinicians, policy makers, and even researchers. To make better decisions about diet, innovative methods that integrate best evidence are needed. We have developed a decision support model that predicts how dietary choices affect life expectancy (LE).Methods and findingsBased on meta-analyses and data from the Global Burden of Disease study (2019), we used life table methodology to estimate how LE changes with sustained changes in the intake of fruits, vegetables, whole grains, refined grains, nuts, legumes, fish, eggs, milk/dairy, red meat, processed meat, and sugar-sweetened beverages. We present estimates (with 95% uncertainty intervals [95% UIs]) for an optimized diet and a feasibility approach diet. An optimal diet had substantially higher intake than a typical diet of whole grains, legumes, fish, fruits, vegetables, and included a handful of nuts, while reducing red and processed meats, sugar-sweetened beverages, and refined grains. A feasibility approach diet was a midpoint between an optimal and a typical Western diet. A sustained change from a typical Western diet to the optimal diet from age 20 years would increase LE by more than a decade for women from the United States (10.7 [95% UI 8.4 to 12.3] years) and men (13.0 [95% UI 9.4 to 14.3] years). The largest gains would be made by eating more legumes (females: 2.2 [95% UI 1.1 to 3.4]; males: 2.5 [95% UI 1.1 to 3.9]), whole grains (females: 2.0 [95% UI 1.3 to 2.7]; males: 2.3 [95% UI 1.6 to 3.0]), and nuts (females: 1.7 [95% UI 1.5 to 2.0]; males: 2.0 [95% UI 1.7 to 2.3]), and less red meat (females: 1.6 [95% UI 1.5 to 1.8]; males: 1.9 [95% UI 1.7 to 2.1]) and processed meat (females: 1.6 [95% UI 1.5 to 1.8]; males: 1.9 [95% UI 1.7 to 2.1]). Changing from a typical diet to the optimized diet at age 60 years would increase LE by 8.0 (95% UI 6.2 to 9.3) years for women and 8.8 (95% UI 6.8 to 10.0) years for men, and 80-year-olds would gain 3.4 years (95% UI females: 2.6 to 3.8/males: 2.7 to 3.9). Change from typical to feasibility approach diet would increase LE by 6.2 (95% UI 3.5 to 8.1) years for 20-year-old women from the United States and 7.3 (95% UI 4.7 to 9.5) years for men. Using NutriGrade, the overall quality of evidence was assessed as moderate. The methodology provides population estimates under given assumptions and is not meant as individualized forecasting, with study limitations that include uncertainty for time to achieve full effects, the effect of eggs, white meat, and oils, individual variation in protective and risk factors, uncertainties for future development of medical treatments; and changes in lifestyle.ConclusionsA sustained dietary change may give substantial health gains for people of all ages both for optimized and feasible changes. Gains are predicted to be larger the earlier the dietary changes are initiated in life. The Food4HealthyLife calculator that we provide online could be useful for clinicians, policy makers, and laypeople to understand the health impact of dietary choices.

Lars Fadnes and co-workers estimate the possible benefits to life expectancy from adoption of more healthy diets.     

Decreasing the Burden of Type 2 Diabetes in South Africa: The Impact of Taxing Sugar-Sweetened Beverages

Introduction

Type 2 diabetes poses an increasing public health burden in South Africa (SA) with obesity as the main driver of the epidemic. Consumption of sugar sweetened beverages (SSBs) is linked to weight gain and reducing SSB consumption may significantly impact the prevalence of obesity and related diseases. We estimated the effect of a 20% SSB tax on the burden of diabetes in SA.

Methods and Findings

We constructed a life table-based model in Microsoft Excel (2010). Consumption data from the 2012 SA National Health and Nutrition Examination Survey, previously published own- and cross-price elasticities of SSBs and energy balance equations were used to estimate changes in daily energy intake and its projected impact on BMI arising from increased SSB prices. Diabetes relative risk and prevalent years lived with disability estimates from the Global Burden of Disease Study and modelled disease epidemiology estimates from a previous study were used to estimate the effect of the BMI changes on diabetes burden. Diabetes cost estimates were obtained from the South African Council for Medical Schemes. Over 20 years, a 20% SSB tax could reduce diabetes incident cases by 106 000 in women (95% uncertainty interval (UI) 70 000–142 000) and by 54 000 in men (95% UI: 33 000–80 000); and prevalence in all adults by 4.0% (95% UI: 2.7%-5.3%). Cumulatively over twenty years, approximately 21 000 (95% UI: 14 000–29 000) adult T2DM-related deaths, 374 000 DALYs attributed to T2DM (95% UI: 299 000–463 000) and over ZAR10 billion T2DM healthcare costs (95% UI: ZAR6.8–14.0 billion) equivalent to USD860 million (95% UI: USD570 million–USD1.2 billion) may be averted.

Conclusion

Fiscal policy on SSBs has the potential to mitigate the diabetes epidemic in South Africa and contribute to the National Department of Health goals stated in the National NCD strategic plan.     

Ecological immunology: costly parasite defences and trade-offs in evolutionary ecology

In the face of continuous threats from parasites, hosts have evolved an elaborate series of preventative and controlling measures - the immune system - in order to reduce the fitness costs of parasitism. However, these measures do have associated costs. Viewing an individual's immune response to parasites as being subject to optimization in the face of other demands offers potential insights into mechanisms of life history trade-offs, sexual selection, parasite-mediated selection and population dynamics. We discuss some recent results that have been obtained by practitioners of this approach in natural and semi-natural populations, and suggest some ways in which this field may progress in the near future.     

Domain selection and familywise error rate for functional data: A unified framework

Functional data are smooth, often continuous, random curves, which can be seen as an extreme case of multivariate data with infinite dimensionality. Just as componentwise inference for multivariate data naturally performs feature selection, subsetwise inference for functional data performs domain selection. In this paper, we present a unified testing framework for domain selection on populations of functional data. In detail, p-values of hypothesis tests performed on pointwise evaluations of functional data are suitably adjusted for providing control of the familywise error rate (FWER) over a family of subsets of the domain. We show that several state-of-the-art domain selection methods fit within this framework and differ from each other by the choice of the family over which the control of the FWER is provided. In the existing literature, these families are always defined a priori. In this work, we also propose a novel approach, coined thresholdwise testing, in which the family of subsets is instead built in a data-driven fashion. The method seamlessly generalizes to multidimensional domains in contrast to methods based on a priori defined families. We provide theoretical results with respect to consistency and control of the FWER for the methods within the unified framework. We illustrate the performance of the methods within the unified framework on simulated and real data examples and compare their performance with other existing methods.     

An integrated analysis of phenotypic selection on insect body size and development time

Most studies of phenotypic selection do not estimate selection or fitness surfaces for multiple components of fitness within a unified statistical framework. This makes it difficult or impossible to assess how selection operates on traits through variation in multiple components of fitness. We describe a new generation of aster models that can evaluate phenotypic selection by accounting for timing of life‐history transitions and their effect on population growth rate, in addition to survival and reproductive output. We use this approach to estimate selection on body size and development time for a field population of the herbivorous insect, Manduca sexta (Lepidoptera: Sphingidae). Estimated fitness surfaces revealed strong and significant directional selection favoring both larger adult size (via effects on egg counts) and more rapid rates of early larval development (via effects on larval survival). Incorporating the timing of reproduction and its influence on population growth rate into the analysis resulted in larger values for size in early larval development at which fitness is maximized, and weaker selection on size in early larval development. These results illustrate how the interplay of different components of fitness can influence selection on size and development time. This integrated modeling framework can be readily applied to studies of phenotypic selection via multiple fitness components in other systems.     

Effect of temperature on biofilm formation by Antarctic marine bacteria in a microfluidic device

Polar biofilms have become an increasingly popular biological issue because new materials and phenotypes have been discovered in microorganisms in the polar region. Various environmental factors affect the functionality and adaptation of microorganisms. Because the polar region represents an extremely cold environment, polar microorganisms have a functionality different from that of normal microorganisms. Thus, determining the effective temperature for the development of polar biofilms is crucial. Here, we present a simple, novel one-pot assay for analysis of the effect of temperature on formation of Antarctic bacterial biofilm using a microfluidic system where continuous temperature gradients are generated. We find that a specific range of temperature is required for the growth of biofilms. Thus, this microfluidic approach provides precise information regarding the effective temperature for polar biofilm development with a new high-throughput screening format.     

Functional unit and product functionality—addressing increase in consumption and demand for functionality in sustainability assessment with LCA

Purpose

The static functional unit definition in the current LCA framework has limitations in addressing the changing product functionality and associated environmental impact of constantly evolving product technologies. As a result, it overlooks the changes in consumer behaviour of increased consumption of products in provided services as well as in growing volumes. This article aims to present a new framework in defining a dynamic functional unit of product technologies that caters for changes in consumer behaviour and growing market.

Methods

A new approach to defining the functional unit is proposed that caters for changes in consumer behaviour and the use of technology from a technical performance perspective. A dynamic approach to definition of the functional unit is proposed that is based on Kano’s model of product function and satisfaction.

Results and discussion

The new approach is demonstrated on a case study in which the analysis of historical data for two TV product technologies—CRT and LCD—is used to show how the total environmental impact is increasing due to the increased functionality which triggers an increase in the volume of the market. Despite the efforts of improving product life cycle design, the society is still faced with increasing environmental impact from the product type overall.

Conclusions

This article presents the challenges of using a static, single functional unit definition in an industrial culture with constant evolution of products that influences usage behaviour and demonstrates the vicious circle of improving product efficiency that leads to further consumption and environmental impact. To address this problem, a new framework of dynamic functional unit definition is put forward for performing comparative LCA to manage the development of product life cycle design that helps keep the total environmental impact of the company’s product portfolio within absolute boundaries.

     

Migratory costs and contemporary evolution of reproductive allocation in male chinook salmon

Energetically demanding migrations may impact the resources available for reproductive trait development and activity, and hence favour evolution of new investment strategies for remaining resources. We conducted a large-scale experiment to evaluate the proximate cost of migration on male reproductive investment in chinook salmon (Oncorhynchus tshawytscha) and contemporary evolution of reproductive allocation. Experimentally induced differences in migratory costs (17 km inland and 17 m elevation vs. 100 km and 430 m) influenced dorsal hump size and upper jaw length, two traits influencing male mating success that are developed during migration. Longer migration also reduced tissue energy reserves available for competition and length of breeding life. Corresponding shifts in the balance between natural and sexual selection appear to have been responsible for heritable population divergence in secondary sexual trait investment, in approximately 26 generations, following colonization of spawning sites with different migratory demands.     

NFU-Enabled FASTA: moving bioinformatics applications onto wide area networks

Background  

Advances in Internet technologies have allowed life science researchers to reach beyond the lab-centric research paradigm to create distributed collaborations. Of the existing technologies that support distributed collaborations, there are currently none that simultaneously support data storage and computation as a shared network resource, enabling computational burden to be wholly removed from participating clients. Software using computation-enable logistical networking components of the Internet Backplane Protocol provides a suitable means to accomplish these tasks. Here, we demonstrate software that enables this approach by distributing both the FASTA algorithm and appropriate data sets within the framework of a wide area network.