coevolution sequential counter-adaptations: Topics by Science.gov

Sample records for coevolution sequential counter-adaptations

A Paradigm for Virus–Host Coevolution: Sequential Counter-Adaptations between Endogenous and Exogenous Retroviruses

PubMed Central

Arnaud, Frederick; Caporale, Marco; Varela, Mariana; Biek, Roman; Chessa, Bernardo; Alberti, Alberto; Golder, Matthew; Mura, Manuela; Zhang, Ya-ping; Yu, Li; Pereira, Filipe; DeMartini, James C; Leymaster, Kreg; Spencer, Thomas E; Palmarini, Massimo

2007-01-01

Endogenous retroviruses (ERVs) are remnants of ancient retroviral infections of the host germline transmitted vertically from generation to generation. It is hypothesized that some ERVs are used by the host as restriction factors to block the infection of pathogenic retroviruses. Indeed, some ERVs efficiently interfere with the replication of related exogenous retroviruses. However, data suggesting that these mechanisms have influenced the coevolution of endogenous and/or exogenous retroviruses and their hosts have been more difficult to obtain. Sheep are an interesting model system to study retrovirus-host coevolution because of the coexistence in this animal species of two exogenous (i.e., horizontally transmitted) oncogenic retroviruses, Jaagsiekte sheep retrovirus and Enzootic nasal tumor virus, with highly related and biologically active endogenous retroviruses (enJSRVs). Here, we isolated and characterized the evolutionary history and molecular virology of 27 enJSRV proviruses. enJSRVs have been integrating in the host genome for the last 5–7 million y. Two enJSRV proviruses (enJS56A1 and enJSRV-20), which entered the host genome within the last 3 million y (before and during speciation within the genus Ovis), acquired in two temporally distinct events a defective Gag polyprotein resulting in a transdominant phenotype able to block late replication steps of related exogenous retroviruses. Both transdominant proviruses became fixed in the host genome before or around sheep domestication (∼ 9,000 y ago). Interestingly, a provirus escaping the transdominant enJSRVs has emerged very recently, most likely within the last 200 y. Thus, we determined sequentially distinct events during evolution that are indicative of an evolutionary antagonism between endogenous and exogenous retroviruses. This study strongly suggests that endogenization and selection of ERVs acting as restriction factors is a mechanism used by the host to fight retroviral infections. PMID:17997604
Cuckoos versus hosts in insects and birds: adaptations, counter-adaptations and outcomes.

PubMed

Kilner, Rebecca M; Langmore, Naomi E

2011-11-01

Avian parents and social insect colonies are victimized by interspecific brood parasites-cheats that procure costly care for their dependent offspring by leaving them in another species' nursery. Birds and insects defend themselves from attack by brood parasites; their defences in turn select counter-strategies in the parasite, thus setting in motion antagonistic co-evolution between the two parties. Despite their considerable taxonomic disparity, here we show striking parallels in the way that co-evolution between brood parasites and their hosts proceeds in insects and birds. First, we identify five types of co-evolutionary arms race from the empirical literature, which are common to both systems. These are: (a) directional co-evolution of weaponry and armoury; (b) furtiveness in the parasite countered by strategies in the host to expose the parasite; (c) specialist parasites mimicking hosts who escape by diversifying their genetic signatures; (d) generalist parasites mimicking hosts who escape by favouring signatures that force specialization in the parasite; and (e) parasites using crypsis to evade recognition by hosts who then simplify their signatures to make the parasite more detectable. Arms races a and c are well characterized in the theoretical literature on co-evolution, but the other types have received little or no formal theoretical attention. Empirical work suggests that hosts are doomed to lose arms races b and e to the parasite, in the sense that parasites typically evade host defences and successfully parasitize the nest. Nevertheless hosts may win when the co-evolutionary trajectory follows arms race a, c or d. Next, we show that there are four common outcomes of the co-evolutionary arms race for hosts. These are: (1) successful resistance; (2) the evolution of defence portfolios (or multiple lines of resistance); (3) acceptance of the parasite; and (4) tolerance of the parasite. The particular outcome is not determined by the type of preceding arms race but depends more on whether hosts or parasites control the co-evolutionary trajectory: tolerance is an outcome that parasites inflict on hosts, whereas the other three outcomes are more dependent on properties intrinsic to the host species. Finally, our review highlights considerable interspecific variation in the complexity and depth of host defence portfolios. Whether this variation is adaptive or merely reflects evolutionary lag is unclear. We propose an adaptive explanation, which centres on the relative strength of two opposing processes: strategy-facilitation, in which one line of host defence promotes the evolution of another form of resistance, and strategy-blocking, in which one line of defence may relax selection on another so completely that it causes it to decay. We suggest that when strategy-facilitation outweighs strategy-blocking, hosts will possess complex defence portfolios and we identify selective conditions in which this is likely to be the case. © 2011 The Authors. Biological Reviews © 2011 Cambridge Philosophical Society.
The evolutionary outcome of sexual conflict.

PubMed

Lessells, C M

2006-02-28

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 recognize that such adaptations are in the interest of both sexes can hinder our understanding of the evolutionary outcome of sexual conflict.
Inter-genomic sexual conflict drives antagonistic coevolution in harvester ants

PubMed Central

Herrmann, Michael; Cahan, Sara Helms

2014-01-01

The reproductive interests of males and females are not always aligned, leading to sexual conflict over parental investment, rate of reproduction and mate choice. Traits that increase the genetic interests of one sex often occur at the expense of the other, selecting for counter-adaptations leading to antagonistic coevolution. Reproductive conflict is not limited to intraspecific interactions; interspecific hybridization can produce pronounced sexual conflict between males and females of different species, but it is unclear whether such conflict can drive sexually antagonistic coevolution between reproductively isolated genomes. We tested for hybridization-driven sexually antagonistic adaptations in queens and males of the socially hybridogenetic ‘J’ lineages of Pogonomyrmex harvester ants, whose mating system promotes hybridization in queens but selects against it in males. We conducted no-choice mating assays to compare patterns of mating behaviour and sperm transfer between inter- and intra-lineage pairings. There was no evidence for mate discrimination on the basis of pair type, and the total quantity of sperm transferred did not differ between intra- and inter-lineage pairs; however, further dissection of the sperm transfer process into distinct mechanistic components revealed significant, and opposing, cryptic manipulation of copulatory investment by both sexes. Males of both lineages increased their rate of sperm transfer to high-fitness intra-lineage mates, with a stronger response in the rarer lineage for whom mating mistakes are the most likely. By contrast, the total duration of copulation for intra-lineage mating pairs was significantly shorter than for inter-lineage crosses, suggesting that queens respond to prevent excessive sperm loading by prematurely terminating copulation. These findings demonstrate that sexual conflict can lead to antagonistic coevolution in both intra-genomic and inter-genomic contexts. Indeed, the resolution of sexual conflict may be a key determinant of the long-term evolutionary potential of host-dependent reproductive strategies, counteracting the inherent instabilities arising from such systems. PMID:25355474
Sexual conflict and correlated evolution between male persistence and female resistance traits in the seed beetle Callosobruchus maculatus.

PubMed

Dougherty, Liam R; van Lieshout, Emile; McNamara, Kathryn B; Moschilla, Joe A; Arnqvist, Göran; Simmons, Leigh W

2017-05-31

Traumatic mating (or copulatory wounding) is an extreme form of sexual conflict whereby male genitalia physically harm females during mating. In such species females are expected to evolve counter-adaptations to reduce male-induced harm. Importantly, female counter-adaptations may include both genital and non-genital traits. In this study, we examine evolutionary associations between harmful male genital morphology and female reproductive tract morphology and immune function across 13 populations of the seed beetle Callosobruchus maculatus We detected positive correlated evolution between the injuriousness of male genitalia and putative female resistance adaptations across populations. Moreover, we found evidence for a negative relationship between female immunity and population productivity, which suggests that investment in female resistance may be costly due to the resource trade-offs that are predicted between immunity and reproduction. Finally, the degree of female tract scarring (harm to females) was greater in those populations with both longer aedeagal spines and a thinner female tract lining. Our results are thus consistent with a sexual arms race, which is only apparent when both male and female traits are taken into account. Importantly, our study provides rare evidence for sexually antagonistic coevolution of male and female traits at the within-species level. © 2017 The Author(s).
Sexual conflict and correlated evolution between male persistence and female resistance traits in the seed beetle Callosobruchus maculatus

PubMed Central

van Lieshout, Emile; Moschilla, Joe A.; Arnqvist, Göran

2017-01-01

Traumatic mating (or copulatory wounding) is an extreme form of sexual conflict whereby male genitalia physically harm females during mating. In such species females are expected to evolve counter-adaptations to reduce male-induced harm. Importantly, female counter-adaptations may include both genital and non-genital traits. In this study, we examine evolutionary associations between harmful male genital morphology and female reproductive tract morphology and immune function across 13 populations of the seed beetle Callosobruchus maculatus. We detected positive correlated evolution between the injuriousness of male genitalia and putative female resistance adaptations across populations. Moreover, we found evidence for a negative relationship between female immunity and population productivity, which suggests that investment in female resistance may be costly due to the resource trade-offs that are predicted between immunity and reproduction. Finally, the degree of female tract scarring (harm to females) was greater in those populations with both longer aedeagal spines and a thinner female tract lining. Our results are thus consistent with a sexual arms race, which is only apparent when both male and female traits are taken into account. Importantly, our study provides rare evidence for sexually antagonistic coevolution of male and female traits at the within-species level. PMID:28539510
The evolutionary outcome of sexual conflict

PubMed Central

Lessells, C(Kate). M

2006-01-01

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 recognize that such adaptations are in the interest of both sexes can hinder our understanding of the evolutionary outcome of sexual conflict. PMID:16612889
Female control of paternity in the sexually cannibalistic spider Argiope keyserlingi.

PubMed Central

Elgar, M A; Schneider, J M; Herberstein, M E

2000-01-01

Sexual conflict theory predicts an antagonistic coevolution, with each sex evolving adaptations and counter-adaptations to overcome a temporary dominance of the other sex over the control of paternity. Polyandry allows sexual selection to operate after mating has commenced, with male and female interests competing for control of fertilization. There are numerous examples of male control of paternity, but few studies have unambiguously revealed female control. Attributing variance in paternity to females is often difficult since male and female influences cannot be separated unambiguously. However, we show that polyandrous female orb-web spiders Argiope keserlingi (Arancidae) control the paternity of their offspring by adjusting the timing of sexual cannibalism. Our experiments reveal that females copulating with relatively smaller males delay sexual cannibalism, thereby prolonging the duration of copulation, and that these males consequently fertilize relatively more eggs. PMID:11133035
How Complex, Probable, and Predictable is Genetically Driven Red Queen Chaos?

PubMed

Duarte, Jorge; Rodrigues, Carla; Januário, Cristina; Martins, Nuno; Sardanyés, Josep

2015-12-01

Coevolution between two antagonistic species has been widely studied theoretically for both ecologically- and genetically-driven Red Queen dynamics. A typical outcome of these systems is an oscillatory behavior causing an endless series of one species adaptation and others counter-adaptation. More recently, a mathematical model combining a three-species food chain system with an adaptive dynamics approach revealed genetically driven chaotic Red Queen coevolution. In the present article, we analyze this mathematical model mainly focusing on the impact of species rates of evolution (mutation rates) in the dynamics. Firstly, we analytically proof the boundedness of the trajectories of the chaotic attractor. The complexity of the coupling between the dynamical variables is quantified using observability indices. By using symbolic dynamics theory, we quantify the complexity of genetically driven Red Queen chaos computing the topological entropy of existing one-dimensional iterated maps using Markov partitions. Co-dimensional two bifurcation diagrams are also built from the period ordering of the orbits of the maps. Then, we study the predictability of the Red Queen chaos, found in narrow regions of mutation rates. To extend the previous analyses, we also computed the likeliness of finding chaos in a given region of the parameter space varying other model parameters simultaneously. Such analyses allowed us to compute a mean predictability measure for the system in the explored region of the parameter space. We found that genetically driven Red Queen chaos, although being restricted to small regions of the analyzed parameter space, might be highly unpredictable.
Female burying beetles benefit from male desertion: sexual conflict and counter-adaptation over parental investment.

PubMed

Boncoraglio, Giuseppe; Kilner, Rebecca M

2012-01-01

Sexual conflict drives the coevolution of sexually antagonistic traits, such that an adaptation in one sex selects an opposing coevolutionary response from the other. Although many adaptations and counteradaptations have been identified in sexual conflict over mating interactions, few are known for sexual conflict over parental investment. Here we investigate a possible coevolutionary sequence triggered by mate desertion in the burying beetle Nicrophorus vespilloides, where males commonly leave before their offspring reach independence. Rather than suffer fitness costs as a consequence, our data suggest that females rely on the male's absence to recoup some of the costs of larval care, presumably because they are then free to feed themselves on the carcass employed for breeding. Consequently, forcing males to stay until the larvae disperse reduces components of female fitness to a greater extent than caring for young singlehandedly. Therefore we suggest that females may have co-evolved to anticipate desertion by their partners so that they now benefit from the male's absence.
Female Burying Beetles Benefit from Male Desertion: Sexual Conflict and Counter-Adaptation over Parental Investment

PubMed Central

Boncoraglio, Giuseppe; Kilner, Rebecca M.

2012-01-01

Sexual conflict drives the coevolution of sexually antagonistic traits, such that an adaptation in one sex selects an opposing coevolutionary response from the other. Although many adaptations and counteradaptations have been identified in sexual conflict over mating interactions, few are known for sexual conflict over parental investment. Here we investigate a possible coevolutionary sequence triggered by mate desertion in the burying beetle Nicrophorus vespilloides, where males commonly leave before their offspring reach independence. Rather than suffer fitness costs as a consequence, our data suggest that females rely on the male's absence to recoup some of the costs of larval care, presumably because they are then free to feed themselves on the carcass employed for breeding. Consequently, forcing males to stay until the larvae disperse reduces components of female fitness to a greater extent than caring for young singlehandedly. Therefore we suggest that females may have co-evolved to anticipate desertion by their partners so that they now benefit from the male's absence. PMID:22355390
Co-evolution of Mycobacterium tuberculosis and Homo sapiens

PubMed Central

Brites, Daniela; Gagneux, Sebastien

2015-01-01

The causative agent of human tuberculosis (TB), Mycobacterium tuberculosis, is an obligate pathogen that evolved to exclusively persist in human populations. For M. tuberculosis to transmit from person to person, it has to cause pulmonary disease. Therefore, M. tuberculosis virulence has likely been a significant determinant of the association between M. tuberculosis and humans. Indeed, the evolutionary success of some M. tuberculosis genotypes seems at least partially attributable to their increased virulence. The latter possibly evolved as a consequence of human demographic expansions. If co-evolution occurred, humans would have counteracted to minimize the deleterious effects of M. tuberculosis virulence. The fact that human resistance to infection has a strong genetic basis is a likely consequence of such a counter-response. The genetic architecture underlying human resistance to M. tuberculosis remains largely elusive. However, interactions between human genetic polymorphisms and M. tuberculosis genotypes have been reported. Such interactions are consistent with local adaptation and allow for a better understanding of protective immunity in TB. Future ‘genome-to-genome’ studies, in which locally associated human and M. tuberculosis genotypes are interrogated in conjunction, will help identify new protective antigens for the development of better TB vaccines. PMID:25703549
Darwin and the linguists: the coevolution of mind and language, part 2. The language-thought relationship.

PubMed

Alter, Stephen G

2008-03-01

This paper examines Charles Darwin's idea that language-use and humanity's unique cognitive abilities reinforced each other's evolutionary emergence-an idea Darwin sketched in his early notebooks, set forth in his Descent of man (1871), and qualified in Descent's second (1874) edition. Darwin understood this coevolution process in essentially Lockean terms, based on John Locke's hints about the way language shapes thinking itself. Ironically, the linguist Friedrich Max Müller attacked Darwin's human descent theory by invoking a similar thesis, the German romantic notion of an identity between language and thought. Although Darwin avoided outright contradiction, when he came to defend himself against Müller's attacks, he undercut some of his own argumentation in favor of the coevolution idea. That is, he found it difficult to counter Müller's argument while also making a case for coevolution. Darwin's efforts in this area were further complicated by British and American writers who held a naturalistic view of speech origins yet still taught that language had been invented by fully evolved homo sapiens, thus denying coevolution.
Metabolic coevolution in the bacterial symbiosis of whiteflies and related plant sap-feeding insects

USDA-ARS?s Scientific Manuscript database

In animals dependent on intracellular bacteria with very small genomes, the host cell is adapted to support the function of its bacterial symbionts, but the molecular basis of these adaptations is poorly understood. We investigated the metabolic coevolution between the whitefly Bemisia tabaci and th...
The butterfly plant arms-race escalated by gene and genome duplications

PubMed Central

Edger, Patrick P.; Heidel-Fischer, Hanna M.; Bekaert, Michaël; Rota, Jadranka; Glöckner, Gernot; Platts, Adrian E.; Heckel, David G.; Der, Joshua P.; Wafula, Eric K.; Tang, Michelle; Hofberger, Johannes A.; Smithson, Ann; Hall, Jocelyn C.; Blanchette, Matthieu; Bureau, Thomas E.; Wright, Stephen I.; dePamphilis, Claude W.; Eric Schranz, M.; Barker, Michael S.; Conant, Gavin C.; Wahlberg, Niklas; Vogel, Heiko; Pires, J. Chris; Wheat, Christopher W.

2015-01-01

Coevolutionary interactions are thought to have spurred the evolution of key innovations and driven the diversification of much of life on Earth. However, the genetic and evolutionary basis of the innovations that facilitate such interactions remains poorly understood. We examined the coevolutionary interactions between plants (Brassicales) and butterflies (Pieridae), and uncovered evidence for an escalating evolutionary arms-race. Although gradual changes in trait complexity appear to have been facilitated by allelic turnover, key innovations are associated with gene and genome duplications. Furthermore, we show that the origins of both chemical defenses and of molecular counter adaptations were associated with shifts in diversification rates during the arms-race. These findings provide an important connection between the origins of biodiversity, coevolution, and the role of gene and genome duplications as a substrate for novel traits. PMID:26100883
The butterfly plant arms-race escalated by gene and genome duplications.

PubMed

Edger, Patrick P; Heidel-Fischer, Hanna M; Bekaert, Michaël; Rota, Jadranka; Glöckner, Gernot; Platts, Adrian E; Heckel, David G; Der, Joshua P; Wafula, Eric K; Tang, Michelle; Hofberger, Johannes A; Smithson, Ann; Hall, Jocelyn C; Blanchette, Matthieu; Bureau, Thomas E; Wright, Stephen I; dePamphilis, Claude W; Eric Schranz, M; Barker, Michael S; Conant, Gavin C; Wahlberg, Niklas; Vogel, Heiko; Pires, J Chris; Wheat, Christopher W

2015-07-07

Coevolutionary interactions are thought to have spurred the evolution of key innovations and driven the diversification of much of life on Earth. However, the genetic and evolutionary basis of the innovations that facilitate such interactions remains poorly understood. We examined the coevolutionary interactions between plants (Brassicales) and butterflies (Pieridae), and uncovered evidence for an escalating evolutionary arms-race. Although gradual changes in trait complexity appear to have been facilitated by allelic turnover, key innovations are associated with gene and genome duplications. Furthermore, we show that the origins of both chemical defenses and of molecular counter adaptations were associated with shifts in diversification rates during the arms-race. These findings provide an important connection between the origins of biodiversity, coevolution, and the role of gene and genome duplications as a substrate for novel traits.
The evolution of reduced antagonism--A role for host-parasite coevolution.

PubMed

Gibson, A K; Stoy, K S; Gelarden, I A; Penley, M J; Lively, C M; Morran, L T

2015-11-01

Why do some host-parasite interactions become less antagonistic over evolutionary time? Vertical transmission can select for reduced antagonism. Vertical transmission also promotes coevolution between hosts and parasites. Therefore, we hypothesized that coevolution itself may underlie transitions to reduced antagonism. To test the coevolution hypothesis, we selected for reduced antagonism between the host Caenorhabditis elegans and its parasite Serratia marcescens. This parasite is horizontally transmitted, which allowed us to study coevolution independently of vertical transmission. After 20 generations, we observed a response to selection when coevolution was possible: reduced antagonism evolved in the copassaged treatment. Reduced antagonism, however, did not evolve when hosts or parasites were independently selected without coevolution. In addition, we found strong local adaptation for reduced antagonism between replicate host/parasite lines in the copassaged treatment. Taken together, these results strongly suggest that coevolution was critical to the rapid evolution of reduced antagonism. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.
Colour, vision and coevolution in avian brood parasitism.

PubMed

Stoddard, Mary Caswell; Hauber, Mark E

2017-07-05

The coevolutionary interactions between avian brood parasites and their hosts provide a powerful system for investigating the diversity of animal coloration. Specifically, reciprocal selection pressure applied by hosts and brood parasites can give rise to novel forms and functions of animal coloration, which largely differ from those that arise when selection is imposed by predators or mates. In the study of animal colours, avian brood parasite-host dynamics therefore invite special consideration. Rapid advances across disciplines have paved the way for an integrative study of colour and vision in brood parasite-host systems. We now know that visually driven host defences and host life history have selected for a suite of phenotypic adaptations in parasites, including mimicry, crypsis and supernormal stimuli. This sometimes leads to vision-based host counter-adaptations and increased parasite trickery. Here, we review vision-based adaptations that arise in parasite-host interactions, emphasizing that these adaptations can be visual/sensory, cognitive or phenotypic in nature. We highlight recent breakthroughs in chemistry, genomics, neuroscience and computer vision, and we conclude by identifying important future directions. Moving forward, it will be essential to identify the genetic and neural bases of adaptation and to compare vision-based adaptations to those arising in other sensory modalities.This article is part of the themed issue 'Animal coloration: production, perception, function and application'. © 2017 The Author(s).
Co-evolution with chicken class I genes.

PubMed

Kaufman, Jim

2015-09-01

The concept of co-evolution (or co-adaptation) has a long history, but application at molecular levels (e.g., 'supergenes' in genetics) is more recent, with a consensus definition still developing. One interesting example is the chicken major histocompatibility complex (MHC). In contrast to typical mammals that have many class I and class I-like genes, only two classical class I genes, two CD1 genes and some non-classical Rfp-Y genes are known in chicken, and all are found on the microchromosome that bears the MHC. Rarity of recombination between the closely linked and polymorphic genes encoding classical class I and TAPs allows co-evolution, leading to a single dominantly expressed class I molecule in each MHC haplotype, with strong functional consequences in terms of resistance to infectious pathogens. Chicken tapasin is highly polymorphic, but co-evolution with TAP and class I genes remains unclear. T-cell receptors, natural killer (NK) cell receptors, and CD8 co-receptor genes are found on non-MHC chromosomes, with some evidence for co-evolution of surface residues and number of genes along the avian and mammalian lineages. Over even longer periods, co-evolution has been invoked to explain how the adaptive immune system of jawed vertebrates arose from closely linked receptor, ligand, and antigen-processing genes in the primordial MHC. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.
Novel Designs of Quantum Reversible Counters

NASA Astrophysics Data System (ADS)

Qi, Xuemei; Zhu, Haihong; Chen, Fulong; Zhu, Junru; Zhang, Ziyang

2016-11-01

Reversible logic, as an interesting and important issue, has been widely used in designing combinational and sequential circuits for low-power and high-speed computation. Though a significant number of works have been done on reversible combinational logic, the realization of reversible sequential circuit is still at premature stage. Reversible counter is not only an important part of the sequential circuit but also an essential part of the quantum circuit system. In this paper, we designed two kinds of novel reversible counters. In order to construct counter, the innovative reversible T Flip-flop Gate (TFG), T Flip-flop block (T_FF) and JK flip-flop block (JK_FF) are proposed. Based on the above blocks and some existing reversible gates, the 4-bit binary-coded decimal (BCD) counter and controlled Up/Down synchronous counter are designed. With the help of Verilog hardware description language (Verilog HDL), these counters above have been modeled and confirmed. According to the simulation results, our circuits' logic structures are validated. Compared to the existing ones in terms of quantum cost (QC), delay (DL) and garbage outputs (GBO), it can be concluded that our designs perform better than the others. There is no doubt that they can be used as a kind of important storage components to be applied in future low-power computing systems.

The role of epigenetics in host-parasite coevolution: lessons from the model host insects Galleria mellonella and Tribolium castaneum.

PubMed

Vilcinskas, Andreas

2016-08-01

Recent studies addressing experimental host-parasite coevolution and transgenerational immune priming in insects provide evidence for heritable shifts in host resistance or parasite virulence. These rapid reciprocal adaptations may thus be transferred to offspring generations by either genetic changes or mechanisms that do not involve changes in the germline DNA sequence. Epigenetic inheritance refers to changes in gene expression that are heritable across generations and mediated by epigenetic modifications passed from parents to offspring. Highlighting the role of epigenetics in host-parasite coevolution, this review discusses the involvement of DNA methylation, histone acetylation/deacetylation and microRNAs in the interactions between bacterial or fungal parasites and model host insects such as the greater wax moth Galleria mellonella and the red flour beetle Tribolium castaneum. These epigenetic mechanisms are thought to participate in generation-spanning transcriptional reprogramming in the host insect, often linking immunity with developmentally related gene expression and contributing to the heredity of acquired adaptations. It is proposed that the interactions during host-parasite coevolution can therefore be expanded beyond reciprocal genetic changes to include reciprocal epigenetic changes. Epigenetics is thus a promising and prospering field in the context of host-parasite coevolution. Copyright © 2016 The Author. Published by Elsevier GmbH.. All rights reserved.
The Coevolution of "Tyrannosaurus" & Its Prey: Could "Tyrannosaurus" Chase down & Kill a "Triceratops" for Lunch?

ERIC Educational Resources Information Center

May, S. Randolph

2014-01-01

Students will analyze the coevolution of the predator-prey relationships between "Tyrannosaurus rex" and its prey species using analyses of animal speeds from fossilized trackways, prey-animal armaments, adaptive behaviors, bite marks on prey-animal fossils, predator-prey ratios, and scavenger competition. The students will be asked to…
Networked Workstations and Parallel Processing Utilizing Functional Languages

DTIC Science & Technology

1993-03-01

program . This frees the programmer to concentrate on what the program is to do, not how the program is...traditional ’von Neumann’ architecture uses a timer based (e.g., the program counter), sequentially pro- grammed, single processor approach to problem...traditional ’von Neumann’ architecture uses a timer based (e.g., the program counter), sequentially programmed , single processor approach to
Self-organizing behavior in a lattice model for co-evolution of virus and immune systems

NASA Astrophysics Data System (ADS)

Izmailian, N. Sh.; Papoyan, Vl. V.; Priezzhev, V. B.; Hu, Chin-Kun

2007-04-01

We propose a lattice model for the co-evolution of a virus population and an adaptive immune system. We show that, under some natural assumptions, both probability distribution of the virus population and the distribution of activity of the immune system tend during the evolution to a self-organized critical state.
Within-host co-evolution of chronic viruses and the adaptive immune system

NASA Astrophysics Data System (ADS)

Nourmohammad, Armita

We normally think of evolution occurring in a population of organisms, in response to their external environment. Rapid evolution of cellular populations also occurs within our bodies, as the adaptive immune system works to eliminate infection. Some pathogens, such as HIV, are able to persist in a host for extended periods of time, during which they also evolve to evade the immune response. In this talk I will introduce an analytical framework for the rapid co-evolution of B-cell and viral populations, based on the molecular interactions between them. Since the co-evolution of antibodies and viruses is perpetually out of equilibrium, I will show how to quantify the amount of adaptation in each of the two populations by analysis of their co-evolutionary history. I will discuss the consequences of competition between lineages of antibodies, and characterize the fate of a given lineage dependent on the state of the antibody and viral populations. In particular, I will discuss the conditions for emergence of highly potent broadly neutralizing antibodies, which are now recognized as critical for designing an effective vaccine against HIV.
Invasion fitness for gene-culture co-evolution in family-structured populations and an application to cumulative culture under vertical transmission.

PubMed

Mullon, Charles; Lehmann, Laurent

2017-08-01

Human evolution depends on the co-evolution between genetically determined behaviors and socially transmitted information. Although vertical transmission of cultural information from parent to offspring is common in hominins, its effects on cumulative cultural evolution are not fully understood. Here, we investigate gene-culture co-evolution in a family-structured population by studying the invasion fitness of a mutant allele that influences a deterministic level of cultural information (e.g., amount of knowledge or skill) to which diploid carriers of the mutant are exposed in subsequent generations. We show that the selection gradient on such a mutant, and the concomitant level of cultural information it generates, can be evaluated analytically under the assumption that the cultural dynamic has a single attractor point, thereby making gene-culture co-evolution in family-structured populations with multigenerational effects mathematically tractable. We apply our result to study how genetically determined phenotypes of individual and social learning co-evolve with the level of adaptive information they generate under vertical transmission. We find that vertical transmission increases adaptive information due to kin selection effects, but when information is transmitted as efficiently between family members as between unrelated individuals, this increase is moderate in diploids. By contrast, we show that the way resource allocation into learning trades off with allocation into reproduction (the "learning-reproduction trade-off") significantly influences levels of adaptive information. We also show that vertical transmission prevents evolutionary branching and may therefore play a qualitative role in gene-culture co-evolutionary dynamics. More generally, our analysis of selection suggests that vertical transmission can significantly increase levels of adaptive information under the biologically plausible condition that information transmission between relatives is more efficient than between unrelated individuals. Copyright © 2017 Elsevier Inc. All rights reserved.
The evolutionary ecology of complex lifecycle parasites: linking phenomena with mechanisms

PubMed Central

Auld, S KJR; Tinsley, M C

2015-01-01

Many parasitic infections, including those of humans, are caused by complex lifecycle parasites (CLPs): parasites that sequentially infect different hosts over the course of their lifecycle. CLPs come from a wide range of taxonomic groups—from single-celled bacteria to multicellular flatworms—yet share many common features in their life histories. Theory tells us when CLPs should be favoured by selection, but more empirical studies are required in order to quantify the costs and benefits of having a complex lifecycle, especially in parasites that facultatively vary their lifecycle complexity. In this article, we identify ecological conditions that favour CLPs over their simple lifecycle counterparts and highlight how a complex lifecycle can alter transmission rate and trade-offs between growth and reproduction. We show that CLPs participate in dynamic host–parasite coevolution, as more mobile hosts can fuel CLP adaptation to less mobile hosts. Then, we argue that a more general understanding of the evolutionary ecology of CLPs is essential for the development of effective frameworks to manage the many diseases they cause. More research is needed identifying the genetics of infection mechanisms used by CLPs, particularly into the role of gene duplication and neofunctionalisation in lifecycle evolution. We propose that testing for signatures of selection in infection genes will reveal much about how and when complex lifecycles evolved, and will help quantify complex patterns of coevolution between CLPs and their various hosts. Finally, we emphasise four key areas where new research approaches will provide fertile opportunities to advance this field. PMID:25227255
Biology-Culture Co-evolution in Finite Populations.

PubMed

de Boer, Bart; Thompson, Bill

2018-01-19

Language is the result of two concurrent evolutionary processes: biological and cultural inheritance. An influential evolutionary hypothesis known as the moving target problem implies inherent limitations on the interactions between our two inheritance streams that result from a difference in pace: the speed of cultural evolution is thought to rule out cognitive adaptation to culturally evolving aspects of language. We examine this hypothesis formally by casting it as as a problem of adaptation in time-varying environments. We present a mathematical model of biology-culture co-evolution in finite populations: a generalisation of the Moran process, treating co-evolution as coupled non-independent Markov processes, providing a general formulation of the moving target hypothesis in precise probabilistic terms. Rapidly varying culture decreases the probability of biological adaptation. However, we show that this effect declines with population size and with stronger links between biology and culture: in realistically sized finite populations, stochastic effects can carry cognitive specialisations to fixation in the face of variable culture, especially if the effects of those specialisations are amplified through cultural evolution. These results support the view that language arises from interactions between our two major inheritance streams, rather than from one primary evolutionary process that dominates another.
Coevolution of Cyanogenic Bamboos and Bamboo Lemurs on Madagascar

PubMed Central

Ballhorn, Daniel J.; Rakotoarivelo, Fanny Patrika; Kautz, Stefanie

2016-01-01

Feeding strategies of specialist herbivores often originate from the coevolutionary arms race of plant defenses and counter-adaptations of herbivores. The interaction between bamboo lemurs and cyanogenic bamboos on Madagascar represents a unique system to study diffuse coevolutionary processes between mammalian herbivores and plant defenses. Bamboo lemurs have different degrees of dietary specialization while bamboos show different levels of chemical defense. In this study, we found variation in cyanogenic potential (HCNp) and nutritive characteristics among five sympatric bamboo species in the Ranomafana area, southeastern Madagascar. The HCNp ranged from 209±72 μmol cyanide*g-1 dwt in Cathariostachys madagascariensis to no cyanide in Bambusa madagascariensis. Among three sympatric bamboo lemur species, the greater bamboo lemur (Prolemur simus) has the narrowest food range as it almost exclusively feeds on the highly cyanogenic C. madagascariensis. Our data suggest that high HCNp is the derived state in bamboos. The ancestral state of lemurs is most likely "generalist" while the ancestral state of bamboo lemurs was determined as equivocal. Nevertheless, as recent bamboo lemurs comprise several "facultative specialists" and only one "obligate specialist" adaptive radiation due to increased flexibility is likely. We propose that escaping a strict food plant specialization enabled facultative specialist bamboo lemurs to inhabit diverse geographical areas. PMID:27532127
Divergence in an obligate mutualism is not explained by divergent climatic factors

USGS Publications Warehouse

Godsoe, W.; Strand, Espen; Smith, C.I.; Yoder, J.B.; Esque, T.C.; Pellmyr, O.

2009-01-01

Adaptation to divergent environments creates and maintains biological diversity, but we know little about the importance of different agents of ecological divergence. Coevolution in obligate mutualisms has been hypothesized to drive divergence, but this contention has rarely been tested against alternative ecological explanations. Here, we use a well-established example of coevolution in an obligate pollination mutualism, Yucca brevifolia and its two pollinating yucca moths, to test the hypothesis that divergence in this system is the result of mutualists adapting to different abiotic environments as opposed to coevolution between mutualists. ??? We used a combination of principal component analyses and ecological niche modeling to determine whether varieties of Y. brevifolia associated with different pollinators specialize on different environments. ??? Yucca brevifolia occupies a diverse range of climates. When the two varieties can disperse to similar environments, they occupy similar habitats. ??? This suggests that the two varieties have not specialized on distinct habitats. In turn, this suggests that nonclimatic factors, such as the biotic interaction between Y. brevifolia and its pollinators, are responsible for evolutionary divergence in this system. ?? New Phytologist (2009).
Long-legged bees make adaptive leaps: linking adaptation to coevolution in a plant-pollinator network.

PubMed

Pauw, Anton; Kahnt, Belinda; Kuhlmann, Michael; Michez, Denis; Montgomery, Graham A; Murray, Elizabeth; Danforth, Bryan N

2017-09-13

Adaptation is evolution in response to natural selection. Hence, an adaptation is expected to originate simultaneously with the acquisition of a particular selective environment. Here we test whether long legs evolve in oil-collecting Rediviva bees when they come under selection by long-spurred, oil-secreting flowers. To quantify the selective environment, we drew a large network of the interactions between Rediviva species and oil-secreting plant species. The selective environment of each bee species was summarized as the average spur length of the interacting plant species weighted by interaction frequency. Using phylogenetically independent contrasts, we calculated divergence in selective environment and evolutionary divergence in leg length between sister species (and sister clades) of Rediviva We found that change in the selective environment explained 80% of evolutionary change in leg length, with change in body size contributing an additional 6% of uniquely explained variance. The result is one of four proposed steps in testing for plant-pollinator coevolution. © 2017 The Author(s).
Modeling Co-evolution of Speech and Biology.

PubMed

de Boer, Bart

2016-04-01

Two computer simulations are investigated that model interaction of cultural evolution of language and biological evolution of adaptations to language. Both are agent-based models in which a population of agents imitates each other using realistic vowels. The agents evolve under selective pressure for good imitation. In one model, the evolution of the vocal tract is modeled; in the other, a cognitive mechanism for perceiving speech accurately is modeled. In both cases, biological adaptations to using and learning speech evolve, even though the system of speech sounds itself changes at a more rapid time scale than biological evolution. However, the fact that the available acoustic space is used maximally (a self-organized result of cultural evolution) is constant, and therefore biological evolution does have a stable target. This work shows that when cultural and biological traits are continuous, their co-evolution may lead to cognitive adaptations that are strong enough to detect empirically. Copyright © 2016 Cognitive Science Society, Inc.
Coevolution of Vertex Weights Resolves Social Dilemma in Spatial Networks.

PubMed

Shen, Chen; Chu, Chen; Guo, Hao; Shi, Lei; Duan, Jiangyan

2017-11-09

In realistic social system, the role or influence of each individual varies and adaptively changes in time in the population. Inspired by this fact, we thus consider a new coevolution setup of game strategy and vertex weight on a square lattice. In detail, we model the structured population on a square lattice, on which the role or influence of each individual is depicted by vertex weight, and the prisoner's dilemma game has been applied to describe the social dilemma of pairwise interactions of players. Through numerical simulation, we conclude that our coevolution setup can promote the evolution of cooperation effectively. Especially, there exists a moderate value of δ for each ε that can warrant an optimal resolution of social dilemma. For a further understanding of these results, we find that intermediate value of δ enables the strongest heterogeneous distribution of vertex weight. We hope our coevolution setup of vertex weight will provide new insight for the future research.
Coevolution of CRISPR bacteria and phage in 2 dimensions

NASA Astrophysics Data System (ADS)

Han, Pu; Deem, Michael

2014-03-01

CRISPR (cluster regularly interspaced short palindromic repeats) is a newly discovered adaptive, heritable immune system of prokaryotes. It can prevent infection of prokaryotes by phage. Most bacteria and almost all archae have CRISPR. The CRISPR system incorporates short nucleotide sequences from viruses. These incorporated sequences provide a historical record of the host and predator coevolution. We simulate the coevolution of bacteria and phage in 2 dimensions. Each phage has multiple proto-spacers that the bacteria can incorporate. Each bacterium can store multiple spacers in its CRISPR. Phages can escape recognition by the CRISPR system via point mutation or recombination. We will discuss the different evolutionary consequences of point mutation or recombination on the coevolution of bacteria and phage. We will also discuss an intriguing ``dynamic phase transition'' in the number of phage as a function of time and mutation rate. We will show that due to the arm race between phages and bacteria, the frequency of spacers and proto-spacers in a population can oscillate quite rapidly.
Coevolution of antibiotic production and counter-resistance in soil bacteria.

PubMed

Laskaris, Paris; Tolba, Sahar; Calvo-Bado, Leo; Wellington, Elizabeth M; Wellington, Liz

2010-03-01

We present evidence for the coexistence and coevolution of antibiotic resistance and biosynthesis genes in soil bacteria. The distribution of the streptomycin (strA) and viomycin (vph) resistance genes was examined in Streptomyces isolates. strA and vph were found either within a biosynthetic gene cluster or independently. Streptomyces griseus strains possessing the streptomycin cluster formed part of a clonal complex. All S. griseus strains possessing solely strA belonged to two clades; both were closely related to the streptomycin producers. Other more distantly related S. griseus strains did not contain strA. S. griseus strains with only vph also formed two clades, but they were more distantly related to the producers and to one another. The expression of the strA gene was constitutive in a resistance-only strain whereas streptomycin producers showed peak strA expression in late log phase that correlates with the switch on of streptomycin biosynthesis. While there is evidence that antibiotics have diverse roles in nature, our data clearly support the coevolution of resistance in the presence of antibiotic biosynthetic capability within closely related soil dwelling bacteria. This reinforces the view that, for some antibiotics at least, the primary role is one of antibiosis during competition in soil for resources.
Potential arms race in the coevolution of primates and angiosperms: brazzein sweet proteins and gorilla taste receptors.

PubMed

Guevara, Elaine E; Veilleux, Carrie C; Saltonstall, Kristin; Caccone, Adalgisa; Mundy, Nicholas I; Bradley, Brenda J

2016-09-01

We explored whether variation in the sweet taste receptor protein T1R3 in primates could contribute to differences in sweet taste repertoire among species, potentially reflecting coevolution with local plants. Specifically, we examined which primates are likely to be sweet "tasters" of brazzein, a protein found in the fruit of the African plant Pentadiplandra brazzeana that tastes intensely sweet to humans, but provides little energy. Sweet proteins like brazzein are thought to mimic the taste of sugars to entice seed dispersers. We examined the evolution of T1R3 and assessed whether primates are likely "deceived" by such biochemical mimicry. Using published and new sequence data for TAS1R3, we characterized 57 primates and other mammals at the two amino acid sites necessary to taste brazzein to determine which species are tasters. We further used dN/dS-based methods to look for statistical evidence of accelerated evolution in this protein across primate lineages. The taster genotype is shared across most catarrhines, suggesting that most African primates can be "tricked" into eating and dispersing P. brazzeana's seeds for little caloric gain. Western gorillas (Gorilla gorilla), however, exhibit derived mutations at the two brazzein-critical positions, and although fruit is a substantial portion of the western gorilla diet, they have not been observed to eat P. brazzeana. Our analyses of protein evolution found no signature of positive selection on TAS1R3 along the gorilla lineage. We propose that the gorilla-specific mutations at the TAS1R3 locus encoding T1R3 could be a counter-adaptation to the false sweet signal of brazzein. © 2016 Wiley Periodicals, Inc.
Modelling language evolution: Examples and predictions

NASA Astrophysics Data System (ADS)

Gong, Tao; Shuai, Lan; Zhang, Menghan

2014-06-01

We survey recent computer modelling research of language evolution, focusing on a rule-based model simulating the lexicon-syntax coevolution and an equation-based model quantifying the language competition dynamics. We discuss four predictions of these models: (a) correlation between domain-general abilities (e.g. sequential learning) and language-specific mechanisms (e.g. word order processing); (b) coevolution of language and relevant competences (e.g. joint attention); (c) effects of cultural transmission and social structure on linguistic understandability; and (d) commonalities between linguistic, biological, and physical phenomena. All these contribute significantly to our understanding of the evolutions of language structures, individual learning mechanisms, and relevant biological and socio-cultural factors. We conclude the survey by highlighting three future directions of modelling studies of language evolution: (a) adopting experimental approaches for model evaluation; (b) consolidating empirical foundations of models; and (c) multi-disciplinary collaboration among modelling, linguistics, and other relevant disciplines.
A matching-allele model explains host resistance to parasites.

PubMed

Luijckx, Pepijn; Fienberg, Harris; Duneau, David; Ebert, Dieter

2013-06-17

The maintenance of genetic variation and sex despite its costs has long puzzled biologists. A popular idea, the Red Queen Theory, is that under rapid antagonistic coevolution between hosts and their parasites, the formation of new rare host genotypes through sex can be advantageous as it creates host genotypes to which the prevailing parasite is not adapted. For host-parasite coevolution to lead to an ongoing advantage for rare genotypes, parasites should infect specific host genotypes and hosts should resist specific parasite genotypes. The most prominent genetics capturing such specificity are matching-allele models (MAMs), which have the key feature that resistance for two parasite genotypes can reverse by switching one allele at one host locus. Despite the lack of empirical support, MAMs have played a central role in the theoretical development of antagonistic coevolution, local adaptation, speciation, and sexual selection. Using genetic crosses, we show that resistance of the crustacean Daphnia magna against the parasitic bacterium Pasteuria ramosa follows a MAM. Simulation results show that the observed genetics can explain the maintenance of genetic variation and contribute to the maintenance of sex in the facultatively sexual host as predicted by the Red Queen Theory. Copyright © 2013 Elsevier Ltd. All rights reserved.
The evolution of floral scent and olfactory preferences in pollinators: coevolution or pre-existing bias?

PubMed

Schiestl, Florian P; Dötterl, Stefan

2012-07-01

Coevolution is thought to be a major factor in shaping plant-pollinator interactions. Alternatively, plants may have evolved traits that fitted pre-existing preferences or morphologies in the pollinators. Here, we test these two scenarios in the plant family of Araceae and scarab beetles (Coleoptera, Scarabaeidae) as pollinators. We focused on floral volatile organic compounds (VOCs) and production/detection of VOCs by scarab beetles. We found phylogenetic structure in the production/detection of methoxylated aromatics in scarabs, but not plants. Within the plants, most of the compounds showed a well-supported pattern of correlated evolution with scarab-beetle pollination. In contrast, the scarabs showed no correlation between VOC production/detection and visitation to Araceae flowers, with the exception of the VOC skatole. Moreover, many VOCs were found in nonpollinating beetle groups (e.g., Melolonthinae) that are ancestors of pollinating scarabs. Importantly, none of the tested VOCs were found to have originated in pollinating taxa. Our analysis indicates a Jurassic origin of VOC production/detection in scarabs, but a Cretaceous/Paleocene origin of floral VOCs in plants. Therefore, we argue against coevolution, instead supporting the scenario of sequential evolution of floral VOCs in Araceae driven by pre-existing bias of pollinators. © 2012 The Author(s).
Assembly constraints drive co-evolution among ribosomal constituents.

PubMed

Mallik, Saurav; Akashi, Hiroshi; Kundu, Sudip

2015-06-23

Ribosome biogenesis, a central and essential cellular process, occurs through sequential association and mutual co-folding of protein-RNA constituents in a well-defined assembly pathway. Here, we construct a network of co-evolving nucleotide/amino acid residues within the ribosome and demonstrate that assembly constraints are strong predictors of co-evolutionary patterns. Predictors of co-evolution include a wide spectrum of structural reconstitution events, such as cooperativity phenomenon, protein-induced rRNA reconstitutions, molecular packing of different rRNA domains, protein-rRNA recognition, etc. A correlation between folding rate of small globular proteins and their topological features is known. We have introduced an analogous topological characteristic for co-evolutionary network of ribosome, which allows us to differentiate between rRNA regions subjected to rapid reconstitutions from those hindered by kinetic traps. Furthermore, co-evolutionary patterns provide a biological basis for deleterious mutation sites and further allow prediction of potential antibiotic targeting sites. Understanding assembly pathways of multicomponent macromolecules remains a key challenge in biophysics. Our study provides a 'proof of concept' that directly relates co-evolution to biophysical interactions during multicomponent assembly and suggests predictive power to identify candidates for critical functional interactions as well as for assembly-blocking antibiotic target sites. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Evidence for parasite-mediated selection during short-lasting toxic algal blooms.

PubMed

Blanquart, François; Valero, Myriam; Alves-de-Souza, Catharina; Dia, Aliou; Lepelletier, Frédéric; Bigeard, Estelle; Jeanthon, Christian; Destombe, Christophe; Guillou, Laure

2016-10-26

Parasites play a role in the control of transient algal blooms, but it is not known whether parasite-mediated selection results in coevolution of the host and the parasites over this short time span. We investigated the presence of coevolution between the toxic dinoflagellate Alexandrium minutum and two naturally occurring endoparasites during blooms lasting a month in two river estuaries, using cross-inoculation experiments across time and space. Higher parasite abundance was associated with a large daily reduction in relative A. minutum abundances, demonstrating strong parasite-mediated selection. There was genetic variability in infectivity in both parasite species, and in resistance in the host. We found no evidence for coevolution in one estuary; however, in the other estuary, we found high genetic diversity in the two parasite species, fluctuations in infectivity and suggestion that the two parasites are well adapted to their host, as in 'Red Queen' dynamics. Thus, coevolution is possible over the short time span of a bloom, but geographically variable, and may feedback on community dynamics. © 2016 The Authors.
Dilemma solving by the coevolution of networks and strategy in a 2 x 2 game.

PubMed

Tanimoto, Jun

2007-08-01

A 2 x 2 game model implemented by a coevolution mechanism of both networks and strategy, inspired by the work of Zimmermann and Eguiluz [Phys. Rev. E72, 056118 (2005)] is established. Network adaptation is the manner in which an existing link between two agents is destroyed and how a new one is established to replace it. The strategy is defined as whether an agent offers cooperation (C) or defection (D) . Both the networks and strategy are synchronously renovated in a simulation time step. A series of numerical experiments, considering various 2 x 2 game structures, reveals that the proposed coevolution mechanism can solve dilemmas in several game classes. The effect of solving a dilemma means mutual-cooperation reciprocity (R reciprocity), which is brought about by emerging several cooperative hub agents who have plenty of links. This effect can be primarily observed in game classes of the prisoner's dilemma and stag hunt. The coevolution mechanism, however, seems counterproductive for game classes of leader and hero, where the alternating reciprocity (ST reciprocity) is meaningful.
Co-evolution of Hormone Metabolism and Signaling Networks Expands Plant Adaptive Plasticity.

PubMed

Weng, Jing-Ke; Ye, Mingli; Li, Bin; Noel, Joseph P

2016-08-11

Classically, hormones elicit specific cellular responses by activating dedicated receptors. Nevertheless, the biosynthesis and turnover of many of these hormone molecules also produce chemically related metabolites. These molecules may also possess hormonal activities; therefore, one or more may contribute to the adaptive plasticity of signaling outcomes in host organisms. Here, we show that a catabolite of the plant hormone abscisic acid (ABA), namely phaseic acid (PA), likely emerged in seed plants as a signaling molecule that fine-tunes plant physiology, environmental adaptation, and development. This trait was facilitated by both the emergence-selection of a PA reductase that modulates PA concentrations and by the functional diversification of the ABA receptor family to perceive and respond to PA. Our results suggest that PA serves as a hormone in seed plants through activation of a subset of ABA receptors. This study demonstrates that the co-evolution of hormone metabolism and signaling networks can expand organismal resilience. Copyright © 2016 Elsevier Inc. All rights reserved.
Physical model of the immune response of bacteria against bacteriophage through the adaptive CRISPR-Cas immune system

NASA Astrophysics Data System (ADS)

Han, Pu; Niestemski, Liang Ren; Barrick, Jeffrey E.; Deem, Michael W.

2013-04-01

Bacteria and archaea have evolved an adaptive, heritable immune system that recognizes and protects against viruses or plasmids. This system, known as the CRISPR-Cas system, allows the host to recognize and incorporate short foreign DNA or RNA sequences, called ‘spacers’ into its CRISPR system. Spacers in the CRISPR system provide a record of the history of bacteria and phage coevolution. We use a physical model to study the dynamics of this coevolution as it evolves stochastically over time. We focus on the impact of mutation and recombination on bacteria and phage evolution and evasion. We discuss the effect of different spacer deletion mechanisms on the coevolutionary dynamics. We make predictions about bacteria and phage population growth, spacer diversity within the CRISPR locus, and spacer protection against the phage population.
Prophage-mediated defense against viral attack and viral counter-defense

PubMed Central

Dedrick, Rebekah M.; Jacobs-Sera, Deborah; Guerrero Bustamante, Carlos A.; Garlena, Rebecca A.; Mavrich, Travis N.; Pope, Welkin H.; Reyes, Juan C Cervantes; Russell, Daniel A.; Adair, Tamarah; Alvey, Richard; Bonilla, J. Alfred; Bricker, Jerald S.; Brown, Bryony R.; Byrnes, Deanna; Cresawn, Steven G.; Davis, William B.; Dickson, Leon A.; Edgington, Nicholas P.; Findley, Ann M.; Golebiewska, Urszula; Grose, Julianne H.; Hayes, Cory F.; Hughes, Lee E.; Hutchison, Keith W.; Isern, Sharon; Johnson, Allison A.; Kenna, Margaret A.; Klyczek, Karen K.; Mageeney, Catherine M.; Michael, Scott F.; Molloy, Sally D.; Montgomery, Matthew T.; Neitzel, James; Page, Shallee T.; Pizzorno, Marie C.; Poxleitner, Marianne K.; Rinehart, Claire A.; Robinson, Courtney J.; Rubin, Michael R.; Teyim, Joseph N.; Vazquez, Edwin; Ware, Vassie C.; Washington, Jacqueline; Hatfull, Graham F.

2017-01-01

Temperate phages are common and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses infecting mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity, and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages reveals at least five distinct prophage-expressed viral defense systems that interfere with infection of lytic and temperate phages that are either closely-related (homotypic defense) or unrelated (heterotypic defense). Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defense systems include a single-subunit restriction system, a heterotypic exclusion system, and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival, and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, that acts as a highly effective counter-defense system. Prophage-mediated viral defense offers an efficient mechanism for bacterial success in host-virus dynamics, and counter-defense promotes phage co-evolution. PMID:28067906
Physical mode of bacteria and virus coevolution

NASA Astrophysics Data System (ADS)

Han, Pu; Niestemski, Liang; Deem, Michael

2013-03-01

Single-cell hosts such as bacteria or archaea possess an adaptive, heritable immune system that protects them from viral invasion. This system, known as the CRISPR-Cas system, allows the host to recognize and incorporate short foreign DNA or RNA sequences from viruses or plasmids. The sequences form what are called ``spacers'' in the CRISPR. Spacers in the CRISPR loci provide a record of the host and predator coevolution history. We develop a physical model to study the dynamics of this coevolution due to immune pressure. Hosts and viruses reproduce, die, and evolve due to viral infection pressure, host immune pressure, and mutation. We will discuss the differing effects of point mutation and recombination on CRISPR evolution. We will also discuss the effect of different spacer deletion mechanisms. We will describe population structure of hosts and viruses, how spacer diversity depends on position within CRISPR, and match of the CRISPR spacers to the virus population.
Bats in the Classroom: A Conceptual Guide for Biology Teachers.

ERIC Educational Resources Information Center

Rankin, W. T.; Lewis, Norma G.

2002-01-01

Explains how to use bats to introduce different biological concepts such as classification and phylogeny, altruistic behavior, flight, coevolution, or physiological adaptations. Discusses common myths regarding bats and provides information on additional classroom materials. (YDS)
Effects of adaptive degrees of trust on coevolution of quantum strategies on scale-free networks.

PubMed

Li, Qiang; Chen, Minyou; Perc, Matjaž; Iqbal, Azhar; Abbott, Derek

2013-10-15

We study the impact of adaptive degrees of trust on the evolution of cooperation in the quantum prisoner's dilemma game. In addition to the strategies, links between players are also subject to evolution. Starting with a scale-free interaction network, players adjust trust towards their neighbors based on received payoffs. The latter governs the strategy adoption process, while trust governs the rewiring of links. As soon as the degree of trust towards a neighbor drops to zero, the link is rewired to another randomly chosen player within the network. We find that for small temptations to defect cooperators always dominate, while for intermediate and strong temptations a single quantum strategy is able to outperform all other strategies. In general, reciprocal trust remains within close relationships and favors the dominance of a single strategy. Due to coevolution, the power-law degree distributions transform to Poisson distributions.
Effects of adaptive degrees of trust on coevolution of quantum strategies on scale-free networks

NASA Astrophysics Data System (ADS)

Li, Qiang; Chen, Minyou; Perc, Matjaž; Iqbal, Azhar; Abbott, Derek

2013-10-01

We study the impact of adaptive degrees of trust on the evolution of cooperation in the quantum prisoner's dilemma game. In addition to the strategies, links between players are also subject to evolution. Starting with a scale-free interaction network, players adjust trust towards their neighbors based on received payoffs. The latter governs the strategy adoption process, while trust governs the rewiring of links. As soon as the degree of trust towards a neighbor drops to zero, the link is rewired to another randomly chosen player within the network. We find that for small temptations to defect cooperators always dominate, while for intermediate and strong temptations a single quantum strategy is able to outperform all other strategies. In general, reciprocal trust remains within close relationships and favors the dominance of a single strategy. Due to coevolution, the power-law degree distributions transform to Poisson distributions.
Whole genome-based phylogeny of reptile-associated Helicobacter indicates independent niche adaptation followed by diversification in a poikilothermic host.

PubMed

Gilbert, Maarten J; Duim, Birgitta; Timmerman, Arjen J; Zomer, Aldert L; Wagenaar, Jaap A

2017-08-21

Reptiles have been shown to host a significant Helicobacter diversity. In order to survive, reptile-associated Helicobacter lineages need to be adapted to the thermally dynamic environment encountered in a poikilothermic host. The whole genomes of reptile-associated Helicobacter lineages can provide insights in Helicobacter host adaptation and coevolution. These aspects were explored by comparing the genomes of reptile-, bird-, and mammal-associated Helicobacter lineages. Based on average nucleotide identity, all reptile-associated Helicobacter lineages in this study could be considered distinct species. A whole genome-based phylogeny showed two distinct clades, one associated with chelonians and one associated with lizards. The phylogeny indicates initial adaptation to an anatomical niche, which is followed by an ancient host jump and subsequent diversification. Furthermore, the ability to grow at low temperatures, which might reflect thermal adaptation to a reptilian host, originated at least twice in Helicobacter evolution. A putative tricarballylate catabolism locus was specifically present in Campylobacter and Helicobacter isolates from reptiles. The phylogeny of reptile-associated Helicobacter parallels host association, indicating a high level of host specificity. The high diversity and deep branching within these clades supports long-term coevolution with, and extensive radiation within the respective reptilian host type.
Insect--plant adaptations.

PubMed

Southwood, T R

1984-01-01

The adaptation of insects to plants probably commenced in the early Permian period, though most current associations will be more recent. A major burst of adaptation must have followed the rise of the Angiosperms in the Cretaceous period, though some particular associations are as recent as this century. Living plants form a large proportion of the potential food in most habitats, though insects have had to overcome certain general hurdles to live and feed on them. Insects affect the reproduction and survival of plants, and thus the diversity of plant secondary chemicals may have evolved as a response. Where an insect species has a significant effect on a plant species that is its only host, coevolution may be envisaged. A spectacular example is provided by Heliconius butterflies and passion flower vines, studied by L.E. Gilbert and others. But such cases may be likened to 'vortices in the evolutionary stream': most plant species are influenced by a range of phytophagous insects so that selection will be for general defences--a situation termed diffuse coevolution. Evidence is presented on recent host-plant shifts to illustrate both the restrictions and the flexibility in current insect-plant associations.
Test apparatus for locating shorts during assembly of electrical buses

NASA Technical Reports Server (NTRS)

Deboo, G. J.; Devine, D. L. (Inventor)

1981-01-01

A test apparatus is described for locating electrical shorts that is especially suited for use while an electrical circuit is being fabricated or assembled. A ring counter derives input pulses from a square wave oscillator. The outputs of the counter are fed through transistors to an array of light emitting diodes. Each diode is connected to an electrical conductor, such as a bus bar, that is to be tested. In the absence of a short between the electrical conductors the diodes are sequentially illuminated. When a short occurs, a comparator/multivibrator circuit triggers an alarm and stops the oscillator and the sequential energization of the diodes. The two diodes that remain illuminated identify the electrical conductors that are shorted.
A slowly evolving host moves first in symbiotic interactions

NASA Astrophysics Data System (ADS)

Damore, James; Gore, Jeff

2011-03-01

Symbiotic relationships, both parasitic and mutualistic, are ubiquitous in nature. Understanding how these symbioses evolve, from bacteria and their phages to humans and our gut microflora, is crucial in understanding how life operates. Often, symbioses consist of a slowly evolving host species with each host only interacting with its own sub-population of symbionts. The Red Queen hypothesis describes coevolutionary relationships as constant arms races with each species rushing to evolve an advantage over the other, suggesting that faster evolution is favored. Here, we use a simple game theoretic model of host- symbiont coevolution that includes population structure to show that if the symbionts evolve much faster than the host, the equilibrium distribution is the same as it would be if it were a sequential game where the host moves first against its symbionts. For the slowly evolving host, this will prove to be advantageous in mutualisms and a handicap in antagonisms. The model allows for symbiont adaptation to its host, a result that is robust to changes in the parameters and generalizes to continuous and multiplayer games. Our findings provide insight into a wide range of symbiotic phenomena and help to unify the field of coevolutionary theory.
Sex uncovered special issue: The ecology of sexual reproduction

PubMed Central

LIVELY, C. M.; MORRAN, L. T.

2014-01-01

Sexual reproduction is widely regarded as one of the major unexplained phenomena in biology. Nonetheless, while a general answer may remain elusive, considerable progress has been made in the last few decades. Here we fist review the genesis of, and support for, the major ecological hypotheses for biparental sexual reproduction. We then focus on the idea that host-parasite coevolution can favor cross fertilization over uniparental forms of reproduction, as this hypothesis currently has the most support from natural populations. We also review the results from experimental evolution studies, which tend to show that exposure to novel environments can select for higher levels of sexual reproduction, but that sex decreases in frequency after populations become adapted to the previously novel conditions. In contrast, experimental coevolution studies suggest that host-parasite interactions can lead to the long-term persistence of sex. Taken together, the evidence from natural populations and from laboratory experiments point to antagonistic coevolution as a potent and possibly ubiquitous force of selection favoring cross-fertilization and recombination. PMID:24617324
Cross counter-based adaptive assembly scheme in optical burst switching networks

NASA Astrophysics Data System (ADS)

Zhu, Zhi-jun; Dong, Wen; Le, Zi-chun; Chen, Wan-jun; Sun, Xingshu

2009-11-01

A novel adaptive assembly algorithm called Cross-counter Balance Adaptive Assembly Period (CBAAP) is proposed in this paper. The major difference between CBAAP and other adaptive assembly algorithms is that the threshold of CBAAP can be dynamically adjusted according to the cross counter and step length value. In terms of assembly period and the burst loss probability, we compare the performance of CBAAP with those of three typical algorithms FAP (Fixed Assembly Period), FBL (Fixed Burst Length) and MBMAP (Min-Burst length-Max-Assembly-Period) in the simulation part. The simulation results demonstrate the effectiveness of our algorithm.
Programmable Pulser

NASA Technical Reports Server (NTRS)

Baumann, Eric; Merolla, Anthony

1988-01-01

User controls number of clock pulses to prevent burnout. New digital programmable pulser circuit in three formats; freely running, counted, and single pulse. Operates at frequencies up to 5 MHz, with no special consideration given to layout of components or to terminations. Pulser based on sequential circuit with four states and binary counter with appropriate decoding logic. Number of programmable pulses increased beyond 127 by addition of another counter and decoding logic. For very large pulse counts and/or very high frequencies, use synchronous counters to avoid errors caused by propagation delays. Invaluable tool for initial verification or diagnosis of digital or digitally controlled circuity.
The human as a detector of changes in variance and bandwidth

NASA Technical Reports Server (NTRS)

Curry, R. E.; Govindaraj, T.

1977-01-01

The detection of changes in random process variance and bandwidth was studied. Psychophysical thresholds for these two parameters were determined using an adaptive staircase technique for second order random processes at two nominal periods (1 and 3 seconds) and damping ratios (0.2 and 0.707). Thresholds for bandwidth changes were approximately 9% of nominal except for the (3sec,0.2) process which yielded thresholds of 12%. Variance thresholds averaged 17% of nominal except for the (3sec,0.2) process in which they were 32%. Detection times for suprathreshold changes in the parameters may be roughly described by the changes in RMS velocity of the process. A more complex model is presented which consists of a Kalman filter designed for the nominal process using velocity as the input, and a modified Wald sequential test for changes in the variance of the residual. The model predictions agree moderately well with the experimental data. Models using heuristics, e.g. level crossing counters, were also examined and are found to be descriptive but do not afford the unification of the Kalman filter/sequential test model used for changes in mean.
A sequential adaptation technique and its application to the Mark 12 IFF system

NASA Astrophysics Data System (ADS)

Bailey, John S.; Mallett, John D.; Sheppard, Duane J.; Warner, F. Neal; Adams, Robert

1986-07-01

Sequential adaptation uses only two sets of receivers, correlators, and A/D converters which are time multiplexed to effect spatial adaptation in a system with (N) adaptive degrees of freedom. This technique can substantially reduce the hardware cost over what is realizable in a parallel architecture. A three channel L-band version of the sequential adapter was built and tested for use with the MARK XII IFF (identify friend or foe) system. In this system the sequentially determined adaptive weights were obtained digitally but implemented at RF. As a result, many of the post RF hardware induced sources of error that normally limit cancellation, such as receiver mismatch, are removed by the feedback property. The result is a system that can yield high levels of cancellation and be readily retrofitted to currently fielded equipment.
A snail-eating snake recognizes prey handedness.

PubMed

Danaisawadi, Patchara; Asami, Takahiro; Ota, Hidetoshi; Sutcharit, Chirasak; Panha, Somsak

2016-04-05

Specialized predator-prey interactions can be a driving force for their coevolution. Southeast Asian snail-eating snakes (Pareas) have more teeth on the right mandible and specialize in predation on the clockwise-coiled (dextral) majority in shelled snails by soft-body extraction. Snails have countered the snakes' dextral-predation by recurrent coil reversal, which generates diverse counterclockwise-coiled (sinistral) prey where Pareas snakes live. However, whether the snake predator in turn evolves any response to prey reversal is unknown. We show that Pareas carinatus living with abundant sinistrals avoids approaching or striking at a sinistral that is more difficult and costly to handle than a dextral. Whenever it strikes, however, the snake succeeds in predation by handling dextral and sinistral prey in reverse. In contrast, P. iwasakii with little access to sinistrals on small peripheral islands attempts and frequently misses capturing a given sinistral. Prey-handedness recognition should be advantageous for right-handed snail-eating snakes where frequently encountering sinistrals. Under dextral-predation by Pareas snakes, adaptive fixation of a prey population for a reversal gene instantaneously generates a sinistral species because interchiral mating is rarely possible. The novel warning, instead of sheltering, effect of sinistrality benefitting both predators and prey could further accelerate single-gene ecological speciation by left-right reversal.
The Evolutionary Strategy of Mimcry

ERIC Educational Resources Information Center

Lane, Patricia A.

1977-01-01

Describes methods and materials for an innovative laboratory exercise that centers on the concept of mimicry and illustrates the importance of adaptation, natural selection and coevolution. Students are used as predators and raisins as prey. Included are directions for preparation of unpalatable raisins using alum dissolved in reconstituted lemon…

Arms races between and within species.

PubMed

Dawkins, R; Krebs, J R

1979-09-21

An adaptation in one lineage (e.g. predators) may change the selection pressure on another lineage (e.g. prey), giving rise to a counter-adaptation. If this occurs reciprocally, an unstable runaway escalation or 'arms race' may result. We discuss various factors which might give one side an advantage in an arms race. For example, a lineage under strong selection may out-evolve a weakly selected one (' the life-dinner principle'). We then classify arms races in two independent ways. They may be symmetric or asymmetric, and they may be interspecific or intraspecific. Our example of an asymmetric interspecific arms race is that between brood parasites and their hosts. The arms race concept may help to reduce the mystery of why cuckoo hosts are so good at detecting cuckoo eggs, but so bad at detecting cuckoo nestlings. The evolutionary contest between queen and worker ants over relative parental investment is a good example of an intraspecific asymmetric arms race. Such cases raise special problems because the participants share the same gene pool. Interspecific symmetric arms races are unlikely to be important, because competitors tend to diverge rather than escalate competitive adaptations. Intraspecific symmetric arms races, exemplified by adaptations for male-male competition, may underlie Cope's Rule and even the extinction of lineages. Finally we consider ways in which arms races can end. One lineage may drive the other to extinction; one may reach an optimum, thereby preventing the other from doing so; a particularly interesting possibility, exemplified by flower-bee coevolution, is that both sides may reach a mutual local optimum; lastly, arms races may have no stable and but may cycle continuously. We do not wish necessarily to suggest that all, or even most, evolutionary change results from arms races, but we do suggest that the arms race concept may help to resolve three long-standing questions in evolutionary theory.
Sequential causal inference: Application to randomized trials of adaptive treatment strategies

PubMed Central

Dawson, Ree; Lavori, Philip W.

2009-01-01

SUMMARY Clinical trials that randomize subjects to decision algorithms, which adapt treatments over time according to individual response, have gained considerable interest as investigators seek designs that directly inform clinical decision making. We consider designs in which subjects are randomized sequentially at decision points, among adaptive treatment options under evaluation. We present a sequential method to estimate the comparative effects of the randomized adaptive treatments, which are formalized as adaptive treatment strategies. Our causal estimators are derived using Bayesian predictive inference. We use analytical and empirical calculations to compare the predictive estimators to (i) the ‘standard’ approach that allocates the sequentially obtained data to separate strategy-specific groups as would arise from randomizing subjects at baseline; (ii) the semi-parametric approach of marginal mean models that, under appropriate experimental conditions, provides the same sequential estimator of causal differences as the proposed approach. Simulation studies demonstrate that sequential causal inference offers substantial efficiency gains over the standard approach to comparing treatments, because the predictive estimators can take advantage of the monotone structure of shared data among adaptive strategies. We further demonstrate that the semi-parametric asymptotic variances, which are marginal ‘one-step’ estimators, may exhibit significant bias, in contrast to the predictive variances. We show that the conditions under which the sequential method is attractive relative to the other two approaches are those most likely to occur in real studies. PMID:17914714
Co-evolution of proteins and solutions: protein adaptation versus cytoprotective micromolecules and their roles in marine organisms.

PubMed

Yancey, Paul H; Siebenaller, Joseph F

2015-06-01

Organisms experience a wide range of environmental factors such as temperature, salinity and hydrostatic pressure, which pose challenges to biochemical processes. Studies on adaptations to such factors have largely focused on macromolecules, especially intrinsic adaptations in protein structure and function. However, micromolecular cosolutes can act as cytoprotectants in the cellular milieu to affect biochemical function and they are now recognized as important extrinsic adaptations. These solutes, both inorganic and organic, have been best characterized as osmolytes, which accumulate to reduce osmotic water loss. Singly, and in combination, many cosolutes have properties beyond simple osmotic effects, e.g. altering the stability and function of proteins in the face of numerous stressors. A key example is the marine osmolyte trimethylamine oxide (TMAO), which appears to enhance water structure and is excluded from peptide backbones, favoring protein folding and stability and counteracting destabilizers like urea and temperature. Co-evolution of intrinsic and extrinsic adaptations is illustrated with high hydrostatic pressure in deep-living organisms. Cytosolic and membrane proteins and G-protein-coupled signal transduction in fishes under pressure show inhibited function and stability, while revealing a number of intrinsic adaptations in deep species. Yet, intrinsic adaptations are often incomplete, and those fishes accumulate TMAO linearly with depth, suggesting a role for TMAO as an extrinsic 'piezolyte' or pressure cosolute. Indeed, TMAO is able to counteract the inhibitory effects of pressure on the stability and function of many proteins. Other cosolutes are cytoprotective in other ways, such as via antioxidation. Such observations highlight the importance of considering the cellular milieu in biochemical and cellular adaptation. © 2015. Published by The Company of Biologists Ltd.
The Red Queen in mitochondria: cyto-nuclear co-evolution, hybrid breakdown and human disease

PubMed Central

Chou, Jui-Yu; Leu, Jun-Yi

2015-01-01

Cyto-nuclear incompatibility, a specific form of Dobzhansky-Muller incompatibility caused by incompatible alleles between mitochondrial and nuclear genomes, has been suggested to play a critical role during speciation. Several features of the mitochondrial genome (mtDNA), including high mutation rate, dynamic genomic structure, and uniparental inheritance, make mtDNA more likely to accumulate mutations in the population. Once mtDNA has changed, the nuclear genome needs to play catch-up due to the intimate interactions between these two genomes. In two populations, if cyto-nuclear co-evolution is driven in different directions, it may eventually lead to hybrid incompatibility. Although cyto-nuclear incompatibility has been observed in a wide range of organisms, it remains unclear what type of mutations drives the co-evolution. Currently, evidence supporting adaptive mutations in mtDNA remains limited. On the other hand, it has been known that some mutations allow mtDNA to propagate more efficiently but compromise the host fitness (described as selfish mtDNA). Arms races between such selfish mtDNA and host nuclear genomes can accelerate cyto-nuclear co-evolution and lead to a phenomenon called the Red Queen Effect. Here, we discuss how the Red Queen Effect may contribute to the frequent observation of cyto-nuclear incompatibility and be the underlying driving force of some human mitochondrial diseases. PMID:26042149
Experimental viral evolution to specific host MHC genotypes reveals fitness and virulence trade-offs in alternative MHC types.

PubMed

Kubinak, Jason L; Ruff, James S; Hyzer, Cornelius Whitney; Slev, Patricia R; Potts, Wayne K

2012-02-28

The unprecedented genetic diversity found at vertebrate MHC (major histocompatibility complex) loci influences susceptibility to most infectious and autoimmune diseases. The evolutionary explanation for how these polymorphisms are maintained has been controversial. One leading explanation, antagonistic coevolution (also known as the Red Queen), postulates a never-ending molecular arms race where pathogens evolve to evade immune recognition by common MHC alleles, which in turn provides a selective advantage to hosts carrying rare MHC alleles. This cyclical process leads to negative frequency-dependent selection and promotes MHC diversity if two conditions are met: (i) pathogen adaptation must produce trade-offs that result in pathogen fitness being higher in familiar (i.e., host MHC genotype adapted to) vs. unfamiliar host MHC genotypes; and (ii) this adaptation must produce correlated patterns of virulence (i.e., disease severity). Here we test these fundamental assumptions using an experimental evolutionary approach (serial passage). We demonstrate rapid adaptation and virulence evolution of a mouse-specific retrovirus to its mammalian host across multiple MHC genotypes. Critically, this adaptive response results in trade-offs (i.e., antagonistic pleiotropy) between host MHC genotypes; both viral fitness and virulence is substantially higher in familiar versus unfamiliar MHC genotypes. These data are unique in experimentally confirming the requisite conditions of the antagonistic coevolution model of MHC evolution and providing quantification of fitness effects for pathogen and host. These data help explain the unprecedented diversity of MHC genes, including how disease-causing alleles are maintained.
Coevolution of MHC genes (LMP/TAP/class Ia; NKT-class Ib; NKp30-B7H6): Lessons from cold-blooded vertebrates

PubMed Central

Ohta, Yuko; Flajnik, Martin F.

2015-01-01

Summary Comparative immunology provides the long view of what is conserved across all vertebrate taxa versus what is specific to particular organisms or group of organisms. Regarding the major histocompatibility complex (MHC) and coevolution, three striking cases have been revealed in cold-blooded vertebrates: lineages of class Ia antigen-processing and -presenting genes, evolutionary conservation of NKT-class Ib recognition, and the ancient emergence of the natural cytotoxicity receptor NKp30 and its ligand B7H6. While coevolution of transporter associated with antigen processing (TAP) and class Ia has been documented in endothermic birds and two mammals, lineages of LMP7 are restricted to ectotherms. The unambiguous discovery of natural killer T (NKT) cells in Xenopus demonstrated that NKT cells are not restricted to mammals and are likely to have emerged at the same time in evolution as classical α/β and γ/δ T cells. NK cell receptors evolve at a rapid rate, and orthologues are nearly impossible to identify in different vertebrate classes. By contrast, we have detected NKp30 in all gnathostomes, except in species where it was lost. The recently discovered ligand of NKp30, B7H6, shows strong signs of coevolution with NKp30 throughout evolution, i.e. coincident loss or expansion of both genes in some species. NKp30 also offers an attractive IgSF candidate for the invasion of the RAG transposon, which is believed to have initiated T-cell receptor/immunoglobulin adaptive immunity. Besides reviewing these intriguing features of MHC evolution and coevolution, we offer suggestions for future studies and propose a model for the primordial or proto MHC. PMID:26284468
Coevolution of adaptive technology, maladaptive culture and population size in a producer–scrounger game

PubMed Central

Lehmann, Laurent; Feldman, Marcus W.

2009-01-01

Technology (i.e. tools, methods of cultivation and domestication, systems of construction and appropriation, machines) has increased the vital rates of humans, and is one of the defining features of the transition from Malthusian ecological stagnation to a potentially perpetual rising population growth. Maladaptations, on the other hand, encompass behaviours, customs and practices that decrease the vital rates of individuals. Technology and maladaptations are part of the total stock of culture carried by the individuals in a population. Here, we develop a quantitative model for the coevolution of cumulative adaptive technology and maladaptive culture in a ‘producer–scrounger’ game, which can also usefully be interpreted as an ‘individual–social’ learner interaction. Producers (individual learners) are assumed to invent new adaptations and maladaptations by trial-and-error learning, insight or deduction, and they pay the cost of innovation. Scroungers (social learners) are assumed to copy or imitate (cultural transmission) both the adaptations and maladaptations generated by producers. We show that the coevolutionary dynamics of producers and scroungers in the presence of cultural transmission can have a variety of effects on population carrying capacity. From stable polymorphism, where scroungers bring an advantage to the population (increase in carrying capacity), to periodic cycling, where scroungers decrease carrying capacity, we find that selection-driven cultural innovation and transmission may send a population on the path of indefinite growth or to extinction. PMID:19692409
A coupled human-natural systems analysis of irrigated agriculture under changing climate

NASA Astrophysics Data System (ADS)

Giuliani, M.; Li, Y.; Castelletti, A.; Gandolfi, C.

2016-09-01

Exponentially growing water demands and increasingly uncertain hydrologic regimes due to changes in climate and land use are challenging the sustainability of agricultural water systems. Farmers must adapt their management strategies in order to secure food production and avoid crop failures. Investigating the potential for adaptation policies in agricultural systems requires accounting for their natural and human components, along with their reciprocal interactions. Yet this feedback is generally overlooked in the water resources systems literature. In this work, we contribute a novel modeling approach to study the coevolution of irrigated agriculture under changing climate, advancing the representation of the human component within agricultural systems by using normative meta-models to describe the behaviors of groups of farmers or institutional decisions. These behavioral models, validated against observational data, are then integrated into a coupled human-natural system simulation model to better represent both systems and their coevolution under future changing climate conditions, assuming the adoption of different policy adaptation options, such as cultivating less water demanding crops. The application to the pilot study of the Adda River basin in northern Italy shows that the dynamic coadaptation of water supply and demand allows farmers to avoid estimated potential losses of more than 10 M€/yr under projected climate changes, while unilateral adaptation of either the water supply or the demand are both demonstrated to be less effective. Results also show that the impact of the different policy options varies as function of drought intensity, with water demand adaptation outperforming water supply adaptation when drought conditions become more severe.
Evolutionary escalation: the bat-moth arms race.

PubMed

Ter Hofstede, Hannah M; Ratcliffe, John M

2016-06-01

Echolocation in bats and high-frequency hearing in their insect prey make bats and insects an ideal system for studying the sensory ecology and neuroethology of predator-prey interactions. Here, we review the evolutionary history of bats and eared insects, focusing on the insect order Lepidoptera, and consider the evidence for antipredator adaptations and predator counter-adaptations. Ears evolved in a remarkable number of body locations across insects, with the original selection pressure for ears differing between groups. Although cause and effect are difficult to determine, correlations between hearing and life history strategies in moths provide evidence for how these two variables influence each other. We consider life history variables such as size, sex, circadian and seasonal activity patterns, geographic range and the composition of sympatric bat communities. We also review hypotheses on the neural basis for anti-predator behaviours (such as evasive flight and sound production) in moths. It is assumed that these prey adaptations would select for counter-adaptations in predatory bats. We suggest two levels of support for classifying bat traits as counter-adaptations: traits that allow bats to eat more eared prey than expected based on their availability in the environment provide a low level of support for counter-adaptations, whereas traits that have no other plausible explanation for their origination and maintenance than capturing defended prey constitute a high level of support. Specific predator counter-adaptations include calling at frequencies outside the sensitivity range of most eared prey, changing the pattern and frequency of echolocation calls during prey pursuit, and quiet, or 'stealth', echolocation. © 2016. Published by The Company of Biologists Ltd.
The genetic basis of a plant–insect coevolutionary key innovation

PubMed Central

Wheat, Christopher W.; Vogel, Heiko; Wittstock, Ute; Braby, Michael F.; Underwood, Dessie; Mitchell-Olds, Thomas

2007-01-01

Ehrlich and Raven formally introduced the concept of stepwise coevolution using butterfly and angiosperm interactions in an attempt to account for the impressive biological diversity of these groups. However, many biologists currently envision butterflies evolving 50 to 30 million years (Myr) after the major angiosperm radiation and thus reject coevolutionary origins of butterfly biodiversity. The unresolved central tenet of Ehrlich and Raven's theory is that evolution of plant chemical defenses is followed closely by biochemical adaptation in insect herbivores, and that newly evolved detoxification mechanisms result in adaptive radiation of herbivore lineages. Using one of their original butterfly-host plant systems, the Pieridae, we identify a pierid glucosinolate detoxification mechanism, nitrile-specifier protein (NSP), as a key innovation. Larval NSP activity matches the distribution of glucosinolate in their host plants. Moreover, by using five different temporal estimates, NSP seems to have evolved shortly after the evolution of the host plant group (Brassicales) (≈10 Myr). An adaptive radiation of these glucosinolate-feeding Pierinae followed, resulting in significantly elevated species numbers compared with related clades. Mechanistic understanding in its proper historical context documents more ancient and dynamic plant–insect interactions than previously envisioned. Moreover, these mechanistic insights provide the tools for detailed molecular studies of coevolution from both the plant and insect perspectives. PMID:18077380
An adaptive two-stage sequential design for sampling rare and clustered populations

USGS Publications Warehouse

Brown, J.A.; Salehi, M.M.; Moradi, M.; Bell, G.; Smith, D.R.

2008-01-01

How to design an efficient large-area survey continues to be an interesting question for ecologists. In sampling large areas, as is common in environmental studies, adaptive sampling can be efficient because it ensures survey effort is targeted to subareas of high interest. In two-stage sampling, higher density primary sample units are usually of more interest than lower density primary units when populations are rare and clustered. Two-stage sequential sampling has been suggested as a method for allocating second stage sample effort among primary units. Here, we suggest a modification: adaptive two-stage sequential sampling. In this method, the adaptive part of the allocation process means the design is more flexible in how much extra effort can be directed to higher-abundance primary units. We discuss how best to design an adaptive two-stage sequential sample. ?? 2008 The Society of Population Ecology and Springer.
Comparative modeling of coevolution in communities of unicellular organisms: adaptability and biodiversity.

PubMed

Lashin, Sergey A; Suslov, Valentin V; Matushkin, Yuri G

2010-06-01

We propose an original program "Evolutionary constructor" that is capable of computationally efficient modeling of both population-genetic and ecological problems, combining these directions in one model of required detail level. We also present results of comparative modeling of stability, adaptability and biodiversity dynamics in populations of unicellular haploid organisms which form symbiotic ecosystems. The advantages and disadvantages of two evolutionary strategies of biota formation--a few generalists' taxa-based biota formation and biodiversity-based biota formation--are discussed.
Gene-culture coevolution in the age of genomics

PubMed Central

Richerson, Peter J.; Boyd, Robert; Henrich, Joseph

2010-01-01

The use of socially learned information (culture) is central to human adaptations. We investigate the hypothesis that the process of cultural evolution has played an active, leading role in the evolution of genes. Culture normally evolves more rapidly than genes, creating novel environments that expose genes to new selective pressures. Many human genes that have been shown to be under recent or current selection are changing as a result of new environments created by cultural innovations. Some changed in response to the development of agricultural subsistence systems in the Early and Middle Holocene. Alleles coding for adaptations to diets rich in plant starch (e.g., amylase copy number) and to epidemic diseases evolved as human populations expanded (e.g., sickle cell and G6PD deficiency alleles that provide protection against malaria). Large-scale scans using patterns of linkage disequilibrium to detect recent selection suggest that many more genes evolved in response to agriculture. Genetic change in response to the novel social environment of contemporary modern societies is also likely to be occurring. The functional effects of most of the alleles under selection during the last 10,000 years are currently unknown. Also unknown is the role of paleoenvironmental change in regulating the tempo of hominin evolution. Although the full extent of culture-driven gene-culture coevolution is thus far unknown for the deeper history of the human lineage, theory and some evidence suggest that such effects were profound. Genomic methods promise to have a major impact on our understanding of gene-culture coevolution over the span of hominin evolutionary history. PMID:20445092
Hybrid Computerized Adaptive Testing: From Group Sequential Design to Fully Sequential Design

ERIC Educational Resources Information Center

Wang, Shiyu; Lin, Haiyan; Chang, Hua-Hua; Douglas, Jeff

2016-01-01

Computerized adaptive testing (CAT) and multistage testing (MST) have become two of the most popular modes in large-scale computer-based sequential testing. Though most designs of CAT and MST exhibit strength and weakness in recent large-scale implementations, there is no simple answer to the question of which design is better because different…
Prevailing Negative Soil Biota Effect and No Evidence for Local Adaptation in a Widespread Eurasian Grass

PubMed Central

Wagner, Viktoria; Antunes, Pedro M.; Ristow, Michael; Lechner, Ute; Hensen, Isabell

2011-01-01

Background Soil biota effects are increasingly accepted as an important driver of the abundance and distribution of plants. While biogeographical studies on alien invasive plant species have indicated coevolution with soil biota in their native distribution range, it is unknown whether adaptation to soil biota varies among populations within the native distribution range. The question of local adaptation between plants and their soil biota has important implications for conservation of biodiversity and may justify the use of seed material from local provenances in restoration campaigns. Methodology/Principal Findings We studied soil biota effects in ten populations of the steppe grass Stipa capillata from two distinct regions, Europe and Asia. We tested for local adaptation at two different scales, both within (ca. 10–80 km) and between (ca. 3300 km) regions, using a reciprocal inoculation experiment in the greenhouse for nine months. Generally, negative soil biota effects were consistent. However, we did not find evidence for local adaptation: both within and between regions, growth of plants in their ‘home soil’ was not significantly larger relative to that in soil from other, more distant, populations. Conclusions/Significance Our study suggests that negative soil biota effects can prevail in different parts of a plant species' range. Absence of local adaptation points to the possibility of similar rhizosphere biota composition across populations and regions, sufficient gene flow to prevent coevolution, selection in favor of plasticity, or functional redundancy among different soil biota. From the point of view of plant - soil biota interactions, our findings indicate that the current practice of using seeds exclusively from local provenances in ecosystem restoration campaigns may not be justified. PMID:21479262
Selection on an antagonistic behavioral trait can drive rapid genital coevolution in the burying beetle, Nicrophorus vespilloides

PubMed Central

Hopwood, Paul E.; Head, Megan L.; Jordan, Eleanor J.; Carter, Mauricio J.; Davey, Emma; Moore, Allen J.; Royle, Nick J.

2016-01-01

Male and female genital morphology varies widely across many taxa, and even among populations. Disentangling potential sources of selection on genital morphology is problematic because each sex is predicted to respond to adaptations in the other due to reproductive conflicts of interest. To test how variation in this sexual conflict trait relates to variation in genital morphology we used our previously developed artificial selection lines for high and low repeated mating rates. We selected for high and low repeated mating rates using monogamous pairings to eliminate contemporaneous female choice and male–male competition. Male and female genital shape responded rapidly to selection on repeated mating rate. High and low mating rate lines diverged from control lines after only 10 generations of selection. We also detected significant patterns of male and female genital shape coevolution among selection regimes. We argue that because our selection lines differ in sexual conflict, these results support the hypothesis that sexually antagonistic coevolution can drive the rapid divergence of genital morphology. The greatest divergence in morphology corresponded with lines in which the resolution of sexual conflict over mating rate was biased in favor of male interests. PMID:27144373
Coevolution in action: disruptive selection on egg colour in an avian brood parasite and its host.

PubMed

Yang, Canchao; Liang, Wei; Cai, Yan; Shi, Suhua; Takasu, Fugo; Møller, Anders P; Antonov, Anton; Fossøy, Frode; Moksnes, Arne; Røskaft, Eivin; Stokke, Bård G

2010-05-26

Trait polymorphism can evolve as a consequence of frequency-dependent selection. Coevolutionary interactions between hosts and parasites may lead to selection on both to evolve extreme phenotypes deviating from the norm, through disruptive selection. Here, we show through detailed field studies and experimental procedures that the ashy-throated parrotbill (Paradoxornis alphonsianus) and its avian brood parasite, the common cuckoo (Cuculus canorus), have both evolved egg polymorphism manifested in discrete immaculate white, pale blue, and blue egg phenotypes within a single population. In this host-parasite system the most common egg colours were white and blue, with no significant difference in parasitism rates between hosts laying eggs of either colour. Furthermore, selection on parasites for countering the evolution of host egg types appears to be strong, since ashy-throated parrotbills have evolved rejection abilities for even partially mimetic eggs. The parrotbill-cuckoo system constitutes a clear outcome of disruptive selection on both host and parasite egg phenotypes driven by coevolution, due to the cost of parasitism in the host and by host defences in the parasite. The present study is to our knowledge the first to report the influence of disruptive selection on evolution of discrete phenotypes in both parasite and host traits in an avian brood parasitism system.
Coevolution between Hispaniolan crossbills and pine: does more time allow for greater phenotypic escalation at lower latitude?

PubMed

Parchman, Thomas L; Benkman, Craig W; Mezquida, Eduardo T

2007-09-01

Crossbills (Aves: Loxia) and several conifers have coevolved in predator-prey arms races over the last 10,000 years. However, the extent to which coevolutionary arms races have contributed to the adaptive radiation of crossbills or to any other adaptive radiation is largely unknown. Here we extend our previous studies of geographically structured coevolution by considering a crossbill-conifer interaction that has persisted for a much longer time period and involves a conifer with more variable annual seed production. We examined geographic variation in the cone and seed traits of two sister species of pines, Pinus occidentalis and P. cubensis, on the islands of Hispaniola and Cuba, respectively. We also compared the Hispaniolan crossbill (Loxia megaplaga) to its sister taxa the North American white-winged crossbill (Loxia leucoptera leucoptera). The Hispaniolan crossbill is endemic to Hispaniola whereas Cuba lacks crossbills. In addition and in contrast to previous studies, the variation in selection experienced by these pines due to crossbills is not confounded by the occurrence of selection by tree squirrels (Tamiasciurus and Sciurus). As predicted if P. occidentalis has evolved defenses in response to selection exerted by crossbills, cones of P. occidentalis have scales that are 53% thicker than those of P. cubensis. Cones of P. occidentalis, but not P. cubensis, also have well-developed spines, a known defense against vertebrate seed predators. Consistent with patterns of divergence seen in crossbills coevolving locally with other conifers, the Hispaniolan crossbill has evolved a bill that is 25% deeper than the white-winged crossbill. Together with phylogenetic analyses, our results suggest that predator-prey coevolution between Hispaniolan crossbills and P. occidentalis over approximately 600,000 years has caused substantial morphological evolution in both the crossbill and pine. This also indicates that cone crop fluctuations do not prevent crossbills and conifers from coevolving. Furthermore, because the traits at the phenotypic interface of the interaction apparently remain the same over at least several hundred thousand years, divergence as a result of coevolution is greater at lower latitude where crossbill-conifer interactions have been less interrupted by Pleistocene events.
Adaptive x-ray threat detection using sequential hypotheses testing with fan-beam experimental data (Conference Presentation)

NASA Astrophysics Data System (ADS)

Thamvichai, Ratchaneekorn; Huang, Liang-Chih; Ashok, Amit; Gong, Qian; Coccarelli, David; Greenberg, Joel A.; Gehm, Michael E.; Neifeld, Mark A.

2017-05-01

We employ an adaptive measurement system, based on sequential hypotheses testing (SHT) framework, for detecting material-based threats using experimental data acquired on an X-ray experimental testbed system. This testbed employs 45-degree fan-beam geometry and 15 views over a 180-degree span to generate energy sensitive X-ray projection data. Using this testbed system, we acquire multiple view projection data for 200 bags. We consider an adaptive measurement design where the X-ray projection measurements are acquired in a sequential manner and the adaptation occurs through the choice of the optimal "next" source/view system parameter. Our analysis of such an adaptive measurement design using the experimental data demonstrates a 3x-7x reduction in the probability of error relative to a static measurement design. Here the static measurement design refers to the operational system baseline that corresponds to a sequential measurement using all the available sources/views. We also show that by using adaptive measurements it is possible to reduce the number of sources/views by nearly 50% compared a system that relies on static measurements.
Reliability of Metrics Associated with a Counter-Movement Jump Performed on a Force Plate

ERIC Educational Resources Information Center

Lombard, Wayne; Reid, Sorrel; Pearson, Keagan; Lambert, Michael

2017-01-01

The counter-movement jump is a consequence of maximal force, rate of force developed, and neuromuscular coordination. Thus, the counter-movement jump has been used to monitor various training adaptations. However, the smallest detectable difference of counter-movement jump metrics has yet to be established. The objective of the present study was…

Gene loss, adaptive evolution and the co-evolution of plumage coloration genes with opsins in birds.

PubMed

Borges, Rui; Khan, Imran; Johnson, Warren E; Gilbert, M Thomas P; Zhang, Guojie; Jarvis, Erich D; O'Brien, Stephen J; Antunes, Agostinho

2015-10-06

The wide range of complex photic systems observed in birds exemplifies one of their key evolutionary adaptions, a well-developed visual system. However, genomic approaches have yet to be used to disentangle the evolutionary mechanisms that govern evolution of avian visual systems. We performed comparative genomic analyses across 48 avian genomes that span extant bird phylogenetic diversity to assess evolutionary changes in the 17 representatives of the opsin gene family and five plumage coloration genes. Our analyses suggest modern birds have maintained a repertoire of up to 15 opsins. Synteny analyses indicate that PARA and PARIE pineal opsins were lost, probably in conjunction with the degeneration of the parietal organ. Eleven of the 15 avian opsins evolved in a non-neutral pattern, confirming the adaptive importance of vision in birds. Visual conopsins sw1, sw2 and lw evolved under negative selection, while the dim-light RH1 photopigment diversified. The evolutionary patterns of sw1 and of violet/ultraviolet sensitivity in birds suggest that avian ancestors had violet-sensitive vision. Additionally, we demonstrate an adaptive association between the RH2 opsin and the MC1R plumage color gene, suggesting that plumage coloration has been photic mediated. At the intra-avian level we observed some unique adaptive patterns. For example, barn owl showed early signs of pseudogenization in RH2, perhaps in response to nocturnal behavior, and penguins had amino acid deletions in RH2 sites responsible for the red shift and retinal binding. These patterns in the barn owl and penguins were convergent with adaptive strategies in nocturnal and aquatic mammals, respectively. We conclude that birds have evolved diverse opsin adaptations through gene loss, adaptive selection and coevolution with plumage coloration, and that differentiated selective patterns at the species level suggest novel photic pressures to influence evolutionary patterns of more-recent lineages.
Long sequence correlation coprocessor

NASA Astrophysics Data System (ADS)

Gage, Douglas W.

1994-09-01

A long sequence correlation coprocessor (LSCC) accelerates the bitwise correlation of arbitrarily long digital sequences by calculating in parallel the correlation score for 16, for example, adjacent bit alignments between two binary sequences. The LSCC integrated circuit is incorporated into a computer system with memory storage buffers and a separate general purpose computer processor which serves as its controller. Each of the LSCC's set of sequential counters simultaneously tallies a separate correlation coefficient. During each LSCC clock cycle, computer enable logic associated with each counter compares one bit of a first sequence with one bit of a second sequence to increment the counter if the bits are the same. A shift register assures that the same bit of the first sequence is simultaneously compared to different bits of the second sequence to simultaneously calculate the correlation coefficient by the different counters to represent different alignments of the two sequences.
Biological evolution and statistical physics

NASA Astrophysics Data System (ADS)

Drossel, Barbara

2001-03-01

This review is an introduction to theoretical models and mathematical calculations for biological evolution, aimed at physicists. The methods in the field are naturally very similar to those used in statistical physics, although the majority of publications have appeared in biology journals. The review has three parts, which can be read independently. The first part deals with evolution in fitness landscapes and includes Fisher's theorem, adaptive walks, quasispecies models, effects of finite population sizes, and neutral evolution. The second part studies models of coevolution, including evolutionary game theory, kin selection, group selection, sexual selection, speciation, and coevolution of hosts and parasites. The third part discusses models for networks of interacting species and their extinction avalanches. Throughout the review, attention is paid to giving the necessary biological information, and to pointing out the assumptions underlying the models, and their limits of validity.
Air Proportional Counter

DOEpatents

Simpson, Jr, J A

1950-12-05

A multiple wire counter utilizing air at atmospheric pressure as the ionizing medium and having a window of a nylon sheet of less than 0.5 mil thickness coated with graphite. The window is permeable to alpha particles so that the counter is well adapted to surveying sources of alpha radiation.
Aquatic insects in a multistress environment: cross-tolerance to salinity and desiccation.

PubMed

Pallarés, Susana; Botella-Cruz, María; Arribas, Paula; Millán, Andrés; Velasco, Josefa

2017-04-01

Exposing organisms to a particular stressor may enhance tolerance to a subsequent stress, when protective mechanisms against the two stressors are shared. Such cross-tolerance is a common adaptive response in dynamic multivariate environments and often indicates potential co-evolution of stress traits. Many aquatic insects in inland saline waters from Mediterranean-climate regions are sequentially challenged with salinity and desiccation stress. Thus, cross-tolerance to these physiologically similar stressors could have been positively selected in insects of these regions. We used adults of the saline water beetles Enochrus jesusarribasi (Hydrophilidae) and Nebrioporus baeticus (Dytiscidae) to test cross-tolerance responses to desiccation and salinity. In independent laboratory experiments, we evaluated the effects of (i) salinity stress on the subsequent resistance to desiccation and (ii) desiccation stress (rapid and slow dehydration) on the subsequent tolerance to salinity. Survival, water loss and haemolymph osmolality were measured. Exposure to stressful salinity improved water control under subsequent desiccation stress in both species, with a clear cross-tolerance (enhanced performance) in N. baeticus In contrast, general negative effects on performance were found under the inverse stress sequence. The rapid and slow dehydration produced different water loss and haemolymph osmolality dynamics that were reflected in different survival patterns. Our finding of cross-tolerance to salinity and desiccation in ecologically similar species from distant lineages, together with parallel responses between salinity and thermal stress previously found in several aquatic taxa, highlights the central role of adaption to salinity and co-occurring stressors in arid inland waters, having important implications for the species' persistence under climate change. © 2017. Published by The Company of Biologists Ltd.
AUTOMATIC CALIBRATING SYSTEM FOR PRESSURE TRANSDUCERS

DOEpatents

Amonette, E.L.; Rodgers, G.W.

1958-01-01

An automatic system for calibrating a number of pressure transducers is described. The disclosed embodiment of the invention uses a mercurial manometer to measure the air pressure applied to the transducer. A servo system follows the top of the mercury column as the pressure is changed and operates an analog- to-digital converter This converter furnishes electrical pulses, each representing an increment of pressure change, to a reversible counterThe transducer furnishes a signal at each calibration point, causing an electric typewriter and a card-punch machine to record the pressure at the instant as indicated by the counter. Another counter keeps track of the calibration points so that a number identifying each point is recorded with the corresponding pressure. A special relay control system controls the pressure trend and programs the sequential calibration of several transducers.
Incorporating information on predicted solvent accessibility to the co-evolution-based study of protein interactions.

PubMed

Ochoa, David; García-Gutiérrez, Ponciano; Juan, David; Valencia, Alfonso; Pazos, Florencio

2013-01-27

A widespread family of methods for studying and predicting protein interactions using sequence information is based on co-evolution, quantified as similarity of phylogenetic trees. Part of the co-evolution observed between interacting proteins could be due to co-adaptation caused by inter-protein contacts. In this case, the co-evolution is expected to be more evident when evaluated on the surface of the proteins or the internal layers close to it. In this work we study the effect of incorporating information on predicted solvent accessibility to three methods for predicting protein interactions based on similarity of phylogenetic trees. We evaluate the performance of these methods in predicting different types of protein associations when trees based on positions with different characteristics of predicted accessibility are used as input. We found that predicted accessibility improves the results of two recent versions of the mirrortree methodology in predicting direct binary physical interactions, while it neither improves these methods, nor the original mirrortree method, in predicting other types of interactions. That improvement comes at no cost in terms of applicability since accessibility can be predicted for any sequence. We also found that predictions of protein-protein interactions are improved when multiple sequence alignments with a richer representation of sequences (including paralogs) are incorporated in the accessibility prediction.
Selection on an antagonistic behavioral trait can drive rapid genital coevolution in the burying beetle, Nicrophorus vespilloides.

PubMed

Hopwood, Paul E; Head, Megan L; Jordan, Eleanor J; Carter, Mauricio J; Davey, Emma; Moore, Allen J; Royle, Nick J

2016-06-01

Male and female genital morphology varies widely across many taxa, and even among populations. Disentangling potential sources of selection on genital morphology is problematic because each sex is predicted to respond to adaptations in the other due to reproductive conflicts of interest. To test how variation in this sexual conflict trait relates to variation in genital morphology we used our previously developed artificial selection lines for high and low repeated mating rates. We selected for high and low repeated mating rates using monogamous pairings to eliminate contemporaneous female choice and male-male competition. Male and female genital shape responded rapidly to selection on repeated mating rate. High and low mating rate lines diverged from control lines after only 10 generations of selection. We also detected significant patterns of male and female genital shape coevolution among selection regimes. We argue that because our selection lines differ in sexual conflict, these results support the hypothesis that sexually antagonistic coevolution can drive the rapid divergence of genital morphology. The greatest divergence in morphology corresponded with lines in which the resolution of sexual conflict over mating rate was biased in favor of male interests. © 2016 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.
Coevolution of coloration and colour vision?

PubMed

Lind, Olle; Henze, Miriam J; Kelber, Almut; Osorio, Daniel

2017-07-05

The evolutionary relationship between signals and animal senses has broad significance, with potential consequences for speciation, and for the efficacy and honesty of biological communication. Here we outline current understanding of the diversity of colour vision in two contrasting groups: the phylogenetically conservative birds, and the more variable butterflies. Evidence for coevolution of colour signals and vision exists in both groups, but is limited to observations of phenotypic differences between visual systems, which might be correlated with coloration. Here, to illustrate how one might interpret the evolutionary significance of such differences, we used colour vision modelling based on an avian eye to evaluate the effects of variation in three key characters: photoreceptor spectral sensitivity, oil droplet pigmentation and the proportions of different photoreceptor types. The models predict that physiologically realistic changes in any one character will have little effect, but complementary shifts in all three can substantially affect discriminability of three types of natural spectra. These observations about the adaptive landscape of colour vision may help to explain the general conservatism of photoreceptor spectral sensitivities in birds. This approach can be extended to other types of eye and spectra to inform future work on coevolution of coloration and colour vision.This article is part of the themed issue 'Animal coloration: production, perception, function and application'. © 2017 The Author(s).
Evolution of spatially structured host-parasite interactions.

PubMed

Lion, S; Gandon, S

2015-01-01

Spatial structure has dramatic effects on the demography and the evolution of species. A large variety of theoretical models have attempted to understand how local dispersal may shape the coevolution of interacting species such as host-parasite interactions. The lack of a unifying framework is a serious impediment for anyone willing to understand current theory. Here, we review previous theoretical studies in the light of a single epidemiological model that allows us to explore the effects of both host and parasite migration rates on the evolution and coevolution of various life-history traits. We discuss the impact of local dispersal on parasite virulence, various host defence strategies and local adaptation. Our analysis shows that evolutionary and coevolutionary outcomes crucially depend on the details of the host-parasite life cycle and on which life-history trait is involved in the interaction. We also discuss experimental studies that support the effects of spatial structure on the evolution of host-parasite interactions. This review highlights major similarities between some theoretical results, but it also reveals an important gap between evolutionary and coevolutionary models. We discuss possible ways to bridge this gap within a more unified framework that would reconcile spatial epidemiology, evolution and coevolution. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.
Optimal Sequential Rules for Computer-Based Instruction.

ERIC Educational Resources Information Center

Vos, Hans J.

1998-01-01

Formulates sequential rules for adapting the appropriate amount of instruction to learning needs in the context of computer-based instruction. Topics include Bayesian decision theory, threshold and linear-utility structure, psychometric model, optimal sequential number of test questions, and an empirical example of sequential instructional…
A Bayesian sequential design with adaptive randomization for 2-sided hypothesis test.

PubMed

Yu, Qingzhao; Zhu, Lin; Zhu, Han

2017-11-01

Bayesian sequential and adaptive randomization designs are gaining popularity in clinical trials thanks to their potentials to reduce the number of required participants and save resources. We propose a Bayesian sequential design with adaptive randomization rates so as to more efficiently attribute newly recruited patients to different treatment arms. In this paper, we consider 2-arm clinical trials. Patients are allocated to the 2 arms with a randomization rate to achieve minimum variance for the test statistic. Algorithms are presented to calculate the optimal randomization rate, critical values, and power for the proposed design. Sensitivity analysis is implemented to check the influence on design by changing the prior distributions. Simulation studies are applied to compare the proposed method and traditional methods in terms of power and actual sample sizes. Simulations show that, when total sample size is fixed, the proposed design can obtain greater power and/or cost smaller actual sample size than the traditional Bayesian sequential design. Finally, we apply the proposed method to a real data set and compare the results with the Bayesian sequential design without adaptive randomization in terms of sample sizes. The proposed method can further reduce required sample size. Copyright © 2017 John Wiley & Sons, Ltd.
Hybrid Model Predictive Control for Sequential Decision Policies in Adaptive Behavioral Interventions.

PubMed

Dong, Yuwen; Deshpande, Sunil; Rivera, Daniel E; Downs, Danielle S; Savage, Jennifer S

2014-06-01

Control engineering offers a systematic and efficient method to optimize the effectiveness of individually tailored treatment and prevention policies known as adaptive or "just-in-time" behavioral interventions. The nature of these interventions requires assigning dosages at categorical levels, which has been addressed in prior work using Mixed Logical Dynamical (MLD)-based hybrid model predictive control (HMPC) schemes. However, certain requirements of adaptive behavioral interventions that involve sequential decision making have not been comprehensively explored in the literature. This paper presents an extension of the traditional MLD framework for HMPC by representing the requirements of sequential decision policies as mixed-integer linear constraints. This is accomplished with user-specified dosage sequence tables, manipulation of one input at a time, and a switching time strategy for assigning dosages at time intervals less frequent than the measurement sampling interval. A model developed for a gestational weight gain (GWG) intervention is used to illustrate the generation of these sequential decision policies and their effectiveness for implementing adaptive behavioral interventions involving multiple components.
On the Use of Adaptive Instructional Images Based on the Sequential-Global Dimension of the Felder-Silverman Learning Style Theory

ERIC Educational Resources Information Center

Filippidis, Stavros K.; Tsoukalas, Ioannis A.

2009-01-01

An adaptive educational system that uses adaptive presentation is presented. In this system fragments of different images present the same content and the system can choose the one most relevant to the user based on the sequential-global dimension of Felder-Silverman's learning style theory. In order to retrieve the learning style of each student…
Mass test of AdvanSiD model ASD-NUV3S-P SiliconPMs for the Pixel Timing Counter of the MEG II experiment

NASA Astrophysics Data System (ADS)

Rossella, M.; Bariani, S.; Barnaba, O.; Cattaneo, P. W.; Cervi, T.; Menegolli, A.; Nardò, R.; Prata, M. C.; Romano, E.; Scagliotti, C.; Simonetta, M.; Vercellati, F.

2017-02-01

The MEG II Timing Counter will measure the positron time of arrival with a resolution of 30 ps relying on two arrays of scintillator pixels read out by 6144 Silicon Photomultipliers (SiPMs) from AdvanSiD. They must be characterized, measuring their breakdown voltage, to assure that the gains of the SiPMs of each pixel are as uniform as possible, to maximize the pixel resolution. To do this an automatic test system that can measure sequentially the parameters of 32 devices has been developed.
Older partner selection promotes the prevalence of cooperation in evolutionary games.

PubMed

Yang, Guoli; Huang, Jincai; Zhang, Weiming

2014-10-21

Evolutionary games typically come with the interplays between evolution of individual strategy and adaptation to network structure. How these dynamics in the co-evolution promote (or obstruct) the cooperation is regarded as an important topic in social, economic, and biological fields. Combining spatial selection with partner choice, the focus of this paper is to identify which neighbour should be selected as a role to imitate during the process of co-evolution. Age, an internal attribute and kind of local piece of information regarding the survivability of the agent, is a significant consideration for the selection strategy. The analysis and simulations presented, demonstrate that older partner selection for strategy imitation could foster the evolution of cooperation. The younger partner selection, however, may decrease the level of cooperation. Our model highlights the importance of agent׳s age on the promotion of cooperation in evolutionary games, both efficiently and effectively. Copyright © 2014 Elsevier Ltd. All rights reserved.
Collective evolution of cyanobacteria and cyanophages mediated by horizontal gene transfer

NASA Astrophysics Data System (ADS)

Shih, Hong-Yan; Rogers, Tim; Goldenfeld, Nigel

We describe a model for how antagonistic predator-prey coevolution can lead to mutualistic adaptation to an environment, as a result of horizontal gene transfer. Our model is a simple description of ecosystems such as marine cyanobacteria and their predator cyanophages, which carry photosynthesis genes. These genes evolve more rapidly in the virosphere than the bacterial pan-genome, and thus the bacterial population could potentially benefit from phage predation. By modeling both the barrier to predation and horizontal gene transfer, we study this balance between individual sacrifice and collective benefits. The outcome is an emergent mutualistic coevolution of improved photosynthesis capability, benefiting both bacteria and phage. This form of multi-level selection can contribute to niche stratification in the cyanobacteria-phage ecosystem. This work is supported in part by a cooperative agreement with NASA, Grant NNA13AA91A/A0018.
LOW ENERGY COUNTING CHAMBERS

DOEpatents

Hayes, P.M.

1960-02-16

A beta particle counter adapted to use an end window made of polyethylene terephthalate was designed. The extreme thinness of the film results in a correspondingly high transmission of incident low-energy beta particles by the window. As a consequence, the counting efficiency of the present counter is over 40% greater than counters using conventional mica end windows.
Complexity and health professions education: a basic glossary.

PubMed

Mennin, Stewart

2010-08-01

The study of health professions education in the context of complexity science and complex adaptive systems involves different concepts and terminology that are likely to be unfamiliar to many health professions educators. A list of selected key terms and definitions from the literature of complexity science is provided to assist readers to navigate familiar territory from a different perspective. include agent, attractor, bifurcation, chaos, co-evolution, collective variable, complex adaptive systems, complexity science, deterministic systems, dynamical system, edge of chaos, emergence, equilibrium, far from equilibrium, fuzzy boundaries, linear system, non-linear system, random, self-organization and self-similarity.
Identification of an ancestral resistance gene cluster involved in the coevolution process between Phaseolus vulgaris and its fungal pathogen Colletotrichum lindemuthianum.

PubMed

Geffroy, V; Sicard, D; de Oliveira, J C; Sévignac, M; Cohen, S; Gepts, P; Neema, C; Langin, T; Dron, M

1999-09-01

The recent cloning of plant resistance (R) genes and the sequencing of resistance gene clusters have shed light on the molecular evolution of R genes. However, up to now, no attempt has been made to correlate this molecular evolution with the host-pathogen coevolution process at the population level. Cross-inoculations were carried out between 26 strains of the fungal pathogen Colletotrichum lindemuthianum and 48 Phaseolus vulgaris plants collected in the three centers of diversity of the host species. A high level of diversity for resistance against the pathogen was revealed. Most of the resistance specificities were overcome in sympatric situations, indicating an adaptation of the pathogen to the local host. In contrast, plants were generally resistant to allopatric strains, suggesting that R genes that were efficient against exotic strains but had been overcome locally were maintained in the plant genome. These results indicated that coevolution processes between the two protagonists led to a differentiation for resistance in the three centers of diversity of the host. To improve our understanding of the molecular evolution of these different specificities, a recombinant inbred (RI) population derived from two representative genotypes of the Andean (JaloEEP558) and Mesoamerican (BAT93) gene pools was used to map anthracnose specificities. A gene cluster comprising both Andean (Co-y; Co-z) and Mesoamerican (Co-9) host resistance specificities was identified, suggesting that this locus existed prior to the separation of the two major gene pools of P. vulgaris. Molecular analysis revealed a high level of complexity at this locus. It harbors 11 restriction fragment length polymorphisms when R gene analog (RGA) clones are used. The relationship between the coevolution process and diversification of resistance specificities at resistance gene clusters is discussed.

J-adaptive estimation with estimated noise statistics

NASA Technical Reports Server (NTRS)

Jazwinski, A. H.; Hipkins, C.

1973-01-01

The J-adaptive sequential estimator is extended to include simultaneous estimation of the noise statistics in a model for system dynamics. This extension completely automates the estimator, eliminating the requirement of an analyst in the loop. Simulations in satellite orbit determination demonstrate the efficacy of the sequential estimation algorithm.
The function and response of an improved stratospheric condensation nucleus counter

NASA Technical Reports Server (NTRS)

Wilson, J. C.; Hyun, J. H.; Blackshear, E. D.

1983-01-01

An improved condensation nucleus counter (CNC) for use in the stratosphere is described. The University of Minnesota CNC (UMCNC) has a sequential saturator and condenser and uses n-butyl alcohol as the working fluid. The use of a coaxial saturator flow, with aerosol in the center and filtered, alcohol-laden air around it, speeds the response of this instrument and improves its stability as pressure changes. The counting efficiency has been studied as a function of particle size and pressure. The UMCNC provides an accurate measure of submicron aerosol concentration as long as the number distribution is not dominated by sub-0.02 micron diameter aerosol. The response of the UMCNC is compared with that of other stratospheric condensation nucleus counters, and the results of a (near) comparison with a balloon-borne condensation nucleus counter are presented. The UMCNC has operated 14 times on a NASA U-2 aircraft at altitudes from 8 to 21.5 km.
Comparing cluster-level dynamic treatment regimens using sequential, multiple assignment, randomized trials: Regression estimation and sample size considerations.

PubMed

NeCamp, Timothy; Kilbourne, Amy; Almirall, Daniel

2017-08-01

Cluster-level dynamic treatment regimens can be used to guide sequential treatment decision-making at the cluster level in order to improve outcomes at the individual or patient-level. In a cluster-level dynamic treatment regimen, the treatment is potentially adapted and re-adapted over time based on changes in the cluster that could be impacted by prior intervention, including aggregate measures of the individuals or patients that compose it. Cluster-randomized sequential multiple assignment randomized trials can be used to answer multiple open questions preventing scientists from developing high-quality cluster-level dynamic treatment regimens. In a cluster-randomized sequential multiple assignment randomized trial, sequential randomizations occur at the cluster level and outcomes are observed at the individual level. This manuscript makes two contributions to the design and analysis of cluster-randomized sequential multiple assignment randomized trials. First, a weighted least squares regression approach is proposed for comparing the mean of a patient-level outcome between the cluster-level dynamic treatment regimens embedded in a sequential multiple assignment randomized trial. The regression approach facilitates the use of baseline covariates which is often critical in the analysis of cluster-level trials. Second, sample size calculators are derived for two common cluster-randomized sequential multiple assignment randomized trial designs for use when the primary aim is a between-dynamic treatment regimen comparison of the mean of a continuous patient-level outcome. The methods are motivated by the Adaptive Implementation of Effective Programs Trial which is, to our knowledge, the first-ever cluster-randomized sequential multiple assignment randomized trial in psychiatry.
Real time on-chip sequential adaptive principal component analysis for data feature extraction and image compression

NASA Technical Reports Server (NTRS)

Duong, T. A.

2004-01-01

In this paper, we present a new, simple, and optimized hardware architecture sequential learning technique for adaptive Principle Component Analysis (PCA) which will help optimize the hardware implementation in VLSI and to overcome the difficulties of the traditional gradient descent in learning convergence and hardware implementation.
Host-parasite coevolution beyond the nestling stage? Mimicry of host fledglings by the specialist screaming cowbird.

PubMed

De Mársico, María C; Gantchoff, Mariela G; Reboreda, Juan C

2012-09-07

Egg mimicry by obligate avian brood parasites and host rejection of non-mimetic eggs are well-known textbook examples of host-parasite coevolution. By contrast, reciprocal adaptations and counteradaptations beyond the egg stage in brood parasites and their hosts have received less attention. The screaming cowbird (Molothrus rufoaxillaris) is a specialist obligate brood parasite whose fledglings look identical to those of its primary host, the baywing (Agelaioides badius). Such a resemblance has been proposed as an adaptation in response to host discrimination against odd-looking young, but evidence supporting this idea is scarce. Here, we examined this hypothesis by comparing the survival rates of young screaming cowbirds and non-mimetic shiny cowbirds (Molothrus bonariensis) cross-fostered to baywing nests and quantifying the similarity in plumage colour and begging calls between host and cowbird fledglings. Shiny cowbirds suffered higher post-fledging mortality rates (83%) than screaming cowbirds (0%) owing to host rejection. Visual modelling revealed that screaming cowbirds, but not shiny cowbirds, were indistinguishable from host young in plumage colour. Similarly, screaming cowbirds matched baywings' begging calls more closely than shiny cowbirds. Our results strongly support the occurrence of host fledgling mimicry in screaming cowbirds and suggest a role of visual and vocal cues in fledgling discrimination by baywings.
Directional Selection from Host Plants Is a Major Force Driving Host Specificity in Magnaporthe Species.

PubMed

Zhong, Zhenhui; Norvienyeku, Justice; Chen, Meilian; Bao, Jiandong; Lin, Lianyu; Chen, Liqiong; Lin, Yahong; Wu, Xiaoxian; Cai, Zena; Zhang, Qi; Lin, Xiaoye; Hong, Yonghe; Huang, Jun; Xu, Linghong; Zhang, Honghong; Chen, Long; Tang, Wei; Zheng, Huakun; Chen, Xiaofeng; Wang, Yanli; Lian, Bi; Zhang, Liangsheng; Tang, Haibao; Lu, Guodong; Ebbole, Daniel J; Wang, Baohua; Wang, Zonghua

2016-05-06

One major threat to global food security that requires immediate attention, is the increasing incidence of host shift and host expansion in growing number of pathogenic fungi and emergence of new pathogens. The threat is more alarming because, yield quality and quantity improvement efforts are encouraging the cultivation of uniform plants with low genetic diversity that are increasingly susceptible to emerging pathogens. However, the influence of host genome differentiation on pathogen genome differentiation and its contribution to emergence and adaptability is still obscure. Here, we compared genome sequence of 6 isolates of Magnaporthe species obtained from three different host plants. We demonstrated the evolutionary relationship between Magnaporthe species and the influence of host differentiation on pathogens. Phylogenetic analysis showed that evolution of pathogen directly corresponds with host divergence, suggesting that host-pathogen interaction has led to co-evolution. Furthermore, we identified an asymmetric selection pressure on Magnaporthe species. Oryza sativa-infecting isolates showed higher directional selection from host and subsequently tends to lower the genetic diversity in its genome. We concluded that, frequent gene loss or gain, new transposon acquisition and sequence divergence are host adaptability mechanisms for Magnaporthe species, and this coevolution processes is greatly driven by directional selection from host plants.
Directional Selection from Host Plants Is a Major Force Driving Host Specificity in Magnaporthe Species

PubMed Central

Zhong, Zhenhui; Norvienyeku, Justice; Chen, Meilian; Bao, Jiandong; Lin, Lianyu; Chen, Liqiong; Lin, Yahong; Wu, Xiaoxian; Cai, Zena; Zhang, Qi; Lin, Xiaoye; Hong, Yonghe; Huang, Jun; Xu, Linghong; Zhang, Honghong; Chen, Long; Tang, Wei; Zheng, Huakun; Chen, Xiaofeng; Wang, Yanli; Lian, Bi; Zhang, Liangsheng; Tang, Haibao; Lu, Guodong; Ebbole, Daniel J.; Wang, Baohua; Wang, Zonghua

2016-01-01

One major threat to global food security that requires immediate attention, is the increasing incidence of host shift and host expansion in growing number of pathogenic fungi and emergence of new pathogens. The threat is more alarming because, yield quality and quantity improvement efforts are encouraging the cultivation of uniform plants with low genetic diversity that are increasingly susceptible to emerging pathogens. However, the influence of host genome differentiation on pathogen genome differentiation and its contribution to emergence and adaptability is still obscure. Here, we compared genome sequence of 6 isolates of Magnaporthe species obtained from three different host plants. We demonstrated the evolutionary relationship between Magnaporthe species and the influence of host differentiation on pathogens. Phylogenetic analysis showed that evolution of pathogen directly corresponds with host divergence, suggesting that host-pathogen interaction has led to co-evolution. Furthermore, we identified an asymmetric selection pressure on Magnaporthe species. Oryza sativa-infecting isolates showed higher directional selection from host and subsequently tends to lower the genetic diversity in its genome. We concluded that, frequent gene loss or gain, new transposon acquisition and sequence divergence are host adaptability mechanisms for Magnaporthe species, and this coevolution processes is greatly driven by directional selection from host plants. PMID:27151494
Host–parasite coevolution beyond the nestling stage? Mimicry of host fledglings by the specialist screaming cowbird

PubMed Central

De Mársico, María C.; Gantchoff, Mariela G.; Reboreda, Juan C.

2012-01-01

Egg mimicry by obligate avian brood parasites and host rejection of non-mimetic eggs are well-known textbook examples of host–parasite coevolution. By contrast, reciprocal adaptations and counteradaptations beyond the egg stage in brood parasites and their hosts have received less attention. The screaming cowbird (Molothrus rufoaxillaris) is a specialist obligate brood parasite whose fledglings look identical to those of its primary host, the baywing (Agelaioides badius). Such a resemblance has been proposed as an adaptation in response to host discrimination against odd-looking young, but evidence supporting this idea is scarce. Here, we examined this hypothesis by comparing the survival rates of young screaming cowbirds and non-mimetic shiny cowbirds (Molothrus bonariensis) cross-fostered to baywing nests and quantifying the similarity in plumage colour and begging calls between host and cowbird fledglings. Shiny cowbirds suffered higher post-fledging mortality rates (83%) than screaming cowbirds (0%) owing to host rejection. Visual modelling revealed that screaming cowbirds, but not shiny cowbirds, were indistinguishable from host young in plumage colour. Similarly, screaming cowbirds matched baywings' begging calls more closely than shiny cowbirds. Our results strongly support the occurrence of host fledgling mimicry in screaming cowbirds and suggest a role of visual and vocal cues in fledgling discrimination by baywings. PMID:22648157
CLAss-Specific Subspace Kernel Representations and Adaptive Margin Slack Minimization for Large Scale Classification.

PubMed

Yu, Yinan; Diamantaras, Konstantinos I; McKelvey, Tomas; Kung, Sun-Yuan

2018-02-01

In kernel-based classification models, given limited computational power and storage capacity, operations over the full kernel matrix becomes prohibitive. In this paper, we propose a new supervised learning framework using kernel models for sequential data processing. The framework is based on two components that both aim at enhancing the classification capability with a subset selection scheme. The first part is a subspace projection technique in the reproducing kernel Hilbert space using a CLAss-specific Subspace Kernel representation for kernel approximation. In the second part, we propose a novel structural risk minimization algorithm called the adaptive margin slack minimization to iteratively improve the classification accuracy by an adaptive data selection. We motivate each part separately, and then integrate them into learning frameworks for large scale data. We propose two such frameworks: the memory efficient sequential processing for sequential data processing and the parallelized sequential processing for distributed computing with sequential data acquisition. We test our methods on several benchmark data sets and compared with the state-of-the-art techniques to verify the validity of the proposed techniques.
Vertical Transmission Selects for Reduced Virulence in a Plant Virus and for Increased Resistance in the Host

PubMed Central

Pagán, Israel; Montes, Nuria; Milgroom, Michael G.; García-Arenal, Fernando

2014-01-01

For the last three decades, evolutionary biologists have sought to understand which factors modulate the evolution of parasite virulence. Although theory has identified several of these modulators, their effect has seldom been analysed experimentally. We investigated the role of two such major factors—the mode of transmission, and host adaptation in response to parasite evolution—in the evolution of virulence of the plant virus Cucumber mosaic virus (CMV) in its natural host Arabidopsis thaliana. To do so, we serially passaged three CMV strains under strict vertical and strict horizontal transmission, alternating both modes of transmission. We quantified seed (vertical) transmission rate, virus accumulation, effect on plant growth and virulence of evolved and non-evolved viruses in the original plants and in plants derived after five passages of vertical transmission. Our results indicated that vertical passaging led to adaptation of the virus to greater vertical transmission, which was associated with reductions of virus accumulation and virulence. On the other hand, horizontal serial passages did not significantly modify virus accumulation and virulence. The observed increases in CMV seed transmission, and reductions in virus accumulation and virulence in vertically passaged viruses were due also to reciprocal host adaptation during vertical passages, which additionally reduced virulence and multiplication of vertically passaged viruses. This result is consistent with plant-virus co-evolution. Host adaptation to vertically passaged viruses was traded-off against reduced resistance to the non-evolved viruses. Thus, we provide evidence of the key role that the interplay between mode of transmission and host-parasite co-evolution has in determining the evolution of virulence. PMID:25077948
Culture-gene coevolution of individualism-collectivism and the serotonin transporter gene.

PubMed

Chiao, Joan Y; Blizinsky, Katherine D

2010-02-22

Culture-gene coevolutionary theory posits that cultural values have evolved, are adaptive and influence the social and physical environments under which genetic selection operates. Here, we examined the association between cultural values of individualism-collectivism and allelic frequency of the serotonin transporter functional polymorphism (5-HTTLPR) as well as the role this culture-gene association may play in explaining global variability in prevalence of pathogens and affective disorders. We found evidence that collectivistic cultures were significantly more likely to comprise individuals carrying the short (S) allele of the 5-HTTLPR across 29 nations. Results further show that historical pathogen prevalence predicts cultural variability in individualism-collectivism owing to genetic selection of the S allele. Additionally, cultural values and frequency of S allele carriers negatively predict global prevalence of anxiety and mood disorder. Finally, mediation analyses further indicate that increased frequency of S allele carriers predicted decreased anxiety and mood disorder prevalence owing to increased collectivistic cultural values. Taken together, our findings suggest culture-gene coevolution between allelic frequency of 5-HTTLPR and cultural values of individualism-collectivism and support the notion that cultural values buffer genetically susceptible populations from increased prevalence of affective disorders. Implications of the current findings for understanding culture-gene coevolution of human brain and behaviour as well as how this coevolutionary process may contribute to global variation in pathogen prevalence and epidemiology of affective disorders, such as anxiety and depression, are discussed.
Evolutionary Diversification of Prey and Predator Species Facilitated by Asymmetric Interactions

PubMed Central

Zu, Jian; Wang, Jinliang; Huang, Gang

2016-01-01

We investigate the influence of asymmetric interactions on coevolutionary dynamics of a predator-prey system by using the theory of adaptive dynamics. We assume that the defense ability of prey and the attack ability of predators all can adaptively evolve, either caused by phenotypic plasticity or by behavioral choice, but there are certain costs in terms of their growth rate or death rate. The coevolutionary model is constructed from a deterministic approximation of random mutation-selection process. To sum up, if prey’s trade-off curve is globally weakly concave, then five outcomes of coevolution are demonstrated, which depend on the intensity and shape of asymmetric predator-prey interactions and predator’s trade-off shape. Firstly, we find that if there is a weakly decelerating cost and a weakly accelerating benefit for predator species, then evolutionary branching in the predator species may occur, but after branching further coevolution may lead to extinction of the predator species with a larger trait value. However, if there is a weakly accelerating cost and a weakly accelerating benefit for predator species, then evolutionary branching in the predator species is also possible and after branching the dimorphic predator can evolutionarily stably coexist with a monomorphic prey species. Secondly, if the asymmetric interactions become a little strong, then prey and predators will evolve to an evolutionarily stable equilibrium, at which they can stably coexist on a long-term timescale of evolution. Thirdly, if there is a weakly accelerating cost and a relatively strongly accelerating benefit for prey species, then evolutionary branching in the prey species is possible and the finally coevolutionary outcome contains a dimorphic prey and a monomorphic predator species. Fourthly, if the asymmetric interactions become more stronger, then predator-prey coevolution may lead to cycles in both traits and equilibrium population densities. The Red Queen dynamic is a possible outcome under asymmetric predator-prey interactions. PMID:27685540
Evolutionary Diversification of Prey and Predator Species Facilitated by Asymmetric Interactions.

PubMed

Zu, Jian; Wang, Jinliang; Huang, Gang

We investigate the influence of asymmetric interactions on coevolutionary dynamics of a predator-prey system by using the theory of adaptive dynamics. We assume that the defense ability of prey and the attack ability of predators all can adaptively evolve, either caused by phenotypic plasticity or by behavioral choice, but there are certain costs in terms of their growth rate or death rate. The coevolutionary model is constructed from a deterministic approximation of random mutation-selection process. To sum up, if prey's trade-off curve is globally weakly concave, then five outcomes of coevolution are demonstrated, which depend on the intensity and shape of asymmetric predator-prey interactions and predator's trade-off shape. Firstly, we find that if there is a weakly decelerating cost and a weakly accelerating benefit for predator species, then evolutionary branching in the predator species may occur, but after branching further coevolution may lead to extinction of the predator species with a larger trait value. However, if there is a weakly accelerating cost and a weakly accelerating benefit for predator species, then evolutionary branching in the predator species is also possible and after branching the dimorphic predator can evolutionarily stably coexist with a monomorphic prey species. Secondly, if the asymmetric interactions become a little strong, then prey and predators will evolve to an evolutionarily stable equilibrium, at which they can stably coexist on a long-term timescale of evolution. Thirdly, if there is a weakly accelerating cost and a relatively strongly accelerating benefit for prey species, then evolutionary branching in the prey species is possible and the finally coevolutionary outcome contains a dimorphic prey and a monomorphic predator species. Fourthly, if the asymmetric interactions become more stronger, then predator-prey coevolution may lead to cycles in both traits and equilibrium population densities. The Red Queen dynamic is a possible outcome under asymmetric predator-prey interactions.
Digital-only PLL with adaptive search step

NASA Astrophysics Data System (ADS)

Lin, Ming-Lang; Huang, Shu-Chuan; Liu, Jie-Cherng

2014-06-01

In this paper, an all-digital phase-locked loop (PLL) with adaptively controlled up/down counter serves as the loop filter is presented, and it is implemented on a field-programmable gate array. The detailed circuit of the adaptive up/down counter implementing the adaptive search algorithm is also given, in which the search step for frequency acquisition is adaptively scaled down in half until it is reduced to zero. The phase jitter of the proposed PLL can be lowered, yet keeping with fast lock-in time. Thus, the dilemma between the low phase jitter and fast lock-in time of the traditional PLL can be resolved. Simulation results and circuit implementation show that the locked count, phase jitter and lock-in time of the proposed PLL are consistent with the theoretical predictions.
Self-Organized Terrorist-Counterterrorist Adaptive Coevolutions, Part 1: A Conceptual Design

DTIC Science & Technology

2005-02-01

nodes. Imple- mented in Delphi, it runs in the Windows environment and is being developed by Vladimir Batagelj and Andrej Mrvar . Pajek supports all...Post, January 13, 2002. [22] J. M. Epstein and Robert L. Axtell, Growing Artificial Societies: Social Science from the Bottom Up, MIT Press, 1996 . [23...Mathematical Background and Technical Sourcebook, Center for Naval Analyses Information Manual CIM-461, Unclassified, 1996 . Available on-line, in Adobe’s
Niche construction, sources of selection and trait coevolution.

PubMed

Laland, Kevin; Odling-Smee, John; Endler, John

2017-10-06

Organisms modify and choose components of their local environments. This 'niche construction' can alter ecological processes, modify natural selection and contribute to inheritance through ecological legacies. Here, we propose that niche construction initiates and modifies the selection directly affecting the constructor, and on other species, in an orderly, directed and sustained manner. By dependably generating specific environmental states, niche construction co-directs adaptive evolution by imposing a consistent statistical bias on selection. We illustrate how niche construction can generate this evolutionary bias by comparing it with artificial selection. We suggest that it occupies the middle ground between artificial and natural selection. We show how the perspective leads to testable predictions related to: (i) reduced variance in measures of responses to natural selection in the wild; (ii) multiple trait coevolution, including the evolution of sequences of traits and patterns of parallel evolution; and (iii) a positive association between niche construction and biodiversity. More generally, we submit that evolutionary biology would benefit from greater attention to the diverse properties of all sources of selection.
Clustered marginalization of minorities during social transitions induced by co-evolution of behaviour and network structure

NASA Astrophysics Data System (ADS)

Schleussner, Carl-Friedrich; Donges, Jonathan F.; Engemann, Denis A.; Levermann, Anders

2016-08-01

Large-scale transitions in societies are associated with both individual behavioural change and restructuring of the social network. These two factors have often been considered independently, yet recent advances in social network research challenge this view. Here we show that common features of societal marginalization and clustering emerge naturally during transitions in a co-evolutionary adaptive network model. This is achieved by explicitly considering the interplay between individual interaction and a dynamic network structure in behavioural selection. We exemplify this mechanism by simulating how smoking behaviour and the network structure get reconfigured by changing social norms. Our results are consistent with empirical findings: The prevalence of smoking was reduced, remaining smokers were preferentially connected among each other and formed increasingly marginalized clusters. We propose that self-amplifying feedbacks between individual behaviour and dynamic restructuring of the network are main drivers of the transition. This generative mechanism for co-evolution of individual behaviour and social network structure may apply to a wide range of examples beyond smoking.
Opinion diversity and community formation in adaptive networks

NASA Astrophysics Data System (ADS)

Yu, Y.; Xiao, G.; Li, G.; Tay, W. P.; Teoh, H. F.

2017-10-01

It is interesting and of significant importance to investigate how network structures co-evolve with opinions. In this article, we show that, a simple model integrating consensus formation, link rewiring, and opinion change allows complex system dynamics to emerge, driving the system into a dynamic equilibrium with the co-existence of diversified opinions. Specifically, similar opinion holders may form into communities yet with no strict community consensus; and rather than being separated into disconnected communities, different communities are connected by a non-trivial proportion of inter-community links. More importantly, we show that the complex dynamics may lead to different numbers of communities at the steady state with a given tolerance between different opinion holders. We construct a framework for theoretically analyzing the co-evolution process. Theoretical analysis and extensive simulation results reveal some useful insights into the complex co-evolution process, including the formation of dynamic equilibrium, the transition between different steady states with different numbers of communities, and the dynamics between opinion distribution and network modularity.
Clustered marginalization of minorities during social transitions induced by co-evolution of behaviour and network structure.

PubMed

Schleussner, Carl-Friedrich; Donges, Jonathan F; Engemann, Denis A; Levermann, Anders

2016-08-11

Large-scale transitions in societies are associated with both individual behavioural change and restructuring of the social network. These two factors have often been considered independently, yet recent advances in social network research challenge this view. Here we show that common features of societal marginalization and clustering emerge naturally during transitions in a co-evolutionary adaptive network model. This is achieved by explicitly considering the interplay between individual interaction and a dynamic network structure in behavioural selection. We exemplify this mechanism by simulating how smoking behaviour and the network structure get reconfigured by changing social norms. Our results are consistent with empirical findings: The prevalence of smoking was reduced, remaining smokers were preferentially connected among each other and formed increasingly marginalized clusters. We propose that self-amplifying feedbacks between individual behaviour and dynamic restructuring of the network are main drivers of the transition. This generative mechanism for co-evolution of individual behaviour and social network structure may apply to a wide range of examples beyond smoking.
Network Algorithms for Detection of Radiation Sources

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

Rao, Nageswara S; Brooks, Richard R; Wu, Qishi

In support of national defense, Domestic Nuclear Detection Office s (DNDO) Intelligent Radiation Sensor Systems (IRSS) program supported the development of networks of radiation counters for detecting, localizing and identifying low-level, hazardous radiation sources. Industry teams developed the first generation of such networks with tens of counters, and demonstrated several of their capabilities in indoor and outdoor characterization tests. Subsequently, these test measurements have been used in algorithm replays using various sub-networks of counters. Test measurements combined with algorithm outputs are used to extract Key Measurements and Benchmark (KMB) datasets. We present two selective analyses of these datasets: (a) amore » notional border monitoring scenario that highlights the benefits of a network of counters compared to individual detectors, and (b) new insights into the Sequential Probability Ratio Test (SPRT) detection method, which lead to its adaptations for improved detection. Using KMB datasets from an outdoor test, we construct a notional border monitoring scenario, wherein twelve 2 *2 NaI detectors are deployed on the periphery of 21*21meter square region. A Cs-137 (175 uCi) source is moved across this region, starting several meters from outside and finally moving away. The measurements from individual counters and the network were processed using replays of a particle filter algorithm developed under IRSS program. The algorithm outputs from KMB datasets clearly illustrate the benefits of combining measurements from all networked counters: the source was detected before it entered the region, during its trajectory inside, and until it moved several meters away. When individual counters are used for detection, the source was detected for much shorter durations, and sometimes was missed in the interior region. The application of SPRT for detecting radiation sources requires choosing the detection threshold, which in turn requires a source strength estimate, typically specified as a multiplier of the background radiation level. A judicious selection of this source multiplier is essential to achieve optimal detection probability at a specified false alarm rate. Typically, this threshold is chosen from the Receiver Operating Characteristic (ROC) by varying the source multiplier estimate. ROC is expected to have a monotonically increasing profile between the detection probability and false alarm rate. We derived ROCs for multiple indoor tests using KMB datasets, which revealed an unexpected loop shape: as the multiplier increases, detection probability and false alarm rate both increase until a limit, and then both contract. Consequently, two detection probabilities correspond to the same false alarm rate, and the higher is achieved at a lower multiplier, which is the desired operating point. Using the Chebyshev s inequality we analytically confirm this shape. Then, we present two improved network-SPRT methods by (a) using the threshold off-set as a weighting factor for the binary decisions from individual detectors in a weighted majority voting fusion rule, and (b) applying a composite SPRT derived using measurements from all counters.« less

Gene–culture coevolution and the nature of human sociality

PubMed Central

Gintis, Herbert

2011-01-01

Human characteristics are the product of gene–culture coevolution, which is an evolutionary dynamic involving the interaction of genes and culture over long time periods. Gene–culture coevolution is a special case of niche construction. Gene–culture coevolution is responsible for human other-regarding preferences, a taste for fairness, the capacity to empathize and salience of morality and character virtues. PMID:21320901
Robustness of coevolution in resolving prisoner's dilemma games on interdependent networks subject to attack

NASA Astrophysics Data System (ADS)

Liu, Penghui; Liu, Jing

2017-08-01

Recently, coevolution between strategy and network structure has been established as a rule to resolve social dilemmas and reach optimal situations for cooperation. Many follow-up researches have focused on studying how coevolution helps networks reorganize to deter the defectors and many coevolution methods have been proposed. However, the robustness of the coevolution rules against attacks have not been studied much. Since attacks may directly influence the original evolutionary process of cooperation, the robustness should be an important index while evaluating the quality of a coevolution method. In this paper, we focus on investigating the robustness of an elementary coevolution method in resolving the prisoner's dilemma game upon the interdependent networks. Three different types of time-independent attacks, named as edge attacks, instigation attacks and node attacks have been employed to test its robustness. Through analyzing the simulation results obtained, we find this coevolution method is relatively robust against the edge attack and the node attack as it successfully maintains cooperation in the population over the entire attack range. However, when the instigation probability of the attacked individuals is large or the attack range of instigation attack is wide enough, coevolutionary rule finally fails in maintaining cooperation in the population.
Model of separation performance of bilinear gradients in scanning format counter-flow gradient electrofocusing techniques.

PubMed

Shameli, Seyed Mostafa; Glawdel, Tomasz; Ren, Carolyn L

2015-03-01

Counter-flow gradient electrofocusing allows the simultaneous concentration and separation of analytes by generating a gradient in the total velocity of each analyte that is the sum of its electrophoretic velocity and the bulk counter-flow velocity. In the scanning format, the bulk counter-flow velocity is varying with time so that a number of analytes with large differences in electrophoretic mobility can be sequentially focused and passed by a single detection point. Studies have shown that nonlinear (such as a bilinear) velocity gradients along the separation channel can improve both peak capacity and separation resolution simultaneously, which cannot be realized by using a single linear gradient. Developing an effective separation system based on the scanning counter-flow nonlinear gradient electrofocusing technique usually requires extensive experimental and numerical efforts, which can be reduced significantly with the help of analytical models for design optimization and guiding experimental studies. Therefore, this study focuses on developing an analytical model to evaluate the separation performance of scanning counter-flow bilinear gradient electrofocusing methods. In particular, this model allows a bilinear gradient and a scanning rate to be optimized for the desired separation performance. The results based on this model indicate that any bilinear gradient provides a higher separation resolution (up to 100%) compared to the linear case. This model is validated by numerical studies. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Unfinished Business: Evolution of the MHC and the Adaptive Immune System of Jawed Vertebrates.

PubMed

Kaufman, Jim

2018-04-26

The major histocompatibility complex (MHC) is a large genetic region with many genes, including the highly polymorphic classical class I and II genes that play crucial roles in adaptive as well as innate immune responses. The organization of the MHC varies enormously among jawed vertebrates, but class I and II genes have not been found in other animals. How did the MHC arise, and are there underlying principles that can help us to understand the evolution of the MHC? This review considers what it means to be an MHC and the potential importance of genome-wide duplication, gene linkage, and gene coevolution for the emergence and evolution of an adaptive immune system. Then it considers what the original antigen-specific receptor and MHC molecule might have looked like, how peptide binding might have evolved, and finally the importance of adaptive immunity in general.
Gα and regulator of G-protein signaling (RGS) protein pairs maintain functional compatibility and conserved interaction interfaces throughout evolution despite frequent loss of RGS proteins in plants.

PubMed

Hackenberg, Dieter; McKain, Michael R; Lee, Soon Goo; Roy Choudhury, Swarup; McCann, Tyler; Schreier, Spencer; Harkess, Alex; Pires, J Chris; Wong, Gane Ka-Shu; Jez, Joseph M; Kellogg, Elizabeth A; Pandey, Sona

2017-10-01

Signaling pathways regulated by heterotrimeric G-proteins exist in all eukaryotes. The regulator of G-protein signaling (RGS) proteins are key interactors and critical modulators of the Gα protein of the heterotrimer. However, while G-proteins are widespread in plants, RGS proteins have been reported to be missing from the entire monocot lineage, with two exceptions. A single amino acid substitution-based adaptive coevolution of the Gα:RGS proteins was proposed to enable the loss of RGS in monocots. We used a combination of evolutionary and biochemical analyses and homology modeling of the Gα and RGS proteins to address their expansion and its potential effects on the G-protein cycle in plants. Our results show that RGS proteins are widely distributed in the monocot lineage, despite their frequent loss. There is no support for the adaptive coevolution of the Gα:RGS protein pair based on single amino acid substitutions. RGS proteins interact with, and affect the activity of, Gα proteins from species with or without endogenous RGS. This cross-functional compatibility expands between the metazoan and plant kingdoms, illustrating striking conservation of their interaction interface. We propose that additional proteins or alternative mechanisms may exist which compensate for the loss of RGS in certain plant species. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.
Coevolution between flight morphology, vertical stratification and sexual dimorphism: what can we learn from tropical butterflies?

PubMed

Graça, M B; Pequeno, P A C L; Franklin, E; Morais, J W

2017-10-01

Occurrence patterns are partly shaped by the affinity of species with habitat conditions. For winged organisms, flight-related attributes are vital for ecological performance. However, due to the different reproductive roles of each sex, we expect divergence in flight energy budget, and consequently different selection responses between sexes. We used tropical frugivorous butterflies as models to investigate coevolution between flight morphology, sex dimorphism and vertical stratification. We studied 94 species of Amazonian fruit-feeding butterflies sampled in seven sites across 3341 ha. We used wing-thorax ratio as a proxy for flight capacity and hierarchical Bayesian modelling to estimate stratum preference. We detected a strong phylogenetic signal in wing-thorax ratio in both sexes. Stouter fast-flying species preferred the canopy, whereas more slender slow-flying species preferred the understorey. However, this relationship was stronger in females than in males, suggesting that female phenotype associates more intimately with habitat conditions. Within species, males were stouter than females and sexual dimorphism was sharper in understorey species. Because trait-habitat relationships were independent from phylogeny, the matching between flight morphology and stratum preference is more likely to reflect adaptive radiation than shared ancestry. This study sheds light on the impact of flight and sexual dimorphism on the evolution and ecological adaptation of flying organisms. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.
Strategic variation in mobbing as a front line of defense against brood parasitism.

PubMed

Welbergen, Justin A; Davies, Nicholas B

2009-02-10

Coevolutionary arms races, where adaptations in one party select for counter-adaptations in another and vice versa, are fundamental to interactions between organisms and their predators, pathogens, and parasites [1]. Avian brood parasites and their hosts have emerged as model systems for studying such reciprocal coevolutionary processes [2, 3]. For example, hosts have evolved changes in egg appearance and rejection of foreign eggs in response to brood parasitism from cuckoos, and cuckoos have evolved host-egg mimicry as a counter-response [4-6]. However, the host's front line of defense is protecting the nest from being parasitized in the first place [7-10], yet little is known about the effectiveness of nest defense as an antiparasite adaptation, and its coevolutionary significance remains poorly understood [10]. Here we show first that mobbing of common cuckoos Cuculus canorus by reed warblers Acrocephalus scirpaceus is an effective defense against parasitism. Second, mobbing of cuckoos is a phenotypically plastic trait that is modified strategically according to local parasitism risk. This supports the view that hosts use a "defense in-depth strategy," with successive flexible lines of defense that coevolve with corresponding offensive lines of the parasite. This highlights the need for more holistic research into the coevolutionary consequences when multiple adaptations and counter-adaptations evolve in concert [11].
Comparative Phylogenetic Studies on Schistosoma japonicum and Its Snail Intermediate Host Oncomelania hupensis: Origins, Dispersal and Coevolution

PubMed Central

Attwood, Stephen W.; Ibaraki, Motomu; Saitoh, Yasuhide; Nihei, Naoko; Janies, Daniel A.

2015-01-01

Background Schistosoma japonicum causes major public health problems in China and the Philippines; this parasite, which is transmitted by freshwater snails of the species Oncomelania hupensis, causes the disease intestinal schistosomiasis in humans and cattle. Researchers working on Schistosoma in Africa have described the relationship between the parasites and their snail intermediate hosts as coevolved or even as an evolutionary arms race. In the present study this hypothesis of coevolution is evaluated for S. japonicum and O. hupensis. The origins and radiation of the snails and the parasite across China, and the taxonomic validity of the sub-species of O. hupensis, are also assessed. Methodology/Principal Findings The findings provide no evidence for coevolution between S. japonicum and O. hupensis, and the phylogeographical analysis suggests a heterochronous radiation of the parasites and snails in response to different palaeogeographical and climatic triggers. The results are consistent with a hypothesis of East to West colonisation of China by Oncomelania with a re-invasion of Japan by O. hupensis from China. The Taiwan population of S. japonicum appears to be recently established in comparison with mainland Chinese populations. Conclusions/Significance The snail and parasite populations of the western mountain region of China (Yunnan and Sichuan) appear to have been isolated from Southeast Asian populations since the Pleistocene; this has implications for road and rail links being constructed in the region, which will breach biogeographical barriers between China and Southeast Asia. The results also have implications for the spread of S. japonicum. In the absence of coevolution, the parasite may more readily colonise new snail populations to which it is not locally adapted, or even new intermediate host species; this can facilitate its dispersal into new areas. Additional work is required to assess further the risk of spread of S. japonicum. PMID:26230619
Culture–gene coevolution of individualism–collectivism and the serotonin transporter gene

PubMed Central

Chiao, Joan Y.; Blizinsky, Katherine D.

2010-01-01

Culture–gene coevolutionary theory posits that cultural values have evolved, are adaptive and influence the social and physical environments under which genetic selection operates. Here, we examined the association between cultural values of individualism–collectivism and allelic frequency of the serotonin transporter functional polymorphism (5-HTTLPR) as well as the role this culture–gene association may play in explaining global variability in prevalence of pathogens and affective disorders. We found evidence that collectivistic cultures were significantly more likely to comprise individuals carrying the short (S) allele of the 5-HTTLPR across 29 nations. Results further show that historical pathogen prevalence predicts cultural variability in individualism–collectivism owing to genetic selection of the S allele. Additionally, cultural values and frequency of S allele carriers negatively predict global prevalence of anxiety and mood disorder. Finally, mediation analyses further indicate that increased frequency of S allele carriers predicted decreased anxiety and mood disorder prevalence owing to increased collectivistic cultural values. Taken together, our findings suggest culture–gene coevolution between allelic frequency of 5-HTTLPR and cultural values of individualism–collectivism and support the notion that cultural values buffer genetically susceptible populations from increased prevalence of affective disorders. Implications of the current findings for understanding culture–gene coevolution of human brain and behaviour as well as how this coevolutionary process may contribute to global variation in pathogen prevalence and epidemiology of affective disorders, such as anxiety and depression, are discussed. PMID:19864286
HIGH VOLTAGE GENERATOR

DOEpatents

Zito, G.V.

1959-04-21

This patent relates to high voltage supply circuits adapted for providing operating voltages for GeigerMueller counter tubes, and is especially directed to an arrangement for maintaining uniform voltage under changing conditions of operation. In the usual power supply arrangement for counter tubes the counter voltage is taken from across the power supply output capacitor. If the count rate exceeds the current delivering capaciiy of the capacitor, the capacitor voltage will drop, decreasing the counter voltage. The present invention provides a multivibrator which has its output voltage controlled by a signal proportional to the counting rate. As the counting rate increases beyond the current delivering capacity of the capacitor, the rectified voltage output from the multivibrator is increased to maintain uniform counter voltage.
Coevolution of dynamical states and interactions in dynamic networks

NASA Astrophysics Data System (ADS)

Zimmermann, Martín G.; Eguíluz, Víctor M.; San Miguel, Maxi

2004-06-01

We explore the coupled dynamics of the internal states of a set of interacting elements and the network of interactions among them. Interactions are modeled by a spatial game and the network of interaction links evolves adapting to the outcome of the game. As an example, we consider a model of cooperation in which the adaptation is shown to facilitate the formation of a hierarchical interaction network that sustains a highly cooperative stationary state. The resulting network has the characteristics of a small world network when a mechanism of local neighbor selection is introduced in the adaptive network dynamics. The highly connected nodes in the hierarchical structure of the network play a leading role in the stability of the network. Perturbations acting on the state of these special nodes trigger global avalanches leading to complete network reorganization.
Pathogen and host genotype differently affect pathogen fitness through their effects on different life-history stages.

PubMed

Bruns, Emily; Carson, Martin; May, Georgiana

2012-08-02

Adaptation of pathogens to their hosts depends critically on factors affecting pathogen reproductive rate. While pathogen reproduction is the end result of an intricate interaction between host and pathogen, the relative contributions of host and pathogen genotype to variation in pathogen life history within the host are not well understood. Untangling these contributions allows us to identify traits with sufficient genetic variation for selection to act and to identify mechanisms of coevolution between pathogens and their hosts. We investigated the effects of pathogen and host genotype on three life-history components of pathogen fitness; infection efficiency, latent period, and sporulation capacity, in the oat crown rust fungus, Puccinia coronata f.sp. avenae, as it infects oats (Avena sativa). We show that both pathogen and host genotype significantly affect total spore production but do so through their effects on different life-history stages. Pathogen genotype has the strongest effect on the early stage of infection efficiency, while host genotype most strongly affects the later life-history stages of latent period and sporulation capacity. In addition, host genotype affected the relationship between pathogen density and the later life-history traits of latent period and sporulation capacity. We did not find evidence of pathogen-by-host genotypic (GxG) interactions. Our results illustrate mechanisms by which variation in host populations will affect the evolution of pathogen life history. Results show that different pathogen life-history stages have the potential to respond differently to selection by host or pathogen genotype and suggest mechanisms of antagonistic coevolution. Pathogen populations may adapt to host genotypes through increased infection efficiency while their plant hosts may adapt by limiting the later stages of pathogen growth and spore production within the host.
Evolution of the CRISPR-Cas adaptive immunity systems in prokaryotes: models and observations on virus-host coevolution.

PubMed

Koonin, Eugene V; Wolf, Yuri I

2015-01-01

CRISPR-Cas is an adaptive immunity system in prokaryotes that functions via a unique mechanism which involves incorporation of foreign DNA fragments into CRISPR arrays and subsequent utilization of transcripts of these inserts (known as spacers) as guide RNAs to cleave the cognate selfish element genome. Multiple attempts have been undertaken to explore the coevolution of viruses and microbial hosts carrying CRISPR-Cas using mathematical models that employ either systems of differential equations or an agent-based approach, or combinations thereof. Analysis of these models reveals highly complex co-evolutionary dynamics that ensues from the combination of the heritability of the CRISPR-mediated adaptive immunity with the existence of different degrees of immunity depending on the number of cognate spacers and the cost of carrying a CRISPR-Cas locus. Depending on the details of the models, a variety of testable, sometimes conflicting predictions have been made on the dependence of the degree of immunity and the benefit of maintaining CRISPR-Cas on the abundance and diversity of hosts and viruses. Some of these predictions have already been directly validated experimentally. In particular, both the reality of the virus-host arms race, with viruses escaping resistance and hosts reacquiring it through the capture of new spacers, and the fitness cost of CRISPR-Cas due to the curtailment of beneficial HGT have been reproduced in the laboratory. However, to test the predictions of the models more specifically, detailed studies of coevolving populations of microbes and viruses both in nature and in the laboratory are essential. Such analyses are expected to yield disagreements with the predictions of the current, oversimplified models and to trigger a new round of theoretical developments.
Cable tester

NASA Astrophysics Data System (ADS)

Rammage, Robert L.

1990-10-01

A device for sequentially testing the plurality of connectors in a wiring harness is disclosed. The harness is attached to the tester by means of adapter cables and a rotary switch is used to sequentially, individually test the connectors by passing a current through the connector. If the connector is unbroken, a light will flash to show it is electrically sound. The adapters allow a large number of cable configurations to be tested using a single tester configuration.
The arms race between heliconiine butterflies and Passiflora plants - new insights on an ancient subject.

PubMed

de Castro, Érika C P; Zagrobelny, Mika; Cardoso, Márcio Z; Bak, Søren

2018-02-01

Heliconiines are called passion vine butterflies because they feed exclusively on Passiflora plants during the larval stage. Many features of Passiflora and heliconiines indicate that they have radiated and speciated in association with each other, and therefore this model system was one of the first examples used to exemplify coevolution theory. Three major adaptations of Passiflora plants supported arguments in favour of their coevolution with heliconiines: unusual variation of leaf shape within the genus; the occurrence of yellow structures mimicking heliconiine eggs; and their extensive diversity of defence compounds called cyanogenic glucosides. However, the protection systems of Passiflora plants go beyond these three features. Trichomes, mimicry of pathogen infection through variegation, and production of extrafloral nectar to attract ants and other predators of their herbivores, are morphological defences reported in this plant genus. Moreover, Passiflora plants are well protected chemically, not only by cyanogenic glucosides, but also by other compounds such as alkaloids, flavonoids, saponins, tannins and phenolics. Heliconiines can synthesize cyanogenic glucosides themselves, and their ability to handle these compounds was probably one of the most crucial adaptations that allowed the ancestor of these butterflies to feed on Passiflora plants. Indeed, it has been shown that Heliconius larvae can sequester cyanogenic glucosides and alkaloids from their host plants and utilize them for their own benefit. Recently, it was discovered that Heliconius adults have highly accurate visual and chemosensory systems, and the expansion of brain structures that can process such information allows them to memorize shapes and display elaborate pre-oviposition behaviour in order to defeat visual barriers evolved by Passiflora species. Even though the heliconiine-Passiflora model system has been intensively studied, the forces driving host-plant preference in these butterflies remain unclear. New studies have shown that host-plant preference seems to be genetically controlled, but in many species there is some plasticity in this choice and preferences can even be induced. Although much knowledge regarding the coevolution of Passiflora plants and heliconiine butterflies has accumulated in recent decades, there remain many exciting unanswered questions concerning this model system. © 2017 Cambridge Philosophical Society.
Mixed strategy and coevolution dynamics in social networks

NASA Astrophysics Data System (ADS)

Zhong, Weicai; Abbass, Hussein A.; Bender, Axel; Liu, Jing

2011-01-01

We investigate coevolution dynamics of both individual strategies and social ties as they adapt within the snowdrift game with mixed strategies. We propose a partner selection mechanism based on the concept of trust. Here trust is considered an instrument for an individual both selecting the right partners and being selected amongst other potential partners. Based on her local views of the system, the focal individual dismisses the link from the partner with the lowest trust and rewires to the partner’s partner with the highest trust. It is shown that such a trust-based partner switching mechanism favors the emergence of cooperators. Furthermore, when the number of an individual’s partners is restricted (which is a metaphor of limited capacities and capabilities of an individual in real environments), surprising assortative mixing patterns are formed in the emerging network and change the network’s degree distribution from a power-law distribution to an asymmetrically U-shaped distribution. This plays a leading role in preventing global avalanches triggered by perturbations acting on the state of the highly connected individuals.
Evolutionary dynamics of interactions between plants and their enemies: comparison of herbivorous insects and pathogens.

PubMed

Wininger, Kerry; Rank, Nathan

2017-11-01

Plants colonized land over 400 million years ago. Shortly thereafter, organisms began to consume terrestrial plant tissue as a nutritional resource. Most plant enemies are plant pathogens or herbivores, and they impose natural selection for plants to evolve defenses. These traits generate selection pressures on enemies. Coevolution between terrestrial plants and their enemies is an important element of the evolutionary history of both groups. However, coevolutionary studies of plant-pathogen interactions have tended to focus on different research topics than plant-herbivore interactions. Specifically, studies of plant-pathogen interactions often adopt a "gene-for-gene" conceptual framework. In contrast, studies of plants and herbivores often investigate escalation or elaboration of plant defense and herbivore adaptations to overcome it. The main exceptions to the general pattern are studies that focus on small, sessile herbivores that share many features with plant pathogens, studies that incorporate both herbivores and pathogens into a single investigation, and studies that test aspects of Thompson's geographic mosaic theory for coevolution. We discuss the implications of these findings for future research. © 2017 New York Academy of Sciences.
Clustered marginalization of minorities during social transitions induced by co-evolution of behaviour and network structure

PubMed Central

Schleussner, Carl-Friedrich; Donges, Jonathan F.; Engemann, Denis A.; Levermann, Anders

2016-01-01

Large-scale transitions in societies are associated with both individual behavioural change and restructuring of the social network. These two factors have often been considered independently, yet recent advances in social network research challenge this view. Here we show that common features of societal marginalization and clustering emerge naturally during transitions in a co-evolutionary adaptive network model. This is achieved by explicitly considering the interplay between individual interaction and a dynamic network structure in behavioural selection. We exemplify this mechanism by simulating how smoking behaviour and the network structure get reconfigured by changing social norms. Our results are consistent with empirical findings: The prevalence of smoking was reduced, remaining smokers were preferentially connected among each other and formed increasingly marginalized clusters. We propose that self-amplifying feedbacks between individual behaviour and dynamic restructuring of the network are main drivers of the transition. This generative mechanism for co-evolution of individual behaviour and social network structure may apply to a wide range of examples beyond smoking. PMID:27510641
Climate adaptation and speciation: particular focus on reproductive barriers in Ficedula flycatchers.

PubMed

Qvarnström, Anna; Ålund, Murielle; McFarlane, S Eryn; Sirkiä, Päivi M

2016-01-01

Climate adaptation is surprisingly rarely reported as a cause for the build-up of reproductive isolation between diverging populations. In this review, we summarize evidence for effects of climate adaptation on pre- and postzygotic isolation between emerging species with a particular focus on pied (Ficedula hypoleuca) and collared (Ficedula albicollis) flycatchers as a model for research on speciation. Effects of climate adaptation on prezygotic isolation or extrinsic selection against hybrids have been documented in several taxa, but the combined action of climate adaptation and sexual selection is particularly well explored in Ficedula flycatchers. There is a general lack of evidence for divergent climate adaptation causing intrinsic postzygotic isolation. However, we argue that the profound effects of divergence in climate adaptation on the whole biochemical machinery of organisms and hence many underlying genes should increase the likelihood of genetic incompatibilities arising as side effects. Fast temperature-dependent co-evolution between mitochondrial and nuclear genomes may be particularly likely to lead to hybrid sterility. Thus, how climate adaptation relates to reproductive isolation is best explored in relation to fast-evolving barriers to gene flow, while more research on later stages of divergence is needed to achieve a complete understanding of climate-driven speciation.
Flexible sequential designs for multi-arm clinical trials.

PubMed

Magirr, D; Stallard, N; Jaki, T

2014-08-30

Adaptive designs that are based on group-sequential approaches have the benefit of being efficient as stopping boundaries can be found that lead to good operating characteristics with test decisions based solely on sufficient statistics. The drawback of these so called 'pre-planned adaptive' designs is that unexpected design changes are not possible without impacting the error rates. 'Flexible adaptive designs' on the other hand can cope with a large number of contingencies at the cost of reduced efficiency. In this work, we focus on two different approaches for multi-arm multi-stage trials, which are based on group-sequential ideas, and discuss how these 'pre-planned adaptive designs' can be modified to allow for flexibility. We then show how the added flexibility can be used for treatment selection and sample size reassessment and evaluate the impact on the error rates in a simulation study. The results show that an impressive overall procedure can be found by combining a well chosen pre-planned design with an application of the conditional error principle to allow flexible treatment selection. Copyright © 2014 John Wiley & Sons, Ltd.

Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution.

PubMed

Cavalier-Smith, Thomas

2010-02-04

The transition from prokaryotes to eukaryotes was the most radical change in cell organisation since life began, with the largest ever burst of gene duplication and novelty. According to the coevolutionary theory of eukaryote origins, the fundamental innovations were the concerted origins of the endomembrane system and cytoskeleton, subsequently recruited to form the cell nucleus and coevolving mitotic apparatus, with numerous genetic eukaryotic novelties inevitable consequences of this compartmentation and novel DNA segregation mechanism. Physical and mutational mechanisms of origin of the nucleus are seldom considered beyond the long-standing assumption that it involved wrapping pre-existing endomembranes around chromatin. Discussions on the origin of sex typically overlook its association with protozoan entry into dormant walled cysts and the likely simultaneous coevolutionary, not sequential, origin of mitosis and meiosis. I elucidate nuclear and mitotic coevolution, explaining the origins of dicer and small centromeric RNAs for positionally controlling centromeric heterochromatin, and how 27 major features of the cell nucleus evolved in four logical stages, making both mechanisms and selective advantages explicit: two initial stages (origin of 30 nm chromatin fibres, enabling DNA compaction; and firmer attachment of endomembranes to heterochromatin) protected DNA and nascent RNA from shearing by novel molecular motors mediating vesicle transport, division, and cytoplasmic motility. Then octagonal nuclear pore complexes (NPCs) arguably evolved from COPII coated vesicle proteins trapped in clumps by Ran GTPase-mediated cisternal fusion that generated the fenestrated nuclear envelope, preventing lethal complete cisternal fusion, and allowing passive protein and RNA exchange. Finally, plugging NPC lumens by an FG-nucleoporin meshwork and adopting karyopherins for nucleocytoplasmic exchange conferred compartmentation advantages. These successive changes took place in naked growing cells, probably as indirect consequences of the origin of phagotrophy. The first eukaryote had 1-2 cilia and also walled resting cysts; I outline how encystation may have promoted the origin of meiotic sex. I also explain why many alternative ideas are inadequate. Nuclear pore complexes are evolutionary chimaeras of endomembrane- and mitosis-related chromatin-associated proteins. The keys to understanding eukaryogenesis are a proper phylogenetic context and understanding organelle coevolution: how innovations in one cell component caused repercussions on others.
Mechanisms and Evidence of Genital Coevolution: The Roles of Natural Selection, Mate Choice, and Sexual Conflict

PubMed Central

Brennan, Patricia L.R.; Prum, Richard O.

2015-01-01

Genital coevolution between the sexes is expected to be common because of the direct interaction between male and female genitalia during copulation. Here we review the diverse mechanisms of genital coevolution that include natural selection, female mate choice, male–male competition, and how their interactions generate sexual conflict that can lead to sexually antagonistic coevolution. Natural selection on genital morphology will result in size coevolution to allow for copulation to be mechanically possible, even as other features of genitalia may reflect the action of other mechanisms of selection. Genital coevolution is explicitly predicted by at least three mechanisms of genital evolution: lock and key to prevent hybridization, female choice, and sexual conflict. Although some good examples exist in support of each of these mechanisms, more data on quantitative female genital variation and studies of functional morphology during copulation are needed to understand more general patterns. A combination of different approaches is required to continue to advance our understanding of genital coevolution. Knowledge of the ecology and behavior of the studied species combined with functional morphology, quantitative morphological tools, experimental manipulation, and experimental evolution have been provided in the best-studied species, all of which are invertebrates. Therefore, attention to vertebrates in any of these areas is badly needed. PMID:26134314
Sexual conflict over the maintenance of sex: effects of sexually antagonistic coevolution for reproductive isolation of parthenogenesis.

PubMed

Kawatsu, Kazutaka

2013-01-01

Sexual reproduction involves many costs. Therefore, females acquiring a capacity for parthenogenetic (or asexual) reproduction will gain a reproductive advantage over obligately sexual females. In contrast, for males, any trait coercing parthenogens into sexual reproduction (male coercion) increases their fitness and should be under positive selection because parthenogenesis deprives them of their genetic contribution to future generations. Surprisingly, although such sexual conflict is a possible outcome whenever reproductive isolation is incomplete between parthenogens and the sexual ancestors, it has not been given much attention in the studies of the maintenance of sex. Using two mathematical models, I show here that the evolution of male coercion substantially favours the maintenance of sex even though a female barrier against the coercion can evolve. First, the model based on adaptive-dynamics theory demonstrates that the resultant antagonistic coevolution between male coercion and a female barrier fundamentally ends in either the prevalence of sex or the co-occurrence of two reproductive modes. This is because the coevolution between the two traits additionally involves sex-ratio selection, that is, an increase in parthenogenetic reproduction leads to a female-biased population sex ratio, which will enhance reproductive success of more coercive males and directly promotes the evolution of the coercion among males. Therefore, as shown by the individual-based model, the establishment of obligate parthenogenesis in the population requires the simultaneous evolution of strong reproductive isolation between males and parthenogens. These findings should shed light on the interspecific diversity of reproductive modes as well as help to explain the prevalence of sexual reproduction.
Sexual Conflict over the Maintenance of Sex: Effects of Sexually Antagonistic Coevolution for Reproductive Isolation of Parthenogenesis

PubMed Central

Kawatsu, Kazutaka

2013-01-01

Sexual reproduction involves many costs. Therefore, females acquiring a capacity for parthenogenetic (or asexual) reproduction will gain a reproductive advantage over obligately sexual females. In contrast, for males, any trait coercing parthenogens into sexual reproduction (male coercion) increases their fitness and should be under positive selection because parthenogenesis deprives them of their genetic contribution to future generations. Surprisingly, although such sexual conflict is a possible outcome whenever reproductive isolation is incomplete between parthenogens and the sexual ancestors, it has not been given much attention in the studies of the maintenance of sex. Using two mathematical models, I show here that the evolution of male coercion substantially favours the maintenance of sex even though a female barrier against the coercion can evolve. First, the model based on adaptive-dynamics theory demonstrates that the resultant antagonistic coevolution between male coercion and a female barrier fundamentally ends in either the prevalence of sex or the co-occurrence of two reproductive modes. This is because the coevolution between the two traits additionally involves sex-ratio selection, that is, an increase in parthenogenetic reproduction leads to a female-biased population sex ratio, which will enhance reproductive success of more coercive males and directly promotes the evolution of the coercion among males. Therefore, as shown by the individual-based model, the establishment of obligate parthenogenesis in the population requires the simultaneous evolution of strong reproductive isolation between males and parthenogens. These findings should shed light on the interspecific diversity of reproductive modes as well as help to explain the prevalence of sexual reproduction. PMID:23469150
Counter-propagation network with variable degree variable step size LMS for single switch typing recognition.

PubMed

Yang, Cheng-Huei; Luo, Ching-Hsing; Yang, Cheng-Hong; Chuang, Li-Yeh

2004-01-01

Morse code is now being harnessed for use in rehabilitation applications of augmentative-alternative communication and assistive technology, including mobility, environmental control and adapted worksite access. In this paper, Morse code is selected as a communication adaptive device for disabled persons who suffer from muscle atrophy, cerebral palsy or other severe handicaps. A stable typing rate is strictly required for Morse code to be effective as a communication tool. This restriction is a major hindrance. Therefore, a switch adaptive automatic recognition method with a high recognition rate is needed. The proposed system combines counter-propagation networks with a variable degree variable step size LMS algorithm. It is divided into five stages: space recognition, tone recognition, learning process, adaptive processing, and character recognition. Statistical analyses demonstrated that the proposed method elicited a better recognition rate in comparison to alternative methods in the literature.
Mitochondrial phylogenomics of Hemiptera reveals adaptive innovations driving the diversification of true bugs

PubMed Central

Li, Hu; Leavengood, John M.; Chapman, Eric G.; Burkhardt, Daniel; Song, Fan; Jiang, Pei; Liu, Jinpeng; Cai, Wanzhi

2017-01-01

Hemiptera, the largest non-holometabolous order of insects, represents approximately 7% of metazoan diversity. With extraordinary life histories and highly specialized morphological adaptations, hemipterans have exploited diverse habitats and food sources through approximately 300 Myr of evolution. To elucidate the phylogeny and evolutionary history of Hemiptera, we carried out the most comprehensive mitogenomics analysis on the richest taxon sampling to date covering all the suborders and infraorders, including 34 newly sequenced and 94 published mitogenomes. With optimized branch length and sequence heterogeneity, Bayesian analyses using a site-heterogeneous mixture model resolved the higher-level hemipteran phylogeny as (Sternorrhyncha, (Auchenorrhyncha, (Coleorrhyncha, Heteroptera))). Ancestral character state reconstruction and divergence time estimation suggest that the success of true bugs (Heteroptera) is probably due to angiosperm coevolution, but key adaptive innovations (e.g. prognathous mouthpart, predatory behaviour, and haemelytron) facilitated multiple independent shifts among diverse feeding habits and multiple independent colonizations of aquatic habitats. PMID:28878063
Eco-evolutionary dynamics in a coevolving host-virus system.

PubMed

Frickel, Jens; Sieber, Michael; Becks, Lutz

2016-04-01

Eco-evolutionary dynamics have been shown to be important for understanding population and community stability and their adaptive potential. However, coevolution in the framework of eco-evolutionary theory has not been addressed directly. Combining experiments with an algal host and its viral parasite, and mathematical model analyses we show eco-evolutionary dynamics in antagonistic coevolving populations. The interaction between antagonists initially resulted in arms race dynamics (ARD) with selective sweeps, causing oscillating host-virus population dynamics. However, ARD ended and populations stabilised after the evolution of a general resistant host, whereas a trade-off between host resistance and growth then maintained host diversity over time (trade-off driven dynamics). Most importantly, our study shows that the interaction between ecology and evolution had important consequences for the predictability of the mode and tempo of adaptive change and for the stability and adaptive potential of populations. © 2016 John Wiley & Sons Ltd/CNRS.
Carryover effects from natal habitat type upon competitive ability lead to trait divergence or source-sink dynamics.

PubMed

Kristensen, Nadiah Pardede; Johansson, Jacob; Chisholm, Ryan A; Smith, Henrik G; Kokko, Hanna

2018-06-25

Local adaptation to rare habitats is difficult due to gene flow, but can occur if the habitat has higher productivity. Differences in offspring phenotypes have attracted little attention in this context. We model a scenario where the rarer habitat improves offspring's later competitive ability - a carryover effect that operates on top of local adaptation to one or the other habitat type. Assuming localised dispersal, so the offspring tend to settle in similar habitat to the natal type, the superior competitive ability of offspring remaining in the rarer habitat hampers immigration from the majority habitat. This initiates a positive feedback between local adaptation and trait divergence, which can thereafter be reinforced by coevolution with dispersal traits that match ecotype to habitat type. Rarity strengthens selection on dispersal traits and promotes linkage disequilibrium between locally adapted traits and ecotype-habitat matching dispersal. We propose that carryover effects may initiate isolation by ecology. © 2018 The Authors. Ecology Letters published by CNRS and John Wiley & Sons Ltd.
Macroscopic description of complex adaptive networks coevolving with dynamic node states

NASA Astrophysics Data System (ADS)

Wiedermann, Marc; Donges, Jonathan F.; Heitzig, Jobst; Lucht, Wolfgang; Kurths, Jürgen

2015-05-01

In many real-world complex systems, the time evolution of the network's structure and the dynamic state of its nodes are closely entangled. Here we study opinion formation and imitation on an adaptive complex network which is dependent on the individual dynamic state of each node and vice versa to model the coevolution of renewable resources with the dynamics of harvesting agents on a social network. The adaptive voter model is coupled to a set of identical logistic growth models and we mainly find that, in such systems, the rate of interactions between nodes as well as the adaptive rewiring probability are crucial parameters for controlling the sustainability of the system's equilibrium state. We derive a macroscopic description of the system in terms of ordinary differential equations which provides a general framework to model and quantify the influence of single node dynamics on the macroscopic state of the network. The thus obtained framework is applicable to many fields of study, such as epidemic spreading, opinion formation, or socioecological modeling.
Macroscopic description of complex adaptive networks coevolving with dynamic node states.

PubMed

Wiedermann, Marc; Donges, Jonathan F; Heitzig, Jobst; Lucht, Wolfgang; Kurths, Jürgen

2015-05-01

In many real-world complex systems, the time evolution of the network's structure and the dynamic state of its nodes are closely entangled. Here we study opinion formation and imitation on an adaptive complex network which is dependent on the individual dynamic state of each node and vice versa to model the coevolution of renewable resources with the dynamics of harvesting agents on a social network. The adaptive voter model is coupled to a set of identical logistic growth models and we mainly find that, in such systems, the rate of interactions between nodes as well as the adaptive rewiring probability are crucial parameters for controlling the sustainability of the system's equilibrium state. We derive a macroscopic description of the system in terms of ordinary differential equations which provides a general framework to model and quantify the influence of single node dynamics on the macroscopic state of the network. The thus obtained framework is applicable to many fields of study, such as epidemic spreading, opinion formation, or socioecological modeling.
Exposure Control Using Adaptive Multi-Stage Item Bundles.

ERIC Educational Resources Information Center

Luecht, Richard M.

This paper presents a multistage adaptive testing test development paradigm that promises to handle content balancing and other test development needs, psychometric reliability concerns, and item exposure. The bundled multistage adaptive testing (BMAT) framework is a modification of the computer-adaptive sequential testing framework introduced by…
Detecting sexually antagonistic coevolution with population crosses.

PubMed

Rowe, Locke; Cameron, Erin; Day, Troy

2003-10-07

The result of population crosses on traits such as mating rate, oviposition rate and survivorship are increasingly used to distinguish between modes of coevolution between the sexes. Two key hypotheses, erected from a verbal theory of sexually antagonistic coevolution, have been the subject of several recent tests. First, statistical interactions arising in population crosses are suggested to be indicative of a complex signal/receiver system. In the case of oviposition rates, an interaction between populations (x, y and z) would be indicated by the rank order of female oviposition rates achieved by x, y and z males changing depending upon the female (x, y or z) with which they mated. Second, under sexually antagonistic coevolution females will do 'best' when mated with their own males, where best is defined by the weakest response to the signal and the highest fitness. We test these hypotheses by crossing strains generated from a formal model of sexually antagonistic coevolution. Strains differ in the strength of natural selection acting on male and female traits. In our model, we assume sexually antagonistic coevolution of a single male signal and female receptor. The female receptor is treated as a preference function where both the slope and intercept of the function can evolve. Our results suggest that neither prediction is consistently supported. Interactions are not diagnostic of complex signal-receiver systems, and even under sexually antagonistic coevolution, females may do better mating with males of strains other than their own. These results suggest a reinterpretation of several recent experiments and have important implications for developing theories of speciation when sexually antagonistic coevolution is involved.
A comparison of sequential and spiral scanning techniques in brain CT.

PubMed

Pace, Ivana; Zarb, Francis

2015-01-01

To evaluate and compare image quality and radiation dose of sequential computed tomography (CT) examinations of the brain and spiral CT examinations of the brain imaged on a GE HiSpeed NX/I Dual Slice 2CT scanner. A random sample of 40 patients referred for CT examination of the brain was selected and divided into 2 groups. Half of the patients were scanned using the sequential technique; the other half were scanned using the spiral technique. Radiation dose data—both the computed tomography dose index (CTDI) and the dose length product (DLP)—were recorded on a checklist at the end of each examination. Using the European Guidelines on Quality Criteria for Computed Tomography, 4 radiologists conducted a visual grading analysis and rated the level of visibility of 6 anatomical structures considered necessary to produce images of high quality. The mean CTDI(vol) and DLP values were statistically significantly higher (P <.05) with the sequential scans (CTDI(vol): 22.06 mGy; DLP: 304.60 mGy • cm) than with the spiral scans (CTDI(vol): 14.94 mGy; DLP: 229.10 mGy • cm). The mean image quality rating scores for all criteria of the sequential scanning technique were statistically significantly higher (P <.05) in the visual grading analysis than those of the spiral scanning technique. In this local study, the sequential technique was preferred over the spiral technique for both overall image quality and differentiation between gray and white matter in brain CT scans. Other similar studies counter this finding. The radiation dose seen with the sequential CT scanning technique was significantly higher than that seen with the spiral CT scanning technique. However, image quality with the sequential technique was statistically significantly superior (P <.05).
PULSE COUNTER

DOEpatents

Trumbo, D.E.

1959-02-10

A transistorized pulse-counting circuit adapted for use with nuclear radiation detecting detecting devices to provide a small, light weight portable counter is reported. The small size and low power requirements of the transistor are of particular value in this instance. The circuit provides an adjustable count scale with a single transistor which is triggered by the accumulated charge on a storage capacitor.
Taking a Broad Approach to Public Health Program Adaptation: Adapting a Family-Based Diabetes Education Program

ERIC Educational Resources Information Center

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.

2010-01-01

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…
Molecular mechanisms of adaptation emerging from the physics and evolution of nucleic acids and proteins.

PubMed

Goncearenco, Alexander; Ma, Bin-Guang; Berezovsky, Igor N

2014-03-01

DNA, RNA and proteins are major biological macromolecules that coevolve and adapt to environments as components of one highly interconnected system. We explore here sequence/structure determinants of mechanisms of adaptation of these molecules, links between them, and results of their mutual evolution. We complemented statistical analysis of genomic and proteomic sequences with folding simulations of RNA molecules, unraveling causal relations between compositional and sequence biases reflecting molecular adaptation on DNA, RNA and protein levels. We found many compositional peculiarities related to environmental adaptation and the life style. Specifically, thermal adaptation of protein-coding sequences in Archaea is characterized by a stronger codon bias than in Bacteria. Guanine and cytosine load in the third codon position is important for supporting the aerobic life style, and it is highly pronounced in Bacteria. The third codon position also provides a tradeoff between arginine and lysine, which are favorable for thermal adaptation and aerobicity, respectively. Dinucleotide composition provides stability of nucleic acids via strong base-stacking in ApG dinucleotides. In relation to coevolution of nucleic acids and proteins, thermostability-related demands on the amino acid composition affect the nucleotide content in the second codon position in Archaea.
Molecular mechanisms of adaptation emerging from the physics and evolution of nucleic acids and proteins

PubMed Central

Goncearenco, Alexander; Ma, Bin-Guang; Berezovsky, Igor N.

2014-01-01

DNA, RNA and proteins are major biological macromolecules that coevolve and adapt to environments as components of one highly interconnected system. We explore here sequence/structure determinants of mechanisms of adaptation of these molecules, links between them, and results of their mutual evolution. We complemented statistical analysis of genomic and proteomic sequences with folding simulations of RNA molecules, unraveling causal relations between compositional and sequence biases reflecting molecular adaptation on DNA, RNA and protein levels. We found many compositional peculiarities related to environmental adaptation and the life style. Specifically, thermal adaptation of protein-coding sequences in Archaea is characterized by a stronger codon bias than in Bacteria. Guanine and cytosine load in the third codon position is important for supporting the aerobic life style, and it is highly pronounced in Bacteria. The third codon position also provides a tradeoff between arginine and lysine, which are favorable for thermal adaptation and aerobicity, respectively. Dinucleotide composition provides stability of nucleic acids via strong base-stacking in ApG dinucleotides. In relation to coevolution of nucleic acids and proteins, thermostability-related demands on the amino acid composition affect the nucleotide content in the second codon position in Archaea. PMID:24371267
A protein coevolution method uncovers critical features of the Hepatitis C Virus fusion mechanism

PubMed Central

Douam, Florian; Mancip, Jimmy; Mailly, Laurent; Montserret, Roland; Ding, Qiang; Verhoeyen, Els; Baumert, Thomas F.; Ploss, Alexander; Carbone, Alessandra

2018-01-01

Amino-acid coevolution can be referred to mutational compensatory patterns preserving the function of a protein. Viral envelope glycoproteins, which mediate entry of enveloped viruses into their host cells, are shaped by coevolution signals that confer to viruses the plasticity to evade neutralizing antibodies without altering viral entry mechanisms. The functions and structures of the two envelope glycoproteins of the Hepatitis C Virus (HCV), E1 and E2, are poorly described. Especially, how these two proteins mediate the HCV fusion process between the viral and the cell membrane remains elusive. Here, as a proof of concept, we aimed to take advantage of an original coevolution method recently developed to shed light on the HCV fusion mechanism. When first applied to the well-characterized Dengue Virus (DENV) envelope glycoproteins, coevolution analysis was able to predict important structural features and rearrangements of these viral protein complexes. When applied to HCV E1E2, computational coevolution analysis predicted that E1 and E2 refold interdependently during fusion through rearrangements of the E2 Back Layer (BL). Consistently, a soluble BL-derived polypeptide inhibited HCV infection of hepatoma cell lines, primary human hepatocytes and humanized liver mice. We showed that this polypeptide specifically inhibited HCV fusogenic rearrangements, hence supporting the critical role of this domain during HCV fusion. By combining coevolution analysis and in vitro assays, we also uncovered functionally-significant coevolving signals between E1 and E2 BL/Stem regions that govern HCV fusion, demonstrating the accuracy of our coevolution predictions. Altogether, our work shed light on important structural features of the HCV fusion mechanism and contributes to advance our functional understanding of this process. This study also provides an important proof of concept that coevolution can be employed to explore viral protein mediated-processes, and can guide the development of innovative translational strategies against challenging human-tropic viruses. PMID:29505618
Synthesizing genetic sequential logic circuit with clock pulse generator.

PubMed

Chuang, Chia-Hua; Lin, Chun-Liang

2014-05-28

Rhythmic clock widely occurs in biological systems which controls several aspects of cell physiology. For the different cell types, it is supplied with various rhythmic frequencies. How to synthesize a specific clock signal is a preliminary but a necessary step to further development of a biological computer in the future. This paper presents a genetic sequential logic circuit with a clock pulse generator based on a synthesized genetic oscillator, which generates a consecutive clock signal whose frequency is an inverse integer multiple to that of the genetic oscillator. An analogous electronic waveform-shaping circuit is constructed by a series of genetic buffers to shape logic high/low levels of an oscillation input in a basic sinusoidal cycle and generate a pulse-width-modulated (PWM) output with various duty cycles. By controlling the threshold level of the genetic buffer, a genetic clock pulse signal with its frequency consistent to the genetic oscillator is synthesized. A synchronous genetic counter circuit based on the topology of the digital sequential logic circuit is triggered by the clock pulse to synthesize the clock signal with an inverse multiple frequency to the genetic oscillator. The function acts like a frequency divider in electronic circuits which plays a key role in the sequential logic circuit with specific operational frequency. A cascaded genetic logic circuit generating clock pulse signals is proposed. Based on analogous implement of digital sequential logic circuits, genetic sequential logic circuits can be constructed by the proposed approach to generate various clock signals from an oscillation signal.
Modeling Coevolution between Language and Memory Capacity during Language Origin

PubMed Central

Gong, Tao; Shuai, Lan

2015-01-01

Memory is essential to many cognitive tasks including language. Apart from empirical studies of memory effects on language acquisition and use, there lack sufficient evolutionary explorations on whether a high level of memory capacity is prerequisite for language and whether language origin could influence memory capacity. In line with evolutionary theories that natural selection refined language-related cognitive abilities, we advocated a coevolution scenario between language and memory capacity, which incorporated the genetic transmission of individual memory capacity, cultural transmission of idiolects, and natural and cultural selections on individual reproduction and language teaching. To illustrate the coevolution dynamics, we adopted a multi-agent computational model simulating the emergence of lexical items and simple syntax through iterated communications. Simulations showed that: along with the origin of a communal language, an initially-low memory capacity for acquired linguistic knowledge was boosted; and such coherent increase in linguistic understandability and memory capacities reflected a language-memory coevolution; and such coevolution stopped till memory capacities became sufficient for language communications. Statistical analyses revealed that the coevolution was realized mainly by natural selection based on individual communicative success in cultural transmissions. This work elaborated the biology-culture parallelism of language evolution, demonstrated the driving force of culturally-constituted factors for natural selection of individual cognitive abilities, and suggested that the degree difference in language-related cognitive abilities between humans and nonhuman animals could result from a coevolution with language. PMID:26544876

Mechanisms and Evidence of Genital Coevolution: The Roles of Natural Selection, Mate Choice, and Sexual Conflict.

PubMed

Brennan, Patricia L R; Prum, Richard O

2015-07-01

Genital coevolution between the sexes is expected to be common because of the direct interaction between male and female genitalia during copulation. Here we review the diverse mechanisms of genital coevolution that include natural selection, female mate choice, male-male competition, and how their interactions generate sexual conflict that can lead to sexually antagonistic coevolution. Natural selection on genital morphology will result in size coevolution to allow for copulation to be mechanically possible, even as other features of genitalia may reflect the action of other mechanisms of selection. Genital coevolution is explicitly predicted by at least three mechanisms of genital evolution: lock and key to prevent hybridization, female choice, and sexual conflict. Although some good examples exist in support of each of these mechanisms, more data on quantitative female genital variation and studies of functional morphology during copulation are needed to understand more general patterns. A combination of different approaches is required to continue to advance our understanding of genital coevolution. Knowledge of the ecology and behavior of the studied species combined with functional morphology, quantitative morphological tools, experimental manipulation, and experimental evolution have been provided in the best-studied species, all of which are invertebrates. Therefore, attention to vertebrates in any of these areas is badly needed. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.
Modeling Coevolution between Language and Memory Capacity during Language Origin.

PubMed

Gong, Tao; Shuai, Lan

2015-01-01

Memory is essential to many cognitive tasks including language. Apart from empirical studies of memory effects on language acquisition and use, there lack sufficient evolutionary explorations on whether a high level of memory capacity is prerequisite for language and whether language origin could influence memory capacity. In line with evolutionary theories that natural selection refined language-related cognitive abilities, we advocated a coevolution scenario between language and memory capacity, which incorporated the genetic transmission of individual memory capacity, cultural transmission of idiolects, and natural and cultural selections on individual reproduction and language teaching. To illustrate the coevolution dynamics, we adopted a multi-agent computational model simulating the emergence of lexical items and simple syntax through iterated communications. Simulations showed that: along with the origin of a communal language, an initially-low memory capacity for acquired linguistic knowledge was boosted; and such coherent increase in linguistic understandability and memory capacities reflected a language-memory coevolution; and such coevolution stopped till memory capacities became sufficient for language communications. Statistical analyses revealed that the coevolution was realized mainly by natural selection based on individual communicative success in cultural transmissions. This work elaborated the biology-culture parallelism of language evolution, demonstrated the driving force of culturally-constituted factors for natural selection of individual cognitive abilities, and suggested that the degree difference in language-related cognitive abilities between humans and nonhuman animals could result from a coevolution with language.
Sequential decision making in computational sustainability via adaptive submodularity

USGS Publications Warehouse

Krause, Andreas; Golovin, Daniel; Converse, Sarah J.

2015-01-01

Many problems in computational sustainability require making a sequence of decisions in complex, uncertain environments. Such problems are generally notoriously difficult. In this article, we review the recently discovered notion of adaptive submodularity, an intuitive diminishing returns condition that generalizes the classical notion of submodular set functions to sequential decision problems. Problems exhibiting the adaptive submodularity property can be efficiently and provably near-optimally solved using simple myopic policies. We illustrate this concept in several case studies of interest in computational sustainability: First, we demonstrate how it can be used to efficiently plan for resolving uncertainty in adaptive management scenarios. Secondly, we show how it applies to dynamic conservation planning for protecting endangered species, a case study carried out in collaboration with the US Geological Survey and the US Fish and Wildlife Service.
Accurate Simulation and Detection of Coevolution Signals in Multiple Sequence Alignments

PubMed Central

Ackerman, Sharon H.; Tillier, Elisabeth R.; Gatti, Domenico L.

2012-01-01

Background While the conserved positions of a multiple sequence alignment (MSA) are clearly of interest, non-conserved positions can also be important because, for example, destabilizing effects at one position can be compensated by stabilizing effects at another position. Different methods have been developed to recognize the evolutionary relationship between amino acid sites, and to disentangle functional/structural dependencies from historical/phylogenetic ones. Methodology/Principal Findings We have used two complementary approaches to test the efficacy of these methods. In the first approach, we have used a new program, MSAvolve, for the in silico evolution of MSAs, which records a detailed history of all covarying positions, and builds a global coevolution matrix as the accumulated sum of individual matrices for the positions forced to co-vary, the recombinant coevolution, and the stochastic coevolution. We have simulated over 1600 MSAs for 8 protein families, which reflect sequences of different sizes and proteins with widely different functions. The calculated coevolution matrices were compared with the coevolution matrices obtained for the same evolved MSAs with different coevolution detection methods. In a second approach we have evaluated the capacity of the different methods to predict close contacts in the representative X-ray structures of an additional 150 protein families using only experimental MSAs. Conclusions/Significance Methods based on the identification of global correlations between pairs were found to be generally superior to methods based only on local correlations in their capacity to identify coevolving residues using either simulated or experimental MSAs. However, the significant variability in the performance of different methods with different proteins suggests that the simulation of MSAs that replicate the statistical properties of the experimental MSA can be a valuable tool to identify the coevolution detection method that is most effective in each case. PMID:23091608
The 4A Metric Algorithm: A Unique E-Learning Engineering Solution Designed via Neuroscience to Counter Cheating and Reduce Its Recidivism by Measuring Student Growth through Systemic Sequential Online Learning

ERIC Educational Resources Information Center

Osler, James Edward

2016-01-01

This paper provides a novel instructional methodology that is a unique E-Learning engineered "4A Metric Algorithm" designed to conceptually address the four main challenges faced by 21st century students, who are tempted to cheat in a myriad of higher education settings (face to face, hybrid, and online). The algorithmic online…
Argument structure hierarchy system and method for facilitating analysis and decision-making processes

DOEpatents

Janssen, Terry

2000-01-01

A system and method for facilitating decision-making comprising a computer program causing linkage of data representing a plurality of argument structure units into a hierarchical argument structure. Each argument structure unit comprises data corresponding to a hypothesis and its corresponding counter-hypothesis, data corresponding to grounds that provide a basis for inference of the hypothesis or its corresponding counter-hypothesis, data corresponding to a warrant linking the grounds to the hypothesis or its corresponding counter-hypothesis, and data corresponding to backing that certifies the warrant. The hierarchical argument structure comprises a top level argument structure unit and a plurality of subordinate level argument structure units. Each of the plurality of subordinate argument structure units comprises at least a portion of the grounds of the argument structure unit to which it is subordinate. Program code located on each of a plurality of remote computers accepts input from one of a plurality of contributors. Each input comprises data corresponding to an argument structure unit in the hierarchical argument structure and supports the hypothesis or its corresponding counter-hypothesis. A second programming code is adapted to combine the inputs into a single hierarchical argument structure. A third computer program code is responsive to the second computer program code and is adapted to represent a degree of support for the hypothesis and its corresponding counter-hypothesis in the single hierarchical argument structure.
Raising Darwin's consciousness : Female sexuality and the prehominid origins of patriarchy.

PubMed

Hrdy, S B

1997-03-01

Sociobiologists and feminists agree that men in patriarchal social systems seek to control females, but sociobiologists go further, using Darwin's theory of sexual selection and Trivers's ideas on parental investment to explain why males should attempt to control female sexuality. From this perspective, the stage for the development under some conditions of patriarchal social systems was set over the course of primate evolution.Sexual selection encompasses both competition between males and female choice. But in applying this theory to our "lower origins" (prehominid ancestors), Darwin assumed that choices were made by essentially "coy" females. I argue here that female solicitation of multiple males (either simultaneously or sequentially, depending on the breeding system) characterized prehominid females; this prehominid legacy of cyclical sexual assertiveness, itself possibly a female counter-strategy to male efforts to control the timing of female reproduction, generated further male counter-strategies. This dialectic had important implications for emerging hominid mating systems, human evolution, and the development of patriarchal arrangements in some human societies. For hominid males who will invest in offspring, there would be powerful selection for emotions, behaviors, and customs that ensure them certainty of paternity. The sexual modesty that so struck Darwin can be explained as a recent evolved or learned (perhaps both) adaptation in women to avoid penalties imposed by patrilines on daughters and mates who failed to conform to the patriline's prevailing norms for their sex. Other supposedly innate universals, such as female preferences for wealthy husbands, are also likely to be facultative accommodations by women to constraints set up when patrilines monopolized resources needed by females to survive and reproduce, and passed on intergenerational control of these resources preferentially to sons.
Sequential Modulations in a Combined Horizontal and Vertical Simon Task: Is There ERP Evidence for Feature Integration Effects?

PubMed Central

Hoppe, Katharina; Küper, Kristina; Wascher, Edmund

2017-01-01

In the Simon task, participants respond faster when the task-irrelevant stimulus position and the response position are corresponding, for example on the same side, compared to when they have a non-corresponding relation. Interestingly, this Simon effect is reduced after non-corresponding trials. Such sequential effects can be explained in terms of a more focused processing of the relevant stimulus dimension due to increased cognitive control, which transfers from the previous non-corresponding trial (conflict adaptation effects). Alternatively, sequential modulations of the Simon effect can also be due to the degree of trial-to-trial repetitions and alternations of task features, which is confounded with the correspondence sequence (feature integration effects). In the present study, we used a spatially two-dimensional Simon task with vertical response keys to examine the contribution of adaptive cognitive control and feature integration processes to the sequential modulation of the Simon effect. The two-dimensional Simon task creates correspondences in the vertical as well as in the horizontal dimension. A trial-by-trial alternation of the spatial dimension, for example from a vertical to a horizontal stimulus presentation, generates a subset containing no complete repetitions of task features, but only complete alternations and partial repetitions, which are equally distributed over all correspondence sequences. In line with the assumed feature integration effects, we found sequential modulations of the Simon effect only when the spatial dimension repeated. At least for the horizontal dimension, this pattern was confirmed by the parietal P3b, an event-related potential that is assumed to reflect stimulus–response link processes. Contrary to conflict adaptation effects, cognitive control, measured by the fronto-central N2 component of the EEG, was not sequentially modulated. Overall, our data provide behavioral as well as electrophysiological evidence for feature integration effects contributing to sequential modulations of the Simon effect. PMID:28713305
Sequential Modulations in a Combined Horizontal and Vertical Simon Task: Is There ERP Evidence for Feature Integration Effects?

PubMed

Hoppe, Katharina; Küper, Kristina; Wascher, Edmund

2017-01-01

In the Simon task, participants respond faster when the task-irrelevant stimulus position and the response position are corresponding, for example on the same side, compared to when they have a non-corresponding relation. Interestingly, this Simon effect is reduced after non-corresponding trials. Such sequential effects can be explained in terms of a more focused processing of the relevant stimulus dimension due to increased cognitive control, which transfers from the previous non-corresponding trial (conflict adaptation effects). Alternatively, sequential modulations of the Simon effect can also be due to the degree of trial-to-trial repetitions and alternations of task features, which is confounded with the correspondence sequence (feature integration effects). In the present study, we used a spatially two-dimensional Simon task with vertical response keys to examine the contribution of adaptive cognitive control and feature integration processes to the sequential modulation of the Simon effect. The two-dimensional Simon task creates correspondences in the vertical as well as in the horizontal dimension. A trial-by-trial alternation of the spatial dimension, for example from a vertical to a horizontal stimulus presentation, generates a subset containing no complete repetitions of task features, but only complete alternations and partial repetitions, which are equally distributed over all correspondence sequences. In line with the assumed feature integration effects, we found sequential modulations of the Simon effect only when the spatial dimension repeated. At least for the horizontal dimension, this pattern was confirmed by the parietal P3b, an event-related potential that is assumed to reflect stimulus-response link processes. Contrary to conflict adaptation effects, cognitive control, measured by the fronto-central N2 component of the EEG, was not sequentially modulated. Overall, our data provide behavioral as well as electrophysiological evidence for feature integration effects contributing to sequential modulations of the Simon effect.
Making Career Decisions--A Sequential Elimination Approach.

ERIC Educational Resources Information Center

Gati, Itamar

1986-01-01

Presents a model for career decision making based on the sequential elimination of occupational alternatives, an adaptation for career decisions of Tversky's (1972) elimination-by-aspects theory of choice. The expected utility approach is reviewed as a representative compensatory model for career decisions. Advantages, disadvantages, and…
CACTI: free, open-source software for the sequential coding of behavioral interactions.

PubMed

Glynn, Lisa H; Hallgren, Kevin A; Houck, Jon M; Moyers, Theresa B

2012-01-01

The sequential analysis of client and clinician speech in psychotherapy sessions can help to identify and characterize potential mechanisms of treatment and behavior change. Previous studies required coding systems that were time-consuming, expensive, and error-prone. Existing software can be expensive and inflexible, and furthermore, no single package allows for pre-parsing, sequential coding, and assignment of global ratings. We developed a free, open-source, and adaptable program to meet these needs: The CASAA Application for Coding Treatment Interactions (CACTI). Without transcripts, CACTI facilitates the real-time sequential coding of behavioral interactions using WAV-format audio files. Most elements of the interface are user-modifiable through a simple XML file, and can be further adapted using Java through the terms of the GNU Public License. Coding with this software yields interrater reliabilities comparable to previous methods, but at greatly reduced time and expense. CACTI is a flexible research tool that can simplify psychotherapy process research, and has the potential to contribute to the improvement of treatment content and delivery.
Temporal variation in antibiotic environments slows down resistance evolution in pathogenic Pseudomonas aeruginosa

PubMed Central

Roemhild, Roderich; Barbosa, Camilo; Beardmore, Robert E; Jansen, Gunther; Schulenburg, Hinrich

2015-01-01

Antibiotic resistance is a growing concern to public health. New treatment strategies may alleviate the situation by slowing down the evolution of resistance. Here, we evaluated sequential treatment protocols using two fully independent laboratory-controlled evolution experiments with the human pathogen Pseudomonas aeruginosa PA14 and two pairs of clinically relevant antibiotics (doripenem/ciprofloxacin and cefsulodin/gentamicin). Our results consistently show that the sequential application of two antibiotics decelerates resistance evolution relative to monotherapy. Sequential treatment enhanced population extinction although we applied antibiotics at sublethal dosage. In both experiments, we identified an order effect of the antibiotics used in the sequential protocol, leading to significant variation in the long-term efficacy of the tested protocols. These variations appear to be caused by asymmetric evolutionary constraints, whereby adaptation to one drug slowed down adaptation to the other drug, but not vice versa. An understanding of such asymmetric constraints may help future development of evolutionary robust treatments against infectious disease. PMID:26640520
New Measurement for Correlation of Co-evolution Relationship of Subsequences in Protein.

PubMed

Gao, Hongyun; Yu, Xiaoqing; Dou, Yongchao; Wang, Jun

2015-12-01

Many computational tools have been developed to measure the protein residues co-evolution. Most of them only focus on co-evolution for pairwise residues in a protein sequence. However, number of residues participate in co-evolution might be multiple. And some co-evolved residues are clustered in several distinct regions in primary structure. Therefore, the co-evolution among the adjacent residues and the correlation between the distinct regions offer insights into function and evolution of the protein and residues. Subsequence is used to represent the adjacent multiple residues in one distinct region. In the paper, co-evolution relationship in each subsequence is represented by mutual information matrix (MIM). Then, Pearson's correlation coefficient: R value is developed to measure the similarity correlation of two MIMs. MSAs from Catalytic Data Base (Catalytic Site Atlas, CSA) are used for testing. R value characterizes a specific class of residues. In contrast to individual pairwise co-evolved residues, adjacent residues without high individual MI values are found since the co-evolved relationship among them is similar to that among another set of adjacent residues. These subsequences possess some flexibility in the composition of side chains, such as the catalyzed environment.
Wing patterning genes and coevolution of Müllerian mimicry in Heliconius butterflies: Support from phylogeography, cophylogeny, and divergence times.

PubMed

Hoyal Cuthill, Jennifer F; Charleston, Michael

2015-12-01

Examples of long-term coevolution are rare among free-living organisms. Müllerian mimicry in Heliconius butterflies had been suggested as a key example of coevolution by early genetic studies. However, research over the last two decades has been dominated by the idea that the best-studied comimics, H. erato and H. melpomene, did not coevolve at all. Recently sequenced genes associated with wing color pattern phenotype offer a new opportunity to resolve this controversy. Here, we test the hypothesis of coevolution between H. erato and H. melpomene using Bayesian multilocus analysis of five color pattern genes and five neutral genetic markers. We first explore the extent of phylogenetic agreement versus conflict between the different genes. Coevolution is then tested against three aspects of the mimicry diversifications: phylogenetic branching patterns, divergence times, and, for the first time, phylogeographic histories. We show that all three lines of evidence are compatible with strict coevolution of the diverse mimicry wing patterns, contrary to some recent suggestions. Instead, these findings tally with a coevolutionary diversification driven primarily by the ecological force of Müllerian mimicry. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.
Evolution of speech and evolution of language.

PubMed

de Boer, Bart

2017-02-01

Speech is the physical signal used to convey spoken language. Because of its physical nature, speech is both easier to compare with other species' behaviors and easier to study in the fossil record than other aspects of language. Here I argue that convergent fossil evidence indicates adaptations for complex vocalizations at least as early as the common ancestor of Neanderthals and modern humans. Furthermore, I argue that it is unlikely that language evolved separately from speech, but rather that gesture, speech, and song coevolved to provide both a multimodal communication system and a musical system. Moreover, coevolution must also have played a role by allowing both cognitive and anatomical adaptations to language and speech to evolve in parallel. Although such a coevolutionary scenario is complex, it is entirely plausible from a biological point of view.
How Did the Spider Cross the River? Behavioral Adaptations for River-Bridging Webs in Caerostris darwini (Araneae: Araneidae)

PubMed Central

Gregorič, Matjaž; Agnarsson, Ingi; Blackledge, Todd A.; Kuntner, Matjaž

2011-01-01

Background Interspecific coevolution is well described, but we know significantly less about how multiple traits coevolve within a species, particularly between behavioral traits and biomechanical properties of animals' “extended phenotypes”. In orb weaving spiders, coevolution of spider behavior with ecological and physical traits of their webs is expected. Darwin's bark spider (Caerostris darwini) bridges large water bodies, building the largest known orb webs utilizing the toughest known silk. Here, we examine C. darwini web building behaviors to establish how bridge lines are formed over water. We also test the prediction that this spider's unique web ecology and architecture coevolved with new web building behaviors. Methodology We observed C. darwini in its natural habitat and filmed web building. We observed 90 web building events, and compared web building behaviors to other species of orb web spiders. Conclusions Caerostris darwini uses a unique set of behaviors, some unknown in other spiders, to construct its enormous webs. First, the spiders release unusually large amounts of bridging silk into the air, which is then carried downwind, across the water body, establishing bridge lines. Second, the spiders perform almost no web site exploration. Third, they construct the orb capture area below the initial bridge line. In contrast to all known orb-weavers, the web hub is therefore not part of the initial bridge line but is instead built de novo. Fourth, the orb contains two types of radial threads, with those in the upper half of the web doubled. These unique behaviors result in a giant, yet rather simplified web. Our results continue to build evidence for the coevolution of behavioral (web building), ecological (web microhabitat) and biomaterial (silk biomechanics) traits that combined allow C. darwini to occupy a unique niche among spiders. PMID:22046378
Coevolution of patch-type dependent emigration and patch-type dependent immigration.

PubMed

Weigang, Helene C

2017-08-07

The three phases of dispersal - emigration, transfer and immigration - are affecting each other and the former and latter decisions may depend on patch types. Despite the inevitable fact of the complexity of the dispersal process, patch-type dependencies of dispersal decisions modelled as emigration and immigration are usually missing in theoretical dispersal models. Here, I investigate the coevolution of patch-type dependent emigration and patch-type dependent immigration in an extended Hamilton-May model. The dispersing population inhabits a landscape structured into many patches of two types and disperses during a continuous-time season. The trait under consideration is a four dimensional vector consisting of two values for emigration probability from the patches and two values for immigration probability into the patches of each type. Using the adaptive dynamics approach I show that four qualitatively different dispersal strategies may evolve in different parameter regions, including a counterintuitive strategy, where patches of one type are fully dispersed from (emigration probability is one) but individuals nevertheless always immigrate into them during the dispersal season (immigration probability is one). I present examples of evolutionary branching in a wide parameter range, when the patches with high local death rate during the dispersal season guarantee a high expected disperser output. I find that two dispersal strategies can coexist after evolutionary branching: a strategy with full immigration only into the patches with high expected disperser output coexists with a strategy that immigrates into any patch. Stochastic simulations agree with the numerical predictions. Since evolutionary branching is also found when immigration evolves alone, the present study is adding coevolutionary constraints on the emigration traits and hence finds that the coevolution of a higher dimensional trait sometimes hinders evolutionary diversification. Copyright © 2017 Elsevier Ltd. All rights reserved.
Adaptive Evolution and Divergence of SERPINB3: A Young Duplicate in Great Apes

PubMed Central

Gomes, Sílvia; Marques, Patrícia I.; Matthiesen, Rune; Seixas, Susana

2014-01-01

A series of duplication events led to an expansion of clade B Serine Protease Inhibitors (SERPIN), currently displaying a large repertoire of functions in vertebrates. Accordingly, the recent duplicates SERPINB3 and B4 located in human 18q21.3 SERPIN cluster control the activity of different cysteine and serine proteases, respectively. Here, we aim to assess SERPINB3 and B4 coevolution with their target proteases in order to understand the evolutionary forces shaping the accelerated divergence of these duplicates. Phylogenetic analysis of primate sequences placed the duplication event in a Hominoidae ancestor (∼30 Mya) and the emergence of SERPINB3 in Homininae (∼9 Mya). We detected evidence of strong positive selection throughout SERPINB4/B3 primate tree and target proteases, cathepsin L2 (CTSL2) and G (CTSG) and chymase (CMA1). Specifically, in the Homininae clade a perfect match was observed between the adaptive evolution of SERPINB3 and cathepsin S (CTSS) and most of sites under positive selection were located at the inhibitor/protease interface. Altogether our results seem to favour a coevolution hypothesis for SERPINB3, CTSS and CTSL2 and for SERPINB4 and CTSG and CMA1. A scenario of an accelerated evolution driven by host-pathogen interactions is also possible since SERPINB3/B4 are potent inhibitors of exogenous proteases, released by infectious agents. Finally, similar patterns of expression and the sharing of many regulatory motifs suggest neofunctionalization as the best fitted model of the functional divergence of SERPINB3 and B4 duplicates. PMID:25133778
Generalized antifungal activity and 454-screening of Pseudonocardia and Amycolatopsis bacteria in nests of fungus-growing ants.

PubMed

Sen, Ruchira; Ishak, Heather D; Estrada, Dora; Dowd, Scot E; Hong, Eunki; Mueller, Ulrich G

2009-10-20

In many host-microbe mutualisms, hosts use beneficial metabolites supplied by microbial symbionts. Fungus-growing (attine) ants are thought to form such a mutualism with Pseudonocardia bacteria to derive antibiotics that specifically suppress the coevolving pathogen Escovopsis, which infects the ants' fungal gardens and reduces growth. Here we test 4 key assumptions of this Pseudonocardia-Escovopsis coevolution model. Culture-dependent and culture-independent (tag-encoded 454-pyrosequencing) surveys reveal that several Pseudonocardia species and occasionally Amycolatopsis (a close relative of Pseudonocardia) co-occur on workers from a single nest, contradicting the assumption of a single pseudonocardiaceous strain per nest. Pseudonocardia can occur on males, suggesting that Pseudonocardia could also be horizontally transmitted during mating. Pseudonocardia and Amycolatopsis secretions kill or strongly suppress ant-cultivated fungi, contradicting the previous finding of a growth-enhancing effect of Pseudonocardia on the cultivars. Attine ants therefore may harm their own cultivar if they apply pseudonocardiaceous secretions to actively growing gardens. Pseudonocardia and Amycolatopsis isolates also show nonspecific antifungal activities against saprotrophic, endophytic, entomopathogenic, and garden-pathogenic fungi, contrary to the original report of specific antibiosis against Escovopsis alone. We conclude that attine-associated pseudonocardiaceous bacteria do not exhibit derived antibiotic properties to specifically suppress Escovopsis. We evaluate hypotheses on nonadaptive and adaptive functions of attine integumental bacteria, and develop an alternate conceptual framework to replace the prevailing Pseudonocardia-Escovopsis coevolution model. If association with Pseudonocardia is adaptive to attine ants, alternate roles of such microbes could include the protection of ants or sanitation of the nest.
Generalized antifungal activity and 454-screening of Pseudonocardia and Amycolatopsis bacteria in nests of fungus-growing ants

PubMed Central

Sen, Ruchira; Ishak, Heather D.; Estrada, Dora; Dowd, Scot E.; Hong, Eunki; Mueller, Ulrich G.

2009-01-01

In many host-microbe mutualisms, hosts use beneficial metabolites supplied by microbial symbionts. Fungus-growing (attine) ants are thought to form such a mutualism with Pseudonocardia bacteria to derive antibiotics that specifically suppress the coevolving pathogen Escovopsis, which infects the ants' fungal gardens and reduces growth. Here we test 4 key assumptions of this Pseudonocardia-Escovopsis coevolution model. Culture-dependent and culture-independent (tag-encoded 454-pyrosequencing) surveys reveal that several Pseudonocardia species and occasionally Amycolatopsis (a close relative of Pseudonocardia) co-occur on workers from a single nest, contradicting the assumption of a single pseudonocardiaceous strain per nest. Pseudonocardia can occur on males, suggesting that Pseudonocardia could also be horizontally transmitted during mating. Pseudonocardia and Amycolatopsis secretions kill or strongly suppress ant-cultivated fungi, contradicting the previous finding of a growth-enhancing effect of Pseudonocardia on the cultivars. Attine ants therefore may harm their own cultivar if they apply pseudonocardiaceous secretions to actively growing gardens. Pseudonocardia and Amycolatopsis isolates also show nonspecific antifungal activities against saprotrophic, endophytic, entomopathogenic, and garden-pathogenic fungi, contrary to the original report of specific antibiosis against Escovopsis alone. We conclude that attine-associated pseudonocardiaceous bacteria do not exhibit derived antibiotic properties to specifically suppress Escovopsis. We evaluate hypotheses on nonadaptive and adaptive functions of attine integumental bacteria, and develop an alternate conceptual framework to replace the prevailing Pseudonocardia-Escovopsis coevolution model. If association with Pseudonocardia is adaptive to attine ants, alternate roles of such microbes could include the protection of ants or sanitation of the nest. PMID:19805175

Color plumage polymorphism and predator mimicry in brood parasites

PubMed Central

2013-01-01

Background Plumage polymorphism may evolve during coevolution between brood parasites and their hosts if rare morph(s), by contravening host search image, evade host recognition systems better than common variant(s). Females of the parasitic common cuckoo (Cuculus canorus) are a classic example of discrete color polymorphism: gray females supposedly mimic the sparrowhawk (Accipiter nisus), while rufous females are believed to mimic the kestrel (Falco tinnunculus). Despite many studies on host responses to adult cuckoos comprehensive tests of the “hawk mimicry” and “kestrel mimicry” hypotheses are lacking so far. Results We tested these hypotheses by examining host responses to stuffed dummies of the sparrowhawk, kestrel, cuckoo and the innocuous turtle dove (Streptopelia turtur) as a control at the nest. Our experimental data from an aggressive cuckoo host, the great reed warbler (Acrocephalus arundinaceus), showed low effectiveness of cuckoo-predator mimicry against more aggressive hosts regardless of the type of model and the degree of perfection of the mimic. Specifically, warblers discriminated gray cuckoos from sparrowhawks but did not discriminate rufous cuckoos from kestrels. However, both gray and rufous cuckoos were attacked vigorously and much more than control doves. The ratio of aggression to gray vs. rufous cuckoo was very similar to the ratio between frequencies of gray vs. rufous cuckoo morphs in our study population. Conclusions Overall, our data combined with previous results from other localities suggest polymorphism dynamics are not strongly affected by local predator model frequencies. Instead, hosts responses and discrimination abilities are proportional, other things being equal, to the frequency with which hosts encounter various cuckoo morphs near their nests. This suggests that female cuckoo polymorphism is a counter-adaptation to thwart a specific host adaptation, namely an ability to not be fooled by predator mimicry. We hypothesize the dangerousness of a particular model predator (sparrowhawks are more dangerous to adult birds than kestrels) may be another important factor responsible for better discrimination between the gray cuckoo and its model rather than between the rufous cuckoo and its model. We also provide a review of relevant existing literature, detailed discussion of plumage polymorphism in cuckoos, methodological recommendations and new ideas for future work. PMID:23663311
How Big Is Big Enough? Sample Size Requirements for CAST Item Parameter Estimation

ERIC Educational Resources Information Center

Chuah, Siang Chee; Drasgow, Fritz; Luecht, Richard

2006-01-01

Adaptive tests offer the advantages of reduced test length and increased accuracy in ability estimation. However, adaptive tests require large pools of precalibrated items. This study looks at the development of an item pool for 1 type of adaptive administration: the computer-adaptive sequential test. An important issue is the sample size required…
New frontiers in the study of human cultural and genetic evolution.

PubMed

Ross, Cody T; Richerson, Peter J

2014-12-01

In this review, we discuss the dynamic linkages between culture and the genetic evolution of the human species. We begin by briefly describing the framework of gene-culture coevolutionary (or dual-inheritance) models for human evolutionary change. Until recently, the literature on gene-culture coevolution was composed primarily of mathematical models and formalized theory describing the complex dynamics underlying human behavior, adaptation, and technological evolution, but had little empirical support concerning genetics. The rapid progress in the fields of molecular genetics and genomics, however, is now providing the kinds of data needed to produce rich empirical support for gene-culture coevolutionary models. We briefly outline how theoretical and methodological progress in genome sciences has provided ways for the strength of selection on genes to be evaluated, and then outline how evidence of selection on several key genes can be directly linked to human cultural practices. We then describe some exciting new directions in the empirical study of gene-culture coevolution, and conclude with a discussion of the role of gene-culture evolutionary models in the future integration of medical, biological, and social sciences. Copyright © 2014 Elsevier Ltd. All rights reserved.
An Airway Network Flow Assignment Approach Based on an Efficient Multiobjective Optimization Framework

PubMed Central

Zhang, Xuejun; Lei, Jiaxing

2015-01-01

Considering reducing the airspace congestion and the flight delay simultaneously, this paper formulates the airway network flow assignment (ANFA) problem as a multiobjective optimization model and presents a new multiobjective optimization framework to solve it. Firstly, an effective multi-island parallel evolution algorithm with multiple evolution populations is employed to improve the optimization capability. Secondly, the nondominated sorting genetic algorithm II is applied for each population. In addition, a cooperative coevolution algorithm is adapted to divide the ANFA problem into several low-dimensional biobjective optimization problems which are easier to deal with. Finally, in order to maintain the diversity of solutions and to avoid prematurity, a dynamic adjustment operator based on solution congestion degree is specifically designed for the ANFA problem. Simulation results using the real traffic data from China air route network and daily flight plans demonstrate that the proposed approach can improve the solution quality effectively, showing superiority to the existing approaches such as the multiobjective genetic algorithm, the well-known multiobjective evolutionary algorithm based on decomposition, and a cooperative coevolution multiobjective algorithm as well as other parallel evolution algorithms with different migration topology. PMID:26180840
Biomimicry of symbiotic multi-species coevolution for discrete and continuous optimization in RFID networks.

PubMed

Lin, Na; Chen, Hanning; Jing, Shikai; Liu, Fang; Liang, Xiaodan

2017-03-01

In recent years, symbiosis as a rich source of potential engineering applications and computational model has attracted more and more attentions in the adaptive complex systems and evolution computing domains. Inspired by different symbiotic coevolution forms in nature, this paper proposed a series of multi-swarm particle swarm optimizers called PS 2 Os, which extend the single population particle swarm optimization (PSO) algorithm to interacting multi-swarms model by constructing hierarchical interaction topologies and enhanced dynamical update equations. According to different symbiotic interrelationships, four versions of PS 2 O are initiated to mimic mutualism, commensalism, predation, and competition mechanism, respectively. In the experiments, with five benchmark problems, the proposed algorithms are proved to have considerable potential for solving complex optimization problems. The coevolutionary dynamics of symbiotic species in each PS 2 O version are also studied respectively to demonstrate the heterogeneity of different symbiotic interrelationships that effect on the algorithm's performance. Then PS 2 O is used for solving the radio frequency identification (RFID) network planning (RNP) problem with a mixture of discrete and continuous variables. Simulation results show that the proposed algorithm outperforms the reference algorithms for planning RFID networks, in terms of optimization accuracy and computation robustness.
Computerized Classification Testing with the Rasch Model

ERIC Educational Resources Information Center

Eggen, Theo J. H. M.

2011-01-01

If classification in a limited number of categories is the purpose of testing, computerized adaptive tests (CATs) with algorithms based on sequential statistical testing perform better than estimation-based CATs (e.g., Eggen & Straetmans, 2000). In these computerized classification tests (CCTs), the Sequential Probability Ratio Test (SPRT) (Wald,…
Evaluation of an adaptive detector collimation for prospectively ECG-triggered coronary CT angiography with third-generation dual-source CT.

PubMed

Messerli, Michael; Dewes, Patricia; Scholtz, Jan-Erik; Arendt, Christophe; Wildermuth, Simon; Vogl, Thomas J; Bauer, Ralf W

2018-05-01

To investigate the impact of an adaptive detector collimation on the dose parameters and accurateness of scan length adaption at prospectively ECG-triggered sequential cardiac CT with a wide-detector third-generation dual-source CT. Ideal scan lengths for human hearts were retrospectively derived from 103 triple-rule-out examinations. These measures were entered into the new scanner operated in prospectively ECG-triggered sequential cardiac scan mode with three different detector settings: (1) adaptive collimation, (2) fixed 64 × 0.6-mm collimation, and (3) fixed 96 × 0.6-mm collimation. Differences in effective scan length and deviation from the ideal scan length and dose parameters (CTDIvol, DLP) were documented. The ideal cardiac scan length could be matched by the adaptive collimation in every case while the mean scanned length was longer by 15.4% with the 64 × 0.6 mm and by 27.2% with the fixed 96 × 0.6-mm collimation. While the DLP was almost identical between the adaptive and the 64 × 0.6-mm collimation (83 vs. 89 mGycm at 120 kV), it was 62.7% higher with the 96 × 0.6-mm collimation (135 mGycm), p < 0.001. The adaptive detector collimation for prospectively ECG-triggered sequential acquisition allows for adjusting the scan length as accurate as this can only be achieved with a spiral acquisition. This technique allows keeping patient exposure low where patient dose would significantly increase with the traditional step-and-shoot mode. • Adaptive detector collimation allows keeping patient exposure low in cardiac CT. • With novel detectors the desired scan length can be accurately matched. • Differences in detector settings may cause 62.7% of excessive dose.
AdOn HDP-HMM: An Adaptive Online Model for Segmentation and Classification of Sequential Data.

PubMed

Bargi, Ava; Xu, Richard Yi Da; Piccardi, Massimo

2017-09-21

Recent years have witnessed an increasing need for the automated classification of sequential data, such as activities of daily living, social media interactions, financial series, and others. With the continuous flow of new data, it is critical to classify the observations on-the-fly and without being limited by a predetermined number of classes. In addition, a model should be able to update its parameters in response to a possible evolution in the distributions of the classes. This compelling problem, however, does not seem to have been adequately addressed in the literature, since most studies focus on offline classification over predefined class sets. In this paper, we present a principled solution for this problem based on an adaptive online system leveraging Markov switching models and hierarchical Dirichlet process priors. This adaptive online approach is capable of classifying the sequential data over an unlimited number of classes while meeting the memory and delay constraints typical of streaming contexts. In this paper, we introduce an adaptive ''learning rate'' that is responsible for balancing the extent to which the model retains its previous parameters or adapts to new observations. Experimental results on stationary and evolving synthetic data and two video data sets, TUM Assistive Kitchen and collated Weizmann, show a remarkable performance in terms of segmentation and classification, particularly for sequences from evolutionary distributions and/or those containing previously unseen classes.
Coevolution can reverse predator–prey cycles

PubMed Central

Cortez, Michael H.; Weitz, Joshua S.

2014-01-01

A hallmark of Lotka–Volterra models, and other ecological models of predator–prey interactions, is that in predator–prey cycles, peaks in prey abundance precede peaks in predator abundance. Such models typically assume that species life history traits are fixed over ecologically relevant time scales. However, the coevolution of predator and prey traits has been shown to alter the community dynamics of natural systems, leading to novel dynamics including antiphase and cryptic cycles. Here, using an eco-coevolutionary model, we show that predator–prey coevolution can also drive population cycles where the opposite of canonical Lotka–Volterra oscillations occurs: predator peaks precede prey peaks. These reversed cycles arise when selection favors extreme phenotypes, predator offense is costly, and prey defense is effective against low-offense predators. We present multiple datasets from phage–cholera, mink–muskrat, and gyrfalcon–rock ptarmigan systems that exhibit reversed-peak ordering. Our results suggest that such cycles are a potential signature of predator–prey coevolution and reveal unique ways in which predator–prey coevolution can shape, and possibly reverse, community dynamics. PMID:24799689
Coevolution can reverse predator-prey cycles.

PubMed

Cortez, Michael H; Weitz, Joshua S

2014-05-20

A hallmark of Lotka-Volterra models, and other ecological models of predator-prey interactions, is that in predator-prey cycles, peaks in prey abundance precede peaks in predator abundance. Such models typically assume that species life history traits are fixed over ecologically relevant time scales. However, the coevolution of predator and prey traits has been shown to alter the community dynamics of natural systems, leading to novel dynamics including antiphase and cryptic cycles. Here, using an eco-coevolutionary model, we show that predator-prey coevolution can also drive population cycles where the opposite of canonical Lotka-Volterra oscillations occurs: predator peaks precede prey peaks. These reversed cycles arise when selection favors extreme phenotypes, predator offense is costly, and prey defense is effective against low-offense predators. We present multiple datasets from phage-cholera, mink-muskrat, and gyrfalcon-rock ptarmigan systems that exhibit reversed-peak ordering. Our results suggest that such cycles are a potential signature of predator-prey coevolution and reveal unique ways in which predator-prey coevolution can shape, and possibly reverse, community dynamics.
Synthesizing genetic sequential logic circuit with clock pulse generator

PubMed Central

2014-01-01

Background Rhythmic clock widely occurs in biological systems which controls several aspects of cell physiology. For the different cell types, it is supplied with various rhythmic frequencies. How to synthesize a specific clock signal is a preliminary but a necessary step to further development of a biological computer in the future. Results This paper presents a genetic sequential logic circuit with a clock pulse generator based on a synthesized genetic oscillator, which generates a consecutive clock signal whose frequency is an inverse integer multiple to that of the genetic oscillator. An analogous electronic waveform-shaping circuit is constructed by a series of genetic buffers to shape logic high/low levels of an oscillation input in a basic sinusoidal cycle and generate a pulse-width-modulated (PWM) output with various duty cycles. By controlling the threshold level of the genetic buffer, a genetic clock pulse signal with its frequency consistent to the genetic oscillator is synthesized. A synchronous genetic counter circuit based on the topology of the digital sequential logic circuit is triggered by the clock pulse to synthesize the clock signal with an inverse multiple frequency to the genetic oscillator. The function acts like a frequency divider in electronic circuits which plays a key role in the sequential logic circuit with specific operational frequency. Conclusions A cascaded genetic logic circuit generating clock pulse signals is proposed. Based on analogous implement of digital sequential logic circuits, genetic sequential logic circuits can be constructed by the proposed approach to generate various clock signals from an oscillation signal. PMID:24884665
Meta-analyses and adaptive group sequential designs in the clinical development process.

PubMed

Jennison, Christopher; Turnbull, Bruce W

2005-01-01

The clinical development process can be viewed as a succession of trials, possibly overlapping in calendar time. The design of each trial may be influenced by results from previous studies and other currently proceeding trials, as well as by external information. Results from all of these trials must be considered together in order to assess the efficacy and safety of the proposed new treatment. Meta-analysis techniques provide a formal way of combining the information. We examine how such methods can be used in combining results from: (1) a collection of separate studies, (2) a sequence of studies in an organized development program, and (3) stages within a single study using a (possibly adaptive) group sequential design. We present two examples. The first example concerns the combining of results from a Phase IIb trial using several dose levels or treatment arms with those of the Phase III trial comparing the treatment selected in Phase IIb against a control This enables a "seamless transition" from Phase IIb to Phase III. The second example examines the use of combination tests to analyze data from an adaptive group sequential trial.
A self-adaptive memeplexes robust search scheme for solving stochastic demands vehicle routing problem

NASA Astrophysics Data System (ADS)

Chen, Xianshun; Feng, Liang; Ong, Yew Soon

2012-07-01

In this article, we proposed a self-adaptive memeplex robust search (SAMRS) for finding robust and reliable solutions that are less sensitive to stochastic behaviours of customer demands and have low probability of route failures, respectively, in vehicle routing problem with stochastic demands (VRPSD). In particular, the contribution of this article is three-fold. First, the proposed SAMRS employs the robust solution search scheme (RS 3) as an approximation of the computationally intensive Monte Carlo simulation, thus reducing the computation cost of fitness evaluation in VRPSD, while directing the search towards robust and reliable solutions. Furthermore, a self-adaptive individual learning based on the conceptual modelling of memeplex is introduced in the SAMRS. Finally, SAMRS incorporates a gene-meme co-evolution model with genetic and memetic representation to effectively manage the search for solutions in VRPSD. Extensive experimental results are then presented for benchmark problems to demonstrate that the proposed SAMRS serves as an efficable means of generating high-quality robust and reliable solutions in VRPSD.
Adoptive cellular therapy of cancer: exploring innate and adaptive cellular crosstalk to improve anti-tumor efficacy.

PubMed

Payne, Kyle K; Bear, Harry D; Manjili, Masoud H

2014-08-01

The mammalian immune system has evolved to produce multi-tiered responses consisting of both innate and adaptive immune cells collaborating to elicit a functional response to a pathogen or neoplasm. Immune cells possess a shared ancestry, suggestive of a degree of coevolution that has resulted in optimal functionality as an orchestrated and highly collaborative unit. Therefore, the development of therapeutic modalities that harness the immune system should consider the crosstalk between cells of the innate and adaptive immune systems in order to elicit the most effective response. In this review, the authors will discuss the success achieved using adoptive cellular therapy in the treatment of cancer, recent trends that focus on purified T cells, T cells with genetically modified T-cell receptors and T cells modified to express chimeric antigen receptors, as well as the use of unfractionated immune cell reprogramming to achieve optimal cellular crosstalk upon infusion for adoptive cellular therapy.
Counter Tunnel Exploration, Mapping, and Localization with an Unmanned Ground Vehicle

DTIC Science & Technology

2014-05-01

support terrorist activity. Past robotic tunnel exploration efforts have had limited success in aiding law enforcement to explore and map the suspect...cross-border tunnels. These efforts have made use of adapted explosive ordnance disposal (EOD) or pipe inspection robotic systems that are not ideally... Robotics Enterprise (JGRE) to develop a prototype robotic system for counter-tunnel operations, focusing on exploration, mapping, and characterization of
The Sequential Probability Ratio Test and Binary Item Response Models

ERIC Educational Resources Information Center

Nydick, Steven W.

2014-01-01

The sequential probability ratio test (SPRT) is a common method for terminating item response theory (IRT)-based adaptive classification tests. To decide whether a classification test should stop, the SPRT compares a simple log-likelihood ratio, based on the classification bound separating two categories, to prespecified critical values. As has…
Considering User's Access Pattern in Multimedia File Systems

NASA Astrophysics Data System (ADS)

Cho, KyoungWoon; Ryu, YeonSeung; Won, Youjip; Koh, Kern

2002-12-01

Legacy buffer cache management schemes for multimedia server are grounded at the assumption that the application sequentially accesses the multimedia file. However, user access pattern may not be sequential in some circumstances, for example, in distance learning application, where the user may exploit the VCR-like function(rewind and play) of the system and accesses the particular segments of video repeatedly in the middle of sequential playback. Such a looping reference can cause a significant performance degradation of interval-based caching algorithms. And thus an appropriate buffer cache management scheme is required in order to deliver desirable performance even under the workload that exhibits looping reference behavior. We propose Adaptive Buffer cache Management(ABM) scheme which intelligently adapts to the file access characteristics. For each opened file, ABM applies either the LRU replacement or the interval-based caching depending on the Looping Reference Indicator, which indicates that how strong temporally localized access pattern is. According to our experiment, ABM exhibits better buffer cache miss ratio than interval-based caching or LRU, especially when the workload exhibits not only sequential but also looping reference property.
CACTI: Free, Open-Source Software for the Sequential Coding of Behavioral Interactions

PubMed Central

Glynn, Lisa H.; Hallgren, Kevin A.; Houck, Jon M.; Moyers, Theresa B.

2012-01-01

The sequential analysis of client and clinician speech in psychotherapy sessions can help to identify and characterize potential mechanisms of treatment and behavior change. Previous studies required coding systems that were time-consuming, expensive, and error-prone. Existing software can be expensive and inflexible, and furthermore, no single package allows for pre-parsing, sequential coding, and assignment of global ratings. We developed a free, open-source, and adaptable program to meet these needs: The CASAA Application for Coding Treatment Interactions (CACTI). Without transcripts, CACTI facilitates the real-time sequential coding of behavioral interactions using WAV-format audio files. Most elements of the interface are user-modifiable through a simple XML file, and can be further adapted using Java through the terms of the GNU Public License. Coding with this software yields interrater reliabilities comparable to previous methods, but at greatly reduced time and expense. CACTI is a flexible research tool that can simplify psychotherapy process research, and has the potential to contribute to the improvement of treatment content and delivery. PMID:22815713
Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses.

PubMed

Lagator, Mato; Colegrave, Nick; Neve, Paul

2014-11-07

In rapidly changing environments, selection history may impact the dynamics of adaptation. Mutations selected in one environment may result in pleiotropic fitness trade-offs in subsequent novel environments, slowing the rates of adaptation. Epistatic interactions between mutations selected in sequential stressful environments may slow or accelerate subsequent rates of adaptation, depending on the nature of that interaction. We explored the dynamics of adaptation during sequential exposure to herbicides with different modes of action in Chlamydomonas reinhardtii. Evolution of resistance to two of the herbicides was largely independent of selection history. For carbetamide, previous adaptation to other herbicide modes of action positively impacted the likelihood of adaptation to this herbicide. Furthermore, while adaptation to all individual herbicides was associated with pleiotropic fitness costs in stress-free environments, we observed that accumulation of resistance mechanisms was accompanied by a reduction in overall fitness costs. We suggest that antagonistic epistasis may be a driving mechanism that enables populations to more readily adapt in novel environments. These findings highlight the potential for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug and -pesticide resistance, as well as the potential for epistatic interactions between adaptive mutations to facilitate evolutionary rescue in rapidly changing environments. © 2014 The Author(s) Published by the Royal Society. All rights reserved.
Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution

PubMed Central

2010-01-01

Background The transition from prokaryotes to eukaryotes was the most radical change in cell organisation since life began, with the largest ever burst of gene duplication and novelty. According to the coevolutionary theory of eukaryote origins, the fundamental innovations were the concerted origins of the endomembrane system and cytoskeleton, subsequently recruited to form the cell nucleus and coevolving mitotic apparatus, with numerous genetic eukaryotic novelties inevitable consequences of this compartmentation and novel DNA segregation mechanism. Physical and mutational mechanisms of origin of the nucleus are seldom considered beyond the long-standing assumption that it involved wrapping pre-existing endomembranes around chromatin. Discussions on the origin of sex typically overlook its association with protozoan entry into dormant walled cysts and the likely simultaneous coevolutionary, not sequential, origin of mitosis and meiosis. Results I elucidate nuclear and mitotic coevolution, explaining the origins of dicer and small centromeric RNAs for positionally controlling centromeric heterochromatin, and how 27 major features of the cell nucleus evolved in four logical stages, making both mechanisms and selective advantages explicit: two initial stages (origin of 30 nm chromatin fibres, enabling DNA compaction; and firmer attachment of endomembranes to heterochromatin) protected DNA and nascent RNA from shearing by novel molecular motors mediating vesicle transport, division, and cytoplasmic motility. Then octagonal nuclear pore complexes (NPCs) arguably evolved from COPII coated vesicle proteins trapped in clumps by Ran GTPase-mediated cisternal fusion that generated the fenestrated nuclear envelope, preventing lethal complete cisternal fusion, and allowing passive protein and RNA exchange. Finally, plugging NPC lumens by an FG-nucleoporin meshwork and adopting karyopherins for nucleocytoplasmic exchange conferred compartmentation advantages. These successive changes took place in naked growing cells, probably as indirect consequences of the origin of phagotrophy. The first eukaryote had 1-2 cilia and also walled resting cysts; I outline how encystation may have promoted the origin of meiotic sex. I also explain why many alternative ideas are inadequate. Conclusion Nuclear pore complexes are evolutionary chimaeras of endomembrane- and mitosis-related chromatin-associated proteins. The keys to understanding eukaryogenesis are a proper phylogenetic context and understanding organelle coevolution: how innovations in one cell component caused repercussions on others. Reviewers This article was reviewed by Anthony Poole, Gáspár Jékely and Eugene Koonin. PMID:20132544

Kullback-Leibler information function and the sequential selection of experiments to discriminate among several linear models. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Sidik, S. M.

1972-01-01

A sequential adaptive experimental design procedure for a related problem is studied. It is assumed that a finite set of potential linear models relating certain controlled variables to an observed variable is postulated, and that exactly one of these models is correct. The problem is to sequentially design most informative experiments so that the correct model equation can be determined with as little experimentation as possible. Discussion includes: structure of the linear models; prerequisite distribution theory; entropy functions and the Kullback-Leibler information function; the sequential decision procedure; and computer simulation results. An example of application is given.
A model for sequential decoding overflow due to a noisy carrier reference. [communication performance prediction

NASA Technical Reports Server (NTRS)

Layland, J. W.

1974-01-01

An approximate analysis of the effect of a noisy carrier reference on the performance of sequential decoding is presented. The analysis uses previously developed techniques for evaluating noisy reference performance for medium-rate uncoded communications adapted to sequential decoding for data rates of 8 to 2048 bits/s. In estimating the ten to the minus fourth power deletion probability thresholds for Helios, the model agrees with experimental data to within the experimental tolerances. The computational problem involved in sequential decoding, carrier loop effects, the main characteristics of the medium-rate model, modeled decoding performance, and perspectives on future work are discussed.
Robustness of Ability Estimation to Multidimensionality in CAST with Implications to Test Assembly

ERIC Educational Resources Information Center

Zhang, Yanwei; Nandakumar, Ratna

2006-01-01

Computer Adaptive Sequential Testing (CAST) is a test delivery model that combines features of the traditional conventional paper-and-pencil testing and item-based computerized adaptive testing (CAT). The basic structure of CAST is a panel composed of multiple testlets adaptively administered to examinees at different stages. Current applications…
The effect of the use of a counter-torque device on the abutment-implant complex.

PubMed

Lang, L A; May, K B; Wang, R F

1999-04-01

Little is known about the condition of the abutment-screw joint before loading, after the development of the preload. This study examined the tightening force transmitted to the implant with and without the use of a counter-torque device during the tightening of the abutment screw. Forty Brânemark implants and 10 CeraOne, Estheticone, Procera, and AurAdapt abutments formed the experimental populations. Samples in each group were further divided into 2 groups, 1 group was tightened with a torque controller without the use of a counter-torque device, whereas the other used the counter-torque device. Samples were positioned in a special holder within the grips of a Tohnichi BTG-6 torque gauge for measuring transmitted forces. There were significant differences (P =. 0001) in the tightening forces transmitted to the implant with and without the use of a counter-torque device when tightening the abutment screws. An average of 91% of the recommended preload tightening torque was transmitted to the implant-bone interface in the absence of a counter-torque device. In all abutment systems, less than 10% of the recommended preload tightening torque was transmitted to the implant when the counter-torque device was used.
Repeated exposure to two stressors in sequence demonstrates that corticosterone and paraventricular nucleus of the hypothalamus interleukin-1β responses habituate independently.

PubMed

Lovelock, D F; Deak, T

2017-09-01

A wide range of stress-related pathologies such as post-traumatic stress disorder are considered to arise from aberrant or maladaptive forms of stress adaptation. The hypothalamic-pituitary-adrenal (HPA) axis readily adapts to repeated stressor exposure, yet little is known about adaptation in neuroimmune responses to repeated or sequential stress challenges. In Experiment 1, rats were exposed to 10 days of restraint alone (60 minutes daily), forced swim alone (30 minutes daily) or daily sequential exposure to restraint (60 minutes) followed immediately by forced swim (30 minutes), termed sequential stress exposure. Habituation of the corticosterone (CORT) response occurred to restraint by 5 days and swim at 10 days, whereas rats exposed to sequential stress exposure failed to display habituation to the combined challenge. Experiment 2 compared 1 or 5 days of forced swim with sequential stress exposure and examined how each affected expression of several neuroimmune and cellular activation genes in the paraventricular nucleus of the hypothalamus (PVN), prefrontal cortex (PFC) and hippocampus (HPC). Sequential exposure to restraint and swim increased interleukin (IL)-1β in the PVN, an effect that was attenuated after 5 days. Sequential stress exposure also elicited IL-6 and tumour necrosis factor-α responses in the HPC and PFC, respectively, which did not habituate after 5 days. Experiment 3 tested whether prior habituation to restraint (5 days) would alter the IL-1β response evoked by swim exposure imposed immediately after the sixth day of restraint. Surprisingly, a history of repeated exposure to restraint attenuated the PVN IL-1β response after swim in comparison to acutely-exposed subjects despite an equivalent CORT response. Overall, these findings suggest that habituation of neuroimmune responses to stress proceeds: (i) independent of HPA axis habituation; (ii) likely requires more daily sessions of stress to develop; and (iii) IL-1β displays a greater tendency to habituate after repeated stress challenges compared to other stress-reactive cytokines. © 2017 British Society for Neuroendocrinology.
Co-evolution of electric and telecommunications networks

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

Rivkin, S.R.

1998-05-01

There are potentially significant societal benefits in co-evolution between electricity and telecommunications in the areas of common infrastructure, accelerated deployment of distributed energy, tighter integration of information flow for energy management and distribution, and improved customer care. With due regard for natural processes that are more potent than any regulation and more real than any ideology, the gains from co-evolution would far outweigh the attenuated and speculative savings from restructuring of electricity that is too simplistic.
Detecting Coevolution in and among Protein Domains

PubMed Central

Yeang, Chen-Hsiang; Haussler, David

2007-01-01

Correlated changes of nucleic or amino acids have provided strong information about the structures and interactions of molecules. Despite the rich literature in coevolutionary sequence analysis, previous methods often have to trade off between generality, simplicity, phylogenetic information, and specific knowledge about interactions. Furthermore, despite the evidence of coevolution in selected protein families, a comprehensive screening of coevolution among all protein domains is still lacking. We propose an augmented continuous-time Markov process model for sequence coevolution. The model can handle different types of interactions, incorporate phylogenetic information and sequence substitution, has only one extra free parameter, and requires no knowledge about interaction rules. We employ this model to large-scale screenings on the entire protein domain database (Pfam). Strikingly, with 0.1 trillion tests executed, the majority of the inferred coevolving protein domains are functionally related, and the coevolving amino acid residues are spatially coupled. Moreover, many of the coevolving positions are located at functionally important sites of proteins/protein complexes, such as the subunit linkers of superoxide dismutase, the tRNA binding sites of ribosomes, the DNA binding region of RNA polymerase, and the active and ligand binding sites of various enzymes. The results suggest sequence coevolution manifests structural and functional constraints of proteins. The intricate relations between sequence coevolution and various selective constraints are worth pursuing at a deeper level. PMID:17983264
Mapping proteins in the presence of paralogs using units of coevolution

PubMed Central

2013-01-01

Background We study the problem of mapping proteins between two protein families in the presence of paralogs. This problem occurs as a difficult subproblem in coevolution-based computational approaches for protein-protein interaction prediction. Results Similar to prior approaches, our method is based on the idea that coevolution implies equal rates of sequence evolution among the interacting proteins, and we provide a first attempt to quantify this notion in a formal statistical manner. We call the units that are central to this quantification scheme the units of coevolution. A unit consists of two mapped protein pairs and its score quantifies the coevolution of the pairs. This quantification allows us to provide a maximum likelihood formulation of the paralog mapping problem and to cast it into a binary quadratic programming formulation. Conclusion CUPID, our software tool based on a Lagrangian relaxation of this formulation, makes it, for the first time, possible to compute state-of-the-art quality pairings in a few minutes of runtime. In summary, we suggest a novel alternative to the earlier available approaches, which is statistically sound and computationally feasible. PMID:24564758
Coevolution of Glauber-like Ising dynamics and topology

NASA Astrophysics Data System (ADS)

Mandrà, Salvatore; Fortunato, Santo; Castellano, Claudio

2009-11-01

We study the coevolution of a generalized Glauber dynamics for Ising spins with tunable threshold and of the graph topology where the dynamics takes place. This simple coevolution dynamics generates a rich phase diagram in the space of the two parameters of the model, the threshold and the rewiring probability. The diagram displays phase transitions of different types: spin ordering, percolation, and connectedness. At variance with traditional coevolution models, in which all spins of each connected component of the graph have equal value in the stationary state, we find that, for suitable choices of the parameters, the system may converge to a state in which spins of opposite sign coexist in the same component organized in compact clusters of like-signed spins. Mean field calculations enable one to estimate some features of the phase diagram.
Game Theory, Adaptation, and Genetic Programming: Some Perspectives on Operations Research for Counter-IED

DTIC Science & Technology

2011-06-01

Books. Dawkins , R. (1989), The Selfish Gene , 2 nd ed., Oxford University Press. Dekker, A.H. (2010), “Agent-Based Simulation for Counter-IED: A...memes” ( Dawkins , 1989; Gabora, 1995; Boal & Schultz, 2007). As Weeks & Galunic (2003) point out: “Memes are the replicators in cultural evolution...expression) create the macro-level patterns of culture. … Memes are the genes of culture.” Because genetic programs express beliefs, decision
Estimation of parameters and basic reproduction ratio for Japanese encephalitis transmission in the Philippines using sequential Monte Carlo filter

USDA-ARS?s Scientific Manuscript database

We developed a sequential Monte Carlo filter to estimate the states and the parameters in a stochastic model of Japanese Encephalitis (JE) spread in the Philippines. This method is particularly important for its adaptability to the availability of new incidence data. This method can also capture the...
Trial-to-Trial Modulations of the Simon Effect in Conditions of Attentional Limitations : Evidence from Dual Tasks

ERIC Educational Resources Information Center

Fischer, Rico; Plessow, Franziska; Kunde, Wilfried; Kiesel, Andrea

2010-01-01

Interference effects are reduced after trials including response conflict. This sequential modulation has often been attributed to a top-down mediated adaptive control mechanism and/or to feature repetition mechanisms. In the present study we tested whether mechanisms responsible for such sequential modulations are subject to attentional…
Completion processing for data communications instructions

DOEpatents

Blocksome, Michael A.; Kumar, Sameer; Parker, Jeffrey J.

2014-06-03

Completion processing of data communications instructions in a distributed computing environment, including receiving, in an active messaging interface (`AMI`) data communications instructions, at least one instruction specifying a callback function; injecting into an injection FIFO buffer of a data communication adapter, an injection descriptor, each slot in the injection FIFO buffer having a corresponding slot in a pending callback list; listing in the pending callback list any callback function specified by an instruction, incrementing a pending callback counter for each listed callback function; transferring payload data as per each injection descriptor, incrementing a transfer counter upon completion of each transfer; determining from counter values whether the pending callback list presently includes callback functions whose data transfers have been completed; calling by the AMI any such callback functions from the pending callback list, decrementing the pending callback counter for each callback function called.
Body load in heel-strike running: the effect of a firm heel counter.

PubMed

Jørgensen, U

1990-01-01

The effect of a firm heel counter in the shoe was studied in 11 athletes during submaximal heel-strike running on a treadmill under standardized conditions. The runners were tested in identical shoes with and without the distal 2 cm of the firm heel counter. Body load was expressed by absolute and relative VO2, surface EMG on the right leg, and g-force registration from an accelerometer below the right tibial tuberosity. The heel counter caused a 2.4% significant decrease in VO2, a reduction in musculoskeletal transients, and a decrease in the activity of the triceps surae and quadriceps muscles at heel strike. The changes found are expressions of kinematic adaptations in the body to increased or decreased load and provide functional evidence for the loading factor in the pathophysiology of overuse injuries.
Reactance and Coping Responses to Tobacco Counter-Advertisements.

PubMed

Wehbe, Michelle S; Basil, Michael; Basil, Debra

2017-07-01

Tobacco prevention messages generally take one of three tactics: They can be educational, attack the tobacco industry, or attack particular brands. Being a smoker and smoking a particular brand may form an essential part of a person's self-identity. As such, reactance theory suggests that attack messages can unintentionally attack smokers' self-image. A 2 × 2 × 2 × 2 experiment using six different messages and 260 respondents tested whether smokers have different reactions to tobacco counter-advertisements than nonsmokers. It also examined whether attacking a smoker's brand leads to greater reactance and other maladaptive responses compared to attacking other brands. Consistent with predictions, smokers reported more maladaptive coping responses and fewer adaptive coping responses to tobacco counter-ads than nonsmokers. The study also reveals differences attributable to brand identification. These findings suggest that interventions should consider different counter-advertising tactics for smokers and nonsmokers. Similar admonitions may apply to counter-advertising strategies on other health issues.
Rapid sequential determination of Pu, 90Sr and 241Am nuclides in environmental samples using an anion exchange and Sr-Spec resins.

PubMed

Lee, M H; Ahn, H J; Park, J H; Park, Y J; Song, K

2011-02-01

This paper presents a quantitative and rapid method of sequential separation of Pu, (90)Sr and (241)Am nuclides in environmental soil samples with an anion exchange resin and Sr Spec resin. After the sample solution was passed through an anion exchange column connected to a Sr Spec column, Pu isotopes were purified from the anion exchange column. Strontium-90 was separated from other interfering elements by the Sr Spec column. Americium-241 was purified from lanthanides by the anion exchange resin after oxalate co-precipitation. Measurement of Pu and Am isotopes was carried out using an α-spectrometer. Strontium-90 was measured by a low-level liquid scintillation counter. The radiochemical procedure of Pu, (90)Sr and (241)Am nuclides investigated in this study validated by application to IAEA reference materials and environmental soil samples. Copyright © 2010 Elsevier Ltd. All rights reserved.
Coordinated Rates of Evolution between Interacting Plastid and Nuclear Genes in Geraniaceae

PubMed Central

Zhang, Jin; Ruhlman, Tracey A.; Sabir, Jamal; Blazier, J. Chris; Jansen, Robert K.

2015-01-01

Although gene coevolution has been widely observed within individuals and between different organisms, rarely has this phenomenon been investigated within a phylogenetic framework. The Geraniaceae is an attractive system in which to study plastid-nuclear genome coevolution due to the highly elevated evolutionary rates in plastid genomes. In plants, the plastid-encoded RNA polymerase (PEP) is a protein complex composed of subunits encoded by both plastid (rpoA, rpoB, rpoC1, and rpoC2) and nuclear genes (sig1-6). We used transcriptome and genomic data for 27 species of Geraniales in a systematic evaluation of coevolution between genes encoding subunits of the PEP holoenzyme. We detected strong correlations of dN (nonsynonymous substitutions) but not dS (synonymous substitutions) within rpoB/sig1 and rpoC2/sig2, but not for other plastid/nuclear gene pairs, and identified the correlation of dN/dS ratio between rpoB/C1/C2 and sig1/5/6, rpoC1/C2 and sig2, and rpoB/C2 and sig3 genes. Correlated rates between interacting plastid and nuclear sequences across the Geraniales could result from plastid-nuclear genome coevolution. Analyses of coevolved amino acid positions suggest that structurally mediated coevolution is not the major driver of plastid-nuclear coevolution. The detection of strong correlation of evolutionary rates between SIG and RNAP genes suggests a plausible explanation for plastome-genome incompatibility in Geraniaceae. PMID:25724640
Sexually antagonistic coevolution for sexual harassment can act as a barrier to further invasions by parthenogenesis.

PubMed

Kawatsu, Kazutaka

2013-02-01

The assumption of a twofold cost of sex not only complicates the maintenance of sex but also sets conditions for sexual conflict: in organisms with the twofold cost, males often sexually harass females. Sexual harassment is detrimental to female fitness and thus might help maintain sexual populations if male harassment inflicts a harsher cost on parthenogens than on sexual females (asymmetric harassment cost). However, the generality of this concept is now considered doubtful because selective harassment of parthenogens results in loss of mating opportunities for males. Using three mathematical models, I show here that sexual harassment still can impose the asymmetric cost on parthenogens. First, I apply the Lotka-Volterra model to show the degree of asymmetric harassment cost that permits sex to be maintained stably in the population. Second, using adaptive dynamics, I examine whether sexually antagonistic coevolution for sexual harassment, which occurs only in sexual populations, can promote the asymmetric harassment cost. Finally, an individual-based model, which assumes a spatial structure unlike that in the other two, demonstrates that the asymmetric evolution of harassment cost prevents further invasions of parthenogens from different patches into sexual lineages; these mechanisms may account for allopatric distributions of sexual and parthenogenetic lineages as well as the maintenance of sex.
Assessing sexual conflict in the Drosophila melanogaster laboratory model system

PubMed Central

Rice, William R; Stewart, Andrew D; Morrow, Edward H; Linder, Jodell E; Orteiza, Nicole; Byrne, Phillip G

2006-01-01

We describe a graphical model of interlocus coevolution used to distinguish between the interlocus sexual conflict that leads to sexually antagonistic coevolution, and the intrinsic conflict over mating rate that is an integral part of traditional models of sexual selection. We next distinguish the ‘laboratory island’ approach from the study of both inbred lines and laboratory populations that are newly derived from nature, discuss why we consider it to be one of the most fitting forms of laboratory analysis to study interlocus sexual conflict, and then describe four experiments using this approach with Drosophila melanogaster. The first experiment evaluates the efficacy of the laboratory model system to study interlocus sexual conflict by comparing remating rates of females when they are, or are not, provided with a spatial refuge from persistent male courtship. The second experiment tests for a lag-load in males that is due to adaptations that have accumulated in females, which diminish male-induced harm while simultaneously interfering with a male's ability to compete in the context of sexual selection. The third and fourth experiments test for a lag-load in females owing to direct costs from their interactions with males, and for the capacity for indirect benefits to compensate for these direct costs. PMID:16612888
Infanticide as Sexual Conflict: Coevolution of Male Strategies and Female Counterstrategies

PubMed Central

Palombit, Ryne A.

2015-01-01

One of the earliest recognized forms of sexual conflict was infanticide by males, which imposes serious costs on female reproductive success. Here I review two bodies of evidence addressing coevolved strategies of males and females. The original sexual selection hypothesis arguing that infanticide improves male mating success by accelerating the return of females to fertilizable condition has been generally supported in some taxa—notably, some primates, carnivores, rodents, and cetaceans—but not in other taxa. One result of recent research has been to implicate other selective benefits of infanticide by males in various taxa from insects to birds to mammals, such as acquisition of breeding status or improvement of the female breeding condition. In some cases, however, the adaptive significance of male infanticide remains obscure. The second body of data I review is arguably the most important result of recent research: clarifying the possible female counterstrategies to infanticide. These potential counterstrategies span diverse biological systems, ranging from sexual behavior (e.g., polyandrous mating), to physiology (e.g., the Bruce effect), to individual behavior (e.g., maternal aggression), to social strategies (e.g., association with coalitionary defenders of either sex). Although much remains to be studied, these current data provide compelling evidence of sexually antagonistic coevolution surrounding the phenomenon of infanticide. PMID:25986557

ROTOR END CAP

DOEpatents

Rushing, F.C.

1959-02-01

An improved end cap is described for the cylindrical rotor or bowl of a high-speed centrifugal separator adapted to permit free and efficient continuous counter current flow of gas therethrough for isotope separation. The end cap design provides for securely mounting the same to the hollow central shaft and external wall of the centrifuge. Passageways are incorporated and so arranged as to provide for continuous counter current flow of the light and heavy portions of the gas fed to the centrifuge.
Fossilized skin reveals coevolution with feathers and metabolism in feathered dinosaurs and early birds.

PubMed

McNamara, Maria E; Zhang, Fucheng; Kearns, Stuart L; Orr, Patrick J; Toulouse, André; Foley, Tara; Hone, David W E; Rogers, Chris S; Benton, Michael J; Johnson, Diane; Xu, Xing; Zhou, Zhonghe

2018-05-25

Feathers are remarkable evolutionary innovations that are associated with complex adaptations of the skin in modern birds. Fossilised feathers in non-avian dinosaurs and basal birds provide insights into feather evolution, but how associated integumentary adaptations evolved is unclear. Here we report the discovery of fossil skin, preserved with remarkable nanoscale fidelity, in three non-avian maniraptoran dinosaurs and a basal bird from the Cretaceous Jehol biota (China). The skin comprises patches of desquamating epidermal corneocytes that preserve a cytoskeletal array of helically coiled α-keratin tonofibrils. This structure confirms that basal birds and non-avian dinosaurs shed small epidermal flakes as in modern mammals and birds, but structural differences imply that these Cretaceous taxa had lower body heat production than modern birds. Feathered epidermis acquired many, but not all, anatomically modern attributes close to the base of the Maniraptora by the Middle Jurassic.
A screen for immunity genes evolving under positive selection in Drosophila.

PubMed

Jiggins, F M; Kim, K W

2007-05-01

Genes involved in the immune system tend to have higher rates of adaptive evolution than other genes in the genome, probably because they are coevolving with pathogens. We have screened a sample of Drosophila genes to identify those evolving under positive selection. First, we identified rapidly evolving immunity genes by comparing 140 loci in Drosophila erecta and D. yakuba. Secondly, we resequenced 23 of the fastest evolving genes from the independent species pair D. melanogaster and D. simulans, and identified those under positive selection using a McDonald-Kreitman test. There was strong evidence of adaptive evolution in two serine proteases (persephone and spirit) and a homolog of the Anopheles serpin SRPN6, and weaker evidence in another serine protease and the death domain protein dFADD. These results add to mounting evidence that immune signalling pathway molecules often evolve rapidly, possibly because they are sites of host-parasite coevolution.
Reward Modulates Adaptations to Conflict

ERIC Educational Resources Information Center

Braem, Senne; Verguts, Tom; Roggeman, Chantal; Notebaert, Wim

2012-01-01

Both cognitive conflict (e.g. Verguts & Notebaert, 2009) and reward signals (e.g. Waszak & Pholulamdeth, 2009) have been proposed to enhance task-relevant associations. Bringing these two notions together, we predicted that reward modulates conflict-based sequential adaptations in cognitive control. This was tested combining either a single…
Environmentally adaptive processing for shallow ocean applications: A sequential Bayesian approach.

PubMed

Candy, J V

2015-09-01

The shallow ocean is a changing environment primarily due to temperature variations in its upper layers directly affecting sound propagation throughout. The need to develop processors capable of tracking these changes implies a stochastic as well as an environmentally adaptive design. Bayesian techniques have evolved to enable a class of processors capable of performing in such an uncertain, nonstationary (varying statistics), non-Gaussian, variable shallow ocean environment. A solution to this problem is addressed by developing a sequential Bayesian processor capable of providing a joint solution to the modal function tracking and environmental adaptivity problem. Here, the focus is on the development of both a particle filter and an unscented Kalman filter capable of providing reasonable performance for this problem. These processors are applied to hydrophone measurements obtained from a vertical array. The adaptivity problem is attacked by allowing the modal coefficients and/or wavenumbers to be jointly estimated from the noisy measurement data along with tracking of the modal functions while simultaneously enhancing the noisy pressure-field measurements.
Coevolution of strategy-selection time scale and cooperation in spatial prisoner's dilemma game

NASA Astrophysics Data System (ADS)

Rong, Zhihai; Wu, Zhi-Xi; Chen, Guanrong

2013-06-01

In this paper, we investigate a networked prisoner's dilemma game where individuals' strategy-selection time scale evolves based on their historical learning information. We show that the more times the current strategy of an individual is learnt by his neighbors, the longer time he will stick on the successful behavior by adaptively adjusting the lifetime of the adopted strategy. Through characterizing the extent of success of the individuals with normalized payoffs, we show that properly using the learned information can form a positive feedback mechanism between cooperative behavior and its lifetime, which can boost cooperation on square lattices and scale-free networks.
Optimizing trial design in pharmacogenetics research: comparing a fixed parallel group, group sequential, and adaptive selection design on sample size requirements.

PubMed

Boessen, Ruud; van der Baan, Frederieke; Groenwold, Rolf; Egberts, Antoine; Klungel, Olaf; Grobbee, Diederick; Knol, Mirjam; Roes, Kit

2013-01-01

Two-stage clinical trial designs may be efficient in pharmacogenetics research when there is some but inconclusive evidence of effect modification by a genomic marker. Two-stage designs allow to stop early for efficacy or futility and can offer the additional opportunity to enrich the study population to a specific patient subgroup after an interim analysis. This study compared sample size requirements for fixed parallel group, group sequential, and adaptive selection designs with equal overall power and control of the family-wise type I error rate. The designs were evaluated across scenarios that defined the effect sizes in the marker positive and marker negative subgroups and the prevalence of marker positive patients in the overall study population. Effect sizes were chosen to reflect realistic planning scenarios, where at least some effect is present in the marker negative subgroup. In addition, scenarios were considered in which the assumed 'true' subgroup effects (i.e., the postulated effects) differed from those hypothesized at the planning stage. As expected, both two-stage designs generally required fewer patients than a fixed parallel group design, and the advantage increased as the difference between subgroups increased. The adaptive selection design added little further reduction in sample size, as compared with the group sequential design, when the postulated effect sizes were equal to those hypothesized at the planning stage. However, when the postulated effects deviated strongly in favor of enrichment, the comparative advantage of the adaptive selection design increased, which precisely reflects the adaptive nature of the design. Copyright © 2013 John Wiley & Sons, Ltd.
Completion processing for data communications instructions

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

Blocksome, Michael A; Kumar, Sameer; Parker, Jeffrey J

Completion processing of data communications instructions in a distributed computing environment, including receiving, in an active messaging interface (`AMI`) data communications instructions, at least one instruction specifying a callback function; injecting into an injection FIFO buffer of a data communication adapter, an injection descriptor, each slot in the injection FIFO buffer having a corresponding slot in a pending callback list; listing in the pending callback list any callback function specified by an instruction, incrementing a pending callback counter for each listed callback function; transferring payload data as per each injection descriptor, incrementing a transfer counter upon completion of each transfer;more » determining from counter values whether the pending callback list presently includes callback functions whose data transfers have been completed; calling by the AMI any such callback functions from the pending callback list, decrementing the pending callback counter for each callback function called.« less
Bidirectional relationships between client and counselor speech: the importance of reframing.

PubMed

Barnett, Elizabeth; Spruijt-Metz, Donna; Moyers, Theresa B; Smith, Caitlin; Rohrbach, Louise A; Sun, Ping; Sussman, Steve

2014-12-01

In the study of motivational interviewing (MI), counselor skill has been posited to influence client language about change or "change talk." This study investigates the relationship between a specific counselor behavior, valenced reflective listening, and client change talk in a MI intervention with substance-using adolescents. A combination of recorded in-person and telephone (n = 223) sessions were sequentially coded using the Motivational Interviewing Skill Code 2.5. Reflections were categorized by valence, meaning they included content that was either moving toward (i.e., positive reflection) or away from change (i.e., negative reflection). Client language was coded as either moving toward change, away from change, or neutral about change. Probability analyses showed positive reflections were 11 times more likely to be followed by change talk and 71% less likely to be followed by counter change talk. Negative reflections were 19 times more likely to be followed by counter change talk and 65% less likely to be followed by change talk. Client language was also predictive of counselor reflections, such that positive reflections were 10 times more likely to occur after client change talk and negative reflections were 19 times more likely to follow counter change talk. Because the percentage of change talk expressed in a session has been shown to be positively related to improved behavioral outcomes, counselors should avoid unintentional reflections of counter change talk and use reframing techniques to change the valence of client change language. Implications for MI practice and training are discussed.
Coevolution in the Galapagos: An Example for the Biology Classroom.

ERIC Educational Resources Information Center

Biggs, Alton L.

1990-01-01

Several examples of coevolution which can be used in biology classes are presented. Discussed are evolutionary processes in general, giant cacti, and reptile and cacti association. The effects of human interference are briefly described. (CW)
Molecular dynamics simulations and statistical coupling analysis reveal functional coevolution network of oncogenic mutations in the CDKN2A-CDK6 complex.

PubMed

Wang, Jingwen; Zhao, Yuqi; Wang, Yanjie; Huang, Jingfei

2013-01-16

Coevolution between proteins is crucial for understanding protein-protein interaction. Simultaneous changes allow a protein complex to maintain its overall structural-functional integrity. In this study, we combined statistical coupling analysis (SCA) and molecular dynamics simulations on the CDK6-CDKN2A protein complex to evaluate coevolution between proteins. We reconstructed an inter-protein residue coevolution network, consisting of 37 residues and 37 interactions. It shows that most of the coevolved residue pairs are spatially proximal. When the mutations happened, the stable local structures were broken up and thus the protein interaction was decreased or inhibited, with a following increased risk of melanoma. The identification of inter-protein coevolved residues in the CDK6-CDKN2A complex can be helpful for designing protein engineering experiments. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.
Does cross-generational epigenetic inheritance contribute to cultural continuity?

PubMed Central

Pembrey, Marcus E

2018-01-01

Abstract Human studies of cross-generational epigenetic inheritance have to consider confounding by social patterning down the generations, often referred to as ‘cultural inheritance’. This raises the question to what extent is ‘cultural inheritance’ itself epigenetically mediated rather than just learnt. Human studies of non-genetic inheritance have demonstrated that, beyond foetal life, experiences occurring in mid-childhood before puberty are the most likely to be associated with cross-generational responses in the next generation(s). It is proposed that cultural continuity is played out along the axis, or ‘payoff’, between responsiveness and stability. During the formative years of childhood a stable family and/or home permits small children to explore and thereby learn. To counter disruptions to this family home ideal, cultural institutions such as local schools, religious centres and market places emerged to provide ongoing stability, holding the received wisdom of the past in an accessible state. This cultural support allows the growing child to freely indulge their responsiveness. Some of these prepubertal experiences induce epigenetic responses that also transfer molecular signals to the gametes through which they contribute to the conception of future offspring. In parallel co-evolution with growing cultural support for increasing responsiveness, ‘runaway’ responsiveness is countered by the positive selection of genetic variants that dampen responsiveness. Testing these ideas within longitudinal multigenerational cohorts will need information on ancestors/parents’ own communities and experiences (Exposome scans) linked to ongoing Phenome scans on grandchildren; coupled with epigenome analysis, metastable epialleles and DNA methylation age. Interactions with genetic variants affecting responsiveness should help inform the broad hypothesis. PMID:29732169
Does cross-generational epigenetic inheritance contribute to cultural continuity?

PubMed

Pembrey, Marcus E

2018-04-01

Human studies of cross-generational epigenetic inheritance have to consider confounding by social patterning down the generations, often referred to as 'cultural inheritance'. This raises the question to what extent is 'cultural inheritance' itself epigenetically mediated rather than just learnt. Human studies of non-genetic inheritance have demonstrated that, beyond foetal life, experiences occurring in mid-childhood before puberty are the most likely to be associated with cross-generational responses in the next generation(s). It is proposed that cultural continuity is played out along the axis, or 'payoff', between responsiveness and stability. During the formative years of childhood a stable family and/or home permits small children to explore and thereby learn. To counter disruptions to this family home ideal, cultural institutions such as local schools, religious centres and market places emerged to provide ongoing stability, holding the received wisdom of the past in an accessible state. This cultural support allows the growing child to freely indulge their responsiveness. Some of these prepubertal experiences induce epigenetic responses that also transfer molecular signals to the gametes through which they contribute to the conception of future offspring. In parallel co-evolution with growing cultural support for increasing responsiveness, 'runaway' responsiveness is countered by the positive selection of genetic variants that dampen responsiveness. Testing these ideas within longitudinal multigenerational cohorts will need information on ancestors/parents' own communities and experiences (Exposome scans) linked to ongoing Phenome scans on grandchildren; coupled with epigenome analysis, metastable epialleles and DNA methylation age. Interactions with genetic variants affecting responsiveness should help inform the broad hypothesis.
A Centimeter-Scale Investigation of Geochemical Hotspots in a Soil Lysimeter

NASA Astrophysics Data System (ADS)

Umanzor, M.; Wang, Y.; Dontsova, K.; Chorover, J.; Troch, P. A. A.

2016-12-01

Studying the co-evolution of hydrological and biogeochemical processes in the subsurface of natural landscapes can enhance the understanding of coupled Earth-system processes. Such knowledge is imperative for improving predictions of hydro-biogeochemical cycles, especially under climate change scenarios. Hotspots may form in porous media that is undergoing biogeochemical weathering at locations where reactants accumulate to threshold values along hydrologic flow paths. This is expected to occur in weatherable silicate media, like granular basalt. To examine such processes during incipient soil formation, we constructed a sloping weighing lysimeter 2-m in length, 0.5-m in width and 1-m in depth. Mini-LEO was filled with crushed granular basalt rock with a known initial chemical composition. After 18 months of irrigation and intensive hydrological study, the model "landscape" was divided into a 3D matrix of 324 voxels and excavated. Collected samples were subjected to detailed hydro-bio-geochemical analysis to assess the formation of geochemical heterogeneity. A five-step sequential extraction was employed to characterize incongruent mineral weathering, and its relation to the spatial distribution of microbial composition (in a related study). The changes in Fe and Mn concentration and speciation along the lysimeter length and depth (as measured by each step of the sequential extraction) was quantified to characterize spatial distribution of weathering processes. Results are being used to assist in understanding not only spatial and temporal distribution of basalt weathering on the slope, but also, connections between hydrological and biogeochemical cycles that lead to formation of hotspots.
Coordinated rates of evolution between interacting plastid and nuclear genes in Geraniaceae.

PubMed

Zhang, Jin; Ruhlman, Tracey A; Sabir, Jamal; Blazier, J Chris; Jansen, Robert K

2015-03-01

Although gene coevolution has been widely observed within individuals and between different organisms, rarely has this phenomenon been investigated within a phylogenetic framework. The Geraniaceae is an attractive system in which to study plastid-nuclear genome coevolution due to the highly elevated evolutionary rates in plastid genomes. In plants, the plastid-encoded RNA polymerase (PEP) is a protein complex composed of subunits encoded by both plastid (rpoA, rpoB, rpoC1, and rpoC2) and nuclear genes (sig1-6). We used transcriptome and genomic data for 27 species of Geraniales in a systematic evaluation of coevolution between genes encoding subunits of the PEP holoenzyme. We detected strong correlations of dN (nonsynonymous substitutions) but not dS (synonymous substitutions) within rpoB/sig1 and rpoC2/sig2, but not for other plastid/nuclear gene pairs, and identified the correlation of dN/dS ratio between rpoB/C1/C2 and sig1/5/6, rpoC1/C2 and sig2, and rpoB/C2 and sig3 genes. Correlated rates between interacting plastid and nuclear sequences across the Geraniales could result from plastid-nuclear genome coevolution. Analyses of coevolved amino acid positions suggest that structurally mediated coevolution is not the major driver of plastid-nuclear coevolution. The detection of strong correlation of evolutionary rates between SIG and RNAP genes suggests a plausible explanation for plastome-genome incompatibility in Geraniaceae. © 2015 American Society of Plant Biologists. All rights reserved.
Protein contact prediction by integrating deep multiple sequence alignments, coevolution and machine learning.

PubMed

Adhikari, Badri; Hou, Jie; Cheng, Jianlin

2018-03-01

In this study, we report the evaluation of the residue-residue contacts predicted by our three different methods in the CASP12 experiment, focusing on studying the impact of multiple sequence alignment, residue coevolution, and machine learning on contact prediction. The first method (MULTICOM-NOVEL) uses only traditional features (sequence profile, secondary structure, and solvent accessibility) with deep learning to predict contacts and serves as a baseline. The second method (MULTICOM-CONSTRUCT) uses our new alignment algorithm to generate deep multiple sequence alignment to derive coevolution-based features, which are integrated by a neural network method to predict contacts. The third method (MULTICOM-CLUSTER) is a consensus combination of the predictions of the first two methods. We evaluated our methods on 94 CASP12 domains. On a subset of 38 free-modeling domains, our methods achieved an average precision of up to 41.7% for top L/5 long-range contact predictions. The comparison of the three methods shows that the quality and effective depth of multiple sequence alignments, coevolution-based features, and machine learning integration of coevolution-based features and traditional features drive the quality of predicted protein contacts. On the full CASP12 dataset, the coevolution-based features alone can improve the average precision from 28.4% to 41.6%, and the machine learning integration of all the features further raises the precision to 56.3%, when top L/5 predicted long-range contacts are evaluated. And the correlation between the precision of contact prediction and the logarithm of the number of effective sequences in alignments is 0.66. © 2017 Wiley Periodicals, Inc.
Adaptive bill morphology for enhanced tool manipulation in New Caledonian crows

PubMed Central

Matsui, Hiroshi; Hunt, Gavin R.; Oberhofer, Katja; Ogihara, Naomichi; McGowan, Kevin J.; Mithraratne, Kumar; Yamasaki, Takeshi; Gray, Russell D.; Izawa, Ei-Ichi

2016-01-01

Early increased sophistication of human tools is thought to be underpinned by adaptive morphology for efficient tool manipulation. Such adaptive specialisation is unknown in nonhuman primates but may have evolved in the New Caledonian crow, which has sophisticated tool manufacture. The straightness of its bill, for example, may be adaptive for enhanced visually-directed use of tools. Here, we examine in detail the shape and internal structure of the New Caledonian crow’s bill using Principal Components Analysis and Computed Tomography within a comparative framework. We found that the bill has a combination of interrelated shape and structural features unique within Corvus, and possibly birds generally. The upper mandible is relatively deep and short with a straight cutting edge, and the lower mandible is strengthened and upturned. These novel combined attributes would be functional for (i) counteracting the unique loading patterns acting on the bill when manipulating tools, (ii) a strong precision grip to hold tools securely, and (iii) enhanced visually-guided tool use. Our findings indicate that the New Caledonian crow’s innovative bill has been adapted for tool manipulation to at least some degree. Early increased sophistication of tools may require the co-evolution of morphology that provides improved manipulatory skills. PMID:26955788
Dissecting the contributions of plasticity and local adaptation to the phenology of a butterfly and its host plants.

PubMed

Phillimore, Albert B; Stålhandske, Sandra; Smithers, Richard J; Bernard, Rodolphe

2012-11-01

Phenology affects the abiotic and biotic conditions that an organism encounters and, consequently, its fitness. For populations of high-latitude species, spring phenology often occurs earlier in warmer years and regions. Here we apply a novel approach, a comparison of slope of phenology on temperature over space versus over time, to identify the relative roles of plasticity and local adaptation in generating spatial phenological variation in three interacting species, a butterfly, Anthocharis cardamines, and its two host plants, Cardamine pratensis and Alliaria petiolata. All three species overlap in the time window over which mean temperatures best predict variation in phenology, and we find little evidence that a day length requirement causes the sensitive time window to be delayed as latitude increases. The focal species all show pronounced temperature-mediated phenological plasticity of similar magnitude. While we find no evidence for local adaptation in the flowering times of the plants, geographic variation in the phenology of the butterfly is consistent with countergradient local adaptation. The butterfly's phenology appears to be better predicted by temperature than it is by the flowering times of either host plant, and we find no evidence that coevolution has generated geographic variation in adaptive phenological plasticity.
An extension of the coevolution theory of the origin of the genetic code

PubMed Central

Di Giulio, Massimo

2008-01-01

Background The coevolution theory of the origin of the genetic code suggests that the genetic code is an imprint of the biosynthetic relationships between amino acids. However, this theory does not seem to attribute a role to the biosynthetic relationships between the earliest amino acids that evolved along the pathways of energetic metabolism. As a result, the coevolution theory is unable to clearly define the very earliest phases of genetic code origin. In order to remove this difficulty, I here suggest an extension of the coevolution theory that attributes a crucial role to the first amino acids that evolved along these biosynthetic pathways and to their biosynthetic relationships, even when defined by the non-amino acid molecules that are their precursors. Results It is re-observed that the first amino acids to evolve along these biosynthetic pathways are predominantly those codified by codons of the type GNN, and this observation is found to be statistically significant. Furthermore, the close biosynthetic relationships between the sibling amino acids Ala-Ser, Ser-Gly, Asp-Glu, and Ala-Val are not random in the genetic code table and reinforce the hypothesis that the biosynthetic relationships between these six amino acids played a crucial role in defining the very earliest phases of genetic code origin. Conclusion All this leads to the hypothesis that there existed a code, GNS, reflecting the biosynthetic relationships between these six amino acids which, as it defines the very earliest phases of genetic code origin, removes the main difficulty of the coevolution theory. Furthermore, it is here discussed how this code might have naturally led to the code codifying only for the domains of the codons of precursor amino acids, as predicted by the coevolution theory. Finally, the hypothesis here suggested also removes other problems of the coevolution theory, such as the existence for certain pairs of amino acids with an unclear biosynthetic relationship between the precursor and product amino acids and the collocation of Ala between the amino acids Val and Leu belonging to the pyruvate biosynthetic family, which the coevolution theory considered as belonging to different biosyntheses. Reviewers This article was reviewed by Rob Knight, Paul Higgs (nominated by Laura Landweber), and Eugene Koonin. PMID:18775066
Adaptive Parameter Estimation of Person Recognition Model in a Stochastic Human Tracking Process

NASA Astrophysics Data System (ADS)

Nakanishi, W.; Fuse, T.; Ishikawa, T.

2015-05-01

This paper aims at an estimation of parameters of person recognition models using a sequential Bayesian filtering method. In many human tracking method, any parameters of models used for recognize the same person in successive frames are usually set in advance of human tracking process. In real situation these parameters may change according to situation of observation and difficulty level of human position prediction. Thus in this paper we formulate an adaptive parameter estimation using general state space model. Firstly we explain the way to formulate human tracking in general state space model with their components. Then referring to previous researches, we use Bhattacharyya coefficient to formulate observation model of general state space model, which is corresponding to person recognition model. The observation model in this paper is a function of Bhattacharyya coefficient with one unknown parameter. At last we sequentially estimate this parameter in real dataset with some settings. Results showed that sequential parameter estimation was succeeded and were consistent with observation situations such as occlusions.

Our Social Roots: How Local Ecology Shapes Our Social Structures

NASA Astrophysics Data System (ADS)

Mace, Ruth

There is overwhelming evidence that wide-ranging aspects of human biology and human behavior can be considered as adaptations to different subsistence systems. Wider environmental and ecological correlates of behavioral and cultural traits are generally best understood as being mediated by differences in subsistence strategies. Modes of subsistence profoundly influence both human biology, as documented in genetic changes, and human social behavior and cultural norms, such as kinship, marriage, descent, wealth inheritance, and political systems. Thus both cultural and biological factors usually need to be considered together in studies of human evolutionary ecology, combined in specifically defined evolutionary models. Models of cultural adaptation to environmental conditions can be subjected to the same or similar tests that behavioral ecologists have used to seek evidence for adaptive behavior in other species. Phylogenetic comparative methods are proving useful, both for studying co-evolutionary hypotheses (cultural and/or gene-culture co-evolution), and for estimating ancestral states of prehistoric societies. This form of formal cross-cultural comparison is helping to put history back into anthropology, and helping us to understand cultural evolutionary processes at a number of levels.
Ants and antlions: The impact of ecology, coevolution and learning on an insect predator-prey relationship.

PubMed

Hollis, Karen L

2017-06-01

A behavioural ecological approach to the relationship between pit-digging larval antlions and their common prey, ants, provides yet another example of how the specific ecological niche that species inhabit imposes selection pressures leading to unique behavioural adaptations. Antlions rely on multiple strategies to capture prey with a minimal expenditure of energy and extraordinary efficiency while ants employ several different strategies for avoiding capture, including rescue of trapped nestmates. Importantly, both ants and antlions rely heavily on their capacity for learning, a tool that sometimes is overlooked in predator-prey relationships, leading to the implicit assumption that behavioural adaptations are the result of fixed, hard-wired responses. Nonetheless, like hard-wired responses, learned behaviour, too, is uniquely adapted to the ecological niche, a reminder that the expression of associative learning is species-specific. Beyond the study of ants and antlions, per se, this particular predator-prey relationship reveals the important role that the capacity to learn plays in coevolutionary arms races. Copyright © 2016 Elsevier B.V. All rights reserved.
Different gene expressions between cattle and yak provide insights into high-altitude adaptation.

PubMed

Wang, K; Yang, Y; Wang, L; Ma, T; Shang, H; Ding, L; Han, J; Qiu, Q

2016-02-01

DNA sequence variation has been widely reported as the genetic basis for adaptation, in both humans and other animals, to the hypoxic environment experienced at high altitudes. However, little is known about the patterns of gene expression underlying such hypoxic adaptations. In this study, we examined the differences in the transcriptomes of four organs (heart, kidney, liver and lung) between yak and cattle, a pair of closely related species distributed at high and low altitudes respectively. Of the four organs examined, heart shows the greatest differentiation between the two species in terms of gene expression profiles. Detailed analyses demonstrated that some genes associated with the oxygen supply system and the defense systems that respond to threats of hypoxia are differentially expressed. In addition, genes with significantly differentiated patterns of expression in all organs exhibited an unexpected uniformity of regulation along with an elevated frequency of nonsynonymous substitutions. This co-evolution of protein sequences and gene expression patterns is likely to be correlated with the optimization of the yak metabolic system to resist hypoxia. © 2015 Stichting International Foundation for Animal Genetics.
Evolution of the Genetic and Neural Architecture for Vertebrate Odor Perception

PubMed Central

Bear, Daniel M.; Lassance, Jean-Marc; Hoekstra, Hopi E.; Datta, Sandeep Robert

2016-01-01

Evolution sculpts the olfactory nervous system in response to the unique sensory challenges facing each species. In vertebrates, dramatic and diverse adaptations to the chemical environment are possible because of the hierarchical structure of the olfactory receptor (OR) gene superfamily: rapid growth or pruning across the OR gene tree accompany major changes in habitat and lifestyle; independent selection on OR subfamilies can permit local adaptation or conserved chemical communication; and genetic variation in single OR genes among thousands can alter odor percepts and behaviors driven by precise chemical cues. However, this genetic flexibility contrasts with the relatively fixed neural architecture of the vertebrate olfactory system, whose slower rate of divergence mandates that new olfactory receptors integrate into segregated and functionally-distinct neural pathways. This organization allows evolution to couple critical chemical signals with selectively advantageous responses, but also constrains relationships between olfactory receptors and behavior. The coevolution of the OR repertoire and the structure of the olfactory system therefore reveals general principles of how the brain solves specific sensory problems and how it adapts to new ones. PMID:27780046
Resistance to mate guarding scale in women: psychometric properties.

PubMed

Cousins, Alita J; Fugère, Madeleine A; Riggs, Matthew L

2015-02-03

One individual's actions may affect the evolutionary fitness of another individual. Sexually antagonistic coevolution occurs when one partner's behavior decreases the fitness of the other partner (Rice, 1996). This conflict pressures the other partner to counter these disadvantageous actions. Mate guarding is a mate retention tactic aimed at keeping a partner from cheating. Mate guarding may reduce mate choice, especially for extra pair mates. Therefore, some individuals may resist their partner's mate guarding tactics. We developed a scale to measure resistance to mate guarding and tested it in women (N = 1069). Using exploratory factor analysis (EFA), six theoretically sound factors emerged and explained 69% of the variance. Confirmatory Factor Analysis showed strong support for the six original subscales as well as for the overall scale. The subscales had high reliability. The validity of the Resistance to Mate Guarding Scale was also excellent. Women who stated they used more resistance to mate guarding strategies also indicated that they had partners who mate guarded more, were less invested in their relationships, felt their partners were more controlling, had a more avoidant attachment style, and had a more unrestricted sociosexual orientation.
Restoration of fire in managed forests: a model to prioritize landscapes and analyze tradeoffs

Treesearch

Alan A. Ager; Nicole M. Vaillant; Andrew McMahan

2013-01-01

Ongoing forest restoration on public lands in the western US is a concerted effort to counter the growing incidence of uncharacteristic wildfire in fire-adapted ecosystems. Restoration projects cover 725,000 ha annually, and include thinning and underburning to remove ladder and surface fuel, and seeding of fire-adapted native grasses and shrubs. The backlog of areas...
Studying the co-evolution of protein families with the Mirrortree web server.

PubMed

Ochoa, David; Pazos, Florencio

2010-05-15

The Mirrortree server allows to graphically and interactively study the co-evolution of two protein families, and investigate their possible interactions and functional relationships in a taxonomic context. The server includes the possibility of starting from single sequences and hence it can be used by non-expert users. The web server is freely available at http://csbg.cnb.csic.es/mtserver. It was tested in the main web browsers. Adobe Flash Player is required at the client side to perform the interactive assessment of co-evolution. pazos@cnb.csic.es Supplementary data are available at Bioinformatics online.
Coevolution analysis of Hepatitis C virus genome to identify the structural and functional dependency network of viral proteins

NASA Astrophysics Data System (ADS)

Champeimont, Raphaël; Laine, Elodie; Hu, Shuang-Wei; Penin, Francois; Carbone, Alessandra

2016-05-01

A novel computational approach of coevolution analysis allowed us to reconstruct the protein-protein interaction network of the Hepatitis C Virus (HCV) at the residue resolution. For the first time, coevolution analysis of an entire viral genome was realized, based on a limited set of protein sequences with high sequence identity within genotypes. The identified coevolving residues constitute highly relevant predictions of protein-protein interactions for further experimental identification of HCV protein complexes. The method can be used to analyse other viral genomes and to predict the associated protein interaction networks.
The early phase of the SMBH-galaxy coevolution in low-z "young" galaxies

NASA Astrophysics Data System (ADS)

Nagao, Tohru

2014-01-01

It is now widely recognized that most galaxies have a supermassive black hole (SMBH) in their nucleus, and the evolution of SMBHs is closely related with that of their host galaxies (the SMBH-galaxy coevolution). This is suggested by the correlation in the mass of SMBHs and their host galaxies, that has been observed in low redshifts. However, the physics of the coevolution is totally unclear, that prevents us from complete understandings of the galaxy evolution. One possible strategy to tackle this issue is measuring the mass ratio between SMBHs and their host galaxies (M_BH/M_host) at high redshifs, since different scenarios predict different evolution of the ratio ofMBH/Mhost. However it is extremely challenging to measure the mass of the host of high-z quasars, given the faint surface brightness of the host at close to the glaring quasar nucleus. Here we propose a brand-new approach to assess the early phase of the SMBH-galaxy coevolution, by focusing on low-z AGN-hosting "young" galaxies. Specifically, we focus on some very metal-poor galaxies with broadline Balmer lines at z ~ 0.1 - 0.3. By examining the SMBH scaling relations in some low-z metal-poor AGNs through high-resolution IRCS imaging observations, we will discriminate various scenarios for the SMBH-galaxy coevolution.
Host-parasite coevolution can promote the evolution of seed banking as a bet-hedging strategy.

PubMed

Verin, Mélissa; Tellier, Aurélien

2018-04-20

Seed (egg) banking is a common bet-hedging strategy maximizing the fitness of organisms facing environmental unpredictability by the delayed emergence of offspring. Yet, this condition often requires fast and drastic stochastic shifts between good and bad years. We hypothesize that the host seed banking strategy can evolve in response to coevolution with parasites because the coevolutionary cycles promote a gradually changing environment over longer times than seed persistence. We study the evolution of host germination fraction as a quantitative trait using both pairwise competition and multiple mutant competition methods, while the germination locus can be genetically linked or unlinked with the host locus under coevolution. In a gene-for-gene model of coevolution, hosts evolve a seed bank strategy under unstable coevolutionary cycles promoted by moderate to high costs of resistance or strong disease severity. Moreover, when assuming genetic linkage between coevolving and germination loci, the resistant genotype always evolves seed banking in contrast to susceptible hosts. Under a matching-allele interaction, both hosts' genotypes exhibit the same seed banking strategy irrespective of the genetic linkage between loci. We suggest host-parasite coevolution as an additional hypothesis for the evolution of seed banking as a temporal bet-hedging strategy. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.
Adaptive Interventions and SMART Designs: Application to Child Behavior Research in a Community Setting

ERIC Educational Resources Information Center

Kidwell, Kelley M.; Hyde, Luke W.

2016-01-01

Heterogeneity between and within people necessitates the need for sequential personalized interventions to optimize individual outcomes. Personalized or adaptive interventions (AIs) are relevant for diseases and maladaptive behavioral trajectories when one intervention is not curative and success of a subsequent intervention may depend on…
Parallel Algorithm Solves Coupled Differential Equations

NASA Technical Reports Server (NTRS)

Hayashi, A.

1987-01-01

Numerical methods adapted to concurrent processing. Algorithm solves set of coupled partial differential equations by numerical integration. Adapted to run on hypercube computer, algorithm separates problem into smaller problems solved concurrently. Increase in computing speed with concurrent processing over that achievable with conventional sequential processing appreciable, especially for large problems.
An Adaptable Investigative Graduate Laboratory Course for Teaching Protein Purification

ERIC Educational Resources Information Center

Carroll, Christopher W.; Keller, Lani C.

2014-01-01

This adaptable graduate laboratory course on protein purification offers students the opportunity to explore a wide range of techniques while allowing the instructor the freedom to incorporate their own personal research interests. The course design involves two sequential purification schemes performed in a single semester. The first part…
Mutual Information Item Selection in Adaptive Classification Testing

ERIC Educational Resources Information Center

Weissman, Alexander

2007-01-01

A general approach for item selection in adaptive multiple-category classification tests is provided. The approach uses mutual information (MI), a special case of the Kullback-Leibler distance, or relative entropy. MI works efficiently with the sequential probability ratio test and alleviates the difficulties encountered with using other local-…
Sequential congruency effects: disentangling priming and conflict adaptation.

PubMed

Puccioni, Olga; Vallesi, Antonino

2012-09-01

Responding to the color of a word is slower and less accurate if the word refers to a different color (incongruent condition) than if it refers to the same color (congruent condition). This phenomenon, known as the Stroop effect, is modulated by sequential effects: it is bigger when the current trial is preceded by a congruent condition than by an incongruent one in the previous trial. Whether this phenomenon is due to priming mechanisms or to cognitive control is still debated. To disentangle the contribution of priming with respect to conflict adaptation mechanisms in determining sequential effects, two experiments were designed here with a four-alternative forced choice (4-AFC) Stroop task: in the first one only trials with complete alternations of features were used, while in the second experiment all possible types of repetitions were presented. Both response times (RTs) and errors were evaluated. Conflict adaptation effects on RTs were limited to congruent trials and were exclusively due to priming: they disappeared in the priming-free experiment and, in the second experiment, they occurred in sequences with feature repetitions but not in complete alternation sequences. Error results, instead, support the presence of conflict adaptation effects in incongruent trials. In priming-free sequences (experiment 1 and complete alternation sequences of experiment 2) with incongruent previous trials there was no error Stroop effect, while this effect was significant with congruent previous trials. These results indicate that cognitive control may modulate performance above and beyond priming effects.
Climate change and evolutionary adaptation.

PubMed

Hoffmann, Ary A; Sgrò, Carla M

2011-02-24

Evolutionary adaptation can be rapid and potentially help species counter stressful conditions or realize ecological opportunities arising from climate change. The challenges are to understand when evolution will occur and to identify potential evolutionary winners as well as losers, such as species lacking adaptive capacity living near physiological limits. Evolutionary processes also need to be incorporated into management programmes designed to minimize biodiversity loss under rapid climate change. These challenges can be met through realistic models of evolutionary change linked to experimental data across a range of taxa.
Genetic and structural analyses of cytochrome P450 hydroxylases in sex hormone biosynthesis: Sequential origin and subsequent coevolution.

PubMed

Goldstone, Jared V; Sundaramoorthy, Munirathinam; Zhao, Bin; Waterman, Michael R; Stegeman, John J; Lamb, David C

2016-01-01

Biosynthesis of steroid hormones in vertebrates involves three cytochrome P450 hydroxylases, CYP11A1, CYP17A1 and CYP19A1, which catalyze sequential steps in steroidogenesis. These enzymes are conserved in the vertebrates, but their origin and existence in other chordate subphyla (Tunicata and Cephalochordata) have not been clearly established. In this study, selected protein sequences of CYP11A1, CYP17A1 and CYP19A1 were compiled and analyzed using multiple sequence alignment and phylogenetic analysis. Our analyses show that cephalochordates have sequences orthologous to vertebrate CYP11A1, CYP17A1 or CYP19A1, and that echinoderms and hemichordates possess CYP11-like but not CYP19 genes. While the cephalochordate sequences have low identity with the vertebrate sequences, reflecting evolutionary distance, the data show apparent origin of CYP11 prior to the evolution of CYP19 and possibly CYP17, thus indicating a sequential origin of these functionally related steroidogenic CYPs. Co-occurrence of the three CYPs in early chordates suggests that the three genes may have coevolved thereafter, and that functional conservation should be reflected in functionally important residues in the proteins. CYP19A1 has the largest number of conserved residues while CYP11A1 sequences are less conserved. Structural analyses of human CYP11A1, CYP17A1 and CYP19A1 show that critical substrate binding site residues are highly conserved in each enzyme family. The results emphasize that the steroidogenic pathways producing glucocorticoids and reproductive steroids are several hundred million years old and that the catalytic structural elements of the enzymes have been conserved over the same period of time. Analysis of these elements may help to identify when precursor functions linked to these enzymes first arose. Copyright © 2015 Elsevier Inc. All rights reserved.
A coevolution analysis for identifying protein-protein interactions by Fourier transform.

PubMed

Yin, Changchuan; Yau, Stephen S-T

2017-01-01

Protein-protein interactions (PPIs) play key roles in life processes, such as signal transduction, transcription regulations, and immune response, etc. Identification of PPIs enables better understanding of the functional networks within a cell. Common experimental methods for identifying PPIs are time consuming and expensive. However, recent developments in computational approaches for inferring PPIs from protein sequences based on coevolution theory avoid these problems. In the coevolution theory model, interacted proteins may show coevolutionary mutations and have similar phylogenetic trees. The existing coevolution methods depend on multiple sequence alignments (MSA); however, the MSA-based coevolution methods often produce high false positive interactions. In this paper, we present a computational method using an alignment-free approach to accurately detect PPIs and reduce false positives. In the method, protein sequences are numerically represented by biochemical properties of amino acids, which reflect the structural and functional differences of proteins. Fourier transform is applied to the numerical representation of protein sequences to capture the dissimilarities of protein sequences in biophysical context. The method is assessed for predicting PPIs in Ebola virus. The results indicate strong coevolution between the protein pairs (NP-VP24, NP-VP30, NP-VP40, VP24-VP30, VP24-VP40, and VP30-VP40). The method is also validated for PPIs in influenza and E.coli genomes. Since our method can reduce false positive and increase the specificity of PPI prediction, it offers an effective tool to understand mechanisms of disease pathogens and find potential targets for drug design. The Python programs in this study are available to public at URL (https://github.com/cyinbox/PPI).
A coevolution analysis for identifying protein-protein interactions by Fourier transform

PubMed Central

Yin, Changchuan; Yau, Stephen S. -T.

2017-01-01

Protein-protein interactions (PPIs) play key roles in life processes, such as signal transduction, transcription regulations, and immune response, etc. Identification of PPIs enables better understanding of the functional networks within a cell. Common experimental methods for identifying PPIs are time consuming and expensive. However, recent developments in computational approaches for inferring PPIs from protein sequences based on coevolution theory avoid these problems. In the coevolution theory model, interacted proteins may show coevolutionary mutations and have similar phylogenetic trees. The existing coevolution methods depend on multiple sequence alignments (MSA); however, the MSA-based coevolution methods often produce high false positive interactions. In this paper, we present a computational method using an alignment-free approach to accurately detect PPIs and reduce false positives. In the method, protein sequences are numerically represented by biochemical properties of amino acids, which reflect the structural and functional differences of proteins. Fourier transform is applied to the numerical representation of protein sequences to capture the dissimilarities of protein sequences in biophysical context. The method is assessed for predicting PPIs in Ebola virus. The results indicate strong coevolution between the protein pairs (NP-VP24, NP-VP30, NP-VP40, VP24-VP30, VP24-VP40, and VP30-VP40). The method is also validated for PPIs in influenza and E.coli genomes. Since our method can reduce false positive and increase the specificity of PPI prediction, it offers an effective tool to understand mechanisms of disease pathogens and find potential targets for drug design. The Python programs in this study are available to public at URL (https://github.com/cyinbox/PPI). PMID:28430779
Pulsed counter-current ultrasound-assisted extraction and characterization of polysaccharides from Boletus edulis.

PubMed

You, Qinghong; Yin, Xiulian; Ji, Chaowen

2014-01-30

Four methods for extracting polysaccharides from Boletus edulis, namely, hot-water extraction, ultrasonic clearer extraction, static probe ultrasonic extraction, and pulsed counter-current probe ultrasonic extraction (CCPUE), were studied. Results showed that CCPUE has the highest extraction efficiency among the methods studied. Under optimal CCPUE conditions, a B. edulis polysaccharide (BEP) yield of 8.21% was obtained. Three purified fractions, BEP-I, BEP-II, and BEP-III, were obtained through sequential purification by DEAE-52 and Sephadex G-75 chromatography. The average molecular weights of BEP-I, BEP-II, and BEP-III were 10,278, 23,761, and 42,736 Da, respectively. The polysaccharides were mainly composed of xylose, mannose, galactose, and glucose; of these, mannose contents were the highest. The antioxidant activities of the BEPs were further investigated by measurement of their ability to scavenge DPPH and hydroxyl radicals as well as their reducing power. The results indicated that the BEPs have good antioxidant activity. Copyright © 2013 Elsevier Ltd. All rights reserved.

Design of the biosonar simulator for dolphin's clicks waveform reproduction

NASA Astrophysics Data System (ADS)

Ishii, Ken; Akamatsu, Tomonari; Hatakeyama, Yoshimi

1992-03-01

The emitted clicks of Dall's porpoises consist of a pulse train of burst signals with an ultrasonic carrier frequency. The authors have designed a biosonar simulator to reproduce the waveforms associated with a dolphin's clicks underwater. The total reproduction system consists of a click signal acquisition block, a waveform analysis block, a memory unit, a click simulator, and a underwater, ultrasonic wave transmitter. In operation, data stored in an EPROM (Erasable Programmable Read Only Memory) are read out sequentially by a fast clock and converted to analog output signals. Then an ultrasonic power amplifier reproduces these signals through a transmitter. The click signal replaying block is referred to as the BSS (Biosonar Simulator). This is what simulates the clicks. The details of the BSS are described in this report. A unit waveform is defined. The waveform is divided into a burst period and a waiting period. Clicks are a sequence based on a unit waveform, and digital data are sequentially read out from an EPROM of waveform data. The basic parameters of the BSS are as follows: (1) reading clock, 100 ns to 25.4 microseconds; (2) number of reading clock, 34 to 1024 times; (3) counter clock in a waiting period, 100 ns to 25.4 microseconds; (4) number of counter clock, zero to 16,777,215 times; (5) number of burst/waiting repetition cycle, one to 128 times; and (6) transmission level adjustment by a programmable attenuator, zero to 86.5 dB. These basic functions enable the BSS to replay clicks of Dall's porpoise precisely.
Deciphering the role of DC subsets in MCMV infection to better understand immune protection against viral infections

PubMed Central

Alexandre, Yannick O.; Cocita, Clément D.; Ghilas, Sonia; Dalod, Marc

2014-01-01

Infection of mice with murine cytomegalovirus (MCMV) recapitulates many physiopathological characteristics of human CMV infection and enables studying the interactions between a virus and its natural host. Dendritic cells (DC) are mononuclear phagocytes linking innate and adaptive immunity which are both necessary for MCMV control. DC are critical for the induction of cellular immunity because they are uniquely efficient for the activation of naïve T cells during their first encounter with a pathogen. DC are equipped with a variety of innate immune recognition receptors (I2R2) allowing them to detect pathogens or infections and to engulf molecules, microorganisms or cellular debris. The combinatorial engagement of I2R2 during infections controls DC maturation and shapes their response in terms of cytokine production, activation of natural killer (NK) cells and functional polarization of T cells. Several DC subsets exist which express different arrays of I2R2 and are specialized in distinct functions. The study of MCMV infection helped deciphering the physiological roles of DC subsets and their molecular regulation. It allowed the identification and first in vivo studies of mouse plasmacytoid DC which produce high level of interferons-α/β early after infection. Despite its ability to infect DC and dampen their functions, MCMV induces very robust, efficient and long-lasting CD8 T cell responses. Their priming may rely on the unique ability of uninfected XCR1+ DC to cross-present engulfed viral antigens and thus to counter MCMV interference with antigen presentation. A balance appears to have been reached during co-evolution, allowing controlled replication of the virus for horizontal spread without pathological consequences for the immunocompetent host. We will discuss the role of the interplay between the virus and DC in setting this balance, and how advancing this knowledge further could help develop better vaccines against other intracellular infectious agents. PMID:25120535
Spatial variation in disease resistance: from molecules to metapopulations

PubMed Central

Laine, Anna-Liisa; Burdon, Jeremy J.; Dodds, Peter N.; Thrall, Peter H.

2010-01-01

Summary Variation in disease resistance is a widespread phenomenon in wild plant-pathogen associations. Here, we review current literature on natural plant-pathogen associations to determine how diversity in disease resistance is distributed at different hierarchical levels – within host individuals, within host populations, among host populations at the metapopulation scale and at larger regional scales. We find diversity in resistance across all spatial scales examined. Furthermore, variability seems to be the best counter-defence of plants against their rapidly evolving pathogens. We find that higher diversity of resistance phenotypes also results in higher levels of resistance at the population level. Overall, we find that wild plant populations are more likely to be susceptible than resistant to their pathogens. However, the degree of resistance differs strikingly depending on the origin of the pathogen strains used in experimental inoculation studies. Plant populations are on average 16% more resistant to allopatric pathogen strains than they are to strains that occur within the same population (48 % vs. 32 % respectively). Pathogen dispersal mode affects levels of resistance in natural plant populations with lowest levels detected for hosts of airborne pathogens and highest for waterborne pathogens. Detailed analysis of two model systems, Linum marginale infected by Melampsora lini, and Plantago lanceolata infected by Podosphaera plantaginis, show that the amount of variation in disease resistance declines towards higher spatial scales as we move from individual hosts to metapopulations, but evaluation of multiple spatial scales is needed to fully capture the structure of disease resistance. Synthesis: Variation in disease resistance is ubiquitous in wild plant-pathogen associations. While the debate over whether the resistance structure of plant populations is determined by pathogen-imposed selection versus non-adaptive processes remains unresolved, we do report examples of pathogen-imposed selection on host resistance. Here we highlight the importance of measuring resistance across multiple spatial scales, and of using sympatric strains when looking for signs of coevolution in wild plant-pathogen interactions. PMID:21243068
The role of affective evaluation in conflict adaptation: An LRP study.

PubMed

Fröber, Kerstin; Stürmer, Birgit; Frömer, Romy; Dreisbach, Gesine

2017-08-01

Conflict between incompatible response tendencies is typically followed by control adjustments aimed at diminishing subsequent conflicts, a phenomenon often called conflict adaptation. Dreisbach and Fischer (2015, 2016) recently proposed that it is not the conflict per se but the aversive quality of a conflict that originally motivates this kind of sequential control adjustment. With the present study we tested the causal role of aversive signals in conflict adaptation in a more direct way. To this end, after each trial of a vertical Simon task participants rated whether they experienced the last trial as rather pleasant or unpleasant. Conflict adaptation was measured via lateralized readiness potentials as a measure of early motor-related activation that were computed on the basis of event-related brain potentials. Results showed the typical suppression of automatic response activation following trials rated as unpleasant, whereas suppression was relaxed following trials rated as pleasant. That is, sequential control adaptation was not based on previous conflict but on the subjective affective experience. This is taken as evidence that negative affect even in the absence of actual conflict triggers subsequent control adjustments. Copyright © 2017 Elsevier Inc. All rights reserved.
Consumer co-evolution as an important component of the eco-evolutionary feedback.

PubMed

Hiltunen, Teppo; Becks, Lutz

2014-10-22

Rapid evolution in ecologically relevant traits has recently been recognized to significantly alter the interaction between consumers and their resources, a key interaction in all ecological communities. While these eco-evolutionary dynamics have been shown to occur when prey populations are evolving, little is known about the role of predator evolution and co-evolution between predator and prey in this context. Here, we investigate the role of consumer co-evolution for eco-evolutionary feedback in bacteria-ciliate microcosm experiments by manipulating the initial trait variation in the predator populations. With co-evolved predators, prey evolve anti-predatory defences faster, trait values are more variable, and predator and prey population sizes are larger at the end of the experiment compared with the non-co-evolved predators. Most importantly, differences in predator traits results in a shift from evolution driving ecology, to ecology driving evolution. Thus we demonstrate that predator co-evolution has important effects on eco-evolutionary dynamics.
Error Argumentation Enhance Adaptability in Adults With Low Motor Ability.

PubMed

Lee, Chi-Mei; Bo, Jin

2016-01-01

The authors focused on young adults with varying degrees of motor difficulties and examined their adaptability in a visuomotor adaptation task where the visual feedback of participants' movement error was presented with either 1:1 ratio (i.e., regular feedback schedule) or 1:2 ratio (i.e., enhanced feedback schedule). Within-subject design was used with two feedback schedules counter-balanced and separated for 10 days. Results revealed that participants with greater motor difficulties showed less adaptability than those with normal motor abilities in the regular feedback schedule; however, all participants demonstrated similar level of adaptability in the enhanced feedback schedule. The results suggest that error argumentation enhances adaptability in adults with low motor ability.
Effects of Estimation Bias on Multiple-Category Classification with an IRT-Based Adaptive Classification Procedure

ERIC Educational Resources Information Center

Yang, Xiangdong; Poggio, John C.; Glasnapp, Douglas R.

2006-01-01

The effects of five ability estimators, that is, maximum likelihood estimator, weighted likelihood estimator, maximum a posteriori, expected a posteriori, and Owen's sequential estimator, on the performances of the item response theory-based adaptive classification procedure on multiple categories were studied via simulations. The following…
A Sequential Linear Quadratic Approach for Constrained Nonlinear Optimal Control with Adaptive Time Discretization and Application to Higher Elevation Mars Landing Problem

NASA Astrophysics Data System (ADS)

Sandhu, Amit

A sequential quadratic programming method is proposed for solving nonlinear optimal control problems subject to general path constraints including mixed state-control and state only constraints. The proposed algorithm further develops on the approach proposed in [1] with objective to eliminate the use of a high number of time intervals for arriving at an optimal solution. This is done by introducing an adaptive time discretization to allow formation of a desirable control profile without utilizing a lot of intervals. The use of fewer time intervals reduces the computation time considerably. This algorithm is further used in this thesis to solve a trajectory planning problem for higher elevation Mars landing.
Mitigating amphibian disease: strategies to maintain wild populations and control chytridiomycosis

USGS Publications Warehouse

Woodhams, Douglas C.; Bosch, Jaime; Briggs, Cheryl J.; Cashins, Scott; Davis, Leyla R.; Lauer, Antje; Muths, Erin L.; Puschendorf, Robert; Schmidt, Benedikt R.; Sheafor, Brandon; Voyles, Jamie

2011-01-01

Because sustainable conservation of amphibians in nature is dependent on long-term population persistence and co-evolution with potentially lethal pathogens, we suggest that disease mitigation not focus exclusively on the elimination or containment of the pathogen, or on the captive breeding of amphibian hosts. Rather, successful disease mitigation must be context specific with epidemiologically informed strategies to manage already infected populations by decreasing pathogenicity and host susceptibility. We propose population level treatments based on three steps: first, identify mechanisms of disease suppression; second, parameterize epizootiological models of disease and population dynamics for testing under semi-natural conditions; and third, begin a process of adaptive management in field trials with natural populations.
The Coevolution of Life and Environment on Mars: An Ecosystem Perspective on the Robotic Exploration of Biosignatures.

PubMed

Cabrol, Nathalie A

2018-01-01

Earth's biological and environmental evolution are intertwined and inseparable. This coevolution has become a fundamental concept in astrobiology and is key to the search for life beyond our planet. In the case of Mars, whether a coevolution took place is unknown, but analyzing the factors at play shows the uniqueness of each planetary experiment regardless of similarities. Early Earth and early Mars shared traits. However, biological processes on Mars, if any, would have had to proceed within the distinctive context of an irreversible atmospheric collapse, greater climate variability, and specific planetary characteristics. In that, Mars is an important test bed for comparing the effects of a unique set of spatiotemporal changes on an Earth-like, yet different, planet. Many questions remain unanswered about Mars' early environment. Nevertheless, existing data sets provide a foundation for an intellectual framework where notional coevolution models can be explored. In this framework, the focus is shifted from planetary-scale habitability to the prospect of habitats, microbial ecotones, pathways to biological dispersal, biomass repositories, and their meaning for exploration. Critically, as we search for biosignatures, this focus demonstrates the importance of starting to think of early Mars as a biosphere and vigorously integrating an ecosystem approach to landing site selection and exploration. Key Words: Astrobiology-Biosignatures-Coevolution of Earth and life-Mars. Astrobiology 18, 1-27.
Structure-based Markov random field model for representing evolutionary constraints on functional sites.

PubMed

Jeong, Chan-Seok; Kim, Dongsup

2016-02-24

Elucidating the cooperative mechanism of interconnected residues is an important component toward understanding the biological function of a protein. Coevolution analysis has been developed to model the coevolutionary information reflecting structural and functional constraints. Recently, several methods have been developed based on a probabilistic graphical model called the Markov random field (MRF), which have led to significant improvements for coevolution analysis; however, thus far, the performance of these models has mainly been assessed by focusing on the aspect of protein structure. In this study, we built an MRF model whose graphical topology is determined by the residue proximity in the protein structure, and derived a novel positional coevolution estimate utilizing the node weight of the MRF model. This structure-based MRF method was evaluated for three data sets, each of which annotates catalytic site, allosteric site, and comprehensively determined functional site information. We demonstrate that the structure-based MRF architecture can encode the evolutionary information associated with biological function. Furthermore, we show that the node weight can more accurately represent positional coevolution information compared to the edge weight. Lastly, we demonstrate that the structure-based MRF model can be reliably built with only a few aligned sequences in linear time. The results show that adoption of a structure-based architecture could be an acceptable approximation for coevolution modeling with efficient computation complexity.
The Coevolution of Life and Environment on Mars: An Ecosystem Perspective on the Robotic Exploration of Biosignatures

PubMed Central

2018-01-01

Abstract Earth's biological and environmental evolution are intertwined and inseparable. This coevolution has become a fundamental concept in astrobiology and is key to the search for life beyond our planet. In the case of Mars, whether a coevolution took place is unknown, but analyzing the factors at play shows the uniqueness of each planetary experiment regardless of similarities. Early Earth and early Mars shared traits. However, biological processes on Mars, if any, would have had to proceed within the distinctive context of an irreversible atmospheric collapse, greater climate variability, and specific planetary characteristics. In that, Mars is an important test bed for comparing the effects of a unique set of spatiotemporal changes on an Earth-like, yet different, planet. Many questions remain unanswered about Mars' early environment. Nevertheless, existing data sets provide a foundation for an intellectual framework where notional coevolution models can be explored. In this framework, the focus is shifted from planetary-scale habitability to the prospect of habitats, microbial ecotones, pathways to biological dispersal, biomass repositories, and their meaning for exploration. Critically, as we search for biosignatures, this focus demonstrates the importance of starting to think of early Mars as a biosphere and vigorously integrating an ecosystem approach to landing site selection and exploration. Key Words: Astrobiology—Biosignatures—Coevolution of Earth and life—Mars. Astrobiology 18, 1–27. PMID:29252008
Stochastic eco-evolutionary model of a prey-predator community.

PubMed

Costa, Manon; Hauzy, Céline; Loeuille, Nicolas; Méléard, Sylvie

2016-02-01

We are interested in the impact of natural selection in a prey-predator community. We introduce an individual-based model of the community that takes into account both prey and predator phenotypes. Our aim is to understand the phenotypic coevolution of prey and predators. The community evolves as a multi-type birth and death process with mutations. We first consider the infinite particle approximation of the process without mutation. In this limit, the process can be approximated by a system of differential equations. We prove the existence of a unique globally asymptotically stable equilibrium under specific conditions on the interaction among prey individuals. When mutations are rare, the community evolves on the mutational scale according to a Markovian jump process. This process describes the successive equilibria of the prey-predator community and extends the polymorphic evolutionary sequence to a coevolutionary framework. We then assume that mutations have a small impact on phenotypes and consider the evolution of monomorphic prey and predator populations. The limit of small mutation steps leads to a system of two differential equations which is a version of the canonical equation of adaptive dynamics for the prey-predator coevolution. We illustrate these different limits with an example of prey-predator community that takes into account different prey defense mechanisms. We observe through simulations how these various prey strategies impact the community.
Environmentally friendly microwave-assisted sequential extraction method followed by ICP-OES and ion-chromatographic analysis for rapid determination of sulphur forms in coal samples.

PubMed

Mketo, Nomvano; Nomngongo, Philiswa N; Ngila, J Catherine

2018-05-15

A rapid three-step sequential extraction method was developed under microwave radiation followed by inductively coupled plasma-optical emission spectroscopic (ICP-OES) and ion-chromatographic (IC) analysis for the determination of sulphur forms in coal samples. The experimental conditions of the proposed microwave-assisted sequential extraction (MW-ASE) procedure were optimized by using multivariate mathematical tools. Pareto charts generated from 2 3 full factorial design showed that, extraction time has insignificant effect on the extraction of sulphur species, therefore, all the sequential extraction steps were performed for 5 min. The optimum values according to the central composite designs and counter plots of the response surface methodology were 200 °C (microwave temperature) and 0.1 g (coal amount) for all the investigated extracting reagents (H 2 O, HCl and HNO 3 ). When the optimum conditions of the proposed MW-ASE procedure were applied in coal CRMs, SARM 18 showed more organic sulphur (72%) and the other two coal CRMs (SARMs 19 and 20) were dominated by sulphide sulphur species (52-58%). The sum of the sulphur forms from the sequential extraction steps have shown consistent agreement (95-96%) with certified total sulphur values on the coal CRM certificates. This correlation, in addition to the good precision (1.7%) achieved by the proposed procedure, suggests that the sequential extraction method is reliable, accurate and reproducible. To safe-guard the destruction of pyritic and organic sulphur forms in extraction step 1, water was used instead of HCl. Additionally, the notorious acidic mixture (HCl/HNO 3 /HF) was replaced by greener reagent (H 2 O 2 ) in the last extraction step. Therefore, the proposed MW-ASE method can be applied in routine laboratories for the determination of sulphur forms in coal and coal related matrices. Copyright © 2018 Elsevier B.V. All rights reserved.
PHOTOSENSITIVE RELAY CONTROL CIRCUIT

DOEpatents

Martin, C.F.

1958-01-14

adapted for the measurement of the time required for an oscillating member to pass through a preselected number of oscillations, after being damped to a certain maximum amplitude of oscillation. A mirror is attached to the moving member and directs light successively to a photocell which is part of a trigger unit and to first and second photocells which are part of a starter unit, as the member swings to its maximum amplitude. The starter and trigger units comprise thyratrons and relays so interconnected that the trigger circuit, although generating a counter pulse, does not register a count in the counter when the light traverses both photocells of the starter unit. When the amplitude of oscillation of the member decreases to where the second photocell is not transversed, the triggei pulse is received by the counter. The counter taen operates to register the desired number of oscillations and initiates and terminates a timer for measuring the time irterval for the preselected number of oscillations.
Non-periodic multi-slit masking for a single counter rotating 2-disc chopper and channeling guides for high resolution and high intensity neutron TOF spectroscopy

NASA Astrophysics Data System (ADS)

Bartkowiak, M.; Hofmann, T.; Stüßer, N.

2017-02-01

Energy resolution is an important design goal for time-of-flight instruments and neutron spectroscopy. For high-resolution applications, it is required that the burst times of choppers be short, going down to the μs-range. To produce short pulses while maintaining high neutron flux, we propose beam masks with more than two slits on a counter-rotating 2-disc chopper, behind specially adapted focusing multi-channel guides. A novel non-regular arrangement of the slits ensures that the beam opens only once per chopper cycle, when the masks are congruently aligned. Additionally, beam splitting and intensity focusing by guides before and after the chopper position provide high intensities even for small samples. Phase-space analysis and Monte Carlo simulations on examples of four-slit masks with adapted guide geometries show the potential of the proposed setup.
The adaptive safety analysis and monitoring system

NASA Astrophysics Data System (ADS)

Tu, Haiying; Allanach, Jeffrey; Singh, Satnam; Pattipati, Krishna R.; Willett, Peter

2004-09-01

The Adaptive Safety Analysis and Monitoring (ASAM) system is a hybrid model-based software tool for assisting intelligence analysts to identify terrorist threats, to predict possible evolution of the terrorist activities, and to suggest strategies for countering terrorism. The ASAM system provides a distributed processing structure for gathering, sharing, understanding, and using information to assess and predict terrorist network states. In combination with counter-terrorist network models, it can also suggest feasible actions to inhibit potential terrorist threats. In this paper, we will introduce the architecture of the ASAM system, and discuss the hybrid modeling approach embedded in it, viz., Hidden Markov Models (HMMs) to detect and provide soft evidence on the states of terrorist network nodes based on partial and imperfect observations, and Bayesian networks (BNs) to integrate soft evidence from multiple HMMs. The functionality of the ASAM system is illustrated by way of application to the Indian Airlines Hijacking, as modeled from open sources.
Microcomputer Network for Computerized Adaptive Testing (CAT)

DTIC Science & Technology

1984-03-01

PRDC TR 84-33 \\Q.�d-33- \\ MICROCOMPUTER NETWOJlt FOR COMPUTERIZED ADAPTIVE TESTING ( CAT ) Baldwin Quan Thomas A . Park Gary Sandahl John H...ACCEIIION NO NPRDC TR 84-33 4. TITLE (-d Sul>tlllo) MICROCOMP UTER NETWORK FOR COMPUTERIZED ADA PTIVE TESTING ( CAT ) 1. Q B. uan T. A . Park...adaptive testing ( CAT ) Bayesian sequential testing 20. ABSTitACT (Continuo on ro•••• aide II noco .. _, _., ld-tlly ,.,. t.loclt _._.) DO Computerized
Protometric thermometric titrations of sparingly soluble compounds in water in the presence of n-octanol.

PubMed

Burgot, G; Burgot, J-L

2002-10-15

Thermometric titrimetry permits titration of acido-basic compounds in water in the presence of n-octanol. n-Octanol permits the solubilization of protolytes and moreover may also displace the equilibria of the titration reactions. Hydrochlorides of highly insoluble derivatives such as phenothiazine derivatives can be titrated with satisfactory accuracy and precision by sodium hydroxide despite their high pK(a) values. Likewise barbiturate salts can be titrated by hydrochloric acid. In the case of some salts, the methodology may permit the sequential titration of the ion and counter ion. Copyright 2002 Elsevier Science B.V.
Online Sequential Projection Vector Machine with Adaptive Data Mean Update

PubMed Central

Chen, Lin; Jia, Ji-Ting; Zhang, Qiong; Deng, Wan-Yu; Wei, Wei

2016-01-01

We propose a simple online learning algorithm especial for high-dimensional data. The algorithm is referred to as online sequential projection vector machine (OSPVM) which derives from projection vector machine and can learn from data in one-by-one or chunk-by-chunk mode. In OSPVM, data centering, dimension reduction, and neural network training are integrated seamlessly. In particular, the model parameters including (1) the projection vectors for dimension reduction, (2) the input weights, biases, and output weights, and (3) the number of hidden nodes can be updated simultaneously. Moreover, only one parameter, the number of hidden nodes, needs to be determined manually, and this makes it easy for use in real applications. Performance comparison was made on various high-dimensional classification problems for OSPVM against other fast online algorithms including budgeted stochastic gradient descent (BSGD) approach, adaptive multihyperplane machine (AMM), primal estimated subgradient solver (Pegasos), online sequential extreme learning machine (OSELM), and SVD + OSELM (feature selection based on SVD is performed before OSELM). The results obtained demonstrated the superior generalization performance and efficiency of the OSPVM. PMID:27143958

Online Sequential Projection Vector Machine with Adaptive Data Mean Update.

PubMed

Chen, Lin; Jia, Ji-Ting; Zhang, Qiong; Deng, Wan-Yu; Wei, Wei

2016-01-01

We propose a simple online learning algorithm especial for high-dimensional data. The algorithm is referred to as online sequential projection vector machine (OSPVM) which derives from projection vector machine and can learn from data in one-by-one or chunk-by-chunk mode. In OSPVM, data centering, dimension reduction, and neural network training are integrated seamlessly. In particular, the model parameters including (1) the projection vectors for dimension reduction, (2) the input weights, biases, and output weights, and (3) the number of hidden nodes can be updated simultaneously. Moreover, only one parameter, the number of hidden nodes, needs to be determined manually, and this makes it easy for use in real applications. Performance comparison was made on various high-dimensional classification problems for OSPVM against other fast online algorithms including budgeted stochastic gradient descent (BSGD) approach, adaptive multihyperplane machine (AMM), primal estimated subgradient solver (Pegasos), online sequential extreme learning machine (OSELM), and SVD + OSELM (feature selection based on SVD is performed before OSELM). The results obtained demonstrated the superior generalization performance and efficiency of the OSPVM.
Message passing with a limited number of DMA byte counters

DOEpatents

Blocksome, Michael [Rochester, MN; Chen, Dong [Croton on Hudson, NY; Giampapa, Mark E [Irvington, NY; Heidelberger, Philip [Cortlandt Manor, NY; Kumar, Sameer [White Plains, NY; Parker, Jeffrey J [Rochester, MN

2011-10-04

A method for passing messages in a parallel computer system constructed as a plurality of compute nodes interconnected as a network where each compute node includes a DMA engine but includes only a limited number of byte counters for tracking a number of bytes that are sent or received by the DMA engine, where the byte counters may be used in shared counter or exclusive counter modes of operation. The method includes using rendezvous protocol, a source compute node deterministically sending a request to send (RTS) message with a single RTS descriptor using an exclusive injection counter to track both the RTS message and message data to be sent in association with the RTS message, to a destination compute node such that the RTS descriptor indicates to the destination compute node that the message data will be adaptively routed to the destination node. Using one DMA FIFO at the source compute node, the RTS descriptors are maintained for rendezvous messages destined for the destination compute node to ensure proper message data ordering thereat. Using a reception counter at a DMA engine, the destination compute node tracks reception of the RTS and associated message data and sends a clear to send (CTS) message to the source node in a rendezvous protocol form of a remote get to accept the RTS message and message data and processing the remote get (CTS) by the source compute node DMA engine to provide the message data to be sent.
Does the process map influence the outcome of quality improvement work? A comparison of a sequential flow diagram and a hierarchical task analysis diagram.

PubMed

Colligan, Lacey; Anderson, Janet E; Potts, Henry W W; Berman, Jonathan

2010-01-07

Many quality and safety improvement methods in healthcare rely on a complete and accurate map of the process. Process mapping in healthcare is often achieved using a sequential flow diagram, but there is little guidance available in the literature about the most effective type of process map to use. Moreover there is evidence that the organisation of information in an external representation affects reasoning and decision making. This exploratory study examined whether the type of process map - sequential or hierarchical - affects healthcare practitioners' judgments. A sequential and a hierarchical process map of a community-based anti coagulation clinic were produced based on data obtained from interviews, talk-throughs, attendance at a training session and examination of protocols and policies. Clinic practitioners were asked to specify the parts of the process that they judged to contain quality and safety concerns. The process maps were then shown to them in counter-balanced order and they were asked to circle on the diagrams the parts of the process where they had the greatest quality and safety concerns. A structured interview was then conducted, in which they were asked about various aspects of the diagrams. Quality and safety concerns cited by practitioners differed depending on whether they were or were not looking at a process map, and whether they were looking at a sequential diagram or a hierarchical diagram. More concerns were identified using the hierarchical diagram compared with the sequential diagram and more concerns were identified in relation to clinical work than administrative work. Participants' preference for the sequential or hierarchical diagram depended on the context in which they would be using it. The difficulties of determining the boundaries for the analysis and the granularity required were highlighted. The results indicated that the layout of a process map does influence perceptions of quality and safety problems in a process. In quality improvement work it is important to carefully consider the type of process map to be used and to consider using more than one map to ensure that different aspects of the process are captured.
Water System Adaptation to Hydrological Changes: Module 2, Stormwater Management and Sewer Performance under Intense Storms: Case Study from Lawrence, Massachusetts, U.S.A.

EPA Science Inventory

This course focuses on water system adaptation to short-term and long-term climate and hydrologic stressors that affect water availability, water quality, security, and resilience. The course is organized into 15 sequential modules. The lectures will be augmented by weekly assign...
Water System Adaptation To Hydrological Changes: Module 3, Consequences of Prolonged Drought on Urban Water System Resilience: Case Study from Las Vegas, Nevada, USA

EPA Science Inventory

This course focuses on water system adaptation to short-term and long-term climate and hydrologic stressors that affect water availability, water quality, security, and resilience. The course is organized into 15 sequential modules. The lectures will be augmented by weekly assign...
Water System Adaptations To Hydrological Changes: Module 4, Water Quality Response to Land-use and Precipitation Changes : Case Study of Ohio River Valley, USA

EPA Science Inventory

This course focuses on water system adaptation to short-term and long-term climate and hydrologic stressors that affect water availability, water quality, security, and resilience. The course is organized into 15 sequential modules. The lectures will be augmented by weekly assign...
Attachment, Career-Choice Pessimism, and Intrinsic Motivation as Predictors of College Students' Career Adaptability

ERIC Educational Resources Information Center

Shin, Yun-Jeong; Lee, Ji-Yeon

2017-01-01

The purpose of this study was to examine the cross-cultural validity of the effects of attachment, career-choice pessimism, and intrinsic motivation on career adaptability (CA) in American (n = 198) and Korean (n = 294) college students. We hypothesized that the association between attachment and CA is sequentially mediated by career-choice…
EXSPRT: An Expert Systems Approach to Computer-Based Adaptive Testing.

ERIC Educational Resources Information Center

Frick, Theodore W.; And Others

Expert systems can be used to aid decision making. A computerized adaptive test (CAT) is one kind of expert system, although it is not commonly recognized as such. A new approach, termed EXSPRT, was devised that combines expert systems reasoning and sequential probability ratio test stopping rules. EXSPRT-R uses random selection of test items,…
Adapting the Training Site to Training Needs. Self-Paced Instructional Module. Module Number VII-A.

ERIC Educational Resources Information Center

King, Sylvester; Brooks, Kent

One of 33 self-paced instructional modules for training industry services leaders to provide guidance in the performance of manpower services by public agencies to new and expanding private industry, this module contains three sequential learning activities on adapting the training site to training needs. The first learning activity is designed to…
Competition-Colonization Trade-Offs, Competitive Uncertainty, and the Evolutionary Assembly of Species

PubMed Central

Pillai, Pradeep; Guichard, Frédéric

2012-01-01

We utilize a standard competition-colonization metapopulation model in order to study the evolutionary assembly of species. Based on earlier work showing how models assuming strict competitive hierarchies will likely lead to runaway evolution and self-extinction for all species, we adopt a continuous competition function that allows for levels of uncertainty in the outcome of competition. We then, by extending the standard patch-dynamic metapopulation model in order to include evolutionary dynamics, allow for the coevolution of species into stable communities composed of species with distinct limiting similarities. Runaway evolution towards stochastic extinction then becomes a limiting case controlled by the level of competitive uncertainty. We demonstrate how intermediate competitive uncertainty maximizes the equilibrium species richness as well as maximizes the adaptive radiation and self-assembly of species under adaptive dynamics with mutations of non-negligible size. By reconciling competition-colonization tradeoff theory with co-evolutionary dynamics, our results reveal the importance of intermediate levels of competitive uncertainty for the evolutionary assembly of species. PMID:22448253
Adaptive Communication: Languages with More Non-Native Speakers Tend to Have Fewer Word Forms

PubMed Central

Bentz, Christian; Verkerk, Annemarie; Kiela, Douwe; Hill, Felix; Buttery, Paula

2015-01-01

Explaining the diversity of languages across the world is one of the central aims of typological, historical, and evolutionary linguistics. We consider the effect of language contact-the number of non-native speakers a language has-on the way languages change and evolve. By analysing hundreds of languages within and across language families, regions, and text types, we show that languages with greater levels of contact typically employ fewer word forms to encode the same information content (a property we refer to as lexical diversity). Based on three types of statistical analyses, we demonstrate that this variance can in part be explained by the impact of non-native speakers on information encoding strategies. Finally, we argue that languages are information encoding systems shaped by the varying needs of their speakers. Language evolution and change should be modeled as the co-evolution of multiple intertwined adaptive systems: On one hand, the structure of human societies and human learning capabilities, and on the other, the structure of language. PMID:26083380
The Co-evolution of Honesty and Strategic Vigilance

PubMed Central

Heintz, Christophe; Karabegovic, Mia; Molnar, Andras

2016-01-01

We hypothesize that when honesty is not motivated by selfish goals, it reveals social preferences that have evolved for convincing strategically vigilant partners that one is a person worth cooperating with. In particular, we explain how the patterns of dishonest behavior observed in recent experiments can be motivated by preferences for social and self-esteem. These preferences have evolved because they are adaptive in an environment where it is advantageous to be selected as a partner by others and where these others are strategically vigilant: they efficiently evaluate the expected benefit of cooperating with specific partners and attend to their intentions. We specify the adaptive value of strategic vigilance and preferences for social and self-esteem. We argue that evolved preferences for social and self-esteem are satisfied by applying mechanisms of strategic vigilance to one's own behavior. We further argue that such cognitive processes obviate the need for the evolution of preferences for fairness and social norm compliance. PMID:27790162
Free energy computations by minimization of Kullback-Leibler divergence: An efficient adaptive biasing potential method for sparse representations

NASA Astrophysics Data System (ADS)

Bilionis, I.; Koutsourelakis, P. S.

2012-05-01

The present paper proposes an adaptive biasing potential technique for the computation of free energy landscapes. It is motivated by statistical learning arguments and unifies the tasks of biasing the molecular dynamics to escape free energy wells and estimating the free energy function, under the same objective of minimizing the Kullback-Leibler divergence between appropriately selected densities. It offers rigorous convergence diagnostics even though history dependent, non-Markovian dynamics are employed. It makes use of a greedy optimization scheme in order to obtain sparse representations of the free energy function which can be particularly useful in multidimensional cases. It employs embarrassingly parallelizable sampling schemes that are based on adaptive Sequential Monte Carlo and can be readily coupled with legacy molecular dynamics simulators. The sequential nature of the learning and sampling scheme enables the efficient calculation of free energy functions parametrized by the temperature. The characteristics and capabilities of the proposed method are demonstrated in three numerical examples.
Linking environmental risk assessment and communication: An experiment in co-evolving scientific and social knowledge

USGS Publications Warehouse

Graffy, E.A.; Booth, N.L.

2008-01-01

Dissemination of information to decision-makers and enhanced methods of public participation are often put forward as antidotes to a perceived disconnect between risk assessment and risk communication in the public domain. However, mechanisms that support both the provision of routine, timely and relevant technical knowledge to the public and meaningful opportunities for public participation in the evaluation and management of risk are few. We argue for the need to re-conceptualise the institutional context in which risk research and communication occur as one in which scientific knowledge and public understanding are co-evolutionary instead of independent or sequential. Here, we report on an experiment to promote coevolution of environmental risk assessment and risk communication through the instrumental use of a web-based platform that dynamically links expert and public discourses through common information sources, linked scenario evaluations, and opportunities for iterative dialogue. On the basis of technical feasibility, research value and public communication capacity, we conclude that there is potential for further refinement of the methodologies presented here. Copyright ?? 2008 Inderscience Enterprises Ltd.
The arms race between man and Mycobacterium tuberculosis: Time to regroup.

PubMed

Hoal, Eileen G; Dippenaar, Anzaan; Kinnear, Craig; van Helden, Paul D; Möller, Marlo

2017-08-23

An arms race is an appropriate metaphor to use for the interaction of man and Mycobacterium tuberculosis (M.tb) through the millennia. Estimates of the time of infection of modern humans with M.tb often pre-date the Out-of-Africa migration. Humans have adapted to the changing environment during the migration with respect to climate, food sources and encounters with local pathogens. More recently, there has been adaptation to the demographic changes brought about in the majority of the human population by the Neolithic revolution. By chance and/or selection, specific variants in immune defence have arisen in different population groups. These select for M.tb strains more fit to cause disease and be transmitted, sometimes by exploiting defence systems effective on other bacteria. The different selection pressures on the M.tb lineages carried by specific human groups have resulted in a worldwide M.tb population that is geographically structured according to the humans historically found there. A similar structure is seen with pathogens such as M. leprae and Helicobacter pylori. Modern M.tb strains have emerged which may be more fit, such as the Beijing lineage, leading to their rapid spread both in the areas where they arose, and into new areas after recent introduction. The speed at which this is occurring is outpacing coevolution for the time being. By using the results of genome wide and other association studies, as well as admixture mapping and 'natural experiments' in areas where both a number of populations, admixed populations, and a variety of M.tb strains occur, we can investigate the forces that have driven the coevolution of man and M.tb. The diversity of human and bacterial genetic background may be used in the future to discover and target the specific host-pathogen interactions leading to tuberculosis diseases, which suggests the potential for rational design of vaccines and host-directed therapies. Copyright © 2017 Elsevier B.V. All rights reserved.
The Beringian Coevolution Project: Holistic collections of mammals and associated parasites reveal novel perspectives on changing environments in the north

USDA-ARS?s Scientific Manuscript database

The Beringian Coevolution Project (BCP), a field program underway in the Arctic since 1999, has focused on building key scientific infrastructure for integrated specimen-based studies on mammals and their associated parasites. BCP has contributed new insights across temporal and spatial scales into...
The Co-Evolution of Knowledge and Event Memory

ERIC Educational Resources Information Center

Nelson, Angela B.; Shiffrin, Richard M.

2013-01-01

We present a theoretical framework and a simplified simulation model for the co-evolution of knowledge and event memory, both termed SARKAE (Storing and Retrieving Knowledge and Events). Knowledge is formed through the accrual of individual events, a process that operates in tandem with the storage of individual event memories. In 2 studies, new…
A discriminative test among the different theories proposed to explain the origin of the genetic code: the coevolution theory finds additional support.

PubMed

Giulio, Massimo Di

2018-05-19

A discriminative statistical test among the different theories proposed to explain the origin of the genetic code is presented. Gathering the amino acids into polarity and biosynthetic classes that are the first expression of the physicochemical theory of the origin of the genetic code and the second expression of the coevolution theory, these classes are utilized in the Fisher's exact test to establish their significance within the genetic code table. Linking to the rows and columns of the genetic code of probabilities that express the statistical significance of these classes, I have finally been in the condition to be able to calculate a χ value to link to both the physicochemical theory and to the coevolution theory that would express the corroboration level referred to these theories. The comparison between these two χ values showed that the coevolution theory is able to explain - in this strictly empirical analysis - the origin of the genetic code better than that of the physicochemical theory. Copyright © 2018 Elsevier B.V. All rights reserved.
Coevolution between Male and Female Genitalia in the Drosophila melanogaster Species Subgroup

PubMed Central

Yassin, Amir; Orgogozo, Virginie

2013-01-01

In contrast to male genitalia that typically exhibit patterns of rapid and divergent evolution among internally fertilizing animals, female genitalia have been less well studied and are generally thought to evolve slowly among closely-related species. As a result, few cases of male-female genital coevolution have been documented. In Drosophila, female copulatory structures have been claimed to be mostly invariant compared to male structures. Here, we re-examined male and female genitalia in the nine species of the D. melanogaster subgroup. We describe several new species-specific female genital structures that appear to coevolve with male genital structures, and provide evidence that the coevolving structures contact each other during copulation. Several female structures might be defensive shields against apparently harmful male structures, such as cercal teeth, phallic hooks and spines. Evidence for male-female morphological coevolution in Drosophila has previously been shown at the post-copulatory level (e.g., sperm length and sperm storage organ size), and our results provide support for male-female coevolution at the copulatory level. PMID:23451172
Multi-species attributes as the condition for adaptive sampling of rare species using two-stage sequential sampling with an auxiliary variable

USGS Publications Warehouse

Panahbehagh, B.; Smith, D.R.; Salehi, M.M.; Hornbach, D.J.; Brown, D.J.; Chan, F.; Marinova, D.; Anderssen, R.S.

2011-01-01

Assessing populations of rare species is challenging because of the large effort required to locate patches of occupied habitat and achieve precise estimates of density and abundance. The presence of a rare species has been shown to be correlated with presence or abundance of more common species. Thus, ecological community richness or abundance can be used to inform sampling of rare species. Adaptive sampling designs have been developed specifically for rare and clustered populations and have been applied to a wide range of rare species. However, adaptive sampling can be logistically challenging, in part, because variation in final sample size introduces uncertainty in survey planning. Two-stage sequential sampling (TSS), a recently developed design, allows for adaptive sampling, but avoids edge units and has an upper bound on final sample size. In this paper we present an extension of two-stage sequential sampling that incorporates an auxiliary variable (TSSAV), such as community attributes, as the condition for adaptive sampling. We develop a set of simulations to approximate sampling of endangered freshwater mussels to evaluate the performance of the TSSAV design. The performance measures that we are interested in are efficiency and probability of sampling a unit occupied by the rare species. Efficiency measures the precision of population estimate from the TSSAV design relative to a standard design, such as simple random sampling (SRS). The simulations indicate that the density and distribution of the auxiliary population is the most important determinant of the performance of the TSSAV design. Of the design factors, such as sample size, the fraction of the primary units sampled was most important. For the best scenarios, the odds of sampling the rare species was approximately 1.5 times higher for TSSAV compared to SRS and efficiency was as high as 2 (i.e., variance from TSSAV was half that of SRS). We have found that design performance, especially for adaptive designs, is often case-specific. Efficiency of adaptive designs is especially sensitive to spatial distribution. We recommend that simulations tailored to the application of interest are highly useful for evaluating designs in preparation for sampling rare and clustered populations.

Ventromedial prefrontal and anterior cingulate cortex adopt choice and default reference frames during sequential multialternative choice

PubMed Central

Boorman, Erie D; Rushworth, Matthew F; Behrens, Tim E

2013-01-01

Although damage to medial frontal cortex causes profound decision-making impairments, it has been difficult to pinpoint the relative contributions of key anatomical subdivisions. Here we use fMRI to examine the contributions of human ventromedial prefrontal cortex (vmPFC) and dorsal anterior cingulate cortex (dACC) during sequential choices between multiple alternatives – two key features of choices made in ecological settings. By carefully constructing options whose current value at any given decision was dissociable from their longer-term value, we were able to examine choices in current and long-term frames of reference. We present evidence showing that activity at choice and feedback in vmPFC and dACC was tied to the current choice and the best long-term option, respectively. vmPFC, mid-cingulate, and PCC encoded the relative value between the chosen and next-best option at each sequential decision, whereas dACC encoded the relative value of adapting choices from the option with the highest value in the longer-term. Furthermore, at feedback we identify temporally dissociable effects that predict repetition of the current choice and adaptation away from the long-term best option in vmPFC and dACC, respectively. These functional dissociations at choice and feedback suggest that sequential choices are subject to competing cortical mechanisms. PMID:23392656
Method and apparatus for telemetry adaptive bandwidth compression

NASA Technical Reports Server (NTRS)

Graham, Olin L.

1987-01-01

Methods and apparatus are provided for automatic and/or manual adaptive bandwidth compression of telemetry. An adaptive sampler samples a video signal from a scanning sensor and generates a sequence of sampled fields. Each field and range rate information from the sensor are hence sequentially transmitted to and stored in a multiple and adaptive field storage means. The field storage means then, in response to an automatic or manual control signal, transfers the stored sampled field signals to a video monitor in a form for sequential or simultaneous display of a desired number of stored signal fields. The sampling ratio of the adaptive sample, the relative proportion of available communication bandwidth allocated respectively to transmitted data and video information, and the number of fields simultaneously displayed are manually or automatically selectively adjustable in functional relationship to each other and detected range rate. In one embodiment, when relatively little or no scene motion is detected, the control signal maximizes sampling ratio and causes simultaneous display of all stored fields, thus maximizing resolution and bandwidth available for data transmission. When increased scene motion is detected, the control signal is adjusted accordingly to cause display of fewer fields. If greater resolution is desired, the control signal is adjusted to increase the sampling ratio.
The adaptive evolution of the mammalian mitochondrial genome

PubMed Central

da Fonseca, Rute R; Johnson, Warren E; O'Brien, Stephen J; Ramos, Maria João; Antunes, Agostinho

2008-01-01

Background The mitochondria produce up to 95% of a eukaryotic cell's energy through oxidative phosphorylation. The proteins involved in this vital process are under high functional constraints. However, metabolic requirements vary across species, potentially modifying selective pressures. We evaluate the adaptive evolution of 12 protein-coding mitochondrial genes in 41 placental mammalian species by assessing amino acid sequence variation and exploring the functional implications of observed variation in secondary and tertiary protein structures. Results Wide variation in the properties of amino acids were observed at functionally important regions of cytochrome b in species with more-specialized metabolic requirements (such as adaptation to low energy diet or large body size, such as in elephant, dugong, sloth, and pangolin, and adaptation to unusual oxygen requirements, for example diving in cetaceans, flying in bats, and living at high altitudes in alpacas). Signatures of adaptive variation in the NADH dehydrogenase complex were restricted to the loop regions of the transmembrane units which likely function as protons pumps. Evidence of adaptive variation in the cytochrome c oxidase complex was observed mostly at the interface between the mitochondrial and nuclear-encoded subunits, perhaps evidence of co-evolution. The ATP8 subunit, which has an important role in the assembly of F0, exhibited the highest signal of adaptive variation. ATP6, which has an essential role in rotor performance, showed a high adaptive variation in predicted loop areas. Conclusion Our study provides insight into the adaptive evolution of the mtDNA genome in mammals and its implications for the molecular mechanism of oxidative phosphorylation. We present a framework for future experimental characterization of the impact of specific mutations in the function, physiology, and interactions of the mtDNA encoded proteins involved in oxidative phosphorylation. PMID:18318906
Socio-hydrological modelling of floods: investigating community resilience, adaptation capacity and risk

NASA Astrophysics Data System (ADS)

Ciullo, Alessio; Viglione, Alberto; Castellarin, Attilio

2016-04-01

Changes in flood risk occur because of changes in climate and hydrology, and in societal exposure and vulnerability. Research on change in flood risk has demonstrated that the mutual interactions and continuous feedbacks between floods and societies has to be taken into account in flood risk management. The present work builds on an existing conceptual model of an hypothetical city located in the proximity of a river, along whose floodplains the community evolves over time. The model reproduces the dynamic co-evolution of four variables: flooding, population density of the flooplain, amount of structural protection measures and memory of floods. These variables are then combined in a way to mimic the temporal change of community resilience, defined as the (inverse of the) amount of time for the community to recover from a shock, and adaptation capacity, defined as ratio between damages due to subsequent events. Also, temporal changing exposure, vulnerability and probability of flooding are also modelled, which results in a dynamically varying flood-risk. Examples are provided that show how factors such as collective memory and risk taking attitude influence the dynamics of community resilience, adaptation capacity and risk.
Do arms races punctuate evolutionary stasis? Unified insights from phylogeny, phylogeography and microevolutionary processes.

PubMed

Toju, Hirokazu; Sota, Teiji

2009-09-01

One of the major controversies in evolutionary biology concerns the processes underlying macroevolutionary patterns in which prolonged stasis is disrupted by rapid, short-term evolution that leads species to new adaptive zones. Recent advances in the understanding of contemporary evolution have suggested that such rapid evolution can occur in the wild as a result of environmental changes. Here, we examined a novel hypothesis that evolutionary stasis is punctuated by co-evolutionary arms races, which continuously alter adaptive peaks and landscapes. Based on the phylogeny of long-mouthed weevils in the genus Curculio, likelihood ratio tests showed that the macroevolutionary pattern of the weevils coincides with the punctuational evolution model. A coalescent analysis of a species, Curculio camelliae, the mouthpart of which has diverged considerably among populations because of an arms race with its host plant, further suggested that major evolutionary shifts had occurred within 7000 generations. Through a microevolutionary analysis of the species, we also found that natural selection acting through co-evolutionary interactions is potentially strong enough to drive rapid evolutionary shifts between adaptive zones. Overall, we posit that co-evolution is an important factor driving the history of organismal evolution.
Stakeholder Analysis for the CF Counter-IED Training Courses

DTIC Science & Technology

2010-05-01

for more than purely research purposes when the experimenter is present. 3.1.3 Learning Style- based Adaptation The Index of Learning Styles (Felder...student. It is recommended that the Adaption Module uses the same ontology based reasoning approach as the Evaluation Module. RacerPro is the recommended...reasoner. RacerPro is used as a system for managing semantic web ontologies based on Web Ontology Language (OWL). The design phase will confirm
Radiometric liquid level gauge with linear-detection (in German)

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

Glaeser, M.; Emmelmann, K.P.

1973-09-01

A description is given of a radiometric liquid level gauge with linear detection. It consists of a set of radioactive sources (e.g., /sup 137/Cs) with quadratic graduation in their activities, of a scintillation counter with electronic back-up unit and of a slender tube. The tube, sources and scintillation counter form a compact snd easily transportsble liquid level gauge. It is-especially adapted for liquid level measurements in slender, difficulty accessible and opaque containers. The device supplements the different methods for liquid level measurement with a new variant which is adopted for many cases in practice. (auth)
Seed dispersal in limber and southwestern white pine: Comparing core and peripheral populations

Treesearch

Diana F. Tomback; Sheridan Samano; Elizabeth L. Pruett; Anna W. Schoettle

2011-01-01

According to the geographic mosaic theory of coevolution (Thompson 2005), the potential for coevolutionary relationships between interacting species varies with the presence of other species within a community. This implies that the strength of coevolution between two species may vary geographically. In this study, we ask whether there is a shift in vertebrate seed...
Tracing the role of human civilization in the globalization of plant pathogens

Treesearch

Alberto Santini; Andrew Liebhold; Duccio Migliorini; Steve Woodward

2018-01-01

Co-evolution between plants and parasites, including herbivores and pathogens, has arguably generated much of Earthâs biological diversity. Within an ecosystem, coevolution of plants and pathogens is a stepwise reciprocal evolutionary interaction: epidemics result in intense selection pressures on both host and pathogen populations, ultimately allowing long-term...
Convergence Properties of a Class of Probabilistic Adaptive Schemes Called Sequential Reproductive Plans. Psychology and Education Series, Technical Report No. 210.

ERIC Educational Resources Information Center

Martin, Nancy

Presented is a technical report concerning the use of a mathematical model describing certain aspects of the duplication and selection processes in natural genetic adaptation. This reproductive plan/model occurs in artificial genetics (the use of ideas from genetics to develop general problem solving techniques for computers). The reproductive…
Molecular Aspects and Comparative Genomics of Bacteriophage Endolysins

PubMed Central

Oliveira, Hugo; Melo, Luís D. R.; Santos, Sílvio B.; Nóbrega, Franklin L.; Ferreira, Eugénio C.; Cerca, Nuno; Azeredo, Joana

2013-01-01

Phages are recognized as the most abundant and diverse entities on the planet. Their diversity is determined predominantly by their dynamic adaptation capacities when confronted with different selective pressures in an endless cycle of coevolution with a widespread group of bacterial hosts. At the end of the infection cycle, progeny virions are confronted with a rigid cell wall that hinders their release into the environment and the opportunity to start a new infection cycle. Consequently, phages encode hydrolytic enzymes, called endolysins, to digest the peptidoglycan. In this work, we bring to light all phage endolysins found in completely sequenced double-stranded nucleic acid phage genomes and uncover clues that explain the phage-endolysin-host ecology that led phages to recruit unique and specialized endolysins. PMID:23408602
A group sequential adaptive treatment assignment design for proof of concept and dose selection in headache trials.

PubMed

Hall, David B; Meier, Ulrich; Diener, Hans-Cristoph

2005-06-01

The trial objective was to test whether a new mechanism of action would effectively treat migraine headaches and to select a dose range for further investigation. The motivation for a group sequential, adaptive, placebo-controlled trial design was (1) limited information about where across the range of seven doses to focus attention, (2) a need to limit sample size for a complicated inpatient treatment and (3) a desire to reduce exposure of patients to ineffective treatment. A design based on group sequential and up and down designs was developed and operational characteristics were explored by trial simulation. The primary outcome was headache response at 2 h after treatment. Groups of four treated and two placebo patients were assigned to one dose. Adaptive dose selection was based on response rates of 60% seen with other migraine treatments. If more than 60% of treated patients responded, then the next dose was the next lower dose; otherwise, the dose was increased. A stopping rule of at least five groups at the target dose and at least four groups at that dose with more than 60% response was developed to ensure that a selected dose would be statistically significantly (p=0.05) superior to placebo. Simulations indicated good characteristics in terms of control of type 1 error, sufficient power, modest expected sample size and modest bias in estimation. The trial design is attractive for phase 2 clinical trials when response is acute and simple, ideally binary, placebo comparator is required, and patient accrual is relatively slow allowing for the collection and processing of results as a basis for the adaptive assignment of patients to dose groups. The acute migraine trial based on this design was successful in both proof of concept and dose range selection.
Implications of movement-related cortical potential for understanding neural adaptations in muscle strength tasks

PubMed Central

2014-01-01

This systematic review aims to provide information about the implications of the movement-related cortical potential (MRCP) in acute and chronic responses to the counter resistance training. The structuring of the methods of this study followed the proposals of the PRISMA (Preferred Reporting Items for Systematic reviews and Meta-Analyses). It was performed an electronically search in Pubmed/Medline and ISI Web of Knowledge data bases, from 1987 to 2013, besides the manual search in the selected references. The following terms were used: Bereitschaftspotential, MRCP, strength and force. The logical operator “AND” was used to combine descriptors and terms used to search publications. At the end, 11 studies attended all the eligibility criteria and the results demonstrated that the behavior of MRCP is altered because of different factors such as: force level, rate of force development, fatigue induced by exercise, and the specific phase of muscular action, leading to an increase in the amplitude in eccentric actions compared to concentric actions, in acute effects. The long-term adaptations demonstrated that the counter resistance training provokes an attenuation in the amplitude in areas related to the movement, which may be caused by neural adaptation occurred in the motor cortex. PMID:24602228
Evolution in action: climate change, biodiversity dynamics and emerging infectious disease

PubMed Central

Hoberg, Eric P.; Brooks, Daniel R.

2015-01-01

Climatological variation and ecological perturbation have been pervasive drivers of faunal assembly, structure and diversification for parasites and pathogens through recurrent events of geographical and host colonization at varying spatial and temporal scales of Earth history. Episodic shifts in climate and environmental settings, in conjunction with ecological mechanisms and host switching, are often critical determinants of parasite diversification, a view counter to more than a century of coevolutionary thinking about the nature of complex host–parasite assemblages. Parasites are resource specialists with restricted host ranges, yet shifts onto relatively unrelated hosts are common during phylogenetic diversification of parasite lineages and directly observable in real time. The emerging Stockholm Paradigm resolves this paradox: Ecological Fitting (EF)—phenotypic flexibility and phylogenetic conservatism in traits related to resource use, most notably host preference—provides many opportunities for rapid host switching in changing environments, without the evolution of novel host-utilization capabilities. Host shifts via EF fuel the expansion phase of the Oscillation Hypothesis of host range and speciation and, more generally, the generation of novel combinations of interacting species within the Geographic Mosaic Theory of Coevolution. In synergy, an environmental dynamic of Taxon Pulses establishes an episodic context for host and geographical colonization. PMID:25688014
Implicit learning of sequential bias in a guessing task: failure to demonstrate effects of dopamine administration and paranormal belief.

PubMed

Palmer, John; Mohr, Christine; Krummenacher, Peter; Brugger, Peter

2007-06-01

Previous research suggests that implicit sequence learning (ISL) is superior for believers in the paranormal and individuals with increased cerebral dopamine. Thirty-five healthy participants performed feedback-guided anticipations of four arrow directions. A 100-trial random sequence preceded two 100-trial biased sequences in which visual targets (arrows) on trial t tended to be displaced 90 degrees clockwise (CW) or counter-clockwise (CCW) from those on t - 1. ISL was defined as a positive change during the course of the biased run in the difference between pro-bias and counter-bias responses. It was hypothesized that this difference would be greater for believers in the paranormal than for skeptics, for those who received dopamine than for those who received placebo, and for believers who received dopamine than for the other groups. None of the hypotheses were supported by the data. It is suggested that a simple binary guessing task with a focus on prediction accuracy during early trials should be considered for future explorations.
Brave New World of Intelligence Testing.

ERIC Educational Resources Information Center

Rice, Berkeley

1979-01-01

New approaches to assessing intelligence are discussed, as well as new intelligence tests. Among the developments are investigating neurometrics, adapting testing to the effects of technology on children, countering cultural bias, assessing social intelligence, focusing on aspects of cognitive styles, measuring learning potential, and using…
Plastid–Nuclear Interaction and Accelerated Coevolution in Plastid Ribosomal Genes in Geraniaceae

PubMed Central

Weng, Mao-Lun; Ruhlman, Tracey A.; Jansen, Robert K.

2016-01-01

Plastids and mitochondria have many protein complexes that include subunits encoded by organelle and nuclear genomes. In animal cells, compensatory evolution between mitochondrial and nuclear-encoded subunits was identified and the high mitochondrial mutation rates were hypothesized to drive compensatory evolution in nuclear genomes. In plant cells, compensatory evolution between plastid and nucleus has rarely been investigated in a phylogenetic framework. To investigate plastid–nuclear coevolution, we focused on plastid ribosomal protein genes that are encoded by plastid and nuclear genomes from 27 Geraniales species. Substitution rates were compared for five sets of genes representing plastid- and nuclear-encoded ribosomal subunit proteins targeted to the cytosol or the plastid as well as nonribosomal protein controls. We found that nonsynonymous substitution rates (dN) and the ratios of nonsynonymous to synonymous substitution rates (ω) were accelerated in both plastid- (CpRP) and nuclear-encoded subunits (NuCpRP) of the plastid ribosome relative to control sequences. Our analyses revealed strong signals of cytonuclear coevolution between plastid- and nuclear-encoded subunits, in which nonsynonymous substitutions in CpRP and NuCpRP tend to occur along the same branches in the Geraniaceae phylogeny. This coevolution pattern cannot be explained by physical interaction between amino acid residues. The forces driving accelerated coevolution varied with cellular compartment of the sequence. Increased ω in CpRP was mainly due to intensified positive selection whereas increased ω in NuCpRP was caused by relaxed purifying selection. In addition, the many indels identified in plastid rRNA genes in Geraniaceae may have contributed to changes in plastid subunits. PMID:27190001
Coevolution and life cycle specialization of plant cell wall degrading enzymes in a hemibiotrophic pathogen.

PubMed

Brunner, Patrick C; Torriani, Stefano F F; Croll, Daniel; Stukenbrock, Eva H; McDonald, Bruce A

2013-06-01

Zymoseptoria tritici is an important fungal pathogen on wheat that originated in the Fertile Crescent. Its closely related sister species Z. pseudotritici and Z. ardabiliae infect wild grasses in the same region. This recently emerged host-pathogen system provides a rare opportunity to investigate the evolutionary processes shaping the genome of an emerging pathogen. Here, we investigate genetic signatures in plant cell wall degrading enzymes (PCWDEs) that are likely affected by or driving coevolution in plant-pathogen systems. We hypothesize four main evolutionary scenarios and combine comparative genomics, transcriptomics, and selection analyses to assign the majority of PCWDEs in Z. tritici to one of these scenarios. We found widespread differential transcription among different members of the same gene family, challenging the idea of functional redundancy and suggesting instead that specialized enzymatic activity occurs during different stages of the pathogen life cycle. We also find that natural selection has significantly affected at least 19 of the 48 identified PCWDEs. The majority of genes showed signatures of purifying selection, typical for the scenario of conserved substrate optimization. However, six genes showed diversifying selection that could be attributed to either host adaptation or host evasion. This study provides a powerful framework to better understand the roles played by different members of multigene families and to determine which genes are the most appropriate targets for wet laboratory experimentation, for example, to elucidate enzymatic function during relevant phases of a pathogen's life cycle.
Long-Term and Short-Term Evolutionary Impacts of Transposable Elements on Drosophila

PubMed Central

Lee, Yuh Chwen G.; Langley, Charles H.

2012-01-01

Transposable elements (TEs) are considered to be genomic parasites and their interactions with their hosts have been likened to the coevolution between host and other nongenomic, horizontally transferred pathogens. TE families, however, are vertically inherited as integral segments of the nuclear genome. This transmission strategy has been suggested to weaken the selective benefits of host alleles repressing the transposition of specific TE variants. On the other hand, the elevated rates of TE transposition and high incidences of deleterious mutations observed during the rare cases of horizontal transfers of TE families between species could create at least a transient process analogous to the influence of horizontally transmitted pathogens. Here, we formally address this analogy, using empirical and theoretical analysis to specify the mechanism of how host–TE interactions may drive the evolution of host genes. We found that host TE-interacting genes actually have more pervasive evidence of adaptive evolution than immunity genes that interact with nongenomic pathogens in Drosophila. Yet, both our theoretical modeling and empirical observations comparing Drosophila melanogaster populations before and after the horizontal transfer of P elements, which invaded D. melanogaster early last century, demonstrated that horizontally transferred TEs have only a limited influence on host TE-interacting genes. We propose that the more prevalent and constant interaction with multiple vertically transmitted TE families may instead be the main force driving the fast evolution of TE-interacting genes, which is fundamentally different from the gene-for-gene interaction of host–pathogen coevolution. PMID:22997235
The structural basis of chicken, swine and bovine CD8αα dimers provides insight into the co-evolution with MHC I in endotherm species

PubMed Central

Liu, Yanjie; Li, Xin; Qi, Jianxun; Zhang, Nianzhi; Xia, Chun

2016-01-01

It is unclear how the pivotal molecules of the adaptive immune system (AIS) maintain their inherent characteristics and relationships with their co-receptors over the course of co-evolution. CD8α, a fundamental but simple AIS component with only one immunoglobulin variable (IgV) domain, is a good example with which to explore this question because it can fold correctly to form homodimers (CD8αα) and interact with peptide-MHC I (p/MHC I) with low sequence identities between different species. Hereby, we resolved the crystal structures of chicken, swine and bovine CD8αα. They are typical homodimers consisting of two symmetric IgV domains with distinct species specificities. The CD8αα structures indicated that a few highly conserved residues are important in CD8 dimerization and in interacting with p/MHC I. The dimerization of CD8αα mainly depends on the pivotal residues on the dimer interface; in particular, four aromatic residues provide many intermolecular forces and contact areas. Three residues on the surface of CD8α connecting cavities that formed most of the hydrogen bonds with p/MHC I were also completely conserved. Our data propose that a few key conserved residues are able to ensure the CD8α own structural characteristics despite the great sequence variation that occurs during evolution in endotherms. PMID:27122108

Heuristic urban transportation network design method, a multilayer coevolution approach

NASA Astrophysics Data System (ADS)

Ding, Rui; Ujang, Norsidah; Hamid, Hussain bin; Manan, Mohd Shahrudin Abd; Li, Rong; Wu, Jianjun

2017-08-01

The design of urban transportation networks plays a key role in the urban planning process, and the coevolution of urban networks has recently garnered significant attention in literature. However, most of these recent articles are based on networks that are essentially planar. In this research, we propose a heuristic multilayer urban network coevolution model with lower layer network and upper layer network that are associated with growth and stimulate one another. We first use the relative neighbourhood graph and the Gabriel graph to simulate the structure of rail and road networks, respectively. With simulation we find that when a specific number of nodes are added, the total travel cost ratio between an expanded network and the initial lower layer network has the lowest value. The cooperation strength Λ and the changeable parameter average operation speed ratio Θ show that transit users' route choices change dramatically through the coevolution process and that their decisions, in turn, affect the multilayer network structure. We also note that the simulated relation between the Gini coefficient of the betweenness centrality, Θ and Λ have an optimal point for network design. This research could inspire the analysis of urban network topology features and the assessment of urban growth trends.
Coevolution of nutrigenomics and society: ethical considerations.

PubMed

Korthals, Michiel

2011-12-01

To optimize the coevolution of nutrigenomics and society (ie, the reciprocal stimulation of both developments), I analyzed chances for a fruitful match between normative concepts and strategies of both developments. Nutrigenomics embodies ≥ 3 normative concepts. First, food is exclusively interpreted in terms of disease prevention. Second, striving for health is interpreted as the quantification of risks and prevention of diseases through positive food-gene interactions. The third normative idea is that disease prevention by the minimization of risks is an individual's task. My thesis was that these concepts of nutrigenomics would not easily match with concepts of food and health of various food styles in Western societies, which, for instance, parents in the case of metabolic programming endorse and with a philosophical view of the relation between food, health, and the meaning of life. Next, I reflected on the nonsynchronized coevolution of nutrigenomics and society because of this mismatch and introduced the concept of the fair representation of food styles in nutrigenomic developments. To synchronize and optimize the coevolution of nutrigenomics and society, I propose that the research policy of nutrigenomics should change to a research partnership with society on the basis of fair representation.
Coevolution of game and network structure with adjustable linking

NASA Astrophysics Data System (ADS)

Qin, Shao-Meng; Zhang, Guo-Yong; Chen, Yong

2009-12-01

Most papers about the evolutionary game on graph assume the statistic network structure. However, in the real world, social interaction could change the relationship among people. And the change of social structure will also affect people’s strategies. We build a coevolution model of prisoner’s dilemma game and network structure to study the dynamic interaction in the real world. Differing from other coevolution models, players rewire their network connections according to the density of cooperation and other players’ payoffs. We use a parameter α to control the effect of payoff in the process of rewiring. Based on the asynchronous update rule and Monte Carlo simulation, we find that, when players prefer to rewire their links to those who are richer, the temptation can increase the cooperation density.
A Comparison of Mechanical Parameters Between the Counter Movement Jump and Drop Jump in Biathletes

PubMed Central

Król, Henryk; Mynarski, Władysław

2012-01-01

The main objective of the study was to determine to what degree higher muscular activity, achieved by increased load in the extension phase (eccentric muscle action) of the vertical jump, affects the efficiency of the vertical jump. Sixteen elite biathletes participated in this investigation. The biathletes performed tests that consisted of five, single “maximal” vertical jumps (counter movement jump – CMJ) and five, single vertical jumps, in which the task was to touch a bar placed over the jumping biathletes (specific task counter movement jump – SCMJ). Then, they performed five, single drop jumps from an elevation of 0.4m (DJ). Ground reaction forces were registered using the KISTLER 9182C force platform. MVJ software was used for signal processing (Król, 1999) and enabling calculations for kinematic and kinetic parameters of the subject’s jump movements (on-line system). The results indicate that only height of the jump (h) and mean power (Pmean) during the takeoff are statistically significant. Both h and Pmean are higher in the DJ. The results of this study may indicate that elite biathletes are well adapted to eccentric work of the lower limbs, thus reaching greater values of power during the drop jump. These neuromuscular adaptive changes may allow for a more dynamic and efficient running technique. PMID:23487157
Resist Globally, Infect Locally: A Transcontinental Test of Adaptation by Stickleback and Their Tapeworm Parasite.

PubMed

Weber, Jesse N; Kalbe, Martin; Shim, Kum Chuan; Erin, Noémie I; Steinel, Natalie C; Ma, Lei; Bolnick, Daniel I

2017-01-01

Parasite infections are a product of both ecological processes affecting host-parasite encounter rates and evolutionary dynamics affecting host susceptibility. However, few studies examine natural infection variation from both ecological and evolutionary perspectives. Here, we describe the ecological and evolutionary factors generating variation in infection rates by a tapeworm (Schistocephalus solidus) in a vertebrate host, the threespine stickleback (Gasterosteus aculeatus). To explore ecological aspects of infection, we measured tapeworm prevalence in Canadian stickleback inhabiting two distinct environments: marine and freshwater. Consistent with ecological control of infection, the tapeworm is very rare in marine environments, even though marine fish are highly susceptible. Conversely, commonly infected freshwater stickleback exhibit substantial resistance in controlled laboratory trials, suggesting that high exposure risk overwhelms their recently evolved resistance. We also tested for parasite adaptation to its host by performing transcontinental reciprocal infections, using stickleback and tapeworm populations from Europe and western Canada. More infections occurred in same-continent host-parasite combinations, indicating parasite "local" adaptation, at least on the scale of continents. However, the recently evolved immunity of freshwater hosts applies to both local and foreign parasites. The pattern of adaptation described here is not wholly compatible with either of the common models of host-parasite coevolution (i.e., matching infection or targeted recognition). Instead, we propose a hybrid, eco-evolutionary model to explain the remarkable pattern of global host resistance and local parasite infectivity.
Fixed or adapted conditioning intensity for repeated conditioned pain modulation.

PubMed

Hoegh, M; Petersen, K K; Graven-Nielsen, T

2017-12-29

Aims Conditioned pain modulation (CPM) is used to assess descending pain modulation through a test stimulation (TS) and a conditioning stimulation (CS). Due to potential carry-over effects, sequential CPM paradigms might alter the intensity of the CS, which potentially can alter the CPM-effect. This study aimed to investigate the difference between a fixed and adaptive CS intensity on CPM-effect. Methods On the dominant leg of 20 healthy subjects the cuff pressure detection threshold (PDT) was recorded as TS and the pain tolerance threshold (PTT) was assessed on the non-dominant leg for estimating the CS. The difference in PDT before and during CS defined the CPM-effect. The CPM-effect was assessed four times using a CS with intensities of 70% of baseline PTT (fixed) or 70% of PTT measured throughout the session (adaptive). Pain intensity of the conditioning stimulus was assessed on a numeric rating scale (NRS). Data were analyzed with repeated-measures ANOVA. Results No difference was found comparing the four PDTs assessed before CSs for the fixed and the adaptive paradigms. The CS pressure intensity for the adaptive paradigm was increasing during the four repeated assessments (P < 0.01). The pain intensity was similar during the fixed (NRS: 5.8±0.5) and the adjusted paradigm (NRS: 6.0±0.4). The CPM-effect was higher using the fixed condition compared with the adaptive condition (P < 0.05). Conclusions The current study found that sequential CPM paradigms using a fixed conditioning stimulus produced an increased CPM-effect compared with adaptive and increasing conditioning intensities.
Tracing the first step to speciation: ecological and genetic differentiation of a salamander population in a small forest.

PubMed

Steinfartz, Sebastian; Weitere, Markus; Tautz, Diethard

2007-11-01

Mechanisms and processes of ecologically driven adaptive speciation are best studied in natural situations where the splitting process is still occurring, i.e. before complete reproductive isolation is achieved. Here, we present a case of an early stage of adaptive differentiation under sympatric conditions in the fire salamander, Salamandra salamandra, that allows inferring the underlying processes for the split. Larvae of S. salamandra normally mature in small streams until metamorphosis, but in an old, continuous forest area near Bonn (the Kottenforst), we found salamander larvae not only in small streams but also in shallow ponds, which are ecologically very different from small streams. Common-environment experiments with larvae from both habitat types reveal specific adaptations to these different ecological conditions. Mitochondrial and microsatellite analyses show that the two ecologically differentiated groups also show signs of genetic differentiation. A parallel analysis of animals from a neighbouring much larger forest area (the Eifel), in which larvae mature only in streams, shows no signs of genetic differentiation, indicating that gene flow between ecologically similar types can occur over large distances. Hence, geographical factors cannot explain the differential larval habitat adaptations in the Kottenforst, in particular since adult life and mating of S. salamandra is strictly terrestrial and not associated with larval habitats. We propose therefore that the evolution of these adaptations was coupled with the evolution of cues for assortative mating which would be in line with models of sympatric speciation that suggest a co-evolution of habitat adaptations and associated mating signals.
Adaptive sequential controller

DOEpatents

El-Sharkawi, Mohamed A.; Xing, Jian; Butler, Nicholas G.; Rodriguez, Alonso

1994-01-01

An adaptive sequential controller (50/50') for controlling a circuit breaker (52) or other switching device to substantially eliminate transients on a distribution line caused by closing and opening the circuit breaker. The device adaptively compensates for changes in the response time of the circuit breaker due to aging and environmental effects. A potential transformer (70) provides a reference signal corresponding to the zero crossing of the voltage waveform, and a phase shift comparator circuit (96) compares the reference signal to the time at which any transient was produced when the circuit breaker closed, producing a signal indicative of the adaptive adjustment that should be made. Similarly, in controlling the opening of the circuit breaker, a current transformer (88) provides a reference signal that is compared against the time at which any transient is detected when the circuit breaker last opened. An adaptive adjustment circuit (102) produces a compensation time that is appropriately modified to account for changes in the circuit breaker response, including the effect of ambient conditions and aging. When next opened or closed, the circuit breaker is activated at an appropriately compensated time, so that it closes when the voltage crosses zero and opens when the current crosses zero, minimizing any transients on the distribution line. Phase angle can be used to control the opening of the circuit breaker relative to the reference signal provided by the potential transformer.
Sequential Multiple Assignment Randomized Trial (SMART) with Adaptive Randomization for Quality Improvement in Depression Treatment Program

PubMed Central

Chakraborty, Bibhas; Davidson, Karina W.

2015-01-01

Summary 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. PMID:25354029
Two-stage sequential sampling: A neighborhood-free adaptive sampling procedure

USGS Publications Warehouse

Salehi, M.; Smith, D.R.

2005-01-01

Designing an efficient sampling scheme for a rare and clustered population is a challenging area of research. Adaptive cluster sampling, which has been shown to be viable for such a population, is based on sampling a neighborhood of units around a unit that meets a specified condition. However, the edge units produced by sampling neighborhoods have proven to limit the efficiency and applicability of adaptive cluster sampling. We propose a sampling design that is adaptive in the sense that the final sample depends on observed values, but it avoids the use of neighborhoods and the sampling of edge units. Unbiased estimators of population total and its variance are derived using Murthy's estimator. The modified two-stage sampling design is easy to implement and can be applied to a wider range of populations than adaptive cluster sampling. We evaluate the proposed sampling design by simulating sampling of two real biological populations and an artificial population for which the variable of interest took the value either 0 or 1 (e.g., indicating presence and absence of a rare event). We show that the proposed sampling design is more efficient than conventional sampling in nearly all cases. The approach used to derive estimators (Murthy's estimator) opens the door for unbiased estimators to be found for similar sequential sampling designs. ?? 2005 American Statistical Association and the International Biometric Society.
Proposing a sequential comparative analysis for assessing multilateral health agency transformation and sustainable capacity: exploring the advantages of institutional theory

PubMed Central

2014-01-01

Background This article proposes an approach to comparing and assessing the adaptive capacity of multilateral health agencies in meeting country and individual healthcare needs. Most studies comparing multilateral health agencies have failed to clearly propose a method for conducting agency comparisons. Methods This study conducted a qualitative case study methodological approach, such that secondary and primary case study literature was used to conduct case study comparisons of multilateral health agencies. Results Through the proposed Sequential Comparative Analysis (SCA), the author found a more effective way to justify the selection of cases, compare and assess organizational transformative capacity, and to learn from agency success in policy sustainability processes. Conclusions To more affectively understand and explain why some multilateral health agencies are more capable of adapting to country and individual healthcare needs, SCA provides a methodological approach that may help to better understand why these agencies are so different and what we can learn from successful reform processes. As funding challenges continue to hamper these agencies' adaptive capacity, learning from each other will become increasingly important. PMID:24886283
Proposing a sequential comparative analysis for assessing multilateral health agency transformation and sustainable capacity: exploring the advantages of institutional theory.

PubMed

Gómez, Eduardo J

2014-05-20

This article proposes an approach to comparing and assessing the adaptive capacity of multilateral health agencies in meeting country and individual healthcare needs. Most studies comparing multilateral health agencies have failed to clearly propose a method for conducting agency comparisons. This study conducted a qualitative case study methodological approach, such that secondary and primary case study literature was used to conduct case study comparisons of multilateral health agencies. Through the proposed Sequential Comparative Analysis (SCA), the author found a more effective way to justify the selection of cases, compare and assess organizational transformative capacity, and to learn from agency success in policy sustainability processes. To more affectively understand and explain why some multilateral health agencies are more capable of adapting to country and individual healthcare needs, SCA provides a methodological approach that may help to better understand why these agencies are so different and what we can learn from successful reform processes. As funding challenges continue to hamper these agencies' adaptive capacity, learning from each other will become increasingly important.
Co-Evolution of User and Organizational Interfaces: A Longitudinal Case Study of WWW Dissemination of National Statistics.

ERIC Educational Resources Information Center

Marchionini, Gary

2002-01-01

Describes how user interfaces for the Bureau of Labor Statistics (BLS) web site evolved over a 5-year period along with the larger organizational interface and how this co-evolution has influenced the institution. Interviews with BLS staff and transaction log analysis are the foci of this study, as well as user information-seeking studies and user…
The effect of a beta-adrenoceptor antagonist on accommodative adaptation in Hong Kong children.

PubMed

Chen, Jennifer C; Schmid, Katrina L; Brown, Brian; Edwards, Marion H

2005-03-01

Increased susceptibility to nearwork-induced accommodative adaptation has been suggested as a risk factor for myopia development. We investigated whether accommodative adaptation may explain in part the high prevalence of myopia in Hong Kong children and examined the effect of beta-antagonism with topical timolol maleate on accommodative adaptation. Thirty children (10 emmetropes and 20 myopes) aged between 8 and 12 years were recruited. Tonic accommodation was measured before and after 5 min of video game-playing using an open-field Shin-Nippon autorefractor. Measurements were repeated 30 min after timolol instillation. Children with progressing myopia demonstrated accommodative adaptation following the near task, whereas stable myopes showed counter-adaptive, hyperopic accommodative changes. Timolol increased the magnitude of accommodative adaptation in the stable myopes but had little effect on responses of the progressing myopes or emmetropes. Neuropharmacological modulation of the accommodative system may have a possible etiological role in the progression of myopia.
Detection of significant protein coevolution.

PubMed

Ochoa, David; Juan, David; Valencia, Alfonso; Pazos, Florencio

2015-07-01

The evolution of proteins cannot be fully understood without taking into account the coevolutionary linkages entangling them. From a practical point of view, coevolution between protein families has been used as a way of detecting protein interactions and functional relationships from genomic information. The most common approach to inferring protein coevolution involves the quantification of phylogenetic tree similarity using a family of methodologies termed mirrortree. In spite of their success, a fundamental problem of these approaches is the lack of an adequate statistical framework to assess the significance of a given coevolutionary score (tree similarity). As a consequence, a number of ad hoc filters and arbitrary thresholds are required in an attempt to obtain a final set of confident coevolutionary signals. In this work, we developed a method for associating confidence estimators (P values) to the tree-similarity scores, using a null model specifically designed for the tree comparison problem. We show how this approach largely improves the quality and coverage (number of pairs that can be evaluated) of the detected coevolution in all the stages of the mirrortree workflow, independently of the starting genomic information. This not only leads to a better understanding of protein coevolution and its biological implications, but also to obtain a highly reliable and comprehensive network of predicted interactions, as well as information on the substructure of macromolecular complexes using only genomic information. The software and datasets used in this work are freely available at: http://csbg.cnb.csic.es/pMT/. pazos@cnb.csic.es Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
Plastid-Nuclear Interaction and Accelerated Coevolution in Plastid Ribosomal Genes in Geraniaceae.

PubMed

Weng, Mao-Lun; Ruhlman, Tracey A; Jansen, Robert K

2016-06-27

Plastids and mitochondria have many protein complexes that include subunits encoded by organelle and nuclear genomes. In animal cells, compensatory evolution between mitochondrial and nuclear-encoded subunits was identified and the high mitochondrial mutation rates were hypothesized to drive compensatory evolution in nuclear genomes. In plant cells, compensatory evolution between plastid and nucleus has rarely been investigated in a phylogenetic framework. To investigate plastid-nuclear coevolution, we focused on plastid ribosomal protein genes that are encoded by plastid and nuclear genomes from 27 Geraniales species. Substitution rates were compared for five sets of genes representing plastid- and nuclear-encoded ribosomal subunit proteins targeted to the cytosol or the plastid as well as nonribosomal protein controls. We found that nonsynonymous substitution rates (dN) and the ratios of nonsynonymous to synonymous substitution rates (ω) were accelerated in both plastid- (CpRP) and nuclear-encoded subunits (NuCpRP) of the plastid ribosome relative to control sequences. Our analyses revealed strong signals of cytonuclear coevolution between plastid- and nuclear-encoded subunits, in which nonsynonymous substitutions in CpRP and NuCpRP tend to occur along the same branches in the Geraniaceae phylogeny. This coevolution pattern cannot be explained by physical interaction between amino acid residues. The forces driving accelerated coevolution varied with cellular compartment of the sequence. Increased ω in CpRP was mainly due to intensified positive selection whereas increased ω in NuCpRP was caused by relaxed purifying selection. In addition, the many indels identified in plastid rRNA genes in Geraniaceae may have contributed to changes in plastid subunits. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Observer-based monitoring of heat exchangers.

PubMed

Astorga-Zaragoza, Carlos-Manuel; Alvarado-Martínez, Víctor-Manuel; Zavala-Río, Arturo; Méndez-Ocaña, Rafael-Maxim; Guerrero-Ramírez, Gerardo-Vicente

2008-01-01

The goal of this work is to provide a method for monitoring performance degradation in counter-flow double-pipe heat exchangers. The overall heat transfer coefficient is estimated by an adaptive observer and monitored in order to infer when the heat exchanger needs preventive or corrective maintenance. A simplified mathematical model is used to synthesize the adaptive observer and a more complex model is used for simulation. The reliability of the proposed method was demonstrated via numerical simulations and laboratory experiments with a bench-scale pilot plant.
Research on the adaptive optical control technology based on DSP

NASA Astrophysics Data System (ADS)

Zhang, Xiaolu; Xue, Qiao; Zeng, Fa; Zhao, Junpu; Zheng, Kuixing; Su, Jingqin; Dai, Wanjun

2018-02-01

Adaptive optics is a real-time compensation technique using high speed support system for wavefront errors caused by atmospheric turbulence. However, the randomness and instantaneity of atmospheric changing introduce great difficulties to the design of adaptive optical systems. A large number of complex real-time operations lead to large delay, which is an insurmountable problem. To solve this problem, hardware operation and parallel processing strategy are proposed, and a high-speed adaptive optical control system based on DSP is developed. The hardware counter is used to check the system. The results show that the system can complete a closed loop control in 7.1ms, and improve the controlling bandwidth of the adaptive optical system. Using this system, the wavefront measurement and closed loop experiment are carried out, and obtain the good results.
Dose finding with the sequential parallel comparison design.

PubMed

Wang, Jessie J; Ivanova, Anastasia

2014-01-01

The sequential parallel comparison design (SPCD) is a two-stage design recommended for trials with possibly high placebo response. A drug-placebo comparison in the first stage is followed in the second stage by placebo nonresponders being re-randomized between drug and placebo. We describe how SPCD can be used in trials where multiple doses of a drug or multiple treatments are compared with placebo and present two adaptive approaches. We detail how to analyze data in such trials and give recommendations about the allocation proportion to placebo in the two stages of SPCD.
Sequential Insertion Heuristic with Adaptive Bee Colony Optimisation Algorithm for Vehicle Routing Problem with Time Windows

PubMed Central

Jawarneh, Sana; Abdullah, Salwani

2015-01-01

This paper presents a bee colony optimisation (BCO) algorithm to tackle the vehicle routing problem with time window (VRPTW). The VRPTW involves recovering an ideal set of routes for a fleet of vehicles serving a defined number of customers. The BCO algorithm is a population-based algorithm that mimics the social communication patterns of honeybees in solving problems. The performance of the BCO algorithm is dependent on its parameters, so the online (self-adaptive) parameter tuning strategy is used to improve its effectiveness and robustness. Compared with the basic BCO, the adaptive BCO performs better. Diversification is crucial to the performance of the population-based algorithm, but the initial population in the BCO algorithm is generated using a greedy heuristic, which has insufficient diversification. Therefore the ways in which the sequential insertion heuristic (SIH) for the initial population drives the population toward improved solutions are examined. Experimental comparisons indicate that the proposed adaptive BCO-SIH algorithm works well across all instances and is able to obtain 11 best results in comparison with the best-known results in the literature when tested on Solomon’s 56 VRPTW 100 customer instances. Also, a statistical test shows that there is a significant difference between the results. PMID:26132158

Adaptive Online Sequential ELM for Concept Drift Tackling

PubMed Central

Basaruddin, Chan

2016-01-01

A machine learning method needs to adapt to over time changes in the environment. Such changes are known as concept drift. In this paper, we propose concept drift tackling method as an enhancement of Online Sequential Extreme Learning Machine (OS-ELM) and Constructive Enhancement OS-ELM (CEOS-ELM) by adding adaptive capability for classification and regression problem. The scheme is named as adaptive OS-ELM (AOS-ELM). It is a single classifier scheme that works well to handle real drift, virtual drift, and hybrid drift. The AOS-ELM also works well for sudden drift and recurrent context change type. The scheme is a simple unified method implemented in simple lines of code. We evaluated AOS-ELM on regression and classification problem by using concept drift public data set (SEA and STAGGER) and other public data sets such as MNIST, USPS, and IDS. Experiments show that our method gives higher kappa value compared to the multiclassifier ELM ensemble. Even though AOS-ELM in practice does not need hidden nodes increase, we address some issues related to the increasing of the hidden nodes such as error condition and rank values. We propose taking the rank of the pseudoinverse matrix as an indicator parameter to detect “underfitting” condition. PMID:27594879
Methods for the cultural adaptation of a diabetes lifestyle intervention for Latinas: an illustrative project.

PubMed

Osuna, Diego; Barrera, Manuel; Strycker, Lisa A; Toobert, Deborah J; Glasgow, Russell E; Geno, Cristy R; Almeida, Fabio; Perdomo, Malena; King, Diane; Doty, Alyssa Tinley

2011-05-01

Because Latinas experience a high prevalence of type 2 diabetes and its complications, there is an urgent need to reach them with interventions that promote healthful lifestyles. This article illustrates a sequential approach that took an effective multiple-risk-factor behavior-change program and adapted it for Latinas with type 2 diabetes. Adaptation stages include (a) information gathering from literature and focus groups, (b) preliminary adaptation design, and (c) preliminary adaptation test. In this third stage, a pilot study finds that participants were highly satisfied with the intervention and showed improvement across diverse outcomes. Key implications for applications include the importance of a model for guiding cultural adaptations, and the value of procedures for obtaining continuous feedback from staff and participants during the preliminary adaptation test.
Adaptive Interventions and SMART Designs: Application to child behavior research in a community setting.

PubMed

Kidwell, Kelley M; Hyde, Luke W

2016-09-01

Heterogeneity between and within people necessitates the need for sequential personalized interventions to optimize individual outcomes. Personalized or adaptive interventions (AIs) are relevant for diseases and maladaptive behavioral trajectories when one intervention is not curative and success of a subsequent intervention may depend on individual characteristics or response. AIs may be applied to medical settings and to investigate best prevention, education, and community-based practices. AIs can begin with low-cost or low-burden interventions and followed with intensified or alternative interventions for those who need it most. AIs that guide practice over the course of a disease, program, or school year can be investigated through sequential multiple assignment randomized trials (SMARTs). To promote the use of SMARTs, we provide a hypothetical SMART in a Head Start program to address child behavior problems. We describe the advantages and limitations of SMARTs, particularly as they may be applied to the field of evaluation.
Phylogenetic placement of an unusual coral mushroom challenges the classic hypothesis of strict coevolution in the Apterostigma pilosum group ant-fungus mutualism

Treesearch

Bryn T.M. Dentinger; D.Jean Lodge; Andrew B. Munkacsi; Dennis E. Desjardin; David J. McLaughlin

2009-01-01

The ~50 million-year-old fungus-farming ant mutualism is a classic example of coevolution, involving ants that subsist on asexual, fungal biomass, in turn propagating the fungus clonally through nest-to-nest transmission. Most mutualistic ants cultivate two closely related groups of gilled mushrooms, whereas one small group of ants in the genus ...
Coevolution study of mitochondria respiratory chain proteins: toward the understanding of protein--protein interaction.

PubMed

Yang, Ming; Ge, Yan; Wu, Jiayan; Xiao, Jingfa; Yu, Jun

2011-05-20

Coevolution can be seen as the interdependency between evolutionary histories. In the context of protein evolution, functional correlation proteins are ever-present coordinated evolutionary characters without disruption of organismal integrity. As to complex system, there are two forms of protein--protein interactions in vivo, which refer to inter-complex interaction and intra-complex interaction. In this paper, we studied the difference of coevolution characters between inter-complex interaction and intra-complex interaction using "Mirror tree" method on the respiratory chain (RC) proteins. We divided the correlation coefficients of every pairwise RC proteins into two groups corresponding to the binary protein--protein interaction in intra-complex and the binary protein--protein interaction in inter-complex, respectively. A dramatical discrepancy is detected between the coevolution characters of the two sets of protein interactions (Wilcoxon test, p-value = 4.4 × 10(-6)). Our finding reveals some critical information on coevolutionary study and assists the mechanical investigation of protein--protein interaction. Furthermore, the results also provide some unique clue for supramolecular organization of protein complexes in the mitochondrial inner membrane. More detailed binding sites map and genome information of nuclear encoded RC proteins will be extraordinary valuable for the further mitochondria dynamics study. Copyright © 2011. Published by Elsevier Ltd.
Phylogenetic placement of an unusual coral mushroom challenges the classic hypothesis of strict coevolution in the apterostigma pilosum group ant-fungus mutualism.

PubMed

Dentinger, Bryn T M; Lodge, D Jean; Munkacsi, Andrew B; Desjardin, Dennis E; McLaughlin, David J

2009-08-01

The approximately 50 million-year-old fungus-farming ant mutualism is a classic example of coevolution, involving ants that subsist on asexual, fungal biomass, in turn propagating the fungus clonally through nest-to-nest transmission. Most mutualistic ants cultivate two closely related groups of gilled mushrooms, whereas one small group of ants in the genus Apterostigma cultivates a distantly related lineage comprised of the G2 and G4 groups. The G2 and G4 fungi were previously shown to form a monophyletic group sister to the thread-like coral mushroom family Pterulaceae. Here, we identify an enigmatic coral mushroom that produces both fertile and sterile fruiting structures as the closest free-living relative of the G4 fungi, challenging the monophyly of the Apterostigma-cultivated fungi for the first time. Both nonparametric bootstrap and Bayesian posterior probability support the node leading to the G4 cultivars and a free-living Pterula mushroom. These data suggest three scenarios that contradict the hypothesis of strict coevolution: (1) multiple domestications, (2) escape from domestication, (3) selection of single cultivar lineages from an ancestral mixed-fungus garden. These results illustrate how incomplete phylogenies for coevolved symbionts impede our understanding of the patterns and processes of coevolution.
The Coevolution of Life and Environment on Mars: An Ecosystem Perspective on the Robotic Exploration of Biosignatures

NASA Astrophysics Data System (ADS)

Cabrol, Nathalie A.

2018-01-01

Earth's biological and environmental evolution are intertwined and inseparable. This coevolution has become a fundamental concept in astrobiology and is key to the search for life beyond our planet. In the case of Mars, whether a coevolution took place is unknown, but analyzing the factors at play shows the uniqueness of each planetary experiment regardless of similarities. Early Earth and early Mars shared traits. However, biological processes on Mars, if any, would have had to proceed within the distinctive context of an irreversible atmospheric collapse, greater climate variability, and specific planetary characteristics. In that, Mars is an important test bed for comparing the effects of a unique set of spatiotemporal changes on an Earth-like, yet different, planet. Many questions remain unanswered about Mars' early environment. Nevertheless, existing data sets provide a foundation for an intellectual framework where notional coevolution models can be explored. In this framework, the focus is shifted from planetary-scale habitability to the prospect of habitats, microbial ecotones, pathways to biological dispersal, biomass repositories, and their meaning for exploration. Critically, as we search for biosignatures, this focus demonstrates the importance of starting to think of early Mars as a biosphere and vigorously integrating an ecosystem approach to landing site selection and exploration.
The evolution of dinosaurs.

PubMed

Sereno, P C

1999-06-25

The ascendancy of dinosaurs on land near the close of the Triassic now appears to have been as accidental and opportunistic as their demise and replacement by therian mammals at the end of the Cretaceous. The dinosaurian radiation, launched by 1-meter-long bipeds, was slower in tempo and more restricted in adaptive scope than that of therian mammals. A notable exception was the evolution of birds from small-bodied predatory dinosaurs, which involved a dramatic decrease in body size. Recurring phylogenetic trends among dinosaurs include, to the contrary, increase in body size. There is no evidence for co-evolution between predators and prey or between herbivores and flowering plants. As the major land masses drifted apart, dinosaurian biogeography was molded more by regional extinction and intercontinental dispersal than by the breakup sequence of Pangaea.
Bacterial Unculturability and the Formation of Intercellular Metabolic Networks.

PubMed

Pande, Samay; Kost, Christian

2017-05-01

The majority of known bacterial species cannot be cultivated under laboratory conditions. Here we argue that the adaptive emergence of obligate metabolic interactions in natural bacterial communities can explain this pattern. Bacteria commonly release metabolites into the external environment. Accumulating pools of extracellular metabolites create an ecological niche that benefits auxotrophic mutants, which have lost the ability to autonomously produce the corresponding metabolites. In addition to a diffusion-based metabolite transfer, auxotrophic cells can use contact-dependent means to obtain nutrients from other co-occurring cells. Spatial colocalisation and a continuous coevolution further increase the nutritional dependency and optimise fluxes through combined metabolic networks. Thus, bacteria likely function as networks of interacting cells that reciprocally exchange nutrients and biochemical functions rather than as physiologically autonomous units. Copyright © 2017 Elsevier Ltd. All rights reserved.
Changes in coral-reef structure through the Miocene in the Mediterranean province: Adaptive versus environmental influence

NASA Astrophysics Data System (ADS)

Pomar, Luis; Hallock, Pamela

2007-10-01

Well-documented Mediterranean examples of Miocene carbonate platforms, with complete exposures from shallow-water to basinal facies, provide evidence for temporal changes in reef-building capacity of zooxanthellate corals. In pre-late Tortonian platforms, small coralgal patches and mounds occur from platform top to the toe of slope, but they did not build to sea level. In contrast, barrier reefs with unequivocal reef-crest structures that reached sea level are documented in late Tortonian-early Messinian platforms. We suggest that a change in both calcification rates and bathymetric zonation was the result of coevolution of corals and Symbiodinium zooxanthellae, coeval to global cooling and, at least at a regional scale, a geochemical change that supported widespread aragonite precipitation through the late Miocene.
Helminth Infections: Recognition and Modulation of the Immune Response by Innate Immune Cells

PubMed Central

Motran, Claudia Cristina; Silvane, Leonardo; Chiapello, Laura Silvina; Theumer, Martin Gustavo; Ambrosio, Laura Fernanda; Volpini, Ximena; Celias, Daiana Pamela; Cervi, Laura

2018-01-01

The survival of helminths in the host over long periods of time is the result of a process of adaptation or dynamic co-evolution between the host and the parasite. However, infection with helminth parasites causes damage to the host tissues producing the release of danger signals that induce the recruitment of various cells, including innate immune cells such as macrophages (Mo), dendritic cells (DCs), eosinophils, basophils, and mast cells. In this scenario, these cells are able to secrete soluble factors, which orchestrate immune effector mechanisms that depend on the different niches these parasites inhabit. Here, we focus on recent advances in the knowledge of excretory-secretory products (ESP), resulting from helminth recognition by DCs and Mo. Phagocytes and other cells types such as innate lymphocyte T cells 2 (ILC2), when activated by ESP, participate in an intricate cytokine network to generate innate and adaptive Th2 responses. In this review, we also discuss the mechanisms of innate immune cell-induced parasite killing and the tissue repair necessary to assure helminth survival over long periods of time. PMID:29670630
Archaeogenomic insights into the adaptation of plants to the human environment: pushing plant-hominin co-evolution back to the Pliocene.

PubMed

Allaby, Robin G; Kistler, Logan; Gutaker, Rafal M; Ware, Roselyn; Kitchen, James L; Smith, Oliver; Clarke, Andrew C

2015-02-01

The colonization of the human environment by plants, and the consequent evolution of domesticated forms is increasingly being viewed as a co-evolutionary plant-human process that occurred over a long time period, with evidence for the co-evolutionary relationship between plants and humans reaching ever deeper into the hominin past. This developing view is characterized by a change in emphasis on the drivers of evolution in the case of plants. Rather than individual species being passive recipients of artificial selection pressures and ultimately becoming domesticates, entire plant communities adapted to the human environment. This evolutionary scenario leads to systems level genetic expectations from models that can be explored through ancient DNA and Next Generation Sequencing approaches. Emerging evidence suggests that domesticated genomes fit well with these expectations, with periods of stable complex evolution characterized by large amounts of change associated with relatively small selective value, punctuated by periods in which changes in one-half of the plant-hominin relationship cause rapid, low-complexity adaptation in the other. A corollary of a single plant-hominin co-evolutionary process is that clues about the initiation of the domestication process may well lie deep within the hominin lineage. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.
STARS-PAC Accelerated Anxiety Reduction: Rationale and Initial Findings

ERIC Educational Resources Information Center

Driscoll, Richard

2006-01-01

An anxiety desensitization method is presented which counters over-arousal through strenuous muscle stretch-tense, deep breath, release-relax and positive suggestion sequences; and uses positive adaptive images to replace negative cognitions and to promote confidence. The addition of the stretch-tense and positive images components are expected to…
Counter-Narratives of Educational Excellence: Free Schools, Success, and Community-Based Schooling

ERIC Educational Resources Information Center

Gerrard, Jessica

2014-01-01

The notion of "competitive excellence" is an enduring cornerstone of UK educational policy. Most recently, expanding and adapting New Labour's Academy project with the introduction of free schools, the Coalition's approach advances and embeds competitive market-based forms of community engagement in education. Responding to this policy…
Assessment of the Politico-Military Campaign to Counter ISIL and Options for Adaptation

DTIC Science & Technology

2016-01-01

on behalf of the Syrian regime starting September 30, 2015, which greatly strengthened the regime’s faltering hand against its armed opponents. The... minimalist approach to partnering will not likely yield sufficient results. The fundamental premise does seem sound: That the only way to gain
Adaptive decision making in a dynamic environment: a test of a sequential sampling model of relative judgment.

PubMed

Vuckovic, Anita; Kwantes, Peter J; Neal, Andrew

2013-09-01

Research has identified a wide range of factors that influence performance in relative judgment tasks. However, the findings from this research have been inconsistent. Studies have varied with respect to the identification of causal variables and the perceptual and decision-making mechanisms underlying performance. Drawing on the ecological rationality approach, we present a theory of the judgment and decision-making processes involved in a relative judgment task that explains how people judge a stimulus and adapt their decision process to accommodate their own uncertainty associated with those judgments. Undergraduate participants performed a simulated air traffic control conflict detection task. Across two experiments, we systematically manipulated variables known to affect performance. In the first experiment, we manipulated the relative distances of aircraft to a common destination while holding aircraft speeds constant. In a follow-up experiment, we introduced a direct manipulation of relative speed. We then fit a sequential sampling model to the data, and used the best fitting parameters to infer the decision-making processes responsible for performance. Findings were consistent with the theory that people adapt to their own uncertainty by adjusting their criterion and the amount of time they take to collect evidence in order to make a more accurate decision. From a practical perspective, the paper demonstrates that one can use a sequential sampling model to understand performance in a dynamic environment, allowing one to make sense of and interpret complex patterns of empirical findings that would otherwise be difficult to interpret using standard statistical analyses. PsycINFO Database Record (c) 2013 APA, all rights reserved.
Characterization of Sphinx1 ASIC X-ray detector using photon counting and charge integration

NASA Astrophysics Data System (ADS)

Habib, A.; Arques, M.; Moro, J.-L.; Accensi, M.; Stanchina, S.; Dupont, B.; Rohr, P.; Sicard, G.; Tchagaspanian, M.; Verger, L.

2018-01-01

Sphinx1 is a novel pixel architecture adapted for X-ray imaging, it detects radiation by photon counting and charge integration. In photon counting mode, each photon is compensated by one or more counter-charges typically consisting of 100 electrons (e-) each. The number of counter-charges required gives a measure of the incoming photon energy, thus allowing spectrometric detection. Pixels can also detect radiation by integrating the charges deposited by all incoming photons during one image frame and converting this analog value into a digital response with a 100 electrons least significant bit (LSB), based on the counter-charge concept. A proof of concept test chip measuring 5 mm × 5 mm, with 200 μm × 200 μm pixels has been produced and characterized. This paper provides details on the architecture and the counter-charge design; it also describes the two modes of operation: photon counting and charge integration. The first performance measurements for this test chip are presented. Noise was found to be ~80 e-rms in photon counting mode with a power consumption of only 0.9 μW/pixel for the static analog part and 0.3 μW/pixel for the static digital part.
High-throughput selection for cellulase catalysts using chemical complementation.

PubMed

Peralta-Yahya, Pamela; Carter, Brian T; Lin, Hening; Tao, Haiyan; Cornish, Virginia W

2008-12-24

Efficient enzymatic hydrolysis of lignocellulosic material remains one of the major bottlenecks to cost-effective conversion of biomass to ethanol. Improvement of glycosylhydrolases, however, is limited by existing medium-throughput screening technologies. Here, we report the first high-throughput selection for cellulase catalysts. This selection was developed by adapting chemical complementation to provide a growth assay for bond cleavage reactions. First, a URA3 counter selection was adapted to link chemical dimerizer activated gene transcription to cell death. Next, the URA3 counter selection was shown to detect cellulase activity based on cleavage of a tetrasaccharide chemical dimerizer substrate and decrease in expression of the toxic URA3 reporter. Finally, the utility of the cellulase selection was assessed by isolating cellulases with improved activity from a cellulase library created by family DNA shuffling. This application provides further evidence that chemical complementation can be readily adapted to detect different enzymatic activities for important chemical transformations for which no natural selection exists. Because of the large number of enzyme variants that selections can now test as compared to existing medium-throughput screens for cellulases, this assay has the potential to impact the discovery of improved cellulases and other glycosylhydrolases for biomass conversion from libraries of cellulases created by mutagenesis or obtained from natural biodiversity.
A High-throughput Selection for Cellulase Catalysts Using Chemical Complementation

PubMed Central

Peralta-Yahya, Pamela; Carter, Brian T.; Lin, Hening; Tao, Haiyan; Cornish, Virginia W.

2010-01-01

Efficient enzymatic hydrolysis of lignocellulosic material remains one of the major bottlenecks to cost-effective conversion of biomass to ethanol. Improvement of glycosylhydrolases however is limited by existing medium-throughput screening technologies. Here, we report the first high-throughput selection for cellulase catalysts. This selection was developed by adapting chemical complementation to provide a growth assay for bond cleavage reactions. First, a URA3 counter selection was adapted to link chemical dimerizer activated gene transcription to cell death. Next, the URA3 counter selection was shown to detect cellulase activity based on cleavage of a tetrasaccharide chemical dimerizer substrate and decrease in expression of the toxic URA3 reporter. Finally, the utility of the cellulase selection was assessed by isolating cellulases with improved activity from a cellulase library created by family DNA shuffling. This application provides further evidence that chemical complementation can be readily adapted to detect different enzymatic activities for important chemical transformations for which no natural selection exists. Due to the large number of enzyme variants selections can test compared to existing medium-throughput screens for cellulases, this assay has the potential to impact the discovery of improved cellulases and other glycosylhydrolases for biomass conversion from libraries of cellulases created by mutagenesis or obtained from natural biodiversity. PMID:19053460
Noise and LPI radar as part of counter-drone mitigation system measures

NASA Astrophysics Data System (ADS)

Zhang, Yan (Rockee); Huang, Yih-Ru; Thumann, Charles

2017-05-01

With the rapid proliferation of small unmanned aerial systems (UAS) in the national airspace, small operational drones are being sometimes considered as a security threat for critical infrastructures, such as sports stadiums, military facilities, and airports. There have been many civilian counter-drone solutions and products reported, including radar and electromagnetic counter measures. For the current electromagnetic solutions, they are usually limited to particular type of detection and counter-measure scheme, which is usually effective for the specific type of drones. Also, control and communication link technologies used in even RC drones nowadays are more sophisticated, making them more difficult to detect, decode and counter. Facing these challenges, our team proposes a "software-defined" solution based on noise and LPI radar. For the detection, wideband-noise radar has the resolution performance to discriminate possible micro-Doppler features of the drone versus biological scatterers. It also has the benefit of more adaptive to different types of drones, and covertly detecting for security application. For counter-measures, random noise can be combined with "random sweeping" jamming scheme, to achieve the optimal balance between peak power allowed and the effective jamming probabilities. Some theoretical analysis of the proposed solution is provided in this study, a design case study is developed, and initial laboratory experiments, as well as outdoor tests are conducted to validate the basic concepts and theories. The study demonstrates the basic feasibilities of the Drone Detection and Mitigation Radar (DDMR) concept, while there are still much work needs to be done for a complete and field-worthy technology development.

Anaerobic Digestion in a Flooded Densified Leachbed

NASA Technical Reports Server (NTRS)

Chynoweth, David P.; Teixeira, Arthur A.; Owens, John M.; Haley, Patrick J.

2009-01-01

A document discusses the adaptation of a patented biomass-digesting process, denoted sequential batch anaerobic composting (SEBAC), to recycling of wastes aboard a spacecraft. In SEBAC, high-solids-content biomass wastes are converted into methane, carbon dioxide, and compost.
Advances for Studying Clonal Evolution in Cancer

PubMed Central

Raphael, Benjamin J.; Chen, Feng; Wendl, Michael C.

2013-01-01

The “clonal evolution” model of cancer emerged and “evolved” amid ongoing advances in technology, especially in recent years during which next generation sequencing instruments have provided ever higher resolution pictures of the genetic changes in cancer cells and heterogeneity in tumors. It has become increasingly clear that clonal evolution is not a single sequential process, but instead frequently involves simultaneous evolution of multiple subclones that co-exist because they are of similar fitness or are spatially separated. Co-evolution of subclones also occurs when they complement each other’s survival advantages. Recent studies have also shown that clonal evolution is highly heterogeneous: different individual tumors of the same type may undergo very different paths of clonal evolution. New methodological advancements, including deep digital sequencing of a mixed tumor population, single cell sequencing, and the development of more sophisticated computational tools, will continue to shape and reshape the models of clonal evolution. In turn, these will provide both an improved framework for the understanding of cancer progression and a guide for treatment strategies aimed at the elimination of all, rather than just some, of the cancer cells within a patient. PMID:23353056
Advances for studying clonal evolution in cancer.

PubMed

Ding, Li; Raphael, Benjamin J; Chen, Feng; Wendl, Michael C

2013-11-01

The "clonal evolution" model of cancer emerged and "evolved" amid ongoing advances in technology, especially in recent years during which next generation sequencing instruments have provided ever higher resolution pictures of the genetic changes in cancer cells and heterogeneity in tumors. It has become increasingly clear that clonal evolution is not a single sequential process, but instead frequently involves simultaneous evolution of multiple subclones that co-exist because they are of similar fitness or are spatially separated. Co-evolution of subclones also occurs when they complement each other's survival advantages. Recent studies have also shown that clonal evolution is highly heterogeneous: different individual tumors of the same type may undergo very different paths of clonal evolution. New methodological advancements, including deep digital sequencing of a mixed tumor population, single cell sequencing, and the development of more sophisticated computational tools, will continue to shape and reshape the models of clonal evolution. In turn, these will provide both an improved framework for the understanding of cancer progression and a guide for treatment strategies aimed at the elimination of all, rather than just some, of the cancer cells within a patient. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.
Sequential divergence and the multiplicative origin of community diversity

PubMed Central

Hood, Glen R.; Forbes, Andrew A.; Powell, Thomas H. Q.; Egan, Scott P.; Hamerlinck, Gabriela; Smith, James J.; Feder, Jeffrey L.

2015-01-01

Phenotypic and genetic variation in one species can influence the composition of interacting organisms within communities and across ecosystems. As a result, the divergence of one species may not be an isolated process, as the origin of one taxon could create new niche opportunities for other species to exploit, leading to the genesis of many new taxa in a process termed “sequential divergence.” Here, we test for such a multiplicative effect of sequential divergence in a community of host-specific parasitoid wasps, Diachasma alloeum, Utetes canaliculatus, and Diachasmimorpha mellea (Hymenoptera: Braconidae), that attack Rhagoletis pomonella fruit flies (Diptera: Tephritidae). Flies in the R. pomonella species complex radiated by sympatrically shifting and ecologically adapting to new host plants, the most recent example being the apple-infesting host race of R. pomonella formed via a host plant shift from hawthorn-infesting flies within the last 160 y. Using population genetics, field-based behavioral observations, host fruit odor discrimination assays, and analyses of life history timing, we show that the same host-related ecological selection pressures that differentially adapt and reproductively isolate Rhagoletis to their respective host plants (host-associated differences in the timing of adult eclosion, host fruit odor preference and avoidance behaviors, and mating site fidelity) cascade through the ecosystem and induce host-associated genetic divergence for each of the three members of the parasitoid community. Thus, divergent selection at lower trophic levels can potentially multiplicatively and rapidly amplify biodiversity at higher levels on an ecological time scale, which may sequentially contribute to the rich diversity of life. PMID:26499247
A fast and precise indoor localization algorithm based on an online sequential extreme learning machine.

PubMed

Zou, Han; Lu, Xiaoxuan; Jiang, Hao; Xie, Lihua

2015-01-15

Nowadays, developing indoor positioning systems (IPSs) has become an attractive research topic due to the increasing demands on location-based service (LBS) in indoor environments. WiFi technology has been studied and explored to provide indoor positioning service for years in view of the wide deployment and availability of existing WiFi infrastructures in indoor environments. A large body of WiFi-based IPSs adopt fingerprinting approaches for localization. However, these IPSs suffer from two major problems: the intensive costs of manpower and time for offline site survey and the inflexibility to environmental dynamics. In this paper, we propose an indoor localization algorithm based on an online sequential extreme learning machine (OS-ELM) to address the above problems accordingly. The fast learning speed of OS-ELM can reduce the time and manpower costs for the offline site survey. Meanwhile, its online sequential learning ability enables the proposed localization algorithm to adapt in a timely manner to environmental dynamics. Experiments under specific environmental changes, such as variations of occupancy distribution and events of opening or closing of doors, are conducted to evaluate the performance of OS-ELM. The simulation and experimental results show that the proposed localization algorithm can provide higher localization accuracy than traditional approaches, due to its fast adaptation to various environmental dynamics.
On the specificity of sequential congruency effects in implicit learning of motor and perceptual sequences.

PubMed

D'Angelo, Maria C; Jiménez, Luis; Milliken, Bruce; Lupiáñez, Juan

2013-01-01

Individuals experience less interference from conflicting information following events that contain conflicting information. Recently, Jiménez, Lupiáñez, and Vaquero (2009) demonstrated that such adaptations to conflict occur even when the source of conflict arises from implicit knowledge of sequences. There is accumulating evidence that momentary changes in adaptations made in response to conflicting information are conflict-type specific (e.g., Funes, Lupiáñez, & Humphreys, 2010a), suggesting that there are multiple modes of control. The current study examined whether conflict-specific sequential congruency effects occur when the 2 sources of conflict are implicitly learned. Participants implicitly learned a motor sequence while simultaneously learning a perceptual sequence. In a first experiment, after learning the 2 orthogonal sequences, participants expressed knowledge of the 2 sequences independently of each other in a transfer phase. In Experiments 2 and 3, within each sequence, the presence of a single control trial disrupted the expression of this specific type of learning on the following trial. There was no evidence of cross-conflict modulations in the expression of sequence learning. The results suggest that the mechanisms involved in transient shifts in conflict-specific control, as reflected in sequential congruency effects, are also engaged when the source of conflict is implicit. (c) 2013 APA, all rights reserved.
Sequential Adaptive Multi-Modality Target Detection and Classification Using Physics Based Models

DTIC Science & Technology

2006-09-01

estimation," R. Raghuram, R. Raich and A.O. Hero, IEEE Intl. Conf. on Acoustics, Speech , and Signal Processing, Toulouse France, June 2006, <http...can then be solved using off-the-shelf classifiers such as radial basis functions, SVM, or kNN classifier structures. When applied to mine detection we...stage waveform selection for adaptive resource constrained state estimation," 2006 IEEE Intl. Conf. on Acoustics, Speech , and Signal Processing
Coevolution Theory of the Genetic Code at Age Forty: Pathway to Translation and Synthetic Life

PubMed Central

Wong, J. Tze-Fei; Ng, Siu-Kin; Mat, Wai-Kin; Hu, Taobo; Xue, Hong

2016-01-01

The origins of the components of genetic coding are examined in the present study. Genetic information arose from replicator induction by metabolite in accordance with the metabolic expansion law. Messenger RNA and transfer RNA stemmed from a template for binding the aminoacyl-RNA synthetase ribozymes employed to synthesize peptide prosthetic groups on RNAs in the Peptidated RNA World. Coevolution of the genetic code with amino acid biosynthesis generated tRNA paralogs that identify a last universal common ancestor (LUCA) of extant life close to Methanopyrus, which in turn points to archaeal tRNA introns as the most primitive introns and the anticodon usage of Methanopyrus as an ancient mode of wobble. The prediction of the coevolution theory of the genetic code that the code should be a mutable code has led to the isolation of optional and mandatory synthetic life forms with altered protein alphabets. PMID:26999216
Host-parasite coevolution: genetic variation in a virus population and the interaction with a host gene.

PubMed

Wilfert, L; Jiggins, F M

2010-07-01

Host-parasite coevolution is considered to be an important factor in maintaining genetic variation in resistance to pathogens. Drosophila melanogaster is naturally infected by the sigma virus, a vertically transmitted and host-specific pathogen. In fly populations, there is a large amount of genetic variation in the transmission rate from parent to offspring, much of which is caused by major-effect resistance polymorphisms. We have found that there are similarly high levels of genetic variation in the rate of paternal transmission among 95 different isolates of the virus as in the host. However, when we examined a transmission-blocking gene in the host, we found that it was effective across virus isolates. Therefore, the high levels of genetic variation observed in this system do not appear to be maintained because of coevolution resulting from interactions between this host gene and parasite genes.
The role of ecology, neutral processes and antagonistic coevolution in an apparent sexual arms race.

PubMed

Perry, Jennifer C; Garroway, Colin J; Rowe, Locke

2017-09-01

Some of the strongest examples of a sexual 'arms race' come from observations of correlated evolution in sexually antagonistic traits among populations. However, it remains unclear whether these cases truly represent sexually antagonistic coevolution; alternatively, ecological or neutral processes might also drive correlated evolution. To investigate these alternatives, we evaluated the contributions of intersex genetic correlations, ecological context, neutral genetic divergence and sexual coevolution in the correlated evolution of antagonistic traits among populations of Gerris incognitus water striders. We could not detect intersex genetic correlations for these sexually antagonistic traits. Ecological variation was related to population variation in the key female antagonistic trait (spine length, a defence against males), as well as body size. Nevertheless, population covariation between sexually antagonistic traits remained substantial and significant even after accounting for all of these processes. Our results therefore provide strong evidence for a contemporary sexual arms race. © 2017 John Wiley & Sons Ltd/CNRS.
Faradaic AC Electrokinetic Flow and Particle Traps

NASA Astrophysics Data System (ADS)

Ben, Yuxing; Chang, Hsueh-Chia

2004-11-01

Faradaic reaction at higher voltages can produce co-ion polarization at AC electrodes instead of counter-ion polarization due to capacitive charging from the bulk. The Faradaic co-ion polarization also does not screen the external field and hence can produce large net electro-kinetic flows at frequencies lower than the inverse RC time of the double layer. Due to the opposite polarization of capacitve and Faradaic charging, we can reverse the direction of AC flows on electrodes by changing the voltage and frequency. Particles and bacteria are trapped and then dispersed at stagnation lines, at locations predicted by our theory, by using these two flows sequentially. This technique offers a good way to concentrate and detect bacteria.
Learning the Art of Electronics

NASA Astrophysics Data System (ADS)

Hayes, Thomas C.; Horowitz, Paul

2016-03-01

1. DC circuits; 2. RC circuits; 3. Diode circuits; 4. Transistors I; 5. Transistors II; 6. Operational amplifiers I; 7. Operational amplifiers II: nice positive feedback; 8. Operational amplifiers III; 9. Operational amplifiers IV: nasty positive feedback; 10. Operational amplifiers V: PID motor control loop; 11. Voltage regulators; 12. MOSFET switches; 13. Group audio project; 14. Logic gates; 15. Logic compilers, sequential circuits, flip-flops; 16. Counters; 17. Memory: state machines; 18. Analog to digital: phase-locked loop; 19. Microcontrollers and microprocessors I: processor/controller; 20. I/O, first assembly language; 21. Bit operations; 22. Interrupt: ADC and DAC; 23. Moving pointers, serial buses; 24. Dallas Standalone Micro, SiLabs SPI RAM; 25. Toys in the attic; Appendices; Index.
Characterizing the roles of changing population size and selection on the evolution of flux control in metabolic pathways.

PubMed

Orlenko, Alena; Chi, Peter B; Liberles, David A

2017-05-25

Understanding the genotype-phenotype map is fundamental to our understanding of genomes. Genes do not function independently, but rather as part of networks or pathways. In the case of metabolic pathways, flux through the pathway is an important next layer of biological organization up from the individual gene or protein. Flux control in metabolic pathways, reflecting the importance of mutation to individual enzyme genes, may be evolutionarily variable due to the role of mutation-selection-drift balance. The evolutionary stability of rate limiting steps and the patterns of inter-molecular co-evolution were evaluated in a simulated pathway with a system out of equilibrium due to fluctuating selection, population size, or positive directional selection, to contrast with those under stabilizing selection. Depending upon the underlying population genetic regime, fluctuating population size was found to increase the evolutionary stability of rate limiting steps in some scenarios. This result was linked to patterns of local adaptation of the population. Further, during positive directional selection, as with more complex mutational scenarios, an increase in the observation of inter-molecular co-evolution was observed. Differences in patterns of evolution when systems are in and out of equilibrium, including during positive directional selection may lead to predictable differences in observed patterns for divergent evolutionary scenarios. In particular, this result might be harnessed to detect differences between compensatory processes and directional processes at the pathway level based upon evolutionary observations in individual proteins. Detecting functional shifts in pathways reflects an important milestone in predicting when changes in genotypes result in changes in phenotypes.
Origins of altruism diversity II: Runaway co-evolution of altruistic strategies via “reciprocal niche construction”

PubMed Central

Van Dyken, J. David; Wade, Michael J.

2012-01-01

Understanding the evolution of altruism requires knowledge of both its constraints and its drivers. Here we show that, paradoxically, ecological constraints on altruism may ultimately be its strongest driver. We construct a two-trait, co-evolutionary adaptive dynamics model of social evolution in a genetically structured population with local resource competition. The intensity of local resource competition, which influences the direction and strength of social selection and which is typically treated as a static parameter, is here allowed to be an evolvable trait. Evolution of survival/fecundity altruism, which requires weak local competition, increases local competition as it evolves, creating negative environmental feedback that ultimately inhibits its further evolutionary advance. Alternatively, evolution of resource-based altruism, which requires strong local competition, weakens local competition as it evolves, also ultimately causing its own evolution to stall. When evolving independently, these altruistic strategies are intrinsically self-limiting. However, the co-existence of these two altruism types transforms the negative eco-evolutionary feedback generated by each strategy on itself into positive feedback on the other, allowing the presence of one trait to drive the evolution of the other. We call this feedback conversion “reciprocal niche construction”. In the absence of constraints, this process leads to runaway co-evolution of altruism types. We discuss applications to the origins and evolution of eusociality, division of labor, the inordinate ecological success of eusocial species, and the interaction between technology and demography in human evolution. Our theory suggests that the evolution of extreme sociality may often be an autocatalytic process. PMID:22834748
Host adaptation of Chlamydia pecorum towards low virulence evident in co-evolution of the ompA, incA, and ORF663 Loci.

PubMed

Mohamad, Khalil Yousef; Kaltenboeck, Bernhard; Rahman, Kh Shamsur; Magnino, Simone; Sachse, Konrad; Rodolakis, Annie

2014-01-01

Chlamydia (C.) pecorum, an obligate intracellular bacterium, may cause severe diseases in ruminants, swine and koalas, although asymptomatic infections are the norm. Recently, we identified genetic polymorphisms in the ompA, incA and ORF663 genes that potentially differentiate between high-virulence C. pecorum isolates from diseased animals and low-virulence isolates from asymptomatic animals. Here, we expand these findings by including additional ruminant, swine, and koala strains. Coding tandem repeats (CTRs) at the incA locus encoded a variable number of repeats of APA or AGA amino acid motifs. Addition of any non-APA/AGA repeat motif, such as APEVPA, APAVPA, APE, or APAPE, associated with low virulence (P<10-4), as did a high number of amino acids in all incA CTRs (P = 0.0028). In ORF663, high numbers of 15-mer CTRs correlated with low virulence (P = 0.0001). Correction for ompA phylogram position in ORF663 and incA abolished the correlation between genetic changes and virulence, demonstrating co-evolution of ompA, incA, and ORF663 towards low virulence. Pairwise divergence of ompA, incA, and ORF663 among isolates from healthy animals was significantly higher than among strains isolated from diseased animals (P≤10-5), confirming the longer evolutionary path traversed by low-virulence strains. All three markers combined identified 43 unique strains and 4 pairs of identical strains among all 57 isolates tested, demonstrating the suitability of these markers for epidemiological investigations.
Myxomatosis in Australia and Europe: a model for emerging infectious diseases.

PubMed

Kerr, Peter J

2012-03-01

Myxoma virus is a poxvirus naturally found in two American leporid (rabbit) species (Sylvilagus brasiliensis and Sylvilagus bachmani) in which it causes an innocuous localised cutaneous fibroma. However, in European rabbits (Oryctolagus cuniculus) the same virus causes the lethal disseminated disease myxomatosis. The introduction of myxoma virus into the European rabbit population in Australia in 1950 initiated the best known example of what happens when a novel pathogen jumps into a completely naïve new mammalian host species. The short generation time of the rabbit and their vast numbers in Australia meant evolution could be studied in real time. The carefully documented emergence of attenuated strains of virus that were more effectively transmitted by the mosquito vector and the subsequent selection of rabbits with genetic resistance to myxomatosis is the paradigm for pathogen virulence and host-pathogen coevolution. This natural experiment was repeated with the release of a separate strain of myxoma virus in France in 1952. The subsequent spread of the virus throughout Europe and its coevolution with the rabbit essentially paralleled what occurred in Australia. Detailed molecular studies on myxoma virus have dissected the role of virulence genes in the pathogenesis of myxomatosis and when combined with genomic data and reverse genetics should in future enable the understanding of the molecular evolution of the virus as it adapted to its new host. This review describes the natural history and evolution of myxoma virus together with the molecular biology and experimental pathogenesis studies that are informing our understanding of evolution of emerging diseases. Crown Copyright © 2012. Published by Elsevier B.V. All rights reserved.
Varying Herbivore Population Structure Correlates with Lack of Local Adaptation in a Geographic Variable Plant-Herbivore Interaction

PubMed Central

Cogni, Rodrigo; Trigo, José R.; Futuyma, Douglas J.

2011-01-01

Local adaptation of parasites to their hosts due to coevolution is a central prediction of many theories in evolutionary biology. However, empirical studies looking for parasite local adaptation show great variation in outcomes, and the reasons for such variation are largely unknown. In a previous study, we showed adaptive differentiation in the arctiid moth Utetheisa ornatrix to its host plant, the pyrrolizidine alkaloid-bearing legume Crotalaria pallida, at the continental scale, but found no differentiation at the regional scale. In the present study, we sampled the same sites to investigate factors that may contribute to the lack of differentiation at the regional scale. We performed field observations that show that specialist and non-specialist polyphagous herbivore incidence varies among populations at both scales. With a series of common-garden experiments we show that some plant traits that may affect herbivory (pyrrolizidine alkaloids and extrafloral nectaries) vary at the regional scale, while other traits (trichomes and nitrogen content) just vary at the continental scale. These results, combined with our previous evidence for plant population differentiation based on larval performance on fresh fruits, suggest that U. ornatrix is subjected to divergent selection even at the regional scale. Finally, with a microsatellite study we investigated population structure of U. ornatrix. We found that population structure is not stable over time: we found population differentiation at the regional scale in the first year of sampling, but not in the second year. Unstable population structure of the herbivore is the most likely cause of the lack of regional adaptation. PMID:22220208
ECCM Scheme against Interrupted Sampling Repeater Jammer Based on Parameter-Adjusted Waveform Design

PubMed Central

Wei, Zhenhua; Peng, Bo; Shen, Rui

2018-01-01

Interrupted sampling repeater jamming (ISRJ) is an effective way of deceiving coherent radar sensors, especially for linear frequency modulated (LFM) radar. In this paper, for a simplified scenario with a single jammer, we propose a dynamic electronic counter-counter measure (ECCM) scheme based on jammer parameter estimation and transmitted signal design. Firstly, the LFM waveform is transmitted to estimate the main jamming parameters by investigating the discontinuousness of the ISRJ’s time-frequency (TF) characteristics. Then, a parameter-adjusted intra-pulse frequency coded signal, whose ISRJ signal after matched filtering only forms a single false target, is designed adaptively according to the estimated parameters, i.e., sampling interval, sampling duration and repeater times. Ultimately, for typical jamming scenes with different jamming signal ratio (JSR) and duty cycle, we propose two particular ISRJ suppression approaches. Simulation results validate the effective performance of the proposed scheme for countering the ISRJ, and the trade-off relationship between the two approaches is demonstrated. PMID:29642508
Sequential anaerobic-aerobic biological treatment of colored wastewaters: case study of a textile dyeing factory wastewater.

PubMed

Abiri, Fardin; Fallah, Narges; Bonakdarpour, Babak

2017-03-01

In the present study the feasibility of the use of a bacterial batch sequential anaerobic-aerobic process, in which activated sludge was used in both parts of the process, for pretreatment of wastewater generated by a textile dyeing factory has been considered. Activated sludge used in the process was obtained from a municipal wastewater treatment plant and adapted to real dyeing wastewater using either an anaerobic-only or an anaerobic-aerobic process over a period of 90 days. The use of activated sludge adapted using the anaerobic-aerobic process resulted in a higher overall decolorization efficiency compared to that achieved with activated sludge adapted using the anaerobic-only cycles. Anaerobic and aerobic periods of around 34 and 22 hours respectively resulted in an effluent with chemical oxygen demand (COD) and color content which met the standards for discharge into the centralized wastewater treatment plant of the industrial estate in which the dyeing factory was situated. Neutralization of the real dyeing wastewater and addition of carbon source to it, both of which results in significant increase in the cost of the bacterial treatment process, was not found to be necessary to achieve the required discharge standards.
The aminoacyl-tRNA synthetases had only a marginal role in the origin of the organization of the genetic code: Evidence in favor of the coevolution theory.

PubMed

Di Giulio, Massimo

2017-11-07

The coevolution theory of the origin of the genetic code suggests that the organization of the genetic code coevolved with the biosynthetic relationships between amino acids. The mechanism that allowed this coevolution was based on tRNA-like molecules on which-this theory-would postulate the biosynthetic transformations between amino acids to have occurred. This mechanism makes a prediction on how the role conducted by the aminoacyl-tRNA synthetases (ARSs), in the origin of the genetic code, should have been. Indeed, if the biosynthetic transformations between amino acids occurred on tRNA-like molecules, then there was no need to link amino acids to these molecules because amino acids were already charged on tRNA-like molecules, as the coevolution theory suggests. In spite of the fact that ARSs make the genetic code responsible for the first interaction between a component of nucleic acids and that of proteins, for the coevolution theory the role of ARSs should have been entirely marginal in the genetic code origin. Therefore, I have conducted a further analysis of the distribution of the two classes of ARSs and of their subclasses-in the genetic code table-in order to perform a falsification test of the coevolution theory. Indeed, in the case in which the distribution of ARSs within the genetic code would have been highly significant, then the coevolution theory would be falsified since the mechanism on which it is based would not predict a fundamental role of ARSs in the origin of the genetic code. I found that the statistical significance of the distribution of the two classes of ARSs in the table of the genetic code is low or marginal, whereas that of the subclasses of ARSs statistically significant. However, this is in perfect agreement with the postulates of the coevolution theory. Indeed, the only case of statistical significance-regarding the classes of ARSs-is appreciable for the CAG code, whereas for its complement-the UNN/NUN code-only a marginal significance is measurable. These two codes codify roughly for the two ARS classes, in particular, the CAG code for the class II while the UNN/NUN code for the class I. Furthermore, the subclasses of ARSs show a statistical significance of their distribution in the genetic code table. Nevertheless, the more sensible explanation for these observations would be the following. The observation that would link the two classes of ARSs to the CAG and UNN/NUN codes, and the statistical significance of the distribution of the subclasses of ARSs in the genetic code table, would be only a secondary effect due to the highly significant distribution of the polarity of amino acids and their biosynthetic relationships in the genetic code. That is to say, the polarity of amino acids and their biosynthetic relationships would have conditioned the evolution of ARSs so that their presence in the genetic code would have been detectable. Even if the ARSs would not have-on their own-influenced directly the evolutionary organization of the genetic code. In other words, the role that ARSs had in the origin of the genetic code would have been entirely marginal. This conclusion would be in perfect accord with the predictions of the coevolution theory. Conversely, this conclusion would be in contrast-at least partially-with the physicochemical theories of the origin of the genetic code because they would foresee an absolutely more active role of ARSs in the origin of the organization of the genetic code. Copyright © 2017 Elsevier Ltd. All rights reserved.

Estimating the optimal dynamic antipsychotic treatment regime: Evidence from the sequential multiple assignment randomized CATIE Schizophrenia Study

PubMed Central

Shortreed, Susan M.; Moodie, Erica E. M.

2012-01-01

Summary Treatment of schizophrenia is notoriously difficult and typically requires personalized adaption of treatment due to lack of efficacy of treatment, poor adherence, or intolerable side effects. The Clinical Antipsychotic Trials in Intervention Effectiveness (CATIE) Schizophrenia Study is a sequential multiple assignment randomized trial comparing the typical antipsychotic medication, perphenazine, to several newer atypical antipsychotics. This paper describes the marginal structural modeling method for estimating optimal dynamic treatment regimes and applies the approach to the CATIE Schizophrenia Study. Missing data and valid estimation of confidence intervals are also addressed. PMID:23087488
Sexual Harassment by Males Reduces Female Fecundity in the Alfalfa Leafcutting Bee (Megachile rotundata)

USDA-ARS?s Scientific Manuscript database

Under sexual conflict, males evolve traits to increase their mating and reproductive success that impose costs on females. Females evolve counter-adaptations to resist males and reduce those costs. Female resistance may instead serve as a mechanism for mate choice if the male-imposed costs are outwe...
A Pension Giant Reinvents Itself To Adapt to a Changing Market.

ERIC Educational Resources Information Center

Pulley, John L.

2000-01-01

Reports on changes at the Teachers Insurance and Annuity Association - College Retirement Equities Fund (TIAA-CREF), the dominant force in the higher education pension market, to counter declining investment by younger professors. Changes include addition of retail mutual funds and making some products available to the general public. Critics…
First, Don't Be a Jerk: Proactively Creating a Civil and Supportive Classroom

ERIC Educational Resources Information Center

Lightner, Robin

2014-01-01

Instructors may benefit from the framework for understanding student incivility. The framework considers stages of adolescent brain development and behaviors that were adaptive in the context of high school but are counter to collegiate success. Several activities presented here challenge instructors to be purposeful about classroom civility. When…
Coexistence via coevolution driven by reduced allelochemical effects and increased tolerance to competition between invasive and native plants.

PubMed

Huang, Fangfang; Lankau, Richard; Peng, Shaolin

2018-04-01

Coevolution can promote long-term coexistence of two competing species if selection acts to reduce the fitness inequality between competitors and/or strengthen negative frequency dependence within each population. However, clear coevolution between plant competitors has been rarely documented. Plant invasions offer opportunities to capture the process of coevolution. Here we investigated how the developing relationship between an invasive forb, Alliaria petiolata, and a native competitor, Pilea pumila, may affect their long-term coexistence, by testing the competitive effects of populations of varying lengths of co-occurrence on each other across a chronosequence of invasion history. Alliaria petiolata and P. pumila tended to develop greater tolerance to competition over invasion history. Their coexistence was promoted more by increases in stabilizing relative to equalizing processes. These changes likely stem in part from reductions in allelopathic traits in the invader and evolution of tolerance in the native. These results suggested that some native species can evolve tolerance against the competitive effects of strong invaders, which likely promoted their persistence in invaded communities. However, the potential for coevolutionary rescue of competing populations is likely to vary across native species, and evolutionary processes should not be expected to compensate for the ecological consequences of exotic invasions. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.
Practical characteristics of adaptive design in phase 2 and 3 clinical trials.

PubMed

Sato, A; Shimura, M; Gosho, M

2018-04-01

Adaptive design methods are expected to be ethical, reflect real medical practice, increase the likelihood of research and development success and reduce the allocation of patients into ineffective treatment groups by the early termination of clinical trials. However, the comprehensive details regarding which types of clinical trials will include adaptive designs remain unclear. We examined the practical characteristics of adaptive design used in clinical trials. We conducted a literature search of adaptive design clinical trials published from 2012 to 2015 using PubMed, EMBASE, and the Cochrane Central Register of Controlled Trials, with common search terms related to adaptive design. We systematically assessed the types and characteristics of adaptive designs and disease areas employed in the adaptive design trials. Our survey identified 245 adaptive design clinical trials. The number of trials by the publication year increased from 2012 to 2013 and did not greatly change afterwards. The most frequently used adaptive design was group sequential design (n = 222, 90.6%), especially for neoplasm or cardiovascular disease trials. Among the other types of adaptive design, adaptive dose/treatment group selection (n = 21, 8.6%) and adaptive sample-size adjustment (n = 19, 7.8%) were frequently used. The adaptive randomization (n = 8, 3.3%) and adaptive seamless design (n = 6, 2.4%) were less frequent. Adaptive dose/treatment group selection and adaptive sample-size adjustment were frequently used (up to 23%) in "certain infectious and parasitic diseases," "diseases of nervous system," and "mental and behavioural disorders" in comparison with "neoplasms" (<6.6%). For "mental and behavioural disorders," adaptive randomization was used in two trials of eight trials in total (25%). Group sequential design and adaptive sample-size adjustment were used frequently in phase 3 trials or in trials where study phase was not specified, whereas the other types of adaptive designs were used more in phase 2 trials. Approximately 82% (202 of 245 trials) resulted in early termination at the interim analysis. Among the 202 trials, 132 (54% of 245 trials) had fewer randomized patients than initially planned. This result supports the motive to use adaptive design to make study durations shorter and include a smaller number of subjects. We found that adaptive designs have been applied to clinical trials in various therapeutic areas and interventions. The applications were frequently reported in neoplasm or cardiovascular clinical trials. The adaptive dose/treatment group selection and sample-size adjustment are increasingly common, and these adaptations generally follow the Food and Drug Administration's (FDA's) recommendations. © 2017 John Wiley & Sons Ltd.
Evolution in action: climate change, biodiversity dynamics and emerging infectious disease.

PubMed

Hoberg, Eric P; Brooks, Daniel R

2015-04-05

Climatological variation and ecological perturbation have been pervasive drivers of faunal assembly, structure and diversification for parasites and pathogens through recurrent events of geographical and host colonization at varying spatial and temporal scales of Earth history. Episodic shifts in climate and environmental settings, in conjunction with ecological mechanisms and host switching, are often critical determinants of parasite diversification, a view counter to more than a century of coevolutionary thinking about the nature of complex host-parasite assemblages. Parasites are resource specialists with restricted host ranges, yet shifts onto relatively unrelated hosts are common during phylogenetic diversification of parasite lineages and directly observable in real time. The emerging Stockholm Paradigm resolves this paradox: Ecological Fitting (EF)--phenotypic flexibility and phylogenetic conservatism in traits related to resource use, most notably host preference--provides many opportunities for rapid host switching in changing environments, without the evolution of novel host-utilization capabilities. Host shifts via EF fuel the expansion phase of the Oscillation Hypothesis of host range and speciation and, more generally, the generation of novel combinations of interacting species within the Geographic Mosaic Theory of Coevolution. In synergy, an environmental dynamic of Taxon Pulses establishes an episodic context for host and geographical colonization. © 2015 The Author(s) Published by the Royal Society. All rights reserved.
SARS Coronavirus Fusion Peptide-Derived Sequence Suppresses Collagen-Induced Arthritis in DBA/1J Mice.

PubMed

Shen, Zu T; Sigalov, Alexander B

2016-06-28

During the co-evolution of viruses and their hosts, the viruses have evolved numerous strategies to counter and evade host antiviral immune responses in order to establish a successful infection, replicate and persist in the host. Recently, based on our model of immune signaling, the Signaling Chain HOmoOLigomerization (SCHOOL) model, we suggested specific molecular mechanisms used by different viruses such as severe acute respiratory syndrome coronavirus (SARS-CoV) to modulate the host immune response mediated by members of the family of multichain immune recognition receptors (MIRRs). This family includes T cell receptor (TCR) that is critically involved in immune diseases such as autoimmune arthritis. In the present study, we provide compelling experimental in vivo evidence in support of our hypothesis. Using the SCHOOL approach and the SARS-CoV fusion peptide sequence, we rationally designed a novel immunomodulatory peptide that targets TCR. We showed that this peptide ameliorates collagen-induced arthritis in DBA/1J mice and protects against bone and cartilage damage. Incorporation of the peptide into self-assembling lipopeptide nanoparticles that mimic native human high density lipoproteins significantly increases peptide dosage efficacy. Together, our data further confirm that viral immune evasion strategies that target MIRRs can be transferred to therapeutic strategies that require similar functionalities.
Origins and ecological consequences of pollen specialization among desert bees.

PubMed

Minckley, R L; Cane, J H; Kervin, L

2000-02-07

An understanding of the evolutionary origins of insect foraging specialization is often hindered by a poor biogeographical and palaeoecological record. The historical biogeography (20,000 years before present to the present) of the desert-limited plant, creosote bush (Larrea tridentata), is remarkably complete. This history coupled with the distribution pattern of its bee fauna suggests pollen specialization for creosote bush pollen has evolved repeatedly among bees in the Lower Sonoran and Mojave deserts. In these highly xeric, floristically depauperate environments, species of specialist bees surpass generalist bees in diversity, biomass and abundance. The ability of specialist bees to facultatively remain in diapause through resource-poor years and to emerge synchronously with host plant bloom in resource-rich years probably explains their ecological dominance and persistence in these areas. Repeated origins of pollen specialization to one host plant where bloom occurs least predictably is a counter-example to prevailing theories that postulate such traits originate where the plant grows best and blooms most reliably Host-plant synchronization, a paucity of alternative floral hosts, or flowering attributes of creosote bush alone or in concert may account for the diversity of bee specialists that depend on this plant instead of nutritional factors or chemical coevolution between floral rewards and the pollinators they have evolved to attract.
Behavioral biology of mammalian reproduction and development for a space station

NASA Technical Reports Server (NTRS)

Alberts, J. R.

1983-01-01

Space Station research includes two kinds of adaption to space: somatic (the adjustments made by an organism, within its lifetime, in response to local conditions), and transgenerational adaption (continuous exposure across sequential life cycles of genetic descendents). Transgenerational effects are akin to evolutionary process. Areas of a life Sciences Program in a space station address the questions of the behavioral biology of mammalian reproduction and development, using the Norway rat as the focus of experimentation.
HIV-1 protease-substrate coevolution in nelfinavir resistance.

PubMed

Kolli, Madhavi; Ozen, Ayşegül; Kurt-Yilmaz, Nese; Schiffer, Celia A

2014-07-01

Resistance to various human immunodeficiency virus type 1 (HIV-1) protease inhibitors (PIs) challenges the effectiveness of therapies in treating HIV-1-infected individuals and AIDS patients. The virus accumulates mutations within the protease (PR) that render the PIs less potent. Occasionally, Gag sequences also coevolve with mutations at PR cleavage sites contributing to drug resistance. In this study, we investigated the structural basis of coevolution of the p1-p6 cleavage site with the nelfinavir (NFV) resistance D30N/N88D protease mutations by determining crystal structures of wild-type and NFV-resistant HIV-1 protease in complex with p1-p6 substrate peptide variants with L449F and/or S451N. Alterations of residue 30's interaction with the substrate are compensated by the coevolving L449F and S451N cleavage site mutations. This interdependency in the PR-p1-p6 interactions enhances intermolecular contacts and reinforces the overall fit of the substrate within the substrate envelope, likely enabling coevolution to sustain substrate recognition and cleavage in the presence of PR resistance mutations. Resistance to human immunodeficiency virus type 1 (HIV-1) protease inhibitors challenges the effectiveness of therapies in treating HIV-1-infected individuals and AIDS patients. Mutations in HIV-1 protease selected under the pressure of protease inhibitors render the inhibitors less potent. Occasionally, Gag sequences also mutate and coevolve with protease, contributing to maintenance of viral fitness and to drug resistance. In this study, we investigated the structural basis of coevolution at the Gag p1-p6 cleavage site with the nelfinavir (NFV) resistance D30N/N88D protease mutations. Our structural analysis reveals the interdependency of protease-substrate interactions and how coevolution may restore substrate recognition and cleavage in the presence of protease drug resistance mutations. Copyright © 2014, American Society for Microbiology. All Rights Reserved.
Poster - 51: A tumor motion-compensating system with tracking and prediction – a proof-of-concept study

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

Guo, Kaiming; Teo, Peng; Kawalec, Philip

2016-08-15

Purpose: This work reports on the development of a mechanical slider system for the counter-steering of tumor motion in adaptive Radiation Therapy (RT). The tumor motion was tracked using a weighted optical flow algorithm and its position is being predicted with a neural network (NN). Methods: The components of the proposed mechanical counter-steering system includes: (1) an actuator which provides the tumor motion, (2) the motion detection using an optical flow algorithm, (3) motion prediction using a neural network, (4) a control module and (5) a mechanical slider to counter-steer the anticipated motion of the tumor phantom. An asymmetrical cosinemore » function and five patient traces (P1–P5) were used to evaluate the tracking of a 3D printed lung tumor. In the proposed mechanical counter-steering system, both actuator (Zaber NA14D60) and slider (Zaber A-BLQ0070-E01) were programed to move independently with LabVIEW and their positions were recorded by 2 potentiometers (ETI LCP12S-25). The accuracy of this counter-steering system is given by the difference between the two potentiometers. Results: The inherent accuracy of the system, measured using the cosine function, is −0.15 ± 0.06 mm. While the errors when tracking and prediction were included, is (0.04 ± 0.71) mm. Conclusion: A prototype tumor motion counter-steering system with tracking and prediction was implemented. The inherent errors are small in comparison to the tracking and prediction errors, which in turn are small in comparison to the magnitude of tumor motion. The results show that this system is suited for evaluating RT tracking and prediction.« less
Differential transfer processes in incremental visuomotor adaptation.

PubMed

Seidler, Rachel D

2005-01-01

Visuomotor adaptive processes were examined by testing transfer of adaptation between similar conditions. Participants made manual aiming movements with a joystick to hit targets on a computer screen, with real-time feedback display of their movement. They adapted to three different rotations of the display in a sequential fashion, with a return to baseline display conditions between rotations. Adaptation was better when participants had prior adaptive experiences. When performance was assessed using direction error (calculated at the time of peak velocity) and initial endpoint error (error before any overt corrective actions), transfer was greater when the final rotation reflected an addition of previously experienced rotations (adaptation order 30 degrees rotation, 15 degrees, 45 degrees) than when it was a subtraction of previously experienced conditions (adaptation order 45 degrees rotation, 15 degrees, 30 degrees). Transfer was equal regardless of adaptation order when performance was assessed with final endpoint error (error following any discrete, corrective actions). These results imply the existence of multiple independent processes in visuomotor adaptation.
Plant-bacterial pathogen interactions mediated by type III effectors.

PubMed

Feng, Feng; Zhou, Jian-Min

2012-08-01

Effectors secreted by the bacterial type III system play a central role in the interaction between Gram-negative bacterial pathogens and their host plants. Recent advances in the effector studies have helped cementing several key concepts concerning bacterial pathogenesis, plant immunity, and plant-pathogen co-evolution. Type III effectors use a variety of biochemical mechanisms to target specific host proteins or DNA for pathogenesis. The identifications of their host targets led to the identification of novel components of plant innate immune system. Key modules of plant immune signaling pathways such as immune receptor complexes and MAPK cascades have emerged as a major battle ground for host-pathogen adaptation. These modules are attacked by multiple type III effectors, and some components of these modules have evolved to actively sense the effectors and trigger immunity. Copyright © 2012 Elsevier Ltd. All rights reserved.
Life cycle specialization of filamentous pathogens - colonization and reproduction in plant tissues.

PubMed

Haueisen, Janine; Stukenbrock, Eva H

2016-08-01

Filamentous plant pathogens explore host tissues to obtain nutrients for growth and reproduction. Diverse strategies for tissue invasion, defense manipulation, and colonization of inter and intra-cellular spaces have evolved. Most research has focused on effector molecules, which are secreted to manipulate plant immunity and facilitate infection. Effector genes are often found to evolve rapidly in response to the antagonistic host-pathogen co-evolution but other traits are also subject to adaptive evolution during specialization to the anatomy, biochemistry and ecology of different plant hosts. Although not directly related to virulence, these traits are important components of specialization but little is known about them. We present and discuss specific life cycle traits that facilitate exploration of plant tissues and underline the importance of increasing our insight into the biology of plant pathogens. Copyright © 2016. Published by Elsevier Ltd.
Toward a Psychology of Human Agency.

PubMed

Bandura, Albert

2006-06-01

This article presents an agentic theory of human development, adaptation, and change. The evolutionary emergence of advanced symbolizing capacity enabled humans to transcend the dictates of their immediate environment and made them unique in their power to shape their life circumstances and the courses their lives take. In this conception, people are contributors to their life circumstances, not just products of them. Social cognitive theory rejects a duality between human agency and social structure. People create social systems, and these systems, in turn, organize and influence people's lives. This article discusses the core properties of human agency, the different forms it takes, its ontological and epistemological status, its development and role in causal structures, its growing primacy in the coevolution process, and its influential exercise at individual and collective levels across diverse spheres of life and cultural systems. © 2006 Association for Psychological Science.
Big bang in the evolution of extant malaria parasites.

PubMed

Hayakawa, Toshiyuki; Culleton, Richard; Otani, Hiroto; Horii, Toshihiro; Tanabe, Kazuyuki

2008-10-01

Malaria parasites (genus Plasmodium) infect all classes of terrestrial vertebrates and display host specificity in their infections. It is therefore assumed that malaria parasites coevolved intimately with their hosts. Here, we propose a novel scenario of malaria parasite-host coevolution. A phylogenetic tree constructed using the malaria parasite mitochondrial genome reveals that the extant primate, rodent, bird, and reptile parasite lineages rapidly diverged from a common ancestor during an evolutionary short time period. This rapid diversification occurred long after the establishment of the primate, rodent, bird, and reptile host lineages, which implies that host-switch events contributed to the rapid diversification of extant malaria parasite lineages. Interestingly, the rapid diversification coincides with the radiation of the mammalian genera, suggesting that adaptive radiation to new mammalian hosts triggered the rapid diversification of extant malaria parasite lineages.
Temporal presentation protocols in stereoscopic displays: Flicker visibility, perceived motion, and perceived depth

PubMed Central

Hoffman, David M.; Karasev, Vasiliy I.; Banks, Martin S.

2011-01-01

Most stereoscopic displays rely on field-sequential presentation to present different images to the left and right eyes. With sequential presentation, images are delivered to each eye in alternation with dark intervals, and each eye receives its images in counter phase with the other eye. This type of presentation can exacerbate image artifacts including flicker, and the appearance of unsmooth motion. To address the flicker problem, some methods repeat images multiple times before updating to new ones. This greatly reduces flicker visibility, but makes motion appear less smooth. This paper describes an investigation of how different presentation methods affect the visibility of flicker, motion artifacts, and distortions in perceived depth. It begins with an examination of these methods in the spatio-temporal frequency domain. From this examination, it describes a series of predictions for how presentation rate, object speed, simultaneity of image delivery to the two eyes, and other properties ought to affect flicker, motion artifacts, and depth distortions, and reports a series of experiments that tested these predictions. The results confirmed essentially all of the predictions. The paper concludes with a summary and series of recommendations for the best approach to minimize these undesirable effects. PMID:21572544
Parallelization of sequential Gaussian, indicator and direct simulation algorithms

NASA Astrophysics Data System (ADS)

Nunes, Ruben; Almeida, José A.

2010-08-01

Improving the performance and robustness of algorithms on new high-performance parallel computing architectures is a key issue in efficiently performing 2D and 3D studies with large amount of data. In geostatistics, sequential simulation algorithms are good candidates for parallelization. When compared with other computational applications in geosciences (such as fluid flow simulators), sequential simulation software is not extremely computationally intensive, but parallelization can make it more efficient and creates alternatives for its integration in inverse modelling approaches. This paper describes the implementation and benchmarking of a parallel version of the three classic sequential simulation algorithms: direct sequential simulation (DSS), sequential indicator simulation (SIS) and sequential Gaussian simulation (SGS). For this purpose, the source used was GSLIB, but the entire code was extensively modified to take into account the parallelization approach and was also rewritten in the C programming language. The paper also explains in detail the parallelization strategy and the main modifications. Regarding the integration of secondary information, the DSS algorithm is able to perform simple kriging with local means, kriging with an external drift and collocated cokriging with both local and global correlations. SIS includes a local correction of probabilities. Finally, a brief comparison is presented of simulation results using one, two and four processors. All performance tests were carried out on 2D soil data samples. The source code is completely open source and easy to read. It should be noted that the code is only fully compatible with Microsoft Visual C and should be adapted for other systems/compilers.
Outdoor Education Guide-Handbook, Waukesha Public Schools.

ERIC Educational Resources Information Center

Vitale, Joseph A.

Designed by the Waukesha Public Schools (Wisconsin) specifically for an elementary level three-day camping trip at Camp Phantom Lake, this outdoor education guide presents some activities which suggest adaptation. Activity directions, plans, worksheets, evaluation sheets, and illustrations are presented in sequential order for the following…

Adaptive Interventions and SMART Designs: Application to child behavior research in a community setting

PubMed Central

Kidwell, Kelley M.; Hyde, Luke W.

2016-01-01

Heterogeneity between and within people necessitates the need for sequential personalized interventions to optimize individual outcomes. Personalized or adaptive interventions (AIs) are relevant for diseases and maladaptive behavioral trajectories when one intervention is not curative and success of a subsequent intervention may depend on individual characteristics or response. AIs may be applied to medical settings and to investigate best prevention, education, and community-based practices. AIs can begin with low-cost or low-burden interventions and followed with intensified or alternative interventions for those who need it most. AIs that guide practice over the course of a disease, program, or school year can be investigated through sequential multiple assignment randomized trials (SMARTs). To promote the use of SMARTs, we provide a hypothetical SMART in a Head Start program to address child behavior problems. We describe the advantages and limitations of SMARTs, particularly as they may be applied to the field of evaluation. PMID:28239254
Effective Identification of Similar Patients Through Sequential Matching over ICD Code Embedding.

PubMed

Nguyen, Dang; Luo, Wei; Venkatesh, Svetha; Phung, Dinh

2018-04-11

Evidence-based medicine often involves the identification of patients with similar conditions, which are often captured in ICD (International Classification of Diseases (World Health Organization 2013)) code sequences. With no satisfying prior solutions for matching ICD-10 code sequences, this paper presents a method which effectively captures the clinical similarity among routine patients who have multiple comorbidities and complex care needs. Our method leverages the recent progress in representation learning of individual ICD-10 codes, and it explicitly uses the sequential order of codes for matching. Empirical evaluation on a state-wide cancer data collection shows that our proposed method achieves significantly higher matching performance compared with state-of-the-art methods ignoring the sequential order. Our method better identifies similar patients in a number of clinical outcomes including readmission and mortality outlook. Although this paper focuses on ICD-10 diagnosis code sequences, our method can be adapted to work with other codified sequence data.
Comparison of precursor infiltration into polymer thin films via atomic layer deposition and sequential vapor infiltration using in-situ quartz crystal microgravimetry

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

Padbury, Richard P.; Jur, Jesse S., E-mail: jsjur@ncsu.edu

Previous research exploring inorganic materials nucleation behavior on polymers via atomic layer deposition indicates the formation of hybrid organic–inorganic materials that form within the subsurface of the polymer. This has inspired adaptations to the process, such as sequential vapor infiltration, which enhances the diffusion of organometallic precursors into the subsurface of the polymer to promote the formation of a hybrid organic–inorganic coating. This work highlights the fundamental difference in mass uptake behavior between atomic layer deposition and sequential vapor infiltration using in-situ methods. In particular, in-situ quartz crystal microgravimetry is used to compare the mass uptake behavior of trimethyl aluminummore » in poly(butylene terephthalate) and polyamide-6 polymer thin films. The importance of trimethyl aluminum diffusion into the polymer subsurface and the subsequent chemical reactions with polymer functional groups are discussed.« less
Meta-cognitive online sequential extreme learning machine for imbalanced and concept-drifting data classification.

PubMed

Mirza, Bilal; Lin, Zhiping

2016-08-01

In this paper, a meta-cognitive online sequential extreme learning machine (MOS-ELM) is proposed for class imbalance and concept drift learning. In MOS-ELM, meta-cognition is used to self-regulate the learning by selecting suitable learning strategies for class imbalance and concept drift problems. MOS-ELM is the first sequential learning method to alleviate the imbalance problem for both binary class and multi-class data streams with concept drift. In MOS-ELM, a new adaptive window approach is proposed for concept drift learning. A single output update equation is also proposed which unifies various application specific OS-ELM methods. The performance of MOS-ELM is evaluated under different conditions and compared with methods each specific to some of the conditions. On most of the datasets in comparison, MOS-ELM outperforms the competing methods. Copyright © 2016 Elsevier Ltd. All rights reserved.
A Fast and Precise Indoor Localization Algorithm Based on an Online Sequential Extreme Learning Machine †

PubMed Central

Zou, Han; Lu, Xiaoxuan; Jiang, Hao; Xie, Lihua

2015-01-01

Nowadays, developing indoor positioning systems (IPSs) has become an attractive research topic due to the increasing demands on location-based service (LBS) in indoor environments. WiFi technology has been studied and explored to provide indoor positioning service for years in view of the wide deployment and availability of existing WiFi infrastructures in indoor environments. A large body of WiFi-based IPSs adopt fingerprinting approaches for localization. However, these IPSs suffer from two major problems: the intensive costs of manpower and time for offline site survey and the inflexibility to environmental dynamics. In this paper, we propose an indoor localization algorithm based on an online sequential extreme learning machine (OS-ELM) to address the above problems accordingly. The fast learning speed of OS-ELM can reduce the time and manpower costs for the offline site survey. Meanwhile, its online sequential learning ability enables the proposed localization algorithm to adapt in a timely manner to environmental dynamics. Experiments under specific environmental changes, such as variations of occupancy distribution and events of opening or closing of doors, are conducted to evaluate the performance of OS-ELM. The simulation and experimental results show that the proposed localization algorithm can provide higher localization accuracy than traditional approaches, due to its fast adaptation to various environmental dynamics. PMID:25599427
Adaptive management of natural resources-framework and issues

USGS Publications Warehouse

Williams, B.K.

2011-01-01

Adaptive management, an approach for simultaneously managing and learning about natural resources, has been around for several decades. Interest in adaptive decision making has grown steadily over that time, and by now many in natural resources conservation claim that adaptive management is the approach they use in meeting their resource management responsibilities. Yet there remains considerable ambiguity about what adaptive management actually is, and how it is to be implemented by practitioners. The objective of this paper is to present a framework and conditions for adaptive decision making, and discuss some important challenges in its application. Adaptive management is described as a two-phase process of deliberative and iterative phases, which are implemented sequentially over the timeframe of an application. Key elements, processes, and issues in adaptive decision making are highlighted in terms of this framework. Special emphasis is given to the question of geographic scale, the difficulties presented by non-stationarity, and organizational challenges in implementing adaptive management. ?? 2010.
CMCpy: Genetic Code-Message Coevolution Models in Python

PubMed Central

Becich, Peter J.; Stark, Brian P.; Bhat, Harish S.; Ardell, David H.

2013-01-01

Code-message coevolution (CMC) models represent coevolution of a genetic code and a population of protein-coding genes (“messages”). Formally, CMC models are sets of quasispecies coupled together for fitness through a shared genetic code. Although CMC models display plausible explanations for the origin of multiple genetic code traits by natural selection, useful modern implementations of CMC models are not currently available. To meet this need we present CMCpy, an object-oriented Python API and command-line executable front-end that can reproduce all published results of CMC models. CMCpy implements multiple solvers for leading eigenpairs of quasispecies models. We also present novel analytical results that extend and generalize applications of perturbation theory to quasispecies models and pioneer the application of a homotopy method for quasispecies with non-unique maximally fit genotypes. Our results therefore facilitate the computational and analytical study of a variety of evolutionary systems. CMCpy is free open-source software available from http://pypi.python.org/pypi/CMCpy/. PMID:23532367
Dynamical trade-offs arise from antagonistic coevolution and decrease intraspecific diversity.

PubMed

Huang, Weini; Traulsen, Arne; Werner, Benjamin; Hiltunen, Teppo; Becks, Lutz

2017-12-12

Trade-offs play an important role in evolution. Without trade-offs, evolution would maximize fitness of all traits leading to a "master of all traits". The shape of trade-offs has been shown to determine evolutionary trajectories and is often assumed to be static and independent of the actual evolutionary process. Here we propose that coevolution leads to a dynamical trade-off. We test this hypothesis in a microbial predator-prey system and show that the bacterial growth-defense trade-off changes from concave to convex, i.e., defense is effective and cheap initially, but gets costly when predators coevolve. We further explore the impact of such dynamical trade-offs by a novel mathematical model incorporating de novo mutations for both species. Predator and prey populations diversify rapidly leading to higher prey diversity when the trade-off is concave (cheap). Coevolution results in more convex (costly) trade-offs and lower prey diversity compared to the scenario where only the prey evolves.
Co-evolution of upstream waves and accelerated ions at parallel shocks

NASA Astrophysics Data System (ADS)

Fujimoto, M.; Sugiyama, T.

2016-12-01

Shock waves in space plasmas have been considered as the agents for various particle acceleration phenomena. The basic idea behind shock acceleration is that particles are accelerated as they move back-and-forth across a shock front. Detailed studies of ion acceleration at the terrestrial bow shock have been performed, however, the restricted maximum energies attained prevent a straight-forward application of obtained knowledge to more energetic astrophysical situations. Here we show by a large-scale self-consistent particle simulation that the co-evolution of magnetic turbulence and accelerated ion population is the foundation for continuous operation of shock acceleration to ever higher energies. Magnetic turbulence is created by ions reflected back upstream of a parallel shock front. The co-evolution arises because more energetic ions excite waves of longer wavelengths, and because longer wavelength modes are capable of scattering (in the upstream) and reflecting (at the shock front) more energetic ions. Via carefully designed numerical experiments, we show very clearly that this picture is true.
Parallel arms races between garter snakes and newts involving tetrodotoxin as the phenotypic interface of coevolution.

PubMed

Brodie, Edmund D; Feldman, Chris R; Hanifin, Charles T; Motychak, Jeffrey E; Mulcahy, Daniel G; Williams, Becky L; Brodie, Edmund D

2005-02-01

Parallel "arms races" involving the same or similar phenotypic interfaces allow inference about selective forces driving coevolution, as well as the importance of phylogenetic and phenotypic constraints in coevolution. Here, we report the existence of apparent parallel arms races between species pairs of garter snakes and their toxic newt prey that indicate independent evolutionary origins of a key phenotype in the interface. In at least one area of sympatry, the aquatic garter snake, Thamnophis couchii, has evolved elevated resistance to the neurotoxin tetrodotoxin (TTX), present in the newt Taricha torosa. Previous studies have shown that a distantly related garter snake, Thamnophis sirtalis, has coevolved with another newt species that possesses TTX, Taricha granulosa. Patterns of within population variation and phenotypic tradeoffs between TTX resistance and sprint speed suggest that the mechanism of resistance is similar in both species of snake, yet phylogenetic evidence indicates the independent origins of elevated resistance to TTX.
A Pilot Study Assessing Performance and Visual Attention of Teenagers with ASD in a Novel Adaptive Driving Simulator

ERIC Educational Resources Information Center

Wade, Joshua; Weitlauf, Amy; Broderick, Neill; Swanson, Amy; Zhang, Lian; Bian, Dayi; Sarkar, Medha; Warren, Zachary; Sarkar, Nilanjan

2017-01-01

Individuals with Autism Spectrum Disorder (ASD), compared to typically-developed peers, may demonstrate behaviors that are counter to safe driving. The current work examines the use of a novel simulator in two separate studies. Study 1 demonstrates statistically significant performance differences between individuals with (N = 7) and without ASD…
Physiological responses of emerald ash borer larvae to feeding on different ash species reveal putative resistance mechanisms and insect counter-adaptations

Treesearch

C.M. Rigsby; D.N. Showalter; D.A. Herms; J.L. Koch; P. Bonello; D. Cipollini

2015-01-01

Emerald ash borer, Agrilus planipennis Fairmaire, an Asian wood-boring beetle, has devastated ash (Fraxinus spp.) trees in North American forests and landscapes since its discovery there in 2002. In this study, we collected living larvae from EAB-resistant Manchurian ash (Fraxinus mandschurica), and susceptible...
Adaptationism and intuitions about modern criminal justice.

PubMed

Petersen, Michael Bang

2013-02-01

Research indicates that individuals have incoherent intuitions about particular features of the criminal justice system. This could be seen as an argument against the existence of adapted computational systems for counter-exploitation. Here, I outline how the model developed by McCullough et al. readily predicts the production of conflicting intuitions in the context of modern criminal justice issues.
Wire-shaped perovskite solar cell based on TiO2 nanotubes

NASA Astrophysics Data System (ADS)

Wang, Xiaoyan; Kulkarni, Sneha A.; Li, Zhen; Xu, Wenjing; Batabyal, Sudip K.; Zhang, Sam; Cao, Anyuan; Wong, Lydia Helena

2016-05-01

In this work, a wire-shaped perovskite solar cell based on TiO2 nanotube (TNT) arrays is demonstrated for the first time by integrating a perovskite absorber on TNT-coated Ti wire. Anodization was adopted for the conformal growth of TNTs on Ti wire, together with the simultaneous formation of a compact TiO2 layer. A sequential step dipping process is employed to produce a uniform and compact perovskite layer on top of TNTs with conformal coverage as the efficient light absorber. Transparent carbon nanotube film is wrapped around Ti wire as the hole collector and counter electrode. The integrated perovskite solar cell wire by facile fabrication approaches shows a promising future in portable and wearable textile electronics.
Jitter model and signal processing techniques for pulse width modulation optical recording

NASA Technical Reports Server (NTRS)

Liu, Max M.-K.

1991-01-01

A jitter model and signal processing techniques are discussed for data recovery in Pulse Width Modulation (PWM) optical recording. In PWM, information is stored through modulating sizes of sequential marks alternating in magnetic polarization or in material structure. Jitter, defined as the deviation from the original mark size in the time domain, will result in error detection if it is excessively large. A new approach is taken in data recovery by first using a high speed counter clock to convert time marks to amplitude marks, and signal processing techniques are used to minimize jitter according to the jitter model. The signal processing techniques include motor speed and intersymbol interference equalization, differential and additive detection, and differential and additive modulation.
Co-Evolution of Social Learning and Evolutionary Preparedness in Dangerous Environments

PubMed Central

Lindström, Björn; Selbing, Ida; Olsson, Andreas

2016-01-01

Danger is a fundamental aspect of the lives of most animals. Adaptive behavior therefore requires avoiding actions, objects, and environments associated with danger. Previous research has shown that humans and non-human animals can avoid such dangers through two types of behavioral adaptions, (i) genetic preparedness to avoid certain stimuli or actions, and (ii) social learning. These adaptive mechanisms reduce the fitness costs associated with danger but still allow flexible behavior. Despite the empirical prevalence and importance of both these mechanisms, it is unclear when they evolve and how they interact. We used evolutionary agent-based simulations, incorporating empirically based learning mechanisms, to clarify if preparedness and social learning typically both evolve in dangerous environments, and if these mechanisms generally interact synergistically or antagonistically. Our simulations showed that preparedness and social learning often co-evolve because they provide complimentary benefits: genetic preparedness reduced foraging efficiency, but resulted in a higher rate of survival in dangerous environments, while social learning generally came to dominate the population, especially when the environment was stochastic. However, even in this case, genetic preparedness reliably evolved. Broadly, our results indicate that the relationship between preparedness and social learning is important as it can result in trade-offs between behavioral flexibility and safety, which can lead to seemingly suboptimal behavior if the evolutionary environment of the organism is not taken into account. PMID:27487079
Co-evolution in a landrace meta-population: two closely related pathogens interacting with the same host can lead to different adaptive outcomes.

PubMed

Rau, Domenico; Rodriguez, Monica; Leonarda Murgia, Maria; Balmas, Virgilio; Bitocchi, Elena; Bellucci, Elisa; Nanni, Laura; Attene, Giovanna; Papa, Roberto

2015-08-07

We examined the local adaptation patterns in a system comprising several interconnected heterogeneous plant populations from which populations of two phylogenetically closely related pathogens were also sampled. The host is Hordeum vulgare (cultivated barley); the pathogens are Pyrenophora teres f. teres (net form) and Pyrenophora teres f. maculata (spot form), the causal agents of barley net blotch. We integrated two approaches, the comparison between the population structures of the host and the pathogens, and a cross-inoculation test. We demonstrated that two closely related pathogens with very similar niche specialisation and life-styles can give rise to different co-evolutionary outcomes on the same host. Indeed, we detected local adaptation for the net form of the pathogen but not for the spot form. We also provided evidence that an a-priori well-known resistance quantitative-trait-locus on barley chromosome 6H is involved in the co-evolutionary 'arms race' between the plant and the net-form pathogen. Moreover, data suggested latitudinal clines of host resistance and that different ecological conditions can result in differential selective pressures at different sites. Our data are of interest for on-farm conservation of plant genetic resources, as also in establishing efficient breeding programs and strategies for deployment of resistance genes of P. teres.
Co-Evolution of Social Learning and Evolutionary Preparedness in Dangerous Environments.

PubMed

Lindström, Björn; Selbing, Ida; Olsson, Andreas

2016-01-01

Danger is a fundamental aspect of the lives of most animals. Adaptive behavior therefore requires avoiding actions, objects, and environments associated with danger. Previous research has shown that humans and non-human animals can avoid such dangers through two types of behavioral adaptions, (i) genetic preparedness to avoid certain stimuli or actions, and (ii) social learning. These adaptive mechanisms reduce the fitness costs associated with danger but still allow flexible behavior. Despite the empirical prevalence and importance of both these mechanisms, it is unclear when they evolve and how they interact. We used evolutionary agent-based simulations, incorporating empirically based learning mechanisms, to clarify if preparedness and social learning typically both evolve in dangerous environments, and if these mechanisms generally interact synergistically or antagonistically. Our simulations showed that preparedness and social learning often co-evolve because they provide complimentary benefits: genetic preparedness reduced foraging efficiency, but resulted in a higher rate of survival in dangerous environments, while social learning generally came to dominate the population, especially when the environment was stochastic. However, even in this case, genetic preparedness reliably evolved. Broadly, our results indicate that the relationship between preparedness and social learning is important as it can result in trade-offs between behavioral flexibility and safety, which can lead to seemingly suboptimal behavior if the evolutionary environment of the organism is not taken into account.
Canine parvovirus type 2 (CPV-2) and Feline panleukopenia virus (FPV) codon bias analysis reveals a progressive adaptation to the new niche after the host jump.

PubMed

Franzo, Giovanni; Tucciarone, Claudia Maria; Cecchinato, Mattia; Drigo, Michele

2017-09-01

Based on virus dependence from host cell machinery, their codon usage is expected to show a strong relation with the host one. Even if this association has been stated, especially for bacteria viruses, the linkage is considered to be less consistent for more complex organisms and a codon bias adaptation after host jump has never been proven. Canine parvovirus type 2 (CPV-2) was selected as a model because it represents a well characterized case of host jump, originating from Feline panleukopenia virus (FPV). The current study demonstrates that the adaptation to specific tissue and host codon bias affected CPV-2 evolution. Remarkably, FPV and CPV-2 showed a higher closeness toward the codon bias of the tissues they display the higher tropism for. Moreover, after the host jump, a clear and significant trend was evidenced toward a reduction in the distance between CPV-2 and the dog codon bias over time. This evidence was not confirmed for FPV, suggesting that an equilibrium has been reached during the prolonged virus-host co-evolution. Additionally, the presence of an intermediate pattern displayed by some strains infecting wild species suggests that these could have facilitated the host switch also by acting on codon bias. Copyright © 2017 Elsevier Inc. All rights reserved.
Co-evolution in a landrace meta-population: two closely related pathogens interacting with the same host can lead to different adaptive outcomes

PubMed Central

Rau, Domenico; Rodriguez, Monica; Leonarda Murgia, Maria; Balmas, Virgilio; Bitocchi, Elena; Bellucci, Elisa; Nanni, Laura; Attene, Giovanna; Papa, Roberto

2015-01-01

We examined the local adaptation patterns in a system comprising several interconnected heterogeneous plant populations from which populations of two phylogenetically closely related pathogens were also sampled. The host is Hordeum vulgare (cultivated barley); the pathogens are Pyrenophora teres f. teres (net form) and Pyrenophora teres f. maculata (spot form), the causal agents of barley net blotch. We integrated two approaches, the comparison between the population structures of the host and the pathogens, and a cross-inoculation test. We demonstrated that two closely related pathogens with very similar niche specialisation and life-styles can give rise to different co-evolutionary outcomes on the same host. Indeed, we detected local adaptation for the net form of the pathogen but not for the spot form. We also provided evidence that an a-priori well-known resistance quantitative-trait-locus on barley chromosome 6H is involved in the co-evolutionary ‘arms race’ between the plant and the net-form pathogen. Moreover, data suggested latitudinal clines of host resistance and that different ecological conditions can result in differential selective pressures at different sites. Our data are of interest for on-farm conservation of plant genetic resources, as also in establishing efficient breeding programs and strategies for deployment of resistance genes of P. teres. PMID:26248796

Contrasting effects of intralocus sexual conflict on sexually antagonistic coevolution

PubMed Central

Pennell, Tanya M.; de Haas, Freek J. H.; Morrow, Edward H.; van Doorn, G. Sander

2016-01-01

Evolutionary conflict between the sexes can induce arms races in which males evolve traits that are detrimental to the fitness of their female partners, and vice versa. This interlocus sexual conflict (IRSC) has been proposed as a cause of perpetual intersexual antagonistic coevolution with wide-ranging evolutionary consequences. However, theory suggests that the scope for perpetual coevolution is limited, if traits involved in IRSC are subject to pleiotropic constraints. Here, we consider a biologically plausible form of pleiotropy that has hitherto been ignored in treatments of IRSC and arrive at drastically different conclusions. Our analysis is based on a quantitative genetic model of sexual conflict, in which genes controlling IRSC traits have side effects in the other sex, due to incompletely sex-limited gene expression. As a result, the genes are exposed to intralocus sexual conflict (IASC), a tug-of-war between opposing male- and female-specific selection pressures. We find that the interaction between the two forms of sexual conflict has contrasting effects on antagonistic coevolution: Pleiotropic constraints stabilize the dynamics of arms races if the mating traits are close to evolutionary equilibrium but can prevent populations from ever reaching such a state. Instead, the sexes are drawn into a continuous cycle of arms races, causing the buildup of IASC, alternated by phases of IASC resolution that trigger the next arms race. These results encourage an integrative perspective on the biology of sexual conflict and generally caution against relying exclusively on equilibrium stability analysis. PMID:26755609
AFFINE-CORRECTED PARADISE: FREE-BREATHING PATIENT-ADAPTIVE CARDIAC MRI WITH SENSITIVITY ENCODING

PubMed Central

Sharif, Behzad; Bresler, Yoram

2013-01-01

We propose a real-time cardiac imaging method with parallel MRI that allows for free breathing during imaging and does not require cardiac or respiratory gating. The method is based on the recently proposed PARADISE (Patient-Adaptive Reconstruction and Acquisition Dynamic Imaging with Sensitivity Encoding) scheme. The new acquisition method adapts the PARADISE k-t space sampling pattern according to an affine model of the respiratory motion. The reconstruction scheme involves multi-channel time-sequential imaging with time-varying channels. All model parameters are adapted to the imaged patient as part of the experiment and drive both data acquisition and cine reconstruction. Simulated cardiac MRI experiments using the realistic NCAT phantom show high quality cine reconstructions and robustness to modeling inaccuracies. PMID:24390159
Adaptive web sampling.

PubMed

Thompson, Steven K

2006-12-01

A flexible class of adaptive sampling designs is introduced for sampling in network and spatial settings. In the designs, selections are made sequentially with a mixture distribution based on an active set that changes as the sampling progresses, using network or spatial relationships as well as sample values. The new designs have certain advantages compared with previously existing adaptive and link-tracing designs, including control over sample sizes and of the proportion of effort allocated to adaptive selections. Efficient inference involves averaging over sample paths consistent with the minimal sufficient statistic. A Markov chain resampling method makes the inference computationally feasible. The designs are evaluated in network and spatial settings using two empirical populations: a hidden human population at high risk for HIV/AIDS and an unevenly distributed bird population.
Combating speckle in SAR images - Vector filtering and sequential classification based on a multiplicative noise model

NASA Technical Reports Server (NTRS)

Lin, Qian; Allebach, Jan P.

1990-01-01

An adaptive vector linear minimum mean-squared error (LMMSE) filter for multichannel images with multiplicative noise is presented. It is shown theoretically that the mean-squared error in the filter output is reduced by making use of the correlation between image bands. The vector and conventional scalar LMMSE filters are applied to a three-band SIR-B SAR, and their performance is compared. Based on a mutliplicative noise model, the per-pel maximum likelihood classifier was derived. The authors extend this to the design of sequential and robust classifiers. These classifiers are also applied to the three-band SIR-B SAR image.
Kullback-Leibler information function and the sequential selection of experiments to discriminate among several linear models

NASA Technical Reports Server (NTRS)

Sidik, S. M.

1972-01-01

The error variance of the process prior multivariate normal distributions of the parameters of the models are assumed to be specified, prior probabilities of the models being correct. A rule for termination of sampling is proposed. Upon termination, the model with the largest posterior probability is chosen as correct. If sampling is not terminated, posterior probabilities of the models and posterior distributions of the parameters are computed. An experiment was chosen to maximize the expected Kullback-Leibler information function. Monte Carlo simulation experiments were performed to investigate large and small sample behavior of the sequential adaptive procedure.
The evolution of bacterial resistance against bacteriophages in the horse chestnut phyllosphere is general across both space and time.

PubMed

Koskella, Britt; Parr, Nicole

2015-08-19

Insight to the spatial and temporal scales of coevolution is key to predicting the outcome of host-parasite interactions and spread of disease. For bacteria infecting long-lived hosts, selection to overcome host defences is just one factor shaping the course of evolution; populations will also be competing with other microbial species and will themselves be facing infection by bacteriophage viruses. Here, we examine the temporal and spatial patterns of bacterial adaptation against natural phage populations from within leaves of horse chestnut trees. Using a time-shift experiment with both sympatric and allopatric phages from either contemporary or earlier points in the season, we demonstrate that bacterial resistance is higher against phages from the past, regardless of spatial sympatry or how much earlier in the season phages were collected. Similarly, we show that future bacterial hosts are more resistant to both sympatric and allopatric phages than contemporary bacterial hosts. Together, our results suggest the evolution of relatively general bacterial resistance against phages in nature and are contrasting to previously observed patterns of phage adaptation to bacteria from the same tree hosts over the same time frame, indicating a potential asymmetry in coevolutionary dynamics.
The evolution of bacterial resistance against bacteriophages in the horse chestnut phyllosphere is general across both space and time

PubMed Central

Koskella, Britt; Parr, Nicole

2015-01-01

Insight to the spatial and temporal scales of coevolution is key to predicting the outcome of host–parasite interactions and spread of disease. For bacteria infecting long-lived hosts, selection to overcome host defences is just one factor shaping the course of evolution; populations will also be competing with other microbial species and will themselves be facing infection by bacteriophage viruses. Here, we examine the temporal and spatial patterns of bacterial adaptation against natural phage populations from within leaves of horse chestnut trees. Using a time-shift experiment with both sympatric and allopatric phages from either contemporary or earlier points in the season, we demonstrate that bacterial resistance is higher against phages from the past, regardless of spatial sympatry or how much earlier in the season phages were collected. Similarly, we show that future bacterial hosts are more resistant to both sympatric and allopatric phages than contemporary bacterial hosts. Together, our results suggest the evolution of relatively general bacterial resistance against phages in nature and are contrasting to previously observed patterns of phage adaptation to bacteria from the same tree hosts over the same time frame, indicating a potential asymmetry in coevolutionary dynamics. PMID:26150663
[Insulin resistance as a mechanism of adaptation during human evolution].

PubMed

Ricart, W; Fernández-Real, J M

2010-10-01

The recent application of concepts of evolution to human disease is proving useful to understand certain pathophysiological mechanisms of different entities that span genomic alterations of immunity, respiratory and hormone function, and the circulatory and neural systems. However, effort has concentrated on explaining the keys to adaptation that define human metabolism and, since the early 1960s, several theories have been developed. This article reviews some of the hypotheses postulated in recent years on the potential benefit of insulin resistance and discusses the most recent knowledge. The concept of the thrifty gene seems to have been definitively refuted by current knowledge. The current paradigm describes an interaction between the metabolic and the immune systems resulting from their coevolution, promoted by evolutionary pressures triggered by fasting, infection and intake of different foods. The activation and regulation of these ancient mechanisms in integrated and interdependent areas defines insulin resistance as a survival strategy that is critical during fasting and in the fight against infection. The relationship with some components of the diet and, particularly, with the symbiotic intestinal microflora points to new paradigms in understanding the pathophysiology of obesity, metabolic syndrome and type 2 diabetes mellitus. Copyright © 2010 SEEN. Published by Elsevier Espana. All rights reserved.
The Red Queen and the seed bank: pathogen resistance of ex situ and in situ conserved barley.

PubMed

Jensen, Helen R; Dreiseitl, Antonín; Sadiki, Mohammed; Schoen, Daniel J

2012-06-01

Plant geneticists have proposed that the dynamic conservation of crop plants in farm environments (in situ conservation) is complementary to static conservation in seed banks (ex situ conservation) because it may help to ensure adaptation to changing conditions. Here, we test whether collections of a traditional variety of Moroccan barley (Hordeum vulgare ssp. vulgare) conserved ex situ showed differences in qualitative and quantitative resistance to the endemic fungal pathogen, Blumeria graminis f.sp. hordei, compared to collections that were continuously cultivated in situ. In detached-leaf assays for qualitative resistance, there were some significant differences between in situ and ex situ conserved collections from the same localities. Some ex situ conserved collections showed lower resistance levels, while others showed higher resistance levels than their in situ conserved counterparts. In field trials for quantitative resistance, similar results were observed, with the highest resistance observed in situ. Overall, this study identifies some cases where the Red Queen appears to drive the evolution of increased resistance in situ. However, in situ conservation does not always result in improved adaptation to pathogen virulence, suggesting a more complex evolutionary scenario, consistent with several published examples of plant-pathogen co-evolution in wild systems.
Therapeutic targeting of replicative immortality

PubMed Central

Yaswen, Paul; MacKenzie, Karen L.; Keith, W. Nicol; Hentosh, Patricia; Rodier, Francis; Zhu, Jiyue; Firestone, Gary L.; Matheu, Ander; Carnero, Amancio; Bilsland, Alan; Sundin, Tabetha; Honoki, Kanya; Fujii, Hiromasa; Georgakilas, Alexandros G.; Amedei, Amedeo; Amin, Amr; Helferich, Bill; Boosani, Chandra S.; Guha, Gunjan; Ciriolo, Maria Rosa; Chen, Sophie; Mohammed, Sulma I.; Azmi, Asfar S.; Bhakta, Dipita; Halicka, Dorota; Niccolai, Elena; Aquilano, Katia; Ashraf, S. Salman; Nowsheen, Somaira; Yang, Xujuan

2015-01-01

One of the hallmarks of malignant cell populations is the ability to undergo continuous proliferation. This property allows clonal lineages to acquire sequential aberrations that can fuel increasingly autonomous growth, invasiveness, and therapeutic resistance. Innate cellular mechanisms have evolved to regulate replicative potential as a hedge against malignant progression. When activated in the absence of normal terminal differentiation cues, these mechanisms can result in a state of persistent cytostasis. This state, termed “senescence,” can be triggered by intrinsic cellular processes such as telomere dysfunction and oncogene expression, and by exogenous factors such as DNA damaging agents or oxidative environments. Despite differences in upstream signaling, senescence often involves convergent interdependent activation of tumor suppressors p53 and p16/pRB, but can be induced, albeit with reduced sensitivity, when these suppressors are compromised. Doses of conventional genotoxic drugs required to achieve cancer cell senescence are often much lower than doses required to achieve outright cell death. Additional therapies, such as those targeting cyclin dependent kinases or components of the PI3K signaling pathway, may induce senescence specifically in cancer cells by circumventing defects in tumor suppressor pathways or exploiting cancer cells’ heightened requirements for telomerase. Such treatments sufficient to induce cancer cell senescence could provide increased patient survival with fewer and less severe side effects than conventional cytotoxic regimens. This positive aspect is countered by important caveats regarding senescence reversibility, genomic instability, and paracrine effects that may increase heterogeneity and adaptive resistance of surviving cancer cells. Nevertheless, agents that effectively disrupt replicative immortality will likely be valuable components of new combinatorial approaches to cancer therapy. PMID:25869441
Evolution of the B7 family: co-evolution of B7H6 and NKp30, identification of a new B7 family member, B7H7, and of B7's historical relationship with the MHC.

PubMed

Flajnik, Martin F; Tlapakova, Tereza; Criscitiello, Michael F; Krylov, Vladimir; Ohta, Yuko

2012-08-01

The B7 family of genes is essential in the regulation of the adaptive immune system. Most B7 family members contain both variable (V)- and constant (C)-type domains of the immunoglobulin superfamily (IgSF). Through in silico screening of the Xenopus genome and subsequent phylogenetic analysis, we found novel genes belonging to the B7 family, one of which is the recently discovered B7H6. Humans and rats have a single B7H6 gene; however, many B7H6 genes were detected in a single large cluster in the Xenopus genome. The B7H6 expression patterns also varied in a species-specific manner. Human B7H6 binds to the activating natural killer receptor, NKp30. While the NKp30 gene is single-copy and maps to the MHC in most vertebrates, many Xenopus NKp30 genes were found in a cluster on a separate chromosome that does not harbor the MHC. Indeed, in all species so far analyzed from sharks to mammals, the number of NKp30 and B7H6 genes correlates well, suggestive of receptor-ligand co-evolution. Furthermore, we identified a Xenopus-specific B7 homolog (B7HXen) and revealed its close linkage to B2M, which we have demonstrated previously to have been originally encoded in the MHC. Thus, our study provides further proof that the B7 precursor was included in the proto MHC. Additionally, the comparative analysis revealed a new B7 family member, B7H7, which was previously designated in the literature as an unknown gene, HHLA2.
The Role of Time-Scales in Socio-hydrology

NASA Astrophysics Data System (ADS)

Blöschl, Günter; Sivapalan, Murugesu

2016-04-01

Much of the interest in hydrological modeling in the past decades revolved around resolving spatial variability. With the rapid changes brought about by human impacts on the hydrologic cycle, there is now an increasing need to refocus on time dependency. We present a co-evolutionary view of hydrologic systems, in which every part of the system including human systems, co-evolve, albeit at different rates. The resulting coupled human-nature system is framed as a dynamical system, characterized by interactions of fast and slow time scales and feedbacks between environmental and social processes. This gives rise to emergent phenomena such as the levee effect, adaptation to change and system collapse due to resource depletion. Changing human values play a key role in the emergence of these phenomena and should therefore be considered as internal to the system in a dynamic way. The co-evolutionary approach differs from the traditional view of water resource systems analysis as it allows for path dependence, multiple equilibria, lock-in situations and emergent phenomena. The approach may assist strategic water management for long time scales through facilitating stakeholder participation, exploring the possibility space of alternative futures, and helping to synthesise the observed dynamics of different case studies. Future research opportunities include the study of how changes in human values are connected to human-water interactions, historical analyses of trajectories of system co-evolution in individual places and comparative analyses of contrasting human-water systems in different climate and socio-economic settings. Reference Sivapalan, M. and G. Blöschl (2015) Time scale interactions and the coevolution of humans and water. Water Resour. Res., 51, 6988-7022, doi:10.1002/2015WR017896.
Multiscale Modeling of Human-Water Interactions: The Role of Time-Scales

NASA Astrophysics Data System (ADS)

Bloeschl, G.; Sivapalan, M.

2015-12-01

Much of the interest in hydrological modeling in the past decades revolved around resolving spatial variability. With the rapid changes brought about by human impacts on the hydrologic cycle, there is now an increasing need to refocus on time dependency. We present a co-evolutionary view of hydrologic systems, in which every part of the system including human systems, co-evolve, albeit at different rates. The resulting coupled human-nature system is framed as a dynamical system, characterized by interactions of fast and slow time scales and feedbacks between environmental and social processes. This gives rise to emergent phenomena such as the levee effect, adaptation to change and system collapse due to resource depletion. Changing human values play a key role in the emergence of these phenomena and should therefore be considered as internal to the system in a dynamic way. The co-evolutionary approach differs from the traditional view of water resource systems analysis as it allows for path dependence, multiple equilibria, lock-in situations and emergent phenomena. The approach may assist strategic water management for long time scales through facilitating stakeholder participation, exploring the possibility space of alternative futures, and helping to synthesise the observed dynamics of different case studies. Future research opportunities include the study of how changes in human values are connected to human-water interactions, historical analyses of trajectories of system co-evolution in individual places and comparative analyses of contrasting human-water systems in different climate and socio-economic settings. Reference Sivapalan, M. and G. Blöschl (2015) Time Scale Interactions and the Co-evolution of Humans and Water. Water Resour. Res., 51, in press.
Towards generalizing co-evolutionary dynamics of socio-hydrology: Theoretical frameworks of cultural evolution and robustness-fragility tradeoff

NASA Astrophysics Data System (ADS)

Oh, W. S.; Yu, D. J.; Davis, T.; Hillis, V.; Waring, T. M.

2017-12-01

One ongoing challenge to socio-hydrology is the problem of generalization: to what extent do common human-water co-evolutions exist across distinct cases and what are underlying mechanisms of these co-evolutions. This problem stems in part from a lack of unifying theories in socio-hydrology, which hinders the explanation and generalization of results between cases in different regions. Theories help an analyst to make assumptions that are necessary to diagnose a specific phenomenon, to explain the general mechanisms of causation, and, thus, to predict future outcomes. To help address the issue, this study introduces two theories that are increasingly used in the fields of sustainability science and social-ecological systems research: robustness-fragility tradeoff (RFTO) and cultural multi-level selection (CMLS). We apply each of these theories to two distinct cases (water management issues in southwest Bangladesh and the Kissimmee River Basin, Florida) and interpret the phenomena of the levee and adaptation effects. CMLS and RFTO focus on complementary aspects of socio-hydrological phenomena. The theory of RFTO, which is mostly about inherent tradeoffs associated with infrastructure improvements, explains how efforts to increase system robustness can generate hidden endogenous risks. CMLS theory, rooted in the broader theory of cultural evolution, concerns how human cultural dynamics can act as an endogenous driver of system change across multiple levels of social organizations. Using the applied examples, we demonstrate that these two theories can provide an effective way to study social-hydrological systems and to overcome the generalization problem. Our work shows that multiple theories can be synthesized to give a richer understanding of diverse socio-hydrological patterns.
The Co-Evolution of Life & Environment, and the Astrobiological Quest

NASA Astrophysics Data System (ADS)

Cabrol, N. A.

2016-12-01

Physicochemical and environmental conditions determine the range of possible biogeochemistries on planets and moons. Yet, the Earth shows that as soon as life took hold, it modified its environment, from the mineralogy of sediments to the global composition of the atmosphere. In their evolution, life and environment are intertwined and cannot be separated. This coevolution is one of the most fundamental concepts in astrobiology, one that is central to our understanding of what, where, and how to search for life beyond Earth. In that quest, Mars will be the first destination for planetary missions seeking biosignatures. Both Earth and Mars had shared traits during the Archean/Noachian period. However, for Mars, the impact of a different environmental evolution on the development of life and the preservation of biosignatures remains unclear. In addition to an irreversible global climate change, Mars always had greater environmental variability than Earth due to its astronomical characteristics. Biological evolution, if any, would have had to proceed in this distinct context. If parallels can be drawn, the major metabolisms supporting Earth's biogeochemical cycles had evolved early. Understanding the succession of physical and environmental processes and their combination in the first 700 million years of Mars history is, therefore, essential to envision possible metabolisms, adaptation strategies life would have required to survive changes, and the biosignatures that could still be preserved today. Ultimately, the astrobiological significance of exploring Mars is also about teaching us invaluable lessons about the uniqueness of each planetary experiment, regardless of similarities. Beyond the Solar System, this notion can be expanded to the search for earth-like exoplanets, and for what it means to search for life as we know it, simple or complex.
Experimental Design and Primary Data Analysis Methods for Comparing Adaptive Interventions

PubMed Central

Nahum-Shani, Inbal; Qian, Min; Almirall, Daniel; Pelham, William E.; Gnagy, Beth; Fabiano, Greg; Waxmonsky, Jim; Yu, Jihnhee; Murphy, Susan

2013-01-01

In recent years, research in the area of intervention development is shifting from the traditional fixed-intervention approach to adaptive interventions, which allow greater individualization and adaptation of intervention options (i.e., intervention type and/or dosage) over time. Adaptive interventions are operationalized via a sequence of decision rules that specify how intervention options should be adapted to an individual’s characteristics and changing needs, with the general aim to optimize the long-term effectiveness of the intervention. Here, we review adaptive interventions, discussing the potential contribution of this concept to research in the behavioral and social sciences. We then propose the sequential multiple assignment randomized trial (SMART), an experimental design useful for addressing research questions that inform the construction of high-quality adaptive interventions. To clarify the SMART approach and its advantages, we compare SMART with other experimental approaches. We also provide methods for analyzing data from SMART to address primary research questions that inform the construction of a high-quality adaptive intervention. PMID:23025433
Adaptive Sequential Monte Carlo for Multiple Changepoint Analysis

DOE PAGES

Heard, Nicholas A.; Turcotte, Melissa J. M.

2016-05-21

Process monitoring and control requires detection of structural changes in a data stream in real time. This paper introduces an efficient sequential Monte Carlo algorithm designed for learning unknown changepoints in continuous time. The method is intuitively simple: new changepoints for the latest window of data are proposed by conditioning only on data observed since the most recent estimated changepoint, as these observations carry most of the information about the current state of the process. The proposed method shows improved performance over the current state of the art. Another advantage of the proposed algorithm is that it can be mademore » adaptive, varying the number of particles according to the apparent local complexity of the target changepoint probability distribution. This saves valuable computing time when changes in the changepoint distribution are negligible, and enables re-balancing of the importance weights of existing particles when a significant change in the target distribution is encountered. The plain and adaptive versions of the method are illustrated using the canonical continuous time changepoint problem of inferring the intensity of an inhomogeneous Poisson process, although the method is generally applicable to any changepoint problem. Performance is demonstrated using both conjugate and non-conjugate Bayesian models for the intensity. Lastly, appendices to the article are available online, illustrating the method on other models and applications.« less
Finding Feasible Abstract Counter-Examples

NASA Technical Reports Server (NTRS)

Pasareanu, Corina S.; Dwyer, Matthew B.; Visser, Willem; Clancy, Daniel (Technical Monitor)

2002-01-01

A strength of model checking is its ability to automate the detection of subtle system errors and produce traces that exhibit those errors. Given the high computational cost of model checking most researchers advocate the use of aggressive property-preserving abstractions. Unfortunately, the more aggressively a system is abstracted the more infeasible behavior it will have. Thus, while abstraction enables efficient model checking it also threatens the usefulness of model checking as a defect detection tool, since it may be difficult to determine whether a counter-example is feasible and hence worth developer time to analyze. We have explored several strategies for addressing this problem by extending an explicit-state model checker, Java PathFinder (JPF), to search for and analyze counter-examples in the presence of abstractions. We demonstrate that these techniques effectively preserve the defect detection ability of model checking in the presence of aggressive abstraction by applying them to check properties of several abstracted multi-threaded Java programs. These new capabilities are not specific to JPF and can be easily adapted to other model checking frameworks; we describe how this was done for the Bandera toolset.
Item Selection in Multidimensional Computerized Adaptive Testing--Gaining Information from Different Angles

ERIC Educational Resources Information Center

Wang, Chun; Chang, Hua-Hua

2011-01-01

Over the past thirty years, obtaining diagnostic information from examinees' item responses has become an increasingly important feature of educational and psychological testing. The objective can be achieved by sequentially selecting multidimensional items to fit the class of latent traits being assessed, and therefore Multidimensional…
On the Specificity of Sequential Congruency Effects in Implicit Learning of Motor and Perceptual Sequences

ERIC Educational Resources Information Center

D'Angelo, Maria C.; Jimenez, Luis; Milliken, Bruce; Lupianez, Juan

2013-01-01

Individuals experience less interference from conflicting information following events that contain conflicting information. Recently, Jimenez, Lupianez, and Vaquero (2009) demonstrated that such adaptations to conflict occur even when the source of conflict arises from implicit knowledge of sequences. There is accumulating evidence that momentary…

Edge-following algorithm for tracking geological features

NASA Technical Reports Server (NTRS)

Tietz, J. C.

1977-01-01

Sequential edge-tracking algorithm employs circular scanning to point permit effective real-time tracking of coastlines and rivers from earth resources satellites. Technique eliminates expensive high-resolution cameras. System might also be adaptable for application in monitoring automated assembly lines, inspecting conveyor belts, or analyzing thermographs, or x ray images.
Mixed Emotions and Coping: The Benefits of Secondary Emotions

PubMed Central

Braniecka, Anna; Trzebińska, Ewa; Dowgiert, Aneta; Wytykowska, Agata

2014-01-01

The existing empirical literature suggests that during difficult situations, the concurrent experience of positive and negative affects may be ideal for ensuring successful adaptation and well-being. However, different patterns of mixed emotions may have different adaptive consequences. The present research tested the proposition that experiencing a pattern of secondary mixed emotion (i.e., secondary emotion that embrace both positive and negative affects) more greatly promotes adaptive coping than experiencing two other patterns of mixed emotional experiences: simultaneous (i.e., two emotions of opposing affects taking place at the same time) and sequential (i.e., two emotions of opposing affects switching back and forth). Support for this hypothesis was obtained from two experiments (Studies 1 and 2) and a longitudinal survey (Study 3). The results revealed that secondary mixed emotions predominate over sequential and simultaneous mixed emotional experiences in promoting adaptive coping through fostering the motivational and informative functions of emotions; this is done by providing solution-oriented actions rather than avoidance, faster decisions regarding coping strategies (Study 1), easier access to self-knowledge, and better narrative organization (Study 2). Furthermore, individuals characterized as being prone to feeling secondary mixed emotions were more resilient to stress caused by transitions than those who were characterized as being prone to feeling opposing emotions separately (Study 3). Taken together, the preliminary results indicate that the pattern of secondary mixed emotion provides individuals with a higher capacity to handle adversity than the other two patterns of mixed emotional experience. PMID:25084461
Mixed emotions and coping: the benefits of secondary emotions.

PubMed

Braniecka, Anna; Trzebińska, Ewa; Dowgiert, Aneta; Wytykowska, Agata

2014-01-01

The existing empirical literature suggests that during difficult situations, the concurrent experience of positive and negative affects may be ideal for ensuring successful adaptation and well-being. However, different patterns of mixed emotions may have different adaptive consequences. The present research tested the proposition that experiencing a pattern of secondary mixed emotion (i.e., secondary emotion that embrace both positive and negative affects) more greatly promotes adaptive coping than experiencing two other patterns of mixed emotional experiences: simultaneous (i.e., two emotions of opposing affects taking place at the same time) and sequential (i.e., two emotions of opposing affects switching back and forth). Support for this hypothesis was obtained from two experiments (Studies 1 and 2) and a longitudinal survey (Study 3). The results revealed that secondary mixed emotions predominate over sequential and simultaneous mixed emotional experiences in promoting adaptive coping through fostering the motivational and informative functions of emotions; this is done by providing solution-oriented actions rather than avoidance, faster decisions regarding coping strategies (Study 1), easier access to self-knowledge, and better narrative organization (Study 2). Furthermore, individuals characterized as being prone to feeling secondary mixed emotions were more resilient to stress caused by transitions than those who were characterized as being prone to feeling opposing emotions separately (Study 3). Taken together, the preliminary results indicate that the pattern of secondary mixed emotion provides individuals with a higher capacity to handle adversity than the other two patterns of mixed emotional experience.
Autonomous Agent-Based Systems and Their Applications in Fluid Dynamics, Particle Separation, and Co-evolving Networks

NASA Astrophysics Data System (ADS)

Graeser, Oliver

This thesis comprises three parts, reporting research results in Fluid Dynamics (Part I), Particle Separation (Part II) and Co-evolving Networks (Part III). Part I deals with the simulation of fluid dynamics using the lattice-Boltzmann method. Microfluidic devices often feature two-dimensional, repetitive arrays. Flows through such devices are pressure-driven and confined by solid walls. We have defined new adaptive generalised periodic boundary conditions to represent the effects of outer solid walls, and are thus able to exploit the periodicity of the array by simulating the flow through one unit cell in lieu of the entire device. The so-calculated fully developed flow describes the flow through the entire array accurately, but with computational requirements that are reduced according to the dimensions of the array. Part II discusses the problem of separating macromolecules like proteins or DNA coils. The reliable separation of such molecules is a crucial task in molecular biology. The use of Brownian ratchets as mechanisms for the separation of such particles has been proposed and discussed during the last decade. Pressure-driven flows have so far been dismissed as possible driving forces for Brownian ratchets, as they do not generate ratchet asymmetry. We propose a microfluidic design that uses pressure-driven flows to create asymmetry and hence allows particle separation. The dependence of the asymmetry on various factors of the microfluidic geometry is discussed. We further exemplify the feasibility of our approach using Brownian dynamics simulations of particles of different sizes in such a device. The results show that ratchet-based particle separation using flows as the driving force is possible. Simulation results and ratchet theory predictions are in excellent agreement. Part III deals with the co-evolution of networks and dynamic models. A group of agents occupies the nodes of a network, which defines the relationship between these agents. The evolution of the agents is defined by the rules of the dynamic model and depends on the relationship between agents, i.e., the state of the network. In return, the evolution of the network depends on the state of the dynamic model. The concept is introduced through the adaptive SIS model. We show that the previously used criterion determining the critical infected fraction, i.e., the number of infected agents required to sustain the epidemic, is inappropriate for this model. We introduce a different criterion and show that the critical infected fraction so determined is in good agreement with results obtained by numerical simulations. We further discuss the concept of co-evolving dynamics using the Snowdrift Game as a model paradigm. Co-evolution occurs through agents cutting dissatisfied links and rewiring to other agents at random. The effect of co-evolution on the emergence of cooperation is discussed using a mean-field theory and numerical simulations. A transition between a connected and a disconnected, highly cooperative state of the system is observed, and explained using the mean-field model. Quantitative deviations regarding the level of cooperation in the disconnected regime can be fully resolved through an improved mean-field theory that includes the effect of random fluctuations into its model.
Social Science for Counterterrorism: Putting the Pieces Together

DTIC Science & Technology

2009-01-01

Term Communications In countering terrorism or insurgency, short-term communications efforts—such as crisis response or rapid message adaptation in...of time. Within the literature on crisis communications is a generally agreed- on list of preparatory actions an organization should take, including...writing a crisis response plan, assigning crisis spokespersons and teams, training staff for crises, identifying communications risks and vulner
Organic compatible solutes of halotolerant and halophilic microorganisms

PubMed Central

Roberts, Mary F

2005-01-01

Microorganisms that adapt to moderate and high salt environments use a variety of solutes, organic and inorganic, to counter external osmotic pressure. The organic solutes can be zwitterionic, noncharged, or anionic (along with an inorganic cation such as K+). The range of solutes, their diverse biosynthetic pathways, and physical properties of the solutes that effect molecular stability are reviewed. PMID:16176595
Navy Shipboard Lasers for Surface, Air, and Missile Defense: Background and Issues for Congress

DTIC Science & Technology

2013-03-14

absorption and turbulence , suitable for use to evaluate notional maritime beam director subsystems, and shall include studies in adaptive optics for...is good enough in terms of atmospheric transmission to permit the laser to disable targets of interest at tactically useful ranges, and that...Countering Targets ........................................................ 7 Types of Lasers Being Developed for Potential Shipboard Use
Targeting Therapy Resistance: When Glutamine Catabolism Becomes Essential.

PubMed

Lukey, Michael J; Katt, William P; Cerione, Richard A

2018-05-14

Identifying contexts in which cancer cells become addicted to specific nutrients is critical for developing targeted metabolic therapies. In this issue of Cancer Cell, Momcilovic et al. report that suppressed glycolysis following mTOR inhibition is countered by adaptive glutamine catabolism in lung squamous cell carcinoma, sensitizing tumors to glutaminase inhibition. Copyright © 2018 Elsevier Inc. All rights reserved.
Itaukei Indigenous Fijian "Masi" as an Education Framework: Retaining and Adapting Tradition in Epistemology and Pedagogy for a Globalised Culture

ERIC Educational Resources Information Center

Varani-Norton, Eta Emele

2017-01-01

iTaukei (Indigenous Fijians) are experiencing rapid social transformation through urbanisation and globalisation. Indigenous knowledge is being quickly eroded by its conflicts with modern Western knowledge and values. To counter this decay, there is need, in the school curriculum, for teaching methods that can help students achieve, in their own…
Complex trophic interactions in kelp forest ecosystems

USGS Publications Warehouse

Estes, J.A.; Danner, E.M.; Doak, D.F.; Konar, B.; Springer, A.M.; Steinberg, P.D.; Tinker, M. Tim; Williams, T.M.

2004-01-01

The distributions and abundances of species and populations change almost continuously. Understanding the processes responsible is perhaps ecology’s most fundamental challenge. Kelp-forest ecosystems in southwest Alaska have undergone several phase shifts between alga- and herbivore-dominated states in recent decades. Overhunting and recovery of sea otters caused the earlier shifts. Studies focusing on these changes demonstrate the importance of top-down forcing processes, a variety of indirect food-web interactions associated with the otter-urchin-kelp trophic cascade, and the role of food-chain length in the coevolution of defense and resistance in plants and their herbivores. This system unexpectedly shifted back to an herbivore-dominated state during the 1990s, because of a sea-otter population collapse that apparently was driven by increased predation by killer whales. Reasons for this change remain uncertain but seem to be linked to the whole-sale collapse of marine mammals in the North Pacific Ocean and southern Bering Sea. We hypothesize that killer whales sequentially "fished down" pinniped and sea-otter populations after their earlier prey, the great whales, were decimated by commercial whaling. The dynamics of kelp forests in southwest Alaska thus appears to have been influenced by an ecological chain reaction that encompassed numerous species and large scales of space and time.
Genome Dynamics in Legionella: The Basis of Versatility and Adaptation to Intracellular Replication

PubMed Central

Gomez-Valero, Laura; Buchrieser, Carmen

2013-01-01

Legionella pneumophila is a bacterial pathogen present in aquatic environments that can cause a severe pneumonia called Legionnaires’ disease. Soon after its recognition, it was shown that Legionella replicates inside amoeba, suggesting that bacteria replicating in environmental protozoa are able to exploit conserved signaling pathways in human phagocytic cells. Comparative, evolutionary, and functional genomics suggests that the Legionella–amoeba interaction has shaped this pathogen more than previously thought. A complex evolutionary scenario involving mobile genetic elements, type IV secretion systems, and horizontal gene transfer among Legionella, amoeba, and other organisms seems to take place. This long-lasting coevolution led to the development of very sophisticated virulence strategies and a high level of temporal and spatial fine-tuning of bacteria host–cell interactions. We will discuss current knowledge of the evolution of virulence of Legionella from a genomics perspective and propose our vision of the emergence of this human pathogen from the environment. PMID:23732852
Genome-culture coevolution promotes rapid divergence of killer whale ecotypes.

PubMed

Foote, Andrew D; Vijay, Nagarjun; Ávila-Arcos, María C; Baird, Robin W; Durban, John W; Fumagalli, Matteo; Gibbs, Richard A; Hanson, M Bradley; Korneliussen, Thorfinn S; Martin, Michael D; Robertson, Kelly M; Sousa, Vitor C; Vieira, Filipe G; Vinař, Tomáš; Wade, Paul; Worley, Kim C; Excoffier, Laurent; Morin, Phillip A; Gilbert, M Thomas P; Wolf, Jochen B W

2016-05-31

Analysing population genomic data from killer whale ecotypes, which we estimate have globally radiated within less than 250,000 years, we show that genetic structuring including the segregation of potentially functional alleles is associated with socially inherited ecological niche. Reconstruction of ancestral demographic history revealed bottlenecks during founder events, likely promoting ecological divergence and genetic drift resulting in a wide range of genome-wide differentiation between pairs of allopatric and sympatric ecotypes. Functional enrichment analyses provided evidence for regional genomic divergence associated with habitat, dietary preferences and post-zygotic reproductive isolation. Our findings are consistent with expansion of small founder groups into novel niches by an initial plastic behavioural response, perpetuated by social learning imposing an altered natural selection regime. The study constitutes an important step towards an understanding of the complex interaction between demographic history, culture, ecological adaptation and evolution at the genomic level.
Genome-culture coevolution promotes rapid divergence of killer whale ecotypes

PubMed Central

Foote, Andrew D.; Vijay, Nagarjun; Ávila-Arcos, María C.; Baird, Robin W.; Durban, John W.; Fumagalli, Matteo; Gibbs, Richard A.; Hanson, M. Bradley; Korneliussen, Thorfinn S.; Martin, Michael D.; Robertson, Kelly M.; Sousa, Vitor C.; Vieira, Filipe G.; Vinař, Tomáš; Wade, Paul; Worley, Kim C.; Excoffier, Laurent; Morin, Phillip A.; Gilbert, M. Thomas P.; Wolf, Jochen B.W.

2016-01-01

Analysing population genomic data from killer whale ecotypes, which we estimate have globally radiated within less than 250,000 years, we show that genetic structuring including the segregation of potentially functional alleles is associated with socially inherited ecological niche. Reconstruction of ancestral demographic history revealed bottlenecks during founder events, likely promoting ecological divergence and genetic drift resulting in a wide range of genome-wide differentiation between pairs of allopatric and sympatric ecotypes. Functional enrichment analyses provided evidence for regional genomic divergence associated with habitat, dietary preferences and post-zygotic reproductive isolation. Our findings are consistent with expansion of small founder groups into novel niches by an initial plastic behavioural response, perpetuated by social learning imposing an altered natural selection regime. The study constitutes an important step towards an understanding of the complex interaction between demographic history, culture, ecological adaptation and evolution at the genomic level. PMID:27243207
The Co-evolution of Concepts and Motivation

PubMed Central

Delton, Andrew W.; Sell, Aaron

2014-01-01

Does the human mind contain evolved concepts? Many psychologists have doubted this or have investigated only a narrow set (e.g., object, number, cause). Does the human mind contain evolved motivational systems? Many more assent to this claim, holding that there are evolved motivational systems for, among other tasks, social affiliation, aggressive competition, and finding food. An emerging research program, however, reveals that these are not separate questions. Any evolved motivational system needs a wealth of conceptual structure that tethers the motivations to real world entities. For instance, what use is a fear of predators without knowing what predators are and how to respond to them effectively? As we illustrate with case studies of cooperation and conflict, there is no motivation without representation: To generate adaptive behavior, motivational systems must be interwoven with the concepts required to support them, and cannot be understood without explicit reference to those concepts. PMID:25221389
Experimental Evolution with Caenorhabditis Nematodes

PubMed Central

Teotónio, Henrique; Estes, Suzanne; Phillips, Patrick C.; Baer, Charles F.

2017-01-01

The hermaphroditic nematode Caenorhabditis elegans has been one of the primary model systems in biology since the 1970s, but only within the last two decades has this nematode also become a useful model for experimental evolution. Here, we outline the goals and major foci of experimental evolution with C. elegans and related species, such as C. briggsae and C. remanei, by discussing the principles of experimental design, and highlighting the strengths and limitations of Caenorhabditis as model systems. We then review three exemplars of Caenorhabditis experimental evolution studies, underlining representative evolution experiments that have addressed the: (1) maintenance of genetic variation; (2) role of natural selection during transitions from outcrossing to selfing, as well as the maintenance of mixed breeding modes during evolution; and (3) evolution of phenotypic plasticity and its role in adaptation to variable environments, including host–pathogen coevolution. We conclude by suggesting some future directions for which experimental evolution with Caenorhabditis would be particularly informative. PMID:28592504
Co-evolution for Problem Simplification

NASA Technical Reports Server (NTRS)

Haith, Gary L.; Lohn, Jason D.; Cplombano, Silvano P.; Stassinopoulos, Dimitris

1999-01-01

This paper explores a co-evolutionary approach applicable to difficult problems with limited failure/success performance feedback. Like familiar "predator-prey" frameworks this algorithm evolves two populations of individuals - the solutions (predators) and the problems (prey). The approach extends previous work by rewarding only the problems that match their difficulty to the level of solut,ion competence. In complex problem domains with limited feedback, this "tractability constraint" helps provide an adaptive fitness gradient that, effectively differentiates the candidate solutions. The algorithm generates selective pressure toward the evolution of increasingly competent solutions by rewarding solution generality and uniqueness and problem tractability and difficulty. Relative (inverse-fitness) and absolute (static objective function) approaches to evaluating problem difficulty are explored and discussed. On a simple control task, this co-evolutionary algorithm was found to have significant advantages over a genetic algorithm with either a static fitness function or a fitness function that changes on a hand-tuned schedule.
Insect response to plant defensive protease inhibitors.

PubMed

Zhu-Salzman, Keyan; Zeng, Rensen

2015-01-07

Plant protease inhibitors (PIs) are natural plant defense proteins that inhibit proteases of invading insect herbivores. However, their anti-insect efficacy is determined not only by their potency toward a vulnerable insect system but also by the response of the insect to such a challenge. Through the long history of coevolution with their host plants, insects have developed sophisticated mechanisms to circumvent antinutritional effects of dietary challenges. Their response takes the form of changes in gene expression and the protein repertoire in cells lining the alimentary tract, the first line of defense. Research in insect digestive proteases has revealed the crucial roles they play in insect adaptation to plant PIs and has brought about a new appreciation of how phytophagous insects employ this group of molecules in both protein digestion and counterdefense. This review provides researchers in related fields an up-to-date summary of recent advances.
Behavioral Immunity in Insects

PubMed Central

de Roode, Jacobus C.; Lefèvre, Thierry

2012-01-01

Parasites can dramatically reduce the fitness of their hosts, and natural selection should favor defense mechanisms that can protect hosts against disease. Much work has focused on understanding genetic and physiological immunity against parasites, but hosts can also use behaviors to avoid infection, reduce parasite growth or alleviate disease symptoms. It is increasingly recognized that such behaviors are common in insects, providing strong protection against parasites and parasitoids. We review the current evidence for behavioral immunity in insects, present a framework for investigating such behavior, and emphasize that behavioral immunity may act through indirect rather than direct fitness benefits. We also discuss the implications for host-parasite co-evolution, local adaptation, and the evolution of non-behavioral physiological immune systems. Finally, we argue that the study of behavioral immunity in insects has much to offer for investigations in vertebrates, in which this topic has traditionally been studied. PMID:26466629
The Co-evolution of Concepts and Motivation.

PubMed

Delton, Andrew W; Sell, Aaron

2014-04-01

Does the human mind contain evolved concepts? Many psychologists have doubted this or have investigated only a narrow set (e.g., object, number, cause). Does the human mind contain evolved motivational systems? Many more assent to this claim, holding that there are evolved motivational systems for, among other tasks, social affiliation, aggressive competition, and finding food. An emerging research program, however, reveals that these are not separate questions. Any evolved motivational system needs a wealth of conceptual structure that tethers the motivations to real world entities. For instance, what use is a fear of predators without knowing what predators are and how to respond to them effectively? As we illustrate with case studies of cooperation and conflict, there is no motivation without representation: To generate adaptive behavior, motivational systems must be interwoven with the concepts required to support them, and cannot be understood without explicit reference to those concepts.
Host shifts and evolutionary radiations of butterflies

PubMed Central

Fordyce, James A.

2010-01-01

Ehrlich and Raven proposed a model of coevolution where major host plant shifts of butterflies facilitate a burst of diversification driven by their arrival to a new adaptive zone. One prediction of this model is that reconstructions of historical diversification of butterflies should indicate an increase in diversification rate following major host shifts. Using reconstructed histories of 15 butterfly groups, I tested this prediction and found general agreement with Ehrlich and Raven's model. Butterfly lineages with an inferred major historical host shift showed evidence of diversification rate variation, with a significant acceleration following the host shift. Lineages without an inferred major host shift generally agreed with a constant-rate model of diversification. These results are consistent with the view that host plant associations have played a profound role in the evolutionary history of butterflies, and show that major shifts to chemically distinct plant groups leave a historical footprint that remains detectable today. PMID:20610430

The Keck OSIRIS Nearby AGN (KONA) Survey: AGN Fueling and Feedback

NASA Astrophysics Data System (ADS)

Hicks, Erin K. S.; Müller-Sánchez, Francisco; Malkan, Matthew A.; Yu, Po-Chieh

In an effort to better constrain the relevant physical processes dictating the co-evolution of supermassive black holes and the galaxies in which they reside we turn to local Seyfert AGN. It is only with these local AGN that we can reach the spatial resolution needed to adequately characterize the inflow and outflow mechanisms thought to be the driving forces in establishing the relationship between black holes and their host galaxies at higher redshift. We present the first results from the KONA (Keck OSIRIS Nearby AGN) survey, which takes advantage of the integral field unit OSIRIS plus laser and natural guide star adaptive optics to probe down to scales of 5-30 parsecs in a sample of 40 local Seyfert galaxies. With these K-band data we measure the two-dimensional distribution and kinematics of the nuclear stars, molecular gas, and ionized gas within the central few hundred parsecs.
Cuckoos, cowbirds and hosts: adaptations, trade-offs and constraints.

PubMed

Krüger, Oliver

2007-10-29

The interactions between brood parasitic birds and their host species provide one of the best model systems for coevolution. Despite being intensively studied, the parasite-host system provides ample opportunities to test new predictions from both coevolutionary theory as well as life-history theory in general. I identify four main areas that might be especially fruitful: cuckoo female gentes as alternative reproductive strategies, non-random and nonlinear risks of brood parasitism for host individuals, host parental quality and targeted brood parasitism, and differences and similarities between predation risk and parasitism risk. Rather than being a rare and intriguing system to study coevolutionary processes, I believe that avian brood parasites and their hosts are much more important as extreme cases in the evolution of life-history strategies. They provide unique examples of trade-offs and situations where constraints are either completely removed or particularly severe.
Chlamydia Infection Across Host Species Boundaries Promotes Distinct Sets of Transcribed Anti-Apoptotic Factors

PubMed Central

Messinger, Joshua E.; Nelton, Emmalin; Feeney, Colleen; Gondek, David C.

2015-01-01

Chlamydiae, obligate intracellular bacteria, cause significant human and veterinary associated diseases. Having emerged an estimated 700-million years ago, these bacteria have twice adapted to humans as a host species, causing sexually transmitted infection (C. trachomatis) and respiratory associated disease (C. pneumoniae). The principle mechanism of host cell defense against these intracellular bacteria is the induction of cell death via apoptosis. However, in the “arms race” of co-evolution, Chlamydiae have developed mechanisms to promote cell viability and inhibit cell death. Herein we examine the impact of Chlamydiae infection across multiple host species on transcription of anti-apoptotic genes. We found mostly distinct patterns of gene expression (Mcl1 and cIAPs) elicited by each pathogen-host pair indicating Chlamydiae infection across host species boundaries does not induce a universally shared host response. Understanding species specific host-pathogen interactions is paramount to deciphering how potential pathogens become emerging diseases. PMID:26779446
Draft genome sequences of two Bifidobacterium sp. from the honey bee (Apis mellifera).

PubMed

Anderson, Kirk E; Johansson, Andreas; Sheehan, Tim H; Mott, Brendon M; Corby-Harris, Vanessa; Johnstone, Laurel; Sprissler, Ryan; Fitz, William

2013-12-18

Widely considered probiotic organisms, Bifidobacteria are common inhabitants of the alimentary tract of animals including insects. Bifidobacteria identified from the honey bee are found in larval guts and throughout the alimentary tract, but attain their greatest abundance in the adult hind gut. To further understand the role of Bifidobacteria in honey bees, we sequenced two strains of Bifidobacterium cultured from different alimentary tract environments and life stages. Reflecting an oxygen-rich niche, both strains possessed catalase, peroxidase, superoxide-dismutase and respiratory chain enzymes indicative of oxidative metabolism. The strains show markedly different carbohydrate processing capabilities, with one possessing auxiliary and key enzymes of the Entner-Doudoroff pathway. As a result of long term co-evolution, honey bee associated Bifidobacterium may harbor considerable strain diversity reflecting adaptation to a variety of different honey bee microenvironments and hive-mediated vertical transmission between generations.
Genome dynamics in Legionella: the basis of versatility and adaptation to intracellular replication.

PubMed

Gomez-Valero, Laura; Buchrieser, Carmen

2013-06-01

Legionella pneumophila is a bacterial pathogen present in aquatic environments that can cause a severe pneumonia called Legionnaires' disease. Soon after its recognition, it was shown that Legionella replicates inside amoeba, suggesting that bacteria replicating in environmental protozoa are able to exploit conserved signaling pathways in human phagocytic cells. Comparative, evolutionary, and functional genomics suggests that the Legionella-amoeba interaction has shaped this pathogen more than previously thought. A complex evolutionary scenario involving mobile genetic elements, type IV secretion systems, and horizontal gene transfer among Legionella, amoeba, and other organisms seems to take place. This long-lasting coevolution led to the development of very sophisticated virulence strategies and a high level of temporal and spatial fine-tuning of bacteria host-cell interactions. We will discuss current knowledge of the evolution of virulence of Legionella from a genomics perspective and propose our vision of the emergence of this human pathogen from the environment.
Specific inflammatory response of Anemonia sulcata (Cnidaria) after bacterial injection causes tissue reaction and enzymatic activity alteration.

PubMed

Trapani, M R; Parisi, M G; Parrinello, D; Sanfratello, M A; Benenati, G; Palla, F; Cammarata, M

2016-03-01

The evolution of multicellular organisms was marked by adaptations to protect against pathogens. The mechanisms for discriminating the ''self'' from ''non-self" have evolved into a long history of cellular and molecular strategies, from damage repair to the co-evolution of host-pathogen interactions. We investigated the inflammatory response in Anemonia sulcata (Cnidaria: Anthozoa) following injection of substances that varied in type and dimension, and observed clear, strong and specific reactions, especially after injection of Escherichia coli and Vibrio alginolyticus. Moreover, we analyzed enzymatic activity of protease, phosphatase and esterase, showing how the injection of different bacterial strains alters the expression of these enzymes and suggesting a correlation between the appearance of the inflammatory reaction and the modification of enzymatic activities. Our study shows for the first time, a specific reaction and enzymatic responses following injection of bacteria in a cnidarian. Copyright © 2016 Elsevier Inc. All rights reserved.
What chickens would tell you about the evolution of antigen processing and presentation.

PubMed

Kaufman, Jim

2015-06-01

Outside of mammals, antigen processing and presentation have only been investigated in chickens. The chicken MHC is organized differently than mammals, allowing the co-evolution of polymorphic genes, with each MHC haplotype having a set of TAP1, TAP2 and tapasin alleles directed to high expression of a single classical class I molecule. However, the class I alleles vary in the size of peptide-binding repertoire, along with a suite of other properties. The salient features of the chicken MHC are found in many non-mammalian vertebrates, and are likely to have been set at the origin of the adaptive immune system of jawed vertebrates, with unrelated genes co-evolving to set up the original pathways. Half a billion years later, various features of presentation and resistance to disease still reflect this ancestral arrangement. Copyright © 2015 Elsevier Ltd. All rights reserved.
Comparative myology of the unicornfishes, Naso (Acanthuridae, Percomorpha), with implications for phylogenetic analysis.

PubMed

Borden, W Calvin

1999-02-01

Striated muscles of 15 species of unicornfishes (Naso, Acanthuridae) are described in detail. Of 93 muscles dissected, only five demonstrate intrageneric variation, providing only ten characters suitable for phylogenetic analysis. Thus, myology appears to be highly conservative at the species level and has been so for approximately 50-55 million years in this particular group of fishes. Furthermore, myology is static relative to osteology in Naso and at any taxonomic rank within fishes, implying osteology provides a larger but not necessarily more valuable data source for systematic studies. Although important for their epistomological value, these descriptions provide a basis for further studies ranging from functional, comparative, and systematic analyses, ultimately with the potential to address questions of historical ecology (i.e., speciation, adaptation, coevolution) within Naso. J. Morphol. 239:191-224, 1999. © 1999 Wiley-Liss, Inc. Copyright © 1999 Wiley-Liss, Inc.
Developmental aspects of the interaction between narcissism, self-esteem and object relations.

PubMed

Dare, C; Holder, A

1981-01-01

This paper reviews the history, within psycho-analysis, of narcissism and shows that it cannot be understood as a unitary concept. This is reflected in much of the extensive literature on the topic. The definition of narcissism solely in terms of the libidinal drive cathexis of the self representation is rejected. Instead, narcissism is defined as the sum of the positively-coloured feeling states attached to the self-representation. By pursuing a developmental investigation of narcissistic and opposing phenomena, the multiple sources which contribute to or detract from the overall level of self-esteem are demonstrated. Such an investigation clarifies the close relationship between the concepts of self-esteem, well-being and narcissism, and differentiating definitions are put forward. The term 'counter-narcissistic' is introduced to denote the negative contributions to self-esteem which detract from the narcissistic input. The interplay between the contributions to the overall quality of self-esteem, deriving on the one hand from somatic and instinctual drive sources, and on the other from object relationships, exemplifies the multiple origins of its qualities at any one time. This interplay is pursued through the sequential developmental phases from infancy to the oedipal level in order to show the complex epigenesis of narcissism, counter-narcissism and self-esteem.
On Budyko curve as a consequence of climate-soil-vegetation equilibrium hypothesis

NASA Astrophysics Data System (ADS)

Pande, S.

2012-04-01

A hypothesis that Budyko curve is a consequence of stable equilibriums of climate-soil-vegetation co-evolution is tested at biome scale. We assume that i) distribution of vegetation, soil and climate within a biome is a distribution of equilibriums of similar soil-vegetation dynamics and that this dynamics is different across different biomes and ii) soil and vegetation are in dynamic equilibrium with climate while in static equilibrium with each other. In order to test the hypothesis, a two stage regression is considered using MOPEX/Hydrologic Synthesis Project dataset for basins in eastern United States. In the first stage, multivariate regression (Seemingly Unrelated Regression) is performed for each biome with soil (estimated porosity and slope of soil water retention curve) and vegetation characteristics (5-week NDVI gradient) as dependent variables and aridity index, vegetation and soil characteristics as independent variables for respective dependent variables. The regression residuals of the first stage along with aridity index then serve as second stage independent variables while actual vaporization to precipitation ratio (vapor index) serving as dependent variable. Insignificance, if revealed, of a first stage parameter allows us to reject the role of corresponding soil or vegetation characteristics in the co-evolution hypothesis. Meanwhile the significance of second stage regression parameter corresponding to a first stage residual allow us to reject the hypothesis that Budyko curve is a locus "solely" of climate-soil-vegetation co-evolution equilibrium points. Results suggest lack of evidence for soil-vegetation co-evolution in Prairies and Mixed/SouthEast Forests (unlike in Deciduous Forests) though climate plays a dominant role in explaining within biome soil and vegetation characteristics across all the biomes. Preliminary results indicate absence of effects beyond climate-soil-vegetation co-evolution in explaining the ratio of annual total minimum monthly flows to precipitation in Deciduous Forests though other three biome types show presence of effects beyond co-evolutionary. Such an analysis can yield insights into the nature of hydrologic change when assessed along the Budyko curve as well as non co-evolutionary effects such as anthropogenic effects on basin scale annual water balances.
Comparative evaluation of shock absorption ability of custom-fit mouthguards with new-generation polyolefin self-adapting mouthguards in three different maxillary anterior teeth alignments using Fiber Bragg Grating (FBG) sensors.

PubMed

Grewal, Navneet; Kumari, Foolan; Tiwari, Umesh

2015-08-01

Prevention of orofacial injuries is one of the biggest pre-occupations in sports dentistry. The custom-fitted mouthguard is considered the best choice for fit and protection when compared to over-the-counter commercial mouthguards. However, cost and time prohibit their mass production. It is therefore imperative to have an over-the-counter true mouth-formed mouthguard with comparable properties. The present in vitro experimental study was carried out to compare the shock absorption ability of EVA laminate mouthguards with self-adapting polyolefin material mouthguards in three different anterior teeth alignments. Finite element analysis (FEA) was performed to simulate the stress distribution due to impact on the respective mouthguards. Customized pendulum device with three interchangeable standard size impact objects was used. Response of grating was monitored using a FBG interrogation system. Shift in wavelength for each impact was measured. Three standardized jaw models were subjected to a total of 72 impact strikes with three different balls on two specified sites by releasing the objects from two different heights H1 24 cm and H2 48 cm. Two-way ANOVA was applied and comparative values computed. It was found that the percentage shock absorption ability of self-adapted polyolefin mouthguard was highly significant at <0.001 level in both regions. The influence of height on the shock absorption ability of both mouthguards was highly significant at P < 0.001. It was concluded that self-adapting polyolefin mouthguards fulfill similar protection requirement as custom-fit mouthguards and can be used for millions of athletes if properly fitted chairside by a dentist without requiring laboratory fabrication. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.
Effectiveness of ProTaper Universal retreatment instruments used with rotary or reciprocating adaptive motion in the removal of root canal filling material.

PubMed

Capar, I D; Arslan, H; Ertas, H; Gök, T; Saygılı, G

2015-01-01

To compare the effectiveness of ProTaper Universal retreatment instruments with continuous rotation and adaptive motion (AM; a modified reciprocating motion that combines rotational and reciprocating motion) in the removal of filling material. Mesiobuccal root canals in 36 mandibular first molars were instrumented up to size F2 with the ProTaper Universal instrument (Dentsply Maillefer, Ballaigues, Switzerland) and filled using sealer and ProTaper Universal F2 gutta-percha cones. Gutta-percha was then down-packed and the root canal backfilled using the extruder hand-piece of the Elements Obturation System (SybronEndo, Orange, CA, USA). The teeth were assigned to two groups (n = 18), and removal of the root fillings was performed using one of the following techniques: group 1) ProTaper Universal retreatment files used with rotational motion (RM) and group 2) ProTaper Universal retreatment files used with adaptive motion (AM) (600° clockwise/0° counter-clockwise to 370° clockwise/50° counter-clockwise). The teeth were sectioned, and both halves were analysed at 8 × magnification. The percentage of remaining filling material was recorded. The data were analysed statistically using the Student's t-test at a 95% confidence level (P < 0.05). There was no significant difference between the groups with respect to the total time required for retreatment (P = 0.481). The AM technique left significantly less filling material than the RM method (P = 0.013). The use of ProTaper Universal retreatment files with adaptive motion removed more filling materials from root canals than the rotational movement. © 2014 International Endodontic Journal. Published by John Wiley & Sons Ltd.
Successful Sequential Liver and Hematopoietic Stem Cell Transplantation in a Child With CD40 Ligand Deficiency and Cryptosporidium-Induced Liver Cirrhosis.

PubMed

Quarello, Paola; Tandoi, Francesco; Carraro, Francesca; Vassallo, Elena; Pinon, Michele; Romagnoli, Renato; David, Ezio; Dell Olio, Dominic; Salizzoni, Mauro; Fagioli, Franca; Calvo, Pier Luigi

2018-05-01

Hematopoietic stem cell transplantation (HSCT) is curative in patients with primary immunodeficiencies. However, pre-HSCT conditioning entails unacceptably high risks if the liver is compromised. The presence of a recurrent opportunistic infection affecting the biliary tree and determining liver cirrhosis with portal hypertension posed particular decisional difficulties in a 7-year-old child with X-linked CD40-ligand deficiency. We aim at adding to the scanty experience available on such rare cases, as successful management with sequential liver transplantation (LT) and HSCT has been reported in detail only in 1 young adult to date. A closely sequential strategy, with a surgical complication-free LT, followed by reduced-intensity conditioning, allowed HSCT to be performed only one month after LT, preventing Cryptosporidium parvum recolonization of the liver graft. Combined sequential LT and HSCT resolved the cirrhotic evolution and corrected the immunodeficiency so that the infection responsible for the progressive sclerosing cholangitis did not recur. Hopefully, this report of the successful resolution of a potentially fatal combination of immunodeficiency and chronic opportunistic infection with end-stage organ damage in a child will encourage others to adapt a sequential transplant approach to this highly complex pathology. However, caution is to be exercised to carefully balance the risks intrinsic to transplant surgery and immunosuppression in primary immunodeficiencies.
Comparison of human embryomorphokinetic parameters in sequential or global culture media.

PubMed

Kazdar, Nadia; Brugnon, Florence; Bouche, Cyril; Jouve, Guilhem; Veau, Ségolène; Drapier, Hortense; Rousseau, Chloé; Pimentel, Céline; Viard, Patricia; Belaud-Rotureau, Marc-Antoine; Ravel, Célia

2017-08-01

A prospective study on randomized patients was conducted to determine how morphokinetic parameters are altered in embryos grown in sequential versus global culture media. Eleven morphokinetic parameters of 160 single embryos transferred were analyzed by time lapse imaging involving two University-affiliated in vitro fertilization (IVF) centers. We found that the fading of the two pronuclei occurred earlier in global (22.56±2.15 hpi) versus sequential media (23.63±2.71 hpi; p=0.0297). Likewise, the first cleavage started earlier at 24.52±2.33 hpi vs 25.76±2.95 hpi (p=0.0158). Also, the first cytokinesis was shorter in global medium, lasting 18±10.2 minutes in global versus 36±37.8 minutes in sequential culture medium (p <0.0001). We also observed a significant shortening in the duration of the 2-cell stage in sequential medium: 10.64 h±2.75 versus 11.66 h±1.11 in global medium (p=0.0225) which suggested a faster progression of the embryos through their first mitotic cell cycle. In conclusion, morphokinetic analysis of human embryos by Time lapse imaging reveals significant differences in five kinetic variables according to culture medium. Our study highlights the need to adapt morphokinetic analysis accordingly to the type of media used to best support human early embryo development.
Amino acid positions subject to multiple coevolutionary constraints can be robustly identified by their eigenvector network centrality scores.

PubMed

Parente, Daniel J; Ray, J Christian J; Swint-Kruse, Liskin

2015-12-01

As proteins evolve, amino acid positions key to protein structure or function are subject to mutational constraints. These positions can be detected by analyzing sequence families for amino acid conservation or for coevolution between pairs of positions. Coevolutionary scores are usually rank-ordered and thresholded to reveal the top pairwise scores, but they also can be treated as weighted networks. Here, we used network analyses to bypass a major complication of coevolution studies: For a given sequence alignment, alternative algorithms usually identify different, top pairwise scores. We reconciled results from five commonly-used, mathematically divergent algorithms (ELSC, McBASC, OMES, SCA, and ZNMI), using the LacI/GalR and 1,6-bisphosphate aldolase protein families as models. Calculations used unthresholded coevolution scores from which column-specific properties such as sequence entropy and random noise were subtracted; "central" positions were identified by calculating various network centrality scores. When compared among algorithms, network centrality methods, particularly eigenvector centrality, showed markedly better agreement than comparisons of the top pairwise scores. Positions with large centrality scores occurred at key structural locations and/or were functionally sensitive to mutations. Further, the top central positions often differed from those with top pairwise coevolution scores: instead of a few strong scores, central positions often had multiple, moderate scores. We conclude that eigenvector centrality calculations reveal a robust evolutionary pattern of constraints-detectable by divergent algorithms--that occur at key protein locations. Finally, we discuss the fact that multiple patterns coexist in evolutionary data that, together, give rise to emergent protein functions. © 2015 Wiley Periodicals, Inc.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Xiaojian; Qiao, Qiao; Department of Radiotherapy, First Hospital of China Medical University, Shenyang

Purpose: To evaluate the efficiency of standard image-guided radiation therapy (IGRT) to account for lumpectomy cavity (LC) variation during whole-breast irradiation (WBI) and propose an adaptive strategy to improve dosimetry if IGRT fails to address the interfraction LC variations. Methods and Materials: Daily diagnostic-quality CT data acquired during IGRT in the boost stage using an in-room CT for 19 breast cancer patients treated with sequential boost after WBI in the prone position were retrospectively analyzed. Contours of the LC, treated breast, ipsilateral lung, and heart were generated by populating contours from planning CTs to boost fraction CTs using an auto-segmentationmore » tool with manual editing. Three plans were generated on each fraction CT: (1) a repositioning plan by applying the original boost plan with the shift determined by IGRT; (2) an adaptive plan by modifying the original plan according to a fraction CT; and (3) a reoptimization plan by a full-scale optimization. Results: Significant variations were observed in LC. The change in LC volume at the first boost fraction ranged from a 70% decrease to a 50% increase of that on the planning CT. The adaptive and reoptimization plans were comparable. Compared with the repositioning plans, the adaptive plans led to an improvement in target coverage for an increased LC case (1 of 19, 7.5% increase in planning target volume evaluation volume V{sub 95%}), and breast tissue sparing for an LC decrease larger than 35% (3 of 19, 7.5% decrease in breast evaluation volume V{sub 50%}; P=.008). Conclusion: Significant changes in LC shape and volume at the time of boost that deviate from the original plan for WBI with sequential boost can be addressed by adaptive replanning at the first boost fraction.« less
History of antibiotic adaptation influences microbial evolutionary dynamics during subsequent treatment

PubMed Central

Papin, Jason A.

2017-01-01

Antibiotic regimens often include the sequential changing of drugs to limit the development and evolution of resistance of bacterial pathogens. It remains unclear how history of adaptation to one antibiotic can influence the resistance profiles when bacteria subsequently adapt to a different antibiotic. Here, we experimentally evolved Pseudomonas aeruginosa to six 2-drug sequences. We observed drug order–specific effects, whereby adaptation to the first drug can limit the rate of subsequent adaptation to the second drug, adaptation to the second drug can restore susceptibility to the first drug, or final resistance levels depend on the order of the 2-drug sequence. These findings demonstrate how resistance not only depends on the current drug regimen but also the history of past regimens. These order-specific effects may allow for rational forecasting of the evolutionary dynamics of bacteria given knowledge of past adaptations and provide support for the need to consider the history of past drug exposure when designing strategies to mitigate resistance and combat bacterial infections. PMID:28792497
Impact of Load Balancing on Unstructured Adaptive Grid Computations for Distributed-Memory Multiprocessors

NASA Technical Reports Server (NTRS)

Sohn, Andrew; Biswas, Rupak; Simon, Horst D.

1996-01-01

The computational requirements for an adaptive solution of unsteady problems change as the simulation progresses. This causes workload imbalance among processors on a parallel machine which, in turn, requires significant data movement at runtime. We present a new dynamic load-balancing framework, called JOVE, that balances the workload across all processors with a global view. Whenever the computational mesh is adapted, JOVE is activated to eliminate the load imbalance. JOVE has been implemented on an IBM SP2 distributed-memory machine in MPI for portability. Experimental results for two model meshes demonstrate that mesh adaption with load balancing gives more than a sixfold improvement over one without load balancing. We also show that JOVE gives a 24-fold speedup on 64 processors compared to sequential execution.
Endophytic Epichloë species and their grass hosts: from evolution to applications.

PubMed

Saikkonen, Kari; Young, Carolyn A; Helander, Marjo; Schardl, Christopher L

2016-04-01

The closely linked fitness of the Epichloë symbiont and the host grass is presumed to align the coevolution of the species towards specialization and mutually beneficial cooperation. Ecological observations demonstrating that Epichloë-grass symbioses can modulate grassland ecosystems via both above- and belowground ecosystem processes support this. In many cases the detected ecological importance of Epichloë species is directly or indirectly linked to defensive mutualism attributable to alkaloids of fungal-origin. Now, modern genetic and molecular techniques enable the precise studies on evolutionary origin of endophytic Epichloë species, their coevolution with host grasses and identification the genetic variation that explains phenotypic diversity in ecologically relevant characteristics of Epichloë-grass associations. Here we briefly review the most recent findings in these areas of research using the present knowledge of the genetic variation that explains the biosynthetic pathways driving the diversity of alkaloids produced by the endophyte. These findings underscore the importance of genetic interplay between the fungus and the host in shaping their coevolution and ecological role in both natural grass ecosystems, and in the agricultural arena.
Sequence, structure and function relationships in flaviviruses as assessed by evolutive aspects of its conserved non-structural protein domains.

PubMed

da Fonseca, Néli José; Lima Afonso, Marcelo Querino; Pedersolli, Natan Gonçalves; de Oliveira, Lucas Carrijo; Andrade, Dhiego Souto; Bleicher, Lucas

2017-10-28

Flaviviruses are responsible for serious diseases such as dengue, yellow fever, and zika fever. Their genomes encode a polyprotein which, after cleavage, results in three structural and seven non-structural proteins. Homologous proteins can be studied by conservation and coevolution analysis as detected in multiple sequence alignments, usually reporting positions which are strictly necessary for the structure and/or function of all members in a protein family or which are involved in a specific sub-class feature requiring the coevolution of residue sets. This study provides a complete conservation and coevolution analysis on all flaviviruses non-structural proteins, with results mapped on all well-annotated available sequences. A literature review on the residues found in the analysis enabled us to compile available information on their roles and distribution among different flaviviruses. Also, we provide the mapping of conserved and coevolved residues for all sequences currently in SwissProt as a supplementary material, so that particularities in different viruses can be easily analyzed. Copyright © 2017 Elsevier Inc. All rights reserved.

Cooperation enhanced by the coevolution of teaching activity in evolutionary prisoner's dilemma games with voluntary participation.

PubMed

Shen, Chen; Chu, Chen; Geng, Yini; Jin, Jiahua; Chen, Fei; Shi, Lei

2018-01-01

Voluntary participation, as an additional strategy involved in repeated games, has been proved to be an efficient way to promote the evolution of cooperation theoretically and empirically. Besides, current studies show that the coevolution of teaching activity can promote cooperation. Thus, inspired by aforementioned above, we investigate the effect of coevolution of teaching activity on the evolution of cooperation for prisoner's dilemma game with voluntary participation: when the focal player successfully enforces its strategy on the opponent, his teaching ability will get an increase. Through numerical simulation, we have shown that voluntary participation could effectively promote the fraction of cooperation, which is also affected by the value of increment. Furthermore, we investigate the influence of the increment value on the density of different strategies and find that there exists an optimal increment value that plays an utmost role on the evolutionary dynamics. With regard to this observation, we unveil that an optimal value of increment can lead to strongest heterogeneity in agents' teaching ability, further promoting the evolution of cooperation.
Vocal Generalization Depends on Gesture Identity and Sequence

PubMed Central

Sober, Samuel J.

2014-01-01

Generalization, the brain's ability to transfer motor learning from one context to another, occurs in a wide range of complex behaviors. However, the rules of generalization in vocal behavior are poorly understood, and it is unknown how vocal learning generalizes across an animal's entire repertoire of natural vocalizations and sequences. Here, we asked whether generalization occurs in a nonhuman vocal learner and quantified its properties. We hypothesized that adaptive error correction of a vocal gesture produced in one sequence would generalize to the same gesture produced in other sequences. To test our hypothesis, we manipulated the fundamental frequency (pitch) of auditory feedback in Bengalese finches (Lonchura striata var. domestica) to create sensory errors during vocal gestures (song syllables) produced in particular sequences. As hypothesized, error-corrective learning on pitch-shifted vocal gestures generalized to the same gestures produced in other sequential contexts. Surprisingly, generalization magnitude depended strongly on sequential distance from the pitch-shifted syllables, with greater adaptation for gestures produced near to the pitch-shifted syllable. A further unexpected result was that nonshifted syllables changed their pitch in the direction opposite from the shifted syllables. This apparently antiadaptive pattern of generalization could not be explained by correlations between generalization and the acoustic similarity to the pitch-shifted syllable. These findings therefore suggest that generalization depends on the type of vocal gesture and its sequential context relative to other gestures and may reflect an advantageous strategy for vocal learning and maintenance. PMID:24741046
Adaptive sequential Bayesian classification using Page's test

NASA Astrophysics Data System (ADS)

Lynch, Robert S., Jr.; Willett, Peter K.

2002-03-01

In this paper, the previously introduced Mean-Field Bayesian Data Reduction Algorithm is extended for adaptive sequential hypothesis testing utilizing Page's test. In general, Page's test is well understood as a method of detecting a permanent change in distribution associated with a sequence of observations. However, the relationship between detecting a change in distribution utilizing Page's test with that of classification and feature fusion is not well understood. Thus, the contribution of this work is based on developing a method of classifying an unlabeled vector of fused features (i.e., detect a change to an active statistical state) as quickly as possible given an acceptable mean time between false alerts. In this case, the developed classification test can be thought of as equivalent to performing a sequential probability ratio test repeatedly until a class is decided, with the lower log-threshold of each test being set to zero and the upper log-threshold being determined by the expected distance between false alerts. It is of interest to estimate the delay (or, related stopping time) to a classification decision (the number of time samples it takes to classify the target), and the mean time between false alerts, as a function of feature selection and fusion by the Mean-Field Bayesian Data Reduction Algorithm. Results are demonstrated by plotting the delay to declaring the target class versus the mean time between false alerts, and are shown using both different numbers of simulated training data and different numbers of relevant features for each class.
The interference effects of non-rotated versus counter-rotated trials in visuomotor adaptation.

PubMed

Hinder, Mark R; Walk, Laura; Woolley, Daniel G; Riek, Stephan; Carson, Richard G

2007-07-01

An isometric torque-production task was used to investigate interference and retention in adaptation to multiple visuomotor environments. Subjects produced isometric flexion-extension and pronation-supination elbow torques to move a cursor to acquire targets as quickly as possible. Adaptation to a 30 degrees counter-clockwise (CCW) rotation (task A), was followed by a period of rest (control), trials with no rotation (task B0), or trials with a 60 degrees clockwise (CW) rotation (task B60). For all groups, retention of task A was assessed 5 h later. With initial training, all groups reduced the angular deviation of cursor paths early in the movements, indicating feedforward adaptation. For the control group, performance at commencement of the retest was significantly better than that at the beginning of the initial learning. For the B0 group, performance in the retest of task A was not dissimilar to that at the start of the initial learning, while for the B60 group retest performance in task A was markedly worse than initially observed. Our results indicate that close juxtaposition of two visuomotor environments precludes improved retest performance in the initial environment. Data for the B60 group, specifically larger angular errors upon retest compared with initial exposures, are consistent with the presence of anterograde interference. Furthermore, full interference occurred even when the visuomotor environment encountered in the second task was not rotated (B0). This latter novel result differs from those obtained for force field learning, where interference does not occur when task B does not impose perturbing forces, i.e., when B consists of a null field (Brashers-Krug et al., Nature 382:252-255, 1996). The results are consistent with recent proposals suggesting different interference mechanisms for visuomotor (kinematic) compared to force field (dynamic) adaptations, and have implications for the use of washout trials when studying interference between multiple visuomotor environments.
Dissociating Perception from Action during Conscious and Unconscious Conflict Adaptation

ERIC Educational Resources Information Center

Atas, Anne; Desender, Kobe; Gevers, Wim; Cleeremans, Axel

2016-01-01

The detection of a conflict between relevant and irrelevant information on a given trial typically results in a smaller conflict effect on the next trial. This sequential effect has been interpreted as an expression of cognitive control implemented to resolve conflict. In this context, 2 different but related issues have received increasing…
Topology optimization of induction heating model using sequential linear programming based on move limit with adaptive relaxation

NASA Astrophysics Data System (ADS)

Masuda, Hiroshi; Kanda, Yutaro; Okamoto, Yoshifumi; Hirono, Kazuki; Hoshino, Reona; Wakao, Shinji; Tsuburaya, Tomonori

2017-12-01

It is very important to design electrical machineries with high efficiency from the point of view of saving energy. Therefore, topology optimization (TO) is occasionally used as a design method for improving the performance of electrical machinery under the reasonable constraints. Because TO can achieve a design with much higher degree of freedom in terms of structure, there is a possibility for deriving the novel structure which would be quite different from the conventional structure. In this paper, topology optimization using sequential linear programming using move limit based on adaptive relaxation is applied to two models. The magnetic shielding, in which there are many local minima, is firstly employed as firstly benchmarking for the performance evaluation among several mathematical programming methods. Secondly, induction heating model is defined in 2-D axisymmetric field. In this model, the magnetic energy stored in the magnetic body is maximized under the constraint on the volume of magnetic body. Furthermore, the influence of the location of the design domain on the solutions is investigated.
CONTINUOUS DISSOLVER EXTRACTOR FOR PROCESSING METAL

DOEpatents

Lemon, R.B.; Buckham, J.A.

1959-02-01

An apparatus is presented for the continuous dissolution of metal slugs in an aqueous acid and sequential continuous extraction of selected metal values from the acid solution by counter-current contact with an organic solvent. The apparatus comprises a cylindrical tank divided into upper and lower sections. Dissolution of the metal slug takes place in the lower section and the solution so produced is continuously fed to the topmost plate of the upper extraction section. An immiscible organic extractant is continuously passed by a pulsing pump into the lowermost unit of the extraction section. Suitable piping and valving permits of removing the aqueous raffinate solution from the lowermost portion of the extraction section, and simultaneous removal of organic solvent extractant containing the desired product from the uppermost portion of the extraction section.
Accounting for sequential trial effects in the flanker task: conflict adaptation or associative priming?

PubMed

Nieuwenhuis, Sander; Stins, John F; Posthuma, Danielle; Polderman, Tinca J C; Boomsma, Dorret I; de Geus, Eco J

2006-09-01

The conflict-control loop theory proposes that the detection of conflict in information processing triggers an increase in cognitive control, resulting in improved performance on the subsequent trial. This theory seems consistent with the robust finding that conflict susceptibility is reduced following correct trials associated with high conflict: the conflict adaptation effect. However, despite providing favorable conditions for eliciting and detecting conflict-triggered performance adjustments, none of the five experiments reported here provide unequivocal evidence of such adjustments. Instead, the results corroborate and extend earlier findings by demonstrating that the conflict adaptation effect, at least in the flanker task, is only present for a specific subset of trial sequences that is characterized by a response repetition. This pattern of results provides strong evidence that the conflict adaptation effect reflects associative stimulus-response priming instead of conflict-driven adaptations in cognitive control.
A “SMART” Design for Building Individualized Treatment Sequences

PubMed Central

Lei, H.; Nahum-Shani, I.; Lynch, K.; Oslin, D.; Murphy, S.A.

2013-01-01

Interventions often involve a sequence of decisions. For example, clinicians frequently adapt the intervention to an individual’s outcomes. Altering the intensity and type of intervention over time is crucial for many reasons, such as to obtain improvement if the individual is not responding or to reduce costs and burden when intensive treatment is no longer necessary. Adaptive interventions utilize individual variables (severity, preferences) to adapt the intervention and then dynamically utilize individual outcomes (response to treatment, adherence) to readapt the intervention. The Sequential Multiple Assignment Randomized Trial (SMART)provides high-quality data that can be used to construct adaptive interventions. We review the SMART and highlight its advantages in constructing and revising adaptive interventions as compared to alternative experimental designs. Selected examples of SMART studies are described and compared. A data analysis method is provided and illustrated using data from the Extending Treatment Effectiveness of Naltrexone SMART study. PMID:22224838
Pulmonary function adaptation to ozone in subjects with chronic bronchitis

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

Kulle, T.J.; Milman, J.H.; Sauder, L.R.

Twenty smokers with chronic bronchitis were exposed to 0.41 ppm ozone for 3 hr-day for 5 consecutive days and reexposed 4 days later to determine (1) if they are sensitive to ozone, (2) if they adapt, and (3) if the adaptation lasts longer than 4 days. There were significant decrements in forced vital capacity (FVC) and forced expiratory volume in 3 sec (FEV/sub 3/) on the first day of the 5-day repeated exposures and also on reexposure 4 days following cessation of the sequential exposures. Symptoms experienced were mild and did not predominate on any exposure days. These results suggestmore » that individuals with chronic bronchitis adapt rapidly to ozone and lose this adaptive phenomenon within 4 days. The small decreases seen in FVC and FEV/sub 3/ ( less than or equal to 3%) appear to impose no more than minimal limitations on their daily activities.« less
Pulmonary function adaptation to ozone in subjects with chronic bronchitis

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

Kulle, T.J.; Milman, J.H.; Sauder, L.R.

Twenty smokers with chronic bronchitis were exposed to 0.41 ppm ozone for 3 hr-day for 5 consecutive days and reexposed 4 days later to determine (1) if they are sensitive to ozone, (2) if they adapt, and (3) if the adaptation lasts longer than 4 days. There were significant decrements in forced vital capacity (FVC) and forced expiratory volume in 3 sec (FEV3) on the first day of the 5-day repeated exposures and also on reexposure 4 days following cessation of the sequential exposures. Symptoms experienced were mild and did not predominate on any exposure days. These results suggest thatmore » individuals with chronic bronchitis adapt rapidly to ozone and lose the adaptive phenomenon within 4 days. The small decreases seen in FVC and FEV3 appear to impose no more than minimal limitations on their daily activities.« less
PLANNING AND RESPONSE IN THE AFTERMATH OF A LARGE CRISIS: AN AGENT-BASED INFORMATICS FRAMEWORK*

PubMed Central

Barrett, Christopher; Bisset, Keith; Chandan, Shridhar; Chen, Jiangzhuo; Chungbaek, Youngyun; Eubank, Stephen; Evrenosoğlu, Yaman; Lewis, Bryan; Lum, Kristian; Marathe, Achla; Marathe, Madhav; Mortveit, Henning; Parikh, Nidhi; Phadke, Arun; Reed, Jeffrey; Rivers, Caitlin; Saha, Sudip; Stretz, Paula; Swarup, Samarth; Thorp, James; Vullikanti, Anil; Xie, Dawen

2014-01-01

We present a synthetic information and modeling environment that can allow policy makers to study various counter-factual experiments in the event of a large human-initiated crisis. The specific scenario we consider is a ground detonation caused by an improvised nuclear device in a large urban region. In contrast to earlier work in this area that focuses largely on the prompt effects on human health and injury, we focus on co-evolution of individual and collective behavior and its interaction with the differentially damaged infrastructure. This allows us to study short term secondary and tertiary effects. The present environment is suitable for studying the dynamical outcomes over a two week period after the initial blast. A novel computing and data processing architecture is described; the architecture allows us to represent multiple co-evolving infrastructures and social networks at a highly resolved temporal, spatial, and individual scale. The representation allows us to study the emergent behavior of individuals as well as specific strategies to reduce casualties and injuries that exploit the spatial and temporal nature of the secondary and tertiary effects. A number of important conclusions are obtained using the modeling environment. For example, the studies decisively show that deploying ad hoc communication networks to reach individuals in the affected area is likely to have a significant impact on the overall casualties and injuries. PMID:25580055
PLANNING AND RESPONSE IN THE AFTERMATH OF A LARGE CRISIS: AN AGENT-BASED INFORMATICS FRAMEWORK*

PubMed

Barrett, Christopher; Bisset, Keith; Chandan, Shridhar; Chen, Jiangzhuo; Chungbaek, Youngyun; Eubank, Stephen; Evrenosoğlu, Yaman; Lewis, Bryan; Lum, Kristian; Marathe, Achla; Marathe, Madhav; Mortveit, Henning; Parikh, Nidhi; Phadke, Arun; Reed, Jeffrey; Rivers, Caitlin; Saha, Sudip; Stretz, Paula; Swarup, Samarth; Thorp, James; Vullikanti, Anil; Xie, Dawen

2013-01-01

We present a synthetic information and modeling environment that can allow policy makers to study various counter-factual experiments in the event of a large human-initiated crisis. The specific scenario we consider is a ground detonation caused by an improvised nuclear device in a large urban region. In contrast to earlier work in this area that focuses largely on the prompt effects on human health and injury, we focus on co-evolution of individual and collective behavior and its interaction with the differentially damaged infrastructure. This allows us to study short term secondary and tertiary effects. The present environment is suitable for studying the dynamical outcomes over a two week period after the initial blast. A novel computing and data processing architecture is described; the architecture allows us to represent multiple co-evolving infrastructures and social networks at a highly resolved temporal, spatial, and individual scale. The representation allows us to study the emergent behavior of individuals as well as specific strategies to reduce casualties and injuries that exploit the spatial and temporal nature of the secondary and tertiary effects. A number of important conclusions are obtained using the modeling environment. For example, the studies decisively show that deploying ad hoc communication networks to reach individuals in the affected area is likely to have a significant impact on the overall casualties and injuries.
Question 6: coevolution theory of the genetic code: a proven theory.

PubMed

Wong, Jeffrey Tze-Fei

2007-10-01

The coevolution theory proposes that primordial proteins consisted only of those amino acids readily obtainable from the prebiotic environment, representing about half the twenty encoded amino acids of today, and the missing amino acids entered the system as the code expanded along with pathways of amino acid biosynthesis. The isolation of genetic code mutants, and the antiquity of pretran synthesis revealed by the comparative genomics of tRNAs and aminoacyl-tRNA synthetases, have combined to provide a rigorous proof of the four fundamental tenets of the theory, thus solving the riddle of the structure of the universal genetic code.
Computational aspects of helicopter trim analysis and damping levels from Floquet theory

NASA Technical Reports Server (NTRS)

Gaonkar, Gopal H.; Achar, N. S.

1992-01-01

Helicopter trim settings of periodic initial state and control inputs are investigated for convergence of Newton iteration in computing the settings sequentially and in parallel. The trim analysis uses a shooting method and a weak version of two temporal finite element methods with displacement formulation and with mixed formulation of displacements and momenta. These three methods broadly represent two main approaches of trim analysis: adaptation of initial-value and finite element boundary-value codes to periodic boundary conditions, particularly for unstable and marginally stable systems. In each method, both the sequential and in-parallel schemes are used and the resulting nonlinear algebraic equations are solved by damped Newton iteration with an optimally selected damping parameter. The impact of damped Newton iteration, including earlier-observed divergence problems in trim analysis, is demonstrated by the maximum condition number of the Jacobian matrices of the iterative scheme and by virtual elimination of divergence. The advantages of the in-parallel scheme over the conventional sequential scheme are also demonstrated.
Sequential segmental classification of feline congenital heart disease.

PubMed

Scansen, Brian A; Schneider, Matthias; Bonagura, John D

2015-12-01

Feline congenital heart disease is less commonly encountered in veterinary medicine than acquired feline heart diseases such as cardiomyopathy. Understanding the wide spectrum of congenital cardiovascular disease demands a familiarity with a variety of lesions, occurring both in isolation and in combination, along with an appreciation of complex nomenclature and variable classification schemes. This review begins with an overview of congenital heart disease in the cat, including proposed etiologies and prevalence, examination approaches, and principles of therapy. Specific congenital defects are presented and organized by a sequential segmental classification with respect to their morphologic lesions. Highlights of diagnosis, treatment options, and prognosis are offered. It is hoped that this review will provide a framework for approaching congenital heart disease in the cat, and more broadly in other animal species based on the sequential segmental approach, which represents an adaptation of the common methodology used in children and adults with congenital heart disease. Copyright © 2015 Elsevier B.V. All rights reserved.
Use of personalized Dynamic Treatment Regimes (DTRs) and Sequential Multiple Assignment Randomized Trials (SMARTs) in mental health studies

PubMed Central

Liu, Ying; ZENG, Donglin; WANG, Yuanjia

2014-01-01

Summary Dynamic treatment regimens (DTRs) are sequential decision rules tailored at each point where a clinical decision is made based on each patient’s time-varying characteristics and intermediate outcomes observed at earlier points in time. The complexity, patient heterogeneity, and chronicity of mental disorders call for learning optimal DTRs to dynamically adapt treatment to an individual’s response over time. The Sequential Multiple Assignment Randomized Trial (SMARTs) design allows for estimating causal effects of DTRs. Modern statistical tools have been developed to optimize DTRs based on personalized variables and intermediate outcomes using rich data collected from SMARTs; these statistical methods can also be used to recommend tailoring variables for designing future SMART studies. This paper introduces DTRs and SMARTs using two examples in mental health studies, discusses two machine learning methods for estimating optimal DTR from SMARTs data, and demonstrates the performance of the statistical methods using simulated data. PMID:25642116
Sequential ChIP Protocol for Profiling Bivalent Epigenetic Modifications (ReChIP).

PubMed

Desvoyes, Bénédicte; Sequeira-Mendes, Joana; Vergara, Zaida; Madeira, Sofia; Gutierrez, Crisanto

2018-01-01

Identification of chromatin modifications, e.g., histone acetylation and methylation, among others, is widely carried out by using a chromatin immunoprecipitation (ChIP) strategy. The information obtained with these procedures is useful to gain an overall picture of modifications present in all cells of the population under study. It also serves as a basis to figure out the mechanisms of chromatin organization and gene regulation at the population level. However, the ultimate goal is to understand gene regulation at the level of single chromatin fibers. This requires the identification of chromatin modifications that occur at a given genomic location and within the same chromatin fiber. This is achieved by following a sequential ChIP strategy using two antibodies to distinguish different chromatin modifications. Here, we describe a sequential ChIP protocol (Re-ChIP), paying special attention to the controls needed and the required steps to obtain meaningful and reproducible results. The protocol is developed for young Arabidopsis seedlings but could be adapted to other plant materials.
Low dimensional temporal organization of spontaneous eye blinks in adults with developmental disabilities and stereotyped movement disorder.

PubMed

Lee, Mei-Hua; Bodfish, James W; Lewis, Mark H; Newell, Karl M

2010-01-01

This study investigated the mean rate and time-dependent sequential organization of spontaneous eye blinks in adults with intellectual and developmental disability (IDD) and individuals from this group who were additionally categorized with stereotypic movement disorder (IDD+SMD). The mean blink rate was lower in the IDD+SMD group than the IDD group and both of these groups had a lower blink rate than a contrast group of healthy adults. In the IDD group the n to n+1 sequential organization over time of the eye-blink durations showed a stronger compensatory organization than the contrast group suggesting decreased complexity/dimensionality of eye-blink behavior. Very low blink rate (and thus insufficient time series data) precluded analysis of time-dependent sequential properties in the IDD+SMD group. These findings support the hypothesis that both IDD and SMD are associated with a reduction in the dimension and adaptability of movement behavior and that this may serve as a risk factor for the expression of abnormal movements.
Organizing Chaos: The Tactical Assault Kit Collaborative Mission Planner

DTIC Science & Technology

2018-12-01

choice. Case studies , such as the 2017 Presidential Inauguration Collective Security Event, Operation Flaming Sword 2017, and the counter-ISIS campaign...rallied around the Tactical Assault Kit (TAK) as their mission command tool of choice. Case studies , such as the 2017 Presidential Inauguration...authorities ADA Air Defense Artillery ADM Army Design Methodology ADAPT Advanced Digital Advisor Partner Technologies ATAK Android Tactical Assault Kit

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