Image segmentation remains one of the major challenges in image analysis and computer vision. Fuzzy clustering, as a soft segmentation method, has been widely studied and successfully applied in mage clustering and segmentation. The fuzzy c-means (FCM) algorithm is the most popular method used in mage segmentation. However, most clustering algorithms such as the k-means and the FCM clustering algorithms search for the final clusters values based on the predetermined initial centers. The FCM clustering algorithms does not consider the space information of pixels and is sensitive to noise. In the paper, presents a new fuzzy c-means (FCM) algorithm with adaptive evolutionary programming that provides image clustering. The features of this algorithm are: 1) firstly, it need not predetermined initial centers. Evolutionary programming will help FCM search for better center and escape bad centers at local minima. Secondly, the spatial distance and the Euclidean distance is also considered in the FCM clustering. So this algorithm is more robust to the noises. Thirdly, the adaptive evolutionary programming is proposed. The mutation rule is adaptively changed with learning the useful knowledge in the evolving process. Experiment results shows that the new image segmentation algorithm is effective. It is providing robustness to noisy images.
One of the most well known methodological criticisms of evolutionary psychology is Gould's claim that the program pays too much attention to adaptations, and not enough to exaptations. Almost as well known is the standard rebuttal of that criticism: namely, that the study of exaptations in fact depends on the study of adaptations. However, as I try to show in this paper, it is premature to think that this is where this debate ends. First, the notion of exaptation that is commonly used in this debate is different from the one that Gould and Vrba originally defined. Noting this is particularly important, since, second, the standard reply to Gould's criticism only works if the criticism is framed in terms of the former notion of exaptation, and not the latter. However, third, this ultimately does not change the outcome of the debate much, as evolutionary psychologists can respond to the revamped criticism of their program by claiming that the original notion of exaptation is theoretically and empirically uninteresting. By discussing these issues further, I also seek to determine, more generally, which ways of approaching the adaptationism debate in evolutionary biology are useful, and which not.
Ferriere, Regis; Legendre, Stéphane
Adaptive dynamics theory has been devised to account for feedbacks between ecological and evolutionary processes. Doing so opens new dimensions to and raises new challenges about evolutionary rescue. Adaptive dynamics theory predicts that successive trait substitutions driven by eco-evolutionary feedbacks can gradually erode population size or growth rate, thus potentially raising the extinction risk. Even a single trait substitution can suffice to degrade population viability drastically at once and cause 'evolutionary suicide'. In a changing environment, a population may track a viable evolutionary attractor that leads to evolutionary suicide, a phenomenon called 'evolutionary trapping'. Evolutionary trapping and suicide are commonly observed in adaptive dynamics models in which the smooth variation of traits causes catastrophic changes in ecological state. In the face of trapping and suicide, evolutionary rescue requires that the population overcome evolutionary threats generated by the adaptive process itself. Evolutionary repellors play an important role in determining how variation in environmental conditions correlates with the occurrence of evolutionary trapping and suicide, and what evolutionary pathways rescue may follow. In contrast with standard predictions of evolutionary rescue theory, low genetic variation may attenuate the threat of evolutionary suicide and small population sizes may facilitate escape from evolutionary traps.
Luca, F; Perry, G H; Di Rienzo, A
Through cultural innovation and changes in habitat and ecology, there have been a number of major dietary shifts in human evolution, including meat eating, cooking, and those associated with plant and animal domestication. The identification of signatures of adaptations to such dietary changes in the genome of extant primates (including humans) may shed light not only on the evolutionary history of our species, but also on the mechanisms that underlie common metabolic diseases in modern human populations. In this review, we provide a brief overview of the major dietary shifts that occurred during hominin evolution, and we discuss the methods and approaches used to identify signals of natural selection in patterns of sequence variation. We then review the results of studies aimed at detecting the genetic loci that played a major role in dietary adaptations and conclude by outlining the potential of future studies in this area.
Luca, F.; Perry, G.H.; Di Rienzo, A.
Through cultural innovation and changes in habitat and ecology, there have been a number of major dietary shifts in human evolution, including meat eating, cooking, and those associated with plant and animal domestication. The identification of signatures of adaptations to such dietary changes in the genome of extant primates (including humans) may shed light not only on the evolutionary history of our species, but also on the mechanisms that underlie common metabolic diseases in modern human populations. In this review, we provide a brief overview of the major dietary shifts that occurred during hominin evolution, and we discuss the methods and approaches used to identify signals of natural selection in patterns of sequence variation. We then review the results of studies aimed at detecting the genetic loci that played a major role in dietary adaptations and conclude by outlining the potential of future studies in this area. PMID:20420525
Csibra, Gergely; Gergely, György
We propose that the cognitive mechanisms that enable the transmission of cultural knowledge by communication between individuals constitute a system of 'natural pedagogy' in humans, and represent an evolutionary adaptation along the hominin lineage. We discuss three kinds of arguments that support this hypothesis. First, natural pedagogy is likely to be human-specific: while social learning and communication are both widespread in non-human animals, we know of no example of social learning by communication in any other species apart from humans. Second, natural pedagogy is universal: despite the huge variability in child-rearing practices, all human cultures rely on communication to transmit to novices a variety of different types of cultural knowledge, including information about artefact kinds, conventional behaviours, arbitrary referential symbols, cognitively opaque skills and know-how embedded in means-end actions. Third, the data available on early hominin technological culture are more compatible with the assumption that natural pedagogy was an independently selected adaptive cognitive system than considering it as a by-product of some other human-specific adaptation, such as language. By providing a qualitatively new type of social learning mechanism, natural pedagogy is not only the product but also one of the sources of the rich cultural heritage of our species.
Szolnoki, Attila; Perc, Matjaž
Our well-being depends on both our personal success and the success of our society. The realization of this fact makes cooperation an essential trait. Experiments have shown that rewards can elevate our readiness to cooperate, but since giving a reward inevitably entails paying a cost for it, the emergence and stability of such behavior remains elusive. Here we show that allowing for the act of rewarding to self-organize in dependence on the success of cooperation creates several evolutionary advantages that instill new ways through which collaborative efforts are promoted. Ranging from indirect territorial battle to the spontaneous emergence and destruction of coexistence, phase diagrams and the underlying spatial patterns reveal fascinatingly rich social dynamics that explain why this costly behavior has evolved and persevered. Comparisons with adaptive punishment, however, uncover an Achilles heel of adaptive rewarding, coming from over-aggression, which in turn hinders optimal utilization of network reciprocity. This may explain why, despite its success, rewarding is not as firmly embedded into our societal organization as punishment.
Adaptation is one of the central concepts in evolutionary theory, which nonetheless has been given different definitions. Some scholars support a historical definition of adaptation, considering it as a trait that is the outcome of natural selection, whereas others support an ahistorical definition, considering it as a trait that contributes to…
A new model for evolving Evolutionary Algorithms is proposed in this paper. The model is based on the Linear Genetic Programming (LGP) technique. Every LGP chromosome encodes an EA which is used for solving a particular problem. Several Evolutionary Algorithms for function optimization, the Traveling Salesman Problem and the Quadratic Assignment Problem are evolved by using the considered model. Numerical experiments show that the evolved Evolutionary Algorithms perform similarly and sometimes even better than standard approaches for several well-known benchmarking problems.
This paper suggests that the behaviours associated with the formal diagnosis of the "disinhibited" form of reactive attachment disorder (RAD) might be seen as a functional adaptation rather than a mental health problem, a facultative response enhancing the probability of survival that is triggered by certain conditions. Although disinhibited RAD is most commonly observed in institutionalised children, similar behaviours may also be a part of the emotional difficulties displayed by some fostered and adopted children (the latter includes those once institutionalised), and these may demonstrate not so much a discrete attachment disorder as either the need to fend for oneself following loss of dedicated caregiving or a lack of opportunity to build specific intimate relationships with dedicated caregivers. In many cases this may be inextricably mixed with the neurobiological and psychological seqelae of maltreatment. Indiscriminate attachment behaviour, from this proposed evolutionary perspective, is less a syndrome of mental ill-health than an astute survival manoeuvre following being orphaned, abandoned or fecklessly reared. Such a response, allied to the innate facility to access caregiving from different adults, could be expected to be initiated by specific events as are the other attachment configurations. Classing disinhibited RAD as an adaptation has implications for helping children brought up under extreme duress when their caregiving environment has changed for the better.
Hintze, Arend; Olson, Randal S.; Adami, Christoph; Hertwig, Ralph
Risk aversion is a common behavior universal to humans and animals alike. Economists have traditionally defined risk preferences by the curvature of the utility function. Psychologists and behavioral economists also make use of concepts such as loss aversion and probability weighting to model risk aversion. Neurophysiological evidence suggests that loss aversion has its origins in relatively ancient neural circuitries (e.g., ventral striatum). Could there thus be an evolutionary origin to risk aversion? We study this question by evolving strategies that adapt to play the equivalent mean payoff gamble. We hypothesize that risk aversion in this gamble is beneficial as an adaptation to living in small groups, and find that a preference for risk averse strategies only evolves in small populations of less than 1,000 individuals, or in populations segmented into groups of 150 individuals or fewer - numbers thought to be comparable to what humans encountered in the past. We observe that risk aversion only evolves when the gamble is a rare event that has a large impact on the individual's fitness. As such, we suggest that rare, high-risk, high-payoff events such as mating and mate competition could have driven the evolution of risk averse behavior in humans living in small groups.
The Water Resource Adaptation Program (WRAP) contributes to the U.S. Environmental Protection Agency’s (U.S. EPA) efforts to provide water resource managers and decision makers with the tools needed to adapt water resources to demographic and economic development, and future clim...
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Yamamichi, Masato; Miner, Brooks E
Recent studies have increasingly recognized evolutionary rescue (adaptive evolution that prevents extinction following environmental change) as an important process in evolutionary biology and conservation science. Researchers have concentrated on single species living in isolation, but populations in nature exist within communities of interacting species, so evolutionary rescue should also be investigated in a multispecies context. We argue that the persistence or extinction of a focal species can be determined solely by evolutionary change in an interacting species. We demonstrate that prey adaptive evolution can prevent predator extinction in two-species predator-prey models, and we derive the conditions under which this indirect evolutionary interaction is essential to prevent extinction following environmental change. A nonevolving predator can be rescued from extinction by adaptive evolution of its prey due to a trade-off for the prey between defense against predation and population growth rate. As prey typically have larger populations and shorter generations than their predators, prey evolution can be rapid and have profound effects on predator population dynamics. We suggest that this process, which we term 'indirect evolutionary rescue', has the potential to be critically important to the ecological and evolutionary responses of populations and communities to dramatic environmental change.
Oong, Tatt Hee; Isa, Nor Ashidi Mat
This paper presents a new evolutionary approach called the hybrid evolutionary artificial neural network (HEANN) for simultaneously evolving an artificial neural networks (ANNs) topology and weights. Evolutionary algorithms (EAs) with strong global search capabilities are likely to provide the most promising region. However, they are less efficient in fine-tuning the search space locally. HEANN emphasizes the balancing of the global search and local search for the evolutionary process by adapting the mutation probability and the step size of the weight perturbation. This is distinguishable from most previous studies that incorporate EA to search for network topology and gradient learning for weight updating. Four benchmark functions were used to test the evolutionary framework of HEANN. In addition, HEANN was tested on seven classification benchmark problems from the UCI machine learning repository. Experimental results show the superior performance of HEANN in fine-tuning the network complexity within a small number of generations while preserving the generalization capability compared with other algorithms.
van Oudenhove, Louise; Cerdá, Xim; Bernstein, Carlos
This study aims to better understand the evolutionary processes allowing species coexistence in eusocial insect communities. We develop a mathematical model that applies adaptive dynamics theory to the evolutionary dynamics of eusocial insects, focusing on the colony as the unit of selection. The model links long-term evolutionary processes to ecological interactions among colonies and seasonal worker production within the colony. Colony population dynamics is defined by both worker production and colony reproduction. Random mutations occur in strategies, and mutant colonies enter the community. The interactions of colonies at the ecological timescale drive the evolution of strategies at the evolutionary timescale by natural selection. This model is used to study two specific traits in ants: worker body size and the degree of collective foraging. For both traits, trade-offs in competitive ability and other fitness components allows to determine conditions in which selection becomes disruptive. Our results illustrate that asymmetric competition underpins diversity in ant communities. PMID:23469162
van Oudenhove, Louise; Cerdá, Xim; Bernstein, Carlos
This study aims to better understand the evolutionary processes allowing species coexistence in eusocial insect communities. We develop a mathematical model that applies adaptive dynamics theory to the evolutionary dynamics of eusocial insects, focusing on the colony as the unit of selection. The model links long-term evolutionary processes to ecological interactions among colonies and seasonal worker production within the colony. Colony population dynamics is defined by both worker production and colony reproduction. Random mutations occur in strategies, and mutant colonies enter the community. The interactions of colonies at the ecological timescale drive the evolution of strategies at the evolutionary timescale by natural selection. This model is used to study two specific traits in ants: worker body size and the degree of collective foraging. For both traits, trade-offs in competitive ability and other fitness components allows to determine conditions in which selection becomes disruptive. Our results illustrate that asymmetric competition underpins diversity in ant communities.
Cooney, Christopher R; Bright, Jen A; Capp, Elliot J R; Chira, Angela M; Hughes, Emma C; Moody, Christopher J A; Nouri, Lara O; Varley, Zoë K; Thomas, Gavin H
The origin and expansion of biological diversity is regulated by both developmental trajectories and limits on available ecological niches. As lineages diversify, an early and often rapid phase of species and trait proliferation gives way to evolutionary slow-downs as new species pack into ever more densely occupied regions of ecological niche space. Small clades such as Darwin's finches demonstrate that natural selection is the driving force of adaptive radiations, but how microevolutionary processes scale up to shape the expansion of phenotypic diversity over much longer evolutionary timescales is unclear. Here we address this problem on a global scale by analysing a crowdsourced dataset of three-dimensional scanned bill morphology from more than 2,000 species. We find that bill diversity expanded early in extant avian evolutionary history, before transitioning to a phase dominated by packing of morphological space. However, this early phenotypic diversification is decoupled from temporal variation in evolutionary rate: rates of bill evolution vary among lineages but are comparatively stable through time. We find that rare, but major, discontinuities in phenotype emerge from rapid increases in rate along single branches, sometimes leading to depauperate clades with unusual bill morphologies. Despite these jumps between groups, the major axes of within-group bill-shape evolution are remarkably consistent across birds. We reveal that macroevolutionary processes underlying global-scale adaptive radiations support Darwinian and Simpsonian ideas of microevolution within adaptive zones and accelerated evolution between distinct adaptive peaks.
Hong Enriquez, Rolando P.; Do, Trang N.
The evolution of life on earth has been a long process that began nearly 3.5 × 109 years ago. In their initial moments, evolution was mainly influenced by anaerobic environments; with the rise of O2 and the corresponding change in bioavailability of metal ions, new mechanisms of survival were created. Here we review the relationships between ancient atmospheric conditions, metal ion bioavailability and adaptation of metals homeostasis during early evolution. A general picture linking geochemistry, biochemistry and homeostasis is supported by the reviewed literature and is further illustrated in this report using simple database searches. PMID:25371266
Morris, Douglas W
The struggle for existence occurs through the vital rates of population growth. This basic fact demonstrates the tight connection between ecology and evolution that defines the emerging field of eco-evolutionary dynamics. An effective synthesis of the interdependencies between ecology and evolution is grounded in six principles. The mechanics of evolution specifies the origin and rules governing traits and evolutionary strategies. Traits and evolutionary strategies achieve their selective value through their functional relationships with fitness. Function depends on the underlying structure of variation and the temporal, spatial and organizational scales of evolution. An understanding of how changes in traits and strategies occur requires conjoining ecological and evolutionary dynamics. Adaptation merges these five pillars to achieve a comprehensive understanding of ecological and evolutionary change. I demonstrate the value of this world-view with reference to the theory and practice of habitat selection. The theory allows us to assess evolutionarily stable strategies and states of habitat selection, and to draw the adaptive landscapes for habitat-selecting species. The landscapes can then be used to forecast future evolution under a variety of climate change and other scenarios.
Goldsmith, Theodore C
Modern programmed (adaptive) theories of biological aging contend that organisms including mammals have generally evolved mechanisms that purposely limit their lifespans in order to obtain an evolutionary benefit. Modern non-programmed theories contend that mammal aging generally results from natural deteriorative processes, and that lifespan differences between species are explained by differences in the degree to which they resist those processes. Originally proposed in the 19th century, programmed aging in mammals has historically been widely summarily rejected as obviously incompatible with the mechanics of the evolution process. However, relatively recent and continuing developments described here have dramatically changed this situation, and programmed mammal aging now has a better evolutionary basis than non-programmed aging. Resolution of this issue is critically important to medical research because the two theories predict that very different biological mechanisms are ultimately responsible for age-related diseases and conditions.
Lucek, Kay; Sivasundar, Arjun; Seehausen, Ole
Rapid phenotypic diversification during biological invasions can either arise by adaptation to alternative environments or by adaptive phenotypic plasticity. Where experimental evidence for adaptive plasticity is common, support for evolutionary diversification is rare. Here, we performed a controlled laboratory experiment using full-sib crosses between ecologically divergent threespine stickleback populations to test for a genetic basis of adaptation. Our populations are from two very different habitats, lake and stream, of a recently invaded range in Switzerland and differ in ecologically relevant morphological traits. We found that in a lake-like food treatment lake fish grow faster than stream fish, resembling the difference among wild type individuals. In contrast, in a stream-like food treatment individuals from both populations grow similarly. Our experimental data suggest that genetically determined diversification has occurred within less than 140 years after the arrival of stickleback in our studied region. PMID:23152900
Zhou, Xiaojun; Shao, Yimin
Evolutionary digital filtering (EDF) exhibits the advantage of avoiding the local optimum problem by using cloning and mating searching rules in an adaptive noise cancellation system. However, convergence performance is restricted by the large population of individuals and the low level of information communication among them. The special beehive structure enables the individuals on neighbour beehive nodes to communicate with each other and thus enhance the information spread and random search ability of the algorithm. By introducing the beehive pattern evolutionary rules into the original EDF, this paper proposes an improved beehive pattern evolutionary digital filter (BP-EDF) to overcome the defects of the original EDF. In the proposed algorithm, a new evolutionary rule which combines competing cloning, complete cloning and assistance mating methods is constructed to enable the individuals distributed on the beehive to communicate with their neighbours. Simulation results are used to demonstrate the improved performance of the proposed algorithm in terms of convergence speed to the global optimum compared with the original methods. Experimental results also verify the effectiveness of the proposed algorithm in extracting feature signals that are contaminated by significant amounts of noise during the fault diagnosis task.
While phenotypic plasticity -the capability to respond to the environment- is vital to organisms, tests of its adaptation have remained indecisive because constraints and selection in variable environments are unknown and entangled. We show that one can determine the phenotype-fitness landscape that specifies selection on plasticity, by uncoupling the environmental cue and stress in a genetically engineered microbial system. Evolutionary trajectories revealed genetic constraints in a regulatory protein, which imposed cross-environment trade-offs that favored specialization. However, depending on the synchronicity and amplitude of the applied cue and stress variations, adaptation could break constraints, resolve trade-offs, and evolve optimal phenotypes that exhibit qualitatively altered (inverse) responses to the cue. Our results provide a first step to explain the adaptive origins of complex behavior in heterogeneous environments.
Dam, Hans G
Predicting the response of the biota to global change remains a formidable endeavor. Zooplankton face challenges related to global warming, ocean acidification, the proliferation of toxic algal blooms, and increasing pollution, eutrophication, and hypoxia. They can respond to these changes by phenotypic plasticity or genetic adaptation. Using the concept of the evolution of reaction norms, I address how adaptive responses can be unequivocally discerned from phenotypic plasticity. To date, relatively few zooplankton studies have been designed for such a purpose. As case studies, I review the evidence for zooplankton adaptation to toxic algal blooms, hypoxia, and climate change. Predicting the response of zooplankton to global change requires new information to determine (a) the trade-offs and costs of adaptation, (b) the rates of evolution versus environmental change, (c) the consequences of adaptation to stochastic or cyclic (toxic algal blooms, coastal hypoxia) versus directional (temperature, acidification, open ocean hypoxia) environmental change, and (d) the interaction of selective pressures, and evolutionary and ecological processes, in promoting or hindering adaptation.
Das, Anupam; Espinosa-Cantú, Adriana; De Maeyer, Dries; Arslan, Ahmed; Van Pee, Michiel; van der Zande, Elisa; Meert, Wim; Yang, Yudi; Zhu, Bo; Marchal, Kathleen; DeLuna, Alexander; Van Noort, Vera; Jelier, Rob; Verstrepen, Kevin J.
Tolerance to high levels of ethanol is an ecologically and industrially relevant phenotype of microbes, but the molecular mechanisms underlying this complex trait remain largely unknown. Here, we use long-term experimental evolution of isogenic yeast populations of different initial ploidy to study adaptation to increasing levels of ethanol. Whole-genome sequencing of more than 30 evolved populations and over 100 adapted clones isolated throughout this two-year evolution experiment revealed how a complex interplay of de novo single nucleotide mutations, copy number variation, ploidy changes, mutator phenotypes, and clonal interference led to a significant increase in ethanol tolerance. Although the specific mutations differ between different evolved lineages, application of a novel computational pipeline, PheNetic, revealed that many mutations target functional modules involved in stress response, cell cycle regulation, DNA repair and respiration. Measuring the fitness effects of selected mutations introduced in non-evolved ethanol-sensitive cells revealed several adaptive mutations that had previously not been implicated in ethanol tolerance, including mutations in PRT1, VPS70 and MEX67. Interestingly, variation in VPS70 was recently identified as a QTL for ethanol tolerance in an industrial bio-ethanol strain. Taken together, our results show how, in contrast to adaptation to some other stresses, adaptation to a continuous complex and severe stress involves interplay of different evolutionary mechanisms. In addition, our study reveals functional modules involved in ethanol resistance and identifies several mutations that could help to improve the ethanol tolerance of industrial yeasts. PMID:26545090
Bosl, W J
The systems approach to genomics seeks quantitative and predictive descriptions of cells and organisms. However, both the theoretical and experimental methods necessary for such studies still need to be developed. We are far from understanding even the simplest collective behavior of biomolecules, cells or organisms. A key aspect to all biological problems, including environmental microbiology, evolution of infectious diseases, and the adaptation of cancer cells is the evolvability of genomes. This is particularly important for Genomes to Life missions, which tend to focus on the prospect of engineering microorganisms to achieve desired goals in environmental remediation and climate change mitigation, and energy production. All of these will require quantitative tools for understanding the evolvability of organisms. Laboratory biodefense goals will need quantitative tools for predicting complicated host-pathogen interactions and finding counter-measures. In this project, we seek to develop methods to simulate how external and internal signals cause the genetic apparatus to adapt and organize to produce complex biochemical systems to achieve survival. This project is specifically directed toward building a computational methodology for simulating the adaptability of genomes. This project investigated the feasibility of using a novel quantitative approach to studying the adaptability of genomes and biochemical pathways. This effort was intended to be the preliminary part of a larger, long-term effort between key leaders in computational and systems biology at Harvard University and LLNL, with Dr. Bosl as the lead PI. Scientific goals for the long-term project include the development and testing of new hypotheses to explain the observed adaptability of yeast biochemical pathways when the myosin-II gene is deleted and the development of a novel data-driven evolutionary computation as a way to connect exploratory computational simulation with hypothesis
Timothy R. McJunkin; Milos Manic
Tomography, used to create images of the internal properties and features of an object, from phased array ultasonics is improved through many sophisiticated methonds of post processing of data. One approach used to improve tomographic results is to prescribe the collection of more data, from different points of few so that data fusion might have a richer data set to work from. This approach can lead to rapid increase in the data needed to be stored and processed. It also does not necessarily lead to have the needed data. This article describes a novel approach to utilizing the data aquired as a basis for adapting the sensors focusing parameters to locate more precisely the features in the material: specifically, two evolutionary methods of autofocusing on a returned signal are coupled with the derivations of the forumulas for spatially locating the feature are given. Test results of the two novel methods of evolutionary based focusing (EBF) illustrate the improved signal strength and correction of the position of feature using the optimized focal timing parameters, called Focused Delay Identification (FoDI).
Aerobic mitochondria serve as the power sources of eukaryotes by producing ATP through oxidative phosphorylation (OXPHOS). The enzymes involved in OXPHOS are multisubunit complexes encoded by both nuclear and mitochondrial DNA. Thus, regulation of respiration is necessarily a highly coordinated process that must organize production, assembly and function of mitochondria to meet an organism's energetic needs. Here I review the role of OXPHOS in metabolic adaptation and diversification of higher animals. On a physiological timescale, endocrine-initiated signaling pathways allow organisms to modulate respiratory enzyme concentration and function under changing environmental conditions. On an evolutionary timescale, mitochondrial enzymes are targets of natural selection, balancing cytonuclear coevolutionary constraints against physiological innovation. By synthesizing our knowledge of biochemistry, physiology and evolution of respiratory regulation, I propose that we can now explore questions at the interface of these fields, from molecular translation of environmental cues to selection on mitochondrial haplotype variation.
Hill, Jane K; Griffiths, Hannah M; Thomas, Chris D
During recent climate warming, many insect species have shifted their ranges to higher latitudes and altitudes. These expansions mirror those that occurred after the Last Glacial Maximum when species expanded from their ice age refugia. Postglacial range expansions have resulted in clines in genetic diversity across present-day distributions, with a reduction in genetic diversity observed in a wide range of insect taxa as one moves from the historical distribution core to the current range margin. Evolutionary increases in dispersal at expanding range boundaries are commonly observed in virtually all insects that have been studied, suggesting a positive feedback between range expansion and the evolution of traits that accelerate range expansion. The ubiquity of this phenomenon suggests that it is likely to be an important determinant of range changes. A better understanding of the extent and speed of adaptation will be crucial to the responses of biodiversity and ecosystems to climate change.
Hanifin, Charles T.; Gilly, William F.
Understanding the processes that generate novel adaptive phenotypes is central to evolutionary biology. We used comparative analyses to reveal the history of tetrodotoxin (TTX) resistance in TTX-bearing salamanders. Resistance to TTX is a critical component of the ability to use TTX defensively but the origin of the TTX-bearing phenotype is unclear. Skeletal muscle of TTX-bearing salamanders (modern newts, family: Salamandridae) is unaffected by TTX at doses far in excess of those that block action potentials in muscle and nerve of other vertebrates. Skeletal muscle of non-TTX-bearing salamandrids is also resistant to TTX but at lower levels. Skeletal muscle TTX resistance in the Salamandridae results from the expression of TTX-resistant variants of the voltage-gated sodium channel NaV 1.4 (SCN4a). We identified four substitutions in the coding region of salSCN4a that are likely responsible for the TTX resistance measured in TTX-bearing salamanders and variation at one of these sites likely explains variation in TTX resistance among other lineages. Our results suggest that exaptation has played a role in the evolution of the TTX-bearing phenotype and provide empirical evidence that complex physiological adaptations can arise through the accumulation of beneficial mutations in the coding region of conserved proteins. PMID:25346116
Hanifin, Charles T; Gilly, William F
Understanding the processes that generate novel adaptive phenotypes is central to evolutionary biology. We used comparative analyses to reveal the history of tetrodotoxin (TTX) resistance in TTX-bearing salamanders. Resistance to TTX is a critical component of the ability to use TTX defensively but the origin of the TTX-bearing phenotype is unclear. Skeletal muscle of TTX-bearing salamanders (modern newts, family: Salamandridae) is unaffected by TTX at doses far in excess of those that block action potentials in muscle and nerve of other vertebrates. Skeletal muscle of non-TTX-bearing salamandrids is also resistant to TTX but at lower levels. Skeletal muscle TTX resistance in the Salamandridae results from the expression of TTX-resistant variants of the voltage-gated sodium channel NaV 1.4 (SCN4a). We identified four substitutions in the coding region of salSCN4a that are likely responsible for the TTX resistance measured in TTX-bearing salamanders and variation at one of these sites likely explains variation in TTX resistance among other lineages. Our results suggest that exaptation has played a role in the evolution of the TTX-bearing phenotype and provide empirical evidence that complex physiological adaptations can arise through the accumulation of beneficial mutations in the coding region of conserved proteins.
Glynn, P. D.
Human biases and heuristics reflect adaptation over our evolutionary past to frequently experienced situations that affected our survival and that provided sharp distinguished feedbacks at the level of the individual. Human behavior, however, is not well adapted to the more diffusely experienced (i.e. less immediately/locally acute) problems and issues that scientists and society often seek to address today. Several human biases are identified that affect how science is conducted and used. These biases include an innate discounting of less visible phenomena/systems and of long-term perspectives; as well as a general lack of consideration of the coupling between the resources that we use and the waste that we consequently produce. Other biases include strong beliefs in human exceptionalism and separatedness from "nature". Francis Bacon (The New Organon, 1620) provided a classification of the factors, of the "idols of the mind", that bias pursuit of greater knowledge. How can we address these biases and the factors that affect behaviour and pursuit of knowledge; and ultimately impact the sustainability and resilience of human societies, resources and environments? A process for critical analysis is proposed that solicits explicit accounting and cognizance of these potential human biases and factors. Seeking a greater diversity of independant perspectives is essential: in both the conduct of science and in its application to the management of natural resources and environments. Accountability, traceability and structured processes are critical in this endeavor. The scientific methods designed during the industrial revolution are necessary, but insufficient, in addressing the issues of today. A new area of study in "the behavioral biogeosciences" is suggested that counters, or at least closely re-evaluates, our normal (i.e. adapted) human priorities of observation and study, as well as our judgements and decision-making.
Laan, Liedewij; Koschwanez, John H; Murray, Andrew W
Cells are organized by functional modules, which typically contain components whose removal severely compromises the module's function. Despite their importance, these components are not absolutely conserved between parts of the tree of life, suggesting that cells can evolve to perform the same biological functions with different proteins. We evolved Saccharomyces cerevisiae for 1000 generations without the important polarity gene BEM1. Initially the bem1∆ lineages rapidly increase in fitness and then slowly reach >90% of the fitness of their BEM1 ancestors at the end of the evolution. Sequencing their genomes and monitoring polarization reveals a common evolutionary trajectory, with a fixed sequence of adaptive mutations, each improving cell polarization by inactivating proteins. Our results show that organisms can be evolutionarily robust to physiologically destructive perturbations and suggest that recovery by gene inactivation can lead to rapid divergence in the parts list for cell biologically important functions. DOI: http://dx.doi.org/10.7554/eLife.09638.001 PMID:26426479
Eizaguirre, Christophe; Baltazar-Soares, Miguel
Despite intense efforts, biodiversity around the globe continues to decrease. To cease this phenomenon, we urgently need a better knowledge not only of the true extent of biodiversity, but also of the evolutionary potential of species to respond to environmental change. These aims are the heart of the developing field of Evolutionary conservation. Here, after describing problems associated with implementing evolutionary perspectives into management, we outline how evolutionary principles can contribute to efficient conservation programmes. We then introduce articles from this special issue on Evolutionary conservation, outlining how each study or review provides tools and concepts to contribute to efficient management of species or populations. Ultimately, we highlight what we believe can be future research avenues for evolutionary conservation.
Program induction generates a computer program that can produce the desired behavior for a given set of situations. Two of the approaches in program induction are inductive logic programming (ILP) and genetic programming (GP). Since their formalisms are so different, these two approaches cannot be integrated easily, although they share many common goals and functionalities. A unification will greatly enhance their problem-solving power. Moreover, they are restricted in the computer languages in which programs can be induced. In this paper, we present a flexible system called LOGENPRO (The LOgic gramar-based GENetic PROgramming system) that uses some of the techniques of GP and ILP. It is based on a formalism of logic grammars. The system applies logic grammars to control the evolution of programs in various programming languages and represent context-sensitive information and domain-dependent knowledge. Experiments have been performed to demonstrate that LOGENPRO can emulate GP and GP with automatically defined functions (ADFs). Moreover, LOGENPRO can employ knowledge such as argument types in a unified framework. The experiments show that LOGENPRO has superior performance to that of GP and GP with ADFs when more domain-dependent knowledge is available. We have applied LOGENPRO to evolve general recursive functions for the even-n-parity problem from noisy training examples. A number of experiments have been performed to determine the impact of domain-specific knowledge and noise in training examples on the speed of learning.
Krause, Mark A
Inquiry into evolutionary adaptations has flourished since the modern synthesis of evolutionary biology. Comparative methods, genetic techniques, and various experimental and modeling approaches are used to test adaptive hypotheses. In psychology, the concept of adaptation is broadly applied and is central to comparative psychology and cognition. The concept of an adaptive specialization of learning is a proposed account for exceptions to general learning processes, as seen in studies of Pavlovian conditioning of taste aversions, sexual responses, and fear. The evidence generally consists of selective associations forming between biologically relevant conditioned and unconditioned stimuli, with conditioned responses differing in magnitude, persistence, or other measures relative to non-biologically relevant stimuli. Selective associations for biologically relevant stimuli may suggest adaptive specializations of learning, but do not necessarily confirm adaptive hypotheses as conceived of in evolutionary biology. Exceptions to general learning processes do not necessarily default to an adaptive specialization explanation, even if experimental results "make biological sense". This paper examines the degree to which hypotheses of adaptive specializations of learning in sexual and fear response systems have been tested using methodologies developed in evolutionary biology (e.g., comparative methods, quantitative and molecular genetics, survival experiments). A broader aim is to offer perspectives from evolutionary biology for testing adaptive hypotheses in psychological science.
Evolutionary programming (EP) has been demonstrated to be an effective method of system identification of single-input-single-output (SISO) systems...This paper investigates the use of EP in system identification of single-input-multioutput (SIMO) systems. EP is used to identify parameters of a
Birk, Frank T.; Smith, Rogers E.
With the completion of the F-111 test-bed Mission Adaptive Wing (MAW) test program's manual flight control system, emphasis has been shifted to flight testing of MAW automatic control modes. These encompass (1) cruise camber control, (2) maneuver camber control, (3) maneuver load control, and (4) maneuver enhancement and load alleviation control. The aircraft is currently cleared to a 2.5-g maneuvering limit due to generally higher variable-incidence wing pivot loads than had been anticipated, especially at the higher wing-camber settings. Buffet is noted to be somewhat higher than expected at the higher camber settings.
Vaccaro, James M.; Guest, Clark C.; Ross, David O.
Many complex artificial intelligence (IA) problems are goal- driven in nature and the opportunity exists to realize the benefits of a goal-oriented solution. In many cases, such as in command and control, a goal-oriented approach may be the only option. One of many appropriate applications for such an approach is War Gaming. War Gaming is an important tool for command and control because it provides a set of alternative courses of actions so that military leaders can contemplate their next move in the battlefield. For instance, when making decisions that save lives, it is necessary to completely understand the consequences of a given order. A goal-oriented approach provides a slowly evolving tractably reasoned solution that inherently follows one of the principles of war: namely concentration on the objective. Future decision-making will depend not only on the battlefield, but also on a virtual world where military leaders can wage wars and determine their options by playing computer war games much like the real world. The problem with these games is that the built-in AI does not learn nor adapt and many times cheats, because the intelligent player has access to all the information, while the user has access to limited information provided on a display. These games are written for the purpose of entertainment and actions are calculated a priori and off-line, and are made prior or during their development. With these games getting more sophisticated in structure and less domain specific in scope, there needs to be a more general intelligent player that can adapt and learn in case the battlefield situations or the rules of engagement change. One such war game that might be considered is Risk. Risk incorporates the principles of war, is a top-down scalable model, and provides a good application for testing a variety of goal- oriented AI approaches. By integrating a goal-oriented hybrid approach, one can develop a program that plays the Risk game effectively and move
Sunday, Jennifer M.; Crim, Ryan N.; Harley, Christopher D. G.; Hart, Michael W.
The global acidification of the earth's oceans is predicted to impact biodiversity via physiological effects impacting growth, survival, reproduction, and immunology, leading to changes in species abundances and global distributions. However, the degree to which these changes will play out critically depends on the evolutionary rate at which populations will respond to natural selection imposed by ocean acidification, which remains largely unquantified. Here we measure the potential for an evolutionary response to ocean acidification in larval development rate in two coastal invertebrates using a full-factorial breeding design. We show that the sea urchin species Strongylocentrotus franciscanus has vastly greater levels of phenotypic and genetic variation for larval size in future CO2 conditions compared to the mussel species Mytilus trossulus. Using these measures we demonstrate that S. franciscanus may have faster evolutionary responses within 50 years of the onset of predicted year-2100 CO2 conditions despite having lower population turnover rates. Our comparisons suggest that information on genetic variation, phenotypic variation, and key demographic parameters, may lend valuable insight into relative evolutionary potentials across a large number of species. PMID:21857962
Zu, Jian; Wang, Jinliang
In this paper, with the methods of adaptive dynamics and critical function analysis, we investigate the evolutionary branching phenomenon of predator species. We assume that both the prey and predators are density-dependent and the predator's attack ability can adaptively evolve, but this has a cost in terms of its death rate. First, we identify the general properties of trade-off relationships that allow for a continuously stable strategy and evolutionary branching in the predator strategy. It is found that if the trade-off curve is weakly concave near the singular strategy, then the singular strategy may be an evolutionary branching point. Second, we find that after the branching has occurred in the predator strategy, if the trade-off curve is convex-concave-convex, the predator species will eventually evolve into two different types, which can stably coexist on the much longer evolutionary timescale and no further branching is possible.
Innate immunity is present in all metazoans, whereas the evolutionarily more novel adaptive immunity is limited to jawed fishes and their descendants (gnathostomes). We observe that the organisms that possess adaptive immunity lack diversity in their innate pattern recognition receptors (PRRs), rais...
Nevado, Bruno; Atchison, Guy W.; Hughes, Colin E.; Filatov, Dmitry A.
The evolutionary processes that drive rapid species diversification are poorly understood. In particular, it is unclear whether Darwinian adaptation or non-adaptive processes are the primary drivers of explosive species diversifications. Here we show that repeated rapid radiations within New World lupins (Lupinus, Leguminosae) were underpinned by a major increase in the frequency of adaptation acting on coding and regulatory changes genome-wide. This contrasts with far less frequent adaptation in genomes of slowly diversifying lupins and all other plant genera analysed. Furthermore, widespread shifts in optimal gene expression coincided with shifts to high rates of diversification and evolution of perenniality, a putative key adaptation trait thought to have triggered the evolutionary radiations in New World lupins. Our results reconcile long-standing debate about the relative importance of protein-coding and regulatory evolution, and represent the first unambiguous evidence for the rapid onset of lineage- and genome-wide accelerated Darwinian evolution during rapid species diversification. PMID:27498896
Notarnicola, Ippolito; Petrucci, Cristina; De Jesus Barbosa, Maria Rosimar; Giorgi, Fabio; Stievano, Alessandro; Rocco, Gennaro; Lancia, Loreto
This study aimed to analyze the concept of "complex adaptive systems." The construct is still nebulous in the literature, and a further explanation of the idea is needed to have a shared knowledge of it. A concept analysis was conducted utilizing Rodgers evolutionary method. The inclusive years of bibliographic search started from 2005 to 2015. The search was conducted at PubMed©, CINAHL© 2017 John Wiley & Sons Australia, Ltd Nursing is a complex adaptive system, and the nursing profession in practice exhibits complex adaptive system characteristics. Complexity science through complex adaptive systems provides new ways of seeing and understanding the mechanisms that underpin the nursing profession.
Shtulman, Andrew; Neal, Cara; Lindquist, Gabrielle
Research Findings: Evolution by natural selection is often relegated to the high school curriculum on the assumption that younger students cannot grasp its complexity. We sought to test that assumption by teaching children ages 4-12 (n = 96) a selection-based explanation for biological adaptation and comparing their success to that of adults…
Fournier-Level, Alexandre; Perry, Emily O; Wang, Jonathan A; Braun, Peter T; Migneault, Andrew; Cooper, Martha D; Metcalf, C Jessica E; Schmitt, Johanna
Predicting whether and how populations will adapt to rapid climate change is a critical goal for evolutionary biology. To examine the genetic basis of fitness and predict adaptive evolution in novel climates with seasonal variation, we grew a diverse panel of the annual plant Arabidopsis thaliana (multiparent advanced generation intercross lines) in controlled conditions simulating four climates: a present-day reference climate, an increased-temperature climate, a winter-warming only climate, and a poleward-migration climate with increased photoperiod amplitude. In each climate, four successive seasonal cohorts experienced dynamic daily temperature and photoperiod variation over a year. We measured 12 traits and developed a genomic prediction model for fitness evolution in each seasonal environment. This model was used to simulate evolutionary trajectories of the base population over 50 y in each climate, as well as 100-y scenarios of gradual climate change following adaptation to a reference climate. Patterns of plastic and evolutionary fitness response varied across seasons and climates. The increased-temperature climate promoted genetic divergence of subpopulations across seasons, whereas in the winter-warming and poleward-migration climates, seasonal genetic differentiation was reduced. In silico "resurrection experiments" showed limited evolutionary rescue compared with the plastic response of fitness to seasonal climate change. The genetic basis of adaptation and, consequently, the dynamics of evolutionary change differed qualitatively among scenarios. Populations with fewer founding genotypes and populations with genetic diversity reduced by prior selection adapted less well to novel conditions, demonstrating that adaptation to rapid climate change requires the maintenance of sufficient standing variation.
Fournier-Level, Alexandre; Perry, Emily O.; Wang, Jonathan A.; Braun, Peter T.; Migneault, Andrew; Cooper, Martha D.; Metcalf, C. Jessica E.; Schmitt, Johanna
Predicting whether and how populations will adapt to rapid climate change is a critical goal for evolutionary biology. To examine the genetic basis of fitness and predict adaptive evolution in novel climates with seasonal variation, we grew a diverse panel of the annual plant Arabidopsis thaliana (multiparent advanced generation intercross lines) in controlled conditions simulating four climates: a present-day reference climate, an increased-temperature climate, a winter-warming only climate, and a poleward-migration climate with increased photoperiod amplitude. In each climate, four successive seasonal cohorts experienced dynamic daily temperature and photoperiod variation over a year. We measured 12 traits and developed a genomic prediction model for fitness evolution in each seasonal environment. This model was used to simulate evolutionary trajectories of the base population over 50 y in each climate, as well as 100-y scenarios of gradual climate change following adaptation to a reference climate. Patterns of plastic and evolutionary fitness response varied across seasons and climates. The increased-temperature climate promoted genetic divergence of subpopulations across seasons, whereas in the winter-warming and poleward-migration climates, seasonal genetic differentiation was reduced. In silico “resurrection experiments” showed limited evolutionary rescue compared with the plastic response of fitness to seasonal climate change. The genetic basis of adaptation and, consequently, the dynamics of evolutionary change differed qualitatively among scenarios. Populations with fewer founding genotypes and populations with genetic diversity reduced by prior selection adapted less well to novel conditions, demonstrating that adaptation to rapid climate change requires the maintenance of sufficient standing variation. PMID:27140640
Siepielski, Adam M; Nemirov, Alex; Cattivera, Matthew; Nickerson, Avery
Determining how adaptive evolution can be coupled to ecological processes is key for developing a more integrative understanding of the demographic factors that regulate populations. Intraspecific competition is an especially important ecological process because it generates negative density dependence in demographic rates. Although ecological factors are most often investigated to determine the strength of density dependence, evolutionary processes such as local adaptation could also feed back to shape variation in the strength of density dependence among populations. Using an experimental approach with damselflies, a predaceous aquatic insect, we find evidence that both density-dependent intraspecific competition and local adaptation can reduce per capita growth rates. In some cases, the effects of local adaptation on reducing per capita growth rates exceeded the ecological competitive effects of a doubling of density. However, we also found that these ecological and evolutionary properties of populations are coupled, and we offer two interpretations of the causes underlying this pattern: (1) the strength of density-dependent competition depends on the extent of local adaptation, or (2) the extent of local adaptation is shaped by the strength of density-dependent competition. Regardless of the underlying causal pathway, these results show how eco-evolutionary dynamics can affect a key demographic process regulating populations.
Wittler, R.; McBain, S.; Stalnaker, C.; Bizier, P.; DeBarry, P.
Two adaptive management programs, the Glen Canyon Dam Adaptive Management Program (GCDAMP) and the Trinity River Restoration Program (TRRP) are examined. In both cases, the focus is on managing the aquatic and riparian systems downstream of a large dam and water supply project. The status of the two programs, lessons learned by the program managers and the Adaptive Environmental Assessment and Management (AEAM) evolution of the TRRP are discussed. The Trinity River illustrates some of the scientific uncertainities that a program faces and the ways the program evolves from concept through implementation.
Brandon, Jim; Donlevy, Kent; Hanna, Paulette; Gereluk, Dianne; Patterson, Peggy; Rhyason, Kath
This study examined a recently established induction program for new superintendents in the Canadian province of Alberta over a three-year period. In keeping with principles of design-based research data were collected from a variety of sources from the 26 new superintendents and their 25 mentors to assess and adjust programming through three…
Mutyalarao, M.; Raj, M. Xavier James
A safe lunar landing is a key factor to undertake an effective lunar exploration. Lunar lander consists of four phases such as launch phase, the earth-moon transfer phase, circumlunar phase and landing phase. The landing phase can be either hard landing or soft landing. Hard landing means the vehicle lands under the influence of gravity without any deceleration measures. However, soft landing reduces the vertical velocity of the vehicle before landing. Therefore, for the safety of the astronauts as well as the vehicle lunar soft landing with an acceptable velocity is very much essential. So it is important to design the optimal lunar soft landing trajectory with minimum fuel consumption. Optimization of Lunar Soft landing is a complex optimal control problem. In this paper, an analysis related to lunar soft landing from a parking orbit around Moon has been carried out. A two-dimensional trajectory optimization problem is attempted. The problem is complex due to the presence of system constraints. To solve the time-history of control parameters, the problem is converted into two point boundary value problem by using the maximum principle of Pontrygen. Taboo Evolutionary Programming (TEP) technique is a stochastic method developed in recent years and successfully implemented in several fields of research. It combines the features of taboo search and single-point mutation evolutionary programming. Identifying the best unknown parameters of the problem under consideration is the central idea for many space trajectory optimization problems. The TEP technique is used in the present methodology for the best estimation of initial unknown parameters by minimizing objective function interms of fuel requirements. The optimal estimation subsequently results into an optimal trajectory design of a module for soft landing on the Moon from a lunar parking orbit. Numerical simulations demonstrate that the proposed approach is highly efficient and it reduces the minimum fuel
Urban, Jennifer Brown; Hargraves, Monica; Trochim, William M
Evolutionary theory, developmental systems theory, and evolutionary epistemology provide deep theoretical foundations for understanding programs, their development over time, and the role of evaluation. This paper relates core concepts from these powerful bodies of theory to program evaluation. Evolutionary Evaluation is operationalized in terms of program and evaluation evolutionary phases, which are in turn aligned with multiple types of validity. The model of Evolutionary Evaluation incorporates Chen's conceptualization of bottom-up versus top-down program development. The resulting framework has important implications for many program management and evaluation issues. The paper illustrates how an Evolutionary Evaluation perspective can illuminate important controversies in evaluation using the example of the appropriate role of randomized controlled trials that encourages a rethinking of "evidence-based programs". From an Evolutionary Evaluation perspective, prevailing interpretations of rigor and mandates for evidence-based programs pose significant challenges to program evolution. This perspective also illuminates the consequences of misalignment between program and evaluation phases; the importance of supporting both researcher-derived and practitioner-derived programs; and the need for variation and evolutionary phase diversity within portfolios of programs.
Yao, Yao; Marchal, Kathleen; Van de Peer, Yves
One of the important challenges in the field of evolutionary robotics is the development of systems that can adapt to a changing environment. However, the ability to adapt to unknown and fluctuating environments is not straightforward. Here, we explore the adaptive potential of simulated swarm robots that contain a genomic encoding of a bio-inspired gene regulatory network (GRN). An artificial genome is combined with a flexible agent-based system, representing the activated part of the regulatory network that transduces environmental cues into phenotypic behaviour. Using an artificial life simulation framework that mimics a dynamically changing environment, we show that separating the static from the conditionally active part of the network contributes to a better adaptive behaviour. Furthermore, in contrast with most hitherto developed ANN-based systems that need to re-optimize their complete controller network from scratch each time they are subjected to novel conditions, our system uses its genome to store GRNs whose performance was optimized under a particular environmental condition for a sufficiently long time. When subjected to a new environment, the previous condition-specific GRN might become inactivated, but remains present. This ability to store 'good behaviour' and to disconnect it from the novel rewiring that is essential under a new condition allows faster re-adaptation if any of the previously observed environmental conditions is reencountered. As we show here, applying these evolutionary-based principles leads to accelerated and improved adaptive evolution in a non-stable environment.
Haasdijk, Evert; Bredeche, Nicolas; Eiben, A E
Embodied evolutionary robotics is a sub-field of evolutionary robotics that employs evolutionary algorithms on the robotic hardware itself, during the operational period, i.e., in an on-line fashion. This enables robotic systems that continuously adapt, and are therefore capable of (re-)adjusting themselves to previously unknown or dynamically changing conditions autonomously, without human oversight. This paper addresses one of the major challenges that such systems face, viz. that the robots must satisfy two sets of requirements. Firstly, they must continue to operate reliably in their environment (viability), and secondly they must competently perform user-specified tasks (usefulness). The solution we propose exploits the fact that evolutionary methods have two basic selection mechanisms-survivor selection and parent selection. This allows evolution to tackle the two sets of requirements separately: survivor selection is driven by the environment and parent selection is based on task-performance. This idea is elaborated in the Multi-Objective aNd open-Ended Evolution (monee) framework, which we experimentally validate. Experiments with robotic swarms of 100 simulated e-pucks show that monee does indeed promote task-driven behaviour without compromising environmental adaptation. We also investigate an extension of the parent selection process with a 'market mechanism' that can ensure equitable distribution of effort over multiple tasks, a particularly pressing issue if the environment promotes specialisation in single tasks.
Shen, Yan; Shin, Hak Chul; Sung, Won Jun; Khim, Sarang; Kim, Honglak; Rhee, Phill Kyu
We present an evolutionary adaptive eye-tracking framework aiming for low-cost human computer interaction. The main focus is to guarantee eye-tracking performance without using high-cost devices and strongly controlled situations. The performance optimization of eye tracking is formulated into the dynamic control problem of deciding on an eye tracking algorithm structure and associated thresholds/parameters, where the dynamic control space is denoted by genotype and phenotype spaces. The evolutionary algorithm is responsible for exploring the genotype control space, and the reinforcement learning algorithm organizes the evolved genotype into a reactive phenotype. The evolutionary algorithm encodes an eye-tracking scheme as a genetic code based on image variation analysis. Then, the reinforcement learning algorithm defines internal states in a phenotype control space limited by the perceived genetic code and carries out interactive adaptations. The proposed method can achieve optimal performance by compromising the difficulty in the real-time performance of the evolutionary algorithm and the drawback of the huge search space of the reinforcement learning algorithm. Extensive experiments were carried out using webcam image sequences and yielded very encouraging results. The framework can be readily applied to other low-cost vision-based human computer interactions in solving their intrinsic brittleness in unstable operational environments.
Haasdijk, Evert; Bredeche, Nicolas; Eiben, A. E.
Embodied evolutionary robotics is a sub-field of evolutionary robotics that employs evolutionary algorithms on the robotic hardware itself, during the operational period, i.e., in an on-line fashion. This enables robotic systems that continuously adapt, and are therefore capable of (re-)adjusting themselves to previously unknown or dynamically changing conditions autonomously, without human oversight. This paper addresses one of the major challenges that such systems face, viz. that the robots must satisfy two sets of requirements. Firstly, they must continue to operate reliably in their environment (viability), and secondly they must competently perform user-specified tasks (usefulness). The solution we propose exploits the fact that evolutionary methods have two basic selection mechanisms–survivor selection and parent selection. This allows evolution to tackle the two sets of requirements separately: survivor selection is driven by the environment and parent selection is based on task-performance. This idea is elaborated in the Multi-Objective aNd open-Ended Evolution (monee) framework, which we experimentally validate. Experiments with robotic swarms of 100 simulated e-pucks show that monee does indeed promote task-driven behaviour without compromising environmental adaptation. We also investigate an extension of the parent selection process with a ‘market mechanism’ that can ensure equitable distribution of effort over multiple tasks, a particularly pressing issue if the environment promotes specialisation in single tasks. PMID:24901702
In an influential paper, Stephen Jay Gould and Richard Lewontin (1979) contrasted selection-driven adaptation with phylogenetic, architectural, and developmental constraints as distinct causes of phenotypic evolution. In subsequent publications Gould (e.g., 1997a,b, 2002) has elaborated this distinction into one between a narrow "Darwinian Fundamentalist" emphasis on "external functionalist" processes, and a more inclusive "pluralist" emphasis on "internal structuralist" principles. Although theoretical integration of functionalist and structuralist explanations is the ultimate aim, natural selection and internal constraints are treated as distinct causes of evolutionary change. This distinction is now routinely taken for granted in the literature in evolutionary biology. I argue that this distinction is problematic because the effects attributed to non-selective constraints are more parsimoniously explained as the ordinary effects of selection itself. Although it may still be a useful shorthand to speak of phylogenetic, architectural, and developmental constraints on phenotypic evolution, it is important to understand that such "constraints" do not constitute an alternative set of causes of evolutionary change. The result of this analysis is a clearer understanding of the relationship between adaptation, selection and constraints as explanatory concepts in evolutionary theory.
Orsini, Luisa; Schwenk, Klaus; De Meester, Luc; Colbourne, John K.; Pfrender, Michael E.; Weider, Lawrence J.
Evolutionary changes are determined by a complex assortment of ecological, demographic and adaptive histories. Predicting how evolution will shape the genetic structures of populations coping with current (and future) environmental challenges has principally relied on investigations through space, in lieu of time, because long-term phenotypic and molecular data are scarce. Yet, dormant propagules in sediments, soils and permafrost are convenient natural archives of population-histories from which to trace adaptive trajectories along extended time periods. DNA sequence data obtained from these natural archives, combined with pioneering methods for analyzing both ecological and population genomic time-series data, are likely to provide predictive models to forecast evolutionary responses of natural populations to environmental changes resulting from natural and anthropogenic stressors, including climate change. PMID:23395434
Moncla, Louise H; Zhong, Gongxun; Nelson, Chase W; Dinis, Jorge M; Mutschler, James; Hughes, Austin L; Watanabe, Tokiko; Kawaoka, Yoshihiro; Friedrich, Thomas C
Avian influenza virus reassortants resembling the 1918 human pandemic virus can become transmissible among mammals by acquiring mutations in hemagglutinin (HA) and polymerase. Using the ferret model, we trace the evolutionary pathway by which an avian-like virus evolves the capacity for mammalian replication and airborne transmission. During initial infection, within-host HA diversity increased drastically. Then, airborne transmission fixed two polymerase mutations that do not confer a detectable replication advantage. In later transmissions, selection fixed advantageous HA1 variants. Transmission initially involved a "loose" bottleneck, which became strongly selective after additional HA mutations emerged. The stringency and evolutionary forces governing between-host bottlenecks may therefore change throughout host adaptation. Mutations occurred in multiple combinations in transmitted viruses, suggesting that mammalian transmissibility can evolve through multiple genetic pathways despite phenotypic constraints. Our data provide a glimpse into avian influenza virus adaptation in mammals, with broad implications for surveillance on potentially zoonotic viruses.
SCHMIDT, KAREN L.; COHN, JEFFREY F.
The importance of the face in social interaction and social intelligence is widely recognized in anthropology. Yet the adaptive functions of human facial expression remain largely unknown. An evolutionary model of human facial expression as behavioral adaptation can be constructed, given the current knowledge of the phenotypic variation, ecological contexts, and fitness consequences of facial behavior. Studies of facial expression are available, but results are not typically framed in an evolutionary perspective. This review identifies the relevant physical phenomena of facial expression and integrates the study of this behavior with the anthropological study of communication and sociality in general. Anthropological issues with relevance to the evolutionary study of facial expression include: facial expressions as coordinated, stereotyped behavioral phenotypes, the unique contexts and functions of different facial expressions, the relationship of facial expression to speech, the value of facial expressions as signals, and the relationship of facial expression to social intelligence in humans and in nonhuman primates. Human smiling is used as an example of adaptation, and testable hypotheses concerning the human smile, as well as other expressions, are proposed. PMID:11786989
Development of programming languages has to contend with a variety of conflicting criteria. Moreover, as in any other creative field, it is not always possible to arrive at a clear formulation of these criteria. Nevertheless, one of the main criteria is problem orientation, be it numerical algorithms, database management, simulation of hydraulic systems, or other applications. Idealizing, we can say that the programming language is based on a model of the application domain. This model may vary in its scope, covering some aspects of the application domain and ignoring others. Thus, for one application domain we may have a whole spectrum of models and correspondingly a whole spectrum of languages. Some are special-purpose languages designed for a specific class of problems, others are more general. Both special-purpose and general-purpose languages have definite advantages and find their own clientele, who are willing to ignore their shortcomings.
Gresham, David; Desai, Michael M; Tucker, Cheryl M; Jenq, Harry T; Pai, Dave A; Ward, Alexandra; DeSevo, Christopher G; Botstein, David; Dunham, Maitreya J
The experimental evolution of laboratory populations of microbes provides an opportunity to observe the evolutionary dynamics of adaptation in real time. Until very recently, however, such studies have been limited by our inability to systematically find mutations in evolved organisms. We overcome this limitation by using a variety of DNA microarray-based techniques to characterize genetic changes -- including point mutations, structural changes, and insertion variation -- that resulted from the experimental adaptation of 24 haploid and diploid cultures of Saccharomyces cerevisiae to growth in either glucose, sulfate, or phosphate-limited chemostats for approximately 200 generations. We identified frequent genomic amplifications and rearrangements as well as novel retrotransposition events associated with adaptation. Global nucleotide variation detection in ten clonal isolates identified 32 point mutations. On the basis of mutation frequencies, we infer that these mutations and the subsequent dynamics of adaptation are determined by the batch phase of growth prior to initiation of the continuous phase in the chemostat. We relate these genotypic changes to phenotypic outcomes, namely global patterns of gene expression, and to increases in fitness by 5-50%. We found that the spectrum of available mutations in glucose- or phosphate-limited environments combined with the batch phase population dynamics early in our experiments allowed several distinct genotypic and phenotypic evolutionary pathways in response to these nutrient limitations. By contrast, sulfate-limited populations were much more constrained in both genotypic and phenotypic outcomes. Thus, the reproducibility of evolution varies with specific selective pressures, reflecting the constraints inherent in the system-level organization of metabolic processes in the cell. We were able to relate some of the observed adaptive mutations (e.g., transporter gene amplifications) to known features of the relevant
Boyer, C.; Adkins, Sean; Andersen, David R.; Atwood, Jenny; Bo, Yong; Byrnes, Peter; Caputa, Kris; Cavaco, Jeff; Ellerbroek, Brent; Gilles, Luc; Gregory, James; Herriot, Glen; Hickson, Paul; Ljusic, Zoran; Manter, Darren; Marois, Christian; Otárola, Angel; Pagès, Hubert; Schoeck, Matthias; Sinquin, Jean-Christophe; Smith, Malcolm; Spano, Paolo; Szeto, Kei; Tang, Jinlong; Travouillon, Tony; Véran, Jean-Pierre; Wang, Lianqi; Wei, Kai
The TMT first light Adaptive Optics (AO) facility consists of the Narrow Field Infra-Red AO System (NFIRAOS) and the associated Laser Guide Star Facility (LGSF). NFIRAOS is a 60 × 60 laser guide star (LGS) multi-conjugate AO (MCAO) system, which provides uniform, diffraction-limited performance in the J, H, and K bands over 17-30 arc sec diameter fields with 50 per cent sky coverage at the galactic pole, as required to support the TMT science cases. NFIRAOS includes two deformable mirrors, six laser guide star wavefront sensors, and three low-order, infrared, natural guide star wavefront sensors within each client instrument. The first light LGSF system includes six sodium lasers required to generate the NFIRAOS laser guide stars. In this paper, we will provide an update on the progress in designing, modeling and validating the TMT first light AO systems and their components over the last two years. This will include pre-final design and prototyping activities for NFIRAOS, preliminary design and prototyping activities for the LGSF, design and prototyping for the deformable mirrors, fabrication and tests for the visible detectors, benchmarking and comparison of different algorithms and processing architecture for the Real Time Controller (RTC) and development and tests of prototype candidate lasers. Comprehensive and detailed AO modeling is continuing to support the design and development of the first light AO facility. Main modeling topics studied during the last two years include further studies in the area of wavefront error budget, sky coverage, high precision astrometry for the galactic center and other observations, high contrast imaging with NFIRAOS and its first light instruments, Point Spread Function (PSF) reconstruction for LGS MCAO, LGS photon return and sophisticated low order mode temporal filtering.
Smith, Richard J
Explanations of the historical origin of specific individual traits are a key part of the research program in paleontology and evolutionary biology. Why did bipedalism evolve in the human lineage? Why did some dinosaurs and related species have head crests? Why did viviparity evolve in some reptiles? Why did the common ancestor of primates evolve stereoscopic vision, grasping hands and feet, nails instead of claws, and large brains? These are difficult questions. To varying degrees, an explanation must grapple with (1) judgments about changes in fitness that might follow from a change in morphology - without actually observing behavior or measuring reproductive success, (2) the relationship between genes and traits, (3) limitations on doing relevant experiments, (4) the interpretation of causes that are almost certainly contingent, multifactorial, interactive, hierarchical, nonlinear, emergent, and probabilistic rather than deterministic, (5) limited information about variation and ontogeny, (6) a dataset based on the random fortunes of the historical record, including only partial hard-tissue morphology and no soft-tissue morphology, (7) an equally partial and problematic (for example, time-averaged) record of the environment, (8) the compression of all data into a geological time scale that is likely to miss biologically important events or fluctuations, (9) dependence on a process that can only be inferred ("form and even behavior may leave fossil traces, but forces like natural selection do not", (1:130) ) and finally, (10) the assumption of the "adaptationist programme"(2) that the trait in question is in fact an adaptation rather than a consequence of genetic drift, correlated evolution, pleiotropy, exaptation, or other mechanisms.
Jønsson, Knud A; Fabre, Pierre-Henri; Fritz, Susanne A; Etienne, Rampal S; Ricklefs, Robert E; Jørgensen, Tobias B; Fjeldså, Jon; Rahbek, Carsten; Ericson, Per G P; Woog, Friederike; Pasquet, Eric; Irestedt, Martin
Adaptive radiation is the rapid diversification of a single lineage into many species that inhabit a variety of environments or use a variety of resources and differ in traits required to exploit these. Why some lineages undergo adaptive radiation is not well-understood, but filling unoccupied ecological space appears to be a common feature. We construct a complete, dated, species-level phylogeny of the endemic Vangidae of Madagascar. This passerine bird radiation represents a classic, but poorly known, avian adaptive radiation. Our results reveal an initial rapid increase in evolutionary lineages and diversification in morphospace after colonizing Madagascar in the late Oligocene some 25 Mya. A subsequent key innovation involving unique bill morphology was associated with a second increase in diversification rates about 10 Mya. The volume of morphospace occupied by contemporary Madagascan vangas is in many aspects as large (shape variation)--or even larger (size variation)--as that of other better-known avian adaptive radiations, including the much younger Galapagos Darwin's finches and Hawaiian honeycreepers. Morphological space bears a close relationship to diet, substrate use, and foraging movements, and thus our results demonstrate the great extent of the evolutionary diversification of the Madagascan vangas.
Pellerin, André; Anderson-Trocmé, Luke; Whyte, Lyle G; Zane, Grant M; Wall, Judy D; Wing, Boswell A
Dissimilatory sulfate reduction is a microbial catabolic pathway that preferentially processes less massive sulfur isotopes relative to their heavier counterparts. This sulfur isotope fractionation is recorded in ancient sedimentary rocks and generally is considered to reflect a phenotypic response to environmental variations rather than to evolutionary adaptation. Modern sulfate-reducing microorganisms isolated from similar environments can exhibit a wide range of sulfur isotope fractionations, suggesting that adaptive processes influence the sulfur isotope phenotype. To date, the relationship between evolutionary adaptation and isotopic phenotypes has not been explored. We addressed this by studying the covariation of fitness, sulfur isotope fractionation, and growth characteristics in Desulfovibrio vulgaris Hildenborough in a microbial evolution experiment. After 560 generations, the mean fitness of the evolved lineages relative to the starting isogenic population had increased by ∼ 17%. After 927 generations, the mean fitness relative to the initial ancestral population had increased by ∼ 20%. Growth rate in exponential phase increased during the course of the experiment, suggesting that this was a primary influence behind the fitness increases. Consistent changes were observed within different selection intervals between fractionation and fitness. Fitness changes were associated with changes in exponential growth rate but changes in fractionation were not. Instead, they appeared to be a response to changes in the parameters that govern growth rate: yield and cell-specific sulfate respiration rate. We hypothesize that cell-specific sulfate respiration rate, in particular, provides a bridge that allows physiological controls on fractionation to cross over to the adaptive realm.
Pievani, Telmo; Serrelli, Emanuele
Palaeontologists, Stephen J. Gould and Elisabeth Vrba, introduced the term "ex-aptation" with the aim of improving and enlarging the scientific language available to researchers studying the evolution of any useful character, instead of calling it an "adaptation" by default, coming up with what Gould named an "extended taxonomy of fitness". With the extension to functional co-optations from non-adaptive structures ("spandrels"), the notion of exaptation expanded and revised the neo-Darwinian concept of "pre-adaptation" (which was misleading, for Gould and Vrba, suggesting foreordination). Exaptation is neither a "saltationist" nor an "anti-Darwinian" concept and, since 1982, has been adopted by many researchers in evolutionary and molecular biology, and particularly in human evolution. Exaptation has also been contested. Objections include the "non-operationality objection".We analyze the possible operationalization of this concept in two recent studies, and identify six directions of empirical research, which are necessary to test "adaptive vs. exaptive" evolutionary hypotheses. We then comment on a comprehensive survey of literature (available online), and on the basis of this we make a quantitative and qualitative evaluation of the adoption of the term among scientists who study human evolution. We discuss the epistemic conditions that may have influenced the adoption and appropriate use of exaptation, and comment on the benefits of an "extended taxonomy of fitness" in present and future studies concerning human evolution.
Arnold, M L; Ballerini, E S; Brothers, A N
Estimates of hybrid fitness have been used as either a platform for testing the potential role of natural hybridization in the evolution of species and species complexes or, alternatively, as a rationale for dismissing hybridization events as being of any evolutionary significance. From the time of Darwin's publication of The Origin, through the neo-Darwinian synthesis, to the present day, the observation of variability in hybrid fitness has remained a challenge for some models of speciation. Yet, Darwin and others have reported the elevated fitness of hybrid genotypes under certain environmental conditions. In modern scientific terminology, this observation reflects the fact that hybrid genotypes can demonstrate genotype × environment interactions. In the current review, we illustrate the development of one plant species complex, namely the Louisiana Irises, into a 'model system' for investigating hybrid fitness and the role of genetic exchange in adaptive evolution and diversification. In particular, we will argue that a multitude of approaches, involving both experimental and natural environments, and incorporating both manipulative analyses and surveys of natural populations, are necessary to adequately test for the evolutionary significance of introgressive hybridization. An appreciation of the variability of hybrid fitness leads to the conclusion that certain genetic signatures reflect adaptive evolution. Furthermore, tests of the frequency of allopatric versus sympatric/parapatric divergence (that is, divergence with ongoing gene flow) support hybrid genotypes as a mechanism of evolutionary diversification in numerous species complexes.
Arnold, M L; Ballerini, E S; Brothers, A N
Estimates of hybrid fitness have been used as either a platform for testing the potential role of natural hybridization in the evolution of species and species complexes or, alternatively, as a rationale for dismissing hybridization events as being of any evolutionary significance. From the time of Darwin's publication of The Origin, through the neo-Darwinian synthesis, to the present day, the observation of variability in hybrid fitness has remained a challenge for some models of speciation. Yet, Darwin and others have reported the elevated fitness of hybrid genotypes under certain environmental conditions. In modern scientific terminology, this observation reflects the fact that hybrid genotypes can demonstrate genotype × environment interactions. In the current review, we illustrate the development of one plant species complex, namely the Louisiana Irises, into a ‘model system' for investigating hybrid fitness and the role of genetic exchange in adaptive evolution and diversification. In particular, we will argue that a multitude of approaches, involving both experimental and natural environments, and incorporating both manipulative analyses and surveys of natural populations, are necessary to adequately test for the evolutionary significance of introgressive hybridization. An appreciation of the variability of hybrid fitness leads to the conclusion that certain genetic signatures reflect adaptive evolution. Furthermore, tests of the frequency of allopatric versus sympatric/parapatric divergence (that is, divergence with ongoing gene flow) support hybrid genotypes as a mechanism of evolutionary diversification in numerous species complexes. PMID:21792222
Anderson, J. L.; Alton, L. R.; Arno, R. D.; Deerwester, J. M.; Edsinger, L. E.; Sinclair, K. F.; Tindle, E. L.; Wood, R. D.
An evolutionary, gradual, and step-wise spacecraft systems technology development from those used on the Apollos and Skylab 1 to that required for the space station was considered. The four mission spacecraft were dry workshop versions of the Saturn 4-B stage, and each individually configured, outfitted and launched by INT-21 vehicles. These spacecraft were evaluated for crews of three, six and nine men and for mission lifetimes of one year. Two versions of the Apollo CSM, a three man and a four man crew, were considered as the logistic vehicle. The solar cell electrical power system of the first mission evolves into a light weight panel system supplemented by an operating isotope-Brayton system on the later missions. The open life support system of the first mission evolves to a system which recovers both water and oxygen on the last mission. The data handling, communications, radiation shielding, micrometeoroid protection, and orbit keeping systems were determined. The program costs were estimated and, excluding operational costs, the cost for each mission would average about $2 billion of which one-sixth would be for development, one-fourth for experiments, and the balance for vehicle acquisition.
An approach to understanding and managing anadromous salmon, steelhead, and sea-run cutthroat trout (Oncorhynchus spp.) based on life history and evolutionary adaptive capacities of species and stocks is presented. Species, stocks, and local populations are viewed as systems that are continuously adapting to changing environmental conditions. They have the potential capacity to evolve in different ways in different environments through both life history and evolutionary adaptation. Habitat organization forms a template for genus, species, stock, and local population life history organization. Harvesting, habitat alteration resulting from land use practices and other human activities can alter the organization and adaptive capacities of species and stocks, and thus their long term persistence. The adaptive capacity of Oncorhynchus relative to its habitat and management environment is examined at the species, stock, and local population levels. Life history characteristics of representative stocks and local populations are analyzed using Detrended Correspondence Analysis (DECORANA). Fresh water migration distance and latitude are used to [open quotes]explain[close quotes] ordination patterns of Oncorhynchus species in the North Pacific Basin. Fresh water migration difficulty and mean annual runoff as used to interpret life history patterns of Columbia Basin chinook salmon stocks. Upstream migration difficulty and fall water temperatures are used to explain the ordination patterns of local populations of Willamette spring chinook salmon. Fishery management practices are examined in terms of their impacts on the organization and adaptive capacity of species, stocks, and local populations of Oncorhynchus. Management generalizations and guidelines derived from the life history theory are applied to management of Willamette spring chinook salmon.
Vidal, Franck P; Villard, Pierre-Frédéric; Lutton, Evelyne
We present and analyze the behavior of an evolutionary algorithm designed to estimate the parameters of a complex organ behavior model. The model is adaptable to account for patient's specificities. The aim is to finely tune the model to be accurately adapted to various real patient datasets. It can then be embedded, for example, in high fidelity simulations of the human physiology. We present here an application focused on respiration modeling. The algorithm is automatic and adaptive. A compound fitness function has been designed to take into account for various quantities that have to be minimized. The algorithm efficiency is experimentally analyzed on several real test cases: 1) three patient datasets have been acquired with the "breath hold" protocol, and 2) two datasets corresponds to 4-D CT scans. Its performance is compared with two traditional methods (downhill simplex and conjugate gradient descent): a random search and a basic real-valued genetic algorithm. The results show that our evolutionary scheme provides more significantly stable and accurate results.
Whitehead, Andrew; Zhang, Shujun; Roach, Jennifer L; Galvez, Fernando
Environmental salinity presents a key barrier to dispersal for most aquatic organisms, and adaptation to alternate osmotic environments likely enables species diversification. Little is known of the functional basis for derived tolerance to environmental salinity. We integrate comparative physiology and functional genomics to explore the mechanistic underpinnings of evolved variation in osmotic plasticity within and among two species of killifish; Fundulus majalis harbours the ancestral mainly salt-tolerant phenotype, whereas Fundulus heteroclitus harbours a derived physiology that retains extreme salt tolerance but with expanded osmotic plasticity towards the freshwater end of the osmotic continuum. Common-garden comparative hypo-osmotic challenge experiments show that F. heteroclitus is capable of remodelling gill epithelia more quickly and at more extreme osmotic challenge than F. majalis. We detect an unusual pattern of baseline transcriptome divergence, where neutral evolutionary processes appear to govern expression divergence within species, but patterns of divergence for these genes between species do not follow neutral expectations. During acclimation, genome expression profiling identifies mechanisms of acclimation-associated response that are conserved within the genus including regulation of paracellular permeability. In contrast, several responses vary among species including those putatively associated with cell volume regulation, and these same mechanisms are targets for adaptive physiological divergence along osmotic gradients within F. heteroclitus. As such, the genomic and physiological mechanisms that are associated with adaptive fine-tuning within species also contribute to macro-evolutionary divergence as species diversify across osmotic niches.
Cetinbaş, Murat; Shakhnovich, Eugene I
Although molecular chaperones are essential components of protein homeostatic machinery, their mechanism of action and impact on adaptation and evolutionary dynamics remain controversial. Here we developed a physics-based ab initio multi-scale model of a living cell for population dynamics simulations to elucidate the effect of chaperones on adaptive evolution. The 6-loci genomes of model cells encode model proteins, whose folding and interactions in cellular milieu can be evaluated exactly from their genome sequences. A genotype-phenotype relationship that is based on a simple yet non-trivially postulated protein-protein interaction (PPI) network determines the cell division rate. Model proteins can exist in native and molten globule states and participate in functional and all possible promiscuous non-functional PPIs. We find that an active chaperone mechanism, whereby chaperones directly catalyze protein folding, has a significant impact on the cellular fitness and the rate of evolutionary dynamics, while passive chaperones, which just maintain misfolded proteins in soluble complexes have a negligible effect on the fitness. We find that by partially releasing the constraint on protein stability, active chaperones promote a deeper exploration of sequence space to strengthen functional PPIs, and diminish the non-functional PPIs. A key experimentally testable prediction emerging from our analysis is that down-regulation of chaperones that catalyze protein folding significantly slows down the adaptation dynamics.
de Wolf, Elizabeth; Cook, Jonathan
CO2 readily combines with H2O to form and H+. Because an increase of only 100 nM in the concentration of H+ (a decrease of 0.1 unit of pH) in blood can prove fatal, the regulated excretion of CO2 during breathing is an essential life-preserving process. In rodents and humans, this vital process is mediated in part via the direct sensing of CO2 via connexin26 (Cx26). CO2 binds to hemichannels of Cx26 causing them to open and allow release of the neurotransmitter ATP. If Cx26 were to be a universal and important CO2 sensor across all homeothermic animals, then a simple hypothesis would posit that it should exhibit evolutionary adaptation in animals with different homeostatic set points for the regulation of partial pressure of arterial CO2 (PaCO2). In humans and rats, PaCO2 is regulated around a set point of 40 mmHg. By contrast, birds are able to maintain cerebral blood flow and breathing at much lower levels of PaCO2. Fossorial mammals, such as the mole rat, live exclusively underground in burrows that are both hypoxic and hypercapnic and can thrive under very hypercapnic conditions. We have therefore compared the CO2 sensitivity of Cx26 from human, chicken, rat and mole rat (Heterocephalus glaber). We find that both the affinity and cooperativity of CO2 binding to Cx26 have been subjected to evolutionary adaption in a manner consistent with the homeostatic requirements of these four species. This is analogous to the evolutionary adaptation of haemoglobin to the needs of O2 transport across the animal kingdom and supports the hypothesis that Cx26 is an important and universal CO2 sensor in homeotherms. PMID:28148750
de Wolf, Elizabeth; Cook, Jonathan; Dale, Nicholas
CO2 readily combines with H2O to form [Formula: see text] and H(+) Because an increase of only 100 nM in the concentration of H(+) (a decrease of 0.1 unit of pH) in blood can prove fatal, the regulated excretion of CO2 during breathing is an essential life-preserving process. In rodents and humans, this vital process is mediated in part via the direct sensing of CO2 via connexin26 (Cx26). CO2 binds to hemichannels of Cx26 causing them to open and allow release of the neurotransmitter ATP. If Cx26 were to be a universal and important CO2 sensor across all homeothermic animals, then a simple hypothesis would posit that it should exhibit evolutionary adaptation in animals with different homeostatic set points for the regulation of partial pressure of arterial CO2 (PaCO2). In humans and rats, PaCO2 is regulated around a set point of 40 mmHg. By contrast, birds are able to maintain cerebral blood flow and breathing at much lower levels of PaCO2 Fossorial mammals, such as the mole rat, live exclusively underground in burrows that are both hypoxic and hypercapnic and can thrive under very hypercapnic conditions. We have therefore compared the CO2 sensitivity of Cx26 from human, chicken, rat and mole rat (Heterocephalus glaber). We find that both the affinity and cooperativity of CO2 binding to Cx26 have been subjected to evolutionary adaption in a manner consistent with the homeostatic requirements of these four species. This is analogous to the evolutionary adaptation of haemoglobin to the needs of O2 transport across the animal kingdom and supports the hypothesis that Cx26 is an important and universal CO2 sensor in homeotherms.
Background Natural selection and genetic drift are major forces responsible for temporal genetic changes in populations. Furthermore, these evolutionary forces may interact with each other. Here we study the impact of an ongoing adaptive process at the molecular genetic level by analyzing the temporal genetic changes throughout 40 generations of adaptation to a common laboratory environment. Specifically, genetic variability, population differentiation and demographic structure were compared in two replicated groups of Drosophila subobscura populations recently sampled from different wild sources. Results We found evidence for a decline in genetic variability through time, along with an increase in genetic differentiation between all populations studied. The observed decline in genetic variability was higher during the first 14 generations of laboratory adaptation. The two groups of replicated populations showed overall similarity in variability patterns. Our results also revealed changing demographic structure of the populations during laboratory evolution, with lower effective population sizes in the early phase of the adaptive process. One of the ten microsatellites analyzed showed a clearly distinct temporal pattern of allele frequency change, suggesting the occurrence of positive selection affecting the region around that particular locus. Conclusion Genetic drift was responsible for most of the divergence and loss of variability between and within replicates, with most changes occurring during the first generations of laboratory adaptation. We also found evidence suggesting a selective sweep, despite the low number of molecular markers analyzed. Overall, there was a similarity of evolutionary dynamics at the molecular level in our laboratory populations, despite distinct genetic backgrounds and some differences in phenotypic evolution. PMID:18302790
Huang, Bei; Cheng, Qiang; Song, Gang Yong; Cui, Tie Jun
Acoustic metamaterials can manipulate sound waves in surprising ways, including the focusing, cloaking, and extraordinary transmitting of sound waves. With the increasing requirements for acoustic metamaterials with extreme parameters, we propose the design of acoustic meta-atoms with a large refraction index using the covariance matrix adaptation evolutionary optimization strategy. To validate the procedure, we propose an optimized metamaterial to construct an acoustic deflection lens. The full-wave simulation results are consistent with the theoretical predictions, showing the efficacy and accuracy of the proposed method, and indicating that the optimization algorithm is a powerful tool for designing meta-atoms with excellent applications.
Botero, Carlos A.; Weissing, Franz J.; Wright, Jonathan; Rubenstein, Dustin R.
In an era of rapid climate change, there is a pressing need to understand how organisms will cope with faster and less predictable variation in environmental conditions. Here we develop a unifying model that predicts evolutionary responses to environmentally driven fluctuating selection and use this theoretical framework to explore the potential consequences of altered environmental cycles. We first show that the parameter space determined by different combinations of predictability and timescale of environmental variation is partitioned into distinct regions where a single mode of response (reversible phenotypic plasticity, irreversible phenotypic plasticity, bet-hedging, or adaptive tracking) has a clear selective advantage over all others. We then demonstrate that, although significant environmental changes within these regions can be accommodated by evolution, most changes that involve transitions between regions result in rapid population collapse and often extinction. Thus, the boundaries between response mode regions in our model correspond to evolutionary tipping points, where even minor changes in environmental parameters can have dramatic and disproportionate consequences on population viability. Finally, we discuss how different life histories and genetic architectures may influence the location of tipping points in parameter space and the likelihood of extinction during such transitions. These insights can help identify and address some of the cryptic threats to natural populations that are likely to result from any natural or human-induced change in environmental conditions. They also demonstrate the potential value of evolutionary thinking in the study of global climate change. PMID:25422451
Botero, Carlos A; Weissing, Franz J; Wright, Jonathan; Rubenstein, Dustin R
In an era of rapid climate change, there is a pressing need to understand how organisms will cope with faster and less predictable variation in environmental conditions. Here we develop a unifying model that predicts evolutionary responses to environmentally driven fluctuating selection and use this theoretical framework to explore the potential consequences of altered environmental cycles. We first show that the parameter space determined by different combinations of predictability and timescale of environmental variation is partitioned into distinct regions where a single mode of response (reversible phenotypic plasticity, irreversible phenotypic plasticity, bet-hedging, or adaptive tracking) has a clear selective advantage over all others. We then demonstrate that, although significant environmental changes within these regions can be accommodated by evolution, most changes that involve transitions between regions result in rapid population collapse and often extinction. Thus, the boundaries between response mode regions in our model correspond to evolutionary tipping points, where even minor changes in environmental parameters can have dramatic and disproportionate consequences on population viability. Finally, we discuss how different life histories and genetic architectures may influence the location of tipping points in parameter space and the likelihood of extinction during such transitions. These insights can help identify and address some of the cryptic threats to natural populations that are likely to result from any natural or human-induced change in environmental conditions. They also demonstrate the potential value of evolutionary thinking in the study of global climate change.
Maestri, Renan; Monteiro, Leandro Rabello; Fornel, Rodrigo; Upham, Nathan S; Patterson, Bruce D; de Freitas, Thales Renato Ochotorena
Evolutionary radiations on continents are less well-understood and appreciated than those occurring on islands. The extent of ecological influence on species divergence can be evaluated to determine whether a radiation was ultimately the outcome of divergent natural selection or else arose mainly by nonecological divergence. Here, we used phylogenetic comparative methods to test distinct hypotheses corresponding to adaptive and nonadaptive evolutionary scenarios for the morphological evolution of sigmodontine rodents. Results showed that ecological variables (diet and life-mode) explain little of the shape and size variation of sigmodontine skulls and mandibles. A Brownian model with varying rates for insectivory versus all other diets was the most likely evolutionary model. The insectivorous sigmodontines have a faster rate of morphological evolution than mice feeding on other diets, possibly due to stronger selection for features that aid insectivory. We also demonstrate that rapid early-lineage diversification is not accompanied by high morphological divergence among subclades, contrasting with island results. The geographic size of continents permits spatial segregation to a greater extent than on islands, allowing for allopatric distributions and escape from interspecific competition. We suggest that continental radiations of rodents are likely to produce a pattern of high species diversification coupled with a low degree of phenotypic specialization.
Menu, Frédéric; Ginoux, Marine; Rajon, Etienne; Lazzari, Claudio R.; Rabinovich, Jorge E.
Background The developmental time of vector insects is important in population dynamics, evolutionary biology, epidemiology and in their responses to global climatic change. In the triatomines (Triatominae, Reduviidae), vectors of Chagas disease, evolutionary ecology concepts, which may allow for a better understanding of their biology, have not been applied. Despite delay in the molting in some individuals observed in triatomines, no effort was made to explain this variability. Methodology We applied four methods: (1) an e-mail survey sent to 30 researchers with experience in triatomines, (2) a statistical description of the developmental time of eleven triatomine species, (3) a relationship between development time pattern and climatic inter-annual variability, (4) a mathematical optimization model of evolution of developmental delay (diapause). Principal Findings 85.6% of responses informed on prolonged developmental times in 5th instar nymphs, with 20 species identified with remarkable developmental delays. The developmental time analysis showed some degree of bi-modal pattern of the development time of the 5th instars in nine out of eleven species but no trend between development time pattern and climatic inter-annual variability was observed. Our optimization model predicts that the developmental delays could be due to an adaptive risk-spreading diapause strategy, only if survival throughout the diapause period and the probability of random occurrence of “bad” environmental conditions are sufficiently high. Conclusions/Significance Developmental delay may not be a simple non-adaptive phenotypic plasticity in development time, and could be a form of adaptive diapause associated to a physiological mechanism related to the postponement of the initiation of reproduction, as an adaptation to environmental stochasticity through a spreading of risk (bet-hedging) strategy. We identify a series of parameters that can be measured in the field and laboratory to test
Schrode, Katrina M.; Bee, Mark A.
ABSTRACT Sensory systems function most efficiently when processing natural stimuli, such as vocalizations, and it is thought that this reflects evolutionary adaptation. Among the best-described examples of evolutionary adaptation in the auditory system are the frequent matches between spectral tuning in both the peripheral and central auditory systems of anurans (frogs and toads) and the frequency spectra of conspecific calls. Tuning to the temporal properties of conspecific calls is less well established, and in anurans has so far been documented only in the central auditory system. Using auditory-evoked potentials, we asked whether there are species-specific or sex-specific adaptations of the auditory systems of gray treefrogs (Hyla chrysoscelis) and green treefrogs (H. cinerea) to the temporal modulations present in conspecific calls. Modulation rate transfer functions (MRTFs) constructed from auditory steady-state responses revealed that each species was more sensitive than the other to the modulation rates typical of conspecific advertisement calls. In addition, auditory brainstem responses (ABRs) to paired clicks indicated relatively better temporal resolution in green treefrogs, which could represent an adaptation to the faster modulation rates present in the calls of this species. MRTFs and recovery of ABRs to paired clicks were generally similar between the sexes, and we found no evidence that males were more sensitive than females to the temporal modulation patterns characteristic of the aggressive calls used in male–male competition. Together, our results suggest that efficient processing of the temporal properties of behaviorally relevant sounds begins at potentially very early stages of the anuran auditory system that include the periphery. PMID:25617467
Morel, Guillaume; Sterck, Lieven; Swennen, Dominique; Marcet-Houben, Marina; Onesime, Djamila; Levasseur, Anthony; Jacques, Noémie; Mallet, Sandrine; Couloux, Arnaux; Labadie, Karine; Amselem, Joëlle; Beckerich, Jean-Marie; Henrissat, Bernard; Van de Peer, Yves; Wincker, Patrick; Souciet, Jean-Luc; Gabaldón, Toni; Tinsley, Colin R; Casaregola, Serge
The evolutionary history of the characters underlying the adaptation of microorganisms to food and biotechnological uses is poorly understood. We undertook comparative genomics to investigate evolutionary relationships of the dairy yeast Geotrichum candidum within Saccharomycotina. Surprisingly, a remarkable proportion of genes showed discordant phylogenies, clustering with the filamentous fungus subphylum (Pezizomycotina), rather than the yeast subphylum (Saccharomycotina), of the Ascomycota. These genes appear not to be the result of Horizontal Gene Transfer (HGT), but to have been specifically retained by G. candidum after the filamentous fungi-yeasts split concomitant with the yeasts' genome contraction. We refer to these genes as SRAGs (Specifically Retained Ancestral Genes), having been lost by all or nearly all other yeasts, and thus contributing to the phenotypic specificity of lineages. SRAG functions include lipases consistent with a role in cheese making and novel endoglucanases associated with degradation of plant material. Similar gene retention was observed in three other distantly related yeasts representative of this ecologically diverse subphylum. The phenomenon thus appears to be widespread in the Saccharomycotina and argues that, alongside neo-functionalization following gene duplication and HGT, specific gene retention must be recognized as an important mechanism for generation of biodiversity and adaptation in yeasts.
Matthews, Blake; Aebischer, Thierry; Sullam, Karen E; Lundsgaard-Hansen, Bänz; Seehausen, Ole
Differences in how organisms modify their environment can evolve rapidly and might influence adaptive population divergence. In a common garden experiment in aquatic mesocosms, we found that adult stickleback from a recently diverged pair of lake and stream populations had contrasting effects on ecosystem metrics. These modifications were caused by both genetic and plastic differences between populations and were sometimes comparable in magnitude to those caused by the presence/absence of stickleback. Lake and stream fish differentially affected the biomass of zooplankton and phytoplankton, the concentration of phosphorus, and the abundance of several prey (e.g., copepods) and non-prey (e.g., cyanobacteria) species. The adult-mediated effects on mesocosm ecosystems influenced the survival and growth of a subsequent generation of juvenile stickleback reared in the same mesocosms. The prior presence of adults decreased the overall growth rate of juveniles, and the prior presence of stream adults lowered overall juvenile survival. Among the survivors, lake juveniles grew faster than co-occurring stream juveniles, except in mesocosm ecosystems previously modified by adult lake fish that were reared on plankton. Overall, our results provide evidence for reciprocal interactions between ecosystem dynamics and evolutionary change (i.e., eco-evolutionary feedbacks) in the early stages of adaptive population divergence.
Morel, Guillaume; Sterck, Lieven; Swennen, Dominique; Marcet-Houben, Marina; Onesime, Djamila; Levasseur, Anthony; Jacques, Noémie; Mallet, Sandrine; Couloux, Arnaux; Labadie, Karine; Amselem, Joëlle; Beckerich, Jean-Marie; Henrissat, Bernard; Van de Peer, Yves; Wincker, Patrick; Souciet, Jean-Luc; Gabaldón, Toni; Tinsley, Colin R.; Casaregola, Serge
The evolutionary history of the characters underlying the adaptation of microorganisms to food and biotechnological uses is poorly understood. We undertook comparative genomics to investigate evolutionary relationships of the dairy yeast Geotrichum candidum within Saccharomycotina. Surprisingly, a remarkable proportion of genes showed discordant phylogenies, clustering with the filamentous fungus subphylum (Pezizomycotina), rather than the yeast subphylum (Saccharomycotina), of the Ascomycota. These genes appear not to be the result of Horizontal Gene Transfer (HGT), but to have been specifically retained by G. candidum after the filamentous fungi–yeasts split concomitant with the yeasts’ genome contraction. We refer to these genes as SRAGs (Specifically Retained Ancestral Genes), having been lost by all or nearly all other yeasts, and thus contributing to the phenotypic specificity of lineages. SRAG functions include lipases consistent with a role in cheese making and novel endoglucanases associated with degradation of plant material. Similar gene retention was observed in three other distantly related yeasts representative of this ecologically diverse subphylum. The phenomenon thus appears to be widespread in the Saccharomycotina and argues that, alongside neo-functionalization following gene duplication and HGT, specific gene retention must be recognized as an important mechanism for generation of biodiversity and adaptation in yeasts. PMID:26108467
Tooby, John; Cosmides, Leda; Price, Michael E.
Organizations are composed of stable, predominantly cooperative interactions or n-person exchanges. Humans have been engaging in n-person exchanges for a great enough period of evolutionary time that we appear to have evolved a distinct constellation of species-typical mechanisms specialized to solve the adaptive problems posed by this form of social interaction. These mechanisms appear to have been evolutionarily elaborated out of the cognitive infrastructure that initially evolved for dyadic exchange. Key adaptive problems that these mechanisms are designed to solve include coordination among individuals, and defense against exploitation by free riders. Multi-individual cooperation could not have been maintained over evolutionary time if free riders reliably benefited more than contributors to collective enterprises, and so outcompeted them. As a result, humans evolved mechanisms that implement an aversion to exploitation by free riding, and a strategy of conditional cooperation, supplemented by punitive sentiment towards free riders. Because of the design of these mechanisms, how free riding is treated is a central determinant of the survival and health of cooperative organizations. The mapping of the evolved psychology of n-party exchange cooperation may contribute to the construction of a principled theoretical foundation for the understanding of human behavior in organizations. PMID:23814325
Boldin, Barbara; Kisdi, Éva
Evolutionary suicide is a riveting phenomenon in which adaptive evolution drives a viable population to extinction. Gyllenberg and Parvinen (Bull Math Biol 63(5):981-993, 2001) showed that, in a wide class of deterministic population models, a discontinuous transition to extinction is a necessary condition for evolutionary suicide. An implicit assumption of their proof is that the invasion fitness of a rare strategy is well-defined also in the extinction state of the population. Epidemic models with frequency-dependent incidence, which are often used to model the spread of sexually transmitted infections or the dynamics of infectious diseases within herds, violate this assumption. In these models, evolutionary suicide can occur through a non-catastrophic bifurcation whereby pathogen adaptation leads to a continuous decline of host (and consequently pathogen) population size to zero. Evolutionary suicide of pathogens with frequency-dependent transmission can occur in two ways, with pathogen strains evolving either higher or lower virulence.
van Niekerk, Gustav; Engelbrecht, Anna-Mart
Jawless vertebrates utilize a form of adaptive immunity that is functionally based on molecular effectors that are completely different from those of vertebrates. This observation raises an intriguing question: why did vertebrates, representing only 5% of all animals, twice evolve a system as complex as adaptive immunity? Theories aimed at identifying a selective pressure that would 'drive' the development of an adaptive immune system (AIS) fail to explain why invertebrates would not similarly develop an AIS. We argue that an AIS can only be implemented in a certain physiological context, i.e., that an AIS represents an unevolvable trait for invertebrates. The immune system is functionally integrated with other systems; therefore a preexisting physiological innovation unique to vertebrates may have acted as the prerequisite infrastructure that allowed the development of an AIS. We propose that future efforts should be directed toward identifying the evolutionary release that allowed the development of an adaptive immune system in vertebrates. In particular, the advent of specialized adipocytes might have expanded the metabolic scope of vertebrates, allowing the opportunistic incorporation of an AIS. However, physiological innovations, unique to (or more developed in) vertebrates, support the implementation of an AIS. Thus, understanding the interaction between systems (e.g. neural-immune-adipose connection) may illuminate our understanding regarding the perplexing immunological dimorphism within the animal kingdom.
Burgin, George H.
The Adaptive Maneuvering Logic (AML) computer program simulates close-in, one-on-one air-to-air combat between two fighter aircraft. Three important improvements are described. First, the previously available versions of AML were examined for their suitability as a baseline program. The selected program was then revised to eliminate some programming bugs which were uncovered over the years. A listing of this baseline program is included. Second, the equations governing the motion of the aircraft were completely revised. This resulted in a model with substantially higher fidelity than the original equations of motion provided. It also completely eliminated the over-the-top problem, which occurred in the older versions when the AML-driven aircraft attempted a vertical or near vertical loop. Third, the requirements for a versatile generic, yet realistic, aircraft model were studied and implemented in the program. The report contains detailed tables which make the generic aircraft to be either a modern, high performance aircraft, an older high performance aircraft, or a previous generation jet fighter.
Army War College, 7 April 2003. 47Orazia A. Di Marca ; Rejto, Stephen B. Rejto and Thomas Gomez, “ Open System Design and Evolutionary Acquisition...to Military Applications-Report No. D-2002-107. 14 June 2002. Di Marca , Orazia A.; Rejto, StephenB., and Gomez, Thomas, “ Open System Design and
Mäkinen, Hannu; Papakostas, Spiros; Vøllestad, Leif Asbjørn; Leder, Erica H; Primmer, Craig R
Understanding how populations adapt to changing environmental conditions is a long-standing theme in evolutionary biology. Gene expression changes have been recognized as an important driver of local adaptation, but relatively little is known regarding the direction of change and in particular, about the interplay between plastic and evolutionary gene expression. We have previously shown that the gene expression profiles of European grayling (Thymallus thymallus) populations inhabiting different thermal environments include both plastic and evolutionary components. However, whether the plastic and evolutionary responses were in the same direction was not investigated in detail, nor was the identity of the specific genes involved. In this study, we show that the plastic changes in protein expression in response to different temperatures are highly correlated with the evolutionary response in grayling subpopulations adapted to different thermal environments. This finding provides preliminary evidence that the plastic response most likely facilitates adaptation during the early phases of colonization of thermal environments. The proteins that showed significant changes in expression level between warm and cold temperature treatments were mostly related to muscle development, which is consistent with earlier findings demonstrating muscle mass differentiation between cold and warm grayling populations.
Ramakrishnan, Jagdish; Craft, David; Bortfeld, Thomas; Tsitsiklis, John N.
We conduct a theoretical study of various solution methods for the adaptive fractionation problem. The two messages of this paper are as follows: (i) dynamic programming (DP) is a useful framework for adaptive radiation therapy, particularly adaptive fractionation, because it allows us to assess how close to optimal different methods are, and (ii) heuristic methods proposed in this paper are near-optimal, and therefore, can be used to evaluate the best possible benefit of using an adaptive fraction size. The essence of adaptive fractionation is to increase the fraction size when the tumor and organ-at-risk (OAR) are far apart (a ‘favorable’ anatomy) and to decrease the fraction size when they are close together. Given that a fixed prescribed dose must be delivered to the tumor over the course of the treatment, such an approach results in a lower cumulative dose to the OAR when compared to that resulting from standard fractionation. We first establish a benchmark by using the DP algorithm to solve the problem exactly. In this case, we characterize the structure of an optimal policy, which provides guidance for our choice of heuristics. We develop two intuitive, numerically near-optimal heuristic policies, which could be used for more complex, high-dimensional problems. Furthermore, one of the heuristics requires only a statistic of the motion probability distribution, making it a reasonable method for use in a realistic setting. Numerically, we find that the amount of decrease in dose to the OAR can vary significantly (5-85%) depending on the amount of motion in the anatomy, the number of fractions and the range of fraction sizes allowed. In general, the decrease in dose to the OAR is more pronounced when: (i) we have a high probability of large tumor-OAR distances, (ii) we use many fractions (as in a hyper-fractionated setting) and (iii) we allow large daily fraction size deviations.
VanBuren, Collin S; Campione, Nicolás E; Evans, David C
The anterior cervical vertebrae form the skeletal connection between the cranial and postcranial skeletons in higher tetrapods. As a result, the morphology of the atlas-axis complex is likely to be shaped by selection pressures acting on either the head or neck. The neoceratopsian (Reptilia:Dinosauria) syncervical represents one of the most highly modified atlas-axis regions in vertebrates, being formed by the complete coalescence of the three most anterior cervical vertebrae. In ceratopsids, the syncervical has been hypothesized to be an adaptation to support a massive skull, or to act as a buttress during intraspecific head-to-head combat. Here, we test these functional/adaptive hypotheses within a phylogenetic framework and critically examine the previously proposed methods for quantifying relative head size in the fossil record for the first time. Results indicate that neither the evolution of cranial weaponry nor large head size correlates with the origin of cervical fusion in ceratopsians, and we, therefore, reject both adaptive hypotheses for the origin of the syncervical. Anterior cervical fusion has evolved independently in a number of amniote clades, and further research on extant groups with this peculiar anatomy is needed to understand the evolutionary basis for cervical fusion in Neoceratopsia.
Zhang, Xian; Liu, Xueduan; He, Qiang; Dong, Weiling; Zhang, Xiaoxia; Fan, Fenliang; Peng, Deliang; Huang, Wenkun; Yin, Huaqun
A. caldus species that inhabit extremely acidic environments, and shed new light on the contribution of gene turnover to the evolutionary adaptation of acidophiles. PMID:27999570
Billiard, Sylvain; Ferrière, Régis; Méléard, Sylvie; Tran, Viet Chi
How the neutral diversity is affected by selection and adaptation is investigated in an eco-evolutionary framework. In our model, we study a finite population in continuous time, where each individual is characterized by a trait under selection and a completely linked neutral marker. Population dynamics are driven by births and deaths, mutations at birth, and competition between individuals. Trait values influence ecological processes (demographic events, competition), and competition generates selection on trait variation, thus closing the eco-evolutionary feedback loop. The demographic effects of the trait are also expected to influence the generation and maintenance of neutral variation. We consider a large population limit with rare mutation, under the assumption that the neutral marker mutates faster than the trait under selection. We prove the convergence of the stochastic individual-based process to a new measure-valued diffusive process with jumps that we call Substitution Fleming-Viot Process (SFVP). When restricted to the trait space this process is the Trait Substitution Sequence first introduced by Metz et al. (1996). During the invasion of a favorable mutation, a genetical bottleneck occurs and the marker associated with this favorable mutant is hitchhiked. By rigorously analysing the hitchhiking effect and how the neutral diversity is restored afterwards, we obtain the condition for a time-scale separation; under this condition, we show that the marker distribution is approximated by a Fleming-Viot distribution between two trait substitutions. We discuss the implications of the SFVP for our understanding of the dynamics of neutral variation under eco-evolutionary feedbacks and illustrate the main phenomena with simulations. Our results highlight the joint importance of mutations, ecological parameters, and trait values in the restoration of neutral diversity after a selective sweep.
Pereira, Joana; Johnson, Warren E.; O’Brien, Stephen J.; Jarvis, Erich D.; Zhang, Guojie; Gilbert, M. Thomas P.; Vasconcelos, Vitor; Antunes, Agostinho
The Hedgehog (Hh) gene family codes for a class of secreted proteins composed of two active domains that act as signalling molecules during embryo development, namely for the development of the nervous and skeletal systems and the formation of the testis cord. While only one Hh gene is found typically in invertebrate genomes, most vertebrates species have three (Sonic hedgehog – Shh; Indian hedgehog – Ihh; and Desert hedgehog – Dhh), each with different expression patterns and functions, which likely helped promote the increasing complexity of vertebrates and their successful diversification. In this study, we used comparative genomic and adaptive evolutionary analyses to characterize the evolution of the Hh genes in vertebrates following the two major whole genome duplication (WGD) events. To overcome the lack of Hh-coding sequences on avian publicly available databases, we used an extensive dataset of 45 avian and three non-avian reptilian genomes to show that birds have all three Hh paralogs. We find suggestions that following the WGD events, vertebrate Hh paralogous genes evolved independently within similar linkage groups and under different evolutionary rates, especially within the catalytic domain. The structural regions around the ion-binding site were identified to be under positive selection in the signaling domain. These findings contrast with those observed in invertebrates, where different lineages that experienced gene duplication retained similar selective constraints in the Hh orthologs. Our results provide new insights on the evolutionary history of the Hh gene family, the functional roles of these paralogs in vertebrate species, and on the location of mutational hotspots. PMID:25549322
Pereira, Joana; Johnson, Warren E; O'Brien, Stephen J; Jarvis, Erich D; Zhang, Guojie; Gilbert, M Thomas P; Vasconcelos, Vitor; Antunes, Agostinho
The Hedgehog (Hh) gene family codes for a class of secreted proteins composed of two active domains that act as signalling molecules during embryo development, namely for the development of the nervous and skeletal systems and the formation of the testis cord. While only one Hh gene is found typically in invertebrate genomes, most vertebrates species have three (Sonic hedgehog--Shh; Indian hedgehog--Ihh; and Desert hedgehog--Dhh), each with different expression patterns and functions, which likely helped promote the increasing complexity of vertebrates and their successful diversification. In this study, we used comparative genomic and adaptive evolutionary analyses to characterize the evolution of the Hh genes in vertebrates following the two major whole genome duplication (WGD) events. To overcome the lack of Hh-coding sequences on avian publicly available databases, we used an extensive dataset of 45 avian and three non-avian reptilian genomes to show that birds have all three Hh paralogs. We find suggestions that following the WGD events, vertebrate Hh paralogous genes evolved independently within similar linkage groups and under different evolutionary rates, especially within the catalytic domain. The structural regions around the ion-binding site were identified to be under positive selection in the signaling domain. These findings contrast with those observed in invertebrates, where different lineages that experienced gene duplication retained similar selective constraints in the Hh orthologs. Our results provide new insights on the evolutionary history of the Hh gene family, the functional roles of these paralogs in vertebrate species, and on the location of mutational hotspots.
McDowell, J J; Popa, Andrei
One theory of behavior dynamics instantiates the idea that behavior evolves in response to selection pressure from the environment in the form of reinforcement. This computational theory implements Darwinian principles of selection, reproduction, and mutation, which operate on a population of potential behaviors by means of a genetic algorithm. The behavior of virtual organisms animated by this theory may be studied in any experimental environment. The evolutionary theory was tested by comparing the steady-state behavior it generated on concurrent schedules to the description of steady state behavior provided by modern matching theory. Ensemble fits of modern matching theory that enforced its constant-k requirement and the parametric identities required by its equations, accounted for large proportions of data variance, left random residuals, and yielded parameter estimates with values and properties similar to those obtained in experiments with live organisms. These results indicate that the dynamics of the evolutionary theory and the statics of modern matching theory together constitute a good candidate for a mechanics of adaptive behavior.
McDowell, J.J; Popa, Andrei
One theory of behavior dynamics instantiates the idea that behavior evolves in response to selection pressure from the environment in the form of reinforcement. This computational theory implements Darwinian principles of selection, reproduction, and mutation, which operate on a population of potential behaviors by means of a genetic algorithm. The behavior of virtual organisms animated by this theory may be studied in any experimental environment. The evolutionary theory was tested by comparing the steady-state behavior it generated on concurrent schedules to the description of steady state behavior provided by modern matching theory. Ensemble fits of modern matching theory that enforced its constant-k requirement and the parametric identities required by its equations, accounted for large proportions of data variance, left random residuals, and yielded parameter estimates with values and properties similar to those obtained in experiments with live organisms. These results indicate that the dynamics of the evolutionary theory and the statics of modern matching theory together constitute a good candidate for a mechanics of adaptive behavior. PMID:21451751
Biswas, Rupak; Biegel, Bryan (Technical Monitor)
Achieving scalable performance for dynamic irregular applications is eminently challenging. Traditional message-passing approaches have been making steady progress towards this goal; however, they suffer from complex implementation requirements. The use of a global address space greatly simplifies the programming task, but can degrade the performance for such computations. In this work, we examine two typical irregular adaptive applications, Dynamic Remeshing and N-Body, under competing programming methodologies and across various parallel architectures. The Dynamic Remeshing application simulates flow over an airfoil, and refines localized regions of the underlying unstructured mesh. The N-Body experiment models two neighboring Plummer galaxies that are about to undergo a merger. Both problems demonstrate dramatic changes in processor workloads and interprocessor communication with time; thus, dynamic load balancing is a required component.
Long, J H; Koob, T J; Irving, K; Combie, K; Engel, V; Livingston, N; Lammert, A; Schumacher, J
For early vertebrates, a long-standing hypothesis is that vertebrae evolved as a locomotor adaptation, stiffening the body axis and enhancing swimming performance. While supported by biomechanical data, this hypothesis has not been tested using an evolutionary approach. We did so by extending biomimetic evolutionary analysis (BEA), which builds physical simulations of extinct systems, to include use of autonomous robots as proxies of early vertebrates competing in a forage navigation task. Modeled after free-swimming larvae of sea squirts (Chordata, Urochordata), three robotic tadpoles (;Tadros'), each with a propulsive tail bearing a biomimetic notochord of variable spring stiffness, k (N m(-1)), searched for, oriented to, and orbited in two dimensions around a light source. Within each of ten generations, we selected for increased swimming speed, U (m s(-1)) and decreased time to the light source, t (s), average distance from the source, R (m) and wobble maneuvering, W (rad s(-2)). In software simulation, we coded two quantitative trait loci (QTL) that determine k: bending modulus, E (Nm(-2)) and length, L (m). Both QTL were mutated during replication, independently assorted during meiosis and, as haploid gametes, entered into the gene pool in proportion to parental fitness. After random mating created three new diploid genotypes, we fabricated three new offspring tails. In the presence of both selection and chance events (mutation, genetic drift), the phenotypic means of this small population evolved. The classic hypothesis was supported in that k was positively correlated (r(2)=0.40) with navigational prowess, NP, the dimensionless ratio of U to the product of R, t and W. However, the plausible adaptive scenario, even in this simplified system, is more complex, since the remaining variance in NP was correlated with the residuals of R and U taken with respect to k, suggesting that changes in k alone are insufficient to explain the evolution of NP.
De Leenheer, Patrick; Mohapatra, Anushaya; Ohms, Haley A; Lytle, David A; Cushing, J M
We consider the phenomenon of partial migration which is exhibited by populations in which some individuals migrate between habitats during their lifetime, but others do not. First, using an adaptive dynamics approach, we show that partial migration can be explained on the basis of negative density dependence in the per capita fertilities alone, provided that this density dependence is attenuated for increasing abundances of the subtypes that make up the population. We present an exact formula for the optimal proportion of migrants which is expressed in terms of the vital rates of migrant and non-migrant subtypes only. We show that this allocation strategy is both an evolutionary stable strategy (ESS) as well as a convergence stable strategy (CSS). To establish the former, we generalize the classical notion of an ESS because it is based on invasion exponents obtained from linearization arguments, which fail to capture the stabilizing effects of the nonlinear density dependence. These results clarify precisely when the notion of a "weak ESS", as proposed in Lundberg (2013) for a related model, is a genuine ESS. Secondly, we use an evolutionary game theory approach, and confirm, once again, that partial migration can be attributed to negative density dependence alone. In this context, the result holds even when density dependence is not attenuated. In this case, the optimal allocation strategy towards migrants is the same as the ESS stemming from the analysis based on the adaptive dynamics. The key feature of the population models considered here is that they are monotone dynamical systems, which enables a rather comprehensive mathematical analysis.
Moalem, S; Storey, K B; Percy, M E; Peros, M C; Perl, D P
The reasons for the uneven worldwide distribution of Type 1 diabetes mellitus have yet to be fully explained. Epidemiological studies have shown a higher prevalence of Type 1 diabetes in northern Europe, particularly in Scandinavian countries, and Sardinia. Recent animal research has uncovered the importance of the generation of elevated levels of glucose, glycerol and other sugar derivatives as a physiological means for cold adaptation. High concentrations of these substances depress the freezing point of body fluids and prevent the formation of ice crystals in cells through supercooling, thus acting as a cryoprotectant or antifreeze for vital organs as well as in their muscle tissue. In this paper, we hypothesize that factors predisposing to elevated levels of glucose, glycerol and other sugar derivatives may have been selected for, in part, as adaptive measures in exceedingly cold climates. This cryoprotective adaptation would have protected ancestral northern Europeans from the effects of suddenly increasingly colder climates, such as those believed to have arisen around 14,000 years ago and culminating in the Younger Dryas. When life expectancy was short, factors predisposing to Type 1 diabetes provided a survival advantage. However, deleterious consequences of this condition have become significant only in more modern times, as life expectancy has increased, thus outweighing their protective value. Examples of evolutionary adaptations conferring selection advantages against human pathogens that result in deleterious effects have been previously reported as epidemic pathogenic selection (EPS). Such proposed examples include the cystic fibrosis mutations in the CFTR gene bestowing resistance to Salmonella typhi and hemochromatosis mutations conferring protection against iron-seeking intracellular pathogens. This paper is one of the first accounts of a metabolic disorder providing a selection advantage not against a pathogenic stressor alone, but rather against
Alexander, Roger P; Jouline, Igor B
As an important model for transmembrane signaling, methyl-accepting chemotaxis proteins (MCPs) have been extensively studied by using genetic, biochemical, and structural techniques. However, details of the molecular mechanism of signaling are still not well understood. The availability of genomic information for hundreds of species enables the identification of features in protein sequences that are conserved over long evolutionary distances and thus are critically important for function. We carried out a large-scale comparative genomic analysis of the MCP signaling and adaptation domain family and identified features that appear to be critical for receptor structure and function. Based on domain length and sequence conservation, we identified seven major MCP classes and three distinct structural regions within the cytoplasmic domain: signaling, methylation, and flexible bundle subdomains. The flexible bundle subdomain, not previously recognized in MCPs, is a conserved element that appears to be important for signal transduction. Remarkably, the N- and C-terminal helical arms of the cytoplasmic domain maintain symmetry in length and register despite dramatic variation, from 24 to 64 7-aa heptads in overall domain length. Loss of symmetry is observed in some MCPs, where it is concomitant with specific changes in the sensory module. Each major MCP class has a distinct pattern of predicted methylation sites that is well supported by experimental data. Our findings indicate that signaling and adaptation functions within the MCP cytoplasmic domain are tightly coupled, and that their coevolution has contributed to the significant diversity in chemotaxis mechanisms among different organisms.
Stefansson, Tryggvi S; McDonald, Bruce A; Willi, Yvonne
To predict the response of plant pathogens to climate warming, data are needed on current thermal adaptation, the pathogen's evolutionary potential, and the link between them. We conducted a common garden experiment using isolates of the fungal pathogen Rhynchosporium commune from nine barley populations representing climatically diverse locations. Clonal replicates of 126 genetically distinct isolates were assessed for their growth rate at 12°C, 18°C, and 22°C. Populations originating from climates with higher monthly temperature variation had higher growth rate at all three temperatures compared with populations from climates with less temperature fluctuation. Population differentiation in growth rate (QST) was significantly higher at 22°C than population differentiation for neutral microsatellite loci (GST), consistent with local adaptation for growth at higher temperatures. At 18°C, we found evidence for stabilizing selection for growth rate as QST was significantly lower than GST. Heritability of growth rate under the three temperatures was substantial in all populations (0.58–0.76). Genetic variation was lower in populations with higher growth rate at the three temperatures and evolvability increased under heat stress in seven of nine populations. Our findings imply that the distribution of this pathogen is unlikely to be genetically limited under climate warming, due to its high genetic variation and plasticity for thermal tolerance. PMID:23745143
Stucker, Karla M.; Pagan, Israel; Cifuente, Javier O.; Kaelber, Jason T.; Lillie, Tyler D.; Hafenstein, Susan; Holmes, Edward C.
The adaptation of viruses to new hosts is a poorly understood process likely involving a variety of viral structures and functions that allow efficient replication and spread. Canine parvovirus (CPV) emerged in the late 1970s as a host-range variant of a virus related to feline panleukopenia virus (FPV). Within a few years of its emergence in dogs, there was a worldwide replacement of the initial virus strain (CPV type 2) by a variant (CPV type 2a) characterized by four amino acid differences in the capsid protein. However, the evolutionary processes that underlie the acquisition of these four mutations, as well as their effects on viral fitness, both singly and in combination, are still uncertain. Using a comprehensive experimental analysis of multiple intermediate mutational combinations, we show that these four capsid mutations act in concert to alter antigenicity, cell receptor binding, and relative in vitro growth in feline cells. Hence, host adaptation involved complex interactions among both surface-exposed and buried capsid mutations that together altered cell infection and immune escape properties of the viruses. Notably, most intermediate viral genotypes containing different combinations of the four key amino acids possessed markedly lower fitness than the wild-type viruses. PMID:22114336
Janikow, Cezary Z.
An evolutionary algorithm applies evolution-based principles to problem solving. To solve a problem, the user defines the space of potential solutions, the representation space. Sample solutions are encoded in a chromosome-like structure. The algorithm maintains a population of such samples, which undergo simulated evolution by means of mutation, crossover, and survival of the fittest principles. Genetic Programming (GP) uses tree-like chromosomes, providing very rich representation suitable for many problems of interest. GP has been successfully applied to a number of practical problems such as learning Boolean functions and designing hardware circuits. To apply GP to a problem, the user needs to define the actual representation space, by defining the atomic functions and terminals labeling the actual trees. The sufficiency principle requires that the label set be sufficient to build the desired solution trees. The closure principle allows the labels to mix in any arity-consistent manner. To satisfy both principles, the user is often forced to provide a large label set, with ad hoc interpretations or penalties to deal with undesired local contexts. This unfortunately enlarges the actual representation space, and thus usually slows down the search. In the past few years, three different methodologies have been proposed to allow the user to alleviate the closure principle by providing means to define, and to process, constraints on mixing the labels in the trees. Last summer we proposed a new methodology to further alleviate the problem by discovering local heuristics for building quality solution trees. A pilot system was implemented last summer and tested throughout the year. This summer we have implemented a new revision, and produced a User's Manual so that the pilot system can be made available to other practitioners and researchers. We have also designed, and partly implemented, a larger system capable of dealing with much more powerful heuristics.
Hendrie, C A; Pickles, A R
Currently available antidepressant treatments are no longer seen as the panaceas they once were. Only a proportion of the depressed population respond to them, they have a high relapse rate and a therapeutic lag of several weeks. The notable lack of progress in developing more efficacious drug-based antidepressant therapies over the past half century is a clear signal for the need to adopt new approaches. The current manuscript outlines the proposal that depression is an evolutionary adaptation that emerged where displaced dominants needed to make a transition to lower social status and that is now triggered, in those individuals that have this adaptation, by damage to reproductive potential from any source. The behavioural cluster associated with depression includes adoption of a hunched posture, avoidance of eye contact, loss of appetite for food and sex and sleep disruption. This behavioural cluster serves to reduce an individuals' attack provoking stimuli and so facilitates this social change. When viewed in this context, it becomes clear that many of the brain areas that mediate these behaviours (e.g. the pineal, hypothalamus and amygdala, whose main output, the stria terminalis passes through) all lie in close physical proximity to the third ventricle. In consequence, it is proposed that depression has its origins within this ventricle. Disruption of circadian rhythms, appetite for sex and food and fear/defence responses would all ensue if structures that border the third ventricle, or whose main connections pass through it, were damaged. Therefore, it is hypothesised that the behavioural expression of this adaptation is mediated by a single or pulsatile release of a yet to be identified noxious factor into the ventricular space. This extreme response reflects the severity of the emergency that was faced by our ancestral stock in this situation and has parallels with the development of other adaptations where the preservation of life (and hence the chance for
Ten Brummelaar, Theo; Che, Xiao; McAlister, Harold A.; Ireland, Michael; Monnier, John D.; Mourard, Denis; Ridgway, Stephen T.; sturmann, judit; Sturmann, Laszlo; Turner, Nils H.; Tuthill, Peter
The CHARA array is an optical/near infrared interferometer consisting of six 1-meter diameter telescopes the longest baseline of which is 331 meters. With sub-millisecond angular resolution, the CHARA array is able to spatially resolve nearby stellar systems to reveal the detailed structures. To improve the sensitivity and scientific throughput, the CHARA array was funded by NSF-ATI in 2011, and by NSF-MRI in 2015, for an upgrade of adaptive optics (AO) systems to all six telescopes. The initial grant covers Phase I of the adaptive optics system, which includes an on-telescope Wavefront Sensor and non-common-path (NCP) error correction. The WFS use a fairly standard Shack-Hartman design and will initially close the tip tilt servo and log wavefront errors for use in data reduction and calibration. The second grant provides the funding for deformable mirrors for each telescope which will be used closed loop to remove atmospheric aberrations from the beams. There are then over twenty reflections after the WFS at the telescopes that bring the light several hundred meters into the beam combining laboratory. Some of these, including the delay line and beam reducing optics, are powered elements, and some of them, in particular the delay lines and telescope Coude optics, are continually moving. This means that the NCP problems in an interferometer are much greater than those found in more standard telescope systems. A second, slow AO system is required in the laboratory to correct for these NCP errors. We will breifly describe the AO system, and it's current status, as well as discuss the new science enabled by the system with a focus on our YSO program.
A systematic approach for the aberration correction of zoom systems is presented. It is assumed that the powers and movements of the components of the zoom systems are known. Each component is considered as a system of thin lenses in contact. An evolutionary algorithm is developed to explore the multivariate hyperspace of design variables formed by spherical aberration, central coma, and longitudinal chromatic aberration of each component for infinite conjugate. The primary aberrations for each component at any zoom position are deduced from three central aberration coefficients of the component for infinite conjugate using conjugate shift formulas. Overall system aberrations of the zoom systems are determined by using stop shift formulas. In most of the zoom lens systems it is important to achieve stability in the primary aberrations of the system over the zoom range. This is facilitated by proper formulation of the merit function for the optimization process. Investigations have been carried out on four-component zoom lenses, and an ab initio structure of a four-component zoom lens is presented.
McGavin, Martin J.; Arsic, Benjamin; Nickerson, Nicholas N.
Staphylococcus aureus clonal complex CC30 has caused infectious epidemics for more than 60 years, and, therefore, provides a model system to evaluate how evolution has influenced the disease potential of closely related strains. In previous multiple genome comparisons, phylogenetic analyses established three major branches that evolved from a common ancestor. Clade 1, comprised of historic pandemic phage type 80/81 methicillin susceptible S. aureus (MSSA), and Clade 2 comprised of contemporary community acquired methicillin resistant S. aureus (CA-MRSA) were hyper-virulent in murine infection models. Conversely, Clade 3 strains comprised of contemporary hospital associated MRSA (HA-MRSA) and clinical MSSA exhibited attenuated virulence, due to common single nucleotide polymorphisms (SNP's) that abrogate production of α-hemolysin Hla, and interfere with signaling of the accessory gene regulator agr. We have now completed additional in silico genome comparisons of 15 additional CC30 genomes in the public domain, to assess the hypothesis that Clade 3 has evolved to favor niche adaptation. In addition to SNP's that influence agr and hla, other common traits of Clade 3 include tryptophan auxotrophy due to a di-nucleotide deletion within trpD, a premature stop codon within isdH encoding an immunogenic cell surface protein involved in iron acquisition, loss of a genomic toxin–antitoxin (TA) addiction module, acquisition of S. aureus pathogenicity islands SaPI4, and SaPI2 encoding toxic shock syndrome toxin tst, and increased copy number of insertion sequence ISSau2, which appears to target transcription terminators. Compared to other Clade 3 MSSA, S. aureus MN8, which is associated with Staphylococcal toxic shock syndrome, exhibited a unique ISSau2 insertion, and enhanced production of toxic shock syndrome toxin encoded by SaPI2. Cumulatively, our data support the notion that Clade 3 strains are following an evolutionary blueprint toward niche-adaptation. PMID:22919639
Sikosek, Tobias; Bornberg-Bauer, Erich; Chan, Hue Sun
Experimental studies have shown that some proteins exist in two alternative native-state conformations. It has been proposed that such bi-stable proteins can potentially function as evolutionary bridges at the interface between two neutral networks of protein sequences that fold uniquely into the two different native conformations. Under adaptive conflict scenarios, bi-stable proteins may be of particular advantage if they simultaneously provide two beneficial biological functions. However, computational models that simulate protein structure evolution do not yet recognize the importance of bi-stability. Here we use a biophysical model to analyze sequence space to identify bi-stable or multi-stable proteins with two or more equally stable native-state structures. The inclusion of such proteins enhances phenotype connectivity between neutral networks in sequence space. Consideration of the sequence space neighborhood of bridge proteins revealed that bi-stability decreases gradually with each mutation that takes the sequence further away from an exactly bi-stable protein. With relaxed selection pressures, we found that bi-stable proteins in our model are highly successful under simulated adaptive conflict. Inspired by these model predictions, we developed a method to identify real proteins in the PDB with bridge-like properties, and have verified a clear bi-stability gradient for a series of mutants studied by Alexander et al. (Proc Nat Acad Sci USA 2009, 106:21149–21154) that connect two sequences that fold uniquely into two different native structures via a bridge-like intermediate mutant sequence. Based on these findings, new testable predictions for future studies on protein bi-stability and evolution are discussed. PMID:23028272
The endocannabinoid system (ECS) is a major lipid signalling network that plays important pro-homeostatic (allostatic) roles not only in the nervous system but also in peripheral organs. There is increasing evidence that there is a dietary component in the modulation of the ECS. Cannabinoid receptors in hominids co-evolved with diet, and the ECS constitutes a feedback loop for food selection and energy metabolism. Here, it is postulated that the mismatch of ancient lipid genes of hunter-gatherers and pastoralists with the high-carbohydrate diet introduced by agriculture could be compensated for via dietary modulation of the ECS. In addition to the fatty acid precursors of endocannabinoids, the potential role of dietary cannabimimetic phytochemicals in agriculturist nutrition is discussed. Dietary secondary metabolites from vegetables and spices able to enhance the activity of cannabinoid-type 2 (CB2 ) receptors may provide adaptive metabolic advantages and counteract inflammation. In contrast, chronic CB1 receptor activation in hedonic obese individuals may enhance pathophysiological processes related to hyperlipidaemia, diabetes, hepatorenal inflammation and cardiometabolic risk. Food able to modulate the CB1 /CB2 receptor activation ratio may thus play a role in the nutrition transition of Western high-calorie diets. In this review, the interplay between diet and the ECS is highlighted from an evolutionary perspective. The emerging potential of cannabimimetic food as a nutraceutical strategy is critically discussed.
Feng, Han-Zhong; Chen, Xuequn; Hossain, M Moazzem; Jin, Jian-Ping
The three isoforms of vertebrate troponin T (TnT) are normally expressed in a muscle type-specific manner. Here we report an exception that the cardiac muscle of toad (Bufo) expresses exclusively slow skeletal muscle TnT (ssTnT) together with cardiac forms of troponin I and myosin as determined using immunoblotting, cDNA cloning, and/or LC-MS/MS. Using RT-PCR and 3'- and 5'-rapid amplification of cDNA ends on toad cardiac mRNA, we cloned full-length cDNAs encoding two alternatively spliced variants of ssTnT. Expression of the cloned cDNAs in Escherichia coli confirmed that the toad cardiac muscle expresses solely ssTnT, predominantly the low molecular weight variant with the exon 5-encoded NH(2)-terminal segment spliced out. Functional studies were performed in ex vivo working toad hearts and compared with the frog (Rana) hearts. The results showed that toad hearts had higher contractile and relaxation velocities and were able to work against a significantly higher afterload than that of frog hearts. Therefore, the unique evolutionary adaptation of utilizing exclusively ssTnT in toad cardiac muscle corresponded to a fitness value from improving systolic function of the heart. The data demonstrated a physiological importance of the functional diversity of TnT isoforms. The structure-function relationship of TnT may be explored for the development of new treatment of heart failure.
Boucher, Nathalie; Noll, Kenneth M
The Thermotogae possess a large number of ATP-binding cassette (ABC) transporters, including two mannan binding proteins, ManD and CelE (previously called ManE). We show that a gene encoding an ancestor of these was acquired by the Thermotogae from the archaea followed by gene duplication. To address the functional evolution of these proteins as a consequence of their evolutionary histories, we measured the binding affinities of ManD and CelE orthologs from representative Thermotogae. Both proteins bind cellobiose, cellotriose, cellotetraose, β-1,4-mannotriose, and β-1,4-mannotetraose. The CelE orthologs additionally bind β-1,4-mannobiose, laminaribiose, laminaritriose and sophorose while the ManD orthologs additionally only weakly bind β-1,4-mannobiose. The CelE orthologs have higher unfolding temperatures than the ManD orthologs. An examination of codon sites under positive selection revealed that many of these encode residues located near or in the binding site, suggesting that the proteins experienced selective pressures in regions that might have changed their functions. The gene arrangement, phylogeny, binding properties, and putative regulatory networks suggest that the ancestral mannan binding protein was a CelE ortholog which gave rise to the ManD orthologs. This study provides a window on how one class of proteins adapted to new functions and temperatures to fit the physiologies of their new hosts.
Berkhout, Jan; Bosdriesz, Evert; Nikerel, Emrah; Molenaar, Douwe; de Ridder, Dick; Teusink, Bas; Bruggeman, Frank J
Evolutionary adaptations in metabolic networks are fundamental to evolution of microbial growth. Studies on unneeded-protein synthesis indicate reductions in fitness upon nonfunctional protein synthesis, showing that cell growth is limited by constraints acting on cellular protein content. Here, we present a theory for optimal metabolic enzyme activity when cells are selected for maximal growth rate given such growth-limiting biochemical constraints. We show how optimal enzyme levels can be understood to result from an enzyme benefit minus cost optimization. The constraints we consider originate from different biochemical aspects of microbial growth, such as competition for limiting amounts of ribosomes or RNA polymerases, or limitations in available energy. Enzyme benefit is related to its kinetics and its importance for fitness, while enzyme cost expresses to what extent resource consumption reduces fitness through constraint-induced reductions of other enzyme levels. A metabolic fitness landscape is introduced to define the fitness potential of an enzyme. This concept is related to the selection coefficient of the enzyme and can be expressed in terms of its fitness benefit and cost.
Kelly, Luke E.
"Designing and Implementing Effective Adapted Physical Education Programs" was written to assist adapted and general physical educators who are dedicated to ensuring that the physical and motor needs of all their students are addressed in physical education. While it is anticipated that adapted physical educators, where available, will typically…
Moore, Julia E; Bumbarger, Brian K; Cooper, Brittany Rhoades
When evidence-based programs (EBPs) are scaled up in natural, or non-research, settings, adaptations are commonly made. Given the fidelity-versus-adaptation debate, theoretical rationales have been provided for the pros and cons of adaptations. Yet the basis of this debate is theoretical; thus, empirical evidence is needed to understand the types of adaptations made in natural settings. In the present study, we introduce a taxonomy for understanding adaptations. This taxonomy addresses several aspects of adaptations made to programs including the fit (philosophical or logistical), timing (proactive or reactive), and valence, or the degree to which the adaptations align with the program's goals and theory, (positive, negative, or neutral). Self-reported qualitative data from communities delivering one of ten state-funded EBPs were coded based on the taxonomy constructs; additionally, quantitative data were used to examine the types and reasons for making adaptations under natural conditions. Forty-four percent of respondents reported making adaptations. Adaptations to the procedures, dosage, and content were cited most often. Lack of time, limited resources, and difficulty retaining participants were listed as the most common reasons for making adaptations. Most adaptations were made reactively, as a result of issues of logistical fit, and were not aligned with, or deviated from, the program's goals and theory.
McClure, Michelle M; Utter, Fred M; Baldwin, Casey; Carmichael, Richard W; Hassemer, Peter F; Howell, Philip J; Spruell, Paul; Cooney, Thomas D; Schaller, Howard A; Petrosky, Charles E
Most hatchery programs for anadromous salmonids have been initiated to increase the numbers of fish for harvest, to mitigate for habitat losses, or to increase abundance in populations at low abundance. However, the manner in which these programs are implemented can have significant impacts on the evolutionary trajectory and long-term viability of populations. In this paper, we review the potential benefits and risks of hatchery programs relative to the conservation of species listed under the US Endangered Species Act. To illustrate, we present the range of potential effects within a population as well as among populations of Chinook salmon (Oncorhynchus tshawytscha) where changes to major hatchery programs are being considered. We apply evolutionary considerations emerging from these examples to suggest broader principles for hatchery uses that are consistent with conservation goals. We conclude that because of the evolutionary risks posed by artificial propagation programs, they should not be viewed as a substitute for addressing other limiting factors that prevent achieving viability. At the population level, artificial propagation programs that are implemented as a short-term approach to avoid imminent extinction are more likely to achieve long-term population viability than approaches that rely on long-term supplementation. In addition, artificial propagation programs can have out-of-population impacts that should be considered in conservation planning. PMID:25567637
This paper analyzes rancher participation in conservation programs in the context of a social-ecological framework for adaptive rangeland management. We argue that conservation programs are best understood as one of many strategies of adaptively managing rangelands in ways that sustain livelihoods a...
Quan, Baldwin; And Others
This program listing is a supplement to the Microcomputer Network for Computerized Adaptive Testing (CAT). The driver textfile program allows access to major subprograms of the CAT project. The test administration textfile program gives examinees a prescribed set of subtests. The parameter management textfile program establishes a file containing…
Brodersen, Jakob; Seehausen, Ole
While ecological monitoring and biodiversity assessment programs are widely implemented and relatively well developed to survey and monitor the structure and dynamics of populations and communities in many ecosystems, quantitative assessment and monitoring of genetic and phenotypic diversity that is important to understand evolutionary dynamics is only rarely integrated. As a consequence, monitoring programs often fail to detect changes in these key components of biodiversity until after major loss of diversity has occurred. The extensive efforts in ecological monitoring have generated large data sets of unique value to macro-scale and long-term ecological research, but the insights gained from such data sets could be multiplied by the inclusion of evolutionary biological approaches. We argue that the lack of process-based evolutionary thinking in ecological monitoring means a significant loss of opportunity for research and conservation. Assessment of genetic and phenotypic variation within and between species needs to be fully integrated to safeguard biodiversity and the ecological and evolutionary dynamics in natural ecosystems. We illustrate our case with examples from fishes and conclude with examples of ongoing monitoring programs and provide suggestions on how to improve future quantitative diversity surveys. PMID:25553061
Venne, Vickie L; Coleman, Darrell
They are the Millennials--Generation Y. Over the next few decades, they will be entering genetic counseling graduate training programs and the workforce. As a group, they are unlike previous youth generations in many ways, including the way they learn. Therefore, genetic counselors who teach and supervise need to understand the Millennials and explore new ways of teaching to ensure that the next cohort of genetic counselors has both skills and knowledge to represent our profession well. This paper will summarize the distinguishing traits of the Millennial generation as well as authentic learning and evolutionary scaffolding theories of learning that can enhance teaching and supervision. We will then use specific aspects of case preparation during clinical rotations to demonstrate how incorporating authentic learning theory into evolutionary scaffolding results in experiential evolutionary scaffolding, a method that potentially offers a more effective approach when teaching Millennials. We conclude with suggestions for future research.
Wander, Katherine; Shell-Duncan, Bettina; McDade, Thomas W
An evolutionary perspective suggests that iron deficiency may have opposing effects on infectious disease risk, decreasing susceptibility by restricting iron availability to pathogens, and increasing susceptibility by compromising cellular immunocompetence. In some environments, the trade-off between these effects may result in optimal iron intake that is inadequate to fully meet body iron needs. Thus, it has been suggested that moderate iron deficiency may protect against acute infection, and may represent a nutritional adaptation to endemic infectious disease stress. To test this assertion, we examined the association between infection, reflected by C-reactive protein, a biomarker of inflammation, and iron status, reflected by transferrin receptor (TfR) and zinc protoporphyrin to heme ratio (ZPP:H), among school-age Kenyan children, and evaluated the hypothesis that moderate iron deficiency is associated with lower odds of infectious disease. TfR > 5.0 mg/l, with sensitivity and specificity for iron deficiency (ZPP:H > 80 micromol/mol) of 0.807 and 0.815, was selected as the TfR definition of iron deficiency. Controlling for age and triceps skinfold thickness (TSF), the odds ratio (OR) for acute viral or bacterial infection associated with iron deficiency (compared to normal/replete) was 0.50 (P = 0.11). Controlling for age and TSF, the OR for infection associated with an unequivocally iron replete state (compared to all others) was 2.9 (P = 0.01). We conclude that iron deficiency may protect against acute infection in children.
Reinschmidt, Kerstin M; Teufel-Shone, Nicolette I; Bradford, Gail; Drummond, Rebecca L; Torres, Emma; Redondo, Floribella; Elenes, Jo Jean; Sanders, Alicia; Gastelum, Sylvia; Moore-Monroy, Martha; Barajas, Salvador; Fernandez, Lourdes; Alvidrez, Rosy; de Zapien, Jill Guernsey; Staten, Lisa K
Diabetes health disparities among Hispanic populations have been countered with federally funded health promotion and disease prevention programs. Dissemination has focused on program adaptation to local cultural contexts for greater acceptability and sustainability. Taking a broader approach and drawing on our experience in Mexican American communities at the U.S.-Mexico Border, we demonstrate how interventions are adapted at the intersection of multiple cultural contexts: the populations targeted, the community- and university-based entities designing and implementing interventions, and the field team delivering the materials. Program adaptation involves negotiations between representatives of all contexts and is imperative in promoting local ownership and program sustainability.
Bikard, David; Marraffini, Luciano A
Bacteria are constantly challenged by bacteriophages (viruses that infect bacteria), the most abundant microorganism on earth. Bacteria have evolved a variety of immunity mechanisms to resist bacteriophage infection. In response, bacteriophages can evolve counter-resistance mechanisms and launch a 'virus versus host' evolutionary arms race. In this context, rapid evolution is fundamental for the survival of the bacterial cell. Programmed genetic variation mechanisms at loci involved in immunity against bacteriophages generate diversity at a much faster rate than random point mutation and enable bacteria to quickly adapt and repel infection. Diversity-generating retroelements (DGRs) and phase variation mechanisms enhance the generic (innate) immune response against bacteriophages. On the other hand, the integration of small bacteriophage sequences in CRISPR loci provide bacteria with a virus-specific and sequence-specific adaptive immune response. Therefore, although using different molecular mechanisms, both prokaryotes and higher organisms rely on programmed genetic variation to increase genetic diversity and fight rapidly evolving infectious agents.
Monteiro, Leandro R; Nogueira, Marcelo R
The evolutionary integration of complex morphological structures is a macroevolutionary pattern in which morphogenetic components evolve in a coordinated fashion, which can result from the interplay among processes of developmental, genetic integration, and different types of selection. We tested hypotheses of ecological versus developmental factors underlying patterns of within-species and evolutionary integration in the mandible of phyllostomid bats, during the most impressive ecological and morphological radiation among mammals. Shape variation of mandibular morphogenetic components was associated with diet, and the transition of integration patterns from developmental to within-species to evolutionary was examined. Within-species (as a proxy to genetic) integration in different lineages resembled developmental integration regardless of diet specialization, however, evolutionary integration patterns reflected selection in different mandibular components. For dietary specializations requiring extensive functional changes in mastication patterns or biting, such as frugivores and sanguivores, the evolutionary integration pattern was not associated with expected within-species or developmental integration. On the other hand, specializations with lower mastication demands or without major functional reorganization (such as nectarivores and carnivores), presented evolutionary integration patterns similar to the expected developmental pattern. These results show that evolutionary integration patterns are largely a result of independent selection on specific components regardless of developmental modules.
This document is a resource for coastal communities to start planning to adapt to climate change. It describes elements, such as vulnerability assessments and stakeholder outreach, and provides examples as well as suggestions for additional resources.
The instructor of an adapted physical education program describes his experiences and suggests guidelines for implementing other programs. Reviewed are such aspects as program orientation, class procedures, identification of student participants, and grading procedures. Objectives, lesson plans and evaluations are presented for the following units…
Fragata, I; Lopes-Cunha, M; Bárbaro, M; Kellen, B; Lima, M; Santos, M A; Faria, G S; Santos, M; Matos, M; Simões, P
Chromosomal inversions are present in a wide range of animals and plants, having an important role in adaptation and speciation. Although empirical evidence of their adaptive value is abundant, the role of different processes underlying evolution of chromosomal polymorphisms is not fully understood. History and selection are likely to shape inversion polymorphism variation to an extent yet largely unknown. Here, we perform a real-time evolution study addressing the role of historical constraints and selection in the evolution of these polymorphisms. We founded laboratory populations of Drosophila subobscura derived from three locations along the European cline and followed the evolutionary dynamics of inversion polymorphisms throughout the first 40 generations. At the beginning, populations were highly differentiated and remained so throughout generations. We report evidence of positive selection for some inversions, variable between foundations. Signs of negative selection were more frequent, in particular for most cold-climate standard inversions across the three foundations. We found that previously observed convergence at the phenotypic level in these populations was not associated with convergence in inversion frequencies. In conclusion, our study shows that selection has shaped the evolutionary dynamics of inversion frequencies, but doing so within the constraints imposed by previous history. Both history and selection are therefore fundamental to predict the evolutionary potential of different populations to respond to global environmental changes.
Mace, Ruth; Jordan, Fiona M
A growing body of theoretical and empirical research has examined cultural transmission and adaptive cultural behaviour at the individual, within-group level. However, relatively few studies have tried to examine proximate transmission or test ultimate adaptive hypotheses about behavioural or cultural diversity at a between-societies macro-level. In both the history of anthropology and in present-day work, a common approach to examining adaptive behaviour at the macro-level has been through correlating various cultural traits with features of ecology. We discuss some difficulties with simple ecological associations, and then review cultural phylogenetic studies that have attempted to go beyond correlations to understand the underlying cultural evolutionary processes. We conclude with an example of a phylogenetically controlled approach to understanding proximate transmission pathways in Austronesian cultural diversity.
Mace, Ruth; Jordan, Fiona M.
A growing body of theoretical and empirical research has examined cultural transmission and adaptive cultural behaviour at the individual, within-group level. However, relatively few studies have tried to examine proximate transmission or test ultimate adaptive hypotheses about behavioural or cultural diversity at a between-societies macro-level. In both the history of anthropology and in present-day work, a common approach to examining adaptive behaviour at the macro-level has been through correlating various cultural traits with features of ecology. We discuss some difficulties with simple ecological associations, and then review cultural phylogenetic studies that have attempted to go beyond correlations to understand the underlying cultural evolutionary processes. We conclude with an example of a phylogenetically controlled approach to understanding proximate transmission pathways in Austronesian cultural diversity. PMID:21199844
Recent technical papers explore whether adaptive management (AM) is useful for environmental management and restoration efforts and discuss the many challenges to overcome for successful implementation, especially for large-scale restoration programs (McLain and Lee 1996; Levine ...
When the Comprehensive Everglades Restoration Plan (CERP) was authorized in 2000, adaptive management (AM) was recognized as a necessary tool to address uncertainty in achieving the broad goals and objectives for restoring a highly managed system. The Everglades covers18,000 squ...
Diz, A P; Páez de la Cadena, M; Rolán-Alvarez, E
The exposed and sheltered ecotypes of the marine snail Littorina saxatilis from European rocky shores are considered a key model system to study adaptation and ecological speciation. Previous studies showed that two ecotypes (RB and SU) of this species in NW Spain have adapted differently to different shore levels and microhabitats. In order to understand how this divergent adaptive process has been accomplished, we followed a quantitative proteomic approach to investigate the proteome variation in a number of different biological factors, that is, ecotype, ontogeny and their interactions. This approach allowed testing the hypothesis that one of the ecotypes has evolved by paedomorphosis, and also whether or not the molecular mechanisms related to ecotype differentiation are set up in early developmental stages. Additionally, the identification of some candidate proteins using mass spectrometry provides some functional insights into these evolutionary processes. Results from this study provided evidence of higher ontogenetic differentiation at proteome level in the RB (metamorphic) than in SU (paedomorphic) ecotype that point to the possibility of juvenile stage retention in this latter ecotype. The level of protein expression (proteome) differences between ecotypes maintained nearly constant from late embryonic stages to adulthood, although some proteins involved in these changes considerably differed in embryonic compared to other ontogenetic stages. Paedomorphosis may be the evolutionary response of the SU ecotype of solving the trade-off during sexually immaturity that is caused by the evolution of small size arising from adaptation to the wave-exposed habitat. Some potential candidate genes of adaptation related to energetic metabolism have been identified, providing a promising baseline for future functional analyses.
Alam, Mohammad Shafiul; Islam, Md Monirul; Yao, Xin; Murase, Kazuyuki
In the application of evolutionary algorithms (EAs) to complex problem solving, it is essential to maintain proper balance between global exploration and local exploitation to achieve a good near-optimum solution to the problem. This paper presents a recurring two-stage evolutionary programming (RTEP) to balance the explorative and exploitative features of the conventional EAs. Unlike most previous works, RTEP is based on repeated and alternated execution of two different stages, namely, the exploration and exploitation stages, each with its own mutation operator, selection strategy, and explorative/exploitative objective. Both analytical and empirical studies have been carried out to understand the necessity of repeated and alternated exploration and exploitation operations in EAs. A suite of 48 benchmark numerical optimization problems has been used in the empirical studies. The experimental results show the remarkable effectiveness of the repeated exploration and exploitation operations employed by RTEP.
The evolution of object-oriented programming languages includes update of their own versions, update of development environments, and reform of new languages upon old languages. In this paper, the evolution analysis of object-oriented programming languages is presented in term of the characters and development. The notion of adaptive teaching upon…
Thomas, Robert G.; Thomas, R. Murray
Describes an adaptive-health program created by officials at the California Men's Colony in San Luis Obispo for inmates who suffer physical or psychological disabilities. Discusses program goals, admission requirements, learning activities, techniques for motivating participants, evaluation methods, and staffing. (JOW)
Crawford, D L; Powers, D A
At the extremes of its natural distribution, populations of the common killifish Fundulus heteroclitus experience a difference of more than 15 degrees C in mean annual temperature. These populations are virtually fixed for two different codominant alleles at the heart-type lactate dehydrogenase locus (Ldh-B) which code for allozymes with different and adaptive kinetic responses to temperature. Two populations near the extremes of the species range (i.e., Maine and Georgia) were further studied for thermal adaptation at this locus. In the absence of any kinetic differences one would predict that to maintain a constant reaction velocity, 2 to 3 times as much enzyme would be required for each 10 degrees C decrease in environmental temperature. Consistent with this adaptive strategy and in addition to the adaptive kinetic characteristics, the LDH-B4 enzyme (EC 184.108.40.206) concentration and its mRNA concentration were approximately twice as great in the northern population as in the southern population. Acclimation experiments allow us to conclude that these differences are due to a combination of fixed genetic traits (evolutionary adaptation) and plastic responses to temperature (physiological acclimation). Furthermore, our calculations show that the LDH-B4 reaction velocities are essentially equivalent for these two populations, even though they live in significantly different thermal environments. PMID:2594773
He, Tianhua; D’Agui, Haylee; Lim, Sim Lin; Enright, Neal J.; Luo, Yiqi
Substantial climate changes are evident across Australia, with declining rainfall and rising temperature in conjunction with frequent fires. Considerable species loss and range contractions have been predicted; however, our understanding of how genetic variation may promote adaptation in response to climate change remains uncertain. Here we characterized candidate genes associated with rainfall gradients, temperatures, and fire intervals through environmental association analysis. We found that overall population adaptive genetic variation was significantly affected by shortened fire intervals, whereas declining rainfall and rising temperature did not have a detectable influence. Candidate SNPs associated with rainfall and high temperature were diverse, whereas SNPs associated with specific fire intervals were mainly fixed in one allele. Gene annotation further revealed four genes with functions in stress tolerance, the regulation of stomatal opening and closure, energy use, and morphogenesis with adaptation to climate and fire intervals. B. attenuata may tolerate further changes in rainfall and temperature through evolutionary adaptations based on their adaptive genetic variation. However, the capacity to survive future climate change may be compromised by changes in the fire regime.
He, Tianhua; D’Agui, Haylee; Lim, Sim Lin; Enright, Neal J.; Luo, Yiqi
Substantial climate changes are evident across Australia, with declining rainfall and rising temperature in conjunction with frequent fires. Considerable species loss and range contractions have been predicted; however, our understanding of how genetic variation may promote adaptation in response to climate change remains uncertain. Here we characterized candidate genes associated with rainfall gradients, temperatures, and fire intervals through environmental association analysis. We found that overall population adaptive genetic variation was significantly affected by shortened fire intervals, whereas declining rainfall and rising temperature did not have a detectable influence. Candidate SNPs associated with rainfall and high temperature were diverse, whereas SNPs associated with specific fire intervals were mainly fixed in one allele. Gene annotation further revealed four genes with functions in stress tolerance, the regulation of stomatal opening and closure, energy use, and morphogenesis with adaptation to climate and fire intervals. B. attenuata may tolerate further changes in rainfall and temperature through evolutionary adaptations based on their adaptive genetic variation. However, the capacity to survive future climate change may be compromised by changes in the fire regime. PMID:27210077
He, Tianhua; D'Agui, Haylee; Lim, Sim Lin; Enright, Neal J; Luo, Yiqi
Substantial climate changes are evident across Australia, with declining rainfall and rising temperature in conjunction with frequent fires. Considerable species loss and range contractions have been predicted; however, our understanding of how genetic variation may promote adaptation in response to climate change remains uncertain. Here we characterized candidate genes associated with rainfall gradients, temperatures, and fire intervals through environmental association analysis. We found that overall population adaptive genetic variation was significantly affected by shortened fire intervals, whereas declining rainfall and rising temperature did not have a detectable influence. Candidate SNPs associated with rainfall and high temperature were diverse, whereas SNPs associated with specific fire intervals were mainly fixed in one allele. Gene annotation further revealed four genes with functions in stress tolerance, the regulation of stomatal opening and closure, energy use, and morphogenesis with adaptation to climate and fire intervals. B. attenuata may tolerate further changes in rainfall and temperature through evolutionary adaptations based on their adaptive genetic variation. However, the capacity to survive future climate change may be compromised by changes in the fire regime.
Chang, Lei; Mak, Miranda C. K.; Li, Tong; Wu, Bao Pei; Chen, Bin Bin; Lu, Hui Jing
Much research has been conducted to document and sometimes to provide proximate explanations (e.g., Confucianism vs. Western philosophy) for East-West cultural differences. The ultimate evolutionary mechanisms underlying these cross-cultural differences have not been addressed. We propose in this review that East-West cultural differences (e.g.,…
Sturge-Apple, Melissa L.; Davies, Patrick T.; Martin, Meredith J.; Cicchetti, Dante; Hentges, Rochelle F.
The current study tests whether propositions set forth in an evolutionary model of temperament (Korte, Koolhaas, Wingfield, & McEwen, 2005) may enhance our understanding of children's differential susceptibility to unsupportive and harsh caregiving practices. Guided by this model, we examined whether children's behavioral strategies for coping…
Marlowe, Douglas B.; Festinger, David S.; Dugosh, Karen L.; Benasutti, Kathleen M.; Fox, Gloria; Croft, Jason R.
Prior studies in Drug Courts reported improved outcomes when participants were matched to schedules of judicial status hearings based on their criminological risk level. The current experiment determined whether incremental efficacy could be gained by periodically adjusting the schedule of status hearings and clinical case-management sessions in response to participants’ ensuing performance in the program. The adjustments were made pursuant to a priori criteria specified in an adaptive algorithm. Results confirmed that participants in the full adaptive condition (n = 62) were more than twice as likely as those assigned to baseline-matching only (n = 63) to be drug-abstinent during the first 18 weeks of the program; however, graduation rates and the average time to case resolution were not significantly different. The positive effects of the adaptive program appear to have stemmed from holding noncompliant participants more accountable for meeting their attendance obligations in the program. Directions for future research and practice implications are discussed. PMID:22923854
Marlowe, Douglas B; Festinger, David S; Dugosh, Karen L; Benasutti, Kathleen M; Fox, Gloria; Croft, Jason R
Prior studies in Drug Courts reported improved outcomes when participants were matched to schedules of judicial status hearings based on their criminological risk level. The current experiment determined whether incremental efficacy could be gained by periodically adjusting the schedule of status hearings and clinical case-management sessions in response to participants' ensuing performance in the program. The adjustments were made pursuant to a priori criteria specified in an adaptive algorithm. Results confirmed that participants in the full adaptive condition (n = 62) were more than twice as likely as those assigned to baseline-matching only (n = 63) to be drug-abstinent during the first 18 weeks of the program; however, graduation rates and the average time to case resolution were not significantly different. The positive effects of the adaptive program appear to have stemmed from holding noncompliant participants more accountable for meeting their attendance obligations in the program. Directions for future research and practice implications are discussed.
Reinschmidt, Kerstin M.; Teufel-Shone, Nicolette I.; Bradford, Gail; Drummond, Rebecca L.; Torres, Emma; Redondo, Floribella; Elenes, Jo Jean; Sanders, Alicia; Gastelum, Sylvia; Moore-Monroy, Martha; Barajas, Salvador; Fernandez, Lourdes; Alvidrez, Rosy; de Zapien, Jill Guernsey; Staten, Lisa K.
Diabetes health disparities among Hispanic populations have been countered with federally funded health promotion and disease prevention programs. Dissemination has focused on program adaptation to local cultural contexts for greater acceptability and sustainability. Taking a broader approach and drawing on our experience in Mexican American…
Broom, Donald M
The term adaptation is used in biology in three different ways. It may refer to changes which occur at the cell and organ level, or at the individual level, or at the level of gene action and evolutionary processes. Adaptation by cells, especially nerve cells helps in: communication within the body, the distinguishing of stimuli, the avoidance of overload and the conservation of energy. The time course and complexity of these mechanisms varies. Adaptive characters of organisms, including adaptive behaviours, increase fitness so this adaptation is evolutionary. The major part of this paper concerns adaptation by individuals and its relationships to welfare. In complex animals, feed forward control is widely used. Individuals predict problems and adapt by acting before the environmental effect is substantial. Much of adaptation involves brain control and animals have a set of needs, located in the brain and acting largely via motivational mechanisms, to regulate life. Needs may be for resources but are also for actions and stimuli which are part of the mechanism which has evolved to obtain the resources. Hence pigs do not just need food but need to be able to carry out actions like rooting in earth or manipulating materials which are part of foraging behaviour. The welfare of an individual is its state as regards its attempts to cope with its environment. This state includes various adaptive mechanisms including feelings and those which cope with disease. The part of welfare which is concerned with coping with pathology is health. Disease, which implies some significant effect of pathology, always results in poor welfare. Welfare varies over a range from very good, when adaptation is effective and there are feelings of pleasure or contentment, to very poor. A key point concerning the concept of individual adaptation in relation to welfare is that welfare may be good or poor while adaptation is occurring. Some adaptation is very easy and energetically cheap and
Genskow, Kenneth D.; Wood, Danielle M.
Environmental planners and managers face unique challenges understanding and documenting the effectiveness of programs that rely on voluntary actions by private landowners. Programs, such as those aimed at reducing nonpoint source pollution or improving habitat, intend to reach those goals by persuading landowners to adopt behaviors and management practices consistent with environmental restoration and protection. Our purpose with this paper is to identify barriers for improving voluntary environmental management programs and ways to overcome them. We first draw upon insights regarding data, learning, and adaptation from the adaptive management and performance management literatures, describing three key issues: overcoming information constraints, structural limitations, and organizational culture. Although these lessons are applicable to a variety of voluntary environmental management programs, we then present the issues in the context of on-going research for nonpoint source water quality pollution. We end the discussion by highlighting important elements for advancing voluntary program efforts.
Pal, Sourav; Hazra, Lakshminarayan
An approach for ab initio synthesis of the thin lens structure of linearly compensated zoom lenses is reported. This method uses evolutionary programming that explores the available configuration space formed by powers of the individual components, the intercomponent separations, and the relative movement parameters of the moving components. Useful thin lens structures of optically and linearly compensated zoom lens systems are obtained by suitable formulation of the merit function of optimization. This paper reports our investigations on three-component zoom lens structures. Illustrative numerical results are presented.
Bloomberg, J. J.; Mulavara, A. P.; Peters, B. T.; Brady, R.; Audas, C.; Ruttley, T. M.; Cohen, H. S.
During the acute phase of adaptation to novel gravitational environments, sensorimotor disturbances have the potential to disrupt the ability of astronauts to perform functional tasks. The goal of this project is to develop a sensorimotor adaptability (SA) training program designed to facilitate recovery of functional capabilities when astronauts transition to different gravitational environments. The project conducted a series of studies that investigated the efficacy of treadmill training combined with a variety of sensory challenges designed to increase adaptability including alterations in visual flow, body loading, and support surface stability.
Storz, Jay F.; Wheat, Christopher W.
Inferences about adaptation at specific loci are often exclusively based on the static analysis of DNA sequence variation. Ideally, population-genetic evidence for positive selection serves as a stepping-off point for experimental studies to elucidate the functional significance of the putatively adaptive variation. We argue that inferences about adaptation at specific loci are best achieved by integrating the indirect, retrospective insights provided by population-genetic analyses with the more direct, mechanistic insights provided by functional experiments. Integrative studies of adaptive genetic variation may sometimes be motivated by experimental insights into molecular function, which then provide the impetus to perform population genetic tests to evaluate whether the functional variation is of adaptive significance. In other cases, studies may be initiated by genome scans of DNA variation to identify candidate loci for recent adaptation. Results of such analyses can then motivate experimental efforts to test whether the identified candidate loci do in fact contribute to functional variation in some fitness-related phenotype. Functional studies can provide corroborative evidence for positive selection at particular loci, and can potentially reveal specific molecular mechanisms of adaptation. PMID:20500215
Barroso-Batista, João; Demengeot, Jocelyne; Gordo, Isabel
Co-evolution between the mammalian immune system and the gut microbiota is believed to have shaped the microbiota's astonishing diversity. Here we test the corollary hypothesis that the adaptive immune system, directly or indirectly, influences the evolution of commensal species. We compare the evolution of Escherichia coli upon colonization of the gut of wild-type and Rag2−/− mice, which lack lymphocytes. We show that bacterial adaptation is slower in immune-compromised animals, a phenomenon explained by differences in the action of natural selection within each host. Emerging mutations exhibit strong beneficial effects in healthy hosts but substantial antagonistic pleiotropy in immune-deficient mice. This feature is due to changes in the composition of the gut microbiota, which differs according to the immune status of the host. Our results indicate that the adaptive immune system influences the tempo and predictability of E. coli adaptation to the mouse gut. PMID:26615893
Atlantic killifish populations have rapidly adapted to normally lethal levels of pollution in four urban estuaries. Through analysis of 384 whole killifish genome sequences and comparative transcriptomics in four pairs of sensitive and tolerant populations, we identify the aryl h...
Wilson, David Sloan; Kauffman, Richard A.; Purdy, Miriam S.
Improving the academic performance of at-risk high school students has proven difficult, often calling for an extended day, extended school year, and other expensive measures. Here we report the results of a program for at-risk 9th and 10th graders in Binghamton, New York, called the Regents Academy that takes place during the normal school day and year. The design of the program is informed by the evolutionary dynamics of cooperation and learning, in general and for our species as a unique product of biocultural evolution. Not only did the Regents Academy students outperform their comparison group in a randomized control design, but they performed on a par with the average high school student in Binghamton on state-mandated exams. All students can benefit from the social environment provided for at-risk students at the Regents Academy, which is within the reach of most public school districts. PMID:22114703
Oohashi, Tsutomu; Maekawa, Tadao; Ueno, Osamu; Kawai, Norie; Nishina, Emi; Honda, Manabu
As part of our research on programmed self-decomposition, we formed the hypothesis that originally immortal terrestrial organisms evolve into ones that are programmed for autonomous death. We then conducted evolutionary simulation experiments in which we examined this hypothesis using an artificial ecosystem that we designed to resemble a terrestrial ecosystem endowed with artificial chemistry. Notable results corroborating our hypothesis were obtained, which showed that mortal organisms emerged from indigenous immortal organisms through mutation; such mortal organisms survived and left behind offspring, albeit very rarely, and, having survived, surpassed immortal organisms without exception. In this article, we report the details of the above findings and also discuss a background framework we previously constructed for approaching altruism.
Huot, Ordom Brian; Nachappa, Punya; Tamborindeguy, Cecilia
Plants have evolved and diversified to reduce the damages imposed by infectious pathogens and herbivorous insects. Living in a sedentary lifestyle, plants are constantly adapting to their environment. They employ various strategies to increase performance and fitness. Thus, plants developed cost-effective strategies to defend against specific insects and pathogens. Plant defense, however, imposes selective pressure on insects and pathogens. This selective pressure provides incentives for pathogens and insects to diversify and develop strategies to counter plant defense. This results in an evolutionary arms race among plants, pathogens and insects. The ever-changing adaptations and physiological alterations among these organisms make studying plant-vector-pathogen interactions a challenging and fascinating field. Studying plant defense and plant protection requires knowledge of the relationship among organisms and the adaptive strategies each organism utilize. Therefore, this review focuses on the integral parts of plant-vector-pathogen interactions in order to understand the factors that affect plant defense and disease development. The review addresses plant-vector-pathogen co-evolution, plant defense strategies, specificity of plant defenses and plant-vector-pathogen interactions. Improving the comprehension of these factors will provide a multi-dimensional perspective for the future research in pest and disease management.
Feldman, Chris R.; Brodie, Edmund D.; Brodie, Edmund D.; Pfrender, Michael E.
Where do the genetic variants underlying adaptive change come from? Are currently adaptive alleles recruited by selection from standing genetic variation within populations, moved through introgression from other populations, or do they arise as novel mutations? Here, we examine the molecular basis of repeated adaptation to the toxin of deadly prey in 3 species of garter snakes (Thamnophis) to determine whether adaptation has evolved through novel mutations, sieving of existing variation, or transmission of beneficial alleles across species. Functional amino acid substitutions in the skeletal muscle sodium channel (Nav1.4) are largely responsible for the physiological resistance of garter snakes to tetrodotoxin found in their newt (Taricha) prey. Phylogenetic analyses reject the hypotheses that the unique resistance alleles observed in multiple Thamnophis species were present before the split of these lineages, or that alleles were shared among species through occasional hybridization events. Our results demonstrate that adaptive evolution has occurred independently multiple times in garter snakes via the de novo acquisition of beneficial mutations. PMID:19666534
Tibayrenc, M; Ayala, F J
We propose that predominant clonal evolution (PCE) in microbial pathogens be defined as restrained recombination on an evolutionary scale, with genetic exchange scarce enough to not break the prevalent pattern of clonal population structure. The main features of PCE are (1) strong linkage disequilibrium, (2) the widespread occurrence of stable genetic clusters blurred by occasional bouts of genetic exchange ('near-clades'), (3) the existence of a "clonality threshold", beyond which recombination is efficiently countered by PCE, and near-clades irreversibly diverge. We hypothesize that the PCE features are not mainly due to natural selection but also chiefly originate from in-built genetic properties of pathogens. We show that the PCE model obtains even in microbes that have been considered as 'highly recombining', such as Neisseria meningitidis, and that some clonality features are observed even in Plasmodium, which has been long described as panmictic. Lastly, we provide evidence that PCE features are also observed in viruses, taking into account their extremely fast genetic turnover. The PCE model provides a convenient population genetic framework for any kind of micropathogen. It makes it possible to describe convenient units of analysis (clones and near-clades) for all applied studies. Due to PCE features, these units of analysis are stable in space and time, and clearly delimited. The PCE model opens up the possibility of revisiting the problem of species definition in these organisms. We hypothesize that PCE constitutes a major evolutionary strategy for protozoa, fungi, bacteria, and viruses to adapt to parasitism.
Sicard, Adrien; Lenhard, Michael
Background In angiosperm evolution, autogamously selfing lineages have been derived from outbreeding ancestors multiple times, and this transition is regarded as one of the most common evolutionary tendencies in flowering plants. In most cases, it is accompanied by a characteristic set of morphological and functional changes to the flowers, together termed the selfing syndrome. Two major areas that have changed during evolution of the selfing syndrome are sex allocation to male vs. female function and flower morphology, in particular flower (mainly petal) size and the distance between anthers and stigma. Scope A rich body of theoretical, taxonomic, ecological and genetic studies have addressed the evolutionary modification of these two trait complexes during or after the transition to selfing. Here, we review our current knowledge about the genetics and evolution of the selfing syndrome. Conclusions We argue that because of its frequent parallel evolution, the selfing syndrome represents an ideal model for addressing basic questions about morphological evolution and adaptation in flowering plants, but that realizing this potential will require the molecular identification of more of the causal genes underlying relevant trait variation. PMID:21303786
Shan, Hong-Zhang; Singh, Jaswinder Pal; Oliker, Leonid; Biswa, Rupak; Kwak, Dochan (Technical Monitor)
We study the performance and programming effort for two major classes of adaptive applications under three leading parallel programming models. We find that all three models can achieve scalable performance on the state-of-the-art multiprocessor machines. The basic parallel algorithms needed for different programming models to deliver their best performance are similar, but the implementations differ greatly, far beyond the fact of using explicit messages versus implicit loads/stores. Compared with MPI and SHMEM, CC-SAS (cache-coherent shared address space) provides substantial ease of programming at the conceptual and program orchestration level, which often leads to the performance gain. However it may also suffer from the poor spatial locality of physically distributed shared data on large number of processors. Our CC-SAS implementation of the PARMETIS partitioner itself runs faster than in the other two programming models, and generates more balanced result for our application.
Tanaka, Midori; Kinney, Dennis K
From an evolutionary perspective, suicide is a puzzle, because it has serious adverse effects, yet is remarkably common and heritable. An hypothesis is proposed to explain this puzzle, by explaining how suicide could be adaptive through reducing risk that individuals will transmit infections to kin. Empirical evidence supports four predictions from the hypothesis. There are well-established mechanisms by which infections and immune factors increase risk for mental disorders that contribute to suicide. Suicide is more prevalent in occupations with greater exposure to infection and immune-compromising factors and at higher latitudes, where key environmental factors increase vulnerability to infection. In several other highly social species, suicide-like behaviors have evolved to reduce transmission of infections. If the hypothesis is correct, detection and treatment of underlying infections and immune dysfunction should help predict and prevent suicidal behavior, while also combating spread of infectious diseases.
Morales Poole, Jose Ricardo; Paganini, Julien; Pontarotti, Pierre
Two different adaptive immune systems (AIS) are present in the two phyla of vertebrates (jawed vertebrates and cyclostomes). The jawed vertebrate system is based on IG/TCR/RAG/MHC while the cyclostome system is based on VLRCs and AID-like enzymes both systems using homologous Cell types (B-cell and B-cell Like, T-cell and T-cell like). We will present our current view of the evolution of these two AISs and present alternative hypotheses that could explain the apparent convergent evolution of the two systems. We will also discuss why comparative immunology analyses should be based on evolutionary biology approaches and not on the scale of progress one.
Graff, Mario; Poli, Riccardo; Flores, Juan J
Modeling the behavior of algorithms is the realm of evolutionary algorithm theory. From a practitioner's point of view, theory must provide some guidelines regarding which algorithm/parameters to use in order to solve a particular problem. Unfortunately, most theoretical models of evolutionary algorithms are difficult to apply to realistic situations. However, in recent work (Graff and Poli, 2008, 2010), where we developed a method to practically estimate the performance of evolutionary program-induction algorithms (EPAs), we started addressing this issue. The method was quite general; however, it suffered from some limitations: it required the identification of a set of reference problems, it required hand picking a distance measure in each particular domain, and the resulting models were opaque, typically being linear combinations of 100 features or more. In this paper, we propose a significant improvement of this technique that overcomes the three limitations of our previous method. We achieve this through the use of a novel set of features for assessing problem difficulty for EPAs which are very general, essentially based on the notion of finite difference. To show the capabilities or our technique and to compare it with our previous performance models, we create models for the same two important classes of problems-symbolic regression on rational functions and Boolean function induction-used in our previous work. We model a variety of EPAs. The comparison showed that for the majority of the algorithms and problem classes, the new method produced much simpler and more accurate models than before. To further illustrate the practicality of the technique and its generality (beyond EPAs), we have also used it to predict the performance of both autoregressive models and EPAs on the problem of wind speed forecasting, obtaining simpler and more accurate models that outperform in all cases our previous performance models.
Although the initial formulation of modern concepts of adaptive radiation arose from consideration of the fossil data, rigorous attempts to identify this phenomenon in the fossil record are largely uncommon. Here I focus on direct evidence of the diet (through tooth-wear patterns) and ecologically-relevant traits of one of the most renowned fossil vertebrates-the Miocene ruminant Hoplitomeryx from the island of Gargano-to deepen our understanding of the most likely causal forces under which adaptive radiations emerge on islands. Results show how accelerated accumulation of species and early-bursts of ecological diversification occur after invading an island, and provide insights on the interplay between diet and demographic (population-density), ecological (competition/food requirements) and abiotic (climate-instability) factors, identified as drivers of adaptive diversification. A pronounced event of overpopulation and a phase of aridity determined most of the rate and magnitude of radiation, and pushed species to expand diets from soft-leafy foods to tougher-harder items. Unexpectedly, results show that herbivorous mammals are restricted to browsing habits on small-islands, even if bursts of ecological diversification and dietary divergence occur. This study deepens our understanding of the mechanisms promoting adaptive radiations, and forces us to reevaluate the role of diet in the origins and evolution of islands mammals. PMID:27405690
Cardoso, Gonçalo C.; Whittaker, Danielle J.; Campbell-Nelson, Samuel; Robertson, Kyle W.; Ketterson, Ellen D.
Novel or changing environments expose animals to diverse stressors that likely require coordinated hormonal and behavioral adaptations. Predicted adaptations to urban environments include attenuated physiological responses to stressors and bolder exploratory behaviors, but few studies to date have evaluated the impact of urban life on codivergence of these hormonal and behavioral traits in natural systems. Here, we demonstrate rapid adaptive shifts in both stress physiology and correlated boldness behaviors in a songbird, the dark-eyed junco, following its colonization of a novel urban environment. We compared elevation in corticosterone (CORT) in response to handling and flight initiation distances in birds from a recently established urban population in San Diego, California to birds from a nearby wildland population in the species' ancestral montane breeding range. We also measured CORT and exploratory behavior in birds raised from early life in a captive common garden study. We found persistent population differences for both reduced CORT responses and bolder exploratory behavior in birds from the colonist population, as well as significant negative covariation between maximum CORT and exploratory behavior. Although early developmental effects cannot be ruled out, these results suggest contemporary adaptive evolution of correlated hormonal and behavioral traits associated with colonization of an urban habitat. PMID:22936840
Although the initial formulation of modern concepts of adaptive radiation arose from consideration of the fossil data, rigorous attempts to identify this phenomenon in the fossil record are largely uncommon. Here I focus on direct evidence of the diet (through tooth-wear patterns) and ecologically-relevant traits of one of the most renowned fossil vertebrates-the Miocene ruminant Hoplitomeryx from the island of Gargano-to deepen our understanding of the most likely causal forces under which adaptive radiations emerge on islands. Results show how accelerated accumulation of species and early-bursts of ecological diversification occur after invading an island, and provide insights on the interplay between diet and demographic (population-density), ecological (competition/food requirements) and abiotic (climate-instability) factors, identified as drivers of adaptive diversification. A pronounced event of overpopulation and a phase of aridity determined most of the rate and magnitude of radiation, and pushed species to expand diets from soft-leafy foods to tougher-harder items. Unexpectedly, results show that herbivorous mammals are restricted to browsing habits on small-islands, even if bursts of ecological diversification and dietary divergence occur. This study deepens our understanding of the mechanisms promoting adaptive radiations, and forces us to reevaluate the role of diet in the origins and evolution of islands mammals.
Wóycicki, Rafał; Witkowicz, Justyna; Gawroński, Piotr; Dąbrowska, Joanna; Lomsadze, Alexandre; Pawełkowicz, Magdalena; Siedlecka, Ewa; Yagi, Kohei; Pląder, Wojciech; Seroczyńska, Anna; Śmiech, Mieczysław; Gutman, Wojciech; Niemirowicz-Szczytt, Katarzyna; Bartoszewski, Grzegorz; Tagashira, Norikazu; Hoshi, Yoshikazu; Borodovsky, Mark; Karpiński, Stanisław; Malepszy, Stefan; Przybecki, Zbigniew
Cucumber (Cucumis sativus L.), a widely cultivated crop, has originated from Eastern Himalayas and secondary domestication regions includes highly divergent climate conditions e.g. temperate and subtropical. We wanted to uncover adaptive genome differences between the cucumber cultivars and what sort of evolutionary molecular mechanisms regulate genetic adaptation of plants to different ecosystems and organism biodiversity. Here we present the draft genome sequence of the Cucumis sativus genome of the North-European Borszczagowski cultivar (line B10) and comparative genomics studies with the known genomes of: C. sativus (Chinese cultivar – Chinese Long (line 9930)), Arabidopsis thaliana, Populus trichocarpa and Oryza sativa. Cucumber genomes show extensive chromosomal rearrangements, distinct differences in quantity of the particular genes (e.g. involved in photosynthesis, respiration, sugar metabolism, chlorophyll degradation, regulation of gene expression, photooxidative stress tolerance, higher non-optimal temperatures tolerance and ammonium ion assimilation) as well as in distributions of abscisic acid-, dehydration- and ethylene-responsive cis-regulatory elements (CREs) in promoters of orthologous group of genes, which lead to the specific adaptation features. Abscisic acid treatment of non-acclimated Arabidopsis and C. sativus seedlings induced moderate freezing tolerance in Arabidopsis but not in C. sativus. This experiment together with analysis of abscisic acid-specific CRE distributions give a clue why C. sativus is much more susceptible to moderate freezing stresses than A. thaliana. Comparative analysis of all the five genomes showed that, each species and/or cultivars has a specific profile of CRE content in promoters of orthologous genes. Our results constitute the substantial and original resource for the basic and applied research on environmental adaptations of plants, which could facilitate creation of new crops with improved growth and yield in
Wóycicki, Rafał; Witkowicz, Justyna; Gawroński, Piotr; Dąbrowska, Joanna; Lomsadze, Alexandre; Pawełkowicz, Magdalena; Siedlecka, Ewa; Yagi, Kohei; Pląder, Wojciech; Seroczyńska, Anna; Śmiech, Mieczysław; Gutman, Wojciech; Niemirowicz-Szczytt, Katarzyna; Bartoszewski, Grzegorz; Tagashira, Norikazu; Hoshi, Yoshikazu; Borodovsky, Mark; Karpiński, Stanisław; Malepszy, Stefan; Przybecki, Zbigniew
Cucumber (Cucumis sativus L.), a widely cultivated crop, has originated from Eastern Himalayas and secondary domestication regions includes highly divergent climate conditions e.g. temperate and subtropical. We wanted to uncover adaptive genome differences between the cucumber cultivars and what sort of evolutionary molecular mechanisms regulate genetic adaptation of plants to different ecosystems and organism biodiversity. Here we present the draft genome sequence of the Cucumis sativus genome of the North-European Borszczagowski cultivar (line B10) and comparative genomics studies with the known genomes of: C. sativus (Chinese cultivar--Chinese Long (line 9930)), Arabidopsis thaliana, Populus trichocarpa and Oryza sativa. Cucumber genomes show extensive chromosomal rearrangements, distinct differences in quantity of the particular genes (e.g. involved in photosynthesis, respiration, sugar metabolism, chlorophyll degradation, regulation of gene expression, photooxidative stress tolerance, higher non-optimal temperatures tolerance and ammonium ion assimilation) as well as in distributions of abscisic acid-, dehydration- and ethylene-responsive cis-regulatory elements (CREs) in promoters of orthologous group of genes, which lead to the specific adaptation features. Abscisic acid treatment of non-acclimated Arabidopsis and C. sativus seedlings induced moderate freezing tolerance in Arabidopsis but not in C. sativus. This experiment together with analysis of abscisic acid-specific CRE distributions give a clue why C. sativus is much more susceptible to moderate freezing stresses than A. thaliana. Comparative analysis of all the five genomes showed that, each species and/or cultivars has a specific profile of CRE content in promoters of orthologous genes. Our results constitute the substantial and original resource for the basic and applied research on environmental adaptations of plants, which could facilitate creation of new crops with improved growth and yield in
Xi, Shibo; Borgna, Lucas Santiago; Zheng, Lirong; Du, Yonghua; Hu, Tiandou
In this report, AI-BL1.0, an open-source Labview-based program for automatic on-line beamline optimization, is presented. The optimization algorithms used in the program are Genetic Algorithm and Differential Evolution. Efficiency was improved by use of a strategy known as Observer Mode for Evolutionary Algorithm. The program was constructed and validated at the XAFCA beamline of the Singapore Synchrotron Light Source and 1W1B beamline of the Beijing Synchrotron Radiation Facility.
Mambrini, Andrea; Sudholt, Dirk
The migration interval is one of the fundamental parameters governing the dynamic behaviour of island models. Yet, there is little understanding on how this parameter affects performance, and how to optimally set it given a problem in hand. We propose schemes for adapting the migration interval according to whether fitness improvements have been found. As long as no improvement is found, the migration interval is increased to minimise communication. Once the best fitness has improved, the migration interval is decreased to spread new best solutions more quickly. We provide a method for obtaining upper bounds on the expected running time and the communication effort, defined as the expected number of migrants sent. Example applications of this method to common example functions show that our adaptive schemes are able to compete with, or even outperform, the optimal fixed choice of the migration interval, with regard to running time and communication effort.
In this study, the vanadium carbide coating in molten borax bath process is modeled by evolutionary genetic programming (GEP) with bath composition (borax percentage, ferro vanadium (Fe-V) percentage, boric acid percentage), bath temperature, immersion time, and layer thickness data. Five inputs and one output data exist in the model. The percentage of borax, Fe-V, and boric acid, temperature, and immersion time parameters are used as input data and the layer thickness value is used as output data. For selected bath components, immersion time, and temperature variables, the layer thicknesses are derived from the mathematical expression. The results of the mathematical expressions are compared to that of experimental data; it is determined that the derived mathematical expression has an accuracy of 89%.
Hagen, Joel B
Bergmann's rule and Allen's rule played important roles in mid-twentieth century discussions of adaptation, variation, and geographical distribution. Although inherited from the nineteenth-century natural history tradition these rules gained significance during the consolidation of the modern synthesis as evolutionary theorists focused attention on populations as units of evolution. For systematists, the rules provided a compelling rationale for identifying geographical races or subspecies, a function that was also picked up by some physical anthropologists. More generally, the rules provided strong evidence for adaptation by natural selection. Supporters of the rules tacitly, or often explicitly, assumed that the clines described by the rules reflected adaptations for thermoregulation. This assumption was challenged by the physiologists Laurence Irving and Per Scholander based on their arctic research conducted after World War II. Their critique spurred a controversy played out in a series of articles in Evolution, in Ernst Mayr's Animal Species and Evolution, and in the writings of other prominent evolutionary biologists and physical anthropologists. Considering this episode highlights the complexity and ambiguity of important biological concepts such as adaptation, homeostasis, and self-regulation. It also demonstrates how different disciplinary orientations and styles of scientific research influenced evolutionary explanations, and the consequent difficulties of constructing a truly synthetic evolutionary biology in the decades immediately following World War II.
Deb, Kalyanmoy; Sinha, Ankur
Bilevel optimization problems involve two optimization tasks (upper and lower level), in which every feasible upper level solution must correspond to an optimal solution to a lower level optimization problem. These problems commonly appear in many practical problem solving tasks including optimal control, process optimization, game-playing strategy developments, transportation problems, and others. However, they are commonly converted into a single level optimization problem by using an approximate solution procedure to replace the lower level optimization task. Although there exist a number of theoretical, numerical, and evolutionary optimization studies involving single-objective bilevel programming problems, not many studies look at the context of multiple conflicting objectives in each level of a bilevel programming problem. In this paper, we address certain intricate issues related to solving multi-objective bilevel programming problems, present challenging test problems, and propose a viable and hybrid evolutionary-cum-local-search based algorithm as a solution methodology. The hybrid approach performs better than a number of existing methodologies and scales well up to 40-variable difficult test problems used in this study. The population sizing and termination criteria are made self-adaptive, so that no additional parameters need to be supplied by the user. The study indicates a clear niche of evolutionary algorithms in solving such difficult problems of practical importance compared to their usual solution by a computationally expensive nested procedure. The study opens up many issues related to multi-objective bilevel programming and hopefully this study will motivate EMO and other researchers to pay more attention to this important and difficult problem solving activity.
Hendrie, C A; Brewer, G
Mouth to mouth sexual kissing is seen in more than 90% of human cultures. Various theories have been put forward to account for this but none offer a full explanation within an evolutionary framework. As mouth to mouth sexual kissing exposes each participant to the diseases of the other, it must confer significant benefit. Human Cytomegalovirus (HCMV) is a ubiquitous infection that carries a severe teratogenic risk if primary infection is acquired during certain critical periods. As HCMV is present in salivary gland epithelial cells and sheds from periodontitis induced lesions, female inoculation with a specific male's HCMV is most efficiently achieved through mouth to mouth contact and saliva exchange, particularly where the flow of saliva is from the male to the typically shorter female. The current hypothesis proposes that mouth to mouth sexual kissing enables females to control when they become infected with a particular male's HCMV and so protect their offspring from the threat of teratogenesis from primary infection during vulnerable times in their development. Females only gain this benefit if they also avoid becoming infected by other males. Hence HCMV induced teratogenesis is a strong viral pressure towards the development of monogamy as well as kissing as a behavioural strategy to protect against it.
Aranda, M.; Li, Y.; Liew, Y. J.; Baumgarten, S.; Simakov, O.; Wilson, M. C.; Piel, J.; Ashoor, H.; Bougouffa, S.; Bajic, V. B.; Ryu, T.; Ravasi, T.; Bayer, T.; Micklem, G.; Kim, H.; Bhak, J.; LaJeunesse, T. C.; Voolstra, C. R.
Despite half a century of research, the biology of dinoflagellates remains enigmatic: they defy many functional and genetic traits attributed to typical eukaryotic cells. Genomic approaches to study dinoflagellates are often stymied due to their large, multi-gigabase genomes. Members of the genus Symbiodinium are photosynthetic endosymbionts of stony corals that provide the foundation of coral reef ecosystems. Their smaller genome sizes provide an opportunity to interrogate evolution and functionality of dinoflagellate genomes and endosymbiosis. We sequenced the genome of the ancestral Symbiodinium microadriaticum and compared it to the genomes of the more derived Symbiodinium minutum and Symbiodinium kawagutii and eukaryote model systems as well as transcriptomes from other dinoflagellates. Comparative analyses of genome and transcriptome protein sets show that all dinoflagellates, not only Symbiodinium, possess significantly more transmembrane transporters involved in the exchange of amino acids, lipids, and glycerol than other eukaryotes. Importantly, we find that only Symbiodinium harbor an extensive transporter repertoire associated with the provisioning of carbon and nitrogen. Analyses of these transporters show species-specific expansions, which provides a genomic basis to explain differential compatibilities to an array of hosts and environments, and highlights the putative importance of gene duplications as an evolutionary mechanism in dinoflagellates and Symbiodinium. PMID:28004835
This paper defines a class of evolutionary algorithms called evolutionary pattern search algorithms (EPSAs) and analyzes their convergence properties. This class of algorithms is closely related to evolutionary programming, evolutionary strategie and real-coded genetic algorithms. EPSAs are self-adapting systems that modify the step size of the mutation operator in response to the success of previous optimization steps. The rule used to adapt the step size can be used to provide a stationary point convergence theory for EPSAs on any continuous function. This convergence theory is based on an extension of the convergence theory for generalized pattern search methods. An experimental analysis of the performance of EPSAs demonstrates that these algorithms can perform a level of global search that is comparable to that of canonical EAs. We also describe a stopping rule for EPSAs, which reliably terminated near stationary points in our experiments. This is the first stopping rule for any class of EAs that can terminate at a given distance from stationary points.
Marroig, Gabriel; Cheverud, James M
New World monkeys (NWM) display substantial variation (two orders of magnitude) in body size. Despite this, variation in skull size and associated shape show a conserved allometric relationship, both within and between genera. Maximum likelihood estimates of quantitative ancestral states were used to compare the direction of morphological differentiation with the phenotypic (p(max)) and genetic (g(max)) lines of least evolutionary resistance (LLER). Diversification in NWM skulls occurred principally along the LLER defined by size variation. We also obtained measures of morphological amount and pace of change using our skull data together with published genetic distances to test whether the LLER influenced the amount and pace of diversification. Moreover, data on an ecological factor (diet) was obtained from the literature and used to test the association of this niche-related measure with the morphological diversification. Two strategies were used to test the association of LLER with the morphological and dietary amount and pace of change, one focusing on both contemporary genera and maximum likelihood reconstructed ancestors and the other using only the 16 contemporary genera in a phylogenetic comparative analysis. Our results suggest that the LLER influenced the path, amount, and pace of morphological change. Evolution also occurred away from the LLER in some taxa but this occurred at a slower pace and resulted in a relatively low amount of morphological change. We found that longer branch lengths (time) are associated with larger differences in p(max) orientation. However, on a macroevolutionary scale there is no such trend. Diet is consistently associated with both absolute size differences and morphological integration patterns, and we suggest that this ecological factor might be driving adaptive radiation in NWM. Invasion of diet-based adaptive zones involves changes in absolute size, due to metabolic and foraging constraints, resulting in simple allometric
Mortimer, Tatum D.; Weber, Alexandra M.
Mycobacteria have a distinct secretion system, termed type VII (T7SS), which is encoded by paralogous chromosomal loci (ESX) and associated with pathogenesis, conjugation, and metal homeostasis. Evolution of paralogous gene families is of interest because duplication is an important mechanism by which novel genes evolve, but there are potential conflicts between adaptive forces that stabilize duplications and those that enable evolution of new functions. Our objective was to delineate the adaptive forces underlying diversification of T7SS. Plasmid-borne ESX were described recently, and we found evidence that the initial duplication and divergence of ESX systems occurred on plasmids and was driven by selection for advantageous mutations. Plasmid conjugation has been linked to T7SS and type IV secretion systems (T4SS) in mycobacteria, and we discovered that T7SS and T4SS genes evolved in concert on the plasmids. We hypothesize that differentiation of plasmid ESX helps to prevent conjugation among cells harboring incompatible plasmids. Plasmid ESX appear to have been repurposed following migration to the chromosome, and there is evidence of positive selection driving further differentiation of chromosomal ESX. We hypothesize that ESX loci were initially stabilized on the chromosome by mediating their own transfer. These results emphasize the diverse adaptive paths underlying evolution of novelty, which in this case involved plasmid duplications, selection for advantageous mutations in the mobile and core genomes, migration of the loci between plasmids and chromosomes, and lateral transfer among chromosomes. We discuss further implications for the choice of model organism to study ESX functions in Mycobacterium tuberculosis. PMID:28391322
Corbally, C. J.; Rappaport, M. B.
The authors, an astronomer/priest and an anthropologist/biologist, describe their use of the dramatic arts at the INSAP VIII meeting in their performance of two short skits on the sighting of a supernova in AD 1054 (creating the beautiful Crab Nebula) and a future “Rho Cas” stellar explosion in the constellation Cassiopeia, in AD 3054. They speculate on the emergence of science, religion, and art as bona fide adaptations, responding to natural selection, which served early hominins well in their struggle for existence. They draw parallels to the continued functions of science, religion, and art in modern society.
Hereditary, environmental, and stochastic factors determine a child’s growth in his unique environment, but their relative contribution to the phenotypic outcome and the extent of stochastic programming that is required to alter human phenotypes is not known because few data are available. This is an attempt to use evolutionary life-history theory in understanding child growth in a broad evolutionary perspective, using the data and theory of evolutionary predictive adaptive growth-related strategies. Transitions from one life-history phase to the next have inherent adaptive plasticity in their timing. Humans evolved to withstand energy crises by decreasing their body size, and evolutionary short-term adaptations to energy crises utilize a plasticity that modifies the timing of transition from infancy into childhood, culminating in short stature in times of energy crisis. Transition to juvenility is part of a strategy of conversion from a period of total dependence on the family and tribe for provision and security to self-supply, and a degree of adaptive plasticity is provided and determines body composition. Transition to adolescence entails plasticity in adapting to energy resources, other environmental cues, and the social needs of the maturing adolescent to determine life-span and the period of fecundity and fertility. Fundamental questions are raised by a life-history approach to the unique growth pattern of each child in his given genetic background and current environment. PMID:23908815
Hereditary, environmental, and stochastic factors determine a child's growth in his unique environment, but their relative contribution to the phenotypic outcome and the extent of stochastic programming that is required to alter human phenotypes is not known because few data are available. This is an attempt to use evolutionary life-history theory in understanding child growth in a broad evolutionary perspective, using the data and theory of evolutionary predictive adaptive growth-related strategies. Transitions from one life-history phase to the next have inherent adaptive plasticity in their timing. Humans evolved to withstand energy crises by decreasing their body size, and evolutionary short-term adaptations to energy crises utilize a plasticity that modifies the timing of transition from infancy into childhood, culminating in short stature in times of energy crisis. Transition to juvenility is part of a strategy of conversion from a period of total dependence on the family and tribe for provision and security to self-supply, and a degree of adaptive plasticity is provided and determines body composition. Transition to adolescence entails plasticity in adapting to energy resources, other environmental cues, and the social needs of the maturing adolescent to determine life-span and the period of fecundity and fertility. Fundamental questions are raised by a life-history approach to the unique growth pattern of each child in his given genetic background and current environment.
Jiang, Yu; Jiang, Zhong-Ping
This paper studies the robust optimal control design for a class of uncertain nonlinear systems from a perspective of robust adaptive dynamic programming (RADP). The objective is to fill up a gap in the past literature of adaptive dynamic programming (ADP) where dynamic uncertainties or unmodeled dynamics are not addressed. A key strategy is to integrate tools from modern nonlinear control theory, such as the robust redesign and the backstepping techniques as well as the nonlinear small-gain theorem, with the theory of ADP. The proposed RADP methodology can be viewed as an extension of ADP to uncertain nonlinear systems. Practical learning algorithms are developed in this paper, and have been applied to the controller design problems for a jet engine and a one-machine power system.
Benazzi, Stefano; Nguyen, Huynh Nhu; Schulz, Dieter; Grosse, Ian R.; Gruppioni, Giorgio; Hublin, Jean-Jacques; Kullmer, Ottmar
Over the last century, humans from industrialized societies have witnessed a radical increase in some dental diseases. A severe problem concerns the loss of dental materials (enamel and dentine) at the buccal cervical region of the tooth. This “modern-day” pathology, called non-carious cervical lesions (NCCLs), is ubiquitous and worldwide spread, but is very sporadic in modern humans from pre-industrialized societies. Scholars believe that several factors are involved, but the real dynamics behind this pathology are far from being understood. Here we use an engineering approach, finite element analysis (FEA), to suggest that the lack of dental wear, characteristic of industrialized societies, might be a major factor leading to NCCLs. Occlusal loads were applied to high resolution finite element models of lower second premolars (P2) to demonstrate that slightly worn P2s envisage high tensile stresses in the buccal cervical region, but when worn down artificially in the laboratory the pattern of stress distribution changes and the tensile stresses decrease, matching the results obtained in naturally worn P2s. In the modern industrialized world, individuals at advanced ages show very moderate dental wear when compared to past societies, and teeth are exposed to high tensile stresses at the buccal cervical region for decades longer. This is the most likely mechanism explaining enamel loss in the cervical region, and may favor the activity of other disruptive processes such as biocorrosion. Because of the lack of dental abrasion, our masticatory apparatus faces new challenges that can only be understood in an evolutionary perspective. PMID:23638020
Aboitiz, Francisco; Montiel, Juan; García, Ricardo R
Mammalian cortical development is preceded by the elaboration of a transient preplate, which is split into a superficial marginal zone and a deep subplate after the arrival of the cortical plate. There has been some controversy in the evolutionary interpretation of this transient structure, as some propose it to represent the ancestral cortex or pallium of non-mammals, while others consider it to be a phylogenetic novelty. The preplate and its derivatives contain components derived by both tangential and radial migration. Tangentially migrating elements include pioneer neurons and interneurons, both of subpallial origin, and Cajal-Retzius cells, mostly of pallial origin. Pioneer neurons were probably present in the ancestors of mammals, but may have changed their original superficial position to one below the developing cortex, thus attracting thalamic afferents in the subcortical white matter, and making them penetrate the cortex radially. In mammals, Cajal-Retzius cells appear to have increased both in number and on their level of reelin expression, perhaps in the context of controlling the final stages of migration in a radially expanding neoocortex. Radial-migrating cells are partly represented by the pyramidal-like cells of the subplate. These neurons resemble the excitatory elements of the adult reptilian cortex, but is not clear whether they are their true homologues. One possibility is that these cells appeared by virtue of a heterochronic process in which the earliest radial elements of the cortical plate began to be produced at progressively earlier developmental stages. Thus, we conclude that the mammalian preplate and its derivatives contain both ancestral and derived elements, all of which have been modified in the course of mammalian evolution to support an increasingly complex cortical plate development.
Foster, Susan A.; Wund, Matthew A.; Baker, John A.
At the end of the 19th century, the suggestion was made by several scientists, including J. M. Baldwin, that behavioral responses to environmental change could both rescue populations from extinction (Baldwin Effect) and influence the course of subsequent evolution. Here we provide the historical and theoretical background for this argument and offer evidence of the importance of these ideas for understanding how animals (and other organisms that exhibit behavior) will respond to the rapid environmental changes caused by human activity. We offer examples from long-term research on the evolution of behavioral and other phenotypes in the adaptive radiation of the threespine stickleback fish (Gasterosteus aculeatus), a radiation in which it is possible to infer ancestral patterns of behavioral plasticity relative to the post-glacial freshwater radiation in northwestern North America, and to use patterns of parallelism and contemporary evolution to understand adaptive causes of responses to environmental modification. Our work offers insights into the complexity of cognitive responses to environmental change, and into the importance of examining multiple aspects of the phenotype simultaneously, if we are to understand how behavioral shifts contribute to the persistence of populations and to subsequent evolution. We conclude by discussing the origins of apparent novelties induced by environmental shifts, and the importance of accounting for geographic variation within species if we are to accurately anticipate the effects of anthropogenic environmental modification on the persistence and evolution of animals. PMID:26163679
Foster, Susan A; Wund, Matthew A; Baker, John A
At the end of the 19th century, the suggestion was made by several scientists, including J. M. Baldwin, that behavioral responses to environmental change could both rescue populations from extinction (Baldwin Effect) and influence the course of subsequent evolution. Here we provide the historical and theoretical background for this argument and offer evidence of the importance of these ideas for understanding how animals (and other organisms that exhibit behavior) will respond to the rapid environmental changes caused by human activity. We offer examples from long-term research on the evolution of behavioral and other phenotypes in the adaptive radiation of the threespine stickleback fish (Gasterosteus aculeatus), a radiation in which it is possible to infer ancestral patterns of behavioral plasticity relative to the post-glacial freshwater radiation in northwestern North America, and to use patterns of parallelism and contemporary evolution to understand adaptive causes of responses to environmental modification. Our work offers insights into the complexity of cognitive responses to environmental change, and into the importance of examining multiple aspects of the phenotype simultaneously, if we are to understand how behavioral shifts contribute to the persistence of populations and to subsequent evolution. We conclude by discussing the origins of apparent novelties induced by environmental shifts, and the importance of accounting for geographic variation within species if we are to accurately anticipate the effects of anthropogenic environmental modification on the persistence and evolution of animals.
Liu, Shiping; Lorenzen, Eline D; Fumagalli, Matteo; Li, Bo; Harris, Kelley; Xiong, Zijun; Zhou, Long; Korneliussen, Thorfinn Sand; Somel, Mehmet; Babbitt, Courtney; Wray, Greg; Li, Jianwen; He, Weiming; Wang, Zhuo; Fu, Wenjing; Xiang, Xueyan; Morgan, Claire C; Doherty, Aoife; O'Connell, Mary J; McInerney, James O; Born, Erik W; Dalén, Love; Dietz, Rune; Orlando, Ludovic; Sonne, Christian; Zhang, Guojie; Nielsen, Rasmus; Willerslev, Eske; Wang, Jun
Polar bears are uniquely adapted to life in the High Arctic and have undergone drastic physiological changes in response to Arctic climates and a hyper-lipid diet of primarily marine mammal prey. We analyzed 89 complete genomes of polar bear and brown bear using population genomic modeling and show that the species diverged only 479-343 thousand years BP. We find that genes on the polar bear lineage have been under stronger positive selection than in brown bears; nine of the top 16 genes under strong positive selection are associated with cardiomyopathy and vascular disease, implying important reorganization of the cardiovascular system. One of the genes showing the strongest evidence of selection, APOB, encodes the primary lipoprotein component of low-density lipoprotein (LDL); functional mutations in APOB may explain how polar bears are able to cope with life-long elevated LDL levels that are associated with high risk of heart disease in humans.
Murray, Andrew J; Montgomery, Hugh E
At extreme altitude (>5,000 - 5,500 m), sustained hypoxia threatens human function and survival, and is associated with marked involuntary weight loss (cachexia). This seems to be a coordinated response: appetite and protein synthesis are suppressed, and muscle catabolism promoted. We hypothesise that, rather than simply being pathophysiological dysregulation, this cachexia is protective. Ketone bodies, synthesised during relative starvation, protect tissues such as the brain from reduced oxygen availability by mechanisms including the reduced generation of reactive oxygen species, improved mitochondrial efficiency and activation of the ATP-sensitive potassium (KATP ) channel. Amino acids released from skeletal muscle also protect cells from hypoxia, and may interact synergistically with ketones to offer added protection. We thus propose that weight loss in hypoxia is an adaptive response: the amino acids and ketone bodies made available act not only as metabolic substrates, but as metabolic modulators, protecting cells from the hypoxic challenge.
Liu, Shiping; Lorenzen, Eline D.; Fumagalli, Matteo; Li, Bo; Harris, Kelley; Xiong, Zijun; Zhou, Long; Korneliussen, Thorfinn Sand; Somel, Mehmet; Babbitt, Courtney; Wray, Greg; Li, Jianwen; He, Weiming; Wang, Zhuo; Fu, Wenjing; Xiang, Xueyan; Morgan, Claire C.; Doherty, Aoife; O’Connell, Mary J.; McInerney, James O.; Born, Erik W.; Dalén, Love; Dietz, Rune; Orlando, Ludovic; Sonne, Christian; Zhang, Guojie; Nielsen, Rasmus; Willerslev, Eske; Wang, Jun
SUMMARY Polar bears are uniquely adapted to life in the High Arctic and have undergone drastic physiological changes in response to Arctic climates and a hyperlipid diet of primarily marine mammal prey. We analyzed 89 complete genomes of polar bear and brown bear using population genomic modeling and show that the species diverged only 479–343 thousand years BP. We find that genes on the polar bear lineage have been under stronger positive selection than in brown bears; nine of the top 16 genes under strong positive selection are associated with cardiomyopathy and vascular disease, implying important reorganization of the cardio-vascular system. One of the genes showing the strongest evidence of selection, APOB, encodes the primary lipoprotein component of low-density lipoprotein (LDL); functional mutations in APOB may explain how polar bears are able to cope with life-long elevated LDL levels that are associated with high risk of heart disease in humans. PMID:24813606
Haliloglu, Turkan; Bahar, Ivet
Several studies in recent years have drawn attention to the ability of proteins to adapt to intermolecular interactions by conformational changes along structure-encoded collective modes of motions. These so-called soft modes, primarily driven by entropic effects, facilitate, if not enable, functional interactions. They represent excursions on the conformational space along principal low-ascent directions/paths away from the original free energy minimum, and they are accessible to the protein even before protein-protein/ligand interactions. An emerging concept from these studies is the evolution of structures or modular domains to favor such modes of motion that will be recruited or integrated for enabling functional interactions. Structural dynamics, including the allosteric switches in conformation that are often stabilized upon formation of complexes and multimeric assemblies, emerge as key properties that are evolutionarily maintained to accomplish biological activities, consistent with the paradigm sequence→structure→dynamics→function where 'dynamics' bridges structure and function.
Murray, Andrew J; Montgomery, Hugh E
At extreme altitude (>5,000 – 5,500 m), sustained hypoxia threatens human function and survival, and is associated with marked involuntary weight loss (cachexia). This seems to be a coordinated response: appetite and protein synthesis are suppressed, and muscle catabolism promoted. We hypothesise that, rather than simply being pathophysiological dysregulation, this cachexia is protective. Ketone bodies, synthesised during relative starvation, protect tissues such as the brain from reduced oxygen availability by mechanisms including the reduced generation of reactive oxygen species, improved mitochondrial efficiency and activation of the ATP-sensitive potassium (KATP) channel. Amino acids released from skeletal muscle also protect cells from hypoxia, and may interact synergistically with ketones to offer added protection. We thus propose that weight loss in hypoxia is an adaptive response: the amino acids and ketone bodies made available act not only as metabolic substrates, but as metabolic modulators, protecting cells from the hypoxic challenge. PMID:24917038
Sabidó, Eduard; Bosch, Elena
Essential trace elements possess vital functions at molecular, cellular, and physiological levels in health and disease, and they are tightly regulated in the human body. In order to assess variability and potential adaptive evolution of trace element homeostasis, we quantified 18 trace elements in 150 liver samples, together with the expression levels of 90 genes and abundances of 40 proteins involved in their homeostasis. Additionally, we genotyped 169 single nucleotide polymorphism (SNPs) in the same sample set. We detected significant associations for 8 protein quantitative trait loci (pQTL), 10 expression quantitative trait loci (eQTLs), and 15 micronutrient quantitative trait loci (nutriQTL). Six of these exceeded the false discovery rate cutoff and were related to essential trace elements: 1) one pQTL for GPX2 (rs10133290); 2) two previously described eQTLs for HFE (rs12346) and SELO (rs4838862) expression; and 3) three nutriQTLs: The pathogenic C282Y mutation at HFE affecting iron (rs1800562), and two SNPs within several clustered metallothionein genes determining selenium concentration (rs1811322 and rs904773). Within the complete set of significant QTLs (which involved 30 SNPs and 20 gene regions), we identified 12 SNPs with extreme patterns of population differentiation (FST values in the top 5% percentile in at least one HapMap population pair) and significant evidence for selective sweeps involving QTLs at GPX1, SELENBP1, GPX3, SLC30A9, and SLC39A8. Overall, this detailed study of various molecular phenotypes illustrates the role of regulatory variants in explaining differences in trace element homeostasis among populations and in the human adaptive response to environmental pressures related to micronutrients. PMID:26582562
Rosa, João P. P.; de Souza, Altay A. L.; de Lima, Giscard H. O.; Rodrigues, Dayane F.; de Aquino Lemos, Valdir; da Silva Alves, Eduardo; Tufik, Sergio; de Mello, Marco T.
Several studies have indicated that motivational level and prior expectations influence one’s commitment to physical activity. Moreover, these aspects are not properly described in terms of proximal (SDT, Self Determination Theory) and distal (evolutionary) explanations in the literature. This paper aims to verify if level of motivation (BREQ-2, Behavioral Regulation in Exercise Questionnaire-2) and expectations regarding regular physical exercise (IMPRAF-54) before starting a 1-year exercise program could determine likelihood of completion. Ninety-four volunteers (53 women) included a completed protocol group (CPG; n = 21) and drop-out group (n = 73). The IMPRAF-54 scale was used to assess six different expectations associated with physical activity, and the BREQ-2 inventory was used to assess the level of motivation in five steps (from amotivation to intrinsic motivation). Both questionnaires were assessed before starting a regular exercise program. The CPG group presented higher sociability and lower pleasure scores according to IMPRAF-54 domains. A logistic regression analysis showed that a one-point increment on sociability score increased the chance of completing the program by 10%, and the same one-point increment on pleasure score reduced the chance of completing the protocol by 16%. ROC curves were also calculated to establish IMPRAF-54 cutoffs for adherence (Sociability – 18.5 points – 81% sensibility/50% specificity) and dropout (Pleasure – 25.5 points – 86% sensibility/20% specificity) of the exercise protocol. Our results indicate that an expectation of social interaction was a positive factor in predicting adherence to exercise. Grounded in SDT and its innate needs (competence, autonomy, relatedness), physical exercise is not an end; it is a means to achieve autonomy and self-cohesion. The association of physical activity with social practices, as occurs in hunter-gathering groups, can engage people to be physically active and can provide
memes ” (Dawkins, 1989; Gabora, 1995; Boal & Schultz, 2007). As Weeks & Galunic (2003) point out: “ Memes are the replicators in cultural evolution ...the process of social and organisational adaptation through meme evolution . It is a more general approach than the evolutionary adaptation of...adaptivity, because of its ability to simulate the innovation and evolution of organisational “ memes .” 8. References Angeline, P.J. & Pollack, J.B
Mabu, Shingo; Hirasawa, Kotaro; Hu, Jinglu
This paper proposes a graph-based evolutionary algorithm called Genetic Network Programming (GNP). Our goal is to develop GNP, which can deal with dynamic environments efficiently and effectively, based on the distinguished expression ability of the graph (network) structure. The characteristics of GNP are as follows. 1) GNP programs are composed of a number of nodes which execute simple judgment/processing, and these nodes are connected by directed links to each other. 2) The graph structure enables GNP to re-use nodes, thus the structure can be very compact. 3) The node transition of GNP is executed according to its node connections without any terminal nodes, thus the past history of the node transition affects the current node to be used and this characteristic works as an implicit memory function. These structural characteristics are useful for dealing with dynamic environments. Furthermore, we propose an extended algorithm, "GNP with Reinforcement Learning (GNPRL)" which combines evolution and reinforcement learning in order to create effective graph structures and obtain better results in dynamic environments. In this paper, we applied GNP to the problem of determining agents' behavior to evaluate its effectiveness. Tileworld was used as the simulation environment. The results show some advantages for GNP over conventional methods.
Wandeler, Peter; Camenisch, Glauco
In natural populations, quantitative trait dynamics often do not appear to follow evolutionary predictions. Despite abundant examples of natural selection acting on heritable traits, conclusive evidence for contemporary adaptive evolution remains rare for wild vertebrate populations, and phenotypic stasis seems to be the norm. This so-called “stasis paradox” highlights our inability to predict evolutionary change, which is especially concerning within the context of rapid anthropogenic environmental change. While the causes underlying the stasis paradox are hotly debated, comprehensive attempts aiming at a resolution are lacking. Here, we apply a quantitative genetic framework to individual-based long-term data for a wild rodent population and show that despite a positive association between body mass and fitness, there has been a genetic change towards lower body mass. The latter represents an adaptive response to viability selection favouring juveniles growing up to become relatively small adults, i.e., with a low potential adult mass, which presumably complete their development earlier. This selection is particularly strong towards the end of the snow-free season, and it has intensified in recent years, coinciding which a change in snowfall patterns. Importantly, neither the negative evolutionary change, nor the selective pressures that drive it, are apparent on the phenotypic level, where they are masked by phenotypic plasticity and a non causal (i.e., non genetic) positive association between body mass and fitness, respectively. Estimating selection at the genetic level enabled us to uncover adaptive evolution in action and to identify the corresponding phenotypic selective pressure. We thereby demonstrate that natural populations can show a rapid and adaptive evolutionary response to a novel selective pressure, and that explicitly (quantitative) genetic models are able to provide us with an understanding of the causes and consequences of selection that is
Smith, Margaret C M; Hendrix, Roger W; Dedrick, Rebekah; Mitchell, Kaitlin; Ko, Ching-Chung; Russell, Daniel; Bell, Emma; Gregory, Matthew; Bibb, Maureen J; Pethick, Florence; Jacobs-Sera, Deborah; Herron, Paul; Buttner, Mark J; Hatfull, Graham F
The genome sequences of eight Streptomyces phages are presented, four of which were isolated for this study. Phages R4, TG1, Hau3, and SV1 were isolated previously and have been exploited as tools for understanding and genetically manipulating Streptomyces spp. We also extracted five apparently intact prophages from recent Streptomyces spp. genome projects and, together with six phage genomes in the database, we analyzed all 19 Streptomyces phage genomes with a view to understanding their relationships to each other and to other actinophages, particularly the mycobacteriophages. Fifteen of the Streptomyces phages group into four clusters of related genomes. Although the R4-like phages do not share nucleotide sequence similarity with other phages, they clearly have common ancestry with cluster A mycobacteriophages, sharing many protein homologues, common gene syntenies, and similar repressor-stoperator regulatory systems. The R4-like phage Hau3 and the prophage StrepC.1 (from Streptomyces sp. strain C) appear to have hijacked a unique adaptation of the streptomycetes, i.e., use of the rare UUA codon, to control translation of the essential phage protein, the terminase. The Streptomyces venezuelae generalized transducing phage SV1 was used to predict the presence of other generalized transducing phages for different Streptomyces species.
Haliloglu, Turkan; Bahar, Ivet
Several studies in recent years have drawn attention to the ability of proteins to adapt to intermolecular interactions by conformational changes along structure-encoded collective modes of motions. These so-called soft modes, primarily driven by entropic effects, facilitate, if not enable, functional interactions. They represent excursions on the conformational space along principal low-ascent directions/paths away from the original free energy minimum, and they are accessible to the protein even prior to protein-protein/ligand interactions. An emerging concept from these studies is the evolution of structures or modular domains to favor such modes of motion that will be recruited or integrated for enabling functional interactions. Structural dynamics, including the allosteric switches in conformation that are often stabilized upon formation of complexes and multimeric assemblies, emerge as key properties that are evolutionarily maintained to accomplish biological activities, consistent with the paradigm sequence → structure → dynamics → function where ‘dynamics’ bridges structure and function. PMID:26254902
Shcherbakov, Denis; Knörzer, Alexandra; Espenhahn, Svenja; Hilbig, Reinhard; Haas, Ulrich; Blum, Martin
Near-infrared (NIR) light constitutes an integrated part of solar radiation. The principal ability to sense NIR under laboratory conditions has previously been demonstrated in fish. The availability of NIR in aquatic habitats, and thus its potential use as a cue for distinct behaviors such as orientation and detection of prey, however, depends on physical and environmental parameters. In clear water, blue and green light represents the dominating part of the illumination. In turbid waters, in contrast, the relative content of red and NIR radiation is enhanced, due to increased scattering and absorption of short and middle range wavelengths by suspended particles and dissolved colored materials. We have studied NIR detection thresholds using a phototactic swimming assay in five fish species, which are exposed to different NIR conditions in their natural habitats. Nile and Mozambique tilapia, which inhabit waters with increased turbidity, displayed the highest spectral sensitivity, with thresholds at wavelengths above 930 nm. Zebrafish, guppy and green swordtail, which prefer clearer waters, revealed significantly lower thresholds of spectral sensitivity with 825–845 nm for green swordtail and 845–910 nm for zebrafish and guppy. The present study revealed a clear correlation between NIR sensation thresholds and availability of NIR in the natural habitats, suggesting that NIR vision, as an integral part of the whole spectrum of visual abilities, can serve as an evolutionarily adaptable trait in fish. PMID:23691215
Zhao, Juan; Li, Xingmei; Wang, Wei; Wu, Guoping
Wireless video transmission encounters higher error rate than in wired network, which introduces distortion into the error-sensitive compressed data, reducing the quality of the playback video. Therefore, to ensure the end-to-end quality, wireless video needs a transmission system including both efficient source coding scheme and transmission technology against the influence of the channel error. This paper tackles a dynamic programming algorithm for robust video streaming over error-prone channels. An auto-resilient multiple-description coding with optimized transmission strategy has been proposed. Further study is done on the computational complexity of rate-distortion optimized video streaming and a dynamic programming algorithm is considered. Experiment results show that video streaming with adaptive dynamic programming gains better playback video quality at the receiver when transmitted through error-prone mobile channel.
Chen, Rubing; Wang, Eryu; Tsetsarkin, Konstantin A.; Weaver, Scott C.
The 3′ untranslated genome region (UTR) of arthropod-borne viruses is characterized by enriched direct repeats (DRs) and stem-loop structures. Despite many years of theoretical and experimental study, on-going positive selection on the 3′UTR had never been observed in ‘real-time,’ and the role of the arbovirus 3′UTR remains poorly understood. We observed a lineage-specific 3′UTR sequence pattern in all available Asian lineage of the mosquito-borne alphavirus, chikungunya virus (CHIKV) (1958–2009), including complicated mutation and duplication patterns of the long DRs. Given that a longer genome is usually associated with less efficient replication, we hypothesized that the fixation of these genetic changes in the Asian lineage 3′UTR was due to their beneficial effects on adaptation to vectors or hosts. Using reverse genetic methods, we examined the functional importance of each direct repeat. Our results suggest that adaptation to mosquitoes, rather than to mammalian hosts, is a major evolutionary force on the CHIKV 3′UTR. Surprisingly, the Asian 3′UTR appeared to be inferior to its predicted ancestral sequence for replication in both mammals and mosquitoes, suggesting that its fixation in Asia was not a result of directional selection. Rather, it may have resulted from a population bottleneck during its introduction from Africa to Asia. We propose that this introduction of a 3′UTR with deletions led to genetic drift and compensatory mutations associated with the loss of structural/functional constraints, followed by two independent beneficial duplications and fixation due to positive selection. Our results provide further evidence that the limited epidemic potential of the Asian CHIKV strains resulted from founder effects that reduced its fitness for efficient transmission by mosquitoes there. PMID:24009512
Xie, Gary; Detter, Chris; Bruce, David; Challacome, Jean F; Brettin, Thomas S; Barabote, Ravi D; Leu, David; Normand, Philippe; Necsula, Anamaria; Daubin, Vincent; Medigue, Claudine; Xu, Xin C; Lapidus, Alla; Pujic, Pierre; Richardson, Paul; Berry, Alison M
We present here the complete 2.4 MB genome of the actinobacterial thermophile, Acidothermus cellulolyticus lIB, that surprisingly reveals thermophilic amino acid usage in only the cytosolic subproteome rather than its whole proteome. Thermophilic amino acid usage in the partial proteome implies a recent, ongoing evolution of the A. cellulolyticus genome since its divergence about 200-250 million years ago from its closest phylogenetic neighbor Frankia, a mesophilic plant symbiont. Differential amino acid usage in the predicted subproteomes of A. cellulolyticus likely reflects a stepwise evolutionary process of modern thermophiles in general. An unusual occurrence of higher G+C in the non-coding DNA than in the transcribed genome reinforces a late evolution from a higher G+C common ancestor. Comparative analyses of the A. cellulolyticus genome with those of Frankia and other closely-related actinobacteria revealed that A. cellulolyticus genes exhibit reciprocal purine preferences at the first and third codon positions, perhaps reflecting a subtle preference for the dinucleotide AG in its mRNAs, a possible adaptation to a thermophilic environment. Other interesting features in the genome of this cellulolytic, hot-springs dwelling prokaryote reveal streamlining for adaptation to its specialized ecological niche. These include a low occurrence of pseudogenes or mobile genetic elements, a flagellar gene complement previously unknown in this organism, and presence of laterally-acquired genomic islands of likely ecophysiological value. New glycoside hydrolases relevant for lignocellulosic biomass deconstruction were identified in the genome, indicating a diverse biomass-degrading enzyme repertoire several-fold greater than previously characterized, and significantly elevating the industrial value of this organism.
Xie, Gary; Detter, John C; Bruce, David C; Challacombe, Jean F; Brettin, Thomas S; Necsulea, Anamaria; Daubin, Vincent; Medigue, Claudine; Adney, William S; Xu, Xin C; Lapidus, Alla; Pujic, Pierre; Berry, Alison M; Barabote, Ravi D; Leu, David; Normand, Phillipe
We present here the complete 2.4 MB genome of the actinobacterial thermophile, Acidothermus cellulolyticus 11B, that surprisingly reveals thermophilic amino acid usage in only the cytosolic subproteome rather than its whole proteome. Thermophilic amino acid usage in the partial proteome implies a recent, ongoing evolution of the A. cellulolyticus genome since its divergence about 200-250 million years ago from its closest phylogenetic neighbor Frankia, a mesophilic plant symbiont. Differential amino acid usage in the predicted subproteomes of A. cellulolyticus likely reflects a stepwise evolutionary process of modern thermophiles in general. An unusual occurrence of higher G+C in the non-coding DNA than in the transcribed genome reinforces a late evolution from a higher G+C common ancestor. Comparative analyses of the A. cellulolyticus genome with those of Frankia and other closely-related actinobacteria revealed that A. cellulolyticus genes exhibit reciprocal purine preferences at the first and third codon positions, perhaps reflecting a subtle preference for the dinucleotide AG in its mRNAs, a possible adaptation to a thermophilic environment. Other interesting features in the genome of this cellulolytic, hot-springs dwelling prokaryote reveal streamlining for adaptation to its specialized ecological niche. These include a low occurrence of pseudo genes or mobile genetic elements, a flagellar gene complement previously unknown in this organism, and presence of laterally-acquired genomic islands of likely ecophysiological value. New glycoside hydrolases relevant for lignocellulosic biomass deconstruction were identified in the genome, indicating a diverse biomass-degrading enzyme repertoire several-fold greater than previously characterized, and significantly elevating the industrial value of this organism.
Tan, Aimee; Petty, Nicola K; Hocking, Dianna; Bennett-Wood, Vicki; Wakefield, Matthew; Praszkier, Judyta; Tauschek, Marija; Yang, Ji; Robins-Browne, Roy
The evolution of pathogenic bacteria is a multifaceted and complex process, which is strongly influenced by the horizontal acquisition of genetic elements and their subsequent expression in their new hosts. A well-studied example is the RegA regulon of the enteric pathogen Citrobacter rodentium. The RegA regulatory protein is a member of the AraC/XylS superfamily, which coordinates the expression of a gene repertoire that is necessary for full pathogenicity of this murine pathogen. Upon stimulation by an exogenous, gut-associated signal, namely, bicarbonate ions, RegA activates the expression of a series of genes, including virulence factors, such as autotransporters, fimbriae, a dispersin-like protein, and the grlRA operon on the locus of enterocyte effacement pathogenicity island. Interestingly, the genes encoding RegA homologues are distributed across the genus Escherichia, encompassing pathogenic and nonpathogenic subtypes. In this study, we carried out a series of bioinformatic, transcriptional, and functional analyses of the RegA regulons of these bacteria. Our results demonstrated that regA has been horizontally transferred to Escherichia spp. and C. rodentium. Comparative studies of two RegA homologues, namely, those from C. rodentium and E. coli SMS-3-5, a multiresistant environmental strain of E. coli, showed that the two regulators acted similarly in vitro but differed in terms of their abilities to activate the virulence of C. rodentium in vivo, which evidently was due to their differential activation of grlRA. Our data indicate that RegA from C. rodentium has strain-specific adaptations that facilitate infection of its murine host. These findings shed new light on the development of virulence by C. rodentium and on the evolution of virulence-regulatory genes of bacterial pathogens in general.
Armbruster, W. Scott; Lee, Joongku; Baldwin, Bruce G.
We conducted phylogenetically informed comparative analyses of 81 taxa of Dalechampia (Euphorbiaceae) vines and shrubs to assess the roles of historical contingency and trait interaction in the evolution of plant-defense and pollinator-attraction systems. We asked whether defenses can originate by exaptation from preexisting pollinator attractants, or vice versa, whether plant defenses show escalation, and if so, whether by enhancing one line of defense or by adding new lines of defense. Two major patterns emerged: (i) correlated evolution of several complementary lines of defense of flowers, seeds, and leaves, and (ii) 5 to 6 losses of the resin reward, followed by redeployment of resin for defense of male flowers in 3 to 4 lineages, apparently in response to herbivore-mediated selection for defense of staminate flowers upon relaxation of pollinator-mediated selection on resin. In all cases, redeployment of resin involved reversion to the inferred ancestral arrangement of flowers and resiniferous bractlets. Triterpene resin has also been deployed for defense of leaves and developing seeds. Other unique defenses against florivores include nocturnal closure of large involucral bracts around receptive flowers and permanent closure around developing fruits (until opening again upon dehiscence). Escalation in one major clade occurred through an early dramatic increase in the number of lines of defense and in the other major clade by more limited increases throughout the group's evolution. We conclude that preaptations played important roles in the evolution of unique defense and attraction systems, and that the evolution of interactions with herbivores can be influenced by adaptations for pollination, and vice versa. PMID:19841278
Armbruster, W Scott; Lee, Joongku; Baldwin, Bruce G
We conducted phylogenetically informed comparative analyses of 81 taxa of Dalechampia (Euphorbiaceae) vines and shrubs to assess the roles of historical contingency and trait interaction in the evolution of plant-defense and pollinator-attraction systems. We asked whether defenses can originate by exaptation from preexisting pollinator attractants, or vice versa, whether plant defenses show escalation, and if so, whether by enhancing one line of defense or by adding new lines of defense. Two major patterns emerged: (i) correlated evolution of several complementary lines of defense of flowers, seeds, and leaves, and (ii) 5 to 6 losses of the resin reward, followed by redeployment of resin for defense of male flowers in 3 to 4 lineages, apparently in response to herbivore-mediated selection for defense of staminate flowers upon relaxation of pollinator-mediated selection on resin. In all cases, redeployment of resin involved reversion to the inferred ancestral arrangement of flowers and resiniferous bractlets. Triterpene resin has also been deployed for defense of leaves and developing seeds. Other unique defenses against florivores include nocturnal closure of large involucral bracts around receptive flowers and permanent closure around developing fruits (until opening again upon dehiscence). Escalation in one major clade occurred through an early dramatic increase in the number of lines of defense and in the other major clade by more limited increases throughout the group's evolution. We conclude that preaptations played important roles in the evolution of unique defense and attraction systems, and that the evolution of interactions with herbivores can be influenced by adaptations for pollination, and vice versa.
Tan, Aimee; Petty, Nicola K.; Hocking, Dianna; Bennett-Wood, Vicki; Wakefield, Matthew; Praszkier, Judyta; Tauschek, Marija; Yang, Ji
The evolution of pathogenic bacteria is a multifaceted and complex process, which is strongly influenced by the horizontal acquisition of genetic elements and their subsequent expression in their new hosts. A well-studied example is the RegA regulon of the enteric pathogen Citrobacter rodentium. The RegA regulatory protein is a member of the AraC/XylS superfamily, which coordinates the expression of a gene repertoire that is necessary for full pathogenicity of this murine pathogen. Upon stimulation by an exogenous, gut-associated signal, namely, bicarbonate ions, RegA activates the expression of a series of genes, including virulence factors, such as autotransporters, fimbriae, a dispersin-like protein, and the grlRA operon on the locus of enterocyte effacement pathogenicity island. Interestingly, the genes encoding RegA homologues are distributed across the genus Escherichia, encompassing pathogenic and nonpathogenic subtypes. In this study, we carried out a series of bioinformatic, transcriptional, and functional analyses of the RegA regulons of these bacteria. Our results demonstrated that regA has been horizontally transferred to Escherichia spp. and C. rodentium. Comparative studies of two RegA homologues, namely, those from C. rodentium and E. coli SMS-3-5, a multiresistant environmental strain of E. coli, showed that the two regulators acted similarly in vitro but differed in terms of their abilities to activate the virulence of C. rodentium in vivo, which evidently was due to their differential activation of grlRA. Our data indicate that RegA from C. rodentium has strain-specific adaptations that facilitate infection of its murine host. These findings shed new light on the development of virulence by C. rodentium and on the evolution of virulence-regulatory genes of bacterial pathogens in general. PMID:25624355
Miya, Masaki; Friedman, Matt; Satoh, Takashi P; Takeshima, Hirohiko; Sado, Tetsuya; Iwasaki, Wataru; Yamanoue, Yusuke; Nakatani, Masanori; Mabuchi, Kohji; Inoue, Jun G; Poulsen, Jan Yde; Fukunaga, Tsukasa; Sato, Yukuto; Nishida, Mutsumi
Uncertainties surrounding the evolutionary origin of the epipelagic fish family Scombridae (tunas and mackerels) are symptomatic of the difficulties in resolving suprafamilial relationships within Percomorpha, a hyperdiverse teleost radiation that contains approximately 17,000 species placed in 13 ill-defined orders and 269 families. Here we find that scombrids share a common ancestry with 14 families based on (i) bioinformatic analyses using partial mitochondrial and nuclear gene sequences from all percomorphs deposited in GenBank (10,733 sequences) and (ii) subsequent mitogenomic analysis based on 57 species from those targeted 15 families and 67 outgroup taxa. Morphological heterogeneity among these 15 families is so extraordinary that they have been placed in six different perciform suborders. However, members of the 15 families are either coastal or oceanic pelagic in their ecology with diverse modes of life, suggesting that they represent a previously undetected adaptive radiation in the pelagic realm. Time-calibrated phylogenies imply that scombrids originated from a deep-ocean ancestor and began to radiate after the end-Cretaceous when large predatory epipelagic fishes were selective victims of the Cretaceous-Paleogene mass extinction. We name this clade of open-ocean fishes containing Scombridae "Pelagia" in reference to the common habitat preference that links the 15 families.
Miya, Masaki; Friedman, Matt; Satoh, Takashi P.; Takeshima, Hirohiko; Sado, Tetsuya; Iwasaki, Wataru; Yamanoue, Yusuke; Nakatani, Masanori; Mabuchi, Kohji; Inoue, Jun G.; Poulsen, Jan Yde; Fukunaga, Tsukasa; Sato, Yukuto; Nishida, Mutsumi
Uncertainties surrounding the evolutionary origin of the epipelagic fish family Scombridae (tunas and mackerels) are symptomatic of the difficulties in resolving suprafamilial relationships within Percomorpha, a hyperdiverse teleost radiation that contains approximately 17,000 species placed in 13 ill-defined orders and 269 families. Here we find that scombrids share a common ancestry with 14 families based on (i) bioinformatic analyses using partial mitochondrial and nuclear gene sequences from all percomorphs deposited in GenBank (10,733 sequences) and (ii) subsequent mitogenomic analysis based on 57 species from those targeted 15 families and 67 outgroup taxa. Morphological heterogeneity among these 15 families is so extraordinary that they have been placed in six different perciform suborders. However, members of the 15 families are either coastal or oceanic pelagic in their ecology with diverse modes of life, suggesting that they represent a previously undetected adaptive radiation in the pelagic realm. Time-calibrated phylogenies imply that scombrids originated from a deep-ocean ancestor and began to radiate after the end-Cretaceous when large predatory epipelagic fishes were selective victims of the Cretaceous-Paleogene mass extinction. We name this clade of open-ocean fishes containing Scombridae “Pelagia” in reference to the common habitat preference that links the 15 families. PMID:24023883
Chouikha, Iman; Hinnebusch, B Joseph
The arthropod-borne transmission route of Yersinia pestis, the bacterial agent of plague, is a recent evolutionary adaptation. Yersinia pseudotuberculosis, the closely related food-and water-borne enteric species from which Y. pestis diverged less than 6,400 y ago, exhibits significant oral toxicity to the flea vectors of plague, whereas Y. pestis does not. In this study, we identify the Yersinia urease enzyme as the responsible oral toxin. All Y. pestis strains, including those phylogenetically closest to the Y. pseudotuberculosis progenitor, contain a mutated ureD allele that eliminated urease activity. Restoration of a functional ureD was sufficient to make Y. pestis orally toxic to fleas. Conversely, deletion of the urease operon in Y. pseudotuberculosis rendered it nontoxic. Enzymatic activity was required for toxicity. Because urease-related mortality eliminates 30-40% of infective flea vectors, ureD mutation early in the evolution of Y. pestis was likely subject to strong positive selection because it significantly increased transmission potential.
Wang, Y.; Pan, Y.
A mediated umuCD genes and double copied ssb gene, these low fidelity DNA polymerase along with Ssb protein may endow MTB high adaptive mutation under stress condition; 4) also, magnetosome crystals (magnetite or greigite) can reduce radiation oxidative damage and protect MTB.
Thiele, R.; Zimmer, R.; Lengauer, T.
We propose a new alignment procedure that is capable of aligning protein sequences and structures in a unified manner. Recursive dynamic programming (RDP) is a hierarchical method which, on each level of the hierarchy, identifies locally optimal solutions and assembles them into partial alignments of sequences and/or structures. In contrast to classical dynamic programming, RDP can also handle alignment problems that use objective functions not obeying the principle of prefix optimality, e.g. scoring schemes derived from energy potentials of mean force. For such alignment problems, RDP aims at computing solutions that are near-optimal with respect to the involved cost function and biologically meaningful at the same time. Towards this goal, RDP maintains a dynamic balance between different factors governing alignment fitness such as evolutionary relationships and structural preferences. As in the RDP method gaps are not scored explicitly, the problematic assignment of gap cost parameters is circumvented. In order to evaluate the RDP approach we analyse whether known and accepted multiple alignments based on structural information can be reproduced with the RDP method.
Ayuk, Paul T-Y
The aetiology of hypertensive disorders of pregnancy remains unknown, despite over 30 years of research. The prevalence and natural history of these disorders and the lack of progress in identifying a cause calls for a radical new approach. It is hypothesised that these disorders arise as a consequence of abnormal maternal regulatory mechanisms. The evolution of the physical characteristics unique to humans (bi-pedal gait and a large brain) resulted in a narrow pelvis and a large head. Such a physique is not conducive to viviparity and caused difficult, prolonged and obstructed labour with post-partum haemorrhage--the commonest causes of maternal mortality in the absence of modern medical care. In such circumstances, up to 6.5% of pregnant women will die as a direct consequence of pregnancy, mainly as a result of obstructed labour and haemorrhage. The death toll would have been much higher over millions of years of evolution. These conditions exerted significant adaptive and evolutionary pressure on our species. The adaptations necessary to mitigate the reproductive consequences of the human physique include activation of the coagulation system to reduce post-partum haemorrhage, increased blood pressure to peak after delivery and maintain cerebral perfusion in the face of post-partum blood loss and restriction of fetal growth to prevent obstructed labour. These adaptations must be regulated to guarantee their occurrence but limit their extent to prevent disease. Evidence for blood pressure regulation during pregnancy and a proposed mechanism to achieve this are presented. Regulation requires a redundant feto-placental signal and a single tightly controlled regulator. To guarantee that blood pressure rises, the feto-placental signal is predicted to be conveyed by several different molecules and to be produced in excess in all pregnancies. Normality is then maintained by a single tightly controlled regulator. This model predicts that the feto-placental factors that
Othman, Muhammad Murtadha; Abd Rahman, Nurulazmi; Musirin, Ismail; Fotuhi-Firuzabad, Mahmud; Rajabi-Ghahnavieh, Abbas
This paper introduces a novel multiobjective approach for capacity benefit margin (CBM) assessment taking into account tie-line reliability of interconnected systems. CBM is the imperative information utilized as a reference by the load-serving entities (LSE) to estimate a certain margin of transfer capability so that a reliable access to generation through interconnected system could be attained. A new Pareto-based evolutionary programming (EP) technique is used to perform a simultaneous determination of CBM for all areas of the interconnected system. The selection of CBM at the Pareto optimal front is proposed to be performed by referring to a heuristic ranking index that takes into account system loss of load expectation (LOLE) in various conditions. Eventually, the power transfer based available transfer capability (ATC) is determined by considering the firm and nonfirm transfers of CBM. A comprehensive set of numerical studies are conducted on the modified IEEE-RTS79 and the performance of the proposed method is numerically investigated in detail. The main advantage of the proposed technique is in terms of flexibility offered to an independent system operator in selecting an appropriate solution of CBM simultaneously for all areas. PMID:25879068
Othman, Muhammad Murtadha; Abd Rahman, Nurulazmi; Musirin, Ismail; Fotuhi-Firuzabad, Mahmud; Rajabi-Ghahnavieh, Abbas
This paper introduces a novel multiobjective approach for capacity benefit margin (CBM) assessment taking into account tie-line reliability of interconnected systems. CBM is the imperative information utilized as a reference by the load-serving entities (LSE) to estimate a certain margin of transfer capability so that a reliable access to generation through interconnected system could be attained. A new Pareto-based evolutionary programming (EP) technique is used to perform a simultaneous determination of CBM for all areas of the interconnected system. The selection of CBM at the Pareto optimal front is proposed to be performed by referring to a heuristic ranking index that takes into account system loss of load expectation (LOLE) in various conditions. Eventually, the power transfer based available transfer capability (ATC) is determined by considering the firm and nonfirm transfers of CBM. A comprehensive set of numerical studies are conducted on the modified IEEE-RTS79 and the performance of the proposed method is numerically investigated in detail. The main advantage of the proposed technique is in terms of flexibility offered to an independent system operator in selecting an appropriate solution of CBM simultaneously for all areas.
Han, Sang-Jun; Cho, Sung-Bae
The process of learning the behavior of a given program by using machine-learning techniques (based on system-call audit data) is effective to detect intrusions. Rule learning, neural networks, statistics, and hidden Markov models (HMMs) are some of the kinds of representative methods for intrusion detection. Among them, neural networks are known for good performance in learning system-call sequences. In order to apply this knowledge to real-world problems successfully, it is important to determine the structures and weights of these call sequences. However, finding the appropriate structures requires very long time periods because there are no suitable analytical solutions. In this paper, a novel intrusion-detection technique based on evolutionary neural networks (ENNs) is proposed. One advantage of using ENNs is that it takes less time to obtain superior neural networks than when using conventional approaches. This is because they discover the structures and weights of the neural networks simultaneously. Experimental results with the 1999 Defense Advanced Research Projects Agency (DARPA) Intrusion Detection Evaluation (IDEVAL) data confirm that ENNs are promising tools for intrusion detection.
Wilson, Jesse W.; Schlup, Philip; Lunacek, Monte; Whitley, Darrell; Bartels, Randy A.
An ultrafast pulse shaper for coherent control applications is described, complete with a simple, reliable calibration technique and an advanced learning control algorithm. The calibration technique makes use of a common-path interferometer, producing less noisy measurements than a conventional Mach-Zehnder interferometer. A covariance matrix adaptation evolutionary strategy (ES) is demonstrated to perform better than a traditional ES for high-dimensional search landscapes.
Liu, Tao; Liu, Yi; Qian, Chen; Qian, Depei
With the development of multi-/many-core processors, applications need to be written as parallel programs to improve execution efficiency. For data-intensive applications that use multiple threads to read/write files simultaneously, an I/O sub-system can easily become a bottleneck when too many of these types of threads exist; on the contrary, too few threads will cause insufficient resource utilization and hurt performance. Therefore, programmers must pay much attention to parallelism control to find the appropriate number of I/O threads for an application. This paper proposes a parallelism control mechanism named IOPA that can adjust the parallelism of applications to adapt to the I/O capability of a system and balance computing resources and I/O bandwidth. The programming interface of IOPA is also provided to programmers to simplify parallel programming. IOPA is evaluated using multiple applications with both solid state and hard disk drives. The results show that the parallel applications using IOPA can achieve higher efficiency than those with a fixed number of threads. PMID:28278236
Yuan, Zhilong; Chen, Gang; Huang, Qin
Many methods have been proposed to account for the potential impact of ethnic/regional factors when extrapolating results from multiregional clinical trials (MRCTs) to targeted ethnic (TE) patients, i.e., "bridging." Most of them either focused on TE patients in the MRCT (i.e., internal bridging) or a separate local clinical trial (LCT) (i.e., external bridging). Huang et al. (2012) integrated both bridging concepts in their method for the Simultaneous Global Drug Development Program (SGDDP) which designs both the MRCT and the LCT prospectively and combines patients in both trials by ethnic origin, i.e., TE vs. non-TE (NTE). The weighted Z test was used to combine information from TE and NTE patients to test with statistical rigor whether a new treatment is effective in the TE population. Practically, the MRCT is often completed before the LCT. Thus to increase the power for the SGDDP and/or obtain more informative data in TE patients, we may use the final results from the MRCT to re-evaluate initial assumptions (e.g., effect sizes, variances, weight), and modify the LCT accordingly. We discuss various adaptive strategies for the LCT such as sample size reassessment, population enrichment, endpoint change, and dose adjustment. As an example, we extend a popular adaptive design method to re-estimate the sample size for the LCT, and illustrate it for a normally distributed endpoint.
Olson, Jonathan R.; Welsh, Janet A.; Perkins, Daniel F.
In this article, we describe how the recent movement towards evidence-based programming has impacted Extension. We review how the emphasis on implementing such programs with strict fidelity to an underlying program model may be at odds with Extension's strong history of adapting programming to meet the unique needs of children, youth, families,…
Taussig, Heather; Weiler, Lindsey; Rhodes, Tara; Hambrick, Erin; Wertheimer, Robyn; Fireman, Orah; Combs, Melody
Objective This article describes the process of adapting and implementing a complex, multicomponent intervention for a new population. Specifically, the article delineates the development and implementation of the Fostering Healthy Futures for Teens (FHF-T) program, which is an adaptation and extension of the Fostering Healthy Futures® (FHF) preventive intervention. FHF is a 9-month mentoring and skills group program for 9 to 11 year olds recently placed in foster care. Following the designation of FHF as an evidence-based intervention, there was increasing demand for the program. However, the narrow population for which FHF had demonstrated efficacy limited broader implementation of the existing intervention. FHF-T was designed to extend the reach of the program by adapting the FHF intervention for adolescents in the early years of high school who have a history of out-of-home care. Specifically, this adaptation recognizes key developmental differences between preadolescent and adolescent populations. Method After designing a program model and adapting the program components, the FHF-T mentoring program was implemented with 42 youth over 2 program years. Results Of the teens who were offered the program, 75% chose to enroll, and 88% of those graduated 9 months later. Although the program evidenced high rates of uptake and participant satisfaction, some unexpected challenges were encountered that will need to be addressed in future iterations of the program. Conclusions Too often program adaptations are made without careful consideration of important contextual issues, and too infrequently, these adapted programs are studied. Our process of program adaptation with rigorous measurement of program implementation provides a useful model for other evidence-based programs seeking thoughtful adaptation. PMID:27019678
Thom, Ronald M.; Anderson, Michael G.; Tyre, Drew; Fleming, Craig A.
The paper, “Adaptive Management: Background for Stakeholders in the Missouri River Recovery Program,” introduced the concept of adaptive management (AM), its principles and how they relate to one-another, how AM is applied, and challenges for its implementation. This companion paper describes how the AM principles were applied to specific management actions within the Missouri River Recovery Program to facilitate understanding, decision-making, and stakeholder engagement. For context, we begin with a brief synopsis of the Missouri River Recovery Program (MRRP) and the strategy for implementing adaptive management (AM) within the program; we finish with an example of AM in action within Phase I of the MRPP.
Hendry, Andrew P; Kinnison, Michael T; Heino, Mikko; Day, Troy; Smith, Thomas B; Fitt, Gary; Bergstrom, Carl T; Oakeshott, John; Jørgensen, Peter S; Zalucki, Myron P; Gilchrist, George; Southerton, Simon; Sih, Andrew; Strauss, Sharon; Denison, Robert F; Carroll, Scott P
Evolutionary principles are now routinely incorporated into medicine and agriculture. Examples include the design of treatments that slow the evolution of resistance by weeds, pests, and pathogens, and the design of breeding programs that maximize crop yield or quality. Evolutionary principles are also increasingly incorporated into conservation biology, natural resource management, and environmental science. Examples include the protection of small and isolated populations from inbreeding depression, the identification of key traits involved in adaptation to climate change, the design of harvesting regimes that minimize unwanted life-history evolution, and the setting of conservation priorities based on populations, species, or communities that harbor the greatest evolutionary diversity and potential. The adoption of evolutionary principles has proceeded somewhat independently in these different fields, even though the underlying fundamental concepts are the same. We explore these fundamental concepts under four main themes: variation, selection, connectivity, and eco-evolutionary dynamics. Within each theme, we present several key evolutionary principles and illustrate their use in addressing applied problems. We hope that the resulting primer of evolutionary concepts and their practical utility helps to advance a unified multidisciplinary field of applied evolutionary biology. PMID:25567966
Funk, W Chris; Lovich, Robert E; Hohenlohe, Paul A; Hofman, Courtney A; Morrison, Scott A; Sillett, T Scott; Ghalambor, Cameron K; Maldonado, Jesus E; Rick, Torben C; Day, Mitch D; Polato, Nicholas R; Fitzpatrick, Sarah W; Coonan, Timothy J; Crooks, Kevin R; Dillon, Adam; Garcelon, David K; King, Julie L; Boser, Christina L; Gould, Nicholas; Andelt, William F
The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small Ne (range = 2.1-89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests identified 3.6-6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential.
Title of adaptation: ADAPT HFS FOR MSXALPHA Adaptation number: 0001 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland (see application form in this issue) Reference to original program Cat. number: ACQI; Title: H.F.S. SELF-CONSISTENT FIELD; Ref. in CPC: 1 (1969) 216 Author of original program: J.-P. Desclaux Computer: Amdahl 470/V7; Installation: University of Alberta, Edmonton, Canada Operating system: MTS Programming language used in adapted program: FORTRAN IV High-speed core required: 75656 bytes Number of bits in a byte: 8 Peripherals used: card reader, line printer, disk No. of cards required to effect adaptation (including directive cards): 254 Card punching code: EBCDIC 027
Ortega, Enrique; Giannotta, Fabrizia; Latina, Delia; Ciairano, Silvia
Background: The family context has proven to be a useful target in which to apply prevention efforts aimed at child and adolescent health risk behaviors. There are currently a variety of cultural adaptation models that serve to guide the international adaptation of intervention programs. Objective: The cultural adaptation process and program…
Coyle-Rogers, Patricia G.
Adaptive competencies are the skills required to effectively complete a particular task and are the congruencies (balance) between personal skills and task demands. The differences between the adaptive competency acquisition of students in licensed practical nurse (LPN) programs and associate degree nurse (ADN) programs were examined in a…
Massachusetts Inst. of Tech., Cambridge. Dept. of Urban Studies and Planning.
The report of Project ADAPT (Aerospace and Defense Adaptation to Public Technology), describes the design, execution, and forthcoming evaluation of the program. The program's objective was to demonstrate the feasibility of redeploying surplus technical manpower into public service at State and local levels of government. The development of the…
As wild environments are often inhospitable, many species have to be captive-bred to save them from extinction. In captivity, species adapt genetically to the captive environment and these genetic adaptations are overwhelmingly deleterious when populations are returned to wild environments. I review empirical evidence on (i) the genetic basis of adaptive changes in captivity, (ii) factors affecting the extent of genetic adaptation to captivity, and (iii) means for minimizing its deleterious impacts. Genetic adaptation to captivity is primarily due to rare alleles that in the wild were deleterious and partially recessive. The extent of adaptation to captivity depends upon selection intensity, genetic diversity, effective population size and number of generation in captivity, as predicted by quantitative genetic theory. Minimizing generations in captivity provides a highly effective means for minimizing genetic adaptation to captivity, but is not a practical option for most animal species. Population fragmentation and crossing replicate captive populations provide practical means for minimizing the deleterious effects of genetic adaptation to captivity upon populations reintroduced into the wild. Surprisingly, equalization of family sizes reduces the rate of genetic adaptation, but not the deleterious impacts upon reintroduced populations. Genetic adaptation to captivity is expected to have major effects on reintroduction success for species that have spent many generations in captivity. This issue deserves a much higher priority than it is currently receiving.
Curtis, Jim; Graham, Alex; Ghafoori, Eraj; Pyke, Susan; Kaufman, Stefan; Boulet, Mark
Interim evaluations of government programs can sometimes reveal lower than expected outcomes, leading to the question of how adjustments can be made while the program is still underway. Although adaptive management frameworks can provide a practical roadmap to address this question, a lack of successful learnings and poor implementation have hampered the progress and wider application of adaptive management. Using a case study involving an energy efficiency government program targeting low-income households, this article provides supporting evidence on how adaptive management can be facilitated and applied. Factors such as proactive and responsive leadership, establishing a research-practice interface, and recognizing the skills, expertise, and contributions of multiple stakeholders guided adjustments to the program, and later paved the way for longer-term organizational learning that impacted how other programs are delivered. Implications for knowledge and practice, and a discussion of the challenges faced in the program, advance current thinking in adaptive management.
Bloomquist, Lorraine E.
This manual provides guidelines for aquatic teachers of people with disabilities. It is based on experience in teaching American Red Cross Adapted Aquatics and is to be used to complement and accompany the Red Cross Adapted Aquatics materials. Emphasis is placed on successful experiences in a positive, safe, reinforcing environment stressing…
Xu, Shuqing; Schlüter, Philipp M
Divergent selection by pollinators can bring about strong reproductive isolation via changes at few genes of large effect. This has recently been demonstrated in sexually deceptive orchids, where studies (1) quantified the strength of reproductive isolation in the field; (2) identified genes that appear to be causal for reproductive isolation; and (3) demonstrated selection by analysis of natural variation in gene sequence and expression. In a group of closely related Ophrys orchids, specific floral scent components, namely n-alkenes, are the key floral traits that control specific pollinator attraction by chemical mimicry of insect sex pheromones. The genetic basis of species-specific differences in alkene production mainly lies in two biosynthetic genes encoding stearoyl–acyl carrier protein desaturases (SAD) that are associated with floral scent variation and reproductive isolation between closely related species, and evolve under pollinator-mediated selection. However, the implications of this genetic architecture of key floral traits on the evolutionary processes of pollinator adaptation and speciation in this plant group remain unclear. Here, we expand on these recent findings to model scenarios of adaptive evolutionary change at SAD2 and SAD5, their effects on plant fitness (i.e., offspring number), and the dynamics of speciation. Our model suggests that the two-locus architecture of reproductive isolation allows for rapid sympatric speciation by pollinator shift; however, the likelihood of such pollinator-mediated speciation is asymmetric between the two orchid species O. sphegodes and O. exaltata due to different fitness effects of their predominant SAD2 and SAD5 alleles. Our study not only provides insight into pollinator adaptation and speciation mechanisms of sexually deceptive orchids but also demonstrates the power of applying a modeling approach to the study of pollinator-driven ecological speciation. PMID:25691974
Xu, Shuqing; Schlüter, Philipp M
Divergent selection by pollinators can bring about strong reproductive isolation via changes at few genes of large effect. This has recently been demonstrated in sexually deceptive orchids, where studies (1) quantified the strength of reproductive isolation in the field; (2) identified genes that appear to be causal for reproductive isolation; and (3) demonstrated selection by analysis of natural variation in gene sequence and expression. In a group of closely related Ophrys orchids, specific floral scent components, namely n-alkenes, are the key floral traits that control specific pollinator attraction by chemical mimicry of insect sex pheromones. The genetic basis of species-specific differences in alkene production mainly lies in two biosynthetic genes encoding stearoyl-acyl carrier protein desaturases (SAD) that are associated with floral scent variation and reproductive isolation between closely related species, and evolve under pollinator-mediated selection. However, the implications of this genetic architecture of key floral traits on the evolutionary processes of pollinator adaptation and speciation in this plant group remain unclear. Here, we expand on these recent findings to model scenarios of adaptive evolutionary change at SAD2 and SAD5, their effects on plant fitness (i.e., offspring number), and the dynamics of speciation. Our model suggests that the two-locus architecture of reproductive isolation allows for rapid sympatric speciation by pollinator shift; however, the likelihood of such pollinator-mediated speciation is asymmetric between the two orchid species O. sphegodes and O. exaltata due to different fitness effects of their predominant SAD2 and SAD5 alleles. Our study not only provides insight into pollinator adaptation and speciation mechanisms of sexually deceptive orchids but also demonstrates the power of applying a modeling approach to the study of pollinator-driven ecological speciation.
Fiscian, Vivian Sarpomaa; Obeng, E. Kwame; Goldstein, Karen; Shea, Judy A.; Turner, Barbara J.
We adapted a U.S. HIV prevention program to address knowledge gaps and cultural pressures that increase the risk of infection in adolescent Ghanaian girls. The theory-based nine-module HIV prevention program combines didactics and games, an interactive computer program about sugar daddies, and tie-and-dye training to demonstrate an economic…
Buckanavage, Robert, Ed.; And Others
Guidelines are presented for organizing programs and modifying activities in physical education programs for children with a wide range of physical and emotional disabilities. The guidelines should result in a program that allows students to work to their maximum potential within the framework of regular physical education classes. In planning the…
Sims, Katharine R E; Alix-Garcia, Jennifer M; Shapiro-Garza, Elizabeth; Fine, Leah R; Radeloff, Volker C; Aronson, Glen; Castillo, Selene; Ramirez-Reyes, Carlos; Yañez-Pagans, Patricia
Natural resource managers are often expected to achieve both environmental protection and economic development even when there are fundamental trade-offs between these goals. Adaptive management provides a theoretical structure for program administrators to balance social priorities in the presence of trade-offs and to improve conservation targeting. We used the case of Mexico's federal Payments for Hydrological Services program (PSAH) to illustrate the importance of adaptive management for improving program targeting. We documented adaptive elements of PSAH and corresponding changes in program eligibility and selection criteria. To evaluate whether these changes resulted in enrollment of lands of high environmental and social priority, we compared the environmental and social characteristics of the areas enrolled in the program with the characteristics of all forested areas in Mexico, all areas eligible for the program, and all areas submitted for application to the program. The program successfully enrolled areas of both high ecological and social priority, and over time, adaptive changes in the program's criteria for eligibility and selection led to increased enrollment of land scoring high on both dimensions. Three factors facilitated adaptive management in Mexico and are likely to be generally important for conservation managers: a supportive political environment, including financial backing and encouragement to experiment from the federal government; availability of relatively good social and environmental data; and active participation in the review process by stakeholders and outside evaluators.
Jirina, Marcel; Krayem, M. Said; Jirina, Marcel, Jr.
The Random Forest is a well-known method and also a program for data clustering and classification. Unfortunately, the original Random Forest program is rather difficult to use. Here we describe a new version of this program originally written in Fortran 77. The modified program in Fortran 95 needs to be compiled only once and information for different tasks is passed with help of arguments. The program was tested with 24 data sets from UCI MLR and results are available on the net.
The corrector module of the RAEIOS program and the IMP dynamics computer program were combined to achieve a date-fitting capability with the more general spacecraft dynamics models of the IMP program. The IMP dynamics program presents models of spacecraft dynamics for satellites with long, flexible booms. The properties of the corrector are discussed and a description is presented of the performance criteria and search logic for parameter estimation. A description is also given of the modifications made to add the corrector to the IMP program. This includes subroutine descriptions, common definitions, definition of input, and a description of output.
Nebraska Univ., Lincoln.
College students need a learning environment that encourages them to develop their reasoning abilities, as well as to master course content. This booklet discusses an attempt to create such an environment: the ADAPT program at the University of Nebraska. ADAPT, Accent on Developing Abstract Processes of Thought, is a comprehensive,…
Atkinson, A.J.; Trenham, P.C.; Fisher, R.N.; Hathaway, S.A.; Johnson, B.S.; Torres, S.G.; Moore, Y.C.
critical management uncertainties; and 3) implementing long-term monitoring and adaptive management. Ultimately, the success of regional conservation planning depends on the ability of monitoring programs to confront the challenges of adaptively managing and monitoring complex ecosystems and diverse arrays of sensitive species.
Gary, Gretchen; Allred, Shorna; LoGiudice, Elizabeth
Education is an important tool to increase the capacity of local government officials for community flood adaptation. To address flood adaptation and post-flood stream management in municipalities, Cornell Cooperative Extension and collaborators developed an educational program to increase municipal officials' knowledge about how to work…
Leko, Melinda M.; Roberts, Carly A.; Pek, Yvonne
This study examined the causes and consequences of secondary teachers' adaptations when implementing a research-based reading intervention program. Interview, observation, and artifact data were collected on five middle school intervention teachers, leading to a grounded theory composed of the core component, reconciliation through adaptation, and…
Sequence 03705-001B 30 September 1991 (3 SOFTWARE TECHNOLOGY FOR ADAPTABLE, RELIABLE SYSTEMS ( STARS ) PROGRAM ELEGTE m AUG15 1991 Ö I 0 SPMS Training...September 1991 SOFTWARE TECHNOLOGY FOR ADAPTABLE, RELIABLE SYSTEMS ( STARS ) PROGRAM SPMS Training Class: Student Handout Addendum to: Software...document is the student handout prepared for the "SEI/ STARS P.3 Asset Acquisition Sub-task" training class. The student handout covers basic aspects
Scraba, Paula J.; Bloomquist, Lorraine E.
An overview is presented of the aquatics course, adapted for persons with disabilities, at the University of Rhode Island. A description of the course includes information on course requirements, objectives, content and learning activities, assignments, modules used in the course, and a course syllabus. A description of the course organization and…
Rudner, Lawrence M.; Guo, Fanmin
This study investigates measurement decision theory (MDT) as an underlying model for computer adaptive testing when the goal is to classify examinees into one of a finite number of groups. The first analysis compares MDT with a popular item response theory model and finds little difference in terms of the percentage of correct classifications. The…
Community programs associated with the Paralympic movement provide recreational or competitive opportunities for individuals with a disability who wish to participate in a sport or leisure activity. These community programs provide the background knowledge and specialized equipment needed for individuals with disabilities to participate safely and…
Prater, Greg; And Others
The Rural Special Education Program (RSEP), a partnership between Northern Arizona University (NAU) and Kayenta Unified School District (KUSD), provides training for preservice special education teachers to work with Native American students and their families. To date, the program has provided training for 63 preservice special education…
MCNEIL, JOHN D.
A BEGINNING READING PROGRAM FOR SPANISH-SPEAKING CHILDREN IS REPORTED. A STUDY, SPONSORED BY THE SOUTHWEST REGIONAL LABORATORY FOR EDUCATIONAL RESEARCH AND DEVELOPMENT (SWRL), DEVELOPED LEARNING SEQUENCES FOR A BEGINNING READING PROGRAM FOR KINDERGARTEN CLASSROOMS WITH SPANISH-SPEAKING CHILDREN THROUGHOUT THE SOUTHWEST REGION. EACH OF 21 10-MINUTE…
Shaykhian, Linda H.; Shaykhian, Gholam Ali
There are numerous ways for engineers and students to become better problem-solvers. The use of command line and visual programming tools can help to model a problem and formulate a solution through visualization. The analysis of problem attributes and constraints provide insight into the scope and complexity of the problem. The visualization aspect of the problem-solving approach tends to make students and engineers more systematic in their thought process and help them catch errors before proceeding too far in the wrong direction. The problem-solver identifies and defines important terms, variables, rules, and procedures required for solving a problem. Every step required to construct the problem solution can be defined in program commands that produce intermediate output. This paper advocates improved problem solving skills through using a programming tool. MatLab created by MathWorks, is an interactive numerical computing environment and programming language. It is a matrix-based system that easily lends itself to matrix manipulation, and plotting of functions and data. MatLab can be used as an interactive command line or a sequence of commands that can be saved in a file as a script or named functions. Prior programming experience is not required to use MatLab commands. The GNU Octave, part of the GNU project, a free computer program for performing numerical computations, is comparable to MatLab. MatLab visual and command programming are presented here.
Henesian, M.A.; Haney, S.W.; Trenholme, J.B.; Thomas, M.
We discuss aspects of adaptive optics optimization for large fusion laser systems such as the 192-arm National Ignition Facility (NIF) at LLNL. By way of example, we considered the discrete actuator deformable mirror and Hartmann sensor system used on the Beamlet laser. Beamlet is a single-aperture prototype of the 11-0-5 slab amplifier design for NIF, and so we expect similar optical distortion levels and deformable mirror correction requirements. We are now in the process of developing a numerically efficient object oriented C++ language implementation of our adaptive optics and wavefront sensor code, but this code is not yet operational. Results are based instead on the prototype algorithms, coded-up in an interpreted array processing computer language.
Ray, L.; Loucks, C.
ADAPTUBL involves adaptively machining cast turbine blades. Due to uncontrollable warpage during solidification of cast parts, each part has unique dimensions. A structured lighting sensor, added to the workspace of a 5-axis machining center, discerns the unique geometry of each part. The processed sensor data is then used to generate the unique, 5-axis tool paths required to perform a high precision machining operation on the tip of each blade.
Cacioppo, John T.; Cacioppo, Stephanie; Boomsma, Dorret I.
Robert Weiss (1973) conceptualized loneliness as perceived social isolation, which he described as a gnawing, chronic disease without redeeming features. On the scale of everyday life, it is understandable how something as personally aversive as loneliness could be regarded as a blight on human existence. However, evolutionary time and evolutionary forces operate at such a different scale of organization than we experience in everyday life that personal experience is not sufficient to understand the role of loneliness in human existence. Research over the past decade suggests a very different view of loneliness than suggested by personal experience, one in which loneliness serves a variety of adaptive functions in specific habitats. We review evidence on the heritability of loneliness and outline an evolutionary theory of loneliness, with an emphasis on its potential adaptive value in an evolutionary timescale. PMID:24067110
Cacioppo, John T; Cacioppo, Stephanie; Boomsma, Dorret I
Robert Weiss (1973) conceptualised loneliness as perceived social isolation, which he described as a gnawing, chronic disease without redeeming features. On the scale of everyday life, it is understandable how something as personally aversive as loneliness could be regarded as a blight on human existence. However, evolutionary time and evolutionary forces operate at such a different scale of organisation than we experience in everyday life that personal experience is not sufficient to understand the role of loneliness in human existence. Research over the past decade suggests a very different view of loneliness than suggested by personal experience, one in which loneliness serves a variety of adaptive functions in specific habitats. We review evidence on the heritability of loneliness and outline an evolutionary theory of loneliness, with an emphasis on its potential adaptive value in an evolutionary timescale.
Delaney, Angela; Padmanabhan, Vasantha; Rezvani, Geoffrey; Chen, Weiping; Forcinito, Patricia; Cheung, Crystal S.F.; Baron, Jeffrey; Lui, Julian C.K.
Body size varies enormously among mammalian species. In small mammals, body growth is typically suppressed rapidly, within weeks, whereas in large mammals, growth is suppressed slowly, over years, allowing for a greater adult size. We recently reported evidence that body growth suppression in rodents is caused in part by a juvenile genetic program that occurs in multiple tissues simultaneously and involves the downregulation of a large set of growth-promoting genes. We hypothesized that this genetic program is conserved in large mammals but that its time course is evolutionarily modulated such that it plays out more slowly, allowing for more prolonged growth. Consistent with this hypothesis, using expression microarray analysis, we identified a set of genes that are downregulated with age in both juvenile sheep kidney and lung. This overlapping gene set was enriched for genes involved in cell proliferation and growth and showed striking similarity to a set of genes downregulated with age in multiple organs of the juvenile mouse and rat, indicating that the multiorgan juvenile genetic program previously described in rodents has been conserved in the 80 million years since sheep and rodents diverged in evolution. Using microarray and real-time PCR, we found that the pace of this program was most rapid in mice, more gradual in rats, and most gradual in sheep. The findings support the hypothesis that a growth-regulating genetic program is conserved among mammalian species but that its pace is modulated to allow more prolonged growth and therefore greater adult body size in larger mammals. PMID:24776848
projects (e.g., Yellowstone Intake, Montana). The Sub-Programs and projects that comprise the MRRP, as well as the congressional authorities can... Yellowstone Intake). The role of the SPgM is to ensure successful implementation of the overall program through communication of the USACE strategic...effects of the Annual Operating Plan [AOP]) in coordination with the ISP. 1.2.10 PM for Other Congressionally and WRDA Directed Work (e.g. Yellowstone
Ross, Steven M.; Rakow, Ernest A.
Subjects completed a self-paced lesson on math rules in which the number of supporting examples was adapted to pretest scores through program control, selected through learner control, or kept constant (nonadaptive). Program control means were consistently highest while learner control means were lowest. (Author/BW)
Raiche, Gilles; Blais, Jean-Guy
Monte Carlo methodologies are frequently applied to study the sampling distribution of the estimated proficiency level in adaptive testing. These methods eliminate real situational constraints. However, these Monte Carlo methodologies are not currently supported by the available software programs, and when these programs are available, their…
Foshee, Vangie A; Dixon, Kimberly S; Ennett, Susan T; Moracco, Kathryn E; Bowling, J Michael; Chang, Ling-Yin; Moss, Jennifer L
Adolescents exposed to domestic violence are at increased risk of dating abuse, yet no evaluated dating abuse prevention programs have been designed specifically for this high-risk population. This article describes the process of adapting Families for Safe Dates (FSD), an evidenced-based universal dating abuse prevention program, to this high-risk population, including conducting 12 focus groups and 107 interviews with the target audience. FSD includes six booklets of dating abuse prevention information, and activities for parents and adolescents to do together at home. We adapted FSD for mothers who were victims of domestic violence, but who no longer lived with the abuser, to do with their adolescents who had been exposed to the violence. Through the adaptation process, we learned that families liked the program structure and valued being offered the program and that some of our initial assumptions about this population were incorrect. We identified practices and beliefs of mother victims and attributes of these adolescents that might increase their risk of dating abuse that we had not previously considered. In addition, we learned that some of the content of the original program generated negative family interactions for some. The findings demonstrate the utility of using a careful process to adapt evidence-based interventions (EBIs) to cultural sub-groups, particularly the importance of obtaining feedback on the program from the target audience. Others can follow this process to adapt EBIs to groups other than the ones for which the original EBI was designed.
Jacobson, S.K.; Morris, J.K.; Sanders, J.S.; Wiley, E.N.; Brooks, M.; Bennetts, R.E.; Percival, H.F.; Marynowski, S.
The Florida Fish and Wildlife Conservation Commission manages over 650,000 ha, including 26 wildlife management and environmental areas. To improve management, they developed an objective-based vegetation management (OBVM) process that focuses on desired conditions of plant communities through an adaptive management framework. Our goals were to understand potential barriers to implementing OBVM and to recommend strategies to overcome barriers. A literature review identified 47 potential barriers in six categories to implementation of adaptive and ecosystem management: logistical, communication, attitudinal, institutional, conceptual, and educational. We explored these barriers through a bureau-wide survey of 90 staff involved in OBVM and personal interviews with area managers, scientists, and administrators. The survey incorporated an organizational culture assessment instrument to gauge how institutional factors might influence OBVM implementation. The survey response rate was 69%. Logistics and communications were the greatest barriers to implementing OBVM. Respondents perceived that the agency had inadequate resources for implementing OBVM and provided inadequate information. About one-third of the respondents believed OBVM would decrease their job flexibility and perceived greater institutional barriers to the approach. The 43% of respondents who believed they would have more responsibility under OBVM also had greater attitudinal barriers. A similar percentage of respondents reported OBVM would not give enough priority to wildlife. Staff believed that current agency culture was hierarchical but preferred a culture that would provide more flexibility for adaptive management and would foster learning from land management activities. In light of the barriers to OBVM, we recommend the following: (1) mitigation of logistical barriers by addressing real and perceived constraints of staff, funds, and other resources in a participatory manner; (2) mitigation of
Kenaley, Christopher P; Devaney, Shannon C; Fjeran, Taylor T
The vast majority of deep-sea fishes have retinas composed of only rod cells sensitive to only shortwave blue light, approximately 480-490 nm. A group of deep-sea dragonfishes, the loosejaws (family Stomiidae), possesses far-red emitting photophores and rhodopsins sensitive to long-wave emissions greater than 650 nm. In this study, the rhodopsin diversity within the Stomiidae is surveyed based on an analysis of rod opsin-coding sequences from representatives of 23 of the 28 genera. Using phylogenetic inference, fossil-calibrated estimates of divergence times, and a comparative approach scanning the stomiid phylogeny for shared genotypes and substitution histories, we explore the evolution and timing of spectral tuning in the family. Our results challenge both the monophyly of the family Stomiidae and the loosejaws. Despite paraphyly of the loosejaws, we infer for the first time that far-red visual systems have a single evolutionary origin within the family and that this shift in phenotype occurred at approximately 15.4 Ma. In addition, we found strong evidence that at approximately 11.2 Ma the most recent common ancestor of two dragonfish genera reverted to a primitive shortwave visual system during its evolution from a far-red sensitive dragonfish. According to branch-site tests for adaptive evolution, we hypothesize that positive selection may be driving spectral tuning in the Stomiidae. These results indicate that the evolutionary history of visual systems in deep-sea species is complex and a more thorough understanding of this system requires an integrative comparative approach.
Mumme, Ronald L; Galatowitsch, Mark L; Jabłoński, Piotr G; Stawarczyk, Tadeusz M; Cygan, Jakub P
two hypotheses for geographic variation in plumage pattern: (1) that geographic variation is a nonadaptive result of genetic drift, and (2) that selection for enhanced flush-pursuit foraging performance generally favors increased white in the plumage, but evolutionary trade-offs constrain the evolution of extensive patches of white in some geographic regions. Instead, our results suggest that geographic variation in the plumage pattern of Myioborus redstarts reflects adaptation to regional habitat characteristics that enhances flush-pursuit foraging performance.
Steed, Elizabeth A.
Behavior Education Program (BEP) is the most researched targeted intervention that is used in schoolwide positive behavior intervention and supports (PBIS). It is a daily check-in and check-out system in which students receive extra attention for positive social behavior throughout their school day. This extra attention is intended to prevent…
Technical Report 359 January 1991 Abstract Parallel programming involves finding the potential parallelism in an application, choos - ing an...during the development of this paper. 34 References [Albert et ai, 1988] Eugene Albert, Kathleen Knobe, Joan D. Lukas, and Guy L. Steele, Jr
Luo, Yan; Guo, Zhenhua; Li, Lu
MicroRNAs (miRNAs) are post-transcriptional regulators of growth and development in both plants and animals. Flowering is critical for the reproduction of angiosperms. Flower development entails the transition from vegetative growth to reproductive growth, floral organ initiation, and the development of floral organs. These developmental processes are genetically regulated by miRNAs, which participate in complex genetic networks of flower development. A survey of the literature shows that miRNAs, their specific targets, and the regulatory programs in which they participate are conserved throughout the plant kingdom. This review summarizes the role of miRNAs and their targets in the regulation of gene expression during the floral developmental phase, which includes the floral transition stage, followed by floral patterning, and then the development of floral organs. The conservation patterns observed in each component of the miRNA regulatory system suggest that these miRNAs play important roles in the evolution of flower development.
Nosek, Jozef; Tomaska, Lubomir; Burger, Gertraud; Lang, B Franz
Programmed translational bypassing enables ribosomes to 'ignore' a precise mRNA interval of several dozen nucleotides. Well-characterized bypassed sequences include hop and byp elements, present in bacteriophage T4 and mitochondria of the yeast Magnusiomyces capitatus, respectively. The bypassing mechanism of byps is probably similar to that of hop, yet the former appears more effective and less constrained as to sequence context. Furthermore, both elements are mobile but hop moves as part of a cassette including a homing endonuclease, whereas byps seem to spread like miniature DNA transposable elements known as GC clusters. Here, we argue that hop and byps arose independently by convergent evolution, and that byps evolved in magnusiomycete mitochondria due to (as yet unknown) alterations of the mitochondrial translation machinery.
determine which provided the most useful data and provided a set of final materials to AWG based on these results. A third objective was to provide... materials suitable not only for evaluating AWALP but also for evaluating other courses or events that include adaptability training or training that...adaptability train- ing, we recommend that AWG create a training support package for AWALP with a program of instruction and supplementary materials
Cheung, Ying Kuen; Chakraborty, Bibhas; Davidson, Karina W
Implementation study is an important tool for deploying state-of-the-art treatments from clinical efficacy studies into a treatment program, with the dual goals of learning about effectiveness of the treatments and improving the quality of care for patients enrolled into the program. In this article, we deal with the design of a treatment program of dynamic treatment regimens (DTRs) for patients with depression post-acute coronary syndrome. We introduce a novel adaptive randomization scheme for a sequential multiple assignment randomized trial of DTRs. Our approach adapts the randomization probabilities to favor treatment sequences having comparatively superior Q-functions used in Q-learning. The proposed approach addresses three main concerns of an implementation study: it allows incorporation of historical data or opinions, it includes randomization for learning purposes, and it aims to improve care via adaptation throughout the program. We demonstrate how to apply our method to design a depression treatment program using data from a previous study. By simulation, we illustrate that the inputs from historical data are important for the program performance measured by the expected outcomes of the enrollees, but also show that the adaptive randomization scheme is able to compensate poorly specified historical inputs by improving patient outcomes within a reasonable horizon. The simulation results also confirm that the proposed design allows efficient learning of the treatments by alleviating the curse of dimensionality.
Bishop, Dana C; Pankratz, Melinda M; Hansen, William B; Albritton, Jordan; Albritton, Lauren; Strack, Joann
There is a need to standardize methods for assessing fidelity and adaptation. Such standardization would allow program implementation to be examined in a manner that will be useful for understanding the moderating role of fidelity in dissemination research. This article describes a method for collecting data about fidelity of implementation for school-based prevention programs, including measures of adherence, quality of delivery, dosage, participant engagement, and adaptation. We report about the reliability of these methods when applied by four observers who coded video recordings of teachers delivering All Stars, a middle school drug prevention program. Interrater agreement for scaled items was assessed for an instrument designed to evaluate program fidelity. Results indicated sound interrater reliability for items assessing adherence, dosage, quality of teaching, teacher understanding of concepts, and program adaptations. The interrater reliability for items assessing potential program effectiveness, classroom management, achievement of activity objectives, and adaptation valences was improved by dichotomizing the response options for these items. The item that assessed student engagement demonstrated only modest interrater reliability and was not improved through dichotomization. Several coder pairs were discordant on items that overall demonstrated good interrater reliability. Proposed modifications to the coding manual and protocol are discussed.
This manual is intended as a guide and source of ideas for using single switches in adaptive software programming for people with disabilities who cannot use a traditional keyboard. The manual and associated program disk are comprised of over 100 programs, routines and files illustrating various uses of single switch and adaptive input devices.…
Warschefsky, Emily; Penmetsa, R Varma; Cook, Douglas R; von Wettberg, Eric J B
The genetic diversity of our crop plants has been substantially reduced during the process of domestication and breeding. This reduction in diversity necessarily constrains our ability to expand a crop's range of cultivation into environments that are more extreme than those in which it was domesticated, including into "sustainable" agricultural systems with reduced inputs of pesticides, water, and fertilizers. Conversely, the wild progenitors of crop plants typically possess high levels of genetic diversity, which underlie an expanded (relative to domesticates) range of adaptive traits that may be of agricultural relevance, including resistance to pests and pathogens, tolerance to abiotic extremes, and reduced dependence on inputs. Despite their clear potential for crop improvement, wild relatives have rarely been used systematically for crop improvement, and in no cases, have full sets of wild diversity been introgressed into a crop. Instead, most breeding efforts have focused on specific traits and dealt with wild species in a limited and typically ad hoc manner. Although expedient, this approach misses the opportunity to test a large suite of traits and deploy the full potential of crop wild relatives in breeding for the looming challenges of the 21st century. Here we review examples of hybridization in several species, both intentionally produced and naturally occurring, to illustrate the gains that are possible. We start with naturally occurring hybrids, and then examine a range of examples of hybridization in agricultural settings.
Axton, Jacob H.; McCullough, John M.; Harris, Nathan
ABSTRACT Objectives The C282Y allele is the major cause of hemochromatosis as a result of excessive iron absorption. The mutation arose in continental Europe no earlier than 6,000 years ago, coinciding with the arrival of the Neolithic agricultural revolution. Here we hypothesize that this new Neolithic diet, which originated in the sunny warm and dry climates of the Middle East, was carried by migrating farmers into the chilly and damp environments of Europe where iron is a critical micronutrient for effective thermoregulation. We argue that the C282Y allele was an adaptation to this novel environment. Materials and Methods To address our hypothesis, we compiled C282Y allele frequencies, known Neolithic sites in Europe and climatic data on temperature and rainfall for statistical analysis. Results Our findings indicate that the geographic cline for C282Y frequency in Europe increases as average temperatures decrease below 16°C, a critical threshold for thermoregulation, with rainy days intensifying the trend. Discussion The results indicate that the deleterious C282Y allele, responsible for most cases of hemochromatosis, may have evolved as a selective advantage to culture and climate during the European Neolithic. Am J Phys Anthropol 160:86–101, 2016. © 2016 The Authors American Journal of Physical Anthropology Published by Wiley Periodicals, Inc. PMID:26799452
Hammerschmidt, Katrin; Kurtz, Joachim
Many diseases are caused by parasites with complex life cycles that involve several hosts. If parasites cope better with only one of the different types of immune systems of their host species, we might expect a trade-off in parasite performance in the different hosts, that likely influences the evolution of virulence. We tested this hypothesis in a naturally co-evolving host-parasite system consisting of the tapeworm Schistocephalus solidus and its intermediate hosts, a copepod, Macrocyclops albidus, and the three-spined stickleback Gasterosteus aculeatus. We did not find a trade-off between infection success in the two hosts. Rather, tapeworms seem to trade-off adaptation towards different parts of their hosts' immune systems. Worm sibships that performed better in the invertebrate host also seem to be able to evade detection by the fish innate defence systems, i.e. induce lower levels of activation of innate immune components. These worm variants were less harmful for the fish host likely due to reduced costs of an activated innate immune system. These findings substantiate the impact of both hosts' immune systems on parasite performance and virulence.
Hammerschmidt, Katrin; Kurtz, Joachim
Many diseases are caused by parasites with complex life cycles that involve several hosts. If parasites cope better with only one of the different types of immune systems of their host species, we might expect a trade-off in parasite performance in the different hosts, that likely influences the evolution of virulence. We tested this hypothesis in a naturally co-evolving host–parasite system consisting of the tapeworm Schistocephalus solidus and its intermediate hosts, a copepod, Macrocyclops albidus, and the three-spined stickleback Gasterosteus aculeatus. We did not find a trade-off between infection success in the two hosts. Rather, tapeworms seem to trade-off adaptation towards different parts of their hosts' immune systems. Worm sibships that performed better in the invertebrate host also seem to be able to evade detection by the fish innate defence systems, i.e. induce lower levels of activation of innate immune components. These worm variants were less harmful for the fish host likely due to reduced costs of an activated innate immune system. These findings substantiate the impact of both hosts' immune systems on parasite performance and virulence. PMID:16271977
dos Santos, Karina Tonini; Saliba, Nemre Adas; Moimaz, Suzely Adas Saliba; Arcieri, Renato Moreira; Carvalho, Maria de Lourdes
This study analyses the status and work reality of Community Health Agents, with the purpose of contributing to the improvement of the Brazilian Health System (SUS) in small cities. It was discussed aspects related to their participation in the team of the Family Health Program (PSF) and their interaction with the community. It was observed a lack of motivation and experience, which compromises the quality of Agents performance in the community. It is known that these findings are reflex and consequence of an established context. It is necessary the team rethink their practice, specially the managers, having always as a fundament the principles that guide the SUS and PSF.
Wang, Sue-Jane; Hung, H M James; O'Neill, Robert
A clinical research program for drug development often consists of a sequence of clinical trials that may begin with uncontrolled and nonrandomized trials, followed by randomized trials or randomized controlled trials. Adaptive designs are not infrequently proposed for use. In the regulatory setting, the success of a drug development program can be defined to be that the experimental treatment at a specific dose level including regimen and frequency is approved based on replicated evidence from at least two confirmatory trials. In the early stage of clinical research, multiplicity issues are very broad. What is the maximum tolerable dose in an adaptive dose escalation trial? What should the dose range be to consider in an adaptive dose-ranging trial? What is the minimum effective dose in an adaptive dose-response study given the tolerability and the toxicity observable in short term or premarketing trials? Is establishing the dose-response relationship important or the ability to select a superior treatment with high probability more important? In the later stage of clinical research, multiplicity problems can be formulated with better focus, depending on whether the study is for exploration to estimate or select design elements or for labeling consideration. What is the study objective for an early-phase versus a later phase adaptive clinical trial? How many doses are to be studied in the early exploratory adaptive trial versus in the confirmatory adaptive trial? Is the intended patient population well defined or is the applicable patient population yet to be adaptively selected in the trial due to the potential patient and/or disease heterogeneity? Is the primary efficacy endpoint well defined or still under discussion providing room for adaptation? What are the potential treatment indications that may adaptively lead to an intended-to-treat patient population and the primary efficacy endpoint? In this work we stipulate the multiplicity issues with adaptive
Chisholm, Rebecca H; Lorenzi, Tommaso; Lorz, Alexander; Larsen, Annette K; de Almeida, Luís Neves; Escargueil, Alexandre; Clairambault, Jean
In recent experiments on isogenetic cancer cell lines, it was observed that exposure to high doses of anticancer drugs can induce the emergence of a subpopulation of weakly proliferative and drug-tolerant cells, which display markers associated with stem cell-like cancer cells. After a period of time, some of the surviving cells were observed to change their phenotype to resume normal proliferation and eventually repopulate the sample. Furthermore, the drug-tolerant cells could be drug resensitized following drug washout. Here, we propose a theoretical mechanism for the transient emergence of such drug tolerance. In this framework, we formulate an individual-based model and an integro-differential equation model of reversible phenotypic evolution in a cell population exposed to cytotoxic drugs. The outcomes of both models suggest that nongenetic instability, stress-induced adaptation, selection, and the interplay between these mechanisms can push an actively proliferating cell population to transition into a weakly proliferative and drug-tolerant state. Hence, the cell population experiences much less stress in the presence of the drugs and, in the long run, reacquires a proliferative phenotype, due to phenotypic fluctuations and selection pressure. These mechanisms can also reverse epigenetic drug tolerance following drug washout. Our study highlights how the transient appearance of the weakly proliferative and drug-tolerant cells is related to the use of high-dose therapy. Furthermore, we show how stem-like characteristics can act to stabilize the transient, weakly proliferative, and drug-tolerant subpopulation for a longer time window. Finally, using our models as in silico laboratories, we propose new testable hypotheses that could help uncover general principles underlying the emergence of cancer drug tolerance.
Van Doorslaer, Koenraad; DeSalle, Rob; Einstein, Mark H; Burk, Robert D
In order to complete their life cycle, papillomaviruses have evolved to manipulate a plethora of cellular pathways. The products of the human Alphapapillomavirus E6 proteins specifically interact with and target PDZ containing proteins for degradation. This viral phenotype has been suggested to play a role in viral oncogenesis. To analyze the association of HPV E6 mediated PDZ-protein degradation with cervical oncogenesis, a high-throughput cell culture assay was developed. Degradation of an epitope tagged human MAGI1 isoform was visualized by immunoblot. The correlation between HPV E6-induced degradation of hMAGI1 and epidemiologically determined HPV oncogenicity was evaluated using a Bayesian approach within a phylogenetic context. All tested oncogenic types degraded the PDZ-containing protein hMAGI1d; however, E6 proteins isolated from several related albeit non-oncogenic viral types were equally efficient at degrading hMAGI1. The relationship between both traits (oncogenicity and PDZ degradation potential) is best explained by a model in which the potential to degrade PDZ proteins was acquired prior to the oncogenic phenotype. This analysis provides evidence that the ancestor of both oncogenic and non-oncogenic HPVs acquired the potential to degrade human PDZ-containing proteins. This suggests that HPV E6 directed degradation of PDZ-proteins represents an ancient ecological niche adaptation. Phylogenetic modeling indicates that this phenotype is not specifically correlated with oncogenic risk, but may act as an enabling phenotype. The role of PDZ protein degradation in HPV fitness and oncogenesis needs to be interpreted in the context of Alphapapillomavirus evolution.
Sørensen, Iben; Rose, Jocelyn K C; Doyle, Jeff J; Domozych, David S; Willats, William G T
The Charophycean green algae (CGA) occupy a key phylogenetic position as the evolutionary grade that includes the sister group of the land plants (embryophytes), and so provide potentially valuable experimental systems to study the development and evolution of traits that were necessary for terrestrial colonization. The nature and molecular bases of such traits are still being determined, but one critical adaptation is thought to have been the evolution of a complex cell wall. Very little is known about the identity, origins and diversity of the biosynthetic machinery producing the major suites of structural polymers (i. e., cell wall polysaccharides and associated molecules) that must have been in place for land colonization. However, it has been suggested that the success of the earliest land plants was partly based on the frequency of gene duplication, and possibly whole genome duplications, during times of radical habitat changes. Orders of the CGA span early diverging taxa retaining more ancestral characters, through complex multicellular organisms with morphological characteristics resembling those of land plants. Examination of gene diversity and evolution within the CGA could help reveal when and how the molecular pathways required for synthesis of key structural polymers in land plants arose.
Hayward, Matt W; Hayward, Gina J; Tambling, Craig J; Kerley, Graham I H
Research on coursing predators has revealed that actions throughout the predatory behavioral sequence (using encounter rate, hunting rate, and kill rate as proxy measures of decisions) drive observed prey preferences. We tested whether similar actions drive the observed prey preferences of a stalking predator, the African lion Panthera leo. We conducted two 96 hour, continuous follows of lions in Addo Elephant National Park seasonally from December 2003 until November 2005 (16 follows), and compared prey encounter rate with prey abundance, hunt rate with prey encounter rate, and kill rate with prey hunt rate for the major prey species in Addo using Jacobs' electivity index. We found that lions encountered preferred prey species far more frequently than expected based on their abundance, and they hunted these species more frequently than expected based on this higher encounter rate. Lions responded variably to non-preferred and avoided prey species throughout the predatory sequence, although they hunted avoided prey far less frequently than expected based on the number of encounters of them. We conclude that actions of lions throughout the predatory behavioural sequence, but particularly early on, drive the prey preferences that have been documented for this species. Once a hunt is initiated, evolutionary adaptations to the predator-prey interactions drive hunting success.
Caron, Rosemary M; Tutko, Holly
In the last several years, the number of Master of Public Health (MPH) programs has increased rapidly in the US. As such, MPH programs, particularly smaller-sized ones, need to critically examine how their programs are meeting the needs and preferences of local public health practitioners. To assist in this necessity, the University of New Hampshire conducted a comprehensive educational assessment of its effectiveness as a smaller-sized, accredited MPH program. The aim of the assessment was to review the MPH program from the perspective of all stakeholders and then to agree on changes that would contribute to the fulfillment of the program's mission, as well as improve program quality and reach. The program's stakeholders examined the following components: policy development and implementation; target audience; marketing strategies; marketplace position; delivery model; curriculum design; and continuing education. Though assessment activities explored a wide array of program attributes, target audience, curriculum design, and delivery strategy presented significant challenges and opportunities for our smaller MPH Program to remain competitive. The effort put forth into conducting an in-depth assessment of the core components of our program also allowed for a comparison to the increasing number of MPH programs developing regionally. Since public health practice is changing and the education of public health practitioners must be adaptable, we propose that a routine assessment of an institution's MPH program could not only meet this need but also assist with keeping smaller, unbranded MPH programs competitive in a burgeoning marketplace.
Fogel, David B.
Evolutionary computation is becoming a common technique for solving difficult, real-world problems in industry, medicine, and defense. This paper reviews some of the practical advantages to using evolutionary algorithms as compared with classic methods of optimization or artificial intelligence. Specific advantages include the flexibility of the procedures, as well as their ability to self-adapt the search for optimum solutions on the fly. As desktop computers increase in speed, the application of evolutionary algorithms will become routine.
Andersen, Øivind; Johnsen, Hanne; De Rosa, Maria Cristina; Præbel, Kim; Stjelja, Suzana; Kirubakaran, Tina Graceline; Pirolli, Davide; Jentoft, Sissel; Fevolden, Svein-Erik
The synaptophysin (SYP) family comprises integral membrane proteins involved in vesicle-trafficking events, but the physiological function of several members has been enigmatic for decades. The presynaptic SYP protein controls neurotransmitter release, while SYP-like 2 (SYPL2) contributes to maintain normal Ca(2+)-signaling in the skeletal muscles. The polymorphic pantophysin (Pan I) of Atlantic cod shows strong genetic divergence between stationary and migratory populations, which seem to be adapted to local environmental conditions. We have investigated the functional involvement of Pan I in the different ecotypes by analyzing the 1) phylogeny, 2) spatio-temporal gene expression, 3) structure-function relationship of the Pan I(A) and I(B) protein variants, and 4) linkage to rhodopsin (rho) recently proposed to be associated with different light sensitivities in Icelandic populations of Atlantic cod. We searched for SYP family genes in phylogenetic key species and identified a single syp-related gene in three invertebrate chordates, while four members, Syp, Sypl1, Sypl2 and synaptoporin (Synpr), were found in tetrapods, Comoran coelacanth and spotted gar. Teleost fish were shown to possess duplicated syp, sypl2 and synpr genes of which the sypl2b paralog is identical to Pan I. The ubiquitously expressed cod Pan I codes for a tetra-spanning membrane protein possessing five amino acid substitutions in the first intravesicular loop, but only minor structural differences were shown between the allelic variants. Despite sizable genomic distance (>2.5 Mb) between Pan I and rho, highly significant linkage disequilibrium was found by genotyping shallow and deep water juvenile settlers predominated by the Pan I(A)-rho(A) and Pan I(B)-rho(B) haplotypes, respectively. However, the predicted rhodopsin protein showed no amino acid changes, while multiple polymorphic sites in the upstream region might affect the gene expression and pigment levels in stationary and migratory cod
Chiang, Y.; Chiang, W.; Sui, C.; Tung, C.; Ho, H.; Li, M.; Chan, S.; Climate Change Adaptation Technologies Program, National Science Council, Taiwan
Climate changes adaptation needs innovative technological revolution on demand for transdisciplinary studies in various temporal and spatial scales. In our proposed program, a systematic and scientific framework will be developed to promote innovative adaptation technologies with respect to providing decision making information for government sectors, enhancing applicability of scientific research output, strengthening national research capabilities, and integrating both academic and non-academic resources. The objectives of this program are to identify key issues, required technologies, and scientific knowledge for climate change adaptations, and to build a transdisciplinary platform bridging science-supported technologies required by government sectors and demand-oriented scientific research conducted by academic communities. The approach proposed herein will be practiced in vulnerable regions, such as urban, rural, mountain, river basin, and coastal areas, which are particularly sensitive to climate change. The first phase of 3-year (2011~2013) work is to deploy framework and strategies of climate change impact assessment and adaptation measures between related government sectors and researchers from academic communities. The proposed framework involves three principle research groups, namely Environmental System, Vulnerability Assessment, and Risk Management and Adaptation Technology. The goal of the first group, Environmental System, is to combine climate change projections with enhanced scientific and environmental monitoring technologies for better adaptations to future scenarios in different social, economic, and environmental sectors to support adaptation measures planning and to reduce uncertainties on assessing vulnerability. The goal of the second group, Vulnerability Assessment, is to identify interfaces and information structures of climate change vulnerably issues and to develop protocol, models, and indices for vulnerability assessment. The goal of
Schlaepfer, Martin A.; Runge, M.C.; Sherman, P.W.
Organisms often rely on environmental cues to make behavioral and life-history decisions. However, in environments that have been altered suddenly by humans, formerly reliable cues might no longer be associated with adaptive outcomes. In such cases, organisms can become 'trapped' by their evolutionary responses to the cues and experience reduced survival or reproduction. Ecological traps occur when organisms make poor habitat choices based on cues that correlated formerly with habitat quality. Ecological traps are part of a broader phenomenon, evolutionary traps, involving a dissociation between cues that organisms use to make any behavioral or life-history decision and outcomes normally associated with that decision. A trap can lead to extinction if a population falls below a critical size threshold before adaptation to the novel environment occurs. Conservation and management protocols must be designed in light of, rather than in spite of, the behavioral mechanisms and evolutionary history of populations and species to avoid 'trapping' them.
Bopp, Melissa; Saunders, Ruth P; Lattimore, Diana
Researchers across multiple fields have described the iterative and nonlinear phases of the translational research process from program development to dissemination. This process can be conceptualized within a "program life cycle" framework that includes overlapping and nonlinear phases: development, adoption, implementation, maintenance, sustainability or termination, and dissemination or diffusion, characterized by tensions between fidelity to the original plan and adaptation for the setting and population. In this article, we describe the life cycle (phases) for research-based health promotion programs, the key influences at each phase, and the issues related to the tug-of-war between fidelity and adaptation throughout the process using a fictionalized case study based on our previous research. This article suggests the importance of reconceptualizing intervention design, involving stakeholders, and monitoring fidelity and adaptation throughout all phases to maintain implementation fidelity and completeness. Intervention fidelity should be based on causal mechanisms to ensure effectiveness, while allowing for appropriate adaption to ensure maximum implementation and sustainability. Recommendations for future interventions include considering the determinants of implementation including contextual factors at each phase, the roles of stakeholders, and the importance of developing a rigorous, adaptive, and flexible definition of implementation fidelity and completeness.
Geary, David C.; Bjorklund, David F.
Describes evolutionary developmental psychology as the study of the genetic and ecological mechanisms that govern the development of social and cognitive competencies common to all human beings and the epigenetic (gene-environment interactions) processes that adapt these competencies to local conditions. Outlines basic assumptions and domains of…
Describes an interactive computer program which can be used by students to construct adaptive landscapes of two types as an illustration of the expected effects of selection. Simulates effects of selection on populations of this type and changes of gene frequency can be plotted on the same contour map. (Author/MA)
Groff, Diane G.; Kleiber, Douglas A.
Investigated the relationship between involvement in an after-school adapted sports program and identity formation among adolescents with physical disabilities. Participant interviews indicated that participation provided most adolescents with a heightened sense of competence and opportunities to express their true selves. It also led to decreased…
Ryan, Joseph B.; Katsiyannis, Antonis; Cadorette, Deborah; Hodge, Janie; Markham, Michelle
Children with disabilities are at increased risk of health risk factors including obesity, often because of low levels of physical activity and limited participation in sports. However, organized adaptive sports programs are increasingly available for individuals with disabilities. This article provides recommendations for establishing successful…
Zakirova, Venera G.; Gaysina, Guzel I.; Zhumabaeva, Asia
Relevance of the problem stated in the article, conditioned by the fact that the successful adaptation of orphans in a foster family requires specialized knowledge and skills, as well as the need of professional support. Therefore, this article aims at substantiation of the effectiveness of the developed pilot program psycho-pedagogical support of…
Scholl, Mark B.; Cascone, Jason
The authors present the constructivist resume, an original approach developed to promote professional identity development and career adaptability (i.e., concern, curiosity, confidence, and control) in students completing graduate-level counselor training programs. The authors discuss underlying theories, including Super's (1990; Super, Savickas,…
In response to the impact of information and communication technology on traditional business and commerce practices, and the empowerment of individuals by the growth of information available on the Internet, educators are challenged to adapt the curricula and delivery modes of educational programs for knowledge workers, such as tax accountants.…
KANTER, EARL F.; BENDER, RALPH E.
THE PURPOSE OF THIS NATIONAL STUDY WAS TO SUGGEST WAYS OF ADAPTING THE FUTURE FARMERS OF AMERICA (FFA) TO A CHANGING PROGRAM OF VOCATIONAL AGRICULTURE THROUGH IDENTIFYING NEW PURPOSES OF THE FFA AND EVALUATING SELECTED OPERATIONAL GUIDELINES AND NATIONAL AND STATE FFA ACTIVITIES. MEMBERS OF THE UNITED STATES OFFICE OF EDUCATION, HEAD STATE…
Ergül, Cevriye; Akoglu, Gözde; Sarica, Ayse D.; Karaman, Gökçe; Tufan, Mümin; Bahap-Kudret, Zeynep; Zülfikar, Deniz
The study aimed to examine the effectiveness of the Adapted Dialogic Reading Program (ADR) on the language and early literacy skills of Turkish kindergarteners from low socio-economic (SES) backgrounds. The effectiveness of ADR was investigated across six different treatment conditions including classroom and home based implementations in various…
Nath, Sankar Kumar; Chakraborty, Subrata; Singh, Sanjiv Kumar; Ganguly, Nilanjan
The disadvantages of conventional seismic tomographic ray tracing and inversion by calculus-based techniques include the assumption of a single ray path for each source-receiver pair, the non-inclusion of head waves, long computation times, and the difficulty in finding ray paths in a complicated velocity distribution. A ray-tracing algorithm is therefore developed using the reciprocity principle and dynamic programming approach. This robust forward calculation routine is subsequently used for the cross-hole seismic velocity inversion. Seismic transmission tomography can be considered to be a function approximation problem; that is, of mapping the traveltime vector to the velocity vector. This falls under the purview of pattern classification problems, so we propose a forward-only counter-propagation neural network (CPNN) technique for the tomographic imaging of the subsurface. The limitation of neural networks, however, lies in the requirement of exhaustive training for its use in routine interpretation. Since finding the optimal solution, sometimes from poor initial models, is the ultimate goal, global optimization and search techniques such as simulated evolution are also implemented in the cross-well traveltime tomography. Genetic algorithms (GA), evolution strategies and evolutionary programming (EP) are the main avenues of research in simulated evolution. Part of this investigation therefore deals with GA and EP schemes for tomographic applications. In the present work on simulated evolution, a new genetic operator called `region-growing mutation' is introduced to speed up the search process. The potential of the forward-only CPNN, GA and EP methods is demonstrated in three synthetic examples. Velocity tomograms of the first model present plausible images of a diagonally orientated velocity contrast bounding two constant-velocity areas by both the CPNN and GA schemes, but the EP scheme could not image the model completely. In the second case, while GA and EP
Baroth, Edmund C.; Clark, Douglas J.; Losey, Robert W.
An example of the implementation of data fusion using a PC and a graphical programming language is discussed. A schematic of the data acquisition system and user interface panel for an adaptive structure test are presented. The computer programs (a series of icons 'wired' together) are also discussed. The way in which using graphical-based programming software to control a data acquisition system can simplify analysis of data, promote multidisciplinary interaction, and provide users a more visual key to understanding their data are shown.
Shan, Hongzhang; Singh, Jaswinder Pal; Oliker, Leonid; Biswas, Rupak
Adaptive applications have computational workloads and communication patterns which change unpredictably at runtime, requiring dynamic load balancing to achieve scalable performance on parallel machines. Efficient parallel implementations of such adaptive applications is therefore a challenging task. In this paper, we compare the performance of and the programming effort required for two major classes of adaptive applications under three leading parallel programming models on an SGI Origin2000 system, a machine which supports all three models efficiently. Results indicate that the three models deliver comparable performance; however, the implementations differ significantly beyond merely using explicit messages versus implicit loads/stores even though the basic parallel algorithms are similar. Compared with the message-passing (using MPI) and SHMEM programming models, the cache-coherent shared address space (CC-SAS) model provides substantial ease of programming at both the conceptual and program orchestration levels, often accompanied by performance gains. However, CC-SAS currently has portability limitations and may suffer from poor spatial locality of physically distributed shared data on large numbers of processors.
Chai, Runqi; Savvaris, Al; Tsourdos, Antonios
In this paper, a fuzzy physical programming (FPP) method has been introduced for solving multi-objective Space Manoeuvre Vehicles (SMV) skip trajectory optimization problem based on hp-adaptive pseudospectral methods. The dynamic model of SMV is elaborated and then, by employing hp-adaptive pseudospectral methods, the problem has been transformed to nonlinear programming (NLP) problem. According to the mission requirements, the solutions were calculated for each single-objective scenario. To get a compromised solution for each target, the fuzzy physical programming (FPP) model is proposed. The preference function is established with considering the fuzzy factor of the system such that a proper compromised trajectory can be acquired. In addition, the NSGA-II is tested to obtain the Pareto-optimal solution set and verify the Pareto optimality of the FPP solution. Simulation results indicate that the proposed method is effective and feasible in terms of dealing with the multi-objective skip trajectory optimization for the SMV.
Paes, Hugo Costa; Albuquerque, Patrícia; Tavares, Aldo Henrique F. P.; Fernandes, Larissa; Silva-Pereira, Ildinete; Casadevall, Arturo
Virulence of Cryptococcus neoformans for mammals, and in particular its intracellular style, was proposed to emerge from evolutionary pressures on its natural environment by protozoan predation, which promoted the selection of strategies that allow intracellular survival in macrophages. In fact, Acanthamoeba castellanii ingests yeast cells, which then can replicate intracellularly. In addition, most fungal factors needed to establish infection in the mammalian host are also important for survival within the amoeba. To better understand the origin of C. neoformans virulence, we compared the transcriptional profile of yeast cells internalized by amoebae and murine macrophages after 6 h of infection. Our results showed 656 and 293 genes whose expression changed at least 2-fold in response to the intracellular environments of amoebae and macrophages, respectively. Among the genes that were found in both groups, we focused on open reading frame (ORF) CNAG_05662, which was potentially related to sugar transport but had no determined biological function. To characterize its function, we constructed a mutant strain and evaluated its ability to grow on various carbon sources. The results showed that this gene, named PTP1 (polyol transporter protein 1), is involved in the transport of 5- and 6-carbon polyols such as mannitol and sorbitol, but its presence or absence had no effect on cryptococcal virulence for mice or moth larvae. Overall, these results are consistent with the hypothesis that the capacity for mammalian virulence originated from fungus-protozoan interactions in the environment and provide a better understanding of how C. neoformans adapts to the mammalian host. PMID:23524994
Cheviron, Zachary A.; Natarajan, Chandrasekhar; Projecto-Garcia, Joana; Eddy, Douglas K.; Jones, Jennifer; Carling, Matthew D.; Witt, Christopher C.; Moriyama, Hideaki; Weber, Roy E.; Fago, Angela; Storz, Jay F.
In air-breathing vertebrates, the physiologically optimal blood-O2 affinity is jointly determined by the prevailing partial pressure of atmospheric O2, the efficacy of pulmonary O2 transfer, and internal metabolic demands. Consequently, genetic variation in the oxygenation properties of hemoglobin (Hb) may be subject to spatially varying selection in species with broad elevational distributions. Here we report the results of a combined functional and evolutionary analysis of Hb polymorphism in the rufous-collared sparrow (Zonotrichia capensis), a species that is continuously distributed across a steep elevational gradient on the Pacific slope of the Peruvian Andes. We integrated a population genomic analysis that included all postnatally expressed Hb genes with functional studies of naturally occurring Hb variants, as well as recombinant Hb (rHb) mutants that were engineered through site-directed mutagenesis. We identified three clinally varying amino acid polymorphisms: Two in the αA-globin gene, which encodes the α-chain subunits of the major HbA isoform, and one in the αD-globin gene, which encodes the α-chain subunits of the minor HbD isoform. We then constructed and experimentally tested single- and double-mutant rHbs representing each of the alternative αA-globin genotypes that predominate at different elevations. Although the locus-specific patterns of altitudinal differentiation suggested a history of spatially varying selection acting on Hb polymorphism, the experimental tests demonstrated that the observed amino acid mutations have no discernible effect on respiratory properties of the HbA or HbD isoforms. These results highlight the importance of experimentally validating the hypothesized effects of genetic changes in protein function to avoid the pitfalls of adaptive storytelling. PMID:25135942
Barkan, Susan E.; Salazar, Amy M.; Estep, Kara; Mattos, Leah M.; Eichenlaub, Caroline; Haggerty, Kevin P.
The scarcity of caregivers and the unique vulnerability of teens involved with the child welfare system necessitate effective strategies for ensuring that caregivers are prepared and supported in the important role they play with children and youth within the child welfare system. They are in a position, through the establishment of a strong, positive, supportive connection with the youth, to potentially minimize the impacts of recent trauma and interrupt a negative trajectory by preventing the youth’s initiation of high-risk behavior. In this paper we describe the process used to systematically adapt Staying Connected with Your Teen™, an evidence-based, prevention-focused parenting program found in other studies to reduce the initiation of teens‘ risky behaviors, for use with foster teens and their relative or foster caregivers. This work has been guided by the ADAPT-ITT framework developed by Wingood and DiClemente (2008) for adapting evidence-based interventions. Qualitative work conducted in Phase 1 of this study identified the need for the development of a trusted connection between foster youth and their caregivers, as well as tools for helping them access community resources, social services, and educational supports. This paper describes the process used to develop new and adapted program activities in response to the needs identified in Phase 1. We conducted a theater test with dyads of foster youth and their caregivers to get feedback on the new activities. Findings from the theater test are provided and next steps in the research are discussed which include examining program usability, fidelity, feasibility, and testing this new prevention program that has been tailored for child welfare involved youth and their caregivers. This intervention program has the potential to fill an important gap in the availability of preventive programming for caregivers of teens in foster care. PMID:26052172
Bargatze, L. F.
Active Data Archive Product Tracking (ADAPT) is a collection of software routines that permits one to generate XML metadata files to describe and register data products in support of the NASA Heliophysics Virtual Observatory VxO effort. ADAPT is also a philosophy. The ADAPT concept is to use any and all available metadata associated with scientific data to produce XML metadata descriptions in a consistent, uniform, and organized fashion to provide blanket access to the full complement of data stored on a targeted data server. In this poster, we present an application of ADAPT to describe all of the data products that are stored by using the Common Data File (CDF) format served out by the CDAWEB and SPDF data servers hosted at the NASA Goddard Space Flight Center. These data servers are the primary repositories for NASA Heliophysics data. For this purpose, the ADAPT routines have been used to generate data resource descriptions by using an XML schema named Space Physics Archive, Search, and Extract (SPASE). SPASE is the designated standard for documenting Heliophysics data products, as adopted by the Heliophysics Data and Model Consortium. The set of SPASE XML resource descriptions produced by ADAPT includes high-level descriptions of numerical data products, display data products, or catalogs and also includes low-level "Granule" descriptions. A SPASE Granule is effectively a universal access metadata resource; a Granule associates an individual data file (e.g. a CDF file) with a "parent" high-level data resource description, assigns a resource identifier to the file, and lists the corresponding assess URL(s). The CDAWEB and SPDF file systems were queried to provide the input required by the ADAPT software to create an initial set of SPASE metadata resource descriptions. Then, the CDAWEB and SPDF data repositories were queried subsequently on a nightly basis and the CDF file lists were checked for any changes such as the occurrence of new, modified, or deleted
Marlowe, Douglas B.; Festinger, David S.; Dugosh, Karen L.; Benasutti, Kathleen M.; Fox, Gloria; Harron, Ashley
Objectives Test whether an adaptive program improves outcomes in drug court by adjusting the schedule of court hearings and clinical case-management sessions pursuant to a priori performance criteria. Methods Consenting participants in a misdemeanor drug court were randomly assigned to the adaptive program (n = 62) or to a baseline-matching condition (n = 63) in which they attended court hearings based on the results of a criminal risk assessment. Outcome measures were re-arrest rates at 18 months post-entry to the drug court and urine drug test results and structured interview results at 6 and 12 months post-entry. Results Although previously published analyses revealed significantly fewer positive drug tests for participants in the adaptive condition during the first 18 weeks of drug court, current analyses indicate the effects converged during the ensuing year. Between-group differences in new arrest rates, urine drug test results and self-reported psychosocial problems were small and non-statistically significant at 6, 12 and 18 months post-entry. A non-significant trend (p = .10) suggests there may have been a small residual impact (Cramer's ν = .15) on new misdemeanor arrests after 18 months. Conclusions Adaptive programming shows promise for enhancing short-term outcomes in drug courts; however, additional efforts are needed to extend the effects beyond the first 4 to 6 months of enrollment. PMID:25346652
Melis, Theodore S.; Walters, Carl; Korman, Josh
With a focus on resources of the Colorado River ecosystem below Glen Canyon Dam, the Glen Canyon Dam Adaptive Management Program has included a variety of experimental policy tests, ranging from manipulation of water releases from the dam to removal of non-native fish within Grand Canyon National Park. None of these field-scale experiments has yet produced unambiguous results in terms of management prescriptions. But there has been adaptive learning, mostly from unanticipated or surprising resource responses relative to predictions from ecosystem modeling. Surprise learning opportunities may often be viewed with dismay by some stakeholders who might not be clear about the purpose of science and modeling in adaptive management. However, the experimental results from the Glen Canyon Dam program actually represent scientific successes in terms of revealing new opportunities for developing better river management policies. A new long-term experimental management planning process for Glen Canyon Dam operations, started in 2011 by the U.S. Department of the Interior, provides an opportunity to refocus management objectives, identify and evaluate key uncertainties about the influence of dam releases, and refine monitoring for learning over the next several decades. Adaptive learning since 1995 is critical input to this long-term planning effort. Embracing uncertainty and surprise outcomes revealed by monitoring and ecosystem modeling will likely continue the advancement of resource objectives below the dam, and may also promote efficient learning in other complex programs.
Jones, James Holland
Fetal programming is an ontogenetic phenomenon of increasing interest to human biologists. Because the downstream consequences of fetal programming have clear impacts on specific life-history traits (e.g., age at first reproduction and the general age-pattern of reproductive investments), a number of authors have raised the question of the adaptive significance of fetal programming. In this paper, I review in some detail several classical models in life-history theory and discuss their relative merits and weaknesses for human biology. I suggest that an adequate model of human life-history evolution must account for the highly structured nature of the human life cycle, with its late age at first reproduction, large degree of iteroparity, highly overlapping generations, and extensive, post-weaning parental investment. I further suggest that an understanding of stochastic demography is essential for answering the question of the adaptive significance of fetal programming, and specifically the finding of low birth weight on smaller adult body size and earlier age at first reproduction. Using a stage-structured stochastic population model, I show that the downstream consequences of early deprivation may be "making the best of a bad start" rather than an adaptation per se. When a high-investment strategy entails survival costs, the alternate strategy of early reproduction with relatively low investment may have higher fitness than trying to play the high-investment strategy and failing.
Dorband, John E.; Aburdene, Maurice F.
Recently, networked and cluster computation have become very popular. This paper is an introduction to a new C based parallel language for architecture-adaptive programming, aCe C. The primary purpose of aCe (Architecture-adaptive Computing Environment) is to encourage programmers to implement applications on parallel architectures by providing them the assurance that future architectures will be able to run their applications with a minimum of modification. A secondary purpose is to encourage computer architects to develop new types of architectures by providing an easily implemented software development environment and a library of test applications. This new language should be an ideal tool to teach parallel programming. In this paper, we will focus on some fundamental features of aCe C.
Waldrop, Raymond S.; Volz, Richard A.; Smith, Gary W.; Holzbacher-Valero, A. A.; Goldsack, Stephen J.
One purpose of our research is the investigation of the effectiveness and expressiveness of AdaPT(1), a set of language extensions to Ada 83, for distributed systems. As a part of that effort, we are now investigating the subject of replacing, e.g., upgrading, software modules while the software system remains in operation. The AdaPT language extension provide a good basis for this investigation for several reasons: (1) they include the concept of specific, self-contained program modules which can be manipulated; (2) support for program configuration is included in the language; and (3) although the discussion will be in terms of the AdaPT language, the AdaPT to Ada 83 conversion methodology being developed as another part of this project will provide a basis for the application of our findings to Ada 83 systems. The purpose of this investigation is to explore the basic mechanisms to the replacement process. Thus, while replacement in the presence of real-time deadlines, heterogeneous systems, and unreliable networks is certainly a topic of interest, we will first gain an understanding of the basic processes in the absence of such concerns. The extension of the replacement process to more complex situations can be made later. This report will establish an overview of the on-line upgrade problem, and present a taxonomy of the various aspects of the replacement process.
Johnson-Jennings, Michelle; Baumann, Ana A.; Proctor, Enola
Introduction Diabetes disproportionately affects underserved racial/ethnic groups in the United States. Diabetes prevention interventions positively influence health; however, further evaluation is necessary to determine what role culture plays in effective programming. We report on the status of research that examines cultural adaptations of diabetes prevention programs. Methods We conducted database searches in March and April 2014. We included studies that were conducted in the United States and that focused on diabetes prevention among African Americans, American Indians/Alaska Natives, Asian Americans/Pacific Islanders, and Latinos. Results A total of 58 studies were identified for review; 29 were excluded from evaluation. Few adaptations referenced or followed recommendations for cultural adaptation nor did they justify the content modifications by providing a rationale or evidence. Cultural elements unique to racial/ethnic populations were not assessed. Conclusion Future cultural adaptations should use recommended processes to ensure that culture’s role in diabetes prevention–related behavioral changes contributes to research. PMID:25950567
Kim, D.; Ghanem, R.
Multigrid solution technique to solve a material nonlinear problem in a visual programming environment using the finite element method is discussed. The nonlinear equation of equilibrium is linearized to incremental form using Newton-Rapson technique, then multigrid solution technique is used to solve linear equations at each Newton-Rapson step. In the process, adaptive mesh refinement, which is based on the bisection of a pair of triangles, is used to form grid hierarchy for multigrid iteration. The solution process is implemented in a visual programming environment with distributed computing capability, which enables more intuitive understanding of solution process, and more effective use of resources.
Background Depression and anxiety are prevalent among women in low- and lower-middle income countries who are pregnant or have recently given birth. There is promising evidence that culturally-adapted, evidence-informed, perinatal psycho-educational programs implemented in local communities are effective in reducing mental health problems. The Thinking Healthy Program (THP) has proved effective in Pakistan. The aims were to adapt the THP for rural Vietnam; establish the program’s comprehensibility, acceptability and salience for universal use, and investigate whether administration to small groups of women might be of equivalent effectiveness to administration in home visits to individual women. Methods The THP Handbook and Calendar were made available in English by the program developers and translated into Vietnamese. Cultural adaptation and field-testing were undertaken using WHO guidance. Field-testing of the four sessions of THP Module One was undertaken in weekly sessions with a small group in a rural commune and evaluated using baseline, process and endline surveys. Results The adapted Vietnamese version of the Thinking Healthy Program (THP-V) was found to be understandable, meaningful and relevant to pregnant women, and commune health centre and Women’s Union representatives in a rural district. It was delivered effectively by trained local facilitators. Role-play, brainstorming and small-group discussions to find shared solutions to common problems were appraised as helpful learning opportunities. Conclusions The THP-V is safe and comprehensible, acceptable and salient to pregnant women without mental health problems in rural Vietnam. Delivery in facilitated small groups provided valued opportunities for role-play rehearsal and shared problem solving. Local observers found the content and approach highly relevant to local needs and endorsed the approach as a mental health promotion strategy with potential for integration into local universal maternal
the Cameron project. The goal of the Cameron project is to make FPGAs and other adaptive computer systems available to more applications programmers...loops onto an FPGA , but this is invisible. SA-C therefore makes recon- gurable processors accessible to applications programmers with no hardware...happens that for SA-C programs, the host executable off-loads the processing of loops onto an FPGA , but this is invisible. SA-C therefore makes
Bonds, Darya D.; Wolchik, Sharlene A.; Winslow, Emily; Tein, Jenn-Yun; Sandler, Irwin N.; Millsap, Roger E.
Using data from a 6-year longitudinal follow-up sample of 240 youth who participated in a randomized experimental trial of a preventive intervention for divorced families with children ages 9–12, the current study tested alternative cascading pathways by which the intervention decreased symptoms of internalizing disorders, symptoms of externalizing disorders, substance use, and risky sexual behavior, and increased self-esteem and academic performance in mid-to late-adolescence (15–19 years old). It was hypothesized that the impact of the program on adolescent adaptation outcomes would be explained by progressive associations between program-induced changes in parenting and youth adaptation outcomes. The results supported a cascading model of program effects in which the program was related to increased mother-child relationship quality, which was related to subsequent decreases in child internalizing problems, which then was related to subsequent increases in self-esteem and decreases in symptoms of internalizing disorders in adolescence. The results also were consistent with a model in which the program was related to increased maternal effective discipline, which was related to subsequent decreases in child externalizing problems, which then was related to subsequent decreases in symptoms of externalizing disorders, less substance use and better academic performance in adolescence. There were no significant differences in the model based on level of baseline risk or adolescent gender. These results provide support for a cascading pathways model of child and adolescent development. PMID:20883581
Al-Bannay, Hana R.; Jongbloed, Lyn E.; Jarus, Tal; Alabdulwahab, Sami S.; Khoja, Tawfik A.; Dean, Elizabeth
Objective: To explore the outcomes of a pilot intervention of a type 2 diabetes (T2D) education program, based on international standards, and adapted to the cultural and religious contexts of Saudi women. Methods: This study is an experiment of a pilot intervention carried out between August 2011 and January 2012 at the primary health clinics in Dammam. Women at risk of or diagnosed with T2D (N=35 including dropouts) were assigned to one of 2 groups; an intervention group participated in a pilot intervention of T2D education program, based on international standards and tailored to their cultural and religious contexts; and a usual care group received the usual care for diabetes in Saudi Arabia. Outcomes included blood glucose, body composition, 6-minute walk distance, life satisfaction, quality of life, and diabetes knowledge. The intervention group participated in a focus group of their program experience. Data analysis was based on mixed methods. Results: Based on 95% confidence interval comparisons, improvements were noted in blood sugar, 6-minute walk distance, quality of life, and diabetes knowledge in participants of the intervention group. They also reported improvements in lifestyle-related health behaviors after the education program. Conclusion: Saudi women may benefit from a T2D education program based on international standards and adapted to their cultural and religious contexts. PMID:26108595
Adams, Byron J.
Given the task of recovering and representing evolutionary history, nematode taxonomists can choose from among several species concepts. All species concepts have theoretical and (or) operational inconsistencies that can result in failure to accurately recover and represent species. This failure not only obfuscates nematode taxonomy but hinders other research programs in hematology that are dependent upon a phylogenetically correct taxonomy, such as biodiversity, biogeography, cospeciation, coevolution, and adaptation. Three types of systematic errors inherent in different species concepts and their potential effects on these research programs are presented. These errors include overestimating and underestimating the number of species (type I and II error, respectively) and misrepresenting their phylogenetic relationships (type III error). For research programs in hematology that utilize recovered evolutionary history, type II and III errors are the most serious. Linnean, biological, evolutionary, and phylogenefic species concepts are evaluated based on their sensitivity to systematic error. Linnean and biological species concepts are more prone to serious systematic error than evolutionary or phylogenetic concepts. As an alternative to the current paradigm, an amalgamation of evolutionary and phylogenetic species concepts is advocated, along with a set of discovery operations designed to minimize the risk of making systematic errors. Examples of these operations are applied to species and isolates of Heterorhabditis. PMID:19274195
Burgin, G. H.; Owens, A. J.
A detailed description is presented of the computer programs in order to provide an understanding of the mathematical and geometrical relationships as implemented in the programs. The individual sbbroutines and their underlying mathematical relationships are described, and the required input data and the output provided by the program are explained. The relationship of the adaptive maneuvering logic program with the program to drive the differential maneuvering simulator is discussed.
Peisajovich, Sergio G
Signaling networks process vast amounts of environmental information to generate specific cellular responses. As cellular environments change, signaling networks adapt accordingly. Here, I will discuss how the integration of synthetic biology and directed evolution approaches is shedding light on the molecular mechanisms that guide the evolution of signaling networks. In particular, I will review studies that demonstrate how different types of mutations, from the replacement of individual amino acids to the shuffling of modular domains, lead to markedly different evolutionary trajectories and consequently to diverse network rewiring. Moreover, I will argue that intrinsic evolutionary properties of signaling proteins, such as the robustness of wild type functions, the promiscuous nature of evolutionary intermediates, and the modular decoupling between binding and catalysis, play important roles in the evolution of signaling networks. Finally, I will argue that rapid advances in our ability to synthesize DNA will radically alter how we study signaling network evolution at the genome-wide level.
King, Ashley C; Bjorklund, David F
The field of evolutionary developmental psychology can potentially broaden the horizons of mainstream evolutionary psychology by combining the principles of Darwinian evolution by natural selection with the study of human development, focusing on the epigenetic effects that occur between humans and their environment in a way that attempts to explain how evolved psychological mechanisms become expressed in the phenotypes of adults. An evolutionary developmental perspective includes an appreciation of comparative research and we, among others, argue that contrasting the cognition of humans with that of nonhuman primates can provide a framework with which to understand how human cognitive abilities and intelligence evolved. Furthermore, we argue that several
Everhart, J. L.
A program called FLEXWAL for calculating wall modifications for solid, adaptive-wall wind tunnels is presented. The method used is the iterative technique of NASA TP-2081 and is applicable to subsonic and transonic test conditions. The program usage, program listing, and a sample case are given.
BRIGGS, LESLIE J.; CAMPBELL, VINCENT N.
POTENTIAL ECONOMIC FORMS OF ADAPTIVE, SELF-INSTRUCTIONAL PROGRAMS WHICH WOULD BE OF PRACTICAL USE IN ADJUSTING TO INDIVIDUAL DIFFERENCES WERE INVESTIGATED. "PARALLEL" PROGRAMS (ONE STUDENT LEARNING BEST BY ONE PROGRAM AND A SECOND STUDENT BENEFITING MOST FROM ANOTHER) WERE FIRST EXPLORED AS A WAY TO ADJUST TO INDIVIDUAL DIFFERENCES. THIS…
Ayotte, Violaine; Saucier, Jean-Francois; Bowen, Francois; Laurendeau, Marie-Claire; Fournier, Michel; Blais, Jean-Guy
Evaluates a program that promoted adaptation of students in their first year of secondary school. The program focused on developing healthy self-perceptions, and cognitive, affective and behavioral skills. Analyses revealed the predicted positive effects of the program on psychological and social outcomes. Findings underline the need to address…
Allison, Molly; Ramaswamy, Megha
Prison-based animal programs have shown promise when it comes to increased sociability, responsibility, and levels of patience for inmates who participate in these programs. Yet there remains a dearth of scientific research that demonstrates the impact of prison-based animal programs on inmates' physical and mental health. Trials of animal-assisted therapy interventions, a form of human-animal interaction therapy most often used with populations affected by depression/anxiety, mental illness, and trauma, may provide models of how prison-based animal program research can have widespread implementation in jail and prison settings, whose populations have high rates of mental health problems. This paper reviews the components of prison-based animal programs most commonly practiced in prisons today, presents five animal-assisted therapy case studies, evaluates them based on their adaptability to prison-based animal programs, and discusses the institutional constraints that act as barriers for rigorous prison-based animal program research implementation. This paper can serve to inform the development of a research approach to animal-assisted therapy that nurses and other public health researchers can use in working with correctional populations.
Gibson, Mhairi A; Lawson, David W
Evolutionary anthropology provides a powerful theoretical framework for understanding how both current environments and legacies of past selection shape human behavioral diversity. This integrative and pluralistic field, combining ethnographic, demographic, and sociological methods, has provided new insights into the ultimate forces and proximate pathways that guide human adaptation and variation. Here, we present the argument that evolutionary anthropological studies of human behavior also hold great, largely untapped, potential to guide the design, implementation, and evaluation of social and public health policy. Focusing on the key anthropological themes of reproduction, production, and distribution we highlight classic and recent research demonstrating the value of an evolutionary perspective to improving human well-being. The challenge now comes in transforming relevance into action and, for that, evolutionary behavioral anthropologists will need to forge deeper connections with other applied social scientists and policy-makers. We are hopeful that these developments are underway and that, with the current tide of enthusiasm for evidence-based approaches to policy, evolutionary anthropology is well positioned to make a strong contribution. PMID:25684561
Gibson, Mhairi A; Lawson, David W
Evolutionary anthropology provides a powerful theoretical framework for understanding how both current environments and legacies of past selection shape human behavioral diversity. This integrative and pluralistic field, combining ethnographic, demographic, and sociological methods, has provided new insights into the ultimate forces and proximate pathways that guide human adaptation and variation. Here, we present the argument that evolutionary anthropological studies of human behavior also hold great, largely untapped, potential to guide the design, implementation, and evaluation of social and public health policy. Focusing on the key anthropological themes of reproduction, production, and distribution we highlight classic and recent research demonstrating the value of an evolutionary perspective to improving human well-being. The challenge now comes in transforming relevance into action and, for that, evolutionary behavioral anthropologists will need to forge deeper connections with other applied social scientists and policy-makers. We are hopeful that these developments are underway and that, with the current tide of enthusiasm for evidence-based approaches to policy, evolutionary anthropology is well positioned to make a strong contribution.
Evolution as an idea has a lengthy history, even though the idea of evolution is generally associated with Darwin today. Rebecca Stott provides an engaging and thoughtful overview of this history of evolutionary thinking in her 2013 book, Darwin's Ghosts: The Secret History of Evolution. Since Darwin, the debate over evolution—both how it takes place and, in a long war of words with religiously-oriented thinkers, whether it takes place—has been sustained and heated. A growing share of this debate is now devoted to examining how evolutionary thinking affects areas outside of biology. How do our lives change when we recognize that all is in flux? What can we learn about life more generally if we study change instead of stasis? Carter Phipps’ book, Evolutionaries: Unlocking the Spiritual and Cultural Potential of Science's Greatest Idea, delves deep into this relatively new development. Phipps generally takes as a given the validity of the Modern Synthesis of evolutionary biology. His story takes us into, as the subtitle suggests, the spiritual and cultural implications of evolutionary thinking. Can religion and evolution be reconciled? Can evolutionary thinking lead to a new type of spirituality? Is our culture already being changed in ways that we don't realize by evolutionary thinking? These are all important questions and Phipps book is a great introduction to this discussion. Phipps is an author, journalist, and contributor to the emerging “integral” or “evolutionary” cultural movement that combines the insights of Integral Philosophy, evolutionary science, developmental psychology, and the social sciences. He has served as the Executive Editor of EnlightenNext magazine (no longer published) and more recently is the co-founder of the Institute for Cultural Evolution, a public policy think tank addressing the cultural roots of America's political challenges. What follows is an email interview with Phipps. PMID:26478766
Missouri, 1978 Acceso • For M.S., Air Force Institute of Technology, 1981 rTIS , D•2 TVAB 0 6y I fivColes Fort Leavenworth, Kansas A j, -dlor 1989 .CIdI...external interfaces at multiple organizational levels, some of which may be inter-Service and multinational (15). Evolutionary Acquisition. This is...and intelligence which serve multiple services (30). The group concluded that the services have not made the necessary commitments to execute joint
Vaamonde, Iago; Souto-López, Álvaro; García-Díaz, Antón
A machine vision system has been developed, validated, and integrated in a commercial laser robot cell. It permits an offline graphical programming of laser cutting of lace. The user interface allows loading CAD designs and aligning them with images of lace pieces. Different thread widths are discriminated to generate proper cutting program templates. During online operation, the system aligns CAD models of pieces and lace images, pre-checks quality of lace cuts and adapts laser parameters to thread widths. For pieces detected with the required quality, the program template is adjusted by transforming the coordinates of every trajectory point. A low-cost lace feeding system was also developed for demonstration of full process automation.
Lowry, David B
Tremendous advances in genetic and genomic techniques have resulted in the capacity to identify genes involved in adaptive evolution across numerous biological systems. One of the next major steps in evolutionary biology will be to determine how landscape-level geographical and environmental features are involved in the distribution of this functional adaptive genetic variation. Here, I outline how an emerging synthesis of multiple disciplines has and will continue to facilitate a deeper understanding of the ways in which heterogeneity of the natural landscapes mould the genomes of organisms.
This article examines how three urban elementary school teachers adapted pedagogical strategies from a school district--adopted core reading program to increase their students' access to the curriculum. Using teacher interviews and classroom observations to construct a descriptive case study of teacher adaptation, analysis reveals that the…
There is no evidence in the literature for direct comparison of the sociocultural adaptation brought by the participation of U.S. students in education abroad programs of different lengths. This study attempts to address this gap by comparing the sociocultural adaptation of education abroad students that results from their participation in both…
Mu, Chaoxu; Ni, Zhen; Sun, Changyin; He, Haibo
In this paper, we propose a data-driven supplementary control approach with adaptive learning capability for air-breathing hypersonic vehicle tracking control based on action-dependent heuristic dynamic programming (ADHDP). The control action is generated by the combination of sliding mode control (SMC) and the ADHDP controller to track the desired velocity and the desired altitude. In particular, the ADHDP controller observes the differences between the actual velocity/altitude and the desired velocity/altitude, and then provides a supplementary control action accordingly. The ADHDP controller does not rely on the accurate mathematical model function and is data driven. Meanwhile, it is capable to adjust its parameters online over time under various working conditions, which is very suitable for hypersonic vehicle system with parameter uncertainties and disturbances. We verify the adaptive supplementary control approach versus the traditional SMC in the cruising flight, and provide three simulation studies to illustrate the improved performance with the proposed approach.
Karemere, Hermès; Ribesse, Nathalie; Kahindo, Jean-Bosco; Macq, Jean
Introduction In many African countries, first referral hospitals received little attention from development agencies until recently. We report the evolution of two of them in an unstable region like Eastern Democratic Republic of Congo when receiving the support from development aid program. Specifically, we aimed at studying how actors’ network and institutional framework evolved over time and what could matter the most when looking at their performance in such an environment. Methods We performed two cases studies between 2006 and 2010. We used multiple sources of data: reports to document events; health information system for hospital services production, and “key-informants” interviews to interpret the relation between interventions and services production. Our analysis was inspired from complex adaptive system theory. It started from the analysis of events implementation, to explore interaction process between the main agents in each hospital, and the consequence it could have on hospital health services production. This led to the development of new theoretical propositions. Results Two events implemented in the frame of the development aid program were identified by most of the key-informants interviewed as having the greatest impact on hospital performance: the development of a hospital plan and the performance based financing. They resulted in contrasting interaction process between the main agents between the two hospitals. Two groups of services production were reviewed: consultation at outpatient department and admissions, and surgery. The evolution of both groups of services production were different between both hospitals. Conclusion By studying two first referral hospitals through the lens of a Complex Adaptive System, their performance in a context of development aid takes a different meaning. Success is not only measured through increased hospital production but through meaningful process of hospital agents’” network adaptation. Expected
Hamill, John F.; Melis, Theodore S.; Boon, Philip J.; Raven, Paul J.
Adaptive management emerged as an important resource management strategy for major river systems in the United States (US) in the early 1990s. The Glen Canyon Dam Adaptive Management Program (‘the Program’) was formally established in 1997 to fulfill a statutory requirement in the 1992 Grand Canyon Protection Act (GCPA). The GCPA aimed to improve natural resource conditions in the Colorado River corridor in the Glen Canyon National Recreation Area and Grand Canyon National Park, Arizona that were affected by the Glen Canyon dam. The Program achieves this by using science and a variety of stakeholder perspectives to inform decisions about dam operations. Since the Program started the ecosystem is now much better understood and several biological and physical improvements have been achieved. These improvements include: (i) an estimated 50% increase in the adult population of endangered humpback chub (Gila cypha) between 2001 and 2008, following previous decline; (ii) a 90% decrease in non-native rainbow trout (Oncorhynchus mykiss), which are known to compete with and prey on native fish, as a result of removal experiments; and (iii) the widespread reappearance of sandbars in response to an experimental high-flow release of dam water in March 2008.Although substantial progress has been made, the Program faces several immediate challenges. These include: (i) defining specific, measurable objectives and desired future conditions for important natural, cultural and recreational attributes to inform science and management decisions; (ii) implementing structural and operational changes to improve collaboration among stakeholders; (iii) establishing a long-term experimental programme and management plan; and (iv) securing long-term funding for monitoring programmes to assess ecosystem and other responses to management actions. Addressing these challenges and building on recent progress will require strong and consistent leadership from the US Department of the Interior
Miranda, Eduardo Reck
This paper introduces three approaches to using Evolutionary Computation (EC) in Music (namely, engineering, creative and musicological approaches) and discusses examples of representative systems that have been developed within the last decade, with emphasis on more recent and innovative works. We begin by reviewing engineering applications of EC in Music Technology such as Genetic Algorithms and Cellular Automata sound synthesis, followed by an introduction to applications where EC has been used to generate musical compositions. Next, we introduce ongoing research into EC models to study the origins of music and detail our own research work on modelling the evolution of melody.
In 1996, Glen Canyon Dam Adaptive Management (GCDAMP) program was established to provide input on Glen Canyon Dam operations and their affect on the Colorado Ecosystem in Grand Canyon. The GCDAMP is a bold experiment in federal resource management that features a governing partnership with all relevant stakeholders sitting at the same table. It is a complicated, difficult process where stakeholder-derived management actions must balance resource protection with water and power delivery compacts, the Endangered Species Act, the National Historical Preservation Act, the Grand Canyon Protection Act, National Park Service Policy, and other stakeholder concerns. The program consists of four entities: the Adaptive Management Workgroup (AMWG), the Technical Workgroup (TWG), the Grand Canyon Monitoring and Research Center (GCMRC), and independent review panels. The AMWG and TWG are federal advisory committees that consists of federal and state resource managers, Native American tribes, power, environmental and recreation interests. The AMWG is develops, evaluates and recommends alternative dam operations to the Secretary. The TWG translates AMWG policy and goals into management objectives and information needs, provides questions that serve as the basis for long-term monitoring and research activities, interprets research results from the GCMRC, and prepares reports as required for the AMWG. The GCMRC is an independent science center that is responsible for all GCDAMP monitoring and research activities. The GCMRC utilizes proposal requests with external peer review and an in-house staff that directs and synthesizes monitoring and research results. The GCMRC meets regularly with the TWG and AMWG and provides scientific information on the consequences of GCDAMP actions. Independent review panels consist of external peer review panels that provide reviews of scientific activities and the program in general, technical advice to the GCMRC, TWG and AMWG, and play a critical
Baer, B; Millar, A H
Evolutionary ecologists are traditionally gene-focused, as genes propagate phenotypic traits across generations and mutations and recombination in the DNA generate genetic diversity required for evolutionary processes. As a consequence, the inheritance of changed DNA provides a molecular explanation for the functional changes associated with natural selection. A direct focus on proteins on the other hand, the actual molecular agents responsible for the expression of a phenotypic trait, receives far less interest from ecologists and evolutionary biologists. This is partially due to the central dogma of molecular biology that appears to define proteins as the 'dead-end of molecular information flow' as well as technical limitations in identifying and studying proteins and their diversity in the field and in many of the more exotic genera often favored in ecological studies. Here we provide an overview of a newly forming field of research that we refer to as 'Evolutionary Proteomics'. We point out that the origins of cellular function are related to the properties of polypeptide and RNA and their interactions with the environment, rather than DNA descent, and that the critical role of horizontal gene transfer in evolution is more about coopting new proteins to impact cellular processes than it is about modifying gene function. Furthermore, post-transcriptional and post-translational processes generate a remarkable diversity of mature proteins from a single gene, and the properties of these mature proteins can also influence inheritance through genetic and perhaps epigenetic mechanisms. The influence of post-transcriptional diversification on evolutionary processes could provide a novel mechanistic underpinning for elements of rapid, directed evolutionary changes and adaptations as observed for a variety of evolutionary processes. Modern state-of the art technologies based on mass spectrometry are now available to identify and quantify peptides, proteins, protein
Neuman, F.; Erzberger, H.
Improvements were made to the Adaptive Maneuvering Logic (AML) computer program, a computer-generated, air-to-air combat opponent. The primary improvement was incorporating a measure of performance, the exchange ratio, defined as the statistical measure of number of enemy kills divided by number of friendly losses. This measure was used to test a new modification of the AML's combat tactics. When the new version of the AML competed against the old version, the new version won with an exchange ratio of 1.4.
Konecny, Robert; Baker, Nathan A.; McCammon, J. A.
The Adaptive Poisson-Boltzmann Solver (APBS) is a state-of-the-art suite for performing Poisson-Boltzmann electrostatic calculations on biomolecules. The iAPBS package provides a modular programmatic interface to the APBS library of electrostatic calculation routines. The iAPBS interface library can be linked with a Fortran or C/C++ program thus making all of the APBS functionality available from within the application. Several application modules for popular molecular dynamics simulation packages -- Amber, NAMD and CHARMM are distributed with iAPBS allowing users of these packages to perform implicit solvent electrostatic calculations with APBS.
Chhabra, Rosy; Springer, Carolyn; Leu, Cheng-Shiun; Ghosh, Shivnath; Sharma, Sunil Kumar; Rapkin, Bruce
Given the current status of HIV infection in youth in India, developing and implementing HIV education and prevention interventions is critical. The goal for School-based Teenage Education Program (STEP) was to demonstrate that a HIV/AIDS and alcohol abuse educational program built with specific cultural, linguistic, and community-specific characteristics could be effective. Utilizing the Train-the-Trainer model, the instructors (17-21 years) were trained to present the 10 session manualized program to primarily rural and tribal youth aged 13-16 years in 23 schools (N = 1,421) in the northern state of Himachal Pradesh in India. The intervention had a greater impact on girls; girls evidenced greater communication skills and a trend towards greater self efficacy and reduced risk taking behavior. The STEP has been successfully adapted by the community organizations that were involved in coordinating the program at the local level. Their intention to continue STEP beyond extra funding shows that utilizing the local community in designing, implementing and evaluating programs promotes ownership and sustainability.
Springer, Carolyn; Leu, Cheng-Shiun; Ghosh, Shivnath; Sharma, Sunil Kumar; Rapkin, Bruce
Given the current status of HIV infection in youth in India, developing and implementing HIV education and prevention interventions is critical. The goal for School-based Teenage Education Program (STEP) was to demonstrate that a HIV/AIDS and alcohol abuse educational program built with specific cultural, linguistic, and community-specific characteristics could be effective. Utilizing the Train-the-Trainer model, the instructors (17–21 years) were trained to present the 10 session manualized program to primarily rural and tribal youth aged 13–16 years in 23 schools (N = 1,421) in the northern state of Himachal Pradesh in India. The intervention had a greater impact on girls; girls evidenced greater communication skills and a trend towards greater self efficacy and reduced risk taking behavior. The STEP has been successfully adapted by the community organizations that were involved in coordinating the program at the local level. Their intention to continue STEP beyond extra funding shows that utilizing the local community in designing, implementing and evaluating programs promotes ownership and sustainability. PMID:20589528
Carey, L. D.; Petersen, W. A.; Deierling, W.; Roeder, W. P.
A new weather radar is being acquired for use in support of America s space program at Cape Canaveral Air Force Station, NASA Kennedy Space Center, and Patrick AFB on the east coast of central Florida. This new radar replaces the modified WSR-74C at Patrick AFB that has been in use since 1984. The new radar is a Radtec TDR 43-250, which has Doppler and dual polarization capability. A new fixed scan strategy was designed to best support the space program. The fixed scan strategy represents a complex compromise between many competing factors and relies on climatological heights of various temperatures that are important for improved lightning forecasting and evaluation of Lightning Launch Commit Criteria (LCC), which are the weather rules to avoid lightning strikes to in-flight rockets. The 0 C to -20 C layer is vital since most generation of electric charge occurs within it and so it is critical in evaluating Lightning LCC and in forecasting lightning. These are two of the most important duties of 45 WS. While the fixed scan strategy that covers most of the climatological variation of the 0 C to -20 C levels with high resolution ensures that these critical temperatures are well covered most of the time, it also means that on any particular day the radar is spending precious time scanning at angles covering less important heights. The goal of this project is to develop a user-friendly, Interactive Data Language (IDL) computer program that will automatically generate optimized radar scan strategies that adapt to user input of the temperature profile and other important parameters. By using only the required scan angles output by the temperature profile adaptive scan strategy program, faster update times for volume scans and/or collection of more samples per gate for better data quality is possible, while maintaining high resolution at the critical temperature levels. The temperature profile adaptive technique will also take into account earth curvature and refraction
Luo, Biao; Wu, Huai-Ning; Li, Han-Xiong
Highly dissipative nonlinear partial differential equations (PDEs) are widely employed to describe the system dynamics of industrial spatially distributed processes (SDPs). In this paper, we consider the optimal control problem of the general highly dissipative SDPs, and propose an adaptive optimal control approach based on neuro-dynamic programming (NDP). Initially, Karhunen-Loève decomposition is employed to compute empirical eigenfunctions (EEFs) of the SDP based on the method of snapshots. These EEFs together with singular perturbation technique are then used to obtain a finite-dimensional slow subsystem of ordinary differential equations that accurately describes the dominant dynamics of the PDE system. Subsequently, the optimal control problem is reformulated on the basis of the slow subsystem, which is further converted to solve a Hamilton-Jacobi-Bellman (HJB) equation. HJB equation is a nonlinear PDE that has proven to be impossible to solve analytically. Thus, an adaptive optimal control method is developed via NDP that solves the HJB equation online using neural network (NN) for approximating the value function; and an online NN weight tuning law is proposed without requiring an initial stabilizing control policy. Moreover, by involving the NN estimation error, we prove that the original closed-loop PDE system with the adaptive optimal control policy is semiglobally uniformly ultimately bounded. Finally, the developed method is tested on a nonlinear diffusion-convection-reaction process and applied to a temperature cooling fin of high-speed aerospace vehicle, and the achieved results show its effectiveness.
Many universities now deliver courses and programs in overseas markets such as China. Often these programs are delivered by foreign academics who teach in these overseas locations. This style and format of educational delivery raises the issue of the degree to which subject material and teaching styles need to be adapted to meet the needs of…
Mutate is a program developed for teaching purposes to impart a virtual laboratory class for undergraduate students of Genetics in Biology. The program emulates the so-called fluctuation test whose aim is to distinguish between spontaneous and adaptive mutation hypotheses in bacteria. The plan is to train students in certain key multidisciplinary…
Kumpfer, Karol L.; Xie, Jing; O'Driscoll, Robert
Background: Evidence-based programs (EBPs) targeting effective family skills are the most cost effective for improving adolescent behavioural health. Cochrane Reviews have found the "Strengthening Families Program" (SFP) to be the most effective substance abuse prevention intervention. Standardized cultural adaptation processes resulted…
Iowa State Dept. of Natural Resources, Des Moines.
This document summarizes materials on aquatic education used by state programs. Emphasis is on materials developed by, or adapted for use with, programs in various states and territories. The 234 entries are categorized as activity books, brochures, newsletters, posters, videos, and other materials. Major subjects include fishing, boating and…
Thom, Ronald; St Clair, Tom; Burns, Rebecca; Anderson, Michael
Adaptive management (AM) is being employed in a number of programs in the United States to guide actions to restore aquatic ecosystems because these programs are both expensive and are faced with significant uncertainties. Many of these uncertainties are associated with prioritizing when, where, and what kind of actions are needed to meet the objectives of enhancing ecosystem services and recovering threatened and endangered species. We interviewed nine large-scale aquatic ecosystem restoration programs across the United States to document the lessons learned from implementing AM. In addition, we recorded information on ecological drivers (e.g., endangered fish species) for the program, and inferred how these drivers reflected more generic ecosystem services. Ecosystem services (e.g., genetic diversity, cultural heritage), albeit not explicit drivers, were either important to the recovery or enhancement of the drivers, or were additional benefits associated with actions to recover or enhance the program drivers. Implementing programs using AM lessons learned has apparently helped achieve better results regarding enhancing ecosystem services and restoring target species populations. The interviews yielded several recommendations. The science and AM program must be integrated into how the overall restoration program operates in order to gain understanding and support, and effectively inform management decision-making. Governance and decision-making varied based on its particular circumstances. Open communication within and among agency and stakeholder groups and extensive vetting lead up to decisions. It was important to have an internal agency staff member to implement the AM plan, and a clear designation of roles and responsibilities, and long-term commitment of other involved parties. The most important management questions and information needs must be identified up front. It was imperative to clearly identify, link and continually reinforce the essential
Mirand, Audrey; Richter, Jan; Schuffenecker, Isabelle; Böttiger, Blenda; Diedrich, Sabine; Terletskaia-Ladwig, Elena; Christodoulou, Christina; Peigue-Lafeuille, Hélène; Bailly, Jean-Luc
The aim of this study was to gain insights into the tempo and mode of the evolutionary processes that sustain genetic diversity in coxsackievirus B5 (CVB5) and into the interplay with virus transmission. We estimated phylodynamic patterns with a large sample of virus strains collected in Europe by Bayesian statistical methods, reconstructed the ancestral states of genealogical nodes, and tested for selection. The genealogies estimated with the structural one-dimensional gene encoding the VP1 protein and nonstructural 3CD locus allowed the precise description of lineages over time and cocirculating virus populations within the two CVB5 clades, genogroups A and B. Strong negative selection shaped the evolution of both loci, but compelling phylogenetic data suggested that immune selection pressure resulted in the emergence of the two genogroups with opposed evolutionary pathways. The genogroups also differed in the temporal occurrence of the amino acid changes. The virus strains of genogroup A were characterized by sequential acquisition of nonsynonymous changes in residues exposed at the virus 5-fold axis. The genogroup B viruses were marked by selection of three changes in a different domain (VP1 C terminus) during its early emergence. These external changes resulted in a selective sweep, which was followed by an evolutionary stasis that is still ongoing after 50 years. The inferred population history of CVB5 showed an alternation of the prevailing genogroup during meningitis epidemics across Europe and is interpreted to be a consequence of partial cross-immunity. PMID:24006446
‘Nothing in biology makes sense except in the light of evolution’ Th. Dobzhansky, 1973 Our understanding of cancer is being transformed by exploring clonal diversity, drug resistance and causation within an evolutionary framework. The therapeutic resilience of advanced cancer is a consequence of its character as complex, dynamic and adaptive ecosystem engendering robustness, underpinned by genetic diversity and epigenetic plasticity. The risk of mutation-driven escape by self-renewing cells is intrinsic to multicellularity but is countered by multiple restraints facilitating increasing complexity and longevity of species. But our own has disrupted this historical narrative by rapidly escalating intrinsic risk. Evolutionary principles illuminate these challenges and provide new avenues to explore for more effective control. PMID:26193902
Bleicher, Lucas; Sasaki, José Marcos; Orloski, Renata Villela; Cardoso, Lisandro Pavie; Hayashi, Marcelo Assaoka; Swart, Jacobus Willibrordus
We present a program that uses an optimization algorithm to fit rocking curves of ion-implanted semiconductors. This is an inverse problem that cannot be solved by simple methods. However, using recursion formulae for rocking curve calculations and a model of ion distribution after implantation, it is possible to fit experimental data with a general-purpose optimization method. In our case, we use a modified version of the genetic algorithm, which has been shown to be a good technique for this problem. The program also calculates rocking curves for a given ion profile, such as those generated by ion implantation simulation programs. Program summaryTitle of program: IonRock, version 1.0 Catalogue identifier: ADTP Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADTP Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer: any computer with Windows95 or later version Operating systems: Windows95/98/2000/NT/XP Programming language used: C++ Memory required to execute with typical data: about 4 MB No. of bytes in distributed program, including test data, etc.: 2 742 530 No of lines in distributed program, including test data etc.: 49 988 Distribution format: tar gzip file Nature of physical problem: strain determination on ion implanted zinc-blend structure semiconductors Method of solution: adapted version of the Genetic Algorithm meta-heuristic Restrictions on the complexity of the problem: strain determination is related to the strain generated by interstitial ions, which causes the left-side distortions on the rocking curve Typical running time: on an Athlon PC computer the computing time for solving the strain gradient using 16 layers takes from 10 to 30 minutes
Patton, Robert M; Cui, Xiaohui; Jiao, Yu; Potok, Thomas E
The rate at which information overwhelms humans is significantly more than the rate at which humans have learned to process, analyze, and leverage this information. To overcome this challenge, new methods of computing must be formulated, and scientist and engineers have looked to nature for inspiration in developing these new methods. Consequently, evolutionary computing has emerged as new paradigm for computing, and has rapidly demonstrated its ability to solve real-world problems where traditional techniques have failed. This field of work has now become quite broad and encompasses areas ranging from artificial life to neural networks. This chapter focuses specifically on two sub-areas of nature-inspired computing: Evolutionary Algorithms and Swarm Intelligence.
Khayatzadeh-Mahani, Akram; Takian, Amirhossein
Nationwide implementation of Family Physician (FP) program started in 2005 and targeted almost 25,000,000 citizens residing in rural areas and cities with less than 20,000 populations in Iran. Despite its blatant initiation that resulted in some modest achievements, the future of FP looks unclear in Iran. Thus far, no longitudinal evaluation of the implementation and impact of FP program has been conducted. However, meager evidence highlights the facilitating role of an existing and strong Primary Health Care (PHC) network in the implementation of FP in rural areas in Iran. A longstanding challenge, however, as emphasized by most stakeholders, remains to be the expansion of FP program into urban settings, where the PHC is undeveloped and fragile as well as the powerful private sector is resistant. Using an adapted conceptual framework of institutions, ideas, and interests, this policy perspective aims to shed light on main difficulties of FP implementation in urban areas of Iran. We analyze FP policy in the context of ongoing interactions and conflicts among institutions (the structures and rules that shape policies), interests (the groups and individuals influencing policy), and ideas (discourses around policies). Our argument will, we envisage, help plan for more appropriate implementation of FP in cities in Iran, and hopefully beyond.
Chen, Yan; Mabu, Shingo; Shimada, Kaoru; Hirasawa, Kotaro
The key in stock trading model is to take the right actions for trading at the right time, primarily based on the accurate forecast of future stock trends. Since an effective trading with given information of stock prices needs an intelligent strategy for the decision making, we applied Genetic Network Programming (GNP) to creating a stock trading model. In this paper, we propose a new method called Real Time Updating Genetic Network Programming (RTU-GNP) for adapting to the change of stock prices. There are three important points in this paper: First, the RTU-GNP method makes a stock trading decision considering both the recommendable information of technical indices and the candlestick charts according to the real time stock prices. Second, we combine RTU-GNP with a Sarsa learning algorithm to create the programs efficiently. Also, sub-nodes are introduced in each judgment and processing node to determine appropriate actions (buying/selling) and to select appropriate stock price information depending on the situation. Third, a Real Time Updating system has been firstly introduced in our paper considering the change of the trend of stock prices. The experimental results on the Japanese stock market show that the trading model with the proposed RTU-GNP method outperforms other models without real time updating. We also compared the experimental results using the proposed method with Buy&Hold method to confirm its effectiveness, and it is clarified that the proposed trading model can obtain much higher profits than Buy&Hold method.
Laland, Kevin N.; Uller, Tobias; Feldman, Marcus W.; Sterelny, Kim; Müller, Gerd B.; Moczek, Armin; Jablonka, Eva; Odling-Smee, John
Scientific activities take place within the structured sets of ideas and assumptions that define a field and its practices. The conceptual framework of evolutionary biology emerged with the Modern Synthesis in the early twentieth century and has since expanded into a highly successful research program to explore the processes of diversification and adaptation. Nonetheless, the ability of that framework satisfactorily to accommodate the rapid advances in developmental biology, genomics and ecology has been questioned. We review some of these arguments, focusing on literatures (evo-devo, developmental plasticity, inclusive inheritance and niche construction) whose implications for evolution can be interpreted in two ways—one that preserves the internal structure of contemporary evolutionary theory and one that points towards an alternative conceptual framework. The latter, which we label the ‘extended evolutionary synthesis' (EES), retains the fundaments of evolutionary theory, but differs in its emphasis on the role of constructive processes in development and evolution, and reciprocal portrayals of causation. In the EES, developmental processes, operating through developmental bias, inclusive inheritance and niche construction, share responsibility for the direction and rate of evolution, the origin of character variation and organism–environment complementarity. We spell out the structure, core assumptions and novel predictions of the EES, and show how it can be deployed to stimulate and advance research in those fields that study or use evolutionary biology. PMID:26246559
Laland, Kevin N; Uller, Tobias; Feldman, Marcus W; Sterelny, Kim; Müller, Gerd B; Moczek, Armin; Jablonka, Eva; Odling-Smee, John
Scientific activities take place within the structured sets of ideas and assumptions that define a field and its practices. The conceptual framework of evolutionary biology emerged with the Modern Synthesis in the early twentieth century and has since expanded into a highly successful research program to explore the processes of diversification and adaptation. Nonetheless, the ability of that framework satisfactorily to accommodate the rapid advances in developmental biology, genomics and ecology has been questioned. We review some of these arguments, focusing on literatures (evo-devo, developmental plasticity, inclusive inheritance and niche construction) whose implications for evolution can be interpreted in two ways—one that preserves the internal structure of contemporary evolutionary theory and one that points towards an alternative conceptual framework. The latter, which we label the 'extended evolutionary synthesis' (EES), retains the fundaments of evolutionary theory, but differs in its emphasis on the role of constructive processes in development and evolution, and reciprocal portrayals of causation. In the EES, developmental processes, operating through developmental bias, inclusive inheritance and niche construction, share responsibility for the direction and rate of evolution, the origin of character variation and organism-environment complementarity. We spell out the structure, core assumptions and novel predictions of the EES, and show how it can be deployed to stimulate and advance research in those fields that study or use evolutionary biology.
Adaptation to environmental change is not a new concept. Humans have shown throughout history a capacity for adapting to different climates and environmental changes. Farmers, foresters, civil engineers, have all been forced to adapt to numerous challenges to overcome adversity...
Wilson, Benjamin A.; Pennings, Pleuni S.; Petrov, Dmitri A.
Evolutionary rescue occurs when a population that is declining in size because of an environmental change is rescued from extinction by genetic adaptation. Evolutionary rescue is an important phenomenon at the intersection of ecology and population genetics, and the study of evolutionary rescue is critical to understanding processes ranging from species conservation to the evolution of drug and pesticide resistance. While most population-genetic models of evolutionary rescue focus on estimating the probability of rescue, we focus on whether one or more adaptive lineages contribute to evolutionary rescue. We find that when evolutionary rescue is likely, it is often driven by soft selective sweeps where multiple adaptive mutations spread through the population simultaneously. We give full analytic results for the probability of evolutionary rescue and the probability that evolutionary rescue occurs via soft selective sweeps. We expect that these results will find utility in understanding the genetic signatures associated with various evolutionary rescue scenarios in large populations, such as the evolution of drug resistance in viral, bacterial, or eukaryotic pathogens. PMID:28213477
This article seeks to unify two subfields of psychology that have hitherto stood separately: evolutionary psychology and intelligence research/differential psychology. I suggest that general intelligence may simultaneously be an evolved adaptation and an individual-difference variable. Tooby and Cosmides's (1990a) notion of random quantitative variation on a monomorphic design allows us to incorporate heritable individual differences in evolved adaptations. The Savanna-IQ Interaction Hypothesis, which is one consequence of the integration of evolutionary psychology and intelligence research, can potentially explain why less intelligent individuals enjoy TV more, why liberals are more intelligent than conservatives, and why night owls are more intelligent than morning larks, among many other findings. The general approach proposed here will allow us to integrate evolutionary psychology with any other aspect of differential psychology.
Liu, Derong; Li, Hongliang; Wang, Ding
In this paper, we establish error bounds of adaptive dynamic programming algorithms for solving undiscounted infinite-horizon optimal control problems of discrete-time deterministic nonlinear systems. We consider approximation errors in the update equations of both value function and control policy. We utilize a new assumption instead of the contraction assumption in discounted optimal control problems. We establish the error bounds for approximate value iteration based on a new error condition. Furthermore, we also establish the error bounds for approximate policy iteration and approximate optimistic policy iteration algorithms. It is shown that the iterative approximate value function can converge to a finite neighborhood of the optimal value function under some conditions. To implement the developed algorithms, critic and action neural networks are used to approximate the value function and control policy, respectively. Finally, a simulation example is given to demonstrate the effectiveness of the developed algorithms.
García-Gen, Santiago; Rodríguez, Jorge; Lema, Juan M
Anaerobic co-digestion of multiple substrates has the potential to enhance biogas productivity by making use of the complementary characteristics of different substrates. A blending strategy based on a linear programming optimisation method is proposed aiming at maximising COD conversion into methane, but simultaneously maintaining a digestate and biogas quality. The method incorporates experimental and heuristic information to define the objective function and the linear restrictions. The active constraints are continuously adapted (by relaxing the restriction boundaries) such that further optimisations in terms of methane productivity can be achieved. The feasibility of the blends calculated with this methodology was previously tested and accurately predicted with an ADM1-based co-digestion model. This was validated in a continuously operated pilot plant, treating for several months different mixtures of glycerine, gelatine and pig manure at organic loading rates from 1.50 to 4.93 gCOD/Ld and hydraulic retention times between 32 and 40 days at mesophilic conditions.
Yang, Yongliang; Wunsch, Donald; Yin, Yixin
This paper presents a Hamiltonian-driven framework of adaptive dynamic programming (ADP) for continuous time nonlinear systems, which consists of evaluation of an admissible control, comparison between two different admissible policies with respect to the corresponding the performance function, and the performance improvement of an admissible control. It is showed that the Hamiltonian can serve as the temporal difference for continuous-time systems. In the Hamiltonian-driven ADP, the critic network is trained to output the value gradient. Then, the inner product between the critic and the system dynamics produces the value derivative. Under some conditions, the minimization of the Hamiltonian functional is equivalent to the value function approximation. An iterative algorithm starting from an arbitrary admissible control is presented for the optimal control approximation with its convergence proof. The implementation is accomplished by a neural network approximation. Two simulation studies demonstrate the effectiveness of Hamiltonian-driven ADP.
Wei, Qing-Lai; Liu, De-Rong; Xu, Yan-Cai
A policy iteration algorithm of adaptive dynamic programming (ADP) is developed to solve the optimal tracking control for a class of discrete-time chaotic systems. By system transformations, the optimal tracking problem is transformed into an optimal regulation one. The policy iteration algorithm for discrete-time chaotic systems is first described. Then, the convergence and admissibility properties of the developed policy iteration algorithm are presented, which show that the transformed chaotic system can be stabilized under an arbitrary iterative control law and the iterative performance index function simultaneously converges to the optimum. By implementing the policy iteration algorithm via neural networks, the developed optimal tracking control scheme for chaotic systems is verified by a simulation. Project supported by the National Natural Science Foundation of China (Grant Nos. 61034002, 61233001, 61273140, 61304086, and 61374105) and the Beijing Natural Science Foundation, China (Grant No. 4132078).
Sahoo, Avimanyu; Jagannathan, Sarangapani
In this paper, an event-driven stochastic adaptive dynamic programming (ADP)-based technique is introduced for nonlinear systems with a communication network within its feedback loop. A near optimal control policy is designed using an actor-critic framework and ADP with event sampled state vector. First, the system dynamics are approximated by using a novel neural network (NN) identifier with event sampled state vector. The optimal control policy is generated via an actor NN by using the NN identifier and value function approximated by a critic NN through ADP. The stochastic NN identifier, actor, and critic NN weights are tuned at the event sampled instants leading to aperiodic weight tuning laws. Above all, an adaptive event sampling condition based on estimated NN weights is designed by using the Lyapunov technique to ensure ultimate boundedness of all the closed-loop signals along with the approximation accuracy. The net result is event-driven stochastic ADP technique that can significantly reduce the computation and network transmissions. Finally, the analytical design is substantiated with simulation results.
This article seeks to unify two subfields of psychology that have hitherto stood separately: evolutionary psychology and intelligence research/differential psychology. I suggest that general intelligence may simultaneously be an evolved adaptation and an individual-difference variable. Tooby and Cosmides's (1990a) notion of random quantitative…
Dumas, Jean E.; Arriaga, Ximena; Begle, Angela Moreland; Longoria, Zayra
This paper describes the Spanish adaptation of PACE—Parenting Our Children to Excellence. Successfully offered in preschools and daycare centers since 2002, PACE is a research-based preventive intervention to support families in their parenting task through discussions and activities that address practical childrearing issues and promote child coping-competence. Developed in response to community calls, the new program is known as CANNE –Criando a Nuestros Niños hacia el Éxito. The paper makes the processes linking original and adapted versions explicit by accounting for the conceptual and practical decisions that were made as CANNE was being developed. We begin by summarizing the challenges of adapting and translating a behavioral intervention, and by describing the coping-competence model that informs both versions of the program. We turn then to a detailed account of the adaptation itself and of its results. Specifically, we describe: (a) the consultation process at the origin of this adaptation, (b) the adaptation of the manual and the steps taken to establish the extent to which the English and Spanish versions correspond (adaptation fidelity), and (c) the translation of the manual and the cross-language comparison of measures to demonstrate that they yield comparable data when administered in English and Spanish. PMID:20607140
Hopson, Laura M.; Holleran Steiker, Lori K.
Although there is a strong evidence base for effective substance abuse prevention programs for youth, there is a need to facilitate the implementation and evaluation of these programs in real world settings. This study evaluates the effectiveness of adapted versions of an evidence-based prevention program, keepin’ it REAL (kiR), with alternative school students. Programs are often adapted when used in schools and other community settings for a variety of reasons. The kiR adaptations, developed during an earlier phase of this study, were created to make the curriculum more appropriate for alternative high school youth. The adaptations were evaluated using a quasi-experimental design in which questionnaires were administered at pretest, posttest, and follow-up, and focus groups were conducted at posttest. MANOVA analyses indicate significantly reduced intentions to accept alcohol and, for younger participants, reduced alcohol use. Focus group data support the need for age appropriate prevention content. The authors discuss implications for practitioners implementing prevention programs in schools. PMID:20622971
Lindberg, Nangel M.; Stevens, Victor J.; Vega-López, Sonia; Kauffman, Tia; Calderón, Mariana Rosales; Cervantes, María Antonieta
Background This study assessed the feasibility of a culturally-appropriate weight-loss intervention targeting obese Spanish-speaking Mexican women. Methods This 12-month weight-loss program was based on behavioral interventions previously used successfully with English-speaking participants. Cultural adaptations included: female interventionists, minimal written materials, emphasis on group activities, focus on Mexican traditions and beliefs, and skill-building approach to food measurement. All sessions were conducted in Spanish. The study had few exclusionary criteria, which allowed participation of women with a wide range of literacy levels. Results Recruitment exceeded expectations, with 47 participants enrolling in the program. Not counting participants who became pregnant during the study, attendance at 6 and 12 months was 62% and 50% respectively. Mean weight loss at 6 and 12 months was 5.3 kg and 7.2 kg, respectively, with a mean reduction in BMI of 4.0 kg/m2 and 5.5 kg/m2 from baseline to 6 and 12 months, respectively. Discussion This pilot study shows that it is feasible to develop and implement culturally-appropriate behavioral lifestyle interventions for obesity treatment in Mexican-American women. PMID:22460538
Lindberg, Nangel M; Stevens, Victor J; Vega-López, Sonia; Kauffman, Tia L; Calderón, Mariana Rosales; Cervantes, María Antonieta
This study assessed the feasibility of a culturally-appropriate weight-loss intervention targeting obese Spanish-speaking Mexican women. This 12-month weight-loss program was based on behavioral interventions previously used successfully with English-speaking participants. Cultural adaptations included: female interventionists, minimal written materials, emphasis on group activities, focus on Mexican traditions and beliefs, and skill-building approach to food measurement. All sessions were conducted in Spanish. The study had few exclusionary criteria, which allowed participation of women with a wide range of literacy levels. Recruitment exceeded expectations, with 47 participants enrolling in the program. Not counting participants who became pregnant during the study, attendance at 6 and 12 months was 62 and 50 % respectively. Mean weight loss at 6 and 12 months was 5.3 and 7.2 kg, respectively, with a mean reduction in BMI of 4.0 and 5.5 kg/m(2) from baseline to 6 and 12 months, respectively. This pilot study shows that it is feasible to develop and implement culturally-appropriate behavioral lifestyle interventions for obesity treatment in Mexican-American women.
Vishnepolsky, Boris; Pirtskhalava, Malak
The presented program ALIGN_MTX makes alignment of two textual sequences with an opportunity to use any several characters for the designation of sequence elements and arbitrary user substitution matrices. It can be used not only for the alignment of amino acid and nucleotide sequences but also for sequence-structure alignment used in threading, amino acid sequence alignment, using preliminary known PSSM matrix, and in other cases when alignment of biological or non-biological textual sequences is required. This distinguishes it from the majority of similar alignment programs that make, as a rule, alignment only of amino acid or nucleotide sequences represented as a sequence of single alphabetic characters. ALIGN_MTX is presented as downloadable zip archive at http://www.imbbp.org/software/ALIGN_MTX/ and available for free use. As application of using the program, the results of comparison of different types of substitution matrix for alignment quality in distantly related protein pair sets were presented. Threading matrix SORDIS, based on side-chain orientation in relation to hydrophobic core centers with evolutionary change-based substitution matrix BLOSUM and using multiple sequence alignment information position-specific score matrices (PSSM) were taken for test alignment accuracy. The best performance shows PSSM matrix, but in the reduced set with lower sequence similarity threading matrix SORDIS shows the same performance and it was shown that combined potential with SORDIS and PSSM can improve alignment quality in evolutionary distantly related protein pairs.
Allison, Andrew B.; Stallknecht, David E.; Holmes, Edward C.
Western equine encephalitis virus (WEEV), Highlands J virus (HJV), and Fort Morgan virus (FMV) are the sole representatives of the WEE antigenic complex of the genus Alphavirus, family Togaviridae, that are endemic to North America. All three viruses have their ancestry in a recombination event involving eastern equine encephalitis virus (EEEV) and a Sindbis (SIN)-like virus that gave rise to a chimeric alphavirus that subsequently diversified into the present-day WEEV, HJV, and FMV. Here, we present a comparative analysis of the genetic, ecological, and evolutionary relationships among these recombinant-origin viruses, including the description of a nsP4 polymerase mutation in FMV that allows it to circumvent the host range barrier to Asian tiger mosquito cells, a vector species that is normally refractory to infection. Notably, we also provide evidence that the recombination event that gave rise to these three WEEV antigenic complex viruses may have occurred in North America. PMID:25463613
Allison, Andrew B; Stallknecht, David E; Holmes, Edward C
Western equine encephalitis virus (WEEV), Highlands J virus (HJV), and Fort Morgan virus (FMV) are the sole representatives of the WEE antigenic complex of the genus Alphavirus, family Togaviridae, that are endemic to North America. All three viruses have their ancestry in a recombination event involving eastern equine encephalitis virus (EEEV) and a Sindbis (SIN)-like virus that gave rise to a chimeric alphavirus that subsequently diversified into the present-day WEEV, HJV, and FMV. Here, we present a comparative analysis of the genetic, ecological, and evolutionary relationships among these recombinant-origin viruses, including the description of a nsP4 polymerase mutation in FMV that allows it to circumvent the host range barrier to Asian tiger mosquito cells, a vector species that is normally refractory to infection. Notably, we also provide evidence that the recombination event that gave rise to these three WEEV antigenic complex viruses may have occurred in North America.
Peace, Diane McClymont; Myers, Erin
Objectives Health Canada's Program for Climate Change and Health Adaptation in Northern First Nation and Inuit Communities is unique among Canadian federal programs in that it enables community-based participatory research by northern communities. Study design The program was designed to build capacity by funding communities to conduct their own research in cooperation with Aboriginal associations, academics, and governments; that way, communities could develop health-related adaptation plans and communication materials that would help in adaptation decision-making at the community, regional, national and circumpolar levels with respect to human health and a changing environment. Methods Community visits and workshops were held to familiarize northerners with the impacts of climate change on their health, as well as methods to develop research proposals and budgets to meet program requirements. Results Since the launch of the Climate Change and Health Adaptation Program in 2008, Health Canada has funded 36 community projects across Canada's North that focus on relevant health issues caused by climate change. In addition, the program supported capacity-building workshops for northerners, as well as a Pan-Arctic Results Workshop to bring communities together to showcase the results of their research. Results include: numerous films and photo-voice products that engage youth and elders and are available on the web; community-based ice monitoring, surveillance and communication networks; and information products on land, water and ice safety, drinking water, food security and safety, and traditional medicine. Conclusions Through these efforts, communities have increased their knowledge and understanding of the health effects related to climate change and have begun to develop local adaptation strategies. PMID:22584509
The development of an evolutionary lunar transportation family (LTF) that can accommodate evolving human exploration goals is discussed. An evolutionary system is aimed at minimizing program costs while preserving programmatic versatility. Technical requirements that affect the design strategy for LTF include aerobraking technology and packaging constraints; mixed, unsymmetrical payload manifests; crew and payload exchange operations; crew and cargo off-loading on the lunar surface; and cryogenic lunar transfer and storage. It is concluded that the LTF is capable of meeting exploration goals, which include the provision for a significant early manned lunar surface science and exploration capability, the avoidance or reduction of some major operational and infrastructure requirements, and the incorporation of common vehicle designs and existing/near-term technology.
Velasco, Veronica; Griffin, Kenneth W; Botvin, Gilbert J
Evidence-based preventive interventions for adolescent substance use, violence, and mental health issues are increasingly being adapted and disseminated internationally. In the present paper, we report the results of an effectiveness study that was part of a comprehensive initiative by a coalition of health promotion organizations in the Lombardy region of Italy to select, culturally adapt, implement, evaluate, and sustain an evidence-based drug abuse prevention program developed in the USA. Findings are presented from a large-scale effectiveness study of the Life Skills Training prevention program among over 3000 students attending 55 middle schools in Italy. The prevention program taught drug refusal skills, antidrug norms, personal self-management skills, and general social skills. Relative to comparison group students, students who received the prevention program were less likely to initiate smoking at the post-test and 2-year follow-up, and less likely to initiate weekly drunkenness at the 1-year follow-up. The program had direct positive effects on several cognitive, attitudinal, and skill variables believed to play a protective role in adolescent substance use. The findings from this study show that a drug abuse prevention program originally designed for adolescents in the USA is effective in a sample of Italian youth when a rigorous and systematic approach to cultural adaptation is followed that incorporates the input of multiple stakeholders.
Runge, Michael C.; Converse, Sarah J.; Lyons, James E.
Natural resource management is plagued with uncertainty of many kinds, but not all uncertainties are equally important to resolve. The promise of adaptive management is that learning in the short-term will improve management in the long-term; that promise is best kept if the focus of learning is on those uncertainties that most impede achievement of management objectives. In this context, an existing tool of decision analysis, the expected value of perfect information (EVPI), is particularly valuable in identifying the most important uncertainties. Expert elicitation can be used to develop preliminary predictions of management response under a series of hypotheses, as well as prior weights for those hypotheses, and the EVPI can be used to determine how much management could improve if uncertainty was resolved. These methods were applied to management of whooping cranes (Grus americana), an endangered migratory bird that is being reintroduced in several places in North America. The Eastern Migratory Population of whooping cranes had exhibited almost no successful reproduction through 2009. Several dozen hypotheses can be advanced to explain this failure, and many of them lead to very different management responses. An expert panel articulated the hypotheses, provided prior weights for them, developed potential management strategies, and made predictions about the response of the population to each strategy under each hypothesis. Multi-criteria decision analysis identified a preferred strategy in the face of uncertainty, and analysis of the expected value of information identified how informative each strategy could be. These results provide the foundation for design of an adaptive management program.
Following construction of Trinity and Lewiston dams on the upper Trinity River in 1964, dam induced changes to streamflows and sediment regime had severely simplified channel morphology and aquatic habitat downstream of the dams. This habitat change, combined with blocked access to over 100 miles of salmon and steelhead habitat upstream of the dams, caused salmon and steelhead populations to quickly plummet. An instream flow study was initiated in 1984 to address the flow needs to restore the fishery, and this study relied on the Physical Habitat Simulation (PHABSIM) Model to quantify instream flow needs. In 1992, geomorphic and riparian studies were integrated into the instream flow study, with the overall study completed in 1999 (USFWS 1999). This 13-year process continued through three presidential administrations, several agency managers, and many turnovers of the agency technical staff responsible for conducting the study. This process culminated in 1996-1998 when a group of scientists were convened to integrate all the studies and data to produce the final instream flow study document. This 13-year, non-linear process, resulted in many uncertainties that could not be resolved in the short amount of time allowed for completing the instream flow study document. Shortly after completion of the instream flow study document, the Secretary of Interior issued a Record of Decision to implement the recommendations contained in the instream flow study document. The uncertainties encountered as the instream flow study report was prepared were highlighted in the report, and the Record of Decision initiated an Adaptive Environmental Assessment and Management program to address these existing uncertainties and improve future river management. There have been many lessons learned going through this process, and the presentation will summarize: 1)The progression of science used to develop the instream flow study report; 2)How the scientists preparing the report addressed
Saint-Laurent, Lise; Giasson, Jocelyne
This article reports on the effects of a family literacy program for first graders that had three main characteristics: (1) book reading with parents that adapts parental intervention to the child's gradually increasing skills in reading during the school year, (2) support for writing activities, and (3) enjoyable home activities complementing the…
Castro-Olivo, Sara M.
The current study evaluated the effects of the culturally adapted "Jóvenes Fuertes" ("Strong Teens") Social-Emotional Learning (SEL) program on the social-emotional outcomes of Latino English language learners (ELLs). A quasi-experimental design with random assignment by classrooms was used to assess the intervention's…
Khunkrai, Naruemon; Sawangboon, Tatsirin; Ketchatturat, Jatuphum
The aim of this research is to study the accurate prediction of comparing test information and evaluation result by multidimensional computerized adaptive scholastic aptitude test program used for grade 9 students under different reviewing test conditions. Grade 9 students of the Secondary Educational Service Area Office in the North-east of…
awards \\#0720882 ( CSR -EHS: PRET), \\#0931843 (CPS: Large: ActionWebs), and \\#1035672 (CPS: Medium: Ptides)), the Naval Research Laboratory (NRL \\#N0013-12...1- G015), and the following companies : Bosch, National Instruments, and Toyota. StreaMorph: A Case for Synthesizing Energy-Efficient Adaptive Programs
Dimitrios, Voutsas; Dimitrios, Kokaridas
The purpose of this action research study was to examine the effect of an adapted swimming program in terms of improving the performance and behaviour of an individual with kyphosis-scoliosis, with the use of an individualised education approach. The sample consisted of an adult woman with kyphosis-scoliosis. The pre-swimming phase included a…
Cameron, Gary; Frensch, Karen; Preyde, Michele; Quosai, Trudy Smit
This article presents the findings from a longitudinal investigation of the prevalence of negative contact with the law for a sample of youth 12-18 months after graduating from residential and intensive children's mental health programming. Results of this study suggest serious community adaptation difficulties face many youth graduating from…
Vonlintel, Drew James
This dissertation examines the efficacy of peer tutor training in adapted physical education (APE). A peer tutor evaluation form was created to assess the skills of untrained peer tutors (n = 12). Once skills were assessed, a peer tutor training protocol was created. The protocol was implemented in a peer tutor training program. After peer tutors…
Vasiliadis, Angelo; Christoulas, Kosmas; Evaggelinou, Christina; Vrabas, Ioannis
The purpose of this study was to investigate the physiological adaptations in cardio respiratory endurance with a personalized exercise program with arm-cranking exercise in a paraplegic person (incomplete T12 spinal cord injury). A 32 year-old man with spinal cord injury (T12) participated in the present study performing 30 minutes arm cranking…
Stein, Dan J
Darwin's seminal publications in the nineteenth century laid the foundation for an evolutionary approach to psychology and psychiatry. Advances in 20th century evolutionary theory facilitated the development of evolutionary psychology and psychiatry as recognized areas of scientific investigation. In this century, advances in understanding the molecular basis of evolution, of the mind, and of psychopathology, offer the possibility of an integrated approach to understanding the proximal (psychobiological) and distal (evolutionary) mechanisms of interest to psychiatry and psychopharmacology. There is, for example, growing interest in the question of whether specific genetic variants mediate psychobiological processes that have evolutionary value in specific contexts, and of the implications of this for understanding the vulnerability to psychopathology and for considering the advantages and limitations of pharmacotherapy. The evolutionary value, and gene-environmental mediation, of early life programming is potentially a particularly rich area of investigation. Although evolutionary approaches to psychology and to medicine face important conceptual and methodological challenges, current work is increasingly sophisticated, and may prove to be an important foundational discipline for clinicians and researchers in psychiatry and psychopharmacology.
Lü, Zhi-Chuang; Gao, Qing-Lei; Wan, Fang-Hao; Yu, Hao; Guo, Jian-Ying
With increasing global climate change, analyses of stress-inducing conditions have important significance in ecological adaptation and the biological distribution of species. To reveal the difference in temperature-adaptive strategy between Turpan and Beijing populations of Bemisia tabaci (Gennadius) Middle East Asia Minor 1 (MEAM1) under high-temperature stress conditions, we compared thermal tolerance and life history traits between Beijing and Turpan populations of MEAM1 after exposure to different heat shock treatments for different times. The experimental design reflected the nature of heat stress conditions suffered by MEAM1. The results showed that eggs, red-eyed pupae, and adults of the Turpan population were more heat tolerant than those of the Beijing population under the same stress conditions. Additionally, it was found that longevity and F1 adult survival rate were significantly higher in the Turpan population than in the Beijing population after heat shock stress, but egg number and F1 female ratio were not significantly different between Turpan population and Beijing population. Overall, it was suggested that heat tolerance and longevity traits were the most relevant for climate characteristics and not reproductive traits, and improved heat tolerance and prolonged longevity were important adaptive strategies that helped MEAM1 to survive in harsh high-temperature conditions such as Turpan arid desert climate. The present results provided further insight into the modes of heat tolerance and the ways in which survival and longevity traits respond to environmental selection pressures.
Wagner, Günter P; Lynch, Vincent J
How novel traits arise in organisms has long been a major problem in biology. Indeed, the sharpest critiques of Darwin's theory of evolution by natural selection often centered on explaining how novel body parts arose. In his response to The Origin of Species, St. George J. Mivart challenged Darwin to explain the origin of evolutionary novelties such as the mammary gland, asking if it was "conceivable that the young of any animal was ever saved from destruction by accidentally sucking a drop of scarcely nutritious fluid from an accidentally hypertrophied cutaneous gland of its mother?" It is only now that modern molecular and genomic tools are being brought to bear on this question that we are finally in a position to answer Mivart's challenge and explain one of the most fundamental questions of biology: how does novelty arise in evolution?
Endler, Anke; Rey, Gunter Daniel; Butz, Martin V.
The objective of this study was to investigate if an e-learning environment may use measurements of the user's current motivation to adapt the level of task difficulty for more effective learning. In the reported study, motivation-based adaptation was applied randomly to collect a wide range of data for different adaptations in a variety of…
Poulin, David; Martinez, David; Aenchbacher, Amy; Aiello, Rocco; Doyle, Mike; Hilgenbrinck, Linda; Busse, Sean; Cappuccio, Jim
In Part III of the feature, physical educators and adapted physical educators offer current best practices as models of implementation for readers. Contributions included are: (1) Answer to the Dear Colleague Letter from the Anchorage School District's Adapted Sport Program (David Poulin); (2) Georgia's Adapted Physical Educators Response to the…
Springer, A. E.
Payments for ecosystems services and watershed investment programs have created new solutions for restoring upland fire-adapted forests to support downstream surface-water and groundwater uses. Water from upland forests supports not only a significant percentage of the public water supplies in the U.S., but also extensive riparian, aquatic, and groundwater dependent ecosystems. Many rare, endemic, threatened, and endangered species are supported by the surface-water and groundwater generated from the forested uplands. In the Ponderosa pine forests of the Southwestern U.S., post Euro-American settlement forest management practices, coupled with climate change, has significantly impacted watershed functionality by increasing vegetation cover and associated evapotranspiration and decreasing runoff and groundwater recharge. A large Collaborative Forest Landscape Restoration Program project known as the Four Forests Restoration Initiative is developing landscape scale processes to make the forests connected to these watersheds more resilient. However, there are challenges in financing the initial forest treatments and subsequent maintenance treatments while garnering supportive public opinion to forest thinning projects. A solution called the Flagstaff Watershed Protection Project is utilizing City tax dollars collected through a public bond to finance forest treatments. Exit polling from the bond election documented the reasons for the 73 % affirmative vote on the bond measure. These forest treatments have included in their actions restoration of associated ephemeral stream channels and spring ecosystems, but resources still need to be identified for these actions. A statewide strategy for developing additional forest restoration resources outside of the federal financing is being explored by state and local business and governmental leaders. Coordination, synthesis, and modeling supported by a NSF Water Sustainability and Climate project has been instrumental in
Gewirtz, Abigail H; DeGarmo, David S; Zamir, Osnat
Few studies have examined whether parenting prevention programs might mitigate risk for suicidality in parents, yet parent suicidality is a strong risk factor for offspring suicidality. We report results from a randomized controlled trial of a parenting program for deployed National Guard and Reserve families with a school-aged child. Intent-to-treat analyses showed that random assignment to the parenting program (ADAPT) was associated with improved parenting locus of control (LOC). Improved parenting LOC was concurrently associated with strengthened emotion regulation which predicted reductions in psychological distress and suicidal ideation at 12 months postbaseline. Results are discussed in the context of ongoing efforts to reduce suicide rates in military populations.
Bowen, Marie Katherine; Taylor, Kathleen P; Marcus-Aiyeku, Ulanda; Krause-Parello, Cheryl A
Addiction rates in nurses are higher than in the general population. The relationship between stress, coping, and adaptation in nurses (N = 82) enrolled in a recovery and monitoring program in the state of New Jersey was examined. Social support, a variable tested as a mediator of this relationship, was also examined. Participants completed the Perceived Stress Scale, Multidimensional Scale of Perceived Social Support, and Psychological General Well-Being Index. Negative relationships were found between stress and social support and stress and well-being, and a positive relationship was found between social support and well-being (all ps < .05). The direct relationship between stress and well-being was decreased in the presence of social support. The findings of this research suggest that, to assist nurses, an increased awareness of stress and its injurious effects on overall well-being must be identified so proactive measures can be implemented to prevent potential untoward consequences. Ultimately, methods to strengthen social support and social networks will enhance the probability of sustained recovery, relapse prevention, and safe reentry into nursing practice. Implications for behavioral health providers and health care practitioners are discussed.
Zhu, Yuanheng; Zhao, Dongbin; Li, Xiangjun
H∞ control is a powerful method to solve the disturbance attenuation problems that occur in some control systems. The design of such controllers relies on solving the zero-sum game (ZSG). But in practical applications, the exact dynamics is mostly unknown. Identification of dynamics also produces errors that are detrimental to the control performance. To overcome this problem, an iterative adaptive dynamic programming algorithm is proposed in this paper to solve the continuous-time, unknown nonlinear ZSG with only online data. A model-free approach to the Hamilton-Jacobi-Isaacs equation is developed based on the policy iteration method. Control and disturbance policies and value are approximated by neural networks (NNs) under the critic-actor-disturber structure. The NN weights are solved by the least-squares method. According to the theoretical analysis, our algorithm is equivalent to a Gauss-Newton method solving an optimization problem, and it converges uniformly to the optimal solution. The online data can also be used repeatedly, which is highly efficient. Simulation results demonstrate its feasibility to solve the unknown nonlinear ZSG. When compared with other algorithms, it saves a significant amount of online measurement time.
Liu, Derong; Wei, Qinglai
This paper is concerned with a new discrete-time policy iteration adaptive dynamic programming (ADP) method for solving the infinite horizon optimal control problem of nonlinear systems. The idea is to use an iterative ADP technique to obtain the iterative control law, which optimizes the iterative performance index function. The main contribution of this paper is to analyze the convergence and stability properties of policy iteration method for discrete-time nonlinear systems for the first time. It shows that the iterative performance index function is nonincreasingly convergent to the optimal solution of the Hamilton-Jacobi-Bellman equation. It is also proven that any of the iterative control laws can stabilize the nonlinear systems. Neural networks are used to approximate the performance index function and compute the optimal control law, respectively, for facilitating the implementation of the iterative ADP algorithm, where the convergence of the weight matrices is analyzed. Finally, the numerical results and analysis are presented to illustrate the performance of the developed method.
Xie, Shengli; Zhong, Weifeng; Xie, Kan; Yu, Rong; Zhang, Yan
Research on the smart grid is being given enormous supports worldwide due to its great significance in solving environmental and energy crises. Electric vehicles (EVs), which are powered by clean energy, are adopted increasingly year by year. It is predictable that the huge charge load caused by high EV penetration will have a considerable impact on the reliability of the smart grid. Therefore, fair energy scheduling for EV charge and discharge is proposed in this paper. By using the vehicle-to-grid technology, the scheduler controls the electricity loads of EVs considering fairness in the residential distribution network. We propose contribution-based fairness, in which EVs with high contributions have high priorities to obtain charge energy. The contribution value is defined by both the charge/discharge energy and the timing of the action. EVs can achieve higher contribution values when discharging during the load peak hours. However, charging during this time will decrease the contribution values seriously. We formulate the fair energy scheduling problem as an infinite-horizon Markov decision process. The methodology of adaptive dynamic programming is employed to maximize the long-term fairness by processing online network training. The numerical results illustrate that the proposed EV energy scheduling is able to mitigate and flatten the peak load in the distribution network. Furthermore, contribution-based fairness achieves a fast recovery of EV batteries that have deeply discharged and guarantee fairness in the full charge time of all EVs.
Wei, Qinglai; Liu, Derong; Lin, Hanquan
In this paper, a value iteration adaptive dynamic programming (ADP) algorithm is developed to solve infinite horizon undiscounted optimal control problems for discrete-time nonlinear systems. The present value iteration ADP algorithm permits an arbitrary positive semi-definite function to initialize the algorithm. A novel convergence analysis is developed to guarantee that the iterative value function converges to the optimal performance index function. Initialized by different initial functions, it is proven that the iterative value function will be monotonically nonincreasing, monotonically nondecreasing, or nonmonotonic and will converge to the optimum. In this paper, for the first time, the admissibility properties of the iterative control laws are developed for value iteration algorithms. It is emphasized that new termination criteria are established to guarantee the effectiveness of the iterative control laws. Neural networks are used to approximate the iterative value function and compute the iterative control law, respectively, for facilitating the implementation of the iterative ADP algorithm. Finally, two simulation examples are given to illustrate the performance of the present method.
Homick, J. L.; Reschke, M. F.; Vanderploeg, J. M.
Better methods for the prediction, prevention, and treatment of the space adaptation syndome (SAS) were developed. A systematic, long range program of operationally oriented data collection on all individuals flying space shuttle missions was initiated. Preflight activities include the use of a motion experience questionnaire, laboratory tests of susceptibility to motion sickness induced by Coriolis stimuli and determinations of antimotion sickness drug efficacy and side effects. During flight, each crewmember is required to provide a daily report of symptom status, use of medications, and other vestibular related sensations. Additional data are obtained postflight. During the first nine shuttle missions, the reported incidence of SAS has been48%. Self-induced head motions and unusual visual orientation attitudes appear to be the principal triggering stimuli. Antimotion sickness medication, was of limited therapeutic value. Complete recovery from symptoms occurred by mission day three or four. Also of relevance is the lack of a statistically significant correlation between the ground based Coriolis test and SAS. The episodes of SAS have resulted in no impact to shuttle mission objectives and, no significant impact to mission timelines.
Kulis, Stephen; Ayers, Stephanie L.; Baker, Tahnee
This study reports the implementation and feasibility of a culturally adapted parenting curriculum, Parenting in 2 Worlds (P2W), which we designed specifically for urban American Indian families by means of community-based participatory research and then pilot tested in three Arizona cities. Data come from matched pre- and post-test surveys completed in 2012 by 75 American Indian parents of adolescents aged 10–17 who participated in the pilot version of P2W. P2W is a 10-workshop program administered twice a week for five weeks by trained American Indian community facilitators. Parents completed pretest surveys during Workshop 1 and post-test surveys five weeks later during Workshop 10. Paired t tests assessed changes in parenting outcomes, cultural identity, and child anti-social behavior. Changes from pre- to post-test demonstrated statistically significant improvements in several parenting outcomes (discipline, involvement, self-agency, and supervision), a strengthened sense of ethnic and cultural identity and Native spirituality, and a decrease in the child’s anti-social behavior. These results, which show significant if preliminary improvements in parenting skills and family functioning, suggest the feasibility of implementing a culturally grounded parenting intervention for urban American Indian parents. PMID:25367804
Kulis, Stephen; Ayers, Stephanie L; Baker, Tahnee
This study reports the implementation and feasibility of a culturally adapted parenting curriculum, Parenting in 2 Worlds (P2W), which we designed specifically for urban American Indian families by means of community-based participatory research and then pilot tested in three Arizona cities. Data come from matched pre- and post-test surveys completed in 2012 by 75 American Indian parents of adolescents aged 10-17 who participated in the pilot version of P2W. P2W is a 10-workshop program administered twice a week for 5 weeks by trained American Indian community facilitators. Parents completed pre-test surveys during Workshop 1 and post-test surveys 5 weeks later during Workshop 10. Paired t tests assessed changes in parenting outcomes, cultural identity, and child anti-social behavior. Changes from pre- to post-test demonstrated statistically significant improvements in several parenting outcomes (discipline, involvement, self-agency, and supervision), a strengthened sense of ethnic and cultural identity and Native spirituality, and a decrease in the child's anti-social behavior. These results, which show significant preliminary improvements in parenting skills and family functioning, suggest the feasibility of implementing a culturally grounded parenting intervention for urban American Indian parents.
Benedetti, Maria Grazia; Berti, Lisa; Presti, Chiara; Frizziero, Antonio; Giannini, Sandro
Background Flexed posture commonly increases with age and is related to musculoskeletal impairment and reduced physical performance. The purpose of this clinical study was to systematically compare the effects of a physical activity program that specifically address the flexed posture that marks a certain percentage of elderly individuals with a non specific exercise program for 3 months. Methods Participants were randomly divided into two groups: one followed an Adapted Physical Activity program for flexed posture and the other one completed a non-specific physical activity protocol for the elderly. A multidimensional clinical assessment was performed at baseline and at 3 months including anthropometric data, clinical profile, measures of musculoskeletal impairment and disability. The instrumental assessment of posture was realized using a stereophotogrammetric system and a specific biomechanical model designed to describe the reciprocal position of the body segments on the sagittal plane in a upright posture. Results The Adapted Physical Activity program determined a significant improvement in several key parameters of the multidimensional assessment in comparison to the non-specific protocol: decreased occiput-to-wall distance, greater lower limb range of motion, better flexibility of pectoralis, hamstrings and hip flexor muscles, increased spine extensor muscles strength. Stereophotogrammetric analysis confirmed a reduced protrusion of the head and revealed a reduction in compensative postural adaptations to flexed posture characterized by knee flexion and ankle dorsiflexion in the participants of the specific program. Conclusion The Adapted Physical Activity program for flexed posture significantly improved postural alignment and musculoskeletal impairment of the elderly. The stereophotogrammetric evaluation of posture was useful to measure the global postural alignment and especially to analyse the possible compensatory strategies at lower limbs in flexed
Esplin, Andrea; Baldwin, Laura-Mae
Introduction Federally Qualified Health Centers (FQHCs) provide primary care to low-income and uninsured patients in the United States. FQHCs are required to report annual measurements and provide evidence of improvement for quality measures; effective methods to improve quality in FQHCs are needed. Systems of Support (SOS) is a proactive, mail-based, colorectal cancer screening program that was developed and tested in an integrated health care system. The objective of this study was to adapt SOS for use in an FQHC system, guided by the Consolidated Framework for Implementation Research (CFIR). Methods We conducted qualitative semi-structured interviews in 2014 with organizational leadership, medical staff, and nursing staff to identify facilitators of and barriers to implementation of SOS in an FQHC system. The interview guide was based on the CFIR framework. Interview transcripts were analyzed using Template Analysis. We adapted SOS and planned implementation strategies to address identified barriers. Results Facilitators of implementation of SOS were previous quality improvement experience and engagement of clinic and administrative leadership. Barriers to implementation were a more diverse patient population, a decentralized administrative structure, and communication challenges throughout the organization. Program adaptations focused on patient instructions and educational materials as well as elimination of follow-up phone calls. Implementation strategies included early and frequent engagement with organizational leadership and a smaller pilot program before organization-wide implementation. Conclusions Use of CFIR identified facilitators of and barriers to implementation of the evidence-based colorectal cancer screening program. Program adaptations and implementation strategies based on this study may generalize to other FQHC systems that are considering implementation of a proactive, mail-based colorectal cancer screening program. PMID:26632954
Wang-Schweig, Meme; Kviz, Frederick J; Altfeld, Susan J; Miller, Arlene M; Miller, Brenda A
The debate on the effectiveness and merit for the amount of time, effort, and resources to culturally adapt health promotion and prevention programs continues. This may be due, in large part, to the lack of theory in commonly used methods to match programmatic content and delivery to the culture of a population, particularly at the deep structural level. This paper asserts that prior to the cultural adaptation of prevention programs, it is necessary to first develop a conceptual framework. We propose a multiphase approach to address key challenges in the science of cultural adaptation by first identifying and exploring relevant cultural factors that may affect the targeted health-related behavior prior to proceeding through steps of a stage model. The first phase involves developing an underlying conceptual framework that integrates cultural factors to ground this process. The second phase employs the different steps of a stage model. For Phase I of our approach, we offer four key steps and use our research study as an example of how these steps were applied to build a framework for the cultural adaptation of a family-based intervention to prevent adolescent alcohol use, Guiding Good Choices (GGC), to Chinese American families. We then provide a summary of the preliminary evidence from a few key relationships that were tested among our sample with the greater purpose of discussing how these findings might be used to culturally adapt GGC.
Lancioni, Giulio E.; Singh, Nirbhay N.; O'Reilly, Mark F.; Sigafoos, Jeff; Oliva, Doretta; Gatti, Michela; Manfredi, Francesco; Megna, Gianfranco; La Martire, Maria L.; Tota, Alessia; Smaldone, Angela; Groeneweg, Jop
A program relying on microswitch clusters (i.e., combinations of microswitches) and preferred stimuli was recently developed to foster adaptive responses and head control in persons with multiple disabilities. In the last version of this program, preferred stimuli (a) are scheduled for adaptive responses occurring in combination with head control…
Shin, Sunwoo; Koh, Myung-sook; Yeo, Moon-Hwan
The purpose of this study was to investigate preliminary intervention effects of the adaptive behavior on the autism intervention program known as the Learning Program for the Development of Children with Autism (LPDCA). The adaptive behavior scores of two groups of students with autism spectrum disorders (ASD) were compared, with one group…
Lancioni, Giulio E.; O'Reilly, Mark F.; Singh, Nirbhay N.; Sigafoos, Jeff; Oliva, Doretta; Cingolani, Eleonora; D'Oro, Lega F.
We evaluated an upgraded version of a microswitch-cluster program used for promoting adaptive foot and head responses and reducing finger mouthing with a boy with multiple disabilities. The boy had been exposed to an early version of the program, which ensured that positive stimulation followed only adaptive responses occurring free from finger…
Battaglia, Giuseppe; Bellafiore, Marianna; Alesi, Marianna; Paoli, Antonio; Bianco, Antonino; Palma, Antonio
Background Several studies have shown the positive effects of adapted physical activity (APA) on physical and mental health (MH) during the lifetime. The aim of this study was to assess the effectiveness of a specific APA intervention program in the improvement of the health-related quality of life (QOL) and functional condition of spine in elderly women. Methods Thirty women were recruited from a senior center and randomly assigned to two groups: control group (CG; age: 69.69±7.94 years, height: 1.57±0.06 m, weight: 68.42±8.18 kg, body mass index [BMI]: 27.88±2.81) and trained group (TG; age: 68.35±6.04 years, height: 1.55±0.05 m, weight: 64.78±10.16 kg, BMI: 26.98±3.07). The APA program was conducted for 8 weeks, with two training sessions/week. CG did not perform any physical activity during the study. Spinal angles were evaluated by SpinalMouse® (Idiag, Volkerswill, Switzerland); health-related QOL was evaluated by SF-36 Health Survey, which assesses physical component summary (PCS-36), mental component summary (MCS-36), and eight subscales: physical functioning, role-physical, bodily pain, general health perception, role-emotional, social functioning, vitality, and MH. All measures were recorded before and after the experimental period. Results In TG, compared to CG, the two-way analysis of variance with repeated measures with Bonferroni post hoc test showed a relevant improvement in lumbar spinal angle (°) and in SF-36 outcomes after the intervention period. We showed a significant increase in physical functioning, bodily pain, and MH subscales and in PCS-36 and MCS-36 scores in TG compared to CG. In particular, from baseline to posttest, we found that in TG, the PCS-36 and MCS-36 scores increased by 13.20% and 11.64%, respectively. Conclusion We believe that an 8-week APA intervention program is able to improve psychophysical heath in elderly people. During the aging process, a dynamic lifestyle, including regular physical activity, is a crucial
Melis, T. S.; Walters, C. J.; Korman, J.
With a focus on resources of the Colorado River ecosystem downstream of Glen Canyon Dam in Glen Canyon National Recreation Area (GCNRA) and Grand Canyon National Park (GCNP) of northern Arizona, the Glen Canyon Dam Adaptive Management Program has evaluated experimental flow and nonflow policy tests since 1990. Flow experiments have consisted of a variety of water releases from the dam within pre-existing annual downstream delivery agreements. The daily experimental dam operation, termed the Modified Low Fluctuating Flow (MLFF), implemented in 1996 to increase daily low flows and decrease daily peaks were intended to limit daily flow range to conserve tributary sand inputs and improve navigation among other objectives, including hydropower energy. Other flow tests have included controlled floods with some larger releases bypassing the dam's hydropower plant to rebuild and maintain eroded sandbars in GCNP. Experimental daily hydropeaking tests beyond MLFF have also been evaluated for managing the exotic recreational rainbow trout fishery in the dam's GCNRA tailwater. Experimental nonflow policies, such as physical removal of exotic fish below the tailwater, and experimental translocation of endangered native humpback chub from spawning habitats in the Little Colorado River (the largest natal origin site for chub in the basin) to other tributaries within GCNP have also been monitored. None of these large-scale field experiments has yet produced unambiguous results in terms of management prescriptions, owing to inadequate monitoring programs and confounding of treatment effects with effects of ongoing natural changes; most notably, a persistent warming of the river resulting from reduced storage in the dam's reservoir after 2003. But there have been several surprising results relative to predictions from models developed to identify monitoring needs and evaluate experimental design options at the start of the adaptive ecosystem assessment and management program in 1997
Johnson, Fred A.; Alhainen, Mikko; Fox, Anthony D.; Madsen, Jesper
This report describes recent progress in specifying the elements of an adaptive harvest program for taiga bean goose. It describes harvest levels appropriate for first rebuilding the population of the Central Management Unit and then maintaining it near the goal specified in the AEWA International Single Species Action Plan (ISSAP). This report also provides estimates of the length of time it would take under ideal conditions (no density dependence and no harvest) to rebuild depleted populations in the Western and Eastern Management Units. We emphasize that our estimates are a first approximation because detailed demographic information is lacking for taiga bean geese. Using allometric relationships, we estimated parameters of a thetalogistic matrix population model. The mean intrinsic rate of growth was estimated as r = 0.150 (90% credible interval: 0.120 – 0.182). We estimated the mean form of density dependence as 2.361 (90% credible interval: 0.473 – 11.778), suggesting the strongest density dependence occurs when the population is near its carrying capacity. Based on expert opinion, carrying capacity (i.e., population size expected in the absence of hunting) for the Central Management Unit was estimated as K 87,900 (90% credible interval: 82,000 – 94,100). The ISSAP specifies a population goal for the Central Management Unit of 60,000 – 80,000 individuals in winter; thus, we specified a preliminary objective function as one which would minimize the difference between this goal and population size. Using the concept of stochastic dominance to explicitly account for uncertainty in demography, we determined that optimal harvest rates for 5, 10, 15, and 20-year time horizons were h = 0.00, 0.02, 0.05, and 0.06, respectively. These optima represent a tradeoff between the harvest rate and the time required to achieve and maintain a population size within desired bounds. We recognize, however, that regulation of absolute harvest rather than
Behera, Shuvashish; Sharma, Nilesh K; Arora, Richa; Kumar, Sachin
Efficient use of xylose along with glucose is necessary for the economic production of lignocellulosic based biofuels. Xylose transporters play an important role in the microorganisms for efficient utilization of xylose. In the present study, a novel method has been developed for a rapid assay of xylose transport activity in the xylose-utilizing isolates and other known yeasts. An assay was conducted to compare the activity of β-xylosidase using p-nitrophenyl-β-D-xylopyranoside (pNPX) in the intact, intracellular, and extracellular yeasts cells showing xylose transporter. Saccharomyces cerevisiae (MTCC 170) showed no xylosidase activity, while little growth was observed in the xylose-containing medium. Although other yeasts, i.e., Kluyveromyces marxianus NIRE-K1 (MTCC 5933), K. marxianus NIRE-K3 (MTCC 5934), and Candida tropicalis (MTCC 230), showed xylosidase activity in intact, intracellular, and extracellular culture. The xylosidase activity in intact cell was higher than that of extracellular and intracellular activity in all the yeast cells. The enzyme activity was higher in case of K. marxianus NIRE-K1 and K. marxianus NIRE-K3 rather than the C. tropicalis. Further, better xylosidase activity was observed in adapted K. marxianus cells which were 2.79-28.46 % higher than that of native (non-adapted) strains, which indicates the significant improvement in xylose transportation.
Klinman, Judith P.; Kohen, Amnon
The role of evolutionary pressure on the chemical step catalyzed by enzymes is somewhat enigmatic, in part because chemistry is not rate-limiting for many optimized systems. Herein, we present studies that examine various aspects of the evolutionary relationship between protein dynamics and the chemical step in two paradigmatic enzyme families, dihydrofolate reductases and alcohol dehydrogenases. Molecular details of both convergent and divergent evolution are beginning to emerge. The findings suggest that protein dynamics across an entire enzyme can play a role in adaptation to differing physiological conditions. The growing tool kit of kinetics, kinetic isotope effects, molecular biology, biophysics, and bioinformatics provides means to link evolutionary changes in structure-dynamics function to the vibrational and conformational states of each protein. PMID:25210031
Vanee, Niti; Fisher, Adam B; Fong, Stephen S
Superficially, evolutionary engineering is a paradoxical field that balances competing interests. In natural settings, evolution iteratively selects and enriches subpopulations that are best adapted to a particular ecological niche using random processes such as genetic mutation. In engineering desired approaches utilize rational prospective design to address targeted problems. When considering details of evolutionary and engineering processes, more commonality can be found. Engineering relies on detailed knowledge of the problem parameters and design properties in order to predict design outcomes that would be an optimized solution. When detailed knowledge of a system is lacking, engineers often employ algorithmic search strategies to identify empirical solutions. Evolution epitomizes this iterative optimization by continuously diversifying design options from a parental design, and then selecting the progeny designs that represent satisfactory solutions. In this chapter, the technique of applying the natural principles of evolution to engineer microbes for industrial applications is discussed to highlight the challenges and principles of evolutionary engineering.
This article explores the adaptive functions of storytelling in the workplace from an evolutionary perspective. Based on the analysis of ethnographic studies on hunter-gatherer and modern work organizations, this article claims that storytelling, as an adapted cognitive device, was selectively retained by natural and sexual selection, because of…
Shackelford, Todd K; Goetz, Aaron T
A comparative evolutionary psychological perspective predicts that species that recurrently faced similar adaptive problems may have evolved similar psychological mechanisms to solve these problems. Sperm competition provides an arena in which to assess the heuristic value of such a comparative evolutionary perspective. The sperm competition that results from female infidelity and polyandry presents a similar class of adaptive problems for individuals across many species. The authors first describe mechanisms of sperm competition in insects and in birds. They suggest that the adaptive problems and evolved solutions in these species provide insight into human anatomy, physiology, psychology, and behavior. The authors then review recent theoretical and empirical arguments for the existence of sperm competition in humans and discuss proposed adaptations in humans that have analogs in insects or birds. The authors conclude by highlighting the heuristic value of a comparative evolutionary psychological approach in this field.
Goldsmith, T C
The programmed vs. non-programmed aging controversy has now existed in some form for at least 150 years. For much of the XX century, it was almost universally believed that evolution theory prohibited programmed (adaptive) aging in mammals and there was little direct experimental or observational evidence favoring it. More recently, multiple new evolutionary mechanics concepts that support programmed aging and steadily increasing direct evidence favoring it overwhelmingly support the existence of programmed aging in humans and other organisms. This issue is important because the different theories suggest very different mechanisms for the aging process that in turn suggest very different paths toward treating and preventing age-related diseases.
Wolf, Jason B.; Wade, Michael J.
Maternal genetic effects (MGEs), where genes expressed by mothers affect the phenotype of their offspring, are important sources of phenotypic diversity in a myriad of organisms. We use a single‐locus model to examine how MGEs contribute patterns of heritable and nonheritable variation and influence evolutionary dynamics in randomly mating and inbreeding populations. We elucidate the influence of MGEs by examining the offspring genotype‐phenotype relationship, which determines how MGEs affect evolutionary dynamics in response to selection on offspring phenotypes. This approach reveals important results that are not apparent from classic quantitative genetic treatments of MGEs. We show that additive and dominance MGEs make different contributions to evolutionary dynamics and patterns of variation, which are differentially affected by inbreeding. Dominance MGEs make the offspring genotype‐phenotype relationship frequency dependent, resulting in the appearance of negative frequency‐dependent selection, while additive MGEs contribute a component of parent‐of‐origin dependent variation. Inbreeding amplifies the contribution of MGEs to the additive genetic variance and, therefore enhances their evolutionary response. Considering evolutionary dynamics of allele frequency change on an adaptive landscape, we show that this landscape differs from the mean fitness surface, and therefore, under some condition, fitness peaks can exist but not be “available” to the evolving population. PMID:26969266
Baroffio, Anne; Vu, Nu V; Gerbase, Margaret W
Implementation of a pedagogical approach is a continuous and evolving process. As an institution with more than 15 years problem-based learning (PBL), we studied how the learning and teaching processes are currently practiced in a 2-year preclinical basic sciences program to assess whether they still match the intended objectives. Using both students' and tutors' evaluations, we analyzed and compared their perceptions on the program content and its organization, on tutors' functioning and on the duration of PBL sessions throughout 11 instructional units of the second and third-year of a 6 years medical curriculum. Whereas both tutors and students indicated that the content and problems selected for the curriculum were well adapted to the PBL process, they felt the references as well as the self-study time as moderately appropriate. Over the course of the 2-year program, tutorial sessions got linearly shorter, whereas reporting sessions got longer. While tutors knew well the PBL approach and were suitably prepared to their tutorials, they however, became less regular in providing feedback and in evaluating group functioning over the 2 years. Our results suggest that the practice of the PBL process evolves within and throughout a 2-year preclinical program and moves away from the original intentions. Possible underlying reasons and their implications are discussed within the context of tutors' and students' concepts of teaching and learning, the medical schools' learning environment and teaching practices and the difficulty of developing and maintaining in the long term a deep and self-directed learning approach.
Iwasaki, Hirotoshi; Sega, Shinichiro; Hiraishi, Hironori; Mizoguchi, Fumio
In recent years, lots of music content can be stored in mobile computing devices, such as a portable digital music player and a car navigation system. Moreover, various information content like news or traffic information can be acquired always anywhere by a cellular communication and a wireless LAN. However, usability issues arise from the simple interfaces of mobile computing devices. Moreover, retrieving and selecting such content poses safety issues, especially while driving. Thus, it is important for the mobile system to recommend content automatically adapted to user's preference and situation. In this paper, we present the user-adapted program scheduling that generates sequences of content (Program) suiting user's preference and situation based on the Bayesian network and the Constraint Satisfaction Problem (CSP) technique. We also describe the design and evaluation of its realization system, the Personal Program Producer (P3). First, preference such as a genre ratio of content in a program is learned as a Bayesian network model using simple operations such as a skip behavior. A model including each content tends to become large-scale. In order to make it small, we present the model separation method that carries out losslessly compression of the model. Using the model, probabilistic distributions of preference to generate constraints are inferred. Finally satisfying the constraints, a program is produced. This kind of CSP has an issue of which the number of variables is not fixedness. In order to make it variable, we propose a method using metavariables. To evaluate the above methods, we applied them to P3 on a car navigation system. User evaluations helped us clarify that the P3 can produce the program that a user prefers and adapt it to the user.
Grain yield since the 1930s has increased more than five-fold in large part due to improvements in adaptation to high plant density. Changes to plant architecture that associated with improved light interception have made a major contribution to improved adaptation to high plant density. Improved ...
Amir, Nader; Kuckertz, Jennie M; Strege, Marlene V
An attentional bias toward threat may be one mechanism underlying clinical anxiety. Attention bias modification (ABM) aims to reduce symptoms of anxiety disorders by directly modifying this deficit. However, existing ABM training programs have not consistently modified attentional bias and may not reflect optimal learning needs of participants (i.e., lack of explicit instruction, training goal unclear to participants, lack of feedback, non-adaptive, inability to differentiate or target different components of attentional bias). In the current study, we introduce a new adaptive ABM program (AABM) and test its feasibility in individuals with social anxiety disorder. We report task characteristics and preliminary evidence that this task consistently modifies attentional bias and that changes in attentional bias (but not number of trials) correlate with the level of symptom reduction. These results suggest that AABM may be a targeted method for the next generation of studies examining the utility of attention training.
Shea, Munyi; Cachelin, Fary M; Gutierrez, Guadalupe; Wang, Sherry; Phimphasone, Phoutdavone
The prevalence of bulimia nervosa (BN) and binge eating disorder (BED) among Latinas is comparable to those of the general population; however, few interventions and treatment trial research have focused on this group. Cognitive-behavioral therapy (CBT) is the treatment of choice for binge eating related disorders. CBT-based guided self-help (CBTgsh)-a low-cost minimal intervention-has also been shown effective in improving binge eating related symptom, but the effectiveness of the CBTgsh among ethnic minority women is not well understood. Cultural adaptation of evidence-based treatments can be an important step for promoting treatment accessibility and engagement among underserved groups. This qualitative study was part of a larger investigation that examined the feasibility and efficacy of a culturally adapted CBTgsh program among Mexican American women with binge eating disorders. Posttreatment focus groups were conducted with 12 Mexican American women with BN or BED who participated in the intervention. Data were analyzed with the grounded theory methodology (Corbin & Strauss, 2008). Three themes emerged from the data: (a) eating behavior and body ideals are socially and culturally constructed, (b) multifaceted support system is crucial to Mexican American women's treatment engagement and success, and (c) the culturally adapted CBTgsh program is feasible and relevant to Mexican American women's experience, but it can be strengthened with increased family and peer involvement. The findings provide suggestions for further adaptation and refinement of the CBTgsh, and implications for future research as well as early intervention for disordered eating in organized care settings.
Castro-Olivo, Sara M
The current study evaluated the effects of the culturally adapted Jóvenes Fuertes (Strong Teens) Social-Emotional Learning (SEL) program on the social-emotional outcomes of Latino English language learners (ELLs). A quasi-experimental design with random assignment by classrooms was used to assess the intervention's effects on students' knowledge of SEL and resiliency. A sample of 102 Spanish-dominant Latino ELLs enrolled in middle or high school participated in this study. The results indicated significant intervention effects on SEL knowledge and social-emotional resiliency. The findings are discussed in terms of their implications for preventive, culturally responsive SEL programs in school settings.
Martin, Erika G; Meehan, Terence; Schackman, Bruce R
With the Affordable Care Act set to expand insurance coverage to millions more Americans next year, existing discretionary health programs that receive federal support might find themselves competing for funds as the health reform law is fully implemented. To assess the implications the Affordable Care Act might have for discretionary health programs, we focused on state AIDS Drug Assistance Programs, which provide free medications to low-income HIV patients. We conducted semistructured interviews with program managers from twenty-two states. Many of the managers predicted that their programs will change focus to provide "wrap-around services," such as helping newly insured clients finance out-of-pocket expenses, including copayments, deductibles, and premiums. Although program managers acknowledged that they must adapt to a changing environment, many said that they were overwhelmed by the complexity of the Affordable Care Act, and some expressed fear that state AIDS Drug Assistance Programs would be eliminated entirely. To remain viable, such programs must identify and justify the need for services in the context of the Affordable Care Act and receive sufficient political support and funding.
Lopez Perez, M.; Barrios, E.; Salinas-Rodriguez, S.; Wickel, B.; Villon, R. A.
-allocation takes place. The strategy is to identify and protect basins with an availability of water that is close to their natural flow regime and that also have a high conservation value (based on prior national conservation priority definitions such as protected areas, and biodiversity conservation gap analyses) in order to implement legal restrictions on water resource development. With such protection, these systems will be best positioned to adjust and respond to water shortages, and regime shifts. To date, 189 basins around the country were identified as potential water reserves. The next step will be the nomination of these water reserves to be integrated in the National Water Reserves Program. This program forms the core of the official Mexican government adaptation strategy towards climate prepared water management, which recognizes that water reserves are the buffer society needs to face uncertainty, and reduce water scarcity risk. The development of activities that alter the natural flow regime such as dams and levees are closely examined, and would potentially be restricted.
Salinas-Rodriguez, S. A.; López Pérez, M.; Barrios Ordóñez, J.; Wickel, B.; Villón Bracamonte, R. A.
allocated, and where the flow regime is then protected before over-allocation takes place. The strategy has been to identify and protect basins with an availability of water that is close to their natural flow regime and that also have a high conservation value (based on prior national conservation priority definitions such as protected areas, and biodiversity conservation gap analyses) in order to implement legal restrictions on water resource development. With such protection, these systems will be best positioned to adjust and respond to water shortages, and regime shifts. To date, 189 basins around the country were identified as potential water reserves. The next step will be the nomination of these water reserves to be integrated in the National Water Reserves Program. This program forms the core of the official Mexican government adaptation strategy towards climate prepared water management, which recognizes that water reserves are the buffer society needs to face uncertainty, imbalance of the man-made, global changes, and thus to reduce water scarcity risk. The development of activities that alter the natural flow regime such as dams and levees are closely examined, and would potentially be restricted.
Gerdes, Alex; Heeren, Bastiaan; Jeuring, Johan; van Binsbergen, L. Thomas
Ask-Elle is a tutor for learning the higher-order, strongly-typed functional programming language Haskell. It supports the stepwise development of Haskell programs by verifying the correctness of incomplete programs, and by providing hints. Programming exercises are added to Ask-Elle by providing a task description for the exercise, one or more…
Bronikowski, A M; Bennett, A F; Lenski, R E
Are enteric bacteria specifically adapted to the thermal environment of their hosts? In particular, do the optimal temperatures and thermal niches of the bacterial flora reflect seasonal, geographic, or phylogenetic differences in their hosts' temperatures? We examined these questions by measuring the relationship between the temperature-dependent growth rates of enteric bacteria in a free-living ectothermic host. We sampled two species of enteric bacteria (Escherichia coli and Salmonella enterica) from three natural populations of slider turtles (Trachemys scripta elegans) seasonally over two years. Despite pronounced differences in turtle body temperatures at different seasons and in different locations, we found no evidence that the thermal growth profiles of these bacteria mirrored this variation. Optimal temperatures and maximal growth rates in rich medium were nearly the same for both bacterial species (35-36 degrees C, 2.5 doublings per hour). The thermal niche (defined as the range of temperatures over which 75% of maximal growth rate occurred) was slightly higher for E. coli (28.5-41.0 degrees C) than for S. enterica (27.7-39.8 degrees C), but the niche breadth was about the same for both. We also measured the thermal dependence of growth rate in these same bacterial species isolated from mammalian hosts. Both bacterial species had temperatures of maximal growth and thermal niches that were about 2 degrees C higher than those of their respective conspecifics sampled from turtles; niche breadths were not different. These data suggest that these bacterial species are thermal generalists that do not track fine-scale changes in their thermal environments. Even major differences in body temperatures, as great as those between ectothermic and endothermic hosts, may result in the evolution of rather modest changes in thermal properties.
Agrebi, Rym; Bellows, Lauren E.; Collet, Jean-François; Kaever, Volkhard
The nucleotide signaling molecule 3′,5′-cyclic adenosine monophosphate (3′,5′-cAMP) plays important physiological roles, ranging from carbon catabolite repression in bacteria to mediating the action of hormones in higher eukaryotes, including human. However, it remains unclear whether 3′,5′-cAMP is universally present in the Firmicutes group of bacteria. We hypothesized that searching for proteins that bind 3′,5′-cAMP might provide new insight into this question. Accordingly, we performed a genome-wide screen and identified the essential Staphylococcus aureus tRNA m1G37 methyltransferase enzyme TrmD, which is conserved in all three domains of life as a tight 3′,5′-cAMP-binding protein. TrmD enzymes are known to use S-adenosyl-l-methionine (AdoMet) as substrate; we have shown that 3′,5′-cAMP binds competitively with AdoMet to the S. aureus TrmD protein, indicating an overlapping binding site. However, the physiological relevance of this discovery remained unclear, as we were unable to identify a functional adenylate cyclase in S. aureus and only detected 2′,3′-cAMP but not 3′,5′-cAMP in cellular extracts. Interestingly, TrmD proteins from Escherichia coli and Mycobacterium tuberculosis, organisms known to synthesize 3′,5′-cAMP, did not bind this signaling nucleotide. Comparative bioinformatics, mutagenesis, and biochemical analyses revealed that the highly conserved Tyr-86 residue in E. coli TrmD is essential to discriminate between 3′,5′-cAMP and the native substrate AdoMet. Combined with a phylogenetic analysis, these results suggest that amino acids in the substrate binding pocket of TrmD underwent an adaptive evolution to accommodate the emergence of adenylate cyclases and thus the signaling molecule 3′,5′-cAMP. Altogether this further indicates that S. aureus does not produce 3′,5′-cAMP, which would otherwise competitively inhibit an essential enzyme. PMID:27881678
Anderson, Melissa L; Bradley, Katharine; An, Lawrence C; Catz, Sheryl L
Background Mobile health (mHealth) interventions hold great promise for helping smokers quit since these programs can have wide reach and facilitate access to comprehensive, interactive, and adaptive treatment content. However, the feasibility, acceptability, and effectiveness of these programs remain largely untested. Objective To assess feasibility and acceptability of the My Mobile Advice Program (MyMAP) smoking cessation program and estimate its effects on smoking cessation and medication adherence to inform future research planning. Methods Sixty-six smokers ready to quit were recruited from a large regional health care system and randomized to one of two mHealth programs: (1) standard self-help including psychoeducational materials and guidance how to quit smoking or (2) an adaptive and interactive program consisting of the same standard mHealth self-help content as controls received plus a) real-time, adaptively tailored advice for managing nicotine withdrawal symptoms and medication side-effects and b) asynchronous secure messaging with a cessation counselor. Participants in both arms were also prescribed a 12-week course of varenicline. Follow-up assessments were conducted at 2 weeks post-target quit date (TQD), 3 months post-TQD, and 5 months post-TQD. Indices of program feasibility and acceptability included acceptability ratings, utilization metrics including use of each MyMAP program component (self-help content, secure messaging, and adaptively tailored advice), and open-ended feedback from participants. Smoking abstinence and medication adherence were also assessed to estimate effects on these treatment outcomes. Results Utilization data indicated the MyMAP program was actively used, with higher mean program log-ins by experimental than control participants (10.6 vs 2.7, P<.001). The majority of experimental respondents thought the MyMAP program could help other people quit smoking (22/24, 92%) and consistently take their stop-smoking medication (17
Levit, Georgy S; Hossfeld, Uwe; Olsson, Lennart
Ivan I. Schmalhausen was one of the central figures in the Russian development of the "Modern Synthesis" in evolutionary biology. He is widely cited internationally even today. Schmalhausen developed the main principles of his theory facing the danger of death in the totalitarian Soviet Union. His great services to evolutionary and theoretical biology are indisputable. However, the received view of Schmalhausen's contributions to evolutionary biology makes an unbiased reading of his texts difficult. Here we show that taking all of his works into consideration (including those only available in Russian) paints a much more dynamic and exciting picture of what he tried to achieve. Schmalhausen pioneered the integration of a developmental perspective into evolutionary thinking. A main tool for achieving this was his approach to living objects as complex multi-level self-regulating systems. Schmalhausen put enormous effort into bringing this idea into fruition during the final stages of his career by combining evolutionary theory with cybernetics. His results and ideas remain thought-provoking, and his texts are of more than just historical interest.
Pierson, Jennifer C; Beissinger, Steven R; Bragg, Jason G; Coates, David J; Oostermeijer, J Gerard B; Sunnucks, Paul; Schumaker, Nathan H; Trotter, Meredith V; Young, Andrew G
We examined how ecological and evolutionary (eco-evo) processes in population dynamics could be better integrated into population viability analysis (PVA). Complementary advances in computation and population genomics can be combined into an eco-evo PVA to offer powerful new approaches to understand the influence of evolutionary processes on population persistence. We developed the mechanistic basis of an eco-evo PVA using individual-based models with individual-level genotype tracking and dynamic genotype-phenotype mapping to model emergent population-level effects, such as local adaptation and genetic rescue. We then outline how genomics can allow or improve parameter estimation for PVA models by providing genotypic information at large numbers of loci for neutral and functional genome regions. As climate change and other threatening processes increase in rate and scale, eco-evo PVAs will become essential research tools to evaluate the effects of adaptive potential, evolutionary rescue, and locally adapted traits on persistence.
Korkmaz, Özgen; Altun, Halis
Students might have different type and different level of perceptions: Positive or negative perceptions on programming; a perception on benefit of programming, perceptions related to difficulties of programming process etc. The perception of student on their own competence is defined as self-efficacy. Based on the discussions reported in…
Min, Jungwon; Kim, Gilsook; Lim, Hyunjung; Carvajal, Nubia A.; Lloyd, Charles W.; Wang, Youfa; Reeves, Katherine
Obesity has become a global epidemic. Childhood obesity is global public health concern including in South Korea where 16.2% of boys and 9.9% of girls are overweight or obese in 2011. Effective and sustainable intervention programs are needed for prevention of childhood obesity. Obesity prevention programs for young children may have a greater intervention effect than in older children. The NASA Mission X: Train Like an Astronaut (MX) program was developed to promote children's exercise and healthy eating by tapping into their excitement for training like an astronaut. This study aimed to examine the feasibility and effectiveness of the adapted NASA MX intervention in promoting PA in young children and in improving parents' related perspectives.
We consider algorithmic design, enhancement, and improvement of evolutionary computation as a mechanism design problem. All individuals or several groups of individuals can be considered as self-interested agents. The individuals in evolutionary computation can manipulate parameter settings and operations by satisfying their own preferences, which are defined by an evolutionary computation algorithm designer, rather than by following a fixed algorithm rule. Evolutionary computation algorithm designers or self-adaptive methods should construct proper rules and mechanisms for all agents (individuals) to conduct their evolution behaviour correctly in order to definitely achieve the desired and preset objective(s). As a case study, we propose a formal framework on parameter setting, strategy selection, and algorithmic design of evolutionary computation by considering the Nash strategy equilibrium of a mechanism design in the search process. The evaluation results present the efficiency of the framework. This primary principle can be implemented in any evolutionary computation algorithm that needs to consider strategy selection issues in its optimization process. The final objective of our work is to solve evolutionary computation design as an algorithmic mechanism design problem and establish its fundamental aspect by taking this perspective. This paper is the first step towards achieving this objective by implementing a strategy equilibrium solution (such as Nash equilibrium) in evolutionary computation algorithm. PMID:26257777
This presentation, ANTHC Rural Alaska Monitoring Program (RAMP): Assessing, Monitoring, and Adapting to Emerging Environmental Human and Wildlife Health Threats, was given at the 2016 STAR Tribal Research Meeting held on Sept. 20-21, 2016.
Schultz, Eric T.; McCormick, Stephen D.; McCormick, Stephen D.; Farrell, Anthony Peter; Brauner, Colin J.
This chapter focuses on the evolutionary importance and taxonomic distribution of euryhalinity. Euryhalinity refers to broad halotolerance and broad halohabitat distribution. Salinity exposure experiments have demonstrated that species vary tenfold in their range of tolerable salinity levels, primarily because of differences in upper limits. Halotolerance breadth varies with the species’ evolutionary history, as represented by its ordinal classification, and with the species’ halohabitat. Freshwater and seawater species tolerate brackish water; their empirically-determined fundamental haloniche is broader than their realized haloniche, as revealed by the halohabitats they occupy. With respect to halohabitat distribution, a minority of species (<10%) are euryhaline. Habitat-euryhalinity is prevalent among basal actinopterygian fishes, is largely absent from orders arising from intermediate nodes, and reappears in the most derived taxa. There is pronounced family-level variability in the tendency to be halohabitat-euryhaline, which may have arisen during a burst of diversification following the Cretaceous-Palaeogene extinction. Low prevalence notwithstanding, euryhaline species are potent sources of evolutionary diversity. Euryhalinity is regarded as a key innovation trait whose evolution enables exploitation of new adaptive zone, triggering cladogenesis. We review phylogenetically-informed studies that demonstrate freshwater species diversifying from euryhaline ancestors through processes such as landlocking. These studies indicate that some euryhaline taxa are particularly susceptible to changes in halohabitat and subsequent diversification, and some geographic regions have been hotspots for transitions to freshwater. Comparative studies on mechanisms among multiple taxa and at multiple levels of biological integration are needed to clarify evolutionary pathways to, and from, euryhalinity.
Fontanesi, John; Martinez, Anthony; Boyo, Toritsesan O; Gish, Robert
Although demands for greater access to hepatology services that are less costly and achieve better outcomes have led to numerous quality improvement initiatives, traditional quality management methods may be inappropriate for hepatology. We empirically tested a model for conducting quality improvement in an academic hepatology program using methods developed to analyze and improve complex adaptive systems. We achieved a 25% increase in volume using 15% more clinical sessions with no change in staff or faculty FTEs, generating a positive margin of 50%. Wait times for next available appointments were reduced from five months to two weeks; unscheduled appointment slots dropped from 7% to less than 1%; "no-show" rates dropped to less than 10%; Press-Ganey scores increased to the 100th percentile. We conclude that framing hepatology as a complex adaptive system may improve our understanding of the complex, interdependent actions required to improve quality of care, patient satisfaction, and cost-effectiveness.
Sharov, Alexei A.
Natural selection is traditionally viewed as a leading factor of evolution, whereas variation is assumed to be random and non-directional. Any order in variation is attributed to epigenetic or developmental constraints that can hinder the action of natural selection. In contrast I consider the positive role of epigenetic mechanisms in evolution because they provide organisms with opportunities for rapid adaptive change. Because the term “constraint” has negative connotations, I use the term “regulated variation” to emphasize the adaptive nature of phenotypic variation, which helps populations and species to survive and evolve in changing environments. The capacity to produce regulated variation is a phenotypic property, which is not described in the genome. Instead, the genome acts as a switchboard, where mostly random mutations switch “on” or “off” preexisting functional capacities of organism components. Thus, there are two channels of heredity: informational (genomic) and structure-functional (phenotypic). Functional capacities of organisms most likely emerged in a chain of modifications and combinations of more simple ancestral functions. The role of DNA has been to keep records of these changes (without describing the result) so that they can be reproduced in the following generations. Evolutionary opportunities include adjustments of individual functions, multitasking, connection between various components of an organism, and interaction between organisms. The adaptive nature of regulated variation can be explained by the differential success of lineages in macro-evolution. Lineages with more advantageous patterns of regulated variation are likely to produce more species and secure more resources (i.e., long-term lineage selection). PMID:24769155
Dumas, Jean E.; Arriaga, Ximena; Begle, Angela Moreland; Longoria, Zayra
This paper describes the Spanish adaptation of PACE--"Parenting Our Children to Excellence." Successfully offered in preschools and daycare centers since 2002, PACE is a research-based preventive intervention to support families in their parenting task through discussions and activities that address practical childrearing issues and promote child…
Ermeling, Bradley A.; Gallimore, Ronald
Making schools learning places for teachers as well as students is a timeless and appealing vision. The growing number of professional learning communities is a hopeful sign that profound change is on the way. This is the challenge learning communities face: Schools and districts need implementation models flexible enough to adapt to local…
Luptak, Marilyn; Kaas, Merrie J.; Artz, Margaret; McCarthy, Teresa
Purpose: We describe and evaluate a project designed to pilot test an evidence-based clinical intervention for assessing and treating depression in older adults in rural primary care clinics. Project ADAPT--Assuring Depression Assessment and Proactive Treatment--utilized existing primary care resources to overcome barriers to sustainability…
It is now recognized that optimal global climate policy is a portfolio of the two key responses for reducing the risks of climate change: mitigation and adaptation. Significant differences between the two responses have inhibited understanding of how to appropriately view these...
Washington Univ., Seattle.
This brochure describes the different types of barriers individuals with mobility impairments, blindness, low vision, hearing impairments, and specific learning disabilities face in providing computer input, interpreting output, and reading documentation. The adaptive hardware and software that has been developed to provide functional alternatives…
Wallace, Anne Elizabeth
Despite the resources and training provided, teachers make decisions to adapt from the written curriculum throughout their day. Some would argue that the teacher's ability to not only recognize when students are struggling, but to also be able to select adequate instructional strategies to reteach the concept, is their most valuable asset. The…
Coyle-Rogers, Patricia G.
Scores on an adaptive competency profile for 30 Licensed Practical Nurse graduate candidates and 41 second-level Associate Degree in Nursing candidates indicated that there was no significant difference between the two groups. Results suggest that a variety of educational backgrounds foster development of nursing competence. (Contains 23…
Teacher quality has been a perennial issue in the field of education. In addition to academic ability, psychological and motivational characteristics are regarded as increasingly important dimensions of teacher quality. This study has established a multidimensional framework of teacher quality including social competency, adaptive ability and…
... assessments, (3) Colorado River Basin hydrology, (4) and the Long-Term Experimental and Management Plan. In... provided to Glen Knowles, Bureau of Reclamation, Upper Colorado Regional Office, 125 South State Street.... Glen Knowles, Chief, Adaptive Management Work Group, Environmental Resources Division, Upper...
Doré-Mazars, Karine; Vergilino-Perez, Dorine; Collins, Thérèse; Bohacova, Katarina; Beauvillain, Cécile
Executing sequences of accurate saccadic eye movements supposes the use of signals carrying information about the first saccade for updating the predetermined motor plan of the subsequent saccades. The present study examines the signals used in planning a second saccade when subjects made two successive saccades towards one long or two short peripheral objects displayed before the first saccade execution. Different first eye movement signals could be used: desired eye movement signals, representing the movement necessary for attaining the intended target, or actual eye movement signals, representing the movement actually executed. Experimental dissociation of desired and actual eye movement signals is made possible by adaptive modifications of the first saccade, obtained by transfer of single saccade adaptation, during which the motor vector was progressively modified in response to the systematic intra-saccadic step of a single target. Whether the second saccade used the actual eye movement signal to compensate or not for the adaptive changes in the first saccade depended on which object properties were relevant for saccade planning. Compensation was observed for saccades that aimed for a new object (between-object saccades) because adaptation modifies relative object location. No compensation was observed for saccades that explored an extended object (within-object saccades). Implications for the on-line control of subsequent eye movements are discussed.
Choi, Seung W.; Podrabsky, Tracy; McKinney, Natalie
Computerized adaptive testing (CAT) enables efficient and flexible measurement of latent constructs. The majority of educational and cognitive measurement constructs are based on dichotomous item response theory (IRT) models. An integral part of developing various components of a CAT system is conducting simulations using both known and empirical…
Risendal, B; Dwyer, A; Seidel, R; Lorig, K; Katzenmeyer, C; Coombs, L; Kellar-Guenther, Y; Warren, L; Franco, A; Ory, M
Self-management in chronic disease has been shown to improve patient-reported and health care-related outcomes. However, relatively little information about its utility in cancer survivorship is known. We evaluated the feasibility and acceptability of the delivery of an adaptation of the evidence-based Chronic Disease Self-management Program (Stanford) called Cancer Thriving and Surviving (CTS). Triangulated mixed methods were used to capture baseline characteristics and post-program experiences using a combination of closed- and open-ended survey items; emergent coding and simple descriptive statistics were used to summarize the data. Twenty-seven workshops were delivered by 22 CTS leaders to 244 participants between August 2011 and January 2013 in a variety of settings (48 % community, 30 % health care, 22 % regional/community cancer center). Representing a variety of cancer types, about half the participants were 1-3 years post-diagnosis and 45 % were 4 or more years from diagnosis. Program attendance was high with 84 % of participants attending four or more of the six sessions in the workshop. Overall, 95 % of the participants were satisfied with the program content and leaders, and would recommend the program to friends and family. These results confirm the feasibility and acceptability of delivery of a high-fidelity, peer-led model for self-management support for cancer survivors. Expansion of the CTS represents a powerful tool toward improving health-related outcomes in this at-risk population.
The Joint Committee on Standards for Educational Evaluation's Program Evaluation Standards is probably the most recognized and applied set of evaluation standards globally. The most recent edition of The Program Evaluation Standards includes five categories and 30 standards. The five categories are Utility, Feasibility, Propriety, Accuracy, and…
Cultural factors significantly influence the effectiveness of pediatric screening that enables the prevention of developmental disturbances. The formulation of intervention programs must match the needs of the child, his or her family, and educators. Recognizing the importance of creating an intervention program accessible to the culture of the…
Murphy-Southwick, Colleen; McBride, Melen
Montana, a predominantly rural state, with a unique blend of geography and history, low population density, and cultural diversity represents the challenges for program development and implementation across remote areas. The paper discusses two statewide multidisciplinary geriatric education programs for health professionals offered by the…
Eberhardt, Lorraine; Sanborn, Laura
The completely waterproof book contains instructions for an alternative form of swimming exercises based on the movements of 19 water creatures. The exercises can be used by groups or individuals to enhance training programs, to serve as part of a structured synchronized swimming program, or to supplement recreational activities. The book provides…
The notion of an RNA world has been introduced for a prebiotic scenario that is dominated by RNA molecules and their properties, in particular their capabilities to act as templates for reproduction and as catalysts for several cleavage and ligation reactions of polynucleotides and polypeptides. This notion is used here also for simple experimental assays which are well suited to study evolution in the test tube. In molecular evolution experiments fitness is determined in essence by the molecular structures of RNA molecules. Evidence is presented for adaptation to environment in cell-free media. RNA based molecular evolution experiments have led to interesting spin-offs in biotechnology, commonly called ‘applied molecular evolution’, which make use of Darwinian trial-and-error strategies in order to synthesize new pharmacological compounds and other advanced materials on a biological basis. Error-propagation in RNA replication leads to formation of mutant spectra called ‘quasispecies’. An increase in the error rate broadens the mutant spectrum. There exists a sharply defined threshold beyond which heredity breaks down and evolutionary adaptation becomes impossible. Almost all RNA viruses studied so far operate at conditions close to this error threshold. Quasispecies and error thresholds are important for an understanding of RNA virus evolution, and they may help to develop novel antiviral strategies. Evolution of RNA molecules can be studied and interpreted by considering secondary structures. The notion of sequence space introduces a distance between pairs of RNA sequences which is tantamount to counting the minimal number of point mutations required to convert the sequences into each other. The mean sensitivity of RNA secondary structures to mutation depends strongly on the base pairing alphabet: structures from sequences which contain only one base pair (GC or AU are much less stable against mutation than those derived from the natural (AUGC) sequences
Osteoporosis is characterised by simultaneous net bone growth and net resorption on different surfaces, suggesting that systemic factors are not the sole explanation for the findings. The main clinical consequence is fracturing in the largely trabecular bones of the spine, hip, and radius, and the key problem in these areas is finding an explanation for the preferential loss of transverse trabeculae. In normal bone, local maintenance depends on a negative feedback response to intermittent compression strain, and it is concluded, from biomechanical analysis of the response required to achieve negative feedback, that a preferential loss of transverse trabeculae is indicative of a selective deficiency of radial compression loading. The only significant source of radial compression in humans is the induced strain produced by axial tension. This is a necessary component of the lifestyles of quadrupeds and arboreal primates, but in humans occurs only on the convex side when the bone is offset loaded. The resulting strain is a function of the range of movement. It is suggested that the asymmetrical pattern of bone loss in cortical and trabecular osteoporosis reflects chronic underuse of movement range, resulting from the adoption of a bipedal lifestyle. Exercise regimens based on using the whole of the available movement range should better prepare the skeleton to adjust to other factors hostile to bone maintenance. PMID:11350841
Goza, B. K.; Hunter, L.; Shaw, J. M.; Metevier, A. J.; Raschke, L.; Espinoza, E.; Geaney, E. R.; Reyes, G.; Rothman, D. L.
This paper describes the interaction of four elements of social science as they have evolved in concert with the Center for Adaptive Optics Professional Development Program (CfAO PDP). We hope these examples persuade early-career scientists and engineers to include social science activities as they develop grant proposals and carry out their research. To frame our discussion we use a metaphor from astronomy. At the University of California Santa Cruz (UCSC), the CfAO PDP and the Educational Partnership Center (EPC) are two young stars in the process of forming a solar system. Together, they are surrounded by a disk of gas and dust made up of program evaluation, applied research, educational assessment, and pedagogy. An idea from the 2001 PDP intensive workshops program evaluation developed into the Assessing Scientific Inquiry and Leadership Skills (AScILS) applied research project. In iterative cycles, AScILS researchers participated in subsequent PDP intensive workshops, teaching social science while piloting AScILS measurement strategies. Subsequent "orbits" of the PDP program evaluation gathered ideas from the applied research and pedagogy. The denser regions of this disk of social science are in the process of forming new protoplanets as tools for research and teaching are developed. These tools include problem-solving exercises or simulations of adaptive optics explanations and scientific reasoning; rubrics to evaluate the scientific reasoning simulation responses, knowledge regarding inclusive science education, and student explanations of science/engineering inquiry investigations; and a scientific reasoning curriculum. Another applied research project is forming with the design of a study regarding how to assess engineering explanations. To illustrate the mutual shaping of the cross-disciplinary, intergenerational group of educational researchers and their projects, the paper ends with a description of the professional trajectories of some of the
Climate-related circumstances pose challenges for permittees and permit writers. Managing discharges to protect water quality can be aided by the refinement of the methods, tools and information used to develop and implement NPDES permits and programs.
synthesis of the evolutionary adaptive Kalman filter. Next, the thesis describes all the aspects related to MATLAB/Simulink modeling and simulation: the performance criterion represented by the Cramer-Rae Lower Bound, the step-by-step modeling of the evolutionary adaptive Kalman filter, and the simulation results that confirm the viability of this approach. The thesis ends with the conclusion and the references. The appendices (the mathematical model of a 6DoF Inertial Measurement Unit, the experimental setup, the Simulink diagrams/MATLAB programs that constitute the evolutionary adaptive Kalman filter, plus the simulation results) are regrouped in a separate document.
Mu, Chaoxu; Ni, Zhen; Sun, Changyin; He, Haibo
A data-driven adaptive tracking control approach is proposed for a class of continuous-time nonlinear systems using a recent developed goal representation heuristic dynamic programming (GrHDP) architecture. The major focus of this paper is on designing a multivariable tracking scheme, including the filter-based action network (FAN) architecture, and the stability analysis in continuous-time fashion. In this design, the FAN is used to observe the system function, and then generates the corresponding control action together with the reference signals. The goal network will provide an internal reward signal adaptively based on the current system states and the control action. This internal reward signal is assigned as the input for the critic network, which approximates the cost function over time. We demonstrate its improved tracking performance in comparison with the existing heuristic dynamic programming (HDP) approach under the same parameter and environment settings. The simulation results of the multivariable tracking control on two examples have been presented to show that the proposed scheme can achieve better control in terms of learning speed and overall performance.
Parke, Tom; Marchenko, Olga; Anisimov, Vladimir; Ivanova, Anastasia; Jennison, Christopher; Perevozskaya, Inna; Song, Guochen
Designing an oncology clinical program is more challenging than designing a single study. The standard approaches have been proven to be not very successful during the last decade; the failure rate of Phase 2 and Phase 3 trials in oncology remains high. Improving a development strategy by applying innovative statistical methods is one of the major objectives of a drug development process. The oncology sub-team on Adaptive Program under the Drug Information Association Adaptive Design Scientific Working Group (DIA ADSWG) evaluated hypothetical oncology programs with two competing treatments and published the work in the Therapeutic Innovation and Regulatory Science journal in January 2014. Five oncology development programs based on different Phase 2 designs, including adaptive designs and a standard two parallel arm Phase 3 design were simulated and compared in terms of the probability of clinical program success and expected net present value (eNPV). In this article, we consider eight Phase2/Phase3 development programs based on selected combinations of five Phase 2 study designs and three Phase 3 study designs. We again used the probability of program success and eNPV to compare simulated programs. For the development strategies, we considered that the eNPV showed robust improvement for each successive strategy, with the highest being for a three-arm response adaptive randomization design in Phase 2 and a group sequential design with 5 analyses in Phase 3.
Press, Maximilian O.; Queitsch, Christine; Borenstein, Elhanan
Evolutionary innovation must occur in the context of some genomic background, which limits available evolutionary paths. For example, protein evolution by sequence substitution is constrained by epistasis between residues. In prokaryotes, evolutionary innovation frequently happens by macrogenomic events such as horizontal gene transfer (HGT). Previous work has suggested that HGT can be influenced by ancestral genomic content, yet the extent of such gene-level constraints has not yet been systematically characterized. Here, we evaluated the evolutionary impact of such constraints in prokaryotes, using probabilistic ancestral reconstructions from 634 extant prokaryotic genomes and a novel framework for detecting evolutionary constraints on HGT events. We identified 8228 directional dependencies between genes and demonstrated that many such dependencies reflect known functional relationships, including for example, evolutionary dependencies of the photosynthetic enzyme RuBisCO. Modeling all dependencies as a network, we adapted an approach from graph theory to establish chronological precedence in the acquisition of different genomic functions. Specifically, we demonstrated that specific functions tend to be gained sequentially, suggesting that evolution in prokaryotes is governed by functional assembly patterns. Finally, we showed that these dependencies are universal rather than clade-specific and are often sufficient for predicting whether or not a given ancestral genome will acquire specific genes. Combined, our results indicate that evolutionary innovation via HGT is profoundly constrained by epistasis and historical contingency, similar to the evolution of proteins and phenotypic characters, and suggest that the emergence of specific metabolic and pathological phenotypes in prokaryotes can be predictable from current genomes. PMID:27197212
Rodríguez-Verdugo, Alejandra; Buckley, James; Stapley, Jessica
Recent recognition that ecological and evolutionary processes can operate on similar timescales has led to a rapid increase in theoretical and empirical studies on eco-evolutionary dynamics. Progress in the fields of evolutionary biology, genomics and ecology is greatly enhancing our understanding of rapid adaptive processes, the predictability of adaptation and the genetics of ecologically important traits. However, progress in these fields has proceeded largely independently of one another. In an attempt to better integrate these fields, the centre for 'Adaptation to a Changing Environment' organized a conference entitled 'The genomic basis of eco-evolutionary change' and brought together experts in ecological genomics and eco-evolutionary dynamics. In this review, we use the work of the invited speakers to summarize eco-evolutionary dynamics and discuss how they are relevant for understanding and predicting responses to contemporary environmental change. Then, we show how recent advances in genomics are contributing to our understanding of eco-evolutionary dynamics. Finally, we highlight the gaps in our understanding of eco-evolutionary dynamics and recommend future avenues of research in eco-evolutionary dynamics.
Allen, Michael R.
A recent focus on contemporary evolution and the connections between communities has sought to more closely integrate ecology with evolutionary biology. Studies of coevolutionary dynamics, life history evolution, and rapid local adaptation demonstrate that ecological circumstances can dictate evolutionary trajectories. Thus, variation in species…
Jansen, Mieke; Coors, Anja; Stoks, Robby; De Meester, Luc
Natural populations that are exposed to pesticides in their environment may at the same time be exposed to natural stressors like parasites and predators, which may interact with pesticide exposure. This may not only impact target pest species but also a wide variety of non-target species. This review reports on a joint research program in the water flea Daphnia magna, a non-target species often used as model organism in ecology and ecotoxicology. The focus is on different aspects that are of key importance to understand the evolutionary ecology of pesticide exposure: (1) the capacity of natural populations to genetically adapt to pesticide exposure (2) the added complexity of synergistic effects caused by simultaneous exposure to natural stressors, and (3) the potential interference of evolutionary costs of adaptation to pesticide exposure. Our results showed that natural populations were able to rapidly evolve resistance to the pesticide carbaryl but at the expense of fitness costs. Individuals selected for carbaryl resistance had higher survival rates when exposed to the pesticide but also a greater susceptibility to the challenge imposed by the bacterial endoparasite Pasteuria ramosa. The evolved resistance to carbaryl was in some cases only expressed in the absence of fish kairomones. Further, it became clear that the responses to both exposure to single and combined stressors was for several life history variables strongly dependent upon past exposure to carbaryl. This indicates that past exposures to pesticides are important and can not be neglected when evaluating responses to current stressors.
Bock, Walter J
Darwin in his On the Origin of species made it clear that evolutionary change depends on the combined action of two different causes, the first being the origin of genetically based phenotypic variation in the individual organisms comprising the population and the second being the action of selective agents of the external environment placing demands on the individual organisms. For over a century following Darwin, most evolutionists focused on the origin of inherited variation and its transmission; many workers continue to regard genetics to be the core of evolutionary theory. Far less attention has been given to the exact nature of the selective agents with most evolutionists still treating this cause imprecisely to the detriment of our understanding of both nomological and historical evolutionary theory. Darwin was vague in the meaning of his new concept of "Natural Selection," using it interchangeably as one of the causes for evolutionary change and as the final outcome (= evolutionary change). In 1930, natural selection was defined clearly as "non-random, differential reproduction of genes" by R. Fisher and J.B.S. Haldane which is a statement of the outcome of evolutionary process and which omits mention of the causes bringing about this change. Evolutionists quickly accepted this outcome definition of natural selection, and have used interchangeably selection both as a cause and as the result of evolutionary change, causing great confusion. Herein, the details will be discussed of how the external environment (i.e., the environment-phenotype interaction) serves as selective agents and exerts demands on the phenotypic organisms. Included are the concepts of fitness and of the components of fitness (= adaptations) which are respectively (a) survival, (b) direct reproductive and (c) indirect reproductive features. Finally, it will be argued that historical-narrative analyses of organisms, including classification and phylogenetic history, are possible only with
Martin, Oliver Y; Gage, Matthew J G
Conflicts between and within species can drive fast evolutionary change. A recent study has documented remarkably rapid counter-adaptations in the wild to an extreme sex-ratio distortion caused by a bacterial symbiont.
Many secondary students hold misconceptions about evolution, even after instruction, that are often inconsistent with what is accepted by evolutionary biologists. Understanding evolution is difficult due to major conceptual difficulties concerning variation, differential survival, adaptation, and natural selection. In this article, the author…
Basel, Nicolai; Harms, Ute; Prechtl, Helmut
A qualitative exploratory study was conducted to reveal students' argumentation skills in the context of the topic of evolution. Transcripts from problem-centred interviews on secondary students' beliefs about evolutionary processes of adaptation were analysed using a content analysis approach. For this purpose two categorical systems were…
Schlaepfer, Martin A.; Sherman, P.W.; Blossey, B.; Runge, M.C.
Invasive species can alter environments in such a way that normal behavioural decision-making rules of native species are no longer adaptive. The evolutionary trap concept provides a useful framework for predicting and managing the impact of harmful invasive species. We discuss how native species can respond to changes in their selective regime via evolution or learning. We also propose novel management strategies to promote the long-term co-existence of native and introduced species in cases where the eradication of the latter is either economically or biologically unrealistic.
Rabbers, Iraes; van Heerden, Johan H.; Nordholt, Niclas; Bachmann, Herwig; Teusink, Bas; Bruggeman, Frank J.
Metabolism is generally required for cellular maintenance and for the generation of offspring under conditions that support growth. The rates, yields (efficiencies), adaptation time and robustness of metabolism are therefore key determinants of cellular fitness. For biotechnological applications and our understanding of the evolution of metabolism, it is necessary to figure out how the functional system properties of metabolism can be optimized, via adjustments of the kinetics and expression of enzymes, and by rewiring metabolism. The trade-offs that can occur during such optimizations then indicate fundamental limits to evolutionary innovations and bioengineering. In this paper, we review several theoretical and experimental findings about mechanisms for metabolic optimization. PMID:26042723
Walsh, David A; Sharma, Adrian K
A common approach for investigating evolutionary relationships between genes and organisms is to compare extant DNA or protein sequences and infer an evolutionary tree. This methodology is known as molecular phylogenetics and may be the most informative means for exploring phage evolution, since there are few morphological features that can be used to differentiate between these tiny biological entities. In addition, phage genomes can be mosaic, meaning different genes or genomic regions can exhibit conflicting evolutionary histories due to lateral gene transfer or homologous recombination between different phage genomes. Molecular phylogenetics can be used to identify and study such genome mosaicism. This chapter provides a general introduction to the theory and methodology used to reconstruct phylogenetic relationships from molecular data. Also included is a discussion on how the evolutionary history of different genes within the same set of genomes can be compared, using a collection of T4-type phage genomes as an example. A compilation of programs and packages that are available for conducting phylogenetic analyses is supplied as an accompanying appendix.
Lessells, C M
Inter-locus sexual conflict occurs by definition when there is sexually antagonistic selection on a trait so that the optimal trait value differs between the sexes. As a result, there is selection on each sex to manipulate the trait towards its own optimum and resist such manipulation by the other sex. Sexual conflict often leads additionally to the evolution of harmful behaviour and to self-reinforcing and even perpetual sexually antagonistic coevolution. In an attempt to understand the determinants of these different outcomes, I compare two groups of traits-those related to parental investment (PI) and to mating-over which there is sexual conflict, but which have to date been explored by largely separate research traditions. A brief review suggests that sexual conflict over PI, particularly over PI per offspring, leads less frequently to the evolution of manipulative behaviour, and rarely to the evolution of harmful behaviour or to the rapid evolutionary changes which may be symptomatic of sexually antagonistic coevolution. The chief determinants of the evolutionary outcome of sexual conflict are the benefits of manipulation and resistance, the costs of manipulation and resistance, and the feasibility of manipulation. All three of these appear to contribute to the differences in the evolutionary outcome of conflicts over PI and mating. A detailed dissection of the evolutionary changes following from sexual conflict exposes greater complexity than a simple adaptation-counter-adaptation cycle and clarifies the role of harm. Not all of the evolutionary changes that follow from sexual conflict are sexually antagonistic, and harm is not necessary for sexually antagonistic coevolution to occur. In particular, whereas selection on the trait over which there is conflict is by definition sexually antagonistic, collateral harm is usually in the interest of neither sex. This creates the opportunity for palliative adaptations which reduce collateral harm. Failure to
Sibbald, Shannon L.; Speechley, Mark; Thind, Amardeep
The goal of any public health education at the Masters level is to transmit knowledge and skills to meet current and future public health challenges. We suggest an innovative multi-modal approach to public health education using a case-based pedagogy combined with competency-based curriculum and a team-based approach to foster truly experiential learning. We describe each pedagogical approach in connection to the relevance of optimal methods for training public health professionals. Western University’s Schulich Interfaculty Masters of Public Health (MPH) program (ON, Canada) provides a unique interprofessional education through case-based learning and competency-based curriculum. This Masters program has attracted applicants from around the world to learn in a supportive interprofessional environment and to foster them as they become learners and leaders in public health changes. To our knowledge, we are the first condensed MPH program using integrated case-based pedagogy as our main pedagogical approach. PMID:27790608
Pifko, A. B.; Ogilvie, P. L.
The conversion of a nonlinear finite element program to the CDC STAR 100 pipeline computer is discussed. The program called DYCAST was developed for the crash simulation of structures. Initial results with the STAR 100 computer indicated that significant gains in computation time are possible for operations on gloval arrays. However, for element level computations that do not lend themselves easily to long vector processing, the STAR 100 was slower than comparable scalar computers. On this basis it is concluded that in order for pipeline computers to impact the economic feasibility of large nonlinear analyses it is absolutely essential that algorithms be devised to improve the efficiency of element level computations.
Cassel, Kevin D; Braun, Kathryn; Ka'opua, Lana; Soa, Fuamaila; Nigg, Claudio
Obesity-associated chronic diseases persist in Samoan populations in the United States. Samoans and African Americans share cultural similarities such as church affiliation, perceptions of weight and body size, and obesity-related health risks. Adapting an effective energy balance intervention originally designed for African Americans--Body and Soul--might be useful in reducing obesity among U.S. Samoans. To determine potential attractiveness and adaptations, we used aspects of grounded theory to analyze key-informant and focus group interviews with 31 purposively selected Samoans in Hawaii. We incorporated participatory features into the research with Samoan community members conducting parts of the study. From interview narratives, we identified relevant themes from Samoan culture, such as "fa'aSamoa", or the Samoan way, and specific energy balance activities to include in an obesity and cancer prevention intervention for U.S.-dwelling Samoans. Our findings describe methods to address health disparities by incorporating culturally appropriate health concepts into existing evidence-based interventions.
Cassel, Kevin D.; Braun, Kathryn; Ka’opua, Lana; Soa, Fuamaila; Nigg, Claudio
Obesity-associated chronic diseases persist in Samoan populations in the United States. Samoans and African Americans share cultural similarities such as church affiliation, perceptions of weight and body size, and obesity-related health risks. Adapting an effective energy balance intervention originally designed for African Americans—Body and Soul— might be useful in reducing obesity among U.S. Samoans. To determine potential attractiveness and adaptations, we used aspects of grounded theory to analyze key-informant and focus group interviews with 31 purposively selected Samoans in Hawaii. We incorporated participatory features into the research with Samoan community members conducting parts of the study. From interview narratives, we identified relevant themes from Samoan culture, such as fa’aSamoa or the Samoan way, and specific energy balance activities to include in an obesity and cancer prevention intervention for U.S.-dwelling Samoans. Our findings describe methods to address health disparities by incorporating culturally appropriate health concepts into existing evidence-based interventions. PMID:25212854
Tomioka, Michiyo; Braun, Kathryn L.; Compton, Merlita; Tanoue, Leslie
Purpose of the Study: Stanford's Chronic Disease Self-Management Program (CDSMP) has been proven to increase patients' ability to manage distress. We describe how we replicated CDSMP in Asian and Pacific Islander (API) communities. Design and Methods: We used the "track changes" tool to deconstruct CDSMP into its various components…
Lennington, R. K.; Rassbach, M. E.
Discussed in this report is the clustering algorithm CLASSY, including detailed descriptions of its general structure and mathematical background and of the various major subroutines. The report provides a development of the logic and equations used with specific reference to program variables. Some comments on timing and proposed optimization techniques are included.
Latham, Gary; Latham, Soosan D.; Whyte, Glen
Many full-time MBA programs limit their effectiveness by clinging to functionalism. At best, they have made incremental changes to meet the market demand for MBA graduates. These changes, in most cases, have failed to integrate the various functional facets of complex business challenges. For insights into how to do so, many business schools need…
Engeswick, Lynnette Marie
This study was conducted to discover the extent dental hygiene educators in 25 entry-level dental hygiene programs from the Upper Midwest demonstrate Emotional Resilience, Flexibility and Openness, Perceptual Acuity, and Personal Autonomy as they relate to their level of education and multicultural experiences. An additional purpose was to examine…
Hojnicki, Jeffrey S.; Kerslake, Thomas W.; Ayres, Mark; Han, Augustina H.; Adamson, Adrian M.
NASA's Constellation Program is embarking on a new era of space exploration, returning to the Moon and beyond. The Constellation architecture will consist of a number of new spacecraft elements, including the Orion crew exploration vehicle, the Altair lunar lander, and the Ares family of launch vehicles. Each of these new spacecraft elements will need an electric power system, and those power systems will need to be designed to fulfill unique mission objectives and to survive the unique environments encountered on a lunar exploration mission. As with any new spacecraft power system development, preliminary design work will rely heavily on analysis to select the proper power technologies, size the power system components, and predict the system performance throughout the required mission profile. Constellation projects have the advantage of leveraging power system modeling developments from other recent programs such as the International Space Station (ISS) and the Mars Exploration Program. These programs have developed mature power system modeling tools, which can be quickly modified to meet the unique needs of Constellation, and thus provide a rapid capability for detailed power system modeling that otherwise would not exist.
Ribbe, Robert, Jr.; Cyrus, Rachael; Langan, Emily
Outdoor orientation programming as a means for orientating students to college has experienced significant growth and expanded use over the past decade. An increase in rigorous research has accompanied this growth as colleges and universities seek to understand and meet the needs of young adults in transition. In this study, two research questions…
The booklet reviews ways in which students with crutches may be helped to successfully participate in four specific sports. General guidelines for modifying programs for this group include the importance of thorough assessment, attention to details of the game play, and consideration of equipment and supply alterations. Each of the four sports is…
were exposed to a spray of polar solvent or polar solvent/ water absorbing polymer . When compared to the control, the doped yarns doubled in... Polymer Nanocomposite Synthesis ................................25 4.6.2 Polymeric Nanocomposite Battery Materials...merged into the ERA bridge program: in-house polymer synthesis and processing projects of graded preceramic polymeric hybrid materials, a laser
Colquitt, Gavin; Walker, Ashley; Alfonso, Moya
With school-aged youth spending less time in physical education, school-community-university partnerships offer potential to promote physical activity among school-aged youth. The VERB™ Summer Scorecard (VSS) program was designed in Lexington, Kentucky, to promote physical activity among "tweens" (8- to 13-year-olds). VSS since has been…
Meinke, Mark W.
Discusses a model of English-as-a-Second-Language (ESL) program evaluation and suggests ESL professionals begin to see themselves within the wider context of training and development and begin applying useful disciplines of the business world to their activities. (four references) (JL)
Davis, Kathy; Hodson, Patricia; Zhang, Guili; Boswell, Boni; Decker, Jim
Research has shown that regular physical activity helps to prevent major health problems, such as heart disease, obesity, and diabetes. However, little research has been conducted on classroom-based physical activity programs for students with disabilities. In North Carolina, the Healthy Active Children Policy was implemented in 2006, requiring…
Fox, Mary Frank; Sonnert, Gerhard; Nikiforova, Irina
This article focuses upon programs for undergraduate women in science and engineering, which are a strategic research site in the study of gender, science, and higher education. The design involves both quantitative and qualitative approaches, linking theory, method, questions, and analyses in ways not undertaken previously. Using a comprehensive,…
Gantt, D G; Rafter, J A
The purpose of this investigation is to evaluate enamel thickness in extant and extinct hominoids. The material used in this study spans the evolutionary history of this group, from 20 million years ago to the present. The objectives of this investigation are to test three hypotheses: (1) the Loading Hypothesis: loading areas of the crown have thicker enamel than non-loading areas; (2) the Phyletic Hypothesis: differences in enamel thickness provide a basis for determining evolutionary relationships; and (3) the Functional Hypothesis: differences among hominoids result from adaptations to differing dietary and ecological habitats, that is from folivory to frugivory to hard object feeding and from tropical to forest to savanna habitats. Thin sections were prepared and polished to approximately 100 microm in thickness. Each section was then enlarged and digitally captured to the computer. Image processing and analysis software, SigmaImage (was used to measure the sections. Subsequent statistical analysis was conducted with SigmaStat and SPSS statistical software programs. The data provides statistical support for all hypotheses. In particular, the data support the proposal that "thick" enamel is the ancestral condition for the great apes and human clade. Therefore, Pongo would have retained its enamel thickness from the common ancestor of the great apes and Gorilla and Pan would have secondarily reduced enamel thickness to "thin." The common ancestor of the hominids, the australopithecines, would have "thick" enamel. The "hyper-thick" enamel of the australopithecines would be a derived character for this clade due to increased crushing and grinding and adaptation to savanna habitat. Homo would have secondarily reduced enamel thickness to "thick." Evolutionary biology of enamel differs markedly in hominids from that found in other hominoids and primates. Increased enamel thickness involved both increases in absolute thickness of enamel and crown size in response to
Welch, John J
There have been periodic claims that evolutionary biology needs urgent reform, and this article tries to account for the volume and persistence of this discontent. It is argued that a few inescapable properties of the field make it prone to criticisms of predictable kinds, whether or not the criticisms have any merit. For example, the variety of living things and the complexity of evolution make it easy to generate data that seem revolutionary (e.g. exceptions to well-established generalizations, or neglected factors in evolution), and lead to disappointment with existing explanatory frameworks (with their high levels of abstraction, and limited predictive power). It is then argued that special discontent stems from misunderstandings and dislike of one well-known but atypical research programme: the study of adaptive function, in the tradition of behavioural ecology. To achieve its goals, this research needs distinct tools, often including imaginary agency, and a partial description of the evolutionary process. This invites mistaken charges of narrowness and oversimplification (which come, not least, from researchers in other subfields), and these chime with anxieties about human agency and overall purpose. The article ends by discussing several ways in which calls to reform evolutionary biology actively hinder progress in the field.
Lee, Carol Eunmi; Gelembiuk, Gregory William
What factors shape the evolution of invasive populations? Recent theoretical and empirical studies suggest that an evolutionary history of disturbance might be an important factor. This perspective presents hypotheses regarding the impact of disturbance on the evolution of invasive populations, based on a synthesis of the existing literature. Disturbance might select for life-history traits that are favorable for colonizing novel habitats, such as rapid population growth and persistence. Theoretical results suggest that disturbance in the form of fluctuating environments might select for organismal flexibility, or alternatively, the evolution of evolvability. Rapidly fluctuating environments might favor organismal flexibility, such as broad tolerance or plasticity. Alternatively, longer fluctuations or environmental stress might lead to the evolution of evolvability by acting on features of the mutation matrix. Once genetic variance is generated via mutations, temporally fluctuating selection across generations might promote the accumulation and maintenance of genetic variation. Deeper insights into how disturbance in native habitats affects evolutionary and physiological responses of populations would give us greater capacity to predict the populations that are most likely to tolerate or adapt to novel environments during habitat invasions. Moreover, we would gain fundamental insights into the evolutionary origins of invasive populations. PMID:25567726
Ohtsuki, Hisashi; Nowak, Martin A.
Evolutionary stability is a fundamental concept in evolutionary game theory. A strategy is called an evolutionarily stable strategy (ESS), if its monomorphic population rejects the invasion of any other mutant strategy. Recent studies have revealed that population structure can considerably affect evolutionary dynamics. Here we derive the conditions of evolutionary stability for games on graphs. We obtain analytical conditions for regular graphs of degree k > 2. Those theoretical predictions are compared with computer simulations for random regular graphs and for lattices. We study three different update rules: birth-death (BD), death-birth (DB), and imitation (IM) updating. Evolutionary stability on sparse graphs does not imply evolutionary stability in a well-mixed population, nor vice versa. We provide a geometrical interpretation of the ESS condition on graphs. PMID:18295801
First Steps School Intervention Module: CLASS-- Contingencies for Learning Academic and Social Skills. (Adapted Preschool Version). An Early School Intervention Program for At-Risk Kindergartners. A Component of the First Steps Program.
Golly, Annemieke; Stiller, Bruce
This report describes the second module of an early intervention program for at-risk kindergartners who show the early signs of antisocial behavior patterns. The second module of the "First Steps" program describes a school intervention involving the target child, peers, and teachers that teaches an adaptive, prosocial pattern of school…
Hinton, D. A.; Shaughnessy, J. D.
A data base was developed for SPIFR operation and the program was run. The outputs indicated that further work was necessary on the workload models. In particular, the workload model for the cognitive channel should be modified as the output workload appears to be too small. Included in the needed refinements are models to show the workload when in turbulence, when overshooting a radial or glideslope, and when copying air traffic control clearances.
Hessberg, R. R.
With the completion of the historic Apollo Program, the significant medical findings will be reviewed and the medical results summarized. The medical objectives of Skylab will be presented. The medical experiments which will be conducted and their relationship to the Apollo medical findings and Skylab objectives will be discussed. The interrelationship of the Skylab medical experiments will be described and the anticipated information to be obtained will be postulated.
Throughout his career as a writer, Sigmund Freud maintained an interest in the evolutionary origins of the human mind and its neurotic and psychotic disorders. In common with many writers then and now, he believed that the evolutionary past is conserved in the mind and the brain. Today the "evolutionary Freud" is nearly forgotten. Even among Freudians, he is regarded to be a red herring, relevant only to the extent that he diverts attention from the enduring achievements of the authentic Freud. There are three ways to explain these attitudes. First, the evolutionary Freud's key work is the "Overview of the Transference Neurosis" (1915). But it was published at an inopportune moment, forty years after the author's death, during the so-called "Freud wars." Second, Freud eventually lost interest in the "Overview" and the prospect of a comprehensive evolutionary theory of psychopathology. The publication of The Ego and the Id (1923), introducing Freud's structural theory of the psyche, marked the point of no return. Finally, Freud's evolutionary theory is simply not credible. It is based on just-so stories and a thoroughly discredited evolutionary mechanism, Lamarckian use-inheritance. Explanations one and two are probably correct but also uninteresting. Explanation number three assumes that there is a fundamental difference between Freud's evolutionary narratives (not credible) and the evolutionary accounts of psychopathology that currently circulate in psychiatry and mainstream journals (credible). The assumption is mistaken but worth investigating.
Kulis, Stephen S; Ayers, Stephanie L; Harthun, Mary L
This article describes a small efficacy trial of the Living in 2 Worlds (L2W) substance use prevention curriculum, a culturally adapted version of keepin' it REAL (kiR) redesigned for urban American Indian (AI) middle school students. Focused on strengthening resiliency and AI cultural engagement, L2W teaches drug resistance skills, decision making, and culturally grounded prevention messages. Using cluster random assignment, the research team randomized three urban middle schools with enrichment classes for AI students. AI teachers of these classes delivered the L2W curriculum in two schools; the remaining school implemented kiR, unadapted, and became the comparison group. AI students (N = 107) completed a pretest questionnaire before they received the manualized curriculum lessons, and a posttest (85% completion) 1 month after the final lesson. We assessed the adapted L2W intervention, compared to kiR, with paired t tests, baseline adjusted general linear models, and effect size estimates (Cohen's d). Differences between the L2W and kiR groups reached statistically significant thresholds for four outcomes. Youth receiving L2W, compared to kiR, reported less growth in cigarette use from pretest to posttest, less frequent use of the Leave drug resistance strategy, and less loss of connections to AI spirituality and cultural traditions. For other substance use behaviors and antecedents, the direction of the non-significant effects in small sample tests was toward more positive outcomes in L2W and small to medium effect sizes. Results suggest that evidence-based substance use prevention programs that are culturally adapted for urban AI adolescents, like L2W, can be a foundation for prevention approaches to help delay initiation and slow increases in substance use. In addition to study limitations, we discuss implementation challenges in delivering school-based interventions for urban AI populations.
Zhang, Huaguang; Jiang, He; Luo, Chaomin; Xiao, Geyang
In this paper, we investigate the nonzero-sum games for a class of discrete-time (DT) nonlinear systems by using a novel policy iteration (PI) adaptive dynamic programming (ADP) method. The main idea of our proposed PI scheme is to utilize the iterative ADP algorithm to obtain the iterative control policies, which not only ensure the system to achieve stability but also minimize the performance index function for each player. This paper integrates game theory, optimal control theory, and reinforcement learning technique to formulate and handle the DT nonzero-sum games for multiplayer. First, we design three actor-critic algorithms, an offline one and two online ones, for the PI scheme. Subsequently, neural networks are employed to implement these algorithms and the corresponding stability analysis is also provided via the Lyapunov theory. Finally, a numerical simulation example is presented to demonstrate the effectiveness of our proposed approach.