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Sample records for adaptive natural density

  1. Natural pedagogy as evolutionary adaptation

    PubMed Central

    Csibra, Gergely; Gergely, György

    2011-01-01

    We propose that the cognitive mechanisms that enable the transmission of cultural knowledge by communication between individuals constitute a system of ‘natural pedagogy’ in humans, and represent an evolutionary adaptation along the hominin lineage. We discuss three kinds of arguments that support this hypothesis. First, natural pedagogy is likely to be human-specific: while social learning and communication are both widespread in non-human animals, we know of no example of social learning by communication in any other species apart from humans. Second, natural pedagogy is universal: despite the huge variability in child-rearing practices, all human cultures rely on communication to transmit to novices a variety of different types of cultural knowledge, including information about artefact kinds, conventional behaviours, arbitrary referential symbols, cognitively opaque skills and know-how embedded in means-end actions. Third, the data available on early hominin technological culture are more compatible with the assumption that natural pedagogy was an independently selected adaptive cognitive system than considering it as a by-product of some other human-specific adaptation, such as language. By providing a qualitatively new type of social learning mechanism, natural pedagogy is not only the product but also one of the sources of the rich cultural heritage of our species. PMID:21357237

  2. Electron density measurements for plasma adaptive optics

    NASA Astrophysics Data System (ADS)

    Neiswander, Brian W.

    Over the past 40 years, there has been growing interest in both laser communications and directed energy weapons that operate from moving aircraft. As a laser beam propagates from an aircraft in flight, it passes through boundary layers, turbulence, and shear layers in the near-region of the aircraft. These fluid instabilities cause strong density gradients which adversely affect the transmission of laser energy to a target. Adaptive optics provides corrective measures for this problem but current technology cannot respond quickly enough to be useful for high speed flight conditions. This research investigated the use of plasma as a medium for adaptive optics for aero-optics applications. When a laser beam passes through plasma, its phase is shifted proportionally to the electron density and gas heating within the plasma. As a result, plasma can be utilized as a dynamically controllable optical medium. Experiments were carried out using a cylindrical dielectric barrier discharge plasma chamber which generated a sub-atmospheric pressure, low-temperature plasma. An electrostatic model of this design was developed and revealed an important design constraint relating to the geometry of the chamber. Optical diagnostic techniques were used to characterize the plasma discharge. Single-wavelength interferometric experiments were performed and demonstrated up to 1.5 microns of optical path difference (OPD) in a 633 nm laser beam. Dual-wavelength interferometry was used to obtain time-resolved profiles of the plasma electron density and gas heating inside the plasma chamber. Furthermore, a new multi-wavelength infrared diagnostic technique was developed and proof-of-concept simulations were conducted to demonstrate the system's capabilities.

  3. Adaptive governance, ecosystem management, and natural capital.

    PubMed

    Schultz, Lisen; Folke, Carl; Österblom, Henrik; Olsson, Per

    2015-06-16

    To gain insights into the effects of adaptive governance on natural capital, we compare three well-studied initiatives; a landscape in Southern Sweden, the Great Barrier Reef in Australia, and fisheries in the Southern Ocean. We assess changes in natural capital and ecosystem services related to these social-ecological governance approaches to ecosystem management and investigate their capacity to respond to change and new challenges. The adaptive governance initiatives are compared with other efforts aimed at conservation and sustainable use of natural capital: Natura 2000 in Europe, lobster fisheries in the Gulf of Maine, North America, and fisheries in Europe. In contrast to these efforts, we found that the adaptive governance cases developed capacity to perform ecosystem management, manage multiple ecosystem services, and monitor, communicate, and respond to ecosystem-wide changes at landscape and seascape levels with visible effects on natural capital. They enabled actors to collaborate across diverse interests, sectors, and institutional arrangements and detect opportunities and problems as they developed while nurturing adaptive capacity to deal with them. They all spanned local to international levels of decision making, thus representing multilevel governance systems for managing natural capital. As with any governance system, internal changes and external drivers of global impacts and demands will continue to challenge the long-term success of such initiatives. PMID:26082542

  4. Adaptive governance, ecosystem management, and natural capital

    PubMed Central

    Schultz, Lisen; Folke, Carl; Österblom, Henrik; Olsson, Per

    2015-01-01

    To gain insights into the effects of adaptive governance on natural capital, we compare three well-studied initiatives; a landscape in Southern Sweden, the Great Barrier Reef in Australia, and fisheries in the Southern Ocean. We assess changes in natural capital and ecosystem services related to these social–ecological governance approaches to ecosystem management and investigate their capacity to respond to change and new challenges. The adaptive governance initiatives are compared with other efforts aimed at conservation and sustainable use of natural capital: Natura 2000 in Europe, lobster fisheries in the Gulf of Maine, North America, and fisheries in Europe. In contrast to these efforts, we found that the adaptive governance cases developed capacity to perform ecosystem management, manage multiple ecosystem services, and monitor, communicate, and respond to ecosystem-wide changes at landscape and seascape levels with visible effects on natural capital. They enabled actors to collaborate across diverse interests, sectors, and institutional arrangements and detect opportunities and problems as they developed while nurturing adaptive capacity to deal with them. They all spanned local to international levels of decision making, thus representing multilevel governance systems for managing natural capital. As with any governance system, internal changes and external drivers of global impacts and demands will continue to challenge the long-term success of such initiatives. PMID:26082542

  5. Adapting overcomplete wavelet models to natural images

    NASA Astrophysics Data System (ADS)

    Sallee, Phil; Olshausen, Bruno A.

    2003-11-01

    Overcomplete wavelet representations have become increasingly popular for their ability to provide highly sparse and robust descriptions of natural signals. We describe a method for incorporating an overcomplete wavelet representation as part of a statistical model of images which includes a sparse prior distribution over the wavelet coefficients. The wavelet basis functions are parameterized by a small set of 2-D functions. These functions are adapted to maximize the average log-likelihood of the model for a large database of natural images. When adapted to natural images, these functions become selective to different spatial orientations, and they achieve a superior degree of sparsity on natural images as compared with traditional wavelet bases. The learned basis is similar to the Steerable Pyramid basis, and yields slightly higher SNR for the same number of active coefficients. Inference with the learned model is demonstrated for applications such as denoising, with results that compare favorably with other methods.

  6. Expression and purification of soluble and stable ectodomain of natural killer cell receptor LLT1 through high-density transfection of suspension adapted HEK293S GnTI(-) cells.

    PubMed

    Bláha, Jan; Pachl, Petr; Novák, Petr; Vaněk, Ondřej

    2015-05-01

    Lectin-like transcript 1 (LLT1, gene clec2d) was identified to be a ligand for the single human NKR-P1 receptor present on NK and NK-T lymphocytes. Naturally, LLT1 is expressed on the surface of NK cells, stimulating IFN-γ production, and is up-regulated upon activation of other immune cells, e.g. TLR-stimulated dendritic cells and B cells or T cell receptor-activated T cells. While in normal tissues LLT1:NKR-P1 interaction (representing an alternative "missing-self" recognition system) play an immunomodulatory role in regulation of crosstalk between NK and antigen presenting cells, LLT1 is upregulated in glioblastoma cells, one of the most lethal tumors, where it acts as a mediator of immune escape of glioma cells. Here we report transient expression and characterization of soluble His176Cys mutant of LLT1 ectodomain in an eukaryotic expression system of human suspension-adapted HEK293S GnTI(-) cell line with uniform N-glycans. The His176Cys mutation is critical for C-type lectin-like domain stability, leading to the reconstruction of third canonical disulfide bridge in LLT1, as shown by mass spectrometry. Purified soluble LLT1 is homogeneous, deglycosylatable and forms a non-covalent homodimer whose dimerization is not dependent on presence of its N-glycans. As a part of production of soluble LLT1, we have adapted HEK293S GnTI(-) cell line to growth in suspension in media facilitating transient transfection and optimized novel high cell density transfection protocol, greatly enhancing protein yields. This transfection protocol is generally applicable for protein production within this cell line, especially for protein crystallography. PMID:25623399

  7. Effect of adaptation and pulp density on bioleaching of mine waste using indigenous acidophilic bacteria

    NASA Astrophysics Data System (ADS)

    Cho, K.; Kim, B.; Lee, D.; Choi, N.; Park, C.

    2011-12-01

    Adaptation to environment is a natural phenomena that takes place in many animals, plants and microorganisms. These adapted organisms achieve stronger applicability than unadapted organisms after habitation in a specific environment for a long time. In the biohydrometallurgical industry, adaptation to special environment conditions by selective culturing is the most popular method for improving bioleaching activity of strains-although that is time consuming. This study investigated the influence of the bioleaching efficiency of mine waste under batch experimental conditions (adaptation and pulp density) using the indigenous acidophilic bacteria collected from acid mine drainage in Go-seong and Yeon-hwa, Korea. We conducted the batch experiments at the influences of parameters, such as the adaptation of bacteria and pulp density of the mine waste. In the adaptation case, the value of pH in 1'st adaptation bacteria sample exhibited lower than in 2'nd adaptation bacteria sample. And the content of both Cu and Zn at 1'st adaptation bacteria sample appeared lower than at 2'nd adaptation bacteria sample. In the SEM analysis, the rod-shaped bacteria with 1μm in length were observed on the filter paper (pore size - 0.45μm). The results of pulp density experiments revealed that the content of both Cu and Zn increased with increasing pulp density, since the increment of pulp density resulted in the enhancement of bioleaching capacity.

  8. Climate adaptation strategy for natural resources released

    NASA Astrophysics Data System (ADS)

    Showstack, Randy

    2013-04-01

    The National Fish, Wildlife, and Plants Climate Adaptation Strategy, released on 26 March by the Obama administration, calls for a series of measures to help public and private decision makers better address the effects of climate change on living natural resources. The measures include conserving habitat to support healthy fish, wildlife, and plant populations and ecosystem functions; managing species and habitats to protect ecosystem functions and provide sustainable commercial, subsistence, recreational, and cultural use; increasing knowledge and information about effects on and responses of fish, wildlife, and plants; and reducing nonclimate stressors to help fish, wildlife, plants, and ecosystems adapt.

  9. A Biologically Inspired Self-Adaptation of Replica Density Control

    NASA Astrophysics Data System (ADS)

    Izumi, Tomoko; Izumi, Taisuke; Ooshita, Fukuhito; Kakugawa, Hirotsugu; Masuzawa, Toshimitsu

    Biologically-inspired approaches are one of the most promising approaches to realize highly-adaptive distributed systems. Biological systems inherently have self-* properties, such as self-stabilization, self-adaptation, self-configuration, self-optimization and self-healing. Thus, the application of biological systems into distributed systems has attracted a lot of attention recently. In this paper, we present one successful result of bio-inspired approach: we propose distributed algorithms for resource replication inspired by the single species population model. Resource replication is a crucial technique for improving system performance of distributed applications with shared resources. In systems using resource replication, generally, a larger number of replicas lead to shorter time to reach a replica of a requested resource but consume more storage of the hosts. Therefore, it is indispensable to adjust the number of replicas appropriately for the resource sharing application. This paper considers the problem for controlling the densities of replicas adaptively in dynamic networks and proposes two bio-inspired distributed algorithms for the problem. In the first algorithm, we try to control the replica density for a single resource. However, in a system where multiple resources coexist, the algorithm needs high network cost and the exact knowledge at each node about all resources in the network. In the second algorithm, the densities of all resources are controlled by the single algorithm without high network cost and the exact knowledge about all resources. This paper shows by simulations that these two algorithms realize self-adaptation of the replica density in dynamic networks.

  10. 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.

  11. Stereopsis is adaptive for the natural environment

    PubMed Central

    Sprague, William W.; Cooper, Emily A.; Tošić, Ivana; Banks, Martin S.

    2015-01-01

    Humans and many animals have forward-facing eyes providing different views of the environment. Precise depth estimates can be derived from the resulting binocular disparities, but determining which parts of the two retinal images correspond to one another is computationally challenging. To aid the computation, the visual system focuses the search on a small range of disparities. We asked whether the disparities encountered in the natural environment match that range. We did this by simultaneously measuring binocular eye position and three-dimensional scene geometry during natural tasks. The natural distribution of disparities is indeed matched to the smaller range of correspondence search. Furthermore, the distribution explains the perception of some ambiguous stereograms. Finally, disparity preferences of macaque cortical neurons are consistent with the natural distribution. PMID:26207262

  12. Adaptive method of realizing natural gradient learning for multilayer perceptrons.

    PubMed

    Amari, S; Park, H; Fukumizu, K

    2000-06-01

    The natural gradient learning method is known to have ideal performances for on-line training of multilayer perceptrons. It avoids plateaus, which give rise to slow convergence of the backpropagation method. It is Fisher efficient, whereas the conventional method is not. However, for implementing the method, it is necessary to calculate the Fisher information matrix and its inverse, which is practically very difficult. This article proposes an adaptive method of directly obtaining the inverse of the Fisher information matrix. It generalizes the adaptive Gauss-Newton algorithms and provides a solid theoretical justification of them. Simulations show that the proposed adaptive method works very well for realizing natural gradient learning. PMID:10935719

  13. Adapting natural resource management to climate change: The South Central Oregon and Northern Rockies Adaptation Partnerships

    NASA Astrophysics Data System (ADS)

    Halofsky, J.; Peterson, D. L.

    2015-12-01

    Concrete ways to adapt to climate change are needed to help natural resource managers take the first steps to incorporate climate change into management and take advantage of opportunities to balance the negative effects of climate change. We recently initiated two science-management climate change adaptation partnerships, one with three national forests and one national park in south central Oregon, and the other with 16 national forests, three national parks and other stakeholders in the northern Rockies region. Goals of both partnerships were to: (1) synthesize published information and data to assess the exposure, sensitivity, and adaptive capacity of key resource areas, including water use, infrastructure, fisheries, and vegetation and disturbance; (2) develop science-based adaptation strategies and tactics that will help to mitigate the negative effects of climate change and assist the transition of biological systems and management to a warmer climate; (3) ensure adaptation strategies and tactics are incorporated into relevant planning documents; and (4) foster an enduring partnership to facilitate ongoing dialogue and activities related to climate change in the partnerships regions. After an initial vulnerability assessment by agency and university scientists and local resource specialists, adaptation strategies and tactics were developed in a series of scientist-manager workshops. The final vulnerability assessments and adaptation actions are incorporated in technical reports. The partnerships produced concrete adaptation options for national forest and other natural resource managers and illustrated the utility of place-based vulnerability assessments and scientist-manager workshops in adapting to climate change.

  14. Adapting Natural Resource Management to Climate Change: The Blue Mountains and Northern Rockies Adaptation Partnerships

    NASA Astrophysics Data System (ADS)

    Halofsky, J.; Peterson, D. L.

    2014-12-01

    Concrete ways to adapt to climate change are needed to help natural resource managers take the first steps to incorporate climate change into management and take advantage of opportunities to balance the negative effects of climate change. We recently initiated two science-management climate change adaptation partnerships, one with three national forests and other key stakeholders in the Blue Mountains region of northeastern Oregon, and the other with 16 national forests, three national parks and other stakeholders in the northern Rockies region. Goals of both partnerships were to: (1) synthesize published information and data to assess the exposure, sensitivity, and adaptive capacity of key resource areas, including water use, infrastructure, fisheries, and vegetation and disturbance; (2) develop science-based adaptation strategies and tactics that will help to mitigate the negative effects of climate change and assist the transition of biological systems and management to a warmer climate; (3) ensure adaptation strategies and tactics are incorporated into relevant planning documents; and (4) foster an enduring partnership to facilitate ongoing dialogue and activities related to climate change in the partnerships regions. After an initial vulnerability assessment by agency and university scientists and local resource specialists, adaptation strategies and tactics were developed in a series of scientist-manager workshops. The final vulnerability assessments and adaptation actions are incorporated in technical reports. The partnerships produced concrete adaptation options for national forest and other natural resource managers and illustrated the utility of place-based vulnerability assessments and scientist-manager workshops in adapting to climate change.

  15. Evolution of behavior by density-dependent natural selection

    SciTech Connect

    Pingzhong Guo; Mueller, L.D.; Ayala, F.J. )

    1991-12-01

    Theories of density-dependent natural selection predict that evolution should favor those genotypes with the highest per capita rates of population growth under the current density conditions. These theories are silent about the mechanisms that may give rise to these increases in density-dependent growth rates. The authors have observed the evolution of six populations of Drosophila melanogaster recently placed in crowded environments after nearly 200 generations at low-population density in the laboratory. After 25 generations in these crowded cultures all six populations showed the predicted increase in population growth rates at high-population density with the concomitant decrease in their growth rates at low densities. These changes in rates of population growth are accompanied by changes in the feeding and pupation behavior of the larvae: those populations that have evolve at high-population densities have higher feeding rates and are less likely to pupate on or near the food surface than populations maintained at low densities. A detailed understanding of the mechanisms by which populations evolve under density-dependent natural selection will provide a framework for understanding that nature of trade-offs in life history evolution.

  16. Non-adaptive plasticity potentiates rapid adaptive evolution of gene expression in nature.

    PubMed

    Ghalambor, Cameron K; Hoke, Kim L; Ruell, Emily W; Fischer, Eva K; Reznick, David N; Hughes, Kimberly A

    2015-09-17

    Phenotypic plasticity is the capacity for an individual genotype to produce different phenotypes in response to environmental variation. Most traits are plastic, but the degree to which plasticity is adaptive or non-adaptive depends on whether environmentally induced phenotypes are closer or further away from the local optimum. Existing theories make conflicting predictions about whether plasticity constrains or facilitates adaptive evolution. Debate persists because few empirical studies have tested the relationship between initial plasticity and subsequent adaptive evolution in natural populations. Here we show that the direction of plasticity in gene expression is generally opposite to the direction of adaptive evolution. We experimentally transplanted Trinidadian guppies (Poecilia reticulata) adapted to living with cichlid predators to cichlid-free streams, and tested for evolutionary divergence in brain gene expression patterns after three to four generations. We find 135 transcripts that evolved parallel changes in expression within the replicated introduction populations. These changes are in the same direction exhibited in a native cichlid-free population, suggesting rapid adaptive evolution. We find 89% of these transcripts exhibited non-adaptive plastic changes in expression when the source population was reared in the absence of predators, as they are in the opposite direction to the evolved changes. By contrast, the remaining transcripts exhibiting adaptive plasticity show reduced population divergence. Furthermore, the most plastic transcripts in the source population evolved reduced plasticity in the introduction populations, suggesting strong selection against non-adaptive plasticity. These results support models predicting that adaptive plasticity constrains evolution, whereas non-adaptive plasticity potentiates evolution by increasing the strength of directional selection. The role of non-adaptive plasticity in evolution has received relatively

  17. Adaptation and the color statistics of natural images.

    PubMed

    Webster, M A; Mollon, J D

    1997-12-01

    Color perception depends profoundly on adaptation processes that adjust sensitivity in response to the prevailing pattern of stimulation. We examined how color sensitivity and appearance might be influenced by adaptation to the color distributions characteristic of natural images. Color distributions were measured for natural scenes by sampling an array of locations within each scene with a spectroradiometer, or by recording each scene with a digital camera successively through 31 interference filters. The images were used to reconstruct the L, M and S cone excitation at each spatial location, and the contrasts along three post-receptoral axes [L + M, L - M or S - (L + M)]. Individual scenes varied substantially in their mean chromaticity and luminance, in the principal color-luminance axes of their distributions, and in the range of contrasts in their distributions. Chromatic contrasts were biased along a relatively narrow range of bluish to yellowish-green angles, lying roughly between the S - (L + M) axis (which was more characteristic of scenes with lush vegetation and little sky) and a unique blue-yellow axis (which was more typical of arid scenes). For many scenes L - M and S - (L + M) signals were highly correlated, with weaker correlations between luminance and chromaticity. We use a two-stage model (von Kries scaling followed by decorrelation) to show how the appearance of colors may be altered by light adaptation to the mean of the distributions and by contrast adaptation to the contrast range and principal axes of the distributions; and we show that such adjustments are qualitatively consistent with empirical measurements of asymmetric color matches obtained after adaptation to successive random samples drawn from natural distributions of chromaticities and lightnesses. Such adaptation effects define the natural range of operating states of the visual system. PMID:9425544

  18. Prism adaptation in virtual and natural contexts: Evidence for a flexible adaptive process.

    PubMed

    Veilleux, Louis-Nicolas; Proteau, Luc

    2015-01-01

    Prism exposure when aiming at a visual target in a virtual condition (e.g., when the hand is represented by a video representation) produces no or only small adaptations (after-effects), whereas prism exposure in a natural condition produces large after-effects. Some researchers suggested that this difference may arise from distinct adaptive processes, but other studies suggested a unique process. The present study reconciled these conflicting interpretations. Forty participants were divided into two groups: One group used visual feedback of their hand (natural context), and the other group used computer-generated representational feedback (virtual context). Visual feedback during adaptation was concurrent or terminal. All participants underwent laterally displacing prism perturbation. The results showed that the after-effects were twice as large in the "natural context" than in the "virtual context". No significant differences were observed between the concurrent and terminal feedback conditions. The after-effects generalized to untested targets and workspace. These results suggest that prism adaptation in virtual and natural contexts involves the same process. The smaller after-effects in the virtual context suggest that the depth of adaptation is a function of the degree of convergence between the proprioceptive and visual information that arises from the hand. PMID:25338188

  19. The dependence of natural graphite anode performance on electrode density

    SciTech Connect

    Shim, Joongpyo; Striebel, Kathryn A.

    2003-11-01

    The effect of electrode density for lithium intercalation and irreversible capacity loss on the natural graphite anode in lithium ion batteries was studied by electrochemical methods. Both the first-cycle reversible and irreversible capacities of the natural graphite anode decreased with an increase in the anode density though compression. The reduction in reversible capacity was attributed to a reduction in the chemical diffusion coefficient for lithium though partially agglomerated particles with a larger stress. For the natural graphite in this study the potentials for Li (de)insertion shifted between the first and second formation cycles and the extent of this shift was dependent on electrode density. The relation between this peak shift and the irreversible capacity loss are probably both due to the decrease in graphite surface area with compression.

  20. Guiding climate change adaptation within vulnerable natural resource management systems.

    PubMed

    Bardsley, Douglas K; Sweeney, Susan M

    2010-05-01

    Climate change has the potential to compromise the sustainability of natural resources in Mediterranean climatic systems, such that short-term reactive responses will increasingly be insufficient to ensure effective management. There is a simultaneous need for both the clear articulation of the vulnerabilities of specific management systems to climate risk, and the development of appropriate short- and long-term strategic planning responses that anticipate environmental change or allow for sustainable adaptive management in response to trends in resource condition. Governments are developing climate change adaptation policy frameworks, but without the recognition of the importance of responding strategically, regional stakeholders will struggle to manage future climate risk. In a partnership between the South Australian Government, the Adelaide and Mt Lofty Ranges Natural Resource Management Board and the regional community, a range of available research approaches to support regional climate change adaptation decision-making, were applied and critically examined, including: scenario modelling; applied and participatory Geographical Information Systems modelling; environmental risk analysis; and participatory action learning. As managers apply ideas for adaptation within their own biophysical and socio-cultural contexts, there would be both successes and failures, but a learning orientation to societal change will enable improvements over time. A base-line target for regional responses to climate change is the ownership of the issue by stakeholders, which leads to an acceptance that effective actions to adapt are now both possible and vitally important. Beyond such baseline knowledge, the research suggests that there is a range of tools from the social and physical sciences available to guide adaptation decision-making. PMID:20383706

  1. Guiding Climate Change Adaptation Within Vulnerable Natural Resource Management Systems

    NASA Astrophysics Data System (ADS)

    Bardsley, Douglas K.; Sweeney, Susan M.

    2010-05-01

    Climate change has the potential to compromise the sustainability of natural resources in Mediterranean climatic systems, such that short-term reactive responses will increasingly be insufficient to ensure effective management. There is a simultaneous need for both the clear articulation of the vulnerabilities of specific management systems to climate risk, and the development of appropriate short- and long-term strategic planning responses that anticipate environmental change or allow for sustainable adaptive management in response to trends in resource condition. Governments are developing climate change adaptation policy frameworks, but without the recognition of the importance of responding strategically, regional stakeholders will struggle to manage future climate risk. In a partnership between the South Australian Government, the Adelaide and Mt Lofty Ranges Natural Resource Management Board and the regional community, a range of available research approaches to support regional climate change adaptation decision-making, were applied and critically examined, including: scenario modelling; applied and participatory Geographical Information Systems modelling; environmental risk analysis; and participatory action learning. As managers apply ideas for adaptation within their own biophysical and socio-cultural contexts, there would be both successes and failures, but a learning orientation to societal change will enable improvements over time. A base-line target for regional responses to climate change is the ownership of the issue by stakeholders, which leads to an acceptance that effective actions to adapt are now both possible and vitally important. Beyond such baseline knowledge, the research suggests that there is a range of tools from the social and physical sciences available to guide adaptation decision-making.

  2. Visuomotor Control of Human Adaptive Locomotion: Understanding the Anticipatory Nature

    PubMed Central

    Higuchi, Takahiro

    2013-01-01

    To maintain balance during locomotion, the central nervous system (CNS) accommodates changes in the constraints of spatial environment (e.g., existence of an obstacle or changes in the surface properties). Locomotion while modifying the basic movement patterns in response to such constraints is referred to as adaptive locomotion. The most powerful means of ensuring balance during adaptive locomotion is to visually perceive the environmental properties at a distance and modify the movement patterns in an anticipatory manner to avoid perturbation altogether. For this reason, visuomotor control of adaptive locomotion is characterized, at least in part, by its anticipatory nature. The purpose of the present article is to review the relevant studies which revealed the anticipatory nature of the visuomotor control of adaptive locomotion. The anticipatory locomotor adjustments for stationary and changeable environment, as well as the spatio-temporal patterns of gaze behavior to support the anticipatory locomotor adjustments are described. Such description will clearly show that anticipatory locomotor adjustments are initiated when an object of interest (e.g., a goal or obstacle) still exists in far space. This review also show that, as a prerequisite of anticipatory locomotor adjustments, environmental properties are accurately perceived from a distance in relation to individual’s action capabilities. PMID:23720647

  3. Perceptual Adaptation to the Correction of Natural Astigmatism

    PubMed Central

    Vinas, Maria; Sawides, Lucie; de Gracia, Pablo; Marcos, Susana

    2012-01-01

    Background The visual system adjusts to changes in the environment, as well as to changes within the observer, adapting continuously to maintain a match between visual coding and visual environment. We evaluated whether the perception of oriented blur is biased by the native astigmatism, and studied the time course of the after-effects following spectacle correction of astigmatism in habitually non-corrected astigmats. Methods and Findings We tested potential shifts of the perceptual judgments of blur orientation in 21 subjects. The psychophysical test consisted on a single interval orientation identification task in order to measure the perceived isotropic point (astigmatism level for which the image did not appear oriented to the subject) from images artificially blurred with constant blur strength (B = 1.5 D), while modifying the orientation of the blur according to the axis of natural astigmatism of the subjects. Measurements were performed after neutral (gray field) adaptation on naked eyes under full correction of low and high order aberrations. Longitudinal measurements (up to 6 months) were performed in three groups of subjects: non-astigmats and corrected and uncorrected astigmats. Uncorrected astigmats were provided with proper astigmatic correction immediately after the first session. Non-astigmats did not show significant bias in their perceived neutral point, while in astigmatic subjects the perceived neutral point was significantly biased, typically towards their axis of natural astigmatism. Previously uncorrected astigmats shifted significantly their perceived neutral point towards more isotropic images shortly (2 hours) after astigmatic correction wear, and, once stabilized, remained constant after 6 months. The shift of the perceived neutral point after correction of astigmatism was highly correlated with the amount of natural astigmatism. Conclusions Non-corrected astigmats appear to be naturally adapted to their astigmatism, and astigmatic

  4. Application of adaptive cluster sampling to low-density populations of freshwater mussels

    USGS Publications Warehouse

    Smith, D.R.; Villella, R.F.; Lemarie, D.P.

    2003-01-01

    Freshwater mussels appear to be promising candidates for adaptive cluster sampling because they are benthic macroinvertebrates that cluster spatially and are frequently found at low densities. We applied adaptive cluster sampling to estimate density of freshwater mussels at 24 sites along the Cacapon River, WV, where a preliminary timed search indicated that mussels were present at low density. Adaptive cluster sampling increased yield of individual mussels and detection of uncommon species; however, it did not improve precision of density estimates. Because finding uncommon species, collecting individuals of those species, and estimating their densities are important conservation activities, additional research is warranted on application of adaptive cluster sampling to freshwater mussels. However, at this time we do not recommend routine application of adaptive cluster sampling to freshwater mussel populations. The ultimate, and currently unanswered, question is how to tell when adaptive cluster sampling should be used, i.e., when is a population sufficiently rare and clustered for adaptive cluster sampling to be efficient and practical? A cost-effective procedure needs to be developed to identify biological populations for which adaptive cluster sampling is appropriate.

  5. Earth formation density measurement from natural gamma ray spectral logs

    SciTech Connect

    Smith Jr., H. D.

    1985-07-02

    Naturally occurring gamma radiations from earth formations in the vicinity of a well borehole are detected and spectrally separated into six energy regions or bands. Borehole compensation techniques are applied to the gamma ray spectra and the attenuation coefficient /eta/ is determined as a result thereof. The attenuation coefficient is used along with predetermined borehole, casing and cement parameters to derive a measure of the density of the earth formations.

  6. Natural frequency identification of smart washer by using adaptive observer

    NASA Astrophysics Data System (ADS)

    Ito, Hitoshi; Okugawa, Masayuki

    2014-04-01

    Bolted joints are used in many machines/structures and some of them have been loosened during long time use, and unluckily these bolt loosening may cause a great accident of machines/structures system. These bolted joint, especially in important places, are main object of maintenance inspection. Maintenance inspection with human- involvement is desired to be improved owing to time-consuming, labor-intensive and high-cost. By remote and full automation monitoring of the bolt loosening, constantly monitoring of bolted joint is achieved. In order to detect loosening of bolted joints without human-involvement, applying a structural health monitoring technique and smart structures/materials concept is the key objective. In this study, a new method of bolt loosening detection by adopting a smart washer has been proposed, and the basic detection principle was discussed with numerical analysis about frequency equation of the system, was confirmed experimentally. The smart washer used in this study is in cantilever type with piezoelectric material, which adds the washer the self-sensing and actuation function. The principle used to detect the loosening of the bolts is a method of a bolt loosening detection noted that the natural frequency of a smart washer system is decreasing by the change of the bolt tightening axial tension. The feature of this proposed method is achieving to identify the natural frequency at current condition on demand by adopting the self-sensing and actuation function and system identification algorithm for varying the natural frequency depending the bolt tightening axial tension. A novel bolt loosening detection method by adopting adaptive observer is proposed in this paper. The numerical simulations are performed to verify the possibility of the adaptive observer-based loosening detection. Improvement of the detection accuracy for a bolt loosening is confirmed by adopting initial parameter and variable adaptive gain by numerical simulation.

  7. Invariant natural killer T cells: bridging innate and adaptive immunity

    PubMed Central

    Parekh, Vrajesh V.; Wu, Lan

    2013-01-01

    Cells of the innate immune system interact with pathogens via conserved pattern-recognition receptors, whereas cells of the adaptive immune system recognize pathogens through diverse, antigen-specific receptors that are generated by somatic DNA rearrangement. Invariant natural killer T (iNKT) cells are a subset of lymphocytes that bridge the innate and adaptive immune systems. Although iNKT cells express T cell receptors that are generated by somatic DNA rearrangement, these receptors are semi-invariant and interact with a limited set of lipid and glycolipid antigens, thus resembling the pattern-recognition receptors of the innate immune system. Functionally, iNKT cells most closely resemble cells of the innate immune system, as they rapidly elicit their effector functions following activation, and fail to develop immunological memory. iNKT cells can become activated in response to a variety of stimuli and participate in the regulation of various immune responses. Activated iNKT cells produce several cytokines with the capacity to jump-start and modulate an adaptive immune response. A variety of glycolipid antigens that can differentially elicit distinct effector functions in iNKT cells have been identified. These reagents have been employed to test the hypothesis that iNKT cells can be harnessed for therapeutic purposes in human diseases. Here, we review the innate-like properties and functions of iNKT cells and discuss their interactions with other cell types of the immune system. PMID:20734065

  8. Spatial aggregation across ephemeral resource patches in insect communities: an adaptive response to natural enemies?

    PubMed

    Rohlfs, Marko; Hoffmeister, Thomas S

    2004-08-01

    Although an increase in competition is a common cost associated with intraspecific crowding, spatial aggregation across food-limited resource patches is a widespread phenomenon in many insect communities. Because intraspecific aggregation of competing insect larvae across, e.show $132#g. fruits, dung, mushrooms etc., is an important means by which many species can coexist (aggregation model of species coexistence), there is a strong need to explore the mechanisms that contribute to the maintenance of this kind of spatial resource exploitation. In the present study, by using Drosophila-parasitoid interactions as a model system, we tested the hypothesis whether intraspecific aggregation reflects an adaptive response to natural enemies. Most of the studies that have hitherto been carried out on Drosophila-parasitoid interactions used an almost two-dimensional artificial host environment, where host larvae could not escape from parasitoid attacks, and have demonstrated positive density-dependent parasitism risk. To test whether these studies captured the essence of such interactions, we used natural breeding substrates (decaying fruits). In a first step, we analysed the parasitism risk of Drosophila larvae on a three-dimensional substrate in natural fly communities in the field, and found that the risk of parasitism decreased with increasing host larval density (inverse density dependence). In a second step, we analysed the parasitism risk of Drosophila subobscura larvae on three breeding substrate types exposed to the larval parasitoids Asobara tabida and Leptopilina heterotoma. We found direct density-dependent parasitism on decaying sloes, inverse density dependence on plums, and a hump-shaped relationship between fly larval density and parasitism risk on crab apples. On crab apples and plums, fly larvae benefited from a density-dependent refuge against the parasitoids. While the proportion of larvae feeding within the fruit tissues increased with larval density

  9. A density-based adaptive quantum mechanical/molecular mechanical method.

    PubMed

    Waller, Mark P; Kumbhar, Sadhana; Yang, Jack

    2014-10-20

    We present a density-based adaptive quantum mechanical/molecular mechanical (DBA-QM/MM) method, whereby molecules can switch layers from the QM to the MM region and vice versa. The adaptive partitioning of the molecular system ensures that the layer assignment can change during the optimization procedure, that is, on the fly. The switch from a QM molecule to a MM molecule is determined if there is an absence of noncovalent interactions to any atom of the QM core region. The presence/absence of noncovalent interactions is determined by analysis of the reduced density gradient. Therefore, the location of the QM/MM boundary is based on physical arguments, and this neatly removes some empiricism inherent in previous adaptive QM/MM partitioning schemes. The DBA-QM/MM method is validated by using a water-in-water setup and an explicitly solvated L-alanyl-L-alanine dipeptide. PMID:24954803

  10. Harnessing nature to help people adapt to climate change

    NASA Astrophysics Data System (ADS)

    Jones, Holly P.; Hole, David G.; Zavaleta, Erika S.

    2012-07-01

    Adapting to climate change is among the biggest challenges humanity faces in the next century. An overwhelming focus of adaptation strategies to reduce climate change-related hazards has been on hard-engineering structures such as sea walls, irrigation infrastructure and dams. Closer attention to a broader spectrum of adaptation options is urgently needed. In particular, ecosystem-based adaptation approaches provide flexible, cost-effective and broadly applicable alternatives for buffering the impacts of climate change, while overcoming many drawbacks of hard infrastructure. As such, they are a critical tool at adaptation planners' disposal for tackling the threats that climate change poses to peoples' lives and livelihoods.

  11. A Newton method with adaptive finite elements for solving phase-change problems with natural convection

    NASA Astrophysics Data System (ADS)

    Danaila, Ionut; Moglan, Raluca; Hecht, Frédéric; Le Masson, Stéphane

    2014-10-01

    We present a new numerical system using finite elements with mesh adaptivity for the simulation of solid-liquid phase change systems. In the liquid phase, the natural convection flow is simulated by solving the incompressible Navier-Stokes equations with Boussinesq approximation. A variable viscosity model allows the velocity to progressively vanish in the solid phase, through an intermediate mushy region. The phase change is modeled by introducing an implicit enthalpy source term in the heat equation. The final system of equations describing the liquid-solid system by a single domain approach is solved using a Newton iterative algorithm. The space discretization is based on a P2-P1 Taylor-Hood finite elements and mesh adaptivity by metric control is used to accurately track the solid-liquid interface or the density inversion interface for water flows. The numerical method is validated against classical benchmarks that progressively add strong non-linearities in the system of equations: natural convection of air, natural convection of water, melting of a phase-change material and water freezing. Very good agreement with experimental data is obtained for each test case, proving the capability of the method to deal with both melting and solidification problems with convection. The presented numerical method is easy to implement using FreeFem++ software using a syntax close to the mathematical formulation.

  12. Accelerating Adaptation of Natural Resource Management to Address Climate Change

    PubMed Central

    Cross, Molly S; McCarthy, Patrick D; Garfin, Gregg; Gori, David; Enquist, Carolyn AF

    2013-01-01

    Abstract Natural resource managers are seeking tools to help them address current and future effects of climate change. We present a model for collaborative planning aimed at identifying ways to adapt management actions to address the effects of climate change in landscapes that cross public and private jurisdictional boundaries. The Southwest Climate Change Initiative (SWCCI) piloted the Adaptation for Conservation Targets (ACT) planning approach at workshops in 4 southwestern U.S. landscapes. This planning approach successfully increased participants’ self-reported capacity to address climate change by providing them with a better understanding of potential effects and guiding the identification of solutions. The workshops fostered cross-jurisdictional and multidisciplinary dialogue on climate change through active participation of scientists and managers in assessing climate change effects, discussing the implications of those effects for determining management goals and activities, and cultivating opportunities for regional coordination on adaptation of management plans. Facilitated application of the ACT framework advanced group discussions beyond assessing effects to devising options to mitigate the effects of climate change on specific species, ecological functions, and ecosystems. Participants addressed uncertainty about future conditions by considering more than one climate-change scenario. They outlined opportunities and identified next steps for implementing several actions, and local partnerships have begun implementing actions and conducting additional planning. Continued investment in adaptation of management plans and actions to address the effects of climate change in the southwestern United States and extension of the approaches used in this project to additional landscapes are needed if biological diversity and ecosystem services are to be maintained in a rapidly changing world. Acelerando la Adaptación del Manejo de Recursos Naturales para

  13. Technical Factors Influencing Cone Packing Density Estimates in Adaptive Optics Flood Illuminated Retinal Images

    PubMed Central

    Lombardo, Marco; Serrao, Sebastiano; Lombardo, Giuseppe

    2014-01-01

    Purpose To investigate the influence of various technical factors on the variation of cone packing density estimates in adaptive optics flood illuminated retinal images. Methods Adaptive optics images of the photoreceptor mosaic were obtained in fifteen healthy subjects. The cone density and Voronoi diagrams were assessed in sampling windows of 320×320 µm, 160×160 µm and 64×64 µm at 1.5 degree temporal and superior eccentricity from the preferred locus of fixation (PRL). The technical factors that have been analyzed included the sampling window size, the corrected retinal magnification factor (RMFcorr), the conversion from radial to linear distance from the PRL, the displacement between the PRL and foveal center and the manual checking of cone identification algorithm. Bland-Altman analysis was used to assess the agreement between cone density estimated within the different sampling window conditions. Results The cone density declined with decreasing sampling area and data between areas of different size showed low agreement. A high agreement was found between sampling areas of the same size when comparing density calculated with or without using individual RMFcorr. The agreement between cone density measured at radial and linear distances from the PRL and between data referred to the PRL or the foveal center was moderate. The percentage of Voronoi tiles with hexagonal packing arrangement was comparable between sampling areas of different size. The boundary effect, presence of any retinal vessels, and the manual selection of cones missed by the automated identification algorithm were identified as the factors influencing variation of cone packing arrangements in Voronoi diagrams. Conclusions The sampling window size is the main technical factor that influences variation of cone density. Clear identification of each cone in the image and the use of a large buffer zone are necessary to minimize factors influencing variation of Voronoi diagrams of the cone

  14. Promoting Positive Adaptation in Adult Survivors of Natural Disasters

    ERIC Educational Resources Information Center

    Warchal, Judith R.; Graham, Louise B.

    2011-01-01

    This article integrates the guidelines of American Red Cross and the "Psychological First Aid: Field Operations Guide" (Brymer et al., 2006) with adult development theories to demonstrate the promotion of adaptive functioning in adults after a disaster. Case examples and recommendations for counselors working in disaster situations are included.

  15. An Efficient Adaptive Weighted Switching Median Filter for Removing High Density Impulse Noise

    NASA Astrophysics Data System (ADS)

    Nair, Madhu S.; Ameera Mol, P. M.

    2014-09-01

    Restoration of images corrupted by impulse noise is a very active research area in image processing. In this paper, an Efficient Adaptive Weighted Switching Median filter for restoration of images that are corrupted by high density impulse noise is proposed. The filtering is performed as a two phase process—a detection phase followed by a filtering phase. In the proposed method, noise detection is done by HEIND algorithm proposed by Duan et al. The filtering algorithm is then applied to the pixels which are detected as noisy by the detection algorithm. All uncorrupted pixels in the image are left unchanged. The filtering window size is chosen adaptively depending on the local noise distribution around each corrupted pixels. Noisy pixels are replaced by a weighted median value of uncorrupted pixels in the filtering window. The weight value assigned to each uncorrupted pixels depends on its closeness to the central pixel.

  16. Communicating for Climate Change Adaptation: Lessons from a Case Study with Nature-Based Tour Operators

    NASA Astrophysics Data System (ADS)

    Timm, K.; Sparrow, E. B.; Pettit, E. C.; Trainor, S. F.; Taylor, K.

    2014-12-01

    Increasing temperatures are projected to have a positive effect on the length of Alaska's tourism season, but the natural attractions that tourism relies on, such as glaciers, wildlife, fish, or other natural resources, may change. In order to continue to derive benefits from these resources, nature-based tour operators may have to adapt to these changes, and communication is an essential, but poorly understood, component of the climate change adaptation process. The goal of this study was to determine how to provide useful climate change information to nature-based tour operators by answering the following questions: 1. What environmental changes do nature-based tour operators perceive? 2. How are nature-based tour operators responding to climate and environmental change? 3. What climate change information do nature-based tour operators need? To answer these questions, twenty-four nature-based tour operators representing 20 different small and medium sized businesses in Juneau, Alaska were interviewed. The results show that many of Juneau's nature-based tour operators are observing, responding to, and in some cases, actively planning for further changes in the environment. The types of responses tended to vary depending on the participants' certainty in climate change and the perceived risks to their organization. Using these two factors, this study proposes a framework to classify climate change responses for the purpose of generating meaningful information and communication processes that promote adaptation and build adaptive capacity. During the course of the study, several other valuable lessons were learned about communicating about adaptation. The results of this study demonstrate that science communication research has an important place in the practice of promoting and fostering climate change adaptation. While the focus of this study was tour operators, the lessons learned may be valuable to other organizations striving to engage unique groups in climate

  17. Dynamic Nature of Noncoding RNA Regulation of Adaptive Immune Response

    PubMed Central

    Curtale, Graziella; Citarella, Franca

    2013-01-01

    Immune response plays a fundamental role in protecting the organism from infections; however, dysregulation often occurs and can be detrimental for the organism, leading to a variety of immune-mediated diseases. Recently our understanding of the molecular and cellular networks regulating the immune response, and, in particular, adaptive immunity, has improved dramatically. For many years, much of the focus has been on the study of protein regulators; nevertheless, recent evidence points to a fundamental role for specific classes of noncoding RNAs (ncRNAs) in regulating development, activation and homeostasis of the immune system. Although microRNAs (miRNAs) are the most comprehensive and well-studied, a number of reports suggest the exciting possibility that long ncRNAs (lncRNAs) could mediate host response and immune function. Finally, evidence is also accumulating that suggests a role for miRNAs and other small ncRNAs in autocrine, paracrine and exocrine signaling events, thus highlighting an elaborate network of regulatory interactions mediated by different classes of ncRNAs during immune response. This review will explore the multifaceted roles of ncRNAs in the adaptive immune response. In particular, we will focus on the well-established role of miRNAs and on the emerging role of lncRNAs and circulating ncRNAs, which all make indispensable contributions to the understanding of the multilayered modulation of the adaptive immune response. PMID:23975170

  18. Adaptive inference for distinguishing credible from incredible patterns in nature

    USGS Publications Warehouse

    Holling, Crawford S.; Allen, C.R.

    2002-01-01

    Strong inference is a powerful and rapid tool that can be used to identify and explain patterns in molecular biology, cell biology, and physiology. It is effective where causes are single and separable and where discrimination between pairwise alternative hypotheses can be determined experimentally by a simple yes or no answer. But causes in ecological systems are multiple and overlapping and are not entirely separable. Frequently, competing hypotheses cannot be distinguished by a single unambiguous test, but only by a suite of tests of different kinds, that produce a body of evidence to support one line of argument and not others. We call this process "adaptive inference". Instead of pitting each member of a pair of hypotheses against each other, adaptive inference relies on the exuberant invention of multiple, competing hypotheses, after which carefully structured comparative data are used to explore the logical consequences of each. Herein we present an example that demonstrates the attributes of adaptive inference that have developed out of a 30-year study of the resilience of ecosystems.

  19. Intermolecular interactions in photodamaged DNA from density functional theory symmetry-adapted perturbation theory.

    PubMed

    Sadeghian, Keyarash; Bocola, Marco; Schütz, Martin

    2011-05-01

    The intermolecular interactions of the photodamaged cyclobutane pyrimidine dimer (CPD) lesion with adjacent nucleobases in the native intrahelical DNA double strand are investigated at the level of density functional theory symmetry-adapted perturbation theory (DFT-SAPT) and compared to the original (or repaired) case with pyrimidines (TpT) instead of CPD. The CPD aggregation is on average destabilized by about 6 kcal mol(-1) relative to that involving TpT. The effect of destabilization is asymmetric, that is, it involves a single H-bonding (Watson-Crick (WC) type) base-pair interaction. PMID:21452189

  20. Aftereffects for Face Attributes with Different Natural Variability: Children Are More Adaptable than Adolescents

    ERIC Educational Resources Information Center

    Hills, Peter J.; Holland, Andrew M.; Lewis, Michael B.

    2010-01-01

    Adults can be adapted to a particular facial distortion in which both eyes are shifted symmetrically (Robbins, R., McKone, E., & Edwards, M. (2007). "Aftereffects for face attributes with different natural variability: Adapter position effects and neural models." "Journal of Experimental Psychology: Human Perception and Performance, 33," 570-592),…

  1. Novel multiresolution mammographic density segmentation using pseudo 3D features and adaptive cluster merging

    NASA Astrophysics Data System (ADS)

    He, Wenda; Juette, Arne; Denton, Erica R. E.; Zwiggelaar, Reyer

    2015-03-01

    Breast cancer is the most frequently diagnosed cancer in women. Early detection, precise identification of women at risk, and application of appropriate disease prevention measures are by far the most effective ways to overcome the disease. Successful mammographic density segmentation is a key aspect in deriving correct tissue composition, ensuring an accurate mammographic risk assessment. However, mammographic densities have not yet been fully incorporated with non-image based risk prediction models, (e.g. the Gail and the Tyrer-Cuzick model), because of unreliable segmentation consistency and accuracy. This paper presents a novel multiresolution mammographic density segmentation, a concept of stack representation is proposed, and 3D texture features were extracted by adapting techniques based on classic 2D first-order statistics. An unsupervised clustering technique was employed to achieve mammographic segmentation, in which two improvements were made; 1) consistent segmentation by incorporating an optimal centroids initialisation step, and 2) significantly reduced the number of missegmentation by using an adaptive cluster merging technique. A set of full field digital mammograms was used in the evaluation. Visual assessment indicated substantial improvement on segmented anatomical structures and tissue specific areas, especially in low mammographic density categories. The developed method demonstrated an ability to improve the quality of mammographic segmentation via clustering, and results indicated an improvement of 26% in segmented image with good quality when compared with the standard clustering approach. This in turn can be found useful in early breast cancer detection, risk-stratified screening, and aiding radiologists in the process of decision making prior to surgery and/or treatment.

  2. Non-iterative adaptive time stepping with truncation error control for simulating variable-density flow

    NASA Astrophysics Data System (ADS)

    Hirthe, E. M.; Graf, T.

    2012-04-01

    Fluid density variations occur due to changes in the solute concentration, temperature and pressure of groundwater. Examples are interaction between freshwater and seawater, radioactive waste disposal, groundwater contamination, and geothermal energy production. The physical coupling between flow and transport introduces non-linearity in the governing mathematical equations, such that solving variable-density flow problems typically requires very long computational time. Computational efficiency can be attained through the use of adaptive time-stepping schemes. The aim of this work is therefore to apply a non-iterative adaptive time-stepping scheme based on local truncation error in variable-density flow problems. That new scheme is implemented into the code of the HydroGeoSphere model (Therrien et al., 2011). The new time-stepping scheme is applied to the Elder (1967) and the Shikaze et al. (1998) problem of free convection in porous and fractured-porous media, respectively. Numerical simulations demonstrate that non-iterative time-stepping based on local truncation error control fully automates the time step size and efficiently limits the temporal discretization error to the user-defined tolerance. Results of the Elder problem show that the new time-stepping scheme presented here is significantly more efficient than uniform time-stepping when high accuracy is required. Results of the Shikaze problem reveal that the new scheme is considerably faster than conventional time-stepping where time step sizes are either constant or controlled by absolute head/concentration changes. Future research will focus on the application of the new time-stepping scheme to variable-density flow in complex real-world fractured-porous rock.

  3. Herbaceous plant species invading natural areas tend to have stronger adaptive root foraging than other naturalized species.

    PubMed

    Keser, Lidewij H; Visser, Eric J W; Dawson, Wayne; Song, Yao-Bin; Yu, Fei-Hai; Fischer, Markus; Dong, Ming; van Kleunen, Mark

    2015-01-01

    Although plastic root-foraging responses are thought to be adaptive, as they may optimize nutrient capture of plants, this has rarely been tested. We investigated whether nutrient-foraging responses are adaptive, and whether they pre-adapt alien species to become natural-area invaders. We grew 12 pairs of congeneric species (i.e., 24 species) native to Europe in heterogeneous and homogeneous nutrient environments, and compared their foraging responses and performance. One species in each pair is a USA natural-area invader, and the other one is not. Within species, individuals with strong foraging responses, measured as plasticity in root diameter and specific root length, had a higher biomass. Among species, the ones with strong foraging responses, measured as plasticity in root length and root biomass, had a higher biomass. Our results therefore suggest that root foraging is an adaptive trait. Invasive species showed significantly stronger root-foraging responses than non-invasive species when measured as root diameter. Biomass accumulation was decreased in the heterogeneous vs. the homogeneous environment. In aboveground, but not belowground and total biomass, this decrease was smaller in invasive than in non-invasive species. Our results show that strong plastic root-foraging responses are adaptive, and suggest that it might aid in pre-adapting species to becoming natural-area invaders. PMID:25964790

  4. Herbaceous plant species invading natural areas tend to have stronger adaptive root foraging than other naturalized species

    PubMed Central

    Keser, Lidewij H.; Visser, Eric J. W.; Dawson, Wayne; Song, Yao-Bin; Yu, Fei-Hai; Fischer, Markus; Dong, Ming; van Kleunen, Mark

    2015-01-01

    Although plastic root-foraging responses are thought to be adaptive, as they may optimize nutrient capture of plants, this has rarely been tested. We investigated whether nutrient-foraging responses are adaptive, and whether they pre-adapt alien species to become natural-area invaders. We grew 12 pairs of congeneric species (i.e., 24 species) native to Europe in heterogeneous and homogeneous nutrient environments, and compared their foraging responses and performance. One species in each pair is a USA natural-area invader, and the other one is not. Within species, individuals with strong foraging responses, measured as plasticity in root diameter and specific root length, had a higher biomass. Among species, the ones with strong foraging responses, measured as plasticity in root length and root biomass, had a higher biomass. Our results therefore suggest that root foraging is an adaptive trait. Invasive species showed significantly stronger root-foraging responses than non-invasive species when measured as root diameter. Biomass accumulation was decreased in the heterogeneous vs. the homogeneous environment. In aboveground, but not belowground and total biomass, this decrease was smaller in invasive than in non-invasive species. Our results show that strong plastic root-foraging responses are adaptive, and suggest that it might aid in pre-adapting species to becoming natural-area invaders. PMID:25964790

  5. Density of muscle spindles in prosimian shoulder muscles reflects locomotor adaptation.

    PubMed

    Higurashi, Yasuo; Taniguchi, Yuki; Kumakura, Hiroo

    2006-01-01

    We examined the correlation between the density of muscle spindles in shoulder muscles and the locomotor mode in three species of prosimian primates: the slow loris (Nycticebus coucang), Garnett's galago (Otolemur garnettii), and the ring-tailed lemur (Lemur catta). The shoulder muscles (supraspinatus, infraspinatus, teres major, teres minor, and subscapularis) were embedded in celloidin and cut into transverse serial thin sections (40 microm); then, every tenth section was stained using the Azan staining technique. The relative muscle weights and the density of the muscle spindles were determined. The slow loris muscles were heavier and had sparser muscle spindles, as compared to Garnett's galago. These features suggest that the shoulder muscles of the slow loris are more adapted to generating propulsive force and stabilizing the shoulder joint during locomotion and play a less controlling role in forelimb movements. In contrast, Garnett's galago possessed smaller shoulder muscles with denser spindles that are suitable for the control of more rapid locomotor movements. The mean relative weight and the mean spindle density in the shoulder muscles of the ring-tailed lemur were between those of the other primates, suggesting that the spindle density is not simply a consequence of taxonomic status. PMID:17361082

  6. Fracture density estimation from petrophysical log data using the adaptive neuro-fuzzy inference system

    NASA Astrophysics Data System (ADS)

    Ja'fari, Ahmad; Kadkhodaie-Ilkhchi, Ali; Sharghi, Yoosef; Ghanavati, Kiarash

    2012-02-01

    Fractures as the most common and important geological features have a significant share in reservoir fluid flow. Therefore, fracture detection is one of the important steps in fractured reservoir characterization. Different tools and methods are introduced for fracture detection from which formation image logs are considered as the common and effective tools. Due to the economical considerations, image logs are available for a limited number of wells in a hydrocarbon field. In this paper, we suggest a model to estimate fracture density from the conventional well logs using an adaptive neuro-fuzzy inference system. Image logs from two wells of the Asmari formation in one of the SW Iranian oil fields are used to verify the results of the model. Statistical data analysis indicates good correlation between fracture density and well log data including sonic, deep resistivity, neutron porosity and bulk density. The results of this study show that there is good agreement (correlation coefficient of 98%) between the measured and neuro-fuzzy estimated fracture density.

  7. Teaching the 'nature of science': modest adaptations or radical reconceptions?

    NASA Astrophysics Data System (ADS)

    Hipkins, Rosemary; Barker, Miles; Bolstad, Rachel

    2005-02-01

    This article explores the nature of a continuing mismatch between curriculum reform rhetoric in science education and actual classroom practice. Lack of philosophical consensus about the nature of science (NOS); lack of appropriate curriculum guidance, classroom materials and pedagogical content knowledge for NOS teaching; teachers' personal theories of learning; and the realities of classroom constraints are all implicated as interacting factors that contribute to the mismatch. Because curriculum policy is political, with pressure brought to bear by many interest groups, it is suggested that the science teaching community cannot adequately address the issues raised in the absence of wider community debate and support.

  8. CLIMATE-RESPONSIVE ADAPTIVE CONTROLS FOR NATURAL VENTILATION

    EPA Science Inventory

    With today’s growing emphasis on minimizing energy use in buildings, energy-efficient active mechanical systems and strategies have admittedly overlooked passive strategies. Critically needed passive cooling or heating can demonstrate that, by maximizing natural resources, qua...

  9. Classification of charge density waves based on their nature

    PubMed Central

    Zhu, Xuetao; Cao, Yanwei; Zhang, Jiandi; Plummer, E. W.; Guo, Jiandong

    2015-01-01

    The concept of a charge density wave (CDW) permeates much of condensed matter physics and chemistry. CDWs have their origin rooted in the instability of a one-dimensional system described by Peierls. The extension of this concept to reduced dimensional systems has led to the concept of Fermi surface nesting (FSN), which dictates the wave vector (q→CDW) of the CDW and the corresponding lattice distortion. The idea is that segments of the Fermi contours are connected by q→CDW, resulting in the effective screening of phonons inducing Kohn anomalies in their dispersion at q→CDW, driving a lattice restructuring at low temperatures. There is growing theoretical and experimental evidence that this picture fails in many real systems and in fact it is the momentum dependence of the electron–phonon coupling (EPC) matrix element that determines the characteristic of the CDW phase. Based on the published results for the prototypical CDW system 2H-NbSe2, we show how well the q→-dependent EPC matrix element, but not the FSN, can describe the origin of the CDW. We further demonstrate a procedure of combing electronic band and phonon measurements to extract the EPC matrix element, allowing the electronic states involved in the EPC to be identified. Thus, we show that a large EPC does not necessarily induce the CDW phase, with Bi2Sr2CaCu2O8+δ as the example, and the charge-ordered phenomena observed in various cuprates are not driven by FSN or EPC. To experimentally resolve the microscopic picture of EPC will lead to a fundamental change in the way we think about, write about, and classify charge density waves. PMID:25646420

  10. Some guidelines for helping natural resources adapt to climate change

    USGS Publications Warehouse

    Baron, Jill S.; Julius, Susan Herrod; West, Jordan M.; Joyce, Linda A.; Blate, Geoffrey; Peterson, Charles H.; Palmer, Margaret; Keller, Brian D.; Kareiva, Peter; Scott, J. Michael; Griffith, Brad

    2008-01-01

    The changes occurring in mountain regions are an epitome of climate change. The dramatic shrinkage of major glaciers over the past century – and especially in the last 30 years – is one of several iconic images that have come to symbolize climate change. Climate creates the context for ecosystems, and climate variables strongly influence the structure, composition, and processes that characterize distinct ecosystems. Climate change, therefore, is having direct and indirect effects on species attributes, ecological interactions, and ecosystem processes. Because changes in the climate system will continue regardless of emissions mitigation, management strategies to enhance the resilience of ecosystems will become increasingly important. It is essential that management responses to climate change proceed using the best available science despite uncertainties associated with the future path of climate change, the response of ecosystems to climate effects, and the effects of management. Given these uncertainties, management adaptation will require flexibility to reflect our growing understanding of climate change impacts and management effectiveness.

  11. Natural selection and self-organization in complex adaptive systems.

    PubMed

    Di Bernardo, Mirko

    2010-01-01

    The central theme of this work is self-organization "interpreted" both from the point of view of theoretical biology, and from a philosophical point of view. By analysing, on the one hand, those which are now considered--not only in the field of physics--some of the most important discoveries, that is complex systems and deterministic chaos and, on the other hand, the new frontiers of systemic biology, this work highlights how large thermodynamic systems which are open can spontaneously stay in an orderly regime. Such systems can represent the natural source of the order required for a stable self-organization, for homoeostasis and for hereditary variations. The order, emerging in enormous randomly interconnected nets of binary variables, is almost certainly only the precursor of similar orders emerging in all the varieties of complex systems. Hence, this work, by finding new foundations for the order pervading the living world, advances the daring hypothesis according to which Darwinian natural selection is not the only source of order in the biosphere. Thus, the article, by examining the passage from Prigogine's dissipative structures theory to the contemporary theory of biological complexity, highlights the development of a coherent and continuous line of research which is set to individuate the general principles marking the profound reality of that mysterious self-organization characterizing the complexity of life. PMID:20882479

  12. Exploring neural directed interactions with transfer entropy based on an adaptive kernel density estimator.

    PubMed

    Zuo, K; Bellanger, J J; Yang, C; Shu, H; Le Bouquin Jeannés, R

    2013-01-01

    This paper aims at estimating causal relationships between signals to detect flow propagation in autoregressive and physiological models. The main challenge of the ongoing work is to discover whether neural activity in a given structure of the brain influences activity in another area during epileptic seizures. This question refers to the concept of effective connectivity in neuroscience, i.e. to the identification of information flows and oriented propagation graphs. Past efforts to determine effective connectivity rooted to Wiener causality definition adapted in a practical form by Granger with autoregressive models. A number of studies argue against such a linear approach when nonlinear dynamics are suspected in the relationship between signals. Consequently, nonlinear nonparametric approaches, such as transfer entropy (TE), have been introduced to overcome linear methods limitations and promoted in many studies dealing with electrophysiological signals. Until now, even though many TE estimators have been developed, further improvement can be expected. In this paper, we investigate a new strategy by introducing an adaptive kernel density estimator to improve TE estimation. PMID:24110694

  13. Saccadic gain adaptation is predicted by the statistics of natural fluctuations in oculomotor function

    PubMed Central

    Albert, Mark V.; Catz, Nicolas; Thier, Peter; Kording, Konrad

    2012-01-01

    Due to multiple factors such as fatigue, muscle strengthening, and neural plasticity, the responsiveness of the motor apparatus to neural commands changes over time. To enable precise movements the nervous system must adapt to compensate for these changes. Recent models of motor adaptation derive from assumptions about the way the motor apparatus changes. Characterizing these changes is difficult because motor adaptation happens at the same time, masking most of the effects of ongoing changes. Here, we analyze eye movements of monkeys with lesions to the posterior cerebellar vermis that impair adaptation. Their fluctuations better reveal the underlying changes of the motor system over time. When these measured, unadapted changes are used to derive optimal motor adaptation rules the prediction precision significantly improves. Among three models that similarly fit single-day adaptation results, the model that also matches the temporal correlations of the non-adapting saccades most accurately predicts multiple day adaptation. Saccadic gain adaptation is well matched to the natural statistics of fluctuations of the oculomotor plant. PMID:23230397

  14. A Time-Critical Adaptive Approach for Visualizing Natural Scenes on Different Devices

    PubMed Central

    Dong, Tianyang; Liu, Siyuan; Xia, Jiajia; Fan, Jing; Zhang, Ling

    2015-01-01

    To automatically adapt to various hardware and software environments on different devices, this paper presents a time-critical adaptive approach for visualizing natural scenes. In this method, a simplified expression of a tree model is used for different devices. The best rendering scheme is intelligently selected to generate a particular scene by estimating the rendering time of trees based on their visual importance. Therefore, this approach can ensure the reality of natural scenes while maintaining a constant frame rate for their interactive display. To verify its effectiveness and flexibility, this method is applied in different devices, such as a desktop computer, laptop, iPad and smart phone. Applications show that the method proposed in this paper can not only adapt to devices with different computing abilities and system resources very well but can also achieve rather good visual realism and a constant frame rate for natural scenes. PMID:25723177

  15. Adaptive Feedback Linearization Control for Asynchronous Machine with Nonlinear for Natural Dynamic Complete Observer

    NASA Astrophysics Data System (ADS)

    Bentaallah, Abderrahim; Massoum, Ahmed; Benhamida, Farid; Meroufel, Abdelkader

    2012-03-01

    This paper studies the nonlinear adaptive control of an induction motor with natural dynamic complete nonlinear observer. The aim of this work is to develop a nonlinear control law and adaptive performance for an asynchronous motor with two main objectives: to improve the continuation of trajectories and the stability, robustness to parametric variations and disturbances rejection. This control law will independently control the speed and flux into the machine by restricting supply. A complete nonlinear observer for dynamic nature ensuring closed loop stability of the entire control and observer has been developed. Several simulations have also been carried out to demonstrate system performance.

  16. Action adaptation during natural unfolding social scenes influences action recognition and inferences made about actor beliefs.

    PubMed

    Keefe, Bruce D; Wincenciak, Joanna; Jellema, Tjeerd; Ward, James W; Barraclough, Nick E

    2016-07-01

    When observing another individual's actions, we can both recognize their actions and infer their beliefs concerning the physical and social environment. The extent to which visual adaptation influences action recognition and conceptually later stages of processing involved in deriving the belief state of the actor remains unknown. To explore this we used virtual reality (life-size photorealistic actors presented in stereoscopic three dimensions) to see how visual adaptation influences the perception of individuals in naturally unfolding social scenes at increasingly higher levels of action understanding. We presented scenes in which one actor picked up boxes (of varying number and weight), after which a second actor picked up a single box. Adaptation to the first actor's behavior systematically changed perception of the second actor. Aftereffects increased with the duration of the first actor's behavior, declined exponentially over time, and were independent of view direction. Inferences about the second actor's expectation of box weight were also distorted by adaptation to the first actor. Distortions in action recognition and actor expectations did not, however, extend across different actions, indicating that adaptation is not acting at an action-independent abstract level but rather at an action-dependent level. We conclude that although adaptation influences more complex inferences about belief states of individuals, this is likely to be a result of adaptation at an earlier action recognition stage rather than adaptation operating at a higher, more abstract level in mentalizing or simulation systems. PMID:27472496

  17. Higher-order adaptive finite-element methods for Kohn–Sham density functional theory

    SciTech Connect

    Motamarri, P.; Nowak, M.R.; Leiter, K.; Knap, J.; Gavini, V.

    2013-11-15

    We present an efficient computational approach to perform real-space electronic structure calculations using an adaptive higher-order finite-element discretization of Kohn–Sham density-functional theory (DFT). To this end, we develop an a priori mesh-adaption technique to construct a close to optimal finite-element discretization of the problem. We further propose an efficient solution strategy for solving the discrete eigenvalue problem by using spectral finite-elements in conjunction with Gauss–Lobatto quadrature, and a Chebyshev acceleration technique for computing the occupied eigenspace. The proposed approach has been observed to provide a staggering 100–200-fold computational advantage over the solution of a generalized eigenvalue problem. Using the proposed solution procedure, we investigate the computational efficiency afforded by higher-order finite-element discretizations of the Kohn–Sham DFT problem. Our studies suggest that staggering computational savings—of the order of 1000-fold—relative to linear finite-elements can be realized, for both all-electron and local pseudopotential calculations, by using higher-order finite-element discretizations. On all the benchmark systems studied, we observe diminishing returns in computational savings beyond the sixth-order for accuracies commensurate with chemical accuracy, suggesting that the hexic spectral-element may be an optimal choice for the finite-element discretization of the Kohn–Sham DFT problem. A comparative study of the computational efficiency of the proposed higher-order finite-element discretizations suggests that the performance of finite-element basis is competing with the plane-wave discretization for non-periodic local pseudopotential calculations, and compares to the Gaussian basis for all-electron calculations to within an order of magnitude. Further, we demonstrate the capability of the proposed approach to compute the electronic structure of a metallic system containing 1688

  18. Higher-order adaptive finite-element methods for Kohn-Sham density functional theory

    NASA Astrophysics Data System (ADS)

    Motamarri, P.; Nowak, M. R.; Leiter, K.; Knap, J.; Gavini, V.

    2013-11-01

    We present an efficient computational approach to perform real-space electronic structure calculations using an adaptive higher-order finite-element discretization of Kohn-Sham density-functional theory (DFT). To this end, we develop an a priori mesh-adaption technique to construct a close to optimal finite-element discretization of the problem. We further propose an efficient solution strategy for solving the discrete eigenvalue problem by using spectral finite-elements in conjunction with Gauss-Lobatto quadrature, and a Chebyshev acceleration technique for computing the occupied eigenspace. The proposed approach has been observed to provide a staggering 100-200-fold computational advantage over the solution of a generalized eigenvalue problem. Using the proposed solution procedure, we investigate the computational efficiency afforded by higher-order finite-element discretizations of the Kohn-Sham DFT problem. Our studies suggest that staggering computational savings-of the order of 1000-fold-relative to linear finite-elements can be realized, for both all-electron and local pseudopotential calculations, by using higher-order finite-element discretizations. On all the benchmark systems studied, we observe diminishing returns in computational savings beyond the sixth-order for accuracies commensurate with chemical accuracy, suggesting that the hexic spectral-element may be an optimal choice for the finite-element discretization of the Kohn-Sham DFT problem. A comparative study of the computational efficiency of the proposed higher-order finite-element discretizations suggests that the performance of finite-element basis is competing with the plane-wave discretization for non-periodic local pseudopotential calculations, and compares to the Gaussian basis for all-electron calculations to within an order of magnitude. Further, we demonstrate the capability of the proposed approach to compute the electronic structure of a metallic system containing 1688 atoms using

  19. Plants adapted to warmer climate do not outperform regional plants during a natural heat wave.

    PubMed

    Bucharova, Anna; Durka, Walter; Hermann, Julia-Maria; Hölzel, Norbert; Michalski, Stefan; Kollmann, Johannes; Bossdorf, Oliver

    2016-06-01

    With ongoing climate change, many plant species may not be able to adapt rapidly enough, and some conservation experts are therefore considering to translocate warm-adapted ecotypes to mitigate effects of climate warming. Although this strategy, called assisted migration, is intuitively plausible, most of the support comes from models, whereas experimental evidence is so far scarce. Here we present data on multiple ecotypes of six grassland species, which we grew in four common gardens in Germany during a natural heat wave, with temperatures 1.4-2.0°C higher than the long-term means. In each garden we compared the performance of regional ecotypes with plants from a locality with long-term summer temperatures similar to what the plants experienced during the summer heat wave. We found no difference in performance between regional and warm-adapted plants in four of the six species. In two species, regional ecotypes even outperformed warm-adapted plants, despite elevated temperatures, which suggests that translocating warm-adapted ecotypes may not only lack the desired effect of increased performance but may even have negative consequences. Even if adaptation to climate plays a role, other factors involved in local adaptation, such as biotic interactions, may override it. Based on our results, we cannot advocate assisted migration as a universal tool to enhance the performance of local plant populations and communities during climate change. PMID:27516871

  20. Studying the Genetics of Behavior and Evolution by Adaptation and Natural Selection.

    ERIC Educational Resources Information Center

    Silverman, Jules

    1998-01-01

    Provides an exercise designed to give students an appreciation for the genetic basis of behavior. Employs the phenomenon of glucose aversion as an example of evolution by mutation and accelerated natural selection, thereby revealing one of the ways in which organisms adapt to human interference. (DDR)

  1. An Experimental Field Study of Delayed Density Dependence in Natural Populations of Aedes albopictus

    PubMed Central

    Walsh, Rachael K.; Bradley, Caitlin; Apperson, Charles S.; Gould, Fred

    2012-01-01

    Aedes albopictus, a species known to transmit dengue and chikungunya viruses, is primarily a container-inhabiting mosquito. The potential for pathogen transmission by Ae. albopictus has increased our need to understand its ecology and population dynamics. Two parameters that we know little about are the impact of direct density-dependence and delayed density-dependence in the larval stage. The present study uses a manipulative experimental design, under field conditions, to understand the impact of delayed density dependence in a natural population of Ae. albopictus in Raleigh, North Carolina. Twenty liter buckets, divided in half prior to experimentation, placed in the field accumulated rainwater and detritus, providing oviposition and larval production sites for natural populations of Ae. albopictus. Two treatments, a larvae present and larvae absent treatment, were produced in each bucket. After five weeks all larvae were removed from both treatments and the buckets were covered with fine mesh cloth. Equal numbers of first instars were added to both treatments in every bucket. Pupae were collected daily and adults were frozen as they emerged. We found a significant impact of delayed density-dependence on larval survival, development time and adult body size in containers with high larval densities. Our results indicate that delayed density-dependence will have negative impacts on the mosquito population when larval densities are high enough to deplete accessible nutrients faster than the rate of natural food accumulation. PMID:22563428

  2. Pattern Recognition With Adaptive-Thresholds For Sleep Spindle In High Density EEG Signals

    PubMed Central

    Gemignani, Jessica; Agrimi, Jacopo; Cheli, Enrico; Gemignani, Angelo; Laurino, Marco; Allegrini, Paolo; Landi, Alberto; Menicucci, Danilo

    2016-01-01

    Sleep spindles are electroencephalographic oscillations peculiar of non-REM sleep, related to neuronal mechanisms underlying sleep restoration and learning consolidation. Based on their very singular morphology, sleep spindles can be visually recognized and detected, even though this approach can lead to significant mis-detections. For this reason, many efforts have been put in developing a reliable algorithm for spindle automatic detection, and a number of methods, based on different techniques, have been tested via visual validation. This work aims at improving current pattern recognition procedures for sleep spindles detection by taking into account their physiological sources of variability. We provide a method as a synthesis of the current state of art that, improving dynamic threshold adaptation, is able to follow modification of spindle characteristics as a function of sleep depth and inter-subjects variability. The algorithm has been applied to physiological data recorded by a high density EEG in order to perform a validation based on visual inspection and on evaluation of expected results from normal night sleep in healthy subjects. PMID:26736332

  3. Insights on Coral Adaptation from Polyp and Colony Morphology, Skeletal Density Banding and Carbonate Depositional Facies

    NASA Astrophysics Data System (ADS)

    Oehlert, A. M.; Hill, C. A.; Piggot, A. M.; Fouke, B. W.

    2008-12-01

    As one of the core reservoirs of primary production in the world's oceans, tropical coral reefs support a complex ecosystem that directly impacts over ninety percent of marine organisms at some point in their life cycle. Corals themselves are highly complex organisms and exhibit a range of growth forms that range from branching to massive, foliaceous, columnar, encrusting, free living and laminar coralla. Fierce competition over scarce resources available to each individual coral species creates niche specialization. Throughout the Phanerozic geological record, this has driven speciation events and created distinct skeletal growth morphologies that have differential abilities in feeding strategy. In turn, this has presumably led to the development of niche specialization that can be quantitatively measured through hierarchical morphological differences from the micrometer to the meter scale. Porter (1976) observed significant differences in skeletal morphology between Caribbean coral species that reflects an adaptive geometry based on feeding strategy. Within the Montastraea species complex there are four major morphologies; columnar, bouldering, irregular mounding, and skirted. Each morphotype can be found forming high abundance along the bathymetric gradient of coral reefs that grow along the leeward coast of Curacao, Netherlands Antilles. We have undertaken a study to determine the relative relationships amongst coral morphology, skeletal density and feeding strategy by comparing the morphometric measurements of individual polyps as well as the entire colony along spatial and bathymetric gradients. Polyp diameter, mouth size, interpolyp area, and interpolyp distance were measured from high-resolution images taken on a stereoscope, and evaluated with AxioVision image analysis software. These high-resolution optical analyses have also revealed new observations regarding folded tissue structures of the outer margin of polyps in the Montastrea complex. Skeletal

  4. Density dynamics of diverse Spiroplasma strains naturally infecting different species of Drosophila

    PubMed Central

    Haselkorn, Tamara S; Watts, Thomas D; Markow, Therese A

    2013-01-01

    Facultative heritable bacterial endosymbionts can have dramatic effects on their hosts, ranging from mutualistic to parasitic. Within-host bacterial endosymbiont density plays a critical role in maintenance of a symbiotic relationship, as it can affect levels of vertical transmission and expression of phenotypic effects, both of which influence the infection prevalence in host populations. Species of genus Drosophila are infected with Spiroplasma, whose characterized phenotypic effects range from that of a male-killing reproductive parasite to beneficial defensive endosymbiont. For many strains of Spiroplasma infecting at least 17 species of Drosophila, however, the phenotypic effects are obscure. The infection prevalence of these Spiroplasma vary within and among Drosophila species, and little is known about the within-host density dynamics of these diverse strains. To characterize the patterns of Spiroplasma density variation among Drosophila we used quantitative PCR to assess bacterial titer at various life stages of three species of Drosophila naturally-infected with two different types of Spiroplasma. For naturally infected Drosophila species we found that non-male-killing infections had consistently lower densities than the male-killing infection. The patterns of Spiroplasma titer change during aging varied among Drosophila species infected with different Spiroplasma strains. Bacterial density varied within and among populations of Drosophila, with individuals from the population with the highest prevalence of infection having the highest density. This density variation underscores the complex interaction of Spiroplasma strain and host genetic background in determining endosymbiont density. PMID:23846301

  5. Does density influence relative growth performance of farm, wild and F1 hybrid Atlantic salmon in semi-natural and hatchery common garden conditions?

    PubMed

    Harvey, Alison C; Juleff, Gareth; Carvalho, Gary R; Taylor, Martin I; Solberg, Monica F; Creer, Simon; Dyrhovden, Lise; Matre, Ivar-Helge; Glover, Kevin A

    2016-07-01

    The conditions encountered by Atlantic salmon, Salmo salar L., in aquaculture are markedly different from the natural environment. Typically, farmed salmon experience much higher densities than wild individuals, and may therefore have adapted to living in high densities. Previous studies have demonstrated that farmed salmon typically outgrow wild salmon by large ratios in the hatchery, but these differences are much less pronounced in the wild. Such divergence in growth may be explained partly by the offspring of wild salmon experiencing higher stress and thus lower growth when compared under high-density farming conditions. Here, growth of farmed, wild and F1 hybrid salmon was studied at contrasting densities within a hatchery and semi-natural environment. Farmed salmon significantly outgrew hybrid and wild salmon in all treatments. Importantly, however, the reaction norms were similar across treatments for all groups. Thus, this study was unable to find evidence that the offspring of farmed salmon have adapted more readily to higher fish densities than wild salmon as a result of domestication. It is suggested that the substantially higher growth rate of farmed salmon observed in the hatchery compared with wild individuals may not solely be caused by differences in their ability to grow in high-density hatchery scenarios. PMID:27493772

  6. Does density influence relative growth performance of farm, wild and F1 hybrid Atlantic salmon in semi-natural and hatchery common garden conditions?

    PubMed Central

    Juleff, Gareth; Carvalho, Gary R.; Taylor, Martin I.; Creer, Simon; Dyrhovden, Lise; Matre, Ivar-Helge; Glover, Kevin A.

    2016-01-01

    The conditions encountered by Atlantic salmon, Salmo salar L., in aquaculture are markedly different from the natural environment. Typically, farmed salmon experience much higher densities than wild individuals, and may therefore have adapted to living in high densities. Previous studies have demonstrated that farmed salmon typically outgrow wild salmon by large ratios in the hatchery, but these differences are much less pronounced in the wild. Such divergence in growth may be explained partly by the offspring of wild salmon experiencing higher stress and thus lower growth when compared under high-density farming conditions. Here, growth of farmed, wild and F1 hybrid salmon was studied at contrasting densities within a hatchery and semi-natural environment. Farmed salmon significantly outgrew hybrid and wild salmon in all treatments. Importantly, however, the reaction norms were similar across treatments for all groups. Thus, this study was unable to find evidence that the offspring of farmed salmon have adapted more readily to higher fish densities than wild salmon as a result of domestication. It is suggested that the substantially higher growth rate of farmed salmon observed in the hatchery compared with wild individuals may not solely be caused by differences in their ability to grow in high-density hatchery scenarios. PMID:27493772

  7. Assessment of Different Sampling Methods for Measuring and Representing Macular Cone Density Using Flood-Illuminated Adaptive Optics

    PubMed Central

    Feng, Shu; Gale, Michael J.; Fay, Jonathan D.; Faridi, Ambar; Titus, Hope E.; Garg, Anupam K.; Michaels, Keith V.; Erker, Laura R.; Peters, Dawn; Smith, Travis B.; Pennesi, Mark E.

    2015-01-01

    Purpose To describe a standardized flood-illuminated adaptive optics (AO) imaging protocol suitable for the clinical setting and to assess sampling methods for measuring cone density. Methods Cone density was calculated following three measurement protocols: 50 × 50-μm sampling window values every 0.5° along the horizontal and vertical meridians (fixed-interval method), the mean density of expanding 0.5°-wide arcuate areas in the nasal, temporal, superior, and inferior quadrants (arcuate mean method), and the peak cone density of a 50 × 50-μm sampling window within expanding arcuate areas near the meridian (peak density method). Repeated imaging was performed in nine subjects to determine intersession repeatability of cone density. Results Cone density montages could be created for 67 of the 74 subjects. Image quality was determined to be adequate for automated cone counting for 35 (52%) of the 67 subjects. We found that cone density varied with different sampling methods and regions tested. In the nasal and temporal quadrants, peak density most closely resembled histological data, whereas the arcuate mean and fixed-interval methods tended to underestimate the density compared with histological data. However, in the inferior and superior quadrants, arcuate mean and fixed-interval methods most closely matched histological data, whereas the peak density method overestimated cone density compared with histological data. Intersession repeatability testing showed that repeatability was greatest when sampling by arcuate mean and lowest when sampling by fixed interval. Conclusions We show that different methods of sampling can significantly affect cone density measurements. Therefore, care must be taken when interpreting cone density results, even in a normal population. PMID:26325414

  8. Direct numerical simulations of particle-laden density currents with adaptive, discontinuous finite elements

    NASA Astrophysics Data System (ADS)

    Parkinson, S. D.; Hill, J.; Piggott, M. D.; Allison, P. A.

    2014-05-01

    High resolution direct numerical simulations (DNS) are an important tool for the detailed analysis of turbidity current dynamics. Models that resolve the vertical structure and turbulence of the flow are typically based upon the Navier-Stokes equations. Two-dimensional simulations are known to produce unrealistic cohesive vortices that are not representative of the real three-dimensional physics. The effect of this phenomena is particularly apparent in the later stages of flow propagation. The ideal solution to this problem is to run the simulation in three dimensions but this is computationally expensive. This paper presents a novel finite-element (FE) DNS turbidity current model that has been built within Fluidity, an open source, general purpose, computational fluid dynamics code. The model is validated through re-creation of a lock release density current at a Grashof number of 5 × 106 in two, and three-dimensions. Validation of the model considers the flow energy budget, sedimentation rate, head speed, wall normal velocity profiles and the final deposit. Conservation of energy in particular is found to be a good metric for measuring mesh performance in capturing the range of dynamics. FE models scale well over many thousands of processors and do not impose restrictions on domain shape, but they are computationally expensive. Use of discontinuous discretisations and adaptive unstructured meshing technologies, which reduce the required element count by approximately two orders of magnitude, results in high resolution DNS models of turbidity currents at a fraction of the cost of traditional FE models. The benefits of this technique will enable simulation of turbidity currents in complex and large domains where DNS modelling was previously unachievable.

  9. The interaction of sexually and naturally selected traits in the adaptive radiations of cichlid fishes.

    PubMed

    Salzburger, Walter

    2009-01-01

    The question of how genetic variation translates into organismal diversity has puzzled biologists for decades. Despite recent advances in evolutionary and developmental genetics, the mechanisms that underlie adaptation, diversification and evolutionary innovation remain largely unknown. The exceptionally diverse species flocks of cichlid fishes are textbook examples of adaptive radiation and explosive speciation and emerge as powerful model systems to study the genetic basis of animal diversification. East Africa's hundreds of endemic cichlid species are akin to a natural mutagenesis screen and differ greatly not only in ecologically relevant (hence naturally selected) characters such as mouth morphology and body shape, but also in sexually selected traits such as coloration. One of the most fascinating aspects of cichlid evolution is the frequent occurrence of evolutionary parallelisms, which has led to the question whether selection alone is sufficient to produce these parallel morphologies, or whether a developmental or genetic bias has influenced the direction of diversification. Here, I review fitness-relevant traits that could be responsible for the cichlids' evolutionary success and assess whether these were shaped by sexual or natural selection. I then focus on the interaction and the relative importance of sexual vs. natural selection in cichlid evolution. Finally, I discuss what is currently known about the genes underlying the morphogenesis of adaptively relevant traits and highlight the importance of the forthcoming cichlid genomes in the quest of the genetic basis of diversification in this group. PMID:18992003

  10. New applications for Coriolis flow and density measurement in the natural gas industry

    SciTech Connect

    Valentine, J.; Keilty, M.

    1995-11-01

    Simultaneous, highly accurate measurement of mass, density and temperature makes the Coriolis instrumentation ideal technology for a wide variety of natural gas applications. This paper describes the technology, discusses the benefits of using Coriolis instrumentation, and describes several applications related to the oil and gas production industries utilizing the Coriolis meter.

  11. Incorporating Natural Capital into Climate Adaptation Planning: Exploring the Role of Habitat in Increasing Coastal Resilience

    NASA Astrophysics Data System (ADS)

    Wedding, L.; Hartge, E. H.; Guannel, G.; Melius, M.; Reiter, S. M.; Ruckelshaus, M.; Guerry, A.; Caldwell, M.

    2014-12-01

    To support decision-makers in their efforts to manage coastal resources in a changing climate the Natural Capital Project and the Center for Ocean Solutions are engaging in, informing, and helping to shape climate adaptation planning at various scales throughout coastal California. Our team is building collaborations with regional planners and local scientific and legal experts to inform local climate adaptation decisions that might minimize the economic and social losses associated with rising seas and more damaging storms. Decision-makers are considering engineered solutions (e.g. seawalls), natural solutions (e.g. dune or marsh restoration), and combinations of the two. To inform decisions about what kinds of solutions might best work in specific locations, we are comparing alternate climate and adaptation scenarios. We will present results from our use of the InVEST ecosystem service models in Sonoma County, with an initial focus on protection from coastal hazards due to erosion and inundation. By strategically choosing adaptation alternatives, communities and agencies can work to protect people and property while also protecting or restoring dwindling critical habitat and the full suite of benefits those habitats provide to people.

  12. Complementary effect of natural and sexual selection against immigrants maintains differentiation between locally adapted fish

    NASA Astrophysics Data System (ADS)

    Plath, Martin; Riesch, Rüdiger; Oranth, Alexandra; Dzienko, Justina; Karau, Nora; Schießl, Angela; Stadler, Stefan; Wigh, Adriana; Zimmer, Claudia; Arias-Rodriguez, Lenin; Schlupp, Ingo; Tobler, Michael

    2010-08-01

    Adaptation to ecologically heterogeneous environments can drive speciation. But what mechanisms maintain reproductive isolation among locally adapted populations? Using poeciliid fishes in a system with naturally occurring toxic hydrogen sulfide, we show that (a) fish from non-sulfidic sites ( Poecilia mexicana) show high mortality (95 %) after 24 h when exposed to the toxicant, while locally adapted fish from sulfidic sites ( Poecilia sulphuraria) experience low mortality (13 %) when transferred to non-sulfidic water. (b) Mate choice tests revealed that P. mexicana females exhibit a preference for conspecific males in non-sulfidic water, but not in sulfidic water, whereas P. sulphuraria females never showed a preference. Increased costs of mate choice in sulfidic, hypoxic water, and the lack of selection for reinforcement due to the low survival of P. mexicana may explain the absence of a preference in P. sulphuraria females. Taken together, our study may be the first to demonstrate independent—but complementary—effects of natural and sexual selection against immigrants maintaining differentiation between locally adapted fish populations.

  13. Naturally occurring diversity helps to reveal genes of adaptive importance in legumes

    PubMed Central

    Gentzbittel, Laurent; Andersen, Stig U.; Ben, Cécile; Rickauer, Martina; Stougaard, Jens; Young, Nevin D.

    2015-01-01

    Environmental changes challenge plants and drive adaptation to new conditions, suggesting that natural biodiversity may be a source of adaptive alleles acting through phenotypic plasticity and/or micro-evolution. Crosses between accessions differing for a given trait have been the most common way to disentangle genetic and environmental components. Interestingly, such man-made crosses may combine alleles that never meet in nature. Another way to discover adaptive alleles, inspired by evolution, is to survey large ecotype collections and to use association genetics to identify loci of interest. Both of these two genetic approaches are based on the use of biodiversity and may eventually help us in identifying the genes that plants use to respond to challenges such as short-term stresses or those due to global climate change. In legumes, two wild species, Medicago truncatula and Lotus japonicus, plus the cultivated soybean (Glycine max) have been adopted as models for genomic studies. In this review, we will discuss the resources, limitations and future plans for a systematic use of biodiversity resources in model legumes to pinpoint genes of adaptive importance in legumes, and their application in breeding. PMID:25954294

  14. Adapting existing natural language processing resources for cardiovascular risk factors identification in clinical notes.

    PubMed

    Khalifa, Abdulrahman; Meystre, Stéphane

    2015-12-01

    The 2014 i2b2 natural language processing shared task focused on identifying cardiovascular risk factors such as high blood pressure, high cholesterol levels, obesity and smoking status among other factors found in health records of diabetic patients. In addition, the task involved detecting medications, and time information associated with the extracted data. This paper presents the development and evaluation of a natural language processing (NLP) application conceived for this i2b2 shared task. For increased efficiency, the application main components were adapted from two existing NLP tools implemented in the Apache UIMA framework: Textractor (for dictionary-based lookup) and cTAKES (for preprocessing and smoking status detection). The application achieved a final (micro-averaged) F1-measure of 87.5% on the final evaluation test set. Our attempt was mostly based on existing tools adapted with minimal changes and allowed for satisfying performance with limited development efforts. PMID:26318122

  15. On the nature of cultural transmission networks: evidence from Fijian villages for adaptive learning biases.

    PubMed

    Henrich, Joseph; Broesch, James

    2011-04-12

    Unlike other animals, humans are heavily dependent on cumulative bodies of culturally learned information. Selective processes operating on this socially learned information can produce complex, functionally integrated, behavioural repertoires-cultural adaptations. To understand such non-genetic adaptations, evolutionary theorists propose that (i) natural selection has favoured the emergence of psychological biases for learning from those individuals most likely to possess adaptive information, and (ii) when these psychological learning biases operate in populations, over generations, they can generate cultural adaptations. Many laboratory experiments now provide evidence for these psychological biases. Here, we bridge from the laboratory to the field by examining if and how these biases emerge in a small-scale society. Data from three cultural domains-fishing, growing yams and using medicinal plants-show that Fijian villagers (ages 10 and up) are biased to learn from others perceived as more successful/knowledgeable, both within and across domains (prestige effects). We also find biases for sex and age, as well as proximity effects. These selective and centralized oblique transmission networks set up the conditions for adaptive cultural evolution. PMID:21357236

  16. Natural Interferon α/β–Producing Cells Link Innate and Adaptive Immunity

    PubMed Central

    Kadowaki, Norimitsu; Antonenko, Svetlana; Lau, Johnson Yiu-Nam; Liu, Yong-Jun

    2000-01-01

    Innate immune responses to pathogens critically impact the development of adaptive immune responses. However, it is not completely understood how innate immunity controls the initiation of adaptive immunities or how it determines which type of adaptive immunity will be induced to eliminate a given pathogen. Here we show that viral stimulation not only triggers natural interferon (IFN)-α/β–producing cells (IPCs) to produce vast amounts of antiviral IFN-α/β but also induces these cells to differentiate into dendritic cells (DCs). IFN-α/β and tumor necrosis factor α produced by virus-activated IPCs act as autocrine survival and DC differentiation factors, respectively. The virus-induced DCs stimulate naive CD4+ T cells to produce IFN-γ and interleukin (IL)-10, in contrast to IL-3–induced DCs, which stimulate naive CD4+ T cells to produce T helper type 2 cytokines IL-4, IL-5, and IL-10. Thus, IPCs may play two master roles in antiviral immune responses: directly inhibiting viral replication by producing large amounts of IFN-α/β, and subsequently triggering adaptive T cell–mediated immunity by differentiating into DCs. IPCs constitute a critical link between innate and adaptive immunity. PMID:10899908

  17. Adaptation.

    PubMed

    Broom, Donald M

    2006-01-01

    The term adaptation is used in biology in three different ways. It may refer to changes which occur at the cell and organ level, or at the individual level, or at the level of gene action and evolutionary processes. Adaptation by cells, especially nerve cells helps in: communication within the body, the distinguishing of stimuli, the avoidance of overload and the conservation of energy. The time course and complexity of these mechanisms varies. Adaptive characters of organisms, including adaptive behaviours, increase fitness so this adaptation is evolutionary. The major part of this paper concerns adaptation by individuals and its relationships to welfare. In complex animals, feed forward control is widely used. Individuals predict problems and adapt by acting before the environmental effect is substantial. Much of adaptation involves brain control and animals have a set of needs, located in the brain and acting largely via motivational mechanisms, to regulate life. Needs may be for resources but are also for actions and stimuli which are part of the mechanism which has evolved to obtain the resources. Hence pigs do not just need food but need to be able to carry out actions like rooting in earth or manipulating materials which are part of foraging behaviour. The welfare of an individual is its state as regards its attempts to cope with its environment. This state includes various adaptive mechanisms including feelings and those which cope with disease. The part of welfare which is concerned with coping with pathology is health. Disease, which implies some significant effect of pathology, always results in poor welfare. Welfare varies over a range from very good, when adaptation is effective and there are feelings of pleasure or contentment, to very poor. A key point concerning the concept of individual adaptation in relation to welfare is that welfare may be good or poor while adaptation is occurring. Some adaptation is very easy and energetically cheap and

  18. Patch Size and Isolation Predict Plant Species Density in a Naturally Fragmented Forest

    PubMed Central

    Munguía-Rosas, Miguel A.; Montiel, Salvador

    2014-01-01

    Studies of the effects of patch size and isolation on plant species density have yielded contrasting results. However, much of the available evidence comes from relatively recent anthropogenic forest fragments which have not reached equilibrium between extinction and immigration. This is a critical issue because the theory clearly states that only when equilibrium has been reached can the number of species be accurately predicted by habitat size and isolation. Therefore, species density could be better predicted by patch size and isolation in an ecosystem that has been fragmented for a very long time. We tested whether patch area, isolation and other spatial variables explain variation among forest patches in plant species density in an ecosystem where the forest has been naturally fragmented for long periods of time on a geological scale. Our main predictions were that plant species density will be positively correlated with patch size, and negatively correlated with isolation (distance to the nearest patch, connectivity, and distance to the continuous forest). We surveyed the vascular flora (except lianas and epiphytes) of 19 forest patches using five belt transects (50×4 m each) per patch (area sampled per patch = 0.1 ha). As predicted, plant species density was positively associated (logarithmically) with patch size and negatively associated (linearly) with patch isolation (distance to the nearest patch). Other spatial variables such as patch elevation and perimeter, did not explain among-patch variability in plant species density. The power of patch area and isolation as predictors of plant species density was moderate (together they explain 43% of the variation), however, a larger sample size may improve the explanatory power of these variables. Patch size and isolation may be suitable predictors of long-term plant species density in terrestrial ecosystems that are naturally and anthropogenically fragmented. PMID:25347818

  19. Automated extraction of natural drainage density patterns for the conterminous United States through high performance computing

    USGS Publications Warehouse

    Stanislawski, Larry V.; Falgout, Jeff T.; Buttenfield, Barbara P.

    2015-01-01

    Hydrographic networks form an important data foundation for cartographic base mapping and for hydrologic analysis. Drainage density patterns for these networks can be derived to characterize local landscape, bedrock and climate conditions, and further inform hydrologic and geomorphological analysis by indicating areas where too few headwater channels have been extracted. But natural drainage density patterns are not consistently available in existing hydrographic data for the United States because compilation and capture criteria historically varied, along with climate, during the period of data collection over the various terrain types throughout the country. This paper demonstrates an automated workflow that is being tested in a high-performance computing environment by the U.S. Geological Survey (USGS) to map natural drainage density patterns at the 1:24,000-scale (24K) for the conterminous United States. Hydrographic network drainage patterns may be extracted from elevation data to guide corrections for existing hydrographic network data. The paper describes three stages in this workflow including data pre-processing, natural channel extraction, and generation of drainage density patterns from extracted channels. The workflow is concurrently implemented by executing procedures on multiple subbasin watersheds within the U.S. National Hydrography Dataset (NHD). Pre-processing defines parameters that are needed for the extraction process. Extraction proceeds in standard fashion: filling sinks, developing flow direction and weighted flow accumulation rasters. Drainage channels with assigned Strahler stream order are extracted within a subbasin and simplified. Drainage density patterns are then estimated with 100-meter resolution and subsequently smoothed with a low-pass filter. The extraction process is found to be of better quality in higher slope terrains. Concurrent processing through the high performance computing environment is shown to facilitate and refine

  20. Contemporary evolution during invasion: evidence for differentiation, natural selection, and local adaptation.

    PubMed

    Colautti, Robert I; Lau, Jennifer A

    2015-05-01

    Biological invasions are 'natural' experiments that can improve our understanding of contemporary evolution. We evaluate evidence for population differentiation, natural selection and adaptive evolution of invading plants and animals at two nested spatial scales: (i) among introduced populations (ii) between native and introduced genotypes. Evolution during invasion is frequently inferred, but rarely confirmed as adaptive. In common garden studies, quantitative trait differentiation is only marginally lower (~3.5%) among introduced relative to native populations, despite genetic bottlenecks and shorter timescales (i.e. millennia vs. decades). However, differentiation between genotypes from the native vs. introduced range is less clear and confounded by nonrandom geographic sampling; simulations suggest this causes a high false-positive discovery rate (>50%) in geographically structured populations. Selection differentials (¦s¦) are stronger in introduced than in native species, although selection gradients (¦β¦) are not, consistent with introduced species experiencing weaker genetic constraints. This could facilitate rapid adaptation, but evidence is limited. For example, rapid phenotypic evolution often manifests as geographical clines, but simulations demonstrate that nonadaptive trait clines can evolve frequently during colonization (~two-thirds of simulations). Additionally, QST-FST studies may often misrepresent the strength and form of natural selection acting during invasion. Instead, classic approaches in evolutionary ecology (e.g. selection analysis, reciprocal transplant, artificial selection) are necessary to determine the frequency of adaptive evolution during invasion and its influence on establishment, spread and impact of invasive species. These studies are rare but crucial for managing biological invasions in the context of global change. PMID:25891044

  1. Adaptive tolerance to a pathogenic fungus drives major histocompatibility complex evolution in natural amphibian populations

    PubMed Central

    Savage, Anna E.; Zamudio, Kelly R.

    2016-01-01

    Amphibians have been affected globally by the disease chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis (Bd), and we are just now beginning to understand how immunogenetic variability contributes to disease susceptibility. Lineages of an expressed major histocompatibility complex (MHC) class II locus involved in acquired immunity are associated with chytridiomycosis susceptibility in controlled laboratory challenge assays. Here, we extend these findings to natural populations that vary both in exposure and response to Bd. We find that MHC alleles and supertypes associated with Bd survival in the field show a molecular signal of positive selection, while those associated with susceptibility do not, supporting the hypothesis that heritable Bd tolerance is rapidly evolving. We compare MHC supertypes to neutral loci to demonstrate where selection versus demography is shaping MHC variability. One population with Bd tolerance in nature shows a significant signal of directional selection for the same allele (allele Q) that was significantly associated with survival in an earlier laboratory study. Our findings indicate that selective pressure for Bd survival drives rapid immunogenetic adaptation in some natural populations, despite differences in environment and demography. Our field-based analysis of immunogenetic variation confirms that natural amphibian populations have the evolutionary potential to adapt to chytridiomycosis. PMID:27009220

  2. Adaptive tolerance to a pathogenic fungus drives major histocompatibility complex evolution in natural amphibian populations.

    PubMed

    Savage, Anna E; Zamudio, Kelly R

    2016-03-30

    Amphibians have been affected globally by the disease chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis (Bd), and we are just now beginning to understand how immunogenetic variability contributes to disease susceptibility. Lineages of an expressed major histocompatibility complex (MHC) class II locus involved in acquired immunity are associated with chytridiomycosis susceptibility in controlled laboratory challenge assays. Here, we extend these findings to natural populations that vary both in exposure and response to Bd We find that MHC alleles and supertypes associated with Bd survival in the field show a molecular signal of positive selection, while those associated with susceptibility do not, supporting the hypothesis that heritable Bd tolerance is rapidly evolving. We compare MHC supertypes to neutral loci to demonstrate where selection versus demography is shaping MHC variability. One population with Bd tolerance in nature shows a significant signal of directional selection for the same allele (allele Q) that was significantly associated with survival in an earlier laboratory study. Our findings indicate that selective pressure for Bd survival drives rapid immunogenetic adaptation in some natural populations, despite differences in environment and demography. Our field-based analysis of immunogenetic variation confirms that natural amphibian populations have the evolutionary potential to adapt to chytridiomycosis. PMID:27009220

  3. Study of Interpolated Timing Recovery Phase-Locked Loop with Linearly Constrained Adaptive Prefilter for Higher-Density Optical Disc

    NASA Astrophysics Data System (ADS)

    Kajiwara, Yoshiyuki; Shiraishi, Junya; Kobayashi, Shoei; Yamagami, Tamotsu

    2009-03-01

    A digital phase-locked loop (PLL) with a linearly constrained adaptive filter (LCAF) has been studied for higher-linear-density optical discs. LCAF has been implemented before an interpolated timing recovery (ITR) PLL unit in order to improve the quality of phase error calculation by using an adaptively equalized partial response (PR) signal. Coefficient update of an asynchronous sampled adaptive FIR filter with a least-mean-square (LMS) algorithm has been constrained by a projection matrix in order to suppress the phase shift of the tap coefficients of the adaptive filter. We have developed projection matrices that are suitable for Blu-ray disc (BD) drive systems by numerical simulation. Results have shown the properties of the projection matrices. Then, we have designed the read channel system of the ITR PLL with an LCAF model on the FPGA board for experiments. Results have shown that the LCAF improves the tilt margins of 30 gigabytes (GB) recordable BD (BD-R) and 33 GB BD read-only memory (BD-ROM) with a sufficient LMS adaptation stability.

  4. The Elusive Nature of Adaptive Mitochondrial DNA Evolution of an Arctic Lineage Prone to Frequent Introgression

    PubMed Central

    Melo-Ferreira, José; Vilela, Joana; Fonseca, Miguel M.; da Fonseca, Rute R.; Boursot, Pierre; Alves, Paulo C.

    2014-01-01

    Mitochondria play a fundamental role in cellular metabolism, being responsible for most of the energy production of the cell in the oxidative phosphorylation (OXPHOS) pathway. Mitochondrial DNA (mtDNA) encodes for key components of this process, but its direct role in adaptation remains far from understood. Hares (Lepus spp.) are privileged models to study the impact of natural selection on mitogenomic evolution because 1) species are adapted to contrasting environments, including arctic, with different metabolic pressures, and 2) mtDNA introgression from arctic into temperate species is widespread. Here, we analyzed the sequences of 11 complete mitogenomes (ten newly obtained) of hares of temperate and arctic origins (including two of arctic origin introgressed into temperate species). The analysis of patterns of codon substitutions along the reconstructed phylogeny showed evidence for positive selection in several codons in genes of the OXPHOS complexes, most notably affecting the arctic lineage. However, using theoretical models, no predictable effect of these differences was found on the structure and physicochemical properties of the encoded proteins, suggesting that the focus of selection may lie on complex interactions with nuclear encoded peptides. Also, a cloverleaf structure was detected in the control region only from the arctic mtDNA lineage, which may influence mtDNA replication and transcription. These results suggest that adaptation impacted the evolution of hare mtDNA and may have influenced the occurrence and consequences of the many reported cases of massive mtDNA introgression. However, the origin of adaptation remains elusive. PMID:24696399

  5. Natural selection fails to optimize mutation rates for long-term adaptation on rugged fitness landscapes.

    PubMed

    Clune, Jeff; Misevic, Dusan; Ofria, Charles; Lenski, Richard E; Elena, Santiago F; Sanjuán, Rafael

    2008-01-01

    The rate of mutation is central to evolution. Mutations are required for adaptation, yet most mutations with phenotypic effects are deleterious. As a consequence, the mutation rate that maximizes adaptation will be some intermediate value. Here, we used digital organisms to investigate the ability of natural selection to adjust and optimize mutation rates. We assessed the optimal mutation rate by empirically determining what mutation rate produced the highest rate of adaptation. Then, we allowed mutation rates to evolve, and we evaluated the proximity to the optimum. Although we chose conditions favorable for mutation rate optimization, the evolved rates were invariably far below the optimum across a wide range of experimental parameter settings. We hypothesized that the reason that mutation rates evolved to be suboptimal was the ruggedness of fitness landscapes. To test this hypothesis, we created a simplified landscape without any fitness valleys and found that, in such conditions, populations evolved near-optimal mutation rates. In contrast, when fitness valleys were added to this simple landscape, the ability of evolving populations to find the optimal mutation rate was lost. We conclude that rugged fitness landscapes can prevent the evolution of mutation rates that are optimal for long-term adaptation. This finding has important implications for applied evolutionary research in both biological and computational realms. PMID:18818724

  6. Natural Selection Fails to Optimize Mutation Rates for Long-Term Adaptation on Rugged Fitness Landscapes

    PubMed Central

    Clune, Jeff; Misevic, Dusan; Ofria, Charles; Lenski, Richard E.; Elena, Santiago F.; Sanjuán, Rafael

    2008-01-01

    The rate of mutation is central to evolution. Mutations are required for adaptation, yet most mutations with phenotypic effects are deleterious. As a consequence, the mutation rate that maximizes adaptation will be some intermediate value. Here, we used digital organisms to investigate the ability of natural selection to adjust and optimize mutation rates. We assessed the optimal mutation rate by empirically determining what mutation rate produced the highest rate of adaptation. Then, we allowed mutation rates to evolve, and we evaluated the proximity to the optimum. Although we chose conditions favorable for mutation rate optimization, the evolved rates were invariably far below the optimum across a wide range of experimental parameter settings. We hypothesized that the reason that mutation rates evolved to be suboptimal was the ruggedness of fitness landscapes. To test this hypothesis, we created a simplified landscape without any fitness valleys and found that, in such conditions, populations evolved near-optimal mutation rates. In contrast, when fitness valleys were added to this simple landscape, the ability of evolving populations to find the optimal mutation rate was lost. We conclude that rugged fitness landscapes can prevent the evolution of mutation rates that are optimal for long-term adaptation. This finding has important implications for applied evolutionary research in both biological and computational realms. PMID:18818724

  7. Adaptation potential of naturally ventilated barns to high temperature extremes: The OptiBarn project

    NASA Astrophysics Data System (ADS)

    Menz, Christoph

    2016-04-01

    Climate change interferes with various aspects of the socio-economic system. One important aspect is its influence on animal husbandry, especially dairy faming. Dairy cows are usually kept in naturally ventilated barns (NVBs) which are particular vulnerable to extreme events due to their low adaptation capabilities. An effective adaptation to high outdoor temperatures for example, is only possible under certain wind and humidity conditions. High temperature extremes are expected to increase in number and strength under climate change. To assess the impact of this change on NVBs and dairy cows also the changes in wind and humidity needs to be considered. Hence we need to consider the multivariate structure of future temperature extremes. The OptiBarn project aims to develop sustainable adaptation strategies for dairy housings under climate change for Europe, by considering the multivariate structure of high temperature extremes. In a first step we identify various multivariate high temperature extremes for three core regions in Europe. With respect to dairy cows in NVBs we will focus on the wind and humidity field during high temperature events. In a second step we will use the CORDEX-EUR-11 ensemble to evaluate the capability of the RCMs to model such events and assess their future change potential. By transferring the outdoor conditions to indoor climate and animal wellbeing the results of this assessment can be used to develop technical, architectural and animal specific adaptation strategies for high temperature extremes.

  8. Testing Local Adaptation in a Natural Great Tit-Malaria System: An Experimental Approach

    PubMed Central

    Jenkins, Tania; Delhaye, Jessica; Christe, Philippe

    2015-01-01

    Finding out whether Plasmodium spp. are coevolving with their vertebrate hosts is of both theoretical and applied interest and can influence our understanding of the effects and dynamics of malaria infection. In this study, we tested for local adaptation as a signature of coevolution between malaria blood parasites, Plasmodium spp. and its host, the great tit, Parus major. We conducted a reciprocal transplant experiment of birds in the field, where we exposed birds from two populations to Plasmodium parasites. This experimental set-up also provided a unique opportunity to study the natural history of malaria infection in the wild and to assess the effects of primary malaria infection on juvenile birds. We present three main findings: i) there was no support for local adaptation; ii) there was a male-biased infection rate; iii) infection occurred towards the end of the summer and differed between sites. There were also site-specific effects of malaria infection on the hosts. Taken together, we present one of the few experimental studies of parasite-host local adaptation in a natural malaria system, and our results shed light on the effects of avian malaria infection in the wild. PMID:26555892

  9. Adaptive Colour Contrast Coding in the Salamander Retina Efficiently Matches Natural Scene Statistics

    PubMed Central

    Vasserman, Genadiy; Schneidman, Elad; Segev, Ronen

    2013-01-01

    The visual system continually adjusts its sensitivity to the statistical properties of the environment through an adaptation process that starts in the retina. Colour perception and processing is commonly thought to occur mainly in high visual areas, and indeed most evidence for chromatic colour contrast adaptation comes from cortical studies. We show that colour contrast adaptation starts in the retina where ganglion cells adjust their responses to the spectral properties of the environment. We demonstrate that the ganglion cells match their responses to red-blue stimulus combinations according to the relative contrast of each of the input channels by rotating their functional response properties in colour space. Using measurements of the chromatic statistics of natural environments, we show that the retina balances inputs from the two (red and blue) stimulated colour channels, as would be expected from theoretical optimal behaviour. Our results suggest that colour is encoded in the retina based on the efficient processing of spectral information that matches spectral combinations in natural scenes on the colour processing level. PMID:24205373

  10. A study of factors affecting the human cone photoreceptor density measured by adaptive optics scanning laser ophthalmoscope

    PubMed Central

    Park, Sung Pyo; Chung, Jae Keun; Greenstein, Vivienne; Tsang, Stephen H.; Chang, Stanley

    2015-01-01

    To investigate the variation in human cone photoreceptor packing density with various demographic or clinical factors, cone packing density was measured using a Canon prototype adaptive optics scanning laser ophthalmoscope and compared as a function of retinal eccentricity, refractive error, axial length, age, gender, race/ethnicity and ocular dominance. We enrolled 192 eyes of 192 subjects with no ocular pathology. Cone packing density was measured at three different retinal eccentricities (0.5 mm, 1.0 mm, and 1.5 mm from the foveal center) along four meridians. Cone density decreased from 32,200 to 11,600 cells/mm2 with retinal eccentricity (0.5 mm to 1.5 mm from the fovea, P < 0.001). A trend towards a slightly negative correlation was observed between age and density (r = −0.117, P = 0.14). There was, however, a statistically significant negative correlation (r = −0.367, P = 0.003) between axial length and cone density. Gender, ocular dominance, and race/ethnicity were not important determinants of cone density (all, P > 0.05). In addition, to assess the spatial arrangement of the cone mosaics, the nearest-neighbor distances (NNDs) and the Voronoi domains were analyzed. The results of NND and Voronoi analysis were significantly correlated with the variation of the cone density. Average NND and Voronoi area were gradually increased (all, P ≤ 0.001) and the degree of regularity of the cone mosaics was decreased (P ≤ 0.001) with increasing retinal eccentricity. In conclusion, we demonstrated cone packing density decreases as a function of retinal eccentricity and axial length and the results of NND and Voronoi analysis is a useful index for cone mosaics arrangements. The results also serve as a reference for further studies designed to detect or monitor cone photoreceptors in patients with retinal diseases. PMID:23276813

  11. Nature of Adaptive Behavior Deficits among Individuals Who Are Moderately-Severely Mentally Retarded in the West Bank.

    ERIC Educational Resources Information Center

    Baker, Ahmad M.

    1989-01-01

    Results of assessing the adaptive behavior of 200 individuals classified as mentally retarded and living in the West Bank region of the Middle East suggest that the nature and development of adaptive behavior of the mentally retarded in Third World areas may not conform to expected trends. (Author/DB)

  12. Adapt

    NASA Astrophysics Data System (ADS)

    Bargatze, L. F.

    2015-12-01

    Active Data Archive Product Tracking (ADAPT) is a collection of software routines that permits one to generate XML metadata files to describe and register data products in support of the NASA Heliophysics Virtual Observatory VxO effort. ADAPT is also a philosophy. The ADAPT concept is to use any and all available metadata associated with scientific data to produce XML metadata descriptions in a consistent, uniform, and organized fashion to provide blanket access to the full complement of data stored on a targeted data server. In this poster, we present an application of ADAPT to describe all of the data products that are stored by using the Common Data File (CDF) format served out by the CDAWEB and SPDF data servers hosted at the NASA Goddard Space Flight Center. These data servers are the primary repositories for NASA Heliophysics data. For this purpose, the ADAPT routines have been used to generate data resource descriptions by using an XML schema named Space Physics Archive, Search, and Extract (SPASE). SPASE is the designated standard for documenting Heliophysics data products, as adopted by the Heliophysics Data and Model Consortium. The set of SPASE XML resource descriptions produced by ADAPT includes high-level descriptions of numerical data products, display data products, or catalogs and also includes low-level "Granule" descriptions. A SPASE Granule is effectively a universal access metadata resource; a Granule associates an individual data file (e.g. a CDF file) with a "parent" high-level data resource description, assigns a resource identifier to the file, and lists the corresponding assess URL(s). The CDAWEB and SPDF file systems were queried to provide the input required by the ADAPT software to create an initial set of SPASE metadata resource descriptions. Then, the CDAWEB and SPDF data repositories were queried subsequently on a nightly basis and the CDF file lists were checked for any changes such as the occurrence of new, modified, or deleted

  13. Centroid gain compensation in Shack-Hartmann adaptive optics systems with natural or laser guide star

    PubMed

    Veran; Herriot

    2000-08-01

    In an adaptive optics system with an undersampled Shack-Hartmann wave-front sensor (WFS), variations in seeing, laser guide star quality, and sodium layer thickness and range distance all combine to vary WFS centroid gain across the pupil during an exposure. While using the minimum of 4 pixels per WFS subaperture improves frame rate and read noise, the WFS centroid gain uncertainty may introduce static aberrations and degrade servo loop phase margin. We present a novel method to estimate and compensate WFS gains of each subaperture individually in real time for both natural and laser guide stars. PMID:10935871

  14. Adaptive nest clustering and density-dependent nest survival in dabbling ducks

    USGS Publications Warehouse

    Ringelman, Kevin M.; Eadie, John M.; Ackerman, Joshua T.

    2014-01-01

    Density-dependent population regulation is observed in many taxa, and understanding the mechanisms that generate density dependence is especially important for the conservation of heavily-managed species. In one such system, North American waterfowl, density dependence is often observed at continental scales, and nest predation has long been implicated as a key factor driving this pattern. However, despite extensive research on this topic, it remains unclear if and how nest density influences predation rates. Part of this confusion may have arisen because previous studies have studied density-dependent predation at relatively large spatial and temporal scales. Because the spatial distribution of nests changes throughout the season, which potentially influences predator behavior, nest survival may vary through time at relatively small spatial scales. As such, density-dependent nest predation might be more detectable at a spatially- and temporally-refined scale and this may provide new insights into nest site selection and predator foraging behavior. Here, we used three years of data on nest survival of two species of waterfowl, mallards and gadwall, to more fully explore the relationship between local nest clustering and nest survival. Throughout the season, we found that the distribution of nests was consistently clustered at small spatial scales (˜50–400 m), especially for mallard nests, and that this pattern was robust to yearly variation in nest density and the intensity of predation. We demonstrated further that local nest clustering had positive fitness consequences – nests with closer nearest neighbors were more likely to be successful, a result that is counter to the general assumption that nest predation rates increase with nest density.

  15. A progressive data compression scheme based upon adaptive transform coding: Mixture block coding of natural images

    NASA Technical Reports Server (NTRS)

    Rost, Martin C.; Sayood, Khalid

    1991-01-01

    A method for efficiently coding natural images using a vector-quantized variable-blocksized transform source coder is presented. The method, mixture block coding (MBC), incorporates variable-rate coding by using a mixture of discrete cosine transform (DCT) source coders. Which coders are selected to code any given image region is made through a threshold driven distortion criterion. In this paper, MBC is used in two different applications. The base method is concerned with single-pass low-rate image data compression. The second is a natural extension of the base method which allows for low-rate progressive transmission (PT). Since the base method adapts easily to progressive coding, it offers the aesthetic advantage of progressive coding without incorporating extensive channel overhead. Image compression rates of approximately 0.5 bit/pel are demonstrated for both monochrome and color images.

  16. Dynamics of the adaptive natural gradient descent method for soft committee machines

    NASA Astrophysics Data System (ADS)

    Inoue, Masato; Park, Hyeyoung; Okada, Masato

    2004-05-01

    Adaptive natural gradient descent (ANGD) method realizes natural gradient descent (NGD) without needing to know the input distribution of learning data and reduces the calculation cost from a cubic order to a square order. However, no performance analysis of ANGD has been done. We have developed a statistical-mechanical theory of the simplified version of ANGD dynamics for soft committee machines in on-line learning; this method provides deterministic learning dynamics expressed through a few order parameters, even though ANGD intrinsically holds a large approximated Fisher information matrix. Numerical results obtained using this theory were consistent with those of a simulation, with respect not only to the learning curve but also to the learning failure. Utilizing this method, we numerically evaluated ANGD efficiency and found that ANGD generally performs as well as NGD. We also revealed the key condition affecting the learning plateau in ANGD.

  17. Stochastic effects in adaptive reconstruction of body damage: implied the creativity of natural selection.

    PubMed

    Xiao, Bo; Cui, Li-Qiang; Chen, Tian-Ming; Lian, Bin

    2015-11-01

    After an injury occurs, mechanical/biochemical loads on muscles influence the composition and structure of recovering muscles; this effect likely occurs in other tissues, cells and biological molecules as well owing to the similarity, interassociation and interaction among biochemical reactions and molecules. The 'damage and reconstruction' model provides an explanation for how an ideal cytoarchitecture is created by reducing components not suitable for bearing loads; in this model, adaptive changes are induced by promoting the stochasticity of biochemical reactions. Biochemical and mechanical loads can direct the stochasticity of biochemical reactions, which can in turn induce cellular changes. Thus, mechanical and biochemical loads, under natural selection pressure, modify the direction of cell- and tissue-level changes and guide the formation of new structures and traits, thereby influencing microevolution. In summary, the 'damage and reconstruction' model accounts for the role of natural selection in the formation of new organisms, helps explain punctuated equilibrium, and illustrates how macroevolution arises from microevolution. PMID:26153081

  18. Adapting Semantic Natural Language Processing Technology to Address Information Overload in Influenza Epidemic Management

    PubMed Central

    Keselman, Alla; Rosemblat, Graciela; Kilicoglu, Halil; Fiszman, Marcelo; Jin, Honglan; Shin, Dongwook; Rindflesch, Thomas C.

    2013-01-01

    Explosion of disaster health information results in information overload among response professionals. The objective of this project was to determine the feasibility of applying semantic natural language processing (NLP) technology to addressing this overload. The project characterizes concepts and relationships commonly used in disaster health-related documents on influenza pandemics, as the basis for adapting an existing semantic summarizer to the domain. Methods include human review and semantic NLP analysis of a set of relevant documents. This is followed by a pilot-test in which two information specialists use the adapted application for a realistic information seeking task. According to the results, the ontology of influenza epidemics management can be described via a manageable number of semantic relationships that involve concepts from a limited number of semantic types. Test users demonstrate several ways to engage with the application to obtain useful information. This suggests that existing semantic NLP algorithms can be adapted to support information summarization and visualization in influenza epidemics and other disaster health areas. However, additional research is needed in the areas of terminology development (as many relevant relationships and terms are not part of existing standardized vocabularies), NLP, and user interface design. PMID:24311971

  19. Adapting Semantic Natural Language Processing Technology to Address Information Overload in Influenza Epidemic Management.

    PubMed

    Keselman, Alla; Rosemblat, Graciela; Kilicoglu, Halil; Fiszman, Marcelo; Jin, Honglan; Shin, Dongwook; Rindflesch, Thomas C

    2010-12-01

    Explosion of disaster health information results in information overload among response professionals. The objective of this project was to determine the feasibility of applying semantic natural language processing (NLP) technology to addressing this overload. The project characterizes concepts and relationships commonly used in disaster health-related documents on influenza pandemics, as the basis for adapting an existing semantic summarizer to the domain. Methods include human review and semantic NLP analysis of a set of relevant documents. This is followed by a pilot-test in which two information specialists use the adapted application for a realistic information seeking task. According to the results, the ontology of influenza epidemics management can be described via a manageable number of semantic relationships that involve concepts from a limited number of semantic types. Test users demonstrate several ways to engage with the application to obtain useful information. This suggests that existing semantic NLP algorithms can be adapted to support information summarization and visualization in influenza epidemics and other disaster health areas. However, additional research is needed in the areas of terminology development (as many relevant relationships and terms are not part of existing standardized vocabularies), NLP, and user interface design. PMID:24311971

  20. Adaptive Transgenerational Plasticity in Plants: Case Studies, Mechanisms, and Implications for Natural Populations

    PubMed Central

    Herman, Jacob J.; Sultan, Sonia E.

    2011-01-01

    Plants respond to environmental conditions not only by plastic changes to their own development and physiology, but also by altering the phenotypes expressed by their offspring. This transgenerational plasticity was initially considered to entail only negative effects of stressful parental environments, such as production of smaller seeds by resource- or temperature-stressed parent plants, and was therefore viewed as environmental noise. Recent evolutionary ecology studies have shown that in some cases, these inherited environmental effects can include specific growth adjustments that are functionally adaptive to the parental conditions that induced them, which can range from contrasting states of controlled laboratory environments to the complex habitat variation encountered by natural plant populations. Preliminary findings suggest that adaptive transgenerational effects can be transmitted by means of diverse mechanisms including changes to seed provisioning and biochemistry, and epigenetic modifications such as DNA methylation that can persist across multiple generations. These non-genetically inherited adaptations can influence the ecological breadth and evolutionary dynamics of plant taxa and promote the spread of invasive plants. Interdisciplinary studies that join mechanistic and evolutionary ecology approaches will be an important source of future insights. PMID:22639624

  1. Ocean Turbulence V: Mesoscale Modeling in Level Coordinates. The Effect of Random Nature of Density

    NASA Technical Reports Server (NTRS)

    Canuto, V. M.; Dubovikov, M. S.

    1998-01-01

    The main result of this paper is the derivation of a new expression for the tracer subgrid term in level coordinates S(l) to be employed in O-GCM. The novel feature is the proper account of the random nature of the density field which strongly affects the transformation from isopycnal to level coordinates of the variables of interest, velocity and tracer fields, their correlation functions and ultimately the subgrid terms. In deriving our result we made use of measured properties of vertical ocean turbulence. The major new results are: 1) the new subgrid expression is different from that of the heuristic GM model, 2) u++(tracer)=1/2u+(thickness), where u++ and u+ are the tracer and thickness bolus velocities. In previous models, u++ = u+, 2) the subgrid for a tracer tau is not the same as that for the density rho even when one accounts for the obvious absence of a diffusion term in the latter. The difference stems from a new treatment of the stochastic nature of the density, 3) the mesoscale diffusivity enters both locally and non-locally, as the integral over all z's from the bottom of the ocean to the level z.

  2. Social and Natural Sciences Differ in Their Research Strategies, Adapted to Work for Different Knowledge Landscapes

    PubMed Central

    Jaffe, Klaus

    2014-01-01

    Do different fields of knowledge require different research strategies? A numerical model exploring different virtual knowledge landscapes, revealed two diverging optimal search strategies. Trend following is maximized when the popularity of new discoveries determine the number of individuals researching it. This strategy works best when many researchers explore few large areas of knowledge. In contrast, individuals or small groups of researchers are better in discovering small bits of information in dispersed knowledge landscapes. Bibliometric data of scientific publications showed a continuous bipolar distribution of these strategies, ranging from natural sciences, with highly cited publications in journals containing a large number of articles, to the social sciences, with rarely cited publications in many journals containing a small number of articles. The natural sciences seem to adapt their research strategies to landscapes with large concentrated knowledge clusters, whereas social sciences seem to have adapted to search in landscapes with many small isolated knowledge clusters. Similar bipolar distributions were obtained when comparing levels of insularity estimated by indicators of international collaboration and levels of country-self citations: researchers in academic areas with many journals such as social sciences, arts and humanities, were the most isolated, and that was true in different regions of the world. The work shows that quantitative measures estimating differences between academic disciplines improve our understanding of different research strategies, eventually helping interdisciplinary research and may be also help improve science policies worldwide. PMID:25426723

  3. An Empirical Analysis of Farm Adaptation Response to Water Security Using a Natural Policy Experiment

    NASA Astrophysics Data System (ADS)

    Brady, M.

    2014-12-01

    The capacity of farm-level adaptation to mitigate the impacts of climate change in arid regions dominated by irrigated agriculture fed by snowpack is a critical challenge for developing accurate integrated engineering-economic modeling tools. Economic optimization models provide a valuable benchmark for the theoretical limit of adaptation given a set of clear objectives, conditions, and constraints. However, a major limitation to specifying tractable and accurate models is the large number of potential adaptation strategies that can be taken. There is a need for more empirical research that reveals preferred adaptation strategies in a way that identifies causal relationships. This research seeks to add to the empirical literature on adaptation by exploiting what in the econometric literature is called a "natural experiment" where a policy has isapplied to one group but not another in a way that is random relative to the variables of interest so as to reduce problems of bias in coefficient estimates caused by unobserved heterogeneity. The region of study is the Yakima Basin in Washington State which is a highly diverse region in terms of crop and irrigation technology. This creates significant complication for modeling adaptation since farmers have a wide array of choices including changing cropping patterns and irrigation technologies. Other strategies including water trading and deficit irrigation. Two irrigation districts in the Yakima Basin, Roza and Sunnyside, are adjacent to each other and are nearly identical in growing conditions. The difference is that Roza is severely curtailed during droughts while Sunnyside is not. With the availability of detailed field level data on cropping patterns, irrigation technologies, and land ownership this presents an opportunity to identify the effect of water security risk on farm-level decision making. Preliminary results show that after controlling for other features, a field in Roza is 5% more likely to have an efficient

  4. On the Nature of Variations in Density and Composition within TATB-based Plastic Bonded Explosives

    SciTech Connect

    Kinney, J H; Willey, T M; Overturf, G

    2006-06-27

    Initiation of insensitive high explosives is affected by porosity in the 100 nm to micron size range. It is also recognized that as-pressed plastic bonded explosives (PBX) are heterogeneous in composition and density at much coarser length scale (10 microns-100 microns). However, variations in density and composition of these explosives have been poorly characterized. Here, we characterize the natural variations in composition and density of TATB-based PBX LX-17 with synchrotron radiation tomography and ultra small angle x-ray scattering. Large scale variations in composition occur as a result of binder enrichment at the prill particle boundaries. The pore fraction is twice as high in the prill particle as in the boundary. The pore distribution is bimodal, with small pores of 50-100 nm in radius and a broader distribution of pores in the 0.5-1.5 micron size range. The higher pore density within the prill particle is attributed to contact asperities between the crystallites that might inhibit complete consolidation and binder infiltration.

  5. Evolutionary adaptations for the temporal processing of natural sounds by the anuran peripheral auditory system.

    PubMed

    Schrode, Katrina M; Bee, Mark A

    2015-03-01

    Sensory systems function most efficiently when processing natural stimuli, such as vocalizations, and it is thought that this reflects evolutionary adaptation. Among the best-described examples of evolutionary adaptation in the auditory system are the frequent matches between spectral tuning in both the peripheral and central auditory systems of anurans (frogs and toads) and the frequency spectra of conspecific calls. Tuning to the temporal properties of conspecific calls is less well established, and in anurans has so far been documented only in the central auditory system. Using auditory-evoked potentials, we asked whether there are species-specific or sex-specific adaptations of the auditory systems of gray treefrogs (Hyla chrysoscelis) and green treefrogs (H. cinerea) to the temporal modulations present in conspecific calls. Modulation rate transfer functions (MRTFs) constructed from auditory steady-state responses revealed that each species was more sensitive than the other to the modulation rates typical of conspecific advertisement calls. In addition, auditory brainstem responses (ABRs) to paired clicks indicated relatively better temporal resolution in green treefrogs, which could represent an adaptation to the faster modulation rates present in the calls of this species. MRTFs and recovery of ABRs to paired clicks were generally similar between the sexes, and we found no evidence that males were more sensitive than females to the temporal modulation patterns characteristic of the aggressive calls used in male-male competition. Together, our results suggest that efficient processing of the temporal properties of behaviorally relevant sounds begins at potentially very early stages of the anuran auditory system that include the periphery. PMID:25617467

  6. Evolutionary adaptations for the temporal processing of natural sounds by the anuran peripheral auditory system

    PubMed Central

    Schrode, Katrina M.; Bee, Mark A.

    2015-01-01

    ABSTRACT Sensory systems function most efficiently when processing natural stimuli, such as vocalizations, and it is thought that this reflects evolutionary adaptation. Among the best-described examples of evolutionary adaptation in the auditory system are the frequent matches between spectral tuning in both the peripheral and central auditory systems of anurans (frogs and toads) and the frequency spectra of conspecific calls. Tuning to the temporal properties of conspecific calls is less well established, and in anurans has so far been documented only in the central auditory system. Using auditory-evoked potentials, we asked whether there are species-specific or sex-specific adaptations of the auditory systems of gray treefrogs (Hyla chrysoscelis) and green treefrogs (H. cinerea) to the temporal modulations present in conspecific calls. Modulation rate transfer functions (MRTFs) constructed from auditory steady-state responses revealed that each species was more sensitive than the other to the modulation rates typical of conspecific advertisement calls. In addition, auditory brainstem responses (ABRs) to paired clicks indicated relatively better temporal resolution in green treefrogs, which could represent an adaptation to the faster modulation rates present in the calls of this species. MRTFs and recovery of ABRs to paired clicks were generally similar between the sexes, and we found no evidence that males were more sensitive than females to the temporal modulation patterns characteristic of the aggressive calls used in male–male competition. Together, our results suggest that efficient processing of the temporal properties of behaviorally relevant sounds begins at potentially very early stages of the anuran auditory system that include the periphery. PMID:25617467

  7. Generating relevant climate adaptation science tools in concert with local natural resource agencies

    NASA Astrophysics Data System (ADS)

    Micheli, L.; Flint, L. E.; Veloz, S.; Heller, N. E.

    2015-12-01

    To create a framework for adapting to climate change, decision makers operating at the urban-wildland interface need to define climate vulnerabilities in the context of site-specific opportunities and constraints relative to water supply, land use suitability, wildfire risks, ecosystem services and quality of life. Pepperwood's TBC3.org is crafting customized climate vulnerability assessments with selected water and natural resource agencies of California's Sonoma, Marin, Napa and Mendocino counties under the auspices of Climate Ready North Bay, a public-private partnership funded by the California Coastal Conservancy. Working directly with managers from the very start of the process to define resource-specific information needs, we are developing high-resolution, spatially-explicit data products to help local governments and agency staff implement informed and effective climate adaptation strategies. Key preliminary findings for the region using the USGS' Basin Characterization Model (at a 270 m spatial resolution) include a unidirectional trend, independent of greater or lesser precipitation, towards increasing climatic water deficits across model scenarios. Therefore a key message is that managers will be facing an increasingly arid environment. Companion models translate the impacts of shifting climate and hydrology on vegetation composition and fire risks. The combination of drought stress on water supplies and native vegetation with an approximate doubling of fire risks may demand new approaches to watershed planning. Working with agencies we are exploring how to build capacity for protection and enhancement of key watershed functions with a focus on groundwater recharge, facilitating greater drought tolerance in forest and rangeland systems, and considering more aggressive approaches to management of fuel loads. Lessons learned about effective engagement include the need for extended in-depth dialog, translation of key climate adaptation questions into

  8. Risks, natural coastal defenses and the Economics of Climate Adaptation in the Gulf Coast

    NASA Astrophysics Data System (ADS)

    Reguero, B. G.; Beck, M.; Bresch, D.; Calil, J.; Meliane, I.

    2014-12-01

    Coastal Development and Climate Change are rapidly altering the world's coastal zones, dramatically increasing risks of catastrophic damage to coastal communities. Natural defenses are increasingly cited as an element of the solution. However, their use and widespread acceptance are still under debate and there are limited data on their cost effectiveness. Our goal is to provide comparable cost effectiveness estimates of 'green' and 'gray' approaches for risk reduction. We follow the Economics of Climate Adaptation (ECA) methodology and further integrates nature-based solutions in to this approach. We propose an ecosystem based risk mitigation perspective and integrate it into local decision making and risk models. A pilot case has been developed for the US Gulf Coast with special emphasis on (1) nature based measures, (2) an open-knowledge approach and (3) on a spatially explicit analyses. We examine potential damage to residential and commercial properties, infrastructure and assets. Our specific goals were to: Assess risks from hurricanes in the Gulf Coast in an holistic manner from hazards to damages and possible solutions Define how cost- effective ecosystems are for coastal defense in the Gulf Coast Quantify how and where natural solutions may reduce risks accounting for coastal engineering indicators Analyze and compare different scenarios including additional risks from climate change such as sea-level rise, potential coastal policy responses and economic growth

  9. Spatio-temporal dynamics of adaptation in the human visual system: A high-density electrical mapping study

    PubMed Central

    Andrade, Gizely N.; Butler, John S.; Mercier, Manuel R.; Molholm, Sophie; Foxe, John J.

    2015-01-01

    When sensory inputs are presented serially, response amplitudes to stimulus repetitions generally decrease as a function of presentation rate, diminishing rapidly as inter-stimulus-intervals (ISIs) fall below a second. This “adaptation” is believed to represent mechanisms by which sensory systems reduce responsivity to consistent environmental inputs, freeing resources to respond to potentially more relevant inputs. While auditory adaptation functions have been relatively well-characterized, considerably less is known about visual adaptation in humans. Here, high-density visual evoked potentials (VEPs) were recorded while two paradigms were used to interrogate visual adaptation. The first presented stimulus pairs with varying ISIs, comparing VEP amplitude to the second stimulus to that of the first (paired-presentation). The second involved blocks of stimulation (N=100) at various ISIs and comparison of VEP amplitude between blocks of differing ISIs (block-presentation). Robust VEP modulations were evident as a function of presentation rate in the block-paradigm with strongest modulations in the 130–150ms and 160–180ms visual processing phases. In paired-presentations, with ISIs of just 200–300 ms, an enhancement of VEP was evident when comparing S2 to S1, with no significant effect of presentation rate. Importantly, in block-presentations, adaptation effects were statistically robust at the individual participant level. These data suggest that a more taxing block-presentation paradigm is better suited to engage visual adaptation mechanisms than a paired-presentation design. The increased sensitivity of the visual processing metric obtained in the block-paradigm has implications for the examination of visual processing deficits in clinical populations. PMID:25688539

  10. Apparatus for adapting a high-pressure light scattering cell to density measurement

    NASA Astrophysics Data System (ADS)

    Abebe, M.; Schoen, P. E.

    1982-04-01

    A new experimental method is presented here by which the density of water, glycerol, HIW (a mixture of isopropyl ammonium nitrate, hydroxyl ammonium nitrate, and water), and solithane 113 was measured at 25 °C and pressure up to 410 MPa.

  11. The effects of density dependence and immigration on local adaptation and niche evolution in a black-hole sink environment.

    PubMed

    Gomulkiewicz, R; Holt, R D; Barfield, M

    1999-06-01

    We examine the effects of density dependence and immigration on local adaptation in a "black-hole sink" habitat, i.e., a habitat in which isolated populations of a species would tend to extinction but where a population is demographically maintained by recurrent one-way migration from a separate source habitat in which the species persists. Using a diploid, one-locus model of a discrete-generation sink population maintained by immigration from a fixed source population, we show that a locally favored allele will spread when rare in the sink if the absolute fitness (or, in some cases, the geometric-mean absolute fitness) of heterozygotes with the favored allele is above one in the sink habitat. With density dependence, the criterion for spread can depend on the rate of immigration, because immigration affects local densities and, hence, absolute fitness. Given the successful establishment of a locally favored allele, it will be maintained by a migration-selection balance and the resulting polymorphic population will be sustained deterministically with either stable or unstable dynamics. The densities of stable polymorphic populations tend to exceed densities that would be maintained in the absence of the favored allele. With strong density regulation, spread of the favored allele may destabilize population dynamics. Our analyses show that polymorphic populations which form subsequent to the establishment of favorable alleles have the capacity to persist deterministically without immigration. Finally, we examined the probabilistic rate at which new favored alleles arise and become established in a sink population. Our results suggest that favored alleles are established most readily at intermediate levels of immigration. PMID:10366553

  12. Curcumin-releasing mechanically adaptive intracortical implants improve the proximal neuronal density and blood-brain barrier stability.

    PubMed

    Potter, Kelsey A; Jorfi, Mehdi; Householder, Kyle T; Foster, E Johan; Weder, Christoph; Capadona, Jeffrey R

    2014-05-01

    The cellular and molecular mechanisms by which neuroinflammatory pathways respond to and propagate the reactive tissue response to intracortical microelectrodes remain active areas of research. We previously demonstrated that both the mechanical mismatch between rigid implants and the much softer brain tissue, as well as oxidative stress, contribute to the neurodegenerative reactive tissue response to intracortical implants. In this study, we utilize physiologically responsive, mechanically adaptive polymer implants based on poly(vinyl alcohol) (PVA), with the capability to also locally administer the antioxidant curcumin. The goal of this study is to investigate if the combination of two independently effective mechanisms - softening of the implant and antioxidant release - leads to synergistic effects in vivo. Over the first 4weeks of the implantation, curcumin-releasing, mechanically adaptive implants were associated with higher neuron survival and a more stable blood-brain barrier at the implant-tissue interface than the neat PVA controls. 12weeks post-implantation, the benefits of the curcumin release were lost, and both sets of compliant materials (with and without curcumin) had no statistically significant differences in neuronal density distribution profiles. Overall, however, the curcumin-releasing softening polymer implants cause minimal implant-mediated neuroinflammation, and embody the new concept of localized drug delivery from mechanically adaptive intracortical implants. PMID:24468582

  13. Amoeboid migration mode adaption in quasi-3D spatial density gradients of varying lattice geometry

    NASA Astrophysics Data System (ADS)

    Gorelashvili, Mari; Emmert, Martin; Hodeck, Kai F.; Heinrich, Doris

    2014-07-01

    Cell migration processes are controlled by sensitive interaction with external cues such as topographic structures of the cell’s environment. Here, we present systematically controlled assays to investigate the specific effects of spatial density and local geometry of topographic structure on amoeboid migration of Dictyostelium discoideum cells. This is realized by well-controlled fabrication of quasi-3D pillar fields exhibiting a systematic variation of inter-pillar distance and pillar lattice geometry. By time-resolved local mean-squared displacement analysis of amoeboid migration, we can extract motility parameters in order to elucidate the details of amoeboid migration mechanisms and consolidate them in a two-state contact-controlled motility model, distinguishing directed and random phases. Specifically, we find that directed pillar-to-pillar runs are found preferably in high pillar density regions, and cells in directed motion states sense pillars as attractive topographic stimuli. In contrast, cell motion in random probing states is inhibited by high pillar density, where pillars act as obstacles for cell motion. In a gradient spatial density, these mechanisms lead to topographic guidance of cells, with a general trend towards a regime of inter-pillar spacing close to the cell diameter. In locally anisotropic pillar environments, cell migration is often found to be damped due to competing attraction by different pillars in close proximity and due to lack of other potential stimuli in the vicinity of the cell. Further, we demonstrate topographic cell guidance reflecting the lattice geometry of the quasi-3D environment by distinct preferences in migration direction. Our findings allow to specifically control amoeboid cell migration by purely topographic effects and thus, to induce active cell guidance. These tools hold prospects for medical applications like improved wound treatment, or invasion assays for immune cells.

  14. Genetic constraints and the adaptive evolution of rabies virus in nature.

    PubMed

    Holmes, Edward C; Woelk, Christopher H; Kassis, Raid; Bourhy, Hervé

    2002-01-20

    We used a molecular evolutionary approach to investigate the species adaptation of rabies virus in nature. A maximum likelihood analysis of selection pressures revealed that the nucleoprotein (N) and glycoprotein (G) genes of natural viral isolates were highly constrained, especially at nonsynonymous sites, in contrast to the higher rates of nonsynonymous evolution observed in viruses subject to laboratory passage. Positive selection was only found at a single amino acid site--position 183 in the ectodomain of the G gene. The low rate of nonsynonymous evolution in natural isolates of rabies virus may be due to constraints imposed by the need to replicate in multiple cell types within the host, which in turn facilitates cross-species transmission, or because viral proteins are not subject to immune selection. Using known dates in the epidemiologic history of European viral isolates, we estimated that overall rates of nucleotide substitution in rabies virus were similar to those observed in other RNA viruses. Assuming that the average rate of synonymous change does not vary among species, we estimated that the current genetic diversity in lyssavirus genotype 1 may have arisen only during the last 500 years. PMID:11878928

  15. Adaptive divergence in body size overrides the effects of plasticity across natural habitats in the brown trout

    PubMed Central

    Rogell, Björn; Dannewitz, Johan; Palm, Stefan; Dahl, Jonas; Petersson, Erik; Laurila, Anssi

    2013-01-01

    The evolution of life-history traits is characterized by trade-offs between different selection pressures, as well as plasticity across environmental conditions. Yet, studies on local adaptation are often performed under artificial conditions, leaving two issues unexplored: (i) how consistent are laboratory inferred local adaptations under natural conditions and (ii) how much phenotypic variation is attributed to phenotypic plasticity and to adaptive evolution, respectively, across environmental conditions? We reared fish from six locally adapted (domesticated and wild) populations of anadromous brown trout (Salmo trutta) in one semi-natural and three natural streams and recorded a key life-history trait (body size at the end of first growth season). We found that population-specific reaction norms were close to parallel across different streams and QST was similar – and larger than FST – within all streams, indicating a consistency of local adaptation in body size across natural environments. The amount of variation explained by population origin exceeded the variation across stream environments, indicating that genetic effects derived from adaptive processes have a stronger effect on phenotypic variation than plasticity induced by environmental conditions. These results suggest that plasticity does not “swamp” the phenotypic variation, and that selection may thus be efficient in generating genetic change. PMID:23919140

  16. Adaptive divergence in body size overrides the effects of plasticity across natural habitats in the brown trout.

    PubMed

    Rogell, Björn; Dannewitz, Johan; Palm, Stefan; Dahl, Jonas; Petersson, Erik; Laurila, Anssi

    2013-07-01

    The evolution of life-history traits is characterized by trade-offs between different selection pressures, as well as plasticity across environmental conditions. Yet, studies on local adaptation are often performed under artificial conditions, leaving two issues unexplored: (i) how consistent are laboratory inferred local adaptations under natural conditions and (ii) how much phenotypic variation is attributed to phenotypic plasticity and to adaptive evolution, respectively, across environmental conditions? We reared fish from six locally adapted (domesticated and wild) populations of anadromous brown trout (Salmo trutta) in one semi-natural and three natural streams and recorded a key life-history trait (body size at the end of first growth season). We found that population-specific reaction norms were close to parallel across different streams and Q ST was similar - and larger than F ST - within all streams, indicating a consistency of local adaptation in body size across natural environments. The amount of variation explained by population origin exceeded the variation across stream environments, indicating that genetic effects derived from adaptive processes have a stronger effect on phenotypic variation than plasticity induced by environmental conditions. These results suggest that plasticity does not "swamp" the phenotypic variation, and that selection may thus be efficient in generating genetic change. PMID:23919140

  17. The neural dynamics of somatosensory processing and adaptation across childhood: a high-density electrical mapping study.

    PubMed

    Uppal, Neha; Foxe, John J; Butler, John S; Acluche, Frantzy; Molholm, Sophie

    2016-03-01

    Young children are often hyperreactive to somatosensory inputs hardly noticed by adults, as exemplified by irritation to seams or labels in clothing. The neurodevelopmental mechanisms underlying changes in sensory reactivity are not well understood. Based on the idea that neurodevelopmental changes in somatosensory processing and/or changes in sensory adaptation might underlie developmental differences in somatosensory reactivity, high-density electroencephalography was used to examine how the nervous system responds and adapts to repeated vibrotactile stimulation over childhood. Participants aged 6-18 yr old were presented with 50-ms vibrotactile stimuli to the right wrist over the median nerve at 5 blocked interstimulus intervals (ranging from ∼7 to ∼1 stimulus per second). Somatosensory evoked potentials (SEPs) revealed three major phases of activation within the first 200 ms, with scalp topographies suggestive of neural generators in contralateral somatosensory cortex. Although overall SEPs were highly similar for younger, middle, and older age groups (6.1-9.8, 10.0-12.9, and 13.0-17.8 yr old), there were significant age-related amplitude differences in initial and later phases of the SEP. In contrast, robust adaptation effects for fast vs. slow presentation rates were observed that did not differ as a function of age. A greater amplitude response in the later portion of the SEP was observed for the youngest group and may be related to developmental changes in responsivity to somatosensory stimuli. These data suggest the protracted development of the somatosensory system over childhood, whereas adaptation, as assayed in this study, is largely in place by ∼7 yr of age. PMID:26763781

  18. Development of an adaptive online fuzzy arbitrator for forecasting short-term natural gas usage

    NASA Astrophysics Data System (ADS)

    Lukas, Richard James, Jr.

    2001-07-01

    The focus of the work is on the development and utilization of a self-assembling Fuzzy logic controller for the purpose of improving short term natural gas load forecasts generated by artificial neural networks (ANN) and linear regression (LR) models. The approach is to form a matrix of dynamic post processors (DPP), composed of ARMAX models, which use load estimates generated by ANNs and LRs as inputs. The problem is to then determine the performance of each DPP under different operating conditions, and to generate a final load estimate using a Fuzzy logic controller. The contributions of this research are as follows. First, as part of a residuals analysis, prefiltering and nonlinear transforms are explored for the purpose of increasing the correlation of environmental input factors with gas load, while decreasing multicollinearity. This has the effect of reducing the covariance of model parameters and increasing forecast confidence. The result of this analysis will be used to develop ARMAX models to postfilter the ANN and LR forecast model estimates. The gas operating regions will be characterized by an adaptive clustering algorithm that will partition operating conditions into distinct patterns with unique consumption characteristics. Finally, an adaptive online Fuzzy controller identifies the characteristics of each DPP under different operating conditions, and generates a weighted average of the DPP estimators to produce the final gas load estimate.

  19. Naturalization of plant populations: the role of cultivation and population size and density.

    PubMed

    Minton, Mark S; Mack, Richard N

    2010-10-01

    Field experimentation is required to assess the effects of environmental stochasticity on small immigrant plant populations-a widely understood but largely unexplored aspect of predicting any species' likelihood of naturalization and potential invasion. Cultivation can mitigate this stochasticity, although the outcome for a population under cultivation nevertheless varies enormously from extinction to persistence. Using factorial experiments, we investigated the effects of population size, density, and cultivation (irrigation) on the fate of founder populations for four alien species with different life history characteristics (Echinochloa frumentacea, Fagopyrum esculentum, Helianthus annuus, and Trifolium incarnatum) in eastern Washington, USA. The fate of founder populations was highly variable within and among the 3 years of experimentation and illustrates the often precarious environment encountered by plant immigrants. Larger founder populations produced more seeds (P < 0.001); the role of founder population size, however, differed among years. Irrigation resulted in higher percent survival (P < 0.001) and correspondingly larger net reproductive rate (R(0); P < 0.001). But the minimum level of irrigation for establishment, R(0) > 1, differed among years and species. Sowing density did not affect the likelihood of establishment for any species. Our results underscore the importance of environmental stochasticity in determining the fate of founder populations and the potential of cultivation and large population size in countering the long odds against naturalization. Any implementation of often proposed post-immigration field trials to assess the risk of an alien species becoming naturalized, a requisite step toward invasion, will need to assess different sizes of founder populations and the extent and character of cultivation (intentional or unintentional) that the immigrants might receive. PMID:20532919

  20. Differential Regulation of Antagonistic Pleiotropy in Synthetic and Natural Populations Suggests Its Role in Adaptation

    PubMed Central

    Yadav, Anupama; Radhakrishnan, Aparna; Bhanot, Gyan; Sinha, Himanshu

    2015-01-01

    Antagonistic pleiotropy (AP), the ability of a gene to show opposing effects in different phenotypes, has been identified in various life history traits and complex disorders, indicating its fundamental role in balancing fitness over the course of evolution. It is intuitive that natural selection might maintain AP to allow organisms phenotypic flexibility in different environments. However, despite several attempts, little evidence exists for its role in adaptation. We performed a meta-analysis in yeast to identify the genetic basis of AP in bi-parental segregants, natural isolates, and a laboratory strain genome-wide deletion collection, by comparing growth in favorable and stress conditions. We found that whereas AP was abundant in the synthetic populations, it was absent in the natural isolates. This finding indicated resolution of trade-offs, i.e., mitigation of trade-offs over evolutionary history, probably through accumulation of compensatory mutations. In the deletion collection, organizational genes showed AP, suggesting ancient resolutions of trade-offs in the basic cellular pathways. We find abundant AP in the segregants, greater than estimated in the deletion collection or observed in previous studies, with IRA2, a negative regulator of the Ras/PKA signaling pathway, showing trade-offs across diverse environments. Additionally, IRA2 and several other Ras/PKA pathway genes showed balancing selection in isolates of S. cerevisiae and S. paradoxus, indicating that multiple alleles maintain AP in this pathway in natural populations. We propose that during AP resolution, retaining the ability to vary signaling pathways such as Ras/PKA, may provide organisms with phenotypic flexibility. However, with increasing organismal complexity AP resolution may become difficult. A partial resolution of AP could manifest as complex human diseases, and the inability to resolve AP may play a role in speciation. Our findings suggest that testing a universal phenomenon like AP

  1. Non-iterative adaptive time-stepping scheme with temporal truncation error control for simulating variable-density flow

    NASA Astrophysics Data System (ADS)

    Hirthe, Eugenia M.; Graf, Thomas

    2012-12-01

    The automatic non-iterative second-order time-stepping scheme based on the temporal truncation error proposed by Kavetski et al. [Kavetski D, Binning P, Sloan SW. Non-iterative time-stepping schemes with adaptive truncation error control for the solution of Richards equation. Water Resour Res 2002;38(10):1211, http://dx.doi.org/10.1029/2001WR000720.] is implemented into the code of the HydroGeoSphere model. This time-stepping scheme is applied for the first time to the low-Rayleigh-number thermal Elder problem of free convection in porous media [van Reeuwijk M, Mathias SA, Simmons CT, Ward JD. Insights from a pseudospectral approach to the Elder problem. Water Resour Res 2009;45:W04416, http://dx.doi.org/10.1029/2008WR007421.], and to the solutal [Shikaze SG, Sudicky EA, Schwartz FW. Density-dependent solute transport in discretely-fractured geological media: is prediction possible? J Contam Hydrol 1998;34:273-91] problem of free convection in fractured-porous media. Numerical simulations demonstrate that the proposed scheme efficiently limits the temporal truncation error to a user-defined tolerance by controlling the time-step size. The non-iterative second-order time-stepping scheme can be applied to (i) thermal and solutal variable-density flow problems, (ii) linear and non-linear density functions, and (iii) problems including porous and fractured-porous media.

  2. Stochastic effects in adaptive reconstruction of body damage: implied the creativity of natural selection

    PubMed Central

    Xiao, Bo; Cui, Li-Qiang; Chen, Tian-Ming; Lian, Bin

    2015-01-01

    After an injury occurs, mechanical/biochemical loads on muscles influence the composition and structure of recovering muscles; this effect likely occurs in other tissues, cells and biological molecules as well owing to the similarity, interassociation and interaction among biochemical reactions and molecules. The ‘damage and reconstruction’ model provides an explanation for how an ideal cytoarchitecture is created by reducing components not suitable for bearing loads; in this model, adaptive changes are induced by promoting the stochasticity of biochemical reactions. Biochemical and mechanical loads can direct the stochasticity of biochemical reactions, which can in turn induce cellular changes. Thus, mechanical and biochemical loads, under natural selection pressure, modify the direction of cell- and tissue-level changes and guide the formation of new structures and traits, thereby influencing microevolution. In summary, the ‘damage and reconstruction’ model accounts for the role of natural selection in the formation of new organisms, helps explain punctuated equilibrium, and illustrates how macroevolution arises from microevolution. PMID:26153081

  3. KAPAO: A Natural Guide Star Adaptive Optics System for Small Aperture Telescopes

    NASA Astrophysics Data System (ADS)

    Severson, Scott A.; Choi, P. I.; Spjut, E.; Contreras, D. S.; Gilbreth, B. N.; McGonigle, L. P.; Morrison, W. A.; Rudy, A. R.; Xue, A.; Baranec, C.; Riddle, R.

    2012-05-01

    We describe KAPAO, our project to develop and deploy a low-cost, remote-access, natural guide star adaptive optics system for the Pomona College Table Mountain Observatory (TMO) 1-meter telescope. The system will offer simultaneous dual-band, diffraction-limited imaging at visible and near-infrared wavelengths and will deliver an order-of-magnitude improvement in point source sensitivity and angular resolution relative to the current TMO seeing limits. We have adopted off-the-shelf core hardware components to ensure reliability, minimize costs and encourage replication efforts. These components include a MEMS deformable mirror, a Shack-Hartmann wavefront sensor and a piezo-electric tip-tilt mirror. We present: project motivation, goals and milestones; the instrument optical design; the instrument opto-mechanical design and tolerances; and an overview of KAPAO Alpha, our on-the-sky testbed using off-the-shelf optics. Beyond the expanded scientific capabilities enabled by AO-enhanced resolution and sensitivity, the interdisciplinary nature of the instrument development effort provides an exceptional opportunity to train a broad range of undergraduate STEM students in AO technologies and techniques. The breadth of our collaboration, which includes both public (Sonoma State University) and private (Pomona and Harvey Mudd Colleges) undergraduate institutions has enabled us to engage students ranging from physics, astronomy, engineering and computer science in the all stages of this project. This material is based upon work supported by the National Science Foundation under Grant No. 0960343.

  4. KAPAO: a MEMS-based natural guide star adaptive optics system

    NASA Astrophysics Data System (ADS)

    Severson, Scott A.; Choi, Philip I.; Contreras, Daniel S.; Gilbreth, Blaine N.; Littleton, Erik; McGonigle, Lorcan P.; Morrison, William A.; Rudy, Alex R.; Wong, Jonathan R.; Xue, Andrew; Spjut, Erik; Baranec, Christoph; Riddle, Reed

    2013-03-01

    We describe KAPAO, our project to develop and deploy a low-cost, remote-access, natural guide star adaptive optics (AO) system for the Pomona College Table Mountain Observatory (TMO) 1-meter telescope. We use a commercially available 140-actuator BMC MEMS deformable mirror and a version of the Robo-AO control software developed by Caltech and IUCAA. We have structured our development around the rapid building and testing of a prototype system, KAPAO-Alpha, while simultaneously designing our more capable final system, KAPAO-Prime. The main differences between these systems are the prototype's reliance on off-the-shelf optics and a single visible-light science camera versus the final design's improved throughput and capabilities due to the use of custom optics and dual-band, visible and near-infrared imaging. In this paper, we present the instrument design and on-sky closed-loop testing of KAPAO-Alpha as well as our plans for KAPAO-Prime. The primarily undergraduate-education nature of our partner institutions, both public (Sonoma State University) and private (Pomona and Harvey Mudd Colleges), has enabled us to engage physics, astronomy, and engineering undergraduates in all phases of this project. This material is based upon work supported by the National Science Foundation under Grant No. 0960343.

  5. Nature and velocity of pyroclastic density currents inferred from models of entrainment of substrate lithic clasts

    NASA Astrophysics Data System (ADS)

    Roche, Olivier

    2015-05-01

    Deposits of pyroclastic density currents (PDCs) often contain accidental lithic clasts of typical size of 0.1-1 m captured from an underlying substrate by the parent flows at distances up to several tens of kilometers from the eruptive vent. In order to gain insights into the nature of PDCs, this study investigates the conditions required for entrainment of particles from a granular substrate by a gas-particle density current, with special emphasis to ignimbrite-forming currents whose dynamics are controversial. The two types of physics of emplacement of PDCs proposed in literature are considered. The first model deals with a hydraulically rough, dilute turbulent PDC of bulk density of ∼1-10 kg/m3 and considers that entrainment through both traction and saltation is controlled by a Shield criterion at high (>104) particle Reynolds number. The second model considers entrainment by a PDC consisting of a dense basal flow of bulk density of the order of 103 kg /m3 and with high interstitial gas pore pressure. This model involves uplift of substrate particles, caused by an upward pressure gradient at the flow-substrate interface, and then transport and deposition on the aggrading basal deposit of the flow as demonstrated by recent laboratory experiments. Results show that a dilute PDC can entrain blocks of maximum size of ∼10-15 cm (for a block density of 2000-3000 kg/m3) if maximum current velocities up to ∼100 m/s are taken into account. This, in turn, suggests that larger (heavier) blocks found in deposits were captured by PDCs if these had a dense basal flow. The dense flow model predicts that PDCs have the potential to entrain metric blocks, whose maximum size (up to ∼2-5 m) decreases with decreasing atmospheric pressure (i.e. increasing altitude). Application of the model considering published data on the characteristics of accidental blocks in several well-studied ignimbrites indicates that the velocity of the parent dense PDCs was up to ∼25-30 m/s.

  6. Sampling-variance effects on detecting density dependence from temporal trends in natural populations

    USGS Publications Warehouse

    Shenk, T.M.; White, Gary C.; Burnham, K.P.

    1998-01-01

    Monte Carlo simulations were conducted to evaluate robustness of four tests to detect density dependence, from series of population abundances, to the addition of sampling variance. Population abundances were generated from random walk, stochastic exponential growth, and density-dependent population models. Population abundance estimates were generated with sampling variances distributed as lognormal and constant coefficients of variation (cv) from 0.00 to 1.00. In general, when data were generated under a random walk, Type I error rates increased rapidly for Bulmer's R, Pollard et al.'s, and Dennis and Taper's tests with increasing magnitude of sampling variance for n > 5 yr and all values of process variation. Bulmer's R* test maintained a constant 5% Type I error rate for n > 5 yr and all magnitudes of sampling variance in the population abundance estimates. When abundances were generated from two stochastic exponential growth models (R = 0.05 and R = 0.10), Type I errors again increased with increasing sampling variance; magnitude of Type I error rates were higher for the slower growing population. Therefore, sampling error inflated Type I error rates, invalidating the tests, for all except Bulmer's R* test. Comparable simulations for abundance estimates generated from a density-dependent growth rate model were conducted to estimate power of the tests. Type II error rates were influenced by the relationship of initial population size to carrying capacity (K), length of time series, as well as sampling error. Given the inflated Type I error rates for all but Bulmer, s R*, power was overestimated for the remaining tests, resulting in density: dependence being detected more often than it existed. Population abundances of natural populations are almost exclusively estimated rather than censused, assuring sampling error. Therefore, because these tests have been shown to be either invalid when only sampling variance occurs in the population abundances (Bulmer's R

  7. Degradation assessment of natural weathering on low density polyethylene/thermoplastic soya spent powder blends

    NASA Astrophysics Data System (ADS)

    Nuradibah, M. A.; Sam, S. T.; Noriman, N. Z.; Ragunathan, S.; Ismail, H.

    2015-07-01

    Soya spent powder was blended with low density polyethylene (LDPE) ranging from 5-25 wt%. Glycerol was added to soya spent powder (SSP) for preparation of thermoplastic soya spent powder (TSSP). Then, the blends were exposed to natural weathering for 6 months. The susceptibility of the LDPE/soya spent powder blends based on its tensile, morphological properties and structural changes was measured every three months. The tensile strength of LDPE/TSSP blends after 6 months of weathering was the lowest compared to the other blends whereas LDPE/SSP blends after 6 months of weathering demonstrated the lowest elongation at break (Eb). Large pore can be seen on the surface of 25 wt% of LDPE/SSP blends.

  8. High-fidelity pulse density modulation in neuromorphic electric circuits utilizing natural heterogeneity

    NASA Astrophysics Data System (ADS)

    Utagawa, Akira; Asai, Tetsuya; Amemiya, Yoshihito

    Hospedales et al. have recently proposed a neural network model of the “vestibulo-ocular reflex” (VOR) in which a common input was given to multiple nonidentical spiking neurons that were exposed to uncorrelated temporal noise, and the output was represented by the sum of these neurons. Although the function of the VOR network is equivalent to pulse density modulation, the neurons' non-uniformity and temporal noises given to the neurons were shown to improve the output spike's fidelity to the analog input. In this paper, we propose a CMOS analog circuit for implementing the VOR network that exploits the non-uniformity of real MOS devices. Through extensive laboratory experiments using discrete MOS devices, we show that the output's fidelity to the input pulses is clearly improved by using multiple neuron circuits, in which the non-uniformity is naturally embedded into the devices.

  9. Analysis of the relationship between photosynthetic photon flux density and natural Taxus baccata seedlings occurrence

    NASA Astrophysics Data System (ADS)

    Iszkuło, Grzegorz; Boratyński, Adam

    2006-01-01

    The aim of the present work was to analyse the relationship of seedlings and saplings of Taxus baccata to the photosynthetic photon flux density (PPFD) reaching the forest floor under natural conditions. Two permanent plots, subdivided into 1 × 1 m square plots, were established in a naturally regenerating population of T. baccata formed during last decades in the Kórnik Arboretum, Poland. All seedlings in every 1 × 1 m plots were counted. Relative PPFD was measured for every plot at the canopy height of the yew seedlings. The dependence of seedling density upon PPFD was examined. We found, that the frequency of the smallest seedlings (to 6.0 cm tall) was highest in the most shaded plots and decreased in plots with increasing PPFD. Thus, the youngest yew seedlings can germinate and grow in very shady conditions. However, the older seedlings (6.1-25.0 and 25.1-100.0 classes) were observed most frequently in 2-7% PPFD. The small numbers of older, taller seedlings in deep shade likely indicate a higher mortality rate of seedlings less than 6 cm in height without promotion to the next height class. Probably the low value of PPFD under the canopy of the stand significantly reduces the competition of other plants with the youngest yew seedlings. At higher light levels they may not be able to compete with more light-demanding plants, such as herbs and seedlings of broad-leaved trees. The seedlings of the second (6.1-25.0 cm) and third (25.1-100.0 cm) height classes were observed most frequently in the plots with 2-7% PPFD ( Fig. 1b and c).

  10. Double Trouble at High Density: Cross-Level Test of Resource-Related Adaptive Plasticity and Crowding-Related Fitness

    PubMed Central

    Gergs, André; Preuss, Thomas G.; Palmqvist, Annemette

    2014-01-01

    Population size is often regulated by negative feedback between population density and individual fitness. At high population densities, animals run into double trouble: they might concurrently suffer from overexploitation of resources and also from negative interference among individuals regardless of resource availability, referred to as crowding. Animals are able to adapt to resource shortages by exhibiting a repertoire of life history and physiological plasticities. In addition to resource-related plasticity, crowding might lead to reduced fitness, with consequences for individual life history. We explored how different mechanisms behind resource-related plasticity and crowding-related fitness act independently or together, using the water flea Daphnia magna as a case study. For testing hypotheses related to mechanisms of plasticity and crowding stress across different biological levels, we used an individual-based population model that is based on dynamic energy budget theory. Each of the hypotheses, represented by a sub-model, is based on specific assumptions on how the uptake and allocation of energy are altered under conditions of resource shortage or crowding. For cross-level testing of different hypotheses, we explored how well the sub-models fit individual level data and also how well they predict population dynamics under different conditions of resource availability. Only operating resource-related and crowding-related hypotheses together enabled accurate model predictions of D. magna population dynamics and size structure. Whereas this study showed that various mechanisms might play a role in the negative feedback between population density and individual life history, it also indicated that different density levels might instigate the onset of the different mechanisms. This study provides an example of how the integration of dynamic energy budget theory and individual-based modelling can facilitate the exploration of mechanisms behind the regulation

  11. Synchronous changes in coral chromatophore tissue density and skeletal banding as an adaptive response to environmental change

    NASA Astrophysics Data System (ADS)

    Ardisana, R. N.; Miller, C. A.; Sivaguru, M.; Fouke, B. W.

    2013-12-01

    Corals are a key reservoir of biodiversity in coastal, shallow water tropical marine environments, and density banding in their aragonite skeletons is used as a sensitive record of paleoclimate. Therefore, the cellular response of corals to environmental change and its expression in skeletal structure is of significant importance. Chromatophores, pigment-bearing cells within the ectoderm of hermatypic corals, serve to both enhance the photosynthetic activity of zooxanthellae symbionts, as well as protect the coral animal from harmful UV radiation. Yet connections have not previously been drawn between chromatophore tissue density and the development of skeletal density bands. A histological analysis of the coral Montastrea faveolata has therefore been conducted across a bathymetric gradient of 1-20 m on the southern Caribbean island of Curaçao. A combination of field and laboratory photography, serial block face imaging (SBFI), two-photon laser scanning microscopy (TPLSM), and 3D image analysis has been applied to test whether M. faveolata adapts to increasing water depth and decreasing photosynthetically active radiation by shifting toward a more heterotrophic lifestyle (decreasing zooxanthellae tissue density, increasing mucocyte tissue density, and decreasing chromatophores density). This study is among the first to collect and evaluate histological data in the spatial context of an entire unprocessed coral polyp. TPLSM was used to optically thin section unprocessed tissue biopsies with quantitative image analysis to yield a nanometer-scale three-dimensional map of the quantity and distribution of the symbionts (zooxanthellae) and a host fluorescent pigments (chromatophores), which is thought to have photoprotective properties, within the context of an entire coral polyp. Preliminary results have offered new insight regarding the three-dimensional distribution and abundance of chromatophores and have identified: (1) M. faveolata tissue collected from 8M SWD do

  12. Exploring the Interaction Natures in Plutonyl (VI) Complexes with Topological Analyses of Electron Density.

    PubMed

    Du, Jiguang; Sun, Xiyuan; Jiang, Gang

    2016-01-01

    The interaction natures between Pu and different ligands in several plutonyl (VI) complexes are investigated by performing topological analyses of electron density. The geometrical structures in both gaseous and aqueous phases are obtained with B3LYP functional, and are generally in agreement with available theoretical and experimental results when combined with all-electron segmented all-electron relativistic contracted (SARC) basis set. The Pu- O y l bond orders show significant linear dependence on bond length and the charge of oxygen atoms in plutonyl moiety. The closed-shell interactions were identified for Pu-Ligand bonds in most complexes with quantum theory of atoms in molecules (QTAIM) analyses. Meanwhile, we found that some Pu-Ligand bonds, like Pu-OH(-), show weak covalent. The interactive nature of Pu-ligand bonds were revealed based on the interaction quantum atom (IQA) energy decomposition approach, and our results indicate that all Pu-Ligand interactions is dominated by the electrostatic attraction interaction as expected. Meanwhile it is also important to note that the quantum mechanical exchange-correlation contributions can not be ignored. By means of the non-covalent interaction (NCI) approach it has been found that some weak and repulsion interactions existed in plutonyl(VI) complexes, which can not be distinguished by QTAIM, can be successfully identified. PMID:27077844

  13. Exploring the Interaction Natures in Plutonyl (VI) Complexes with Topological Analyses of Electron Density

    PubMed Central

    Du, Jiguang; Sun, Xiyuan; Jiang, Gang

    2016-01-01

    The interaction natures between Pu and different ligands in several plutonyl (VI) complexes are investigated by performing topological analyses of electron density. The geometrical structures in both gaseous and aqueous phases are obtained with B3LYP functional, and are generally in agreement with available theoretical and experimental results when combined with all-electron segmented all-electron relativistic contracted (SARC) basis set. The Pu–Oyl bond orders show significant linear dependence on bond length and the charge of oxygen atoms in plutonyl moiety. The closed-shell interactions were identified for Pu-Ligand bonds in most complexes with quantum theory of atoms in molecules (QTAIM) analyses. Meanwhile, we found that some Pu–Ligand bonds, like Pu–OH−, show weak covalent. The interactive nature of Pu–ligand bonds were revealed based on the interaction quantum atom (IQA) energy decomposition approach, and our results indicate that all Pu–Ligand interactions is dominated by the electrostatic attraction interaction as expected. Meanwhile it is also important to note that the quantum mechanical exchange-correlation contributions can not be ignored. By means of the non-covalent interaction (NCI) approach it has been found that some weak and repulsion interactions existed in plutonyl(VI) complexes, which can not be distinguished by QTAIM, can be successfully identified. PMID:27077844

  14. How do age and nature of the motor task influence visuomotor adaptation?

    PubMed

    Nemanich, Samuel T; Earhart, Gammon M

    2015-10-01

    Visuomotor adaptation with prism glasses is a paradigm often used to understand how the motor system responds to visual perturbations. Both reaching and walking adaptation have been documented, but not directly compared. Because the sensorimotor environment and demands are different between reaching and walking, we hypothesized that characteristics of prism adaptation, namely rates and aftereffects, would be different during walking compared to reaching. Furthermore, we aimed to determine the impact of age on motor adaptation. We studied healthy younger and older adults who performed visually guided reaching and walking tasks with and without prism glasses. We noted age effects on visuomotor adaptation, such that older adults adapted and re-adapted slower compared to younger adults, in accord with previous studies of adaptation in older adults. Interestingly, we also noted that both groups adapted slower and showed smaller aftereffects during walking prism adaptation compared to reaching. We propose that walking adaptation is slower because of the complex multi-effector and multi-sensory demands associated with walking. Altogether, these data suggest that humans can adapt various movement types but the rate and extent of adaptation is not the same across movement types nor across ages. PMID:26385199

  15. The Adaptive Significance of Natural Genetic Variation in the DNA Damage Response of Drosophila melanogaster

    PubMed Central

    Svetec, Nicolas; Cridland, Julie M.; Zhao, Li; Begun, David J.

    2016-01-01

    Despite decades of work, our understanding of the distribution of fitness effects of segregating genetic variants in natural populations remains largely incomplete. One form of selection that can maintain genetic variation is spatially varying selection, such as that leading to latitudinal clines. While the introduction of population genomic approaches to understanding spatially varying selection has generated much excitement, little successful effort has been devoted to moving beyond genome scans for selection to experimental analysis of the relevant biology and the development of experimentally motivated hypotheses regarding the agents of selection; it remains an interesting question as to whether the vast majority of population genomic work will lead to satisfying biological insights. Here, motivated by population genomic results, we investigate how spatially varying selection in the genetic model system, Drosophila melanogaster, has led to genetic differences between populations in several components of the DNA damage response. UVB incidence, which is negatively correlated with latitude, is an important agent of DNA damage. We show that sensitivity of early embryos to UVB exposure is strongly correlated with latitude such that low latitude populations show much lower sensitivity to UVB. We then show that lines with lower embryo UVB sensitivity also exhibit increased capacity for repair of damaged sperm DNA by the oocyte. A comparison of the early embryo transcriptome in high and low latitude embryos provides evidence that one mechanism of adaptive DNA repair differences between populations is the greater abundance of DNA repair transcripts in the eggs of low latitude females. Finally, we use population genomic comparisons of high and low latitude samples to reveal evidence that multiple components of the DNA damage response and both coding and non-coding variation likely contribute to adaptive differences in DNA repair between populations. PMID:26950216

  16. The Adaptive Significance of Natural Genetic Variation in the DNA Damage Response of Drosophila melanogaster.

    PubMed

    Svetec, Nicolas; Cridland, Julie M; Zhao, Li; Begun, David J

    2016-03-01

    Despite decades of work, our understanding of the distribution of fitness effects of segregating genetic variants in natural populations remains largely incomplete. One form of selection that can maintain genetic variation is spatially varying selection, such as that leading to latitudinal clines. While the introduction of population genomic approaches to understanding spatially varying selection has generated much excitement, little successful effort has been devoted to moving beyond genome scans for selection to experimental analysis of the relevant biology and the development of experimentally motivated hypotheses regarding the agents of selection; it remains an interesting question as to whether the vast majority of population genomic work will lead to satisfying biological insights. Here, motivated by population genomic results, we investigate how spatially varying selection in the genetic model system, Drosophila melanogaster, has led to genetic differences between populations in several components of the DNA damage response. UVB incidence, which is negatively correlated with latitude, is an important agent of DNA damage. We show that sensitivity of early embryos to UVB exposure is strongly correlated with latitude such that low latitude populations show much lower sensitivity to UVB. We then show that lines with lower embryo UVB sensitivity also exhibit increased capacity for repair of damaged sperm DNA by the oocyte. A comparison of the early embryo transcriptome in high and low latitude embryos provides evidence that one mechanism of adaptive DNA repair differences between populations is the greater abundance of DNA repair transcripts in the eggs of low latitude females. Finally, we use population genomic comparisons of high and low latitude samples to reveal evidence that multiple components of the DNA damage response and both coding and non-coding variation likely contribute to adaptive differences in DNA repair between populations. PMID:26950216

  17. Relative densities of natural enemy and pest insects within California hedgerows.

    PubMed

    Gareau, Tara L Pisani; Letourneau, Deborah K; Shennan, Carol

    2013-08-01

    Research on hedgerow design for supporting communities of natural enemies for biological control lags behind farmer innovation in California, where assemblages of perennial plant species have been used on crop field margins in the last decade. We compared natural enemy to pest ratios between fields with hedgerows and fields with weedy margins by sampling beneficial insects and key pests of vegetables on sticky cards. We used biweekly vacuum samples to measure the distribution of key insect taxa among native perennial plant species with respect to the timing and intensity of bloom. Sticky cards indicated a trend that field margins with hedgerows support a higher ratio of natural enemies to pests compared with weedy borders. Hedgerow plant species hosted different relative densities of a generally overlapping insect community, and the timing and intensity of bloom only explained a small proportion of the variation in insect abundance at plant species and among hedgerows, with the exception of Orius spp. on Achillea millefolium L. and Baccharis pilularis De Candolle. Indicator Species Analysis showed an affinity of parasitic wasps, especially in the super-family Chalcidoidea, for B. pilularis whether or not it was in flower. A. millefolium was attractive to predatory and herbivorous homopterans; Heteromeles arbutifolia (Lindley) Roemer and B. pilularis to Diabrotica undecimpunctata undecimpunctata Mannerheim; and Rhamnus californica Eschsch to Hemerobiidae. Perennial hedgerows can be designed through species selection to support particular beneficial insect taxa, but plant resources beyond floral availability may be critical in providing structural refuges, alternative prey, and other attractive qualities that are often overlooked. PMID:23905731

  18. The Adaptation of the Moth Pheromone Receptor Neuron to its Natural Stimulus

    NASA Astrophysics Data System (ADS)

    Kostal, Lubomir; Lansky, Petr; Rospars, Jean-Pierre

    2008-07-01

    We analyze the first phase of information transduction in the model of the olfactory receptor neuron of the male moth Antheraea polyphemus. We predict such stimulus characteristics that enable the system to perform optimally, i.e., to transfer as much information as possible. Few a priori constraints on the nature of stimulus and stimulus-to-signal transduction are assumed. The results are given in terms of stimulus distributions and intermittency factors which makes direct comparison with experimental data possible. Optimal stimulus is approximatelly described by exponential or log-normal probability density function which is in agreement with experiment and the predicted intermittency factors fall within the lowest range of observed values. The results are discussed with respect to electroantennogram measurements and behavioral observations.

  19. Adaptive exposure estimation for high dynamic range imaging applied to natural scenes and daylight skies.

    PubMed

    Martínez, Miguel A; Valero, Eva M; Hernández-Andrés, Javier

    2015-02-01

    Digital imaging of natural scenes and optical phenomena present on them (such as shadows, twilights, and crepuscular rays) can be a very challenging task because of the range spanned by the radiances impinging on the capture system. We propose a novel method for estimating the set of exposure times (bracketing set) needed to capture the full dynamic range of a scene with high dynamic range (HDR) content. The proposed method is adaptive to scene content and to any camera response and configuration, and it works on-line since the exposure times are estimated as the capturing process is ongoing. Besides, it requires no a priori information about scene content or radiance values. The resulting bracketing sets are minimal in the default method settings, but the user can set a tolerance for the maximum percentage of pixel population that is underexposed or saturated, which allows for a higher number of shots if a better signal-to-noise ratio (SNR) in the HDR scene is desired. This method is based on the use of the camera response function that is needed for building the HDR radiance map by stitching together several differently exposed low dynamic range images of the scene. The use of HDR imaging techniques converts our digital camera into a tool for measuring the relative radiance outgoing from each point of the scene, and for each color channel. This is important for accurate characterization of optical phenomena present in the atmosphere while not suffering any loss of information due to its HDR. We have compared our method with the most similar one developed so far [IEEE Trans. Image Process.17, 1864 (2008)]. Results of the experiments carried out for 30 natural scenes show that our proposed method equals or outperforms the previously developed best approach, with less shots and shorter exposure times, thereby asserting the advantage of being adaptive to scene content for exposure time estimation. As we can also tune the balance between capturing time and the SNR in

  20. Evaluating natural flood management measures using an ecosystem based adaptation framework: a meta-analysis

    NASA Astrophysics Data System (ADS)

    Iacob, Oana; Rowan, John; Brown, Iain; Ellis, Chris

    2014-05-01

    Climate change is projected to alter river flows and the magnitude/frequency characteristics of floods and droughts. As a result flood risk is expected to increase with environmental, social and economic impacts. Traditionally flood risk management has been heavily relying on engineering measures, however with climate change their capacity to provide protection is expected to decrease. Ecosystem-based adaptation highlights the interdependence of human and natural systems, and the potential to buffer the impacts of climate change by maintaining functioning ecosystems that continue to provide multiple societal benefits. Natural flood management measures have the potential to provide a greater adaptive capacity to negate the impacts of climate change and provide ancillary benefits. To understand the impacts of different NFM measures on ecosystem services a meta-analysis was undertaken. Twenty five studies from across the world were pulled together to assess their effectiveness on reducing the flood risk but also on other ecosystems services as defined by the UK National Ecosystem Assessment, which distinguishes between provisioning, regulating, cultural and supporting services. Four categories of NFM measures were considered: (i) afforestation measures, (ii) drainage and blocking the drains, (iii) wetland restoration and (iv) combined measures. Woodland expansion measures provide significant benefits for flood protection more pronounced for low magnitude events, but also for other services such as carbon sequestration and water quality. These measures however will come at a cost for livestock and crop provisioning services as a result of land use changes. Drainage operations and blocking the drains have mixed impacts on carbon sequestration and water quality depending on soil type, landscape settings and local characteristics. Wetland and floodplain restoration measures have generally a few disbenefits and provide improvements for regulating and supporting services

  1. Aftereffects for Face Attributes with Different Natural Variability: Adapter Position Effects and Neural Models

    ERIC Educational Resources Information Center

    Robbins, Rachel; McKone, Elinor; Edwards, Mark

    2007-01-01

    Adaptation to distorted faces is commonly interpreted as a shift in the face-space norm for the adapted attribute. This article shows that the size of the aftereffect varies as a function of the distortion level of the adapter. The pattern differed for different facial attributes, increasing with distortion level for symmetric deviations of eye…

  2. Effects of prepartum stocking density on innate and adaptive leukocyte responses and serum and hair cortisol concentrations.

    PubMed

    Silva, P R B; Lobeck-Luchterhand, K M; Cerri, R L A; Haines, D M; Ballou, M A; Endres, M I; Chebel, R C

    2016-01-01

    Objectives were to evaluate the effects of prepartum stocking density on innate and adaptive leukocyte responses, serum cortisol and haptoglobin concentrations and hair cortisol concentration of Jersey cows. The cows (254 ± 3d of gestation) were balanced for parity (nulliparous vs. parous) and previous lactation projected 305-d mature equivalent milk yield and assigned to one of two treatments: 80SD=80% stocking density (38 animals/48 headlocks) and 100SD=100% stocking density (48 animals/48 headlocks). Pens (n=4) were identical in size and design and each pen received each treatment a total of 2 times (4 replicates; 80SD: n=338; 100SD: n=418). A sub-group of cows (n=48/treatment per parity) was randomly selected on week 1 of each replicate from which blood was sampled weekly from d -14 to 14 (d 0=calving) to determine polymorphonuclear leukocyte (PMNL) phagocytosis, oxidative burst, and expression of CD18 and L-selectin, and hemogram. The same sub-group of cows was treated with chicken egg ovalbumin on d -21, -7, and 7 and had blood sampled weekly from d -21 to 21 for determination of serum IgG anti-ovalbumin concentration. Blood was sampled weekly from d -21 to 21 to determine glucose, cortisol, and haptoglobin concentrations in serum. Hair samples collected at enrollment and within 24h of calving were analyzed for cortisol concentration. The percentage of leukocytes classified as granulocyte and the granulocyte to the lymphocyte ratio were not affected by treatment. Treatment did not affect the percentage of PMNL positive for phagocytosis and oxidative burst or the intensity of phagocytosis and oxidative burst. Similarly, treatment did not affect the percentage of PMNL expressing CD18 and L-selectin or the intensity of expression of CD18 and L-selectin. Concentration of IgG anti-ovalbumin was not affected by treatment. Serum concentrations of haptoglobin and cortisol were not affected by treatment. Similarly, hair cortisol concentration at calving was not

  3. Underground Adaptation to a Hostile Environment: Acute Myeloid Leukemia vs. Natural Killer Cells

    PubMed Central

    Dulphy, Nicolas; Chrétien, Anne-Sophie; Khaznadar, Zena; Fauriat, Cyril; Nanbakhsh, Arash; Caignard, Anne; Chouaib, Salem; Olive, Daniel; Toubert, Antoine

    2016-01-01

    Acute myeloid leukemia (AML) is a heterogeneous group of malignancies which incidence increases with age. The disease affects the differentiation of hematopoietic stem or precursor cells in the bone marrow and can be related to abnormal cytogenetic and/or specific mutational patterns. AML blasts can be sensitive to natural killer (NK) cell antitumor response. However, NK cells are frequently defective in AML patients leading to tumor escape. NK cell defects affect not only the expression of the activating NK receptors, including the natural cytotoxicity receptors, the NK group 2, member D, and the DNAX accessory molecule-1, but also cytotoxicity and IFN-γ release. Such perturbations in NK cell physiology could be related to the adaptation of the AML to the immune pressure and more generally to patient’s clinical features. Various mechanisms are potentially involved in the inhibition of NK-cell functions in AML, including defects in the normal lymphopoiesis, reduced expression of activating receptors through cell-to-cell contacts, and production of immunosuppressive soluble agents by leukemic blasts. Therefore, the continuous cross-talk between AML and NK cells participates to the leukemia immune escape and eventually to patient’s relapse. Methods to restore or stimulate NK cells seem to be attractive strategies to treat patients once the complete remission is achieved. Moreover, our capacity in stimulating the NK cell functions could lead to the development of preemptive strategies to eliminate leukemia-initiating cells before the emergence of the disease in elderly individuals presenting preleukemic mutations in hematopoietic stem cells. PMID:27014273

  4. Local adaptation of a bacterium is as important as its presence in structuring a natural microbial community

    PubMed Central

    Gómez, Pedro; Paterson, Steve; De Meester, Luc; Liu, Xuan; Lenzi, Luca; Sharma, M. D.; McElroy, Kerensa; Buckling, Angus

    2016-01-01

    Local adaptation of a species can affect community composition, yet the importance of local adaptation compared with species presence per se is unknown. Here we determine how a compost bacterial community exposed to elevated temperature changes over 2 months as a result of the presence of a focal bacterium, Pseudomonas fluorescens SBW25, that had been pre-adapted or not to the compost for 48 days. The effect of local adaptation on community composition is as great as the effect of species presence per se, with these results robust to the presence of an additional strong selection pressure: an SBW25-specific virus. These findings suggest that evolution occurring over ecological time scales can be a key driver of the structure of natural microbial communities, particularly in situations where some species have an evolutionary head start following large perturbations, such as exposure to antibiotics or crop planting and harvesting. PMID:27501868

  5. Local adaptation of a bacterium is as important as its presence in structuring a natural microbial community.

    PubMed

    Gómez, Pedro; Paterson, Steve; De Meester, Luc; Liu, Xuan; Lenzi, Luca; Sharma, M D; McElroy, Kerensa; Buckling, Angus

    2016-01-01

    Local adaptation of a species can affect community composition, yet the importance of local adaptation compared with species presence per se is unknown. Here we determine how a compost bacterial community exposed to elevated temperature changes over 2 months as a result of the presence of a focal bacterium, Pseudomonas fluorescens SBW25, that had been pre-adapted or not to the compost for 48 days. The effect of local adaptation on community composition is as great as the effect of species presence per se, with these results robust to the presence of an additional strong selection pressure: an SBW25-specific virus. These findings suggest that evolution occurring over ecological time scales can be a key driver of the structure of natural microbial communities, particularly in situations where some species have an evolutionary head start following large perturbations, such as exposure to antibiotics or crop planting and harvesting. PMID:27501868

  6. Natural history of β-cell adaptation and failure in type 2 diabetes

    PubMed Central

    Alejandro, Emilyn U.; Gregg, Brigid; Blandino-Rosano, Manuel; Cras-Méneur, Corentin; Bernal-Mizrachi, Ernesto

    2014-01-01

    Type 2 diabetes mellitus (T2D) is a complex disease characterized by β-cell failure in the setting of insulin resistance. The current evidence suggests that genetic predisposition, and environmental factors can impair the capacity of the β-cells to respond to insulin resistance and ultimately lead to their failure. However, genetic studies have demonstrated that known variants account for less than 10% of the overall estimated T2D risk, suggesting that additional unidentified factors contribute to susceptibility of this disease. In this review, we will discuss the different stages that contribute to the development of β-cell failure in T2D. We divide the natural history of this process in three major stages: susceptibility, β-cell adaptation and β-cell failure and provide an overview of the molecular mechanisms involved. Further research into mechanisms will reveal key modulators of β-cell failure and thus identify possible novel therapeutic targets and potential interventions to protect against β-cell failure. PMID:25542976

  7. Estimated uncertainty of calculated liquefied natural gas density from a comparison of NBS and Gaz de France densimeter test facilities

    SciTech Connect

    Siegwarth, J.D.; LaBrecque, J.F.; Roncier, M.; Philippe, R.; Saint-Just, J.

    1982-12-16

    Liquefied natural gas (LNG) densities can be measured directly but are usually determined indirectly in custody transfer measurement by using a density correlation based on temperature and composition measurements. An LNG densimeter test facility at the National Bureau of Standards uses an absolute densimeter based on the Archimedes principle, while a test facility at Gaz de France uses a correlation method based on measurement of composition and density. A comparison between these two test facilities using a portable version of the absolute densimeter provides an experimental estimate of the uncertainty of the indirect method of density measurement for the first time, on a large (32 L) sample. The two test facilities agree for pure methane to within about 0.02%. For the LNG-like mixtures consisting of methane, ethane, propane, and nitrogen with the methane concentrations always higher than 86%, the calculated density is within 0.25% of the directly measured density 95% of the time.

  8. Improving performance of natural language processing part-of-speech tagging on clinical narratives through domain adaptation

    PubMed Central

    Ferraro, Jeffrey P; Daumé, Hal; DuVall, Scott L; Chapman, Wendy W; Harkema, Henk; Haug, Peter J

    2013-01-01

    Objective Natural language processing (NLP) tasks are commonly decomposed into subtasks, chained together to form processing pipelines. The residual error produced in these subtasks propagates, adversely affecting the end objectives. Limited availability of annotated clinical data remains a barrier to reaching state-of-the-art operating characteristics using statistically based NLP tools in the clinical domain. Here we explore the unique linguistic constructions of clinical texts and demonstrate the loss in operating characteristics when out-of-the-box part-of-speech (POS) tagging tools are applied to the clinical domain. We test a domain adaptation approach integrating a novel lexical-generation probability rule used in a transformation-based learner to boost POS performance on clinical narratives. Methods Two target corpora from independent healthcare institutions were constructed from high frequency clinical narratives. Four leading POS taggers with their out-of-the-box models trained from general English and biomedical abstracts were evaluated against these clinical corpora. A high performing domain adaptation method, Easy Adapt, was compared to our newly proposed method ClinAdapt. Results The evaluated POS taggers drop in accuracy by 8.5–15% when tested on clinical narratives. The highest performing tagger reports an accuracy of 88.6%. Domain adaptation with Easy Adapt reports accuracies of 88.3–91.0% on clinical texts. ClinAdapt reports 93.2–93.9%. Conclusions ClinAdapt successfully boosts POS tagging performance through domain adaptation requiring a modest amount of annotated clinical data. Improving the performance of critical NLP subtasks is expected to reduce pipeline error propagation leading to better overall results on complex processing tasks. PMID:23486109

  9. Density, Expectation, and Extended Task Performance: An Experiment in the Natural Environment.

    ERIC Educational Resources Information Center

    Glassman, Joel B.; And Others

    1978-01-01

    The effects of density and expectation on academic performance and ratings of spatial and social satisfaction were investigated. Grade point averages and satisfaction measures compiled during the academic quarter were significantly negatively affected by exposure to density, demonstrating that density led to both greater dissatisfaction and more…

  10. Functional Nature of Electrogram Fractionation Demonstrated by Left Atrial High Density Mapping

    PubMed Central

    Jadidi, Amir S.; Duncan, Edward; Miyazaki, Shinsuke; Lellouche, Nicolas; Shah, Ashok J.; Forclaz, Andrei; Nault, Isabelle; Wright, Matthew; Rivard, Lena; Liu, Xingpeng; Scherr, Daniel; Wilton, Stephen; Sacher, Frédéric; Derval, Nicolas; Knecht, Sebastien; Kim, Steven J.; Hocini, Mélèze; Narayan, Sanjiv; Haïssaguerre, Michel; Jaïs, Pierre

    2012-01-01

    Background Complex fractionated electrograms (CFAE) are targets of atrial fibrillation (AF) ablation. Serial high density maps were evaluated to understand the impact of activation direction and rate on electrogram (EGM) fractionation. Methods and Results 18 patients (9 persistent) underwent high density, 3D, left atrial mapping (>400 points/map) during AF, Sinus (SR) and CS-paced (CSp) rhythms. In SR and CSp, fractionation was defined as EGM with ≥4 deflections, while in AF CFEmean <80ms was considered as continuous CFAE. The anatomic distribution of CFAE sites was assessed, quantified and correlated between rhythms. Mechanisms underlying fractionation were investigated by analysis of voltage, activation and propagation maps. A minority of continuous CFAE sites displayed EGM fractionation in SR (15+/−4%) and CSp (12+/(12+/−8%). EGM fractionation did not match between SR and CSp at 70+/−10% sites. Activation maps in SR and CSp showed that wave collision (71%) and regional slow conduction (24%) caused EGM fractionation. EGM voltage during AF (0.59+/−0.58mV) was lower than during SR and CSp (>1.0mV) at all sites. During AF, the EGM voltage was higher at continuous CFAE sites than at non-CFAE sites (0.53mV (Q1, Q3: 0.33–0.83) vs. 0.30 mV (Q1, Q3: 0.18–0.515), p<0.00001). Global LA voltage in AF was lower in persistent vs. paroxysmal AF patients (0.6+/−0.59mV vs. 1.12+/−1.32mV, p<0.01). Conclusions The distribution of fractionated EGMs is highly variable, depending on direction and rate of activation (SR vs. CSp vs. AF). Fractionation in sinus and CSp rhythms mostly resulted from wave collision. All sites with continuous fractionation in AF displayed normal voltage in SR suggesting absence of structural scar. Thus, many fractionated EGMs are functional in nature and their sites dynamic. PMID:22215849

  11. The role of antioxidant enzymes in adaptive responses to sheath blight infestation under different fertilization rates and hill densities.

    PubMed

    Wu, Wei; Wan, Xuejie; Shah, Farooq; Fahad, Shah; Huang, Jianliang

    2014-01-01

    Sheath blight of rice, caused by Rhizoctonia solani, is one of the most devastating rice diseases worldwide. No rice cultivar has been found to be completely resistant to this fungus. Identifying antioxidant enzymes activities (activity of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT)) and malondialdehyde content (MDA) responding to sheath blight infestation is imperative to understand the defensive mechanism systems of rice. In the present study, two inoculation methods (toothpick and agar block method) were tested in double-season rice. Toothpick method had greater lesion length than agar block method in late season. A higher MDA content was found under toothpick method compared with agar block method, which led to greater POD and SOD activities. Dense planting caused higher lesion length resulting in a higher MDA content, which also subsequently stimulated higher POD and SOD activity. Sheath blight severity was significantly related to the activity of antioxidant enzyme during both seasons. The present study implies that rice plants possess a system of antioxidant protective enzymes which helps them in adaptation to sheath blight infection stresses. Several agronomic practices, such as rational use of fertilizers and optimum planting density, involved in regulating antioxidant protective enzyme systems can be regarded as promising strategy to suppress the sheath blight development. PMID:25136671

  12. An adaptive multiple-input multiple-output analog-to-digital converter for high density neuroprosthetic electrode arrays.

    PubMed

    Chakrabartty, Shantanu; Gore, Amit; Oweiss, Karim G

    2006-01-01

    On chip signal compression is one of the key technologies driving development of energy efficient biotelemetry devices. In this paper, we describe a novel architecture for analog-to-digital (A/D) conversion that combines sigma delta conversion with the spatial data compression in a single module. The architecture called multiple-input multiple-output (MIMO) sigma-delta is based on a min-max gradient descent optimization of a regularized cost function that naturally leads to an A/D formulation. Experimental results with simulated and recorded multichannel data demonstrate the effectiveness of the proposed architecture to eliminate cross-channel redundancy in high density microelectrode data, thus superceding the performance of parallel independent data converters in terms of its energy efficiency. PMID:17946414

  13. Computational Design of Non-natural Sugar Alcohols to Increase Thermal Storage Density: Beyond Existing Organic Phase Change Materials.

    PubMed

    Inagaki, Taichi; Ishida, Toyokazu

    2016-09-14

    Thermal storage, a technology that enables us to control thermal energy, makes it possible to reuse a huge amount of waste heat, and materials with the ability to treat larger thermal energy are in high demand for energy-saving societies. Sugar alcohols are now one promising candidate for phase change materials (PCMs) because of their large thermal storage density. In this study, we computationally design experimentally unknown non-natural sugar alcohols and predict their thermal storage density as a basic step toward the development of new high performance PCMs. The non-natural sugar alcohol molecules are constructed in silico in accordance with the previously suggested molecular design guidelines: linear elongation of a carbon backbone, separated distribution of OH groups, and even numbers of carbon atoms. Their crystal structures are then predicted using the random search method and first-principles calculations. Our molecular simulation results clearly demonstrate that the non-natural sugar alcohols have potential ability to have thermal storage density up to ∼450-500 kJ/kg, which is significantly larger than the maximum thermal storage density of the present known organic PCMs (∼350 kJ/kg). This computational study suggests that, even in the case of H-bonded molecular crystals where the electrostatic energy contributes mainly to thermal storage density, the molecular distortion and van der Waals energies are also important factors to increase thermal storage density. In addition, the comparison between the three eight-carbon non-natural sugar alcohol isomers indicates that the selection of preferable isomers is also essential for large thermal storage density. PMID:27505107

  14. Smaller = Denser, and the Brain Knows It: Natural Statistics of Object Density Shape Weight Expectations

    PubMed Central

    Peters, Megan A. K.; Balzer, Jonathan; Shams, Ladan

    2015-01-01

    If one nondescript object’s volume is twice that of another, is it necessarily twice as heavy? As larger objects are typically heavier than smaller ones, one might assume humans use such heuristics in preparing to lift novel objects if other informative cues (e.g., material, previous lifts) are unavailable. However, it is also known that humans are sensitive to statistical properties of our environments, and that such sensitivity can bias perception. Here we asked whether statistical regularities in properties of liftable, everyday objects would bias human observers’ predictions about objects’ weight relationships. We developed state-of-the-art computer vision techniques to precisely measure the volume of everyday objects, and also measured their weight. We discovered that for liftable man-made objects, “twice as large” doesn’t mean “twice as heavy”: Smaller objects are typically denser, following a power function of volume. Interestingly, this “smaller is denser” relationship does not hold for natural or unliftable objects, suggesting some ideal density range for objects designed to be lifted. We then asked human observers to predict weight relationships between novel objects without lifting them; crucially, these weight predictions quantitatively match typical weight relationships shown by similarly-sized objects in everyday environments. These results indicate that the human brain represents the statistics of everyday objects and that this representation can be quantitatively abstracted and applied to novel objects. Finally, that the brain possesses and can use precise knowledge of the nonlinear association between size and weight carries important implications for implementation of forward models of motor control in artificial systems. PMID:25768977

  15. Nature of adsorption on TiC(111) investigated with density-functional calculations

    NASA Astrophysics Data System (ADS)

    Ruberto, Carlo; Lundqvist, Bengt I.

    2007-06-01

    Extensive density-functional calculations are performed for chemisorption of atoms in the three first periods (H, B, C, N, O, F, Al, Si, P, S, and Cl) on the polar TiC(111) surface. Calculations are also performed for O on TiC(001), for full O(1×1) monolayer on TiC(111), as well as for bulk TiC and for the clean TiC(111) and (001) surfaces. Detailed results concerning atomic structures, energetics, and electronic structures are presented. For the bulk and the clean surfaces, previous results are confirmed. In addition, detailed results are given on the presence of C-C bonds in the bulk and at the surface, as well as on the presence of a Ti-based surface resonance (TiSR) at the Fermi level and of C-based surface resonances (CSR’s) in the lower part of the surface upper valence band. For the adsorption, adsorption energies Eads and relaxed geometries are presented, showing great variations characterized by pyramid-shaped Eads trends within each period. An extraordinarily strong chemisorption is found for the O atom, 8.8eV /adatom. On the basis of the calculated electronic structures, a concerted-coupling model for the chemisorption is proposed, in which two different types of adatom-substrate interactions work together to provide the obtained strong chemisorption: (i) adatom-TiSR and (ii) adatom-CSR’s. This model is used to successfully describe the essential features of the calculated Eads trends. The fundamental nature of this model, based on the Newns-Anderson model, should make it apt for general application to transition-metal carbides and nitrides and for predictive purposes in technological applications, such as cutting-tool multilayer coatings and MAX phases.

  16. Water Reserves Program. An adaptation strategy to prevent imbalance of water in nature

    NASA Astrophysics Data System (ADS)

    Salinas-Rodriguez, S. A.; López Pérez, M.; Barrios Ordóñez, J.; Wickel, B.; Villón Bracamonte, R. A.

    2013-12-01

    allocated, and where the flow regime is then protected before over-allocation takes place. The strategy has been to identify and protect basins with an availability of water that is close to their natural flow regime and that also have a high conservation value (based on prior national conservation priority definitions such as protected areas, and biodiversity conservation gap analyses) in order to implement legal restrictions on water resource development. With such protection, these systems will be best positioned to adjust and respond to water shortages, and regime shifts. To date, 189 basins around the country were identified as potential water reserves. The next step will be the nomination of these water reserves to be integrated in the National Water Reserves Program. This program forms the core of the official Mexican government adaptation strategy towards climate prepared water management, which recognizes that water reserves are the buffer society needs to face uncertainty, imbalance of the man-made, global changes, and thus to reduce water scarcity risk. The development of activities that alter the natural flow regime such as dams and levees are closely examined, and would potentially be restricted.

  17. Maximizing the utility of monitoring to the adaptive management of natural resources

    USGS Publications Warehouse

    Kendall, William L.; Moore, Clinton T.

    2012-01-01

    Data collection is an important step in any investigation about the structure or processes related to a natural system. In a purely scientific investigation (experiments, quasi-experiments, observational studies), data collection is part of the scientific method, preceded by the identification of hypotheses and the design of any manipulations of the system to test those hypotheses. Data collection and the manipulations that precede it are ideally designed to maximize the information that is derived from the study. That is, such investigations should be designed for maximum power to evaluate the relative validity of the hypotheses posed. When data collection is intended to inform the management of ecological systems, we call it monitoring. Note that our definition of monitoring encompasses a broader range of data-collection efforts than some alternative definitions – e.g. Chapter 3. The purpose of monitoring as we use the term can vary, from surveillance or “thumb on the pulse” monitoring (see Nichols and Williams 2006), intended to detect changes in a system due to any non-specified source (e.g. the North American Breeding Bird Survey), to very specific and targeted monitoring of the results of specific management actions (e.g. banding and aerial survey efforts related to North American waterfowl harvest management). Although a role of surveillance monitoring is to detect unanticipated changes in a system, the same result is possible from a collection of targeted monitoring programs distributed across the same spatial range (Box 4.1). In the face of limited budgets and many specific management questions, tying monitoring as closely as possible to management needs is warranted (Nichols and Williams 2006). Adaptive resource management (ARM; Walters 1986, Williams 1997, Kendall 2001, Moore and Conroy 2006, McCarthy and Possingham 2007, Conroy et al. 2008a) provides a context and specific purpose for monitoring: to evaluate decisions with respect to achievement

  18. Density Affects the Nature of the Hexatic-Liquid Transition in Two-Dimensional Melting of Soft-Core Systems

    NASA Astrophysics Data System (ADS)

    Zu, Mengjie; Liu, Jun; Tong, Hua; Xu, Ning

    2016-08-01

    We find that both continuous and discontinuous hexatic-liquid transitions can happen in the melting of two-dimensional solids of soft-core disks. For three typical model systems, Hertzian, harmonic, and Gaussian-core models, we observe the same scenarios. These systems exhibit reentrant crystallization (melting) with a maximum melting temperature Tm happening at a crossover density ρm. The hexatic-liquid transition at a density smaller than ρm is discontinuous. Liquid and hexatic phases coexist in a density interval, which becomes narrower with increasing temperature and tends to vanish approximately at Tm. Above ρm, the transition is continuous, in agreement with the Kosterlitz-Thouless-Halperin-Nelson-Young theory. For these soft-core systems, the nature of the hexatic-liquid transition depends on density (pressure), with the melting at ρm being a plausible transition point from discontinuous to continuous hexatic-liquid transition.

  19. Density Affects the Nature of the Hexatic-Liquid Transition in Two-Dimensional Melting of Soft-Core Systems.

    PubMed

    Zu, Mengjie; Liu, Jun; Tong, Hua; Xu, Ning

    2016-08-19

    We find that both continuous and discontinuous hexatic-liquid transitions can happen in the melting of two-dimensional solids of soft-core disks. For three typical model systems, Hertzian, harmonic, and Gaussian-core models, we observe the same scenarios. These systems exhibit reentrant crystallization (melting) with a maximum melting temperature T_{m} happening at a crossover density ρ_{m}. The hexatic-liquid transition at a density smaller than ρ_{m} is discontinuous. Liquid and hexatic phases coexist in a density interval, which becomes narrower with increasing temperature and tends to vanish approximately at T_{m}. Above ρ_{m}, the transition is continuous, in agreement with the Kosterlitz-Thouless-Halperin-Nelson-Young theory. For these soft-core systems, the nature of the hexatic-liquid transition depends on density (pressure), with the melting at ρ_{m} being a plausible transition point from discontinuous to continuous hexatic-liquid transition. PMID:27588868

  20. Water Reserves Program. An adaptation strategy to balance water in nature

    NASA Astrophysics Data System (ADS)

    Lopez Perez, M.; Barrios, E.; Salinas-Rodriguez, S.; Wickel, B.; Villon, R. A.

    2013-05-01

    -allocation takes place. The strategy is to identify and protect basins with an availability of water that is close to their natural flow regime and that also have a high conservation value (based on prior national conservation priority definitions such as protected areas, and biodiversity conservation gap analyses) in order to implement legal restrictions on water resource development. With such protection, these systems will be best positioned to adjust and respond to water shortages, and regime shifts. To date, 189 basins around the country were identified as potential water reserves. The next step will be the nomination of these water reserves to be integrated in the National Water Reserves Program. This program forms the core of the official Mexican government adaptation strategy towards climate prepared water management, which recognizes that water reserves are the buffer society needs to face uncertainty, and reduce water scarcity risk. The development of activities that alter the natural flow regime such as dams and levees are closely examined, and would potentially be restricted.

  1. Evaluation of single and two-stage adaptive sampling designs for estimation of density and abundance of freshwater mussels in a large river

    USGS Publications Warehouse

    Smith, D.R.; Rogala, J.T.; Gray, B.R.; Zigler, S.J.; Newton, T.J.

    2011-01-01

    Reliable estimates of abundance are needed to assess consequences of proposed habitat restoration and enhancement projects on freshwater mussels in the Upper Mississippi River (UMR). Although there is general guidance on sampling techniques for population assessment of freshwater mussels, the actual performance of sampling designs can depend critically on the population density and spatial distribution at the project site. To evaluate various sampling designs, we simulated sampling of populations, which varied in density and degree of spatial clustering. Because of logistics and costs of large river sampling and spatial clustering of freshwater mussels, we focused on adaptive and non-adaptive versions of single and two-stage sampling. The candidate designs performed similarly in terms of precision (CV) and probability of species detection for fixed sample size. Both CV and species detection were determined largely by density, spatial distribution and sample size. However, designs did differ in the rate that occupied quadrats were encountered. Occupied units had a higher probability of selection using adaptive designs than conventional designs. We used two measures of cost: sample size (i.e. number of quadrats) and distance travelled between the quadrats. Adaptive and two-stage designs tended to reduce distance between sampling units, and thus performed better when distance travelled was considered. Based on the comparisons, we provide general recommendations on the sampling designs for the freshwater mussels in the UMR, and presumably other large rivers.

  2. The effect of density ratio on the near field of a naturally occurring oscillating jet

    NASA Astrophysics Data System (ADS)

    England, Grant; Kalt, Peter A. M.; Nathan, Graham J.; Kelso, Richard M.

    2010-01-01

    The triangular oscillating jet nozzle generates a triangular jet partially confined within an axi-symmetric chamber to produce a large scale flow oscillation that has application in thermal processes. Particle image velocimetry and oscillation frequency measurements were conducted to investigate the influence of the jet fluid to ambient fluid density ratio on the resulting oscillating flow. The investigation was conducted with a jet momentum flux of 0.06 kg m s-2 ( Re = 7.3-47.2 × 103) and density ratios ranging from 0.2 to 5.0. The initial spread and decay of the emerging jet was found to depend upon the density ratio but in a more complex way than does an unconfined jet. Both the spread and decay are strongly influenced by the instantaneous angle of jet deflection, with greater deflection leading to increased spreading and decay of the jet. Decreasing the density ratio below unity results in a rapid decrease in the deflection angle, while increasing the density ratio above unity results in an increase in the deflection angle, albeit with less sensitivity. The frequency of oscillation was also shown to depend on the density ratio with an increase in the density ratio causing a decrease in the dominant oscillation frequency.

  3. Interleukin-2 from Adaptive T Cells Enhances Natural Killer Cell Activity against Human Cytomegalovirus-Infected Macrophages

    PubMed Central

    Wu, Zeguang; Frascaroli, Giada; Bayer, Carina; Schmal, Tatjana

    2015-01-01

    ABSTRACT Control of human cytomegalovirus (HCMV) requires a continuous immune surveillance, thus HCMV is the most important viral pathogen in severely immunocompromised individuals. Both innate and adaptive immunity contribute to the control of HCMV. Here, we report that peripheral blood natural killer cells (PBNKs) from HCMV-seropositive donors showed an enhanced activity toward HCMV-infected autologous macrophages. However, this enhanced response was abolished when purified NK cells were applied as effectors. We demonstrate that this enhanced PBNK activity was dependent on the interleukin-2 (IL-2) secretion of CD4+ T cells when reexposed to the virus. Purified T cells enhanced the activity of purified NK cells in response to HCMV-infected macrophages. This effect could be suppressed by IL-2 blocking. Our findings not only extend the knowledge on the immune surveillance in HCMV—namely, that NK cell-mediated innate immunity can be enhanced by a preexisting T cell antiviral immunity—but also indicate a potential clinical implication for patients at risk for severe HCMV manifestations due to immunosuppressive drugs, which mainly suppress IL-2 production and T cell responsiveness. IMPORTANCE Human cytomegalovirus (HCMV) is never cleared by the host after primary infection but instead establishes a lifelong latent infection with possible reactivations when the host′s immunity becomes suppressed. Both innate immunity and adaptive immunity are important for the control of viral infections. Natural killer (NK) cells are main innate effectors providing a rapid response to virus-infected cells. Virus-specific T cells are the main adaptive effectors that are critical for the control of the latent infection and limitation of reinfection. In this study, we found that IL-2 secreted by adaptive CD4+ T cells after reexposure to HCMV enhances the activity of NK cells in response to HCMV-infected target cells. This is the first direct evidence that the adaptive T cells can

  4. Low complexity Reed-Solomon-based low-density parity-check design for software defined optical transmission system based on adaptive puncturing decoding algorithm

    NASA Astrophysics Data System (ADS)

    Pan, Xiaolong; Liu, Bo; Zheng, Jianglong; Tian, Qinghua

    2016-08-01

    We propose and demonstrate a low complexity Reed-Solomon-based low-density parity-check (RS-LDPC) code with adaptive puncturing decoding algorithm for elastic optical transmission system. Partial received codes and the relevant column in parity-check matrix can be punctured to reduce the calculation complexity by adaptive parity-check matrix during decoding process. The results show that the complexity of the proposed decoding algorithm is reduced by 30% compared with the regular RS-LDPC system. The optimized code rate of the RS-LDPC code can be obtained after five times iteration.

  5. Drosophila Regulate Yeast Density and Increase Yeast Community Similarity in a Natural Substrate

    PubMed Central

    Stamps, Judy A.; Yang, Louie H.; Morales, Vanessa M.; Boundy-Mills, Kyria L.

    2012-01-01

    Drosophila melanogaster adults and larvae, but especially larvae, had profound effects on the densities and community structure of yeasts that developed in banana fruits. Pieces of fruit exposed to adult female flies previously fed fly-conditioned bananas developed higher yeast densities than pieces of the same fruits that were not exposed to flies, supporting previous suggestions that adult Drosophila vector yeasts to new substrates. However, larvae alone had dramatic effects on yeast density and species composition. When yeast densities were compared in pieces of the same fruits assigned to different treatments, fruits that developed low yeast densities in the absence of flies developed significantly higher yeast densities when exposed to larvae. Across all of the fruits, larvae regulated yeast densities within narrow limits, as compared to a much wider range of yeast densities that developed in pieces of the same fruits not exposed to flies. Larvae also affected yeast species composition, dramatically reducing species diversity across fruits, reducing variation in yeast communities from one fruit to the next (beta diversity), and encouraging the consistent development of a yeast community composed of three species of yeast (Candida californica, C. zemplinina, and Pichia kluvyeri), all of which were palatable to larvae. Larvae excreted viable cells of these three yeast species in their fecal pools, and discouraged the growth of filamentous fungi, processes which may have contributed to their effects on the yeast communities in banana fruits. These and other findings suggest that D. melanogaster adults and their larval offspring together engage in ‘niche construction’, facilitating a predictable microbial environment in the fruit substrates in which the larvae live and develop. PMID:22860093

  6. Effect of electrode density on cycle performance and irreversible capacity loss for natural graphite anode in lithium ion batteries

    SciTech Connect

    Shim, Joongpyo; Striebel, Kathryn A.

    2002-12-02

    The effect of electrode thickness and density for unpressed and pressed natural graphite electrodes were studied using electrochemical characterization. Pressing the graphite electrode decreases the reversible capacity and the irreversible capacity loss during formation. As electrode density increased, the capacity retention at high rate increased until 0.9g/cm{sup 3}, and then decreased. The cycle performances of the pressed graphite electrodes were more stable than the unpressed one. Pressing graphite electrode affected on its electrochemical characterization such as irreversible capacity loss, high rate cycling and cycle performance.

  7. [Mechanisms of natural variability at adaptation of human physiological systems to conditions of space flight].

    PubMed

    Larina, I M; Nosovskiĭ, A M; Grigor'ev, A I

    2012-01-01

    This article analyzes the physiological data using the principle of invariant relationships, to reveal the mechanisms of adaptive variability. It was used physical-chemical, biochemical, and hormonal blood parameters of cosmonauts who have committed short-term and long space flights. These results suggest that application of the methods of fractal geometry to quantitative estimates of homeostasis allows to allocate the processes depending on the increase/decrease of adaptive variability and fix the state of stability or instability of certain physiological regulatory subsystems, due to mobility and to reduce the level of stability which remains stable internal structure of relationships throughout the body. PMID:22679800

  8. Estimating the density of honeybee colonies across their natural range to fill the gap in pollinator decline censuses.

    PubMed

    Jaffé, Rodolfo; Dietemann, Vincent; Allsopp, Mike H; Costa, Cecilia; Crewe, Robin M; Dall'olio, Raffaele; DE LA Rúa, Pilar; El-Niweiri, Mogbel A A; Fries, Ingemar; Kezic, Nikola; Meusel, Michael S; Paxton, Robert J; Shaibi, Taher; Stolle, Eckart; Moritz, Robin F A

    2010-04-01

    Although pollinator declines are a global biodiversity threat, the demography of the western honeybee (Apis mellifera) has not been considered by conservationists because it is biased by the activity of beekeepers. To fill this gap in pollinator decline censuses and to provide a broad picture of the current status of honeybees across their natural range, we used microsatellite genetic markers to estimate colony densities and genetic diversity at different locations in Europe, Africa, and central Asia that had different patterns of land use. Genetic diversity and colony densities were highest in South Africa and lowest in Northern Europe and were correlated with mean annual temperature. Confounding factors not related to climate, however, are also likely to influence genetic diversity and colony densities in honeybee populations. Land use showed a significantly negative influence over genetic diversity and the density of honeybee colonies over all sampling locations. In Europe honeybees sampled in nature reserves had genetic diversity and colony densities similar to those sampled in agricultural landscapes, which suggests that the former are not wild but may have come from managed hives. Other results also support this idea: putative wild bees were rare in our European samples, and the mean estimated density of honeybee colonies on the continent closely resembled the reported mean number of managed hives. Current densities of European honeybee populations are in the same range as those found in the adverse climatic conditions of the Kalahari and Saharan deserts, which suggests that beekeeping activities do not compensate for the loss of wild colonies. Our findings highlight the importance of reconsidering the conservation status of honeybees in Europe and of regarding beekeeping not only as a profitable business for producing honey, but also as an essential component of biodiversity conservation. PMID:19775273

  9. Adaptive Management

    EPA Science Inventory

    Adaptive management is an approach to natural resource management that emphasizes learning through management where knowledge is incomplete, and when, despite inherent uncertainty, managers and policymakers must act. Unlike a traditional trial and error approach, adaptive managem...

  10. Evidence for parallel adaptation to climate across the natural range of Arabidopsis thaliana

    PubMed Central

    Stearns, Frank W; Fenster, Charles B

    2013-01-01

    How organisms adapt to different climate habitats is a key question in evolutionary ecology and biological conservation. Species distributions are often determined by climate suitability. Consequently, the anthropogenic impact on earth's climate is of key concern to conservation efforts because of our relatively poor understanding of the ability of populations to track and evolve to climate change. Here, we investigate the ability of Arabidopsis thaliana to occupy climate space by quantifying the extent to which different climate regimes are accessible to different A. thaliana genotypes using publicly available data from a large-scale genotyping project and from a worldwide climate database. The genetic distance calculated from 149 single-nucleotide polymorphisms (SNPs) among 60 lineages of A. thaliana was compared to the corresponding climate distance among collection localities calculated from nine different climatic factors. A. thaliana was found to be highly labile when adapting to novel climate space, suggesting that populations may experience few constraints when adapting to changing climates. Our results also provide evidence of a parallel or convergent evolution on the molecular level supporting recent generalizations regarding the genetics of adaptation. PMID:23919166

  11. Local adaptation to temperature and precipitation in naturally fragmented populations of Cephalotaxus oliveri, an endangered conifer endemic to China

    PubMed Central

    Wang, Ting; Wang, Zhen; Xia, Fan; Su, Yingjuan

    2016-01-01

    Cephalotaxus oliveri is an endangered tertiary relict conifer endemic to China. The species survives in a wide range from west to east with heterogeneous climatic conditions. Precipitation and temperature are main restrictive factors for distribution of C. oliveri. In order to comprehend the mechanism of adaptive evolution to climate variation, we employed ISSR markers to detect adaptive evolution loci, to identify the association between variation in temperature and precipitation and adaptive loci, and to investigate the genetic structure for 22 C. oliveri natural populations. In total, 14 outlier loci were identified, of which five were associated with temperature and precipitation. Among outlier loci, linkage disequilibrium (LD) was high (42.86%), which also provided strong evidence for selection. In addition, C. oliveri possessed high genetic variation (93.31%) and population differentiation, which may provide raw material to evolution and accelerate local adaptation, respectively. Ecological niche modeling showed that global warming will cause a shift for populations of C. oliveri from south to north with a shrinkage of southern areas. Our results contribute to understand the potential response of conifers to climatic changes, and provide new insights for conifer resource management and conservation strategies. PMID:27113970

  12. Local adaptation to temperature and precipitation in naturally fragmented populations of Cephalotaxus oliveri, an endangered conifer endemic to China.

    PubMed

    Wang, Ting; Wang, Zhen; Xia, Fan; Su, Yingjuan

    2016-01-01

    Cephalotaxus oliveri is an endangered tertiary relict conifer endemic to China. The species survives in a wide range from west to east with heterogeneous climatic conditions. Precipitation and temperature are main restrictive factors for distribution of C. oliveri. In order to comprehend the mechanism of adaptive evolution to climate variation, we employed ISSR markers to detect adaptive evolution loci, to identify the association between variation in temperature and precipitation and adaptive loci, and to investigate the genetic structure for 22 C. oliveri natural populations. In total, 14 outlier loci were identified, of which five were associated with temperature and precipitation. Among outlier loci, linkage disequilibrium (LD) was high (42.86%), which also provided strong evidence for selection. In addition, C. oliveri possessed high genetic variation (93.31%) and population differentiation, which may provide raw material to evolution and accelerate local adaptation, respectively. Ecological niche modeling showed that global warming will cause a shift for populations of C. oliveri from south to north with a shrinkage of southern areas. Our results contribute to understand the potential response of conifers to climatic changes, and provide new insights for conifer resource management and conservation strategies. PMID:27113970

  13. [Comparison of the adaptive potential for Rhizobium leguminosarum bv. viceae nodule bacterial populations isolated in natural ecosystems and agrocenoses].

    PubMed

    Kurchak, O N; Provorov, N A; Simarov, B V

    2011-04-01

    Polymorphism analysis was performed in Rhizobium leguminosarum bv. viceae populations isolated from geographically distant regions of Ukraine and Middle Asia. Examination of cultural, biochemical, and symbiotic traits revealed interpopulation differences, which were attributed to the difference in conditions between natural ecosystems and agrocenoses. Vetch has high species diversity and is not cultivated in Middle Asia, and the corresponding rhizobial population displayed higher genetic diversity and higher polymorphism of adaptive traits ensuring saprophytic development in soil and the rhizosphere, including melanin synthesis (35%) and active exopolysaccharide production (90%). Strains of the Ukrainian population had a lower exopolysaccharide production (10%), did not produce melanin, had higher herbicide resistance, and utilized glucose and succinate (main components of plant root exudation) as carbon sources. Strains capable of efficient symbiosis with Vicia villosa Roth. had a higher frequency in the Middle Asian than in the Ukrainian population, especially among strains isolated from soil (80 and 35%, respectively). In addition, strains of the Middle Asian population better competed for nodulation. It was assumed that the formation of rhizobial populations in vetch cultivation regions (Ukraine) is aimed at adaptation to ectosymbiotic (rhizospheric) interactions with plants and anthropogenic stress factors, while strains of the vetch original center (Middle Asia) are mostly adapted to the endosymbiotic interaction and to natural edaphic stress factors. PMID:21675237

  14. Natural Disasters and Adaptive Capacity. OECD Development Centre Working Paper No. 237

    ERIC Educational Resources Information Center

    Dayton-Johnson, Jeff

    2004-01-01

    Natural disasters (droughts, earthquakes, epidemics, floods, wind storms) damage wellbeing, both in their immediate and long-term aftermath, and because the insecurity of exposure to disasters is in itself harmful to risk-averse people. As such, mitigating and coping with the risk of natural disasters is a pressing issue for economic development.…

  15. Modelling rainfall interception by vegetation of variable density using an adapted analytical model. Part 2. Model validation for a tropical upland mixed cropping system

    NASA Astrophysics Data System (ADS)

    van Dijk, A. I. J. M.; Bruijnzeel, L. A.

    2001-07-01

    To improve the description of rainfall partitioning by a vegetation canopy that changes in time a number of adaptations to the revised analytical model for rainfall interception by sparse canopies [J. Hydrol., 170 (1995) 79] was proposed in the first of two papers. The current paper presents an application of this adapted analytical model to simulate throughfall, stemflow and interception as measured in a mixed agricultural cropping system involving cassava, maize and rice during two seasons of growth and serial harvesting in upland West Java, Indonesia. Measured interception losses were 18 and 8% during the two measuring periods, while stemflow fractions were estimated at 2 and 4%, respectively. The main reasons for these discrepancies were differences in vegetation density and composition, as well as differences in the exposure of the two sites used in the two respective years. Functions describing the development of the leaf area index of each of the component crops in time were developed. Leaf area index (ranging between 0.7 and 3.8) was related to canopy cover fraction (0.41-0.94). Using average values and time series of the respective parameters, interception losses were modelled using both the revised analytical model and the presently adapted version. The results indicate that the proposed model adaptations substantially improve the performance of the analytical model and provide a more solid base for parameterisation of the analytical model in vegetation of variable density.

  16. Natural enemy density and soil type influence growth and survival of Melaleuca quinquenervia seedlings

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Multiple insects are commonly introduced as biological control agents to reduce growth and spread of invasive plants. Little is known about the species-specific contributions of co-existing agents, and about insect density needed to control invasive plants. We investigated the effects of insect type...

  17. Thermodynamic, energy efficiency, and power density analysis of reverse electrodialysis power generation with natural salinity gradients.

    PubMed

    Yip, Ngai Yin; Vermaas, David A; Nijmeijer, Kitty; Elimelech, Menachem

    2014-05-01

    Reverse electrodialysis (RED) can harness the Gibbs free energy of mixing when fresh river water flows into the sea for sustainable power generation. In this study, we carry out a thermodynamic and energy efficiency analysis of RED power generation, and assess the membrane power density. First, we present a reversible thermodynamic model for RED and verify that the theoretical maximum extractable work in a reversible RED process is identical to the Gibbs free energy of mixing. Work extraction in an irreversible process with maximized power density using a constant-resistance load is then examined to assess the energy conversion efficiency and power density. With equal volumes of seawater and river water, energy conversion efficiency of ∼ 33-44% can be obtained in RED, while the rest is lost through dissipation in the internal resistance of the ion-exchange membrane stack. We show that imperfections in the selectivity of typical ion exchange membranes (namely, co-ion transport, osmosis, and electro-osmosis) can detrimentally lower efficiency by up to 26%, with co-ion leakage being the dominant effect. Further inspection of the power density profile during RED revealed inherent ineffectiveness toward the end of the process. By judicious early discontinuation of the controlled mixing process, the overall power density performance can be considerably enhanced by up to 7-fold, without significant compromise to the energy efficiency. Additionally, membrane resistance was found to be an important factor in determining the power densities attainable. Lastly, the performance of an RED stack was examined for different membrane conductivities and intermembrane distances simulating high performance membranes and stack design. By thoughtful selection of the operating parameters, an efficiency of ∼ 37% and an overall gross power density of 3.5 W/m(2) represent the maximum performance that can potentially be achieved in a seawater-river water RED system with low

  18. Genomic studies on the nature of species: adaptation and speciation in Mimulus.

    PubMed

    Twyford, Alex D; Streisfeld, Matthew A; Lowry, David B; Friedman, Jannice

    2015-06-01

    Evolutionary biology is in an exciting era, in which powerful genomic tools make the answers accessible to long-standing questions about variation, adaptation and speciation. The availability of a suite of genomic resources, a shared knowledge base and a long history of study have made the phenotypically diverse plant genus Mimulus an important system for understanding ecological and evolutionary processes. An international Mimulus Research Meeting was held at Duke University in June 2014 to discuss developments in ecological and evolutionary genetic studies in Mimulus. Here, we report major recent discoveries presented at the meeting that use genomic approaches to advance our understanding of three major themes: the parallel genetic basis of adaptation; the ecological genomics of speciation; and the evolutionary significance of structural genetic variation. We also suggest future research directions for studies of Mimulus and highlight challenges faced when developing new ecological and evolutionary model systems. PMID:25856725

  19. Wide field adaptive optics correction for the GMT using natural guide stars

    NASA Astrophysics Data System (ADS)

    van Dam, Marcos A.; Bouchez, Antonin H.; McLeod, Brian A.

    2014-07-01

    The conceptual design of the Giant Magellan Telescope has four wavefront sensors used to maintain the shape and alignment of the segmented primary and secondary mirrors. In this paper, we show that by reading the sensors at 200 Hz, we can also compensate for low altitude turbulence. As a result, there is a large improvement in image quality, even at visible wavelengths, over the entire science field of view of the telescope. A minimum-variance reconstructor is presented that takes slope measurements from four stars of arbitrary location and magnitude and produces the optimal adaptive secondary mirror commands. The performance of the adaptive optics system in this mode is simulated using YAO, an end-to-end simulation tool. We present the results of trade studies performed to optimize the science return of the telescope.

  20. Socio-ecological Typologies for Understanding Adaptive Capacity of a Region to Natural Disasters

    NASA Astrophysics Data System (ADS)

    Surendran Nair, S.; Preston, B. L.; King, A. W.; Mei, R.

    2015-12-01

    It is expected that the frequency and magnitude of extreme climatic events will increase in coming decades with an anticipated increase in losses from climate hazards. In the Gulf Coastal region of the United States, climate hazards/disasters are common including hurricanes, drought and flooding. However, the capacity to adapt to extreme climatic events varies across the region. This adaptive capacity is linked to the magnitude of the extreme event, exposed infrastructure, and the socio-economic conditions across the region. This study uses hierarchical clustering to quantitatively integrates regional socioeconomic and biophysical factors and develop socio-ecological typologies (SET). The biophysical factors include climatic and topographic variables, and the socio-economic variables include human capital, social capital and man-made resources (infrastructure) of the region. The types of the SET are independent variables in a statistical model of a regional variable of interest. The methodology was applied to US Gulf States to evaluate the social and biophysical determinants of the regional variation in social vulnerability and economic loss to climate hazards. The results show that the SET explains much of the regional variation in social vulnerability, effectively capturing its determinants. In addition, the SET also explains of the variability in economic loss to hazards across of the region. The approach can thus be used to prioritize adaptation strategies to reduce vulnerability and loss across the region.

  1. CONJUGAL TRANSFER AT NATURAL POPULATION DENSITIES IN A MICROCOSM SIMULATING AN ESTUARINE ENVIRONMENT

    EPA Science Inventory

    Estuarine microcosms were used to follow conjugal transfer of a broad host range IncP1 plasmid from a Pseudomonas putida donor to indigenous bacteria. onor cells were added at a concentration similar to the natural abundance of bacteria in the water column (10 6/mi). ransfer was ...

  2. Irradiation-resistance conferred by superoxide dismutase: possible adaptive role of a natural polymorphism in Drosophila melanogaster

    SciTech Connect

    Peng, T.X.; Moya, A.; Ayala, F.J.

    1986-02-01

    The toxic effects of ionizing radiation to DNA are thought to be due to the generation of the superoxide radical, 02-. Superoxide dismutase (SOD), which scavenges 02-., has been invoked as a protecting enzyme against ionizing radiation in viruses, bacteria, mammalian cells in culture, and live mice. We now demonstrate that SOD is involved in the resistance of Drosophila melanogaster against irradiation. The protection is greatest when flies carry the S form of the enzyme (which exhibits highest in vitro specific activity), intermediate when they carry the F form of the enzyme, and lowest when they are homozygous for N, an allele that reduces the amount of the enzyme to 3.5% of the normal level. Natural selection experiments show that the fitness of the high-activity S allele is increased in an irradiated population relative to the nonirradiated control. These results point towards a possible adaptive function of the S/F polymorphism found in natural populations of D. melanogaster.

  3. billingsMentor: Adapting natural family planning to information technology and relieving the user of unnecessary tasks

    PubMed Central

    Smith, Audrey D.; Smith, John L.

    2014-01-01

    BillingsMentor is an automated Web-based service for the Billings Method of natural family planning in which the guidance and interpretation previously communicated from teacher to student is provided by programmed algorithms. There are two functions: (1) to instruct the client to generate proper descriptions of her fertility symptoms; and (2) to interpret the symptoms efficiently according to the Billings Method and to communicate the results to the client. The efficiency of billingsMentor was tested by using the historical records of students who were under the guidance of a teacher to emulate their experience under the guidance of billingsMentor. The results indicate that billingsMentor performs as well as the teacher/student in recognizing the peak of fertility but it is slightly less efficient than the teacher/student in establishing the basic infertile pattern. Advantages that arise from adapting natural family planning to information technology are discussed. PMID:25249704

  4. Effects of hatchery fish density on emigration, growth, survival, and predation risk of natural steelhead parr in an experimental stream channel

    USGS Publications Warehouse

    Tatara, Christopher P.; Riley, Stephen C.; Berejikian, Barry A.

    2011-01-01

    Hatchery supplementation of steelhead Oncorhynchus mykiss raises concerns about the impacts on natural populations, including reduced growth and survival, displacement, and increased predation. The potential risks may be density dependent.We examined how hatchery stocking density and the opportunity to emigrate affect the responses of natural steelhead parr in an experimental stream channel and after 15 d found no density-dependent effects on growth, emigration, or survival at densities ranging from 1-6 hatchery parr/m2. The opportunity for steelhead parr to emigrate reduced predation by coastal cutthroat trout O. clarkii clarkii on both hatchery and natural steelhead parr. The cutthroat trout exhibited a type-I functional response (constant predation rate with increased prey density) for the hatchery and composite populations. In contrast, the predation rate on natural parr decreased as hatchery stocking density increased. Supplementation with hatchery parr at any experimental stocking density reduced the final natural parr density. This decline was explained by increased emigration fromthe supplemented groups. Natural parr had higher mean instantaneous growth rates than hatchery parr. The proportion of parr emigrating decreased as parr size increased over successive experimental trials. Smaller parr had lower survival and suffered higher predation. The final density of the composite population, a measure of supplementation effectiveness, increased with the hatchery steelhead stocking rate. Our results indicate that stocking larger hatchery parr (over 50 d postemergence) at densities within the carrying capacity would have low short-term impact on the growth, survival, and emigration of natural parr while increasing the density of the composite population; in addition, a stocking density greater than 3 fish/m2 might be a good starting point for the evaluation of parr stocking in natural streams.

  5. Smooth statistical torsion angle potential derived from a large conformational database via adaptive kernel density estimation improves the quality of NMR protein structures

    PubMed Central

    Bermejo, Guillermo A; Clore, G Marius; Schwieters, Charles D

    2012-01-01

    Statistical potentials that embody torsion angle probability densities in databases of high-quality X-ray protein structures supplement the incomplete structural information of experimental nuclear magnetic resonance (NMR) datasets. By biasing the conformational search during the course of structure calculation toward highly populated regions in the database, the resulting protein structures display better validation criteria and accuracy. Here, a new statistical torsion angle potential is developed using adaptive kernel density estimation to extract probability densities from a large database of more than 106 quality-filtered amino acid residues. Incorporated into the Xplor-NIH software package, the new implementation clearly outperforms an older potential, widely used in NMR structure elucidation, in that it exhibits simultaneously smoother and sharper energy surfaces, and results in protein structures with improved conformation, nonbonded atomic interactions, and accuracy. PMID:23011872

  6. Animal Density and Track Counts: Understanding the Nature of Observations Based on Animal Movements

    PubMed Central

    Keeping, Derek; Pelletier, Rick

    2014-01-01

    Counting animals to estimate their population sizes is often essential for their management and conservation. Since practitioners frequently rely on indirect observations of animals, it is important to better understand the relationship between such indirect indices and animal abundance. The Formozov-Malyshev-Pereleshin (FMP) formula provides a theoretical foundation for understanding the relationship between animal track counts and the true density of species. Although this analytical method potentially has universal applicability wherever animals are readily detectable by their tracks, it has long been unique to Russia and remains widely underappreciated. In this paper, we provide a test of the FMP formula by isolating the influence of animal travel path tortuosity (i.e., convolutedness) on track counts. We employed simulations using virtual and empirical data, in addition to a field test comparing FMP estimates with independent estimates from line transect distance sampling. We verify that track counts (total intersections between animals and transects) are determined entirely by density and daily movement distances. Hence, the FMP estimator is theoretically robust against potential biases from specific shapes or patterns of animal movement paths if transects are randomly situated with respect to those movements (i.e., the transects do not influence animals’ movements). However, detectability (the detection probability of individual animals) is not determined simply by daily travel distance but also by tortuosity, so ensuring that all intersections with transects are counted regardless of the number of individual animals that made them becomes critical for an accurate density estimate. Additionally, although tortuosity has no bearing on mean track encounter rates, it does affect encounter rate variance and therefore estimate precision. We discuss how these fundamental principles made explicit by the FMP formula have widespread implications for methods of

  7. Advancing interconnect density for spiking neural network hardware implementations using traffic-aware adaptive network-on-chip routers.

    PubMed

    Carrillo, Snaider; Harkin, Jim; McDaid, Liam; Pande, Sandeep; Cawley, Seamus; McGinley, Brian; Morgan, Fearghal

    2012-09-01

    The brain is highly efficient in how it processes information and tolerates faults. Arguably, the basic processing units are neurons and synapses that are interconnected in a complex pattern. Computer scientists and engineers aim to harness this efficiency and build artificial neural systems that can emulate the key information processing principles of the brain. However, existing approaches cannot provide the dense interconnect for the billions of neurons and synapses that are required. Recently a reconfigurable and biologically inspired paradigm based on network-on-chip (NoC) and spiking neural networks (SNNs) has been proposed as a new method of realising an efficient, robust computing platform. However, the use of the NoC as an interconnection fabric for large-scale SNNs demands a good trade-off between scalability, throughput, neuron/synapse ratio and power consumption. This paper presents a novel traffic-aware, adaptive NoC router, which forms part of a proposed embedded mixed-signal SNN architecture called EMBRACE (EMulating Biologically-inspiRed ArChitectures in hardwarE). The proposed adaptive NoC router provides the inter-neuron connectivity for EMBRACE, maintaining router communication and avoiding dropped router packets by adapting to router traffic congestion. Results are presented on throughput, power and area performance analysis of the adaptive router using a 90 nm CMOS technology which outperforms existing NoCs in this domain. The adaptive behaviour of the router is also verified on a Stratix II FPGA implementation of a 4 × 2 router array with real-time traffic congestion. The presented results demonstrate the feasibility of using the proposed adaptive NoC router within the EMBRACE architecture to realise large-scale SNNs on embedded hardware. PMID:22561008

  8. Adaptive significance of natural variations in maternal care in rats: a translational perspective.

    PubMed

    Beery, Annaliese K; Francis, Darlene D

    2011-06-01

    A wealth of data from the last fifty years documents the potency of early life experiences including maternal care on developing offspring. A majority of this research has focused on the developing stress axis and stress-sensitive behaviors in hopes of identifying factors impacting resilience and risk-sensitivity. The power of early life experience to shape later development is profound and has the potential to increase fitness of individuals for their environments. Current findings in a rat maternal care paradigm highlight the complex and dynamic relation between early experiences and a variety of outcomes. In this review we propose adaptive hypotheses for alternate maternal strategies and resulting offspring phenotypes, and suggest means of distinguishing between these hypotheses. We also provide evidence underscoring the critical role of context in interpreting the adaptive significance of early experiences. If our goal is to identify risk-factors relevant to humans, we must better explore the role of the social and physical environment in our basic animal models. PMID:21458485

  9. Efficient reconstruction method for ground layer adaptive optics with mixed natural and laser guide stars.

    PubMed

    Wagner, Roland; Helin, Tapio; Obereder, Andreas; Ramlau, Ronny

    2016-02-20

    The imaging quality of modern ground-based telescopes such as the planned European Extremely Large Telescope is affected by atmospheric turbulence. In consequence, they heavily depend on stable and high-performance adaptive optics (AO) systems. Using measurements of incoming light from guide stars, an AO system compensates for the effects of turbulence by adjusting so-called deformable mirror(s) (DMs) in real time. In this paper, we introduce a novel reconstruction method for ground layer adaptive optics. In the literature, a common approach to this problem is to use Bayesian inference in order to model the specific noise structure appearing due to spot elongation. This approach leads to large coupled systems with high computational effort. Recently, fast solvers of linear order, i.e., with computational complexity O(n), where n is the number of DM actuators, have emerged. However, the quality of such methods typically degrades in low flux conditions. Our key contribution is to achieve the high quality of the standard Bayesian approach while at the same time maintaining the linear order speed of the recent solvers. Our method is based on performing a separate preprocessing step before applying the cumulative reconstructor (CuReD). The efficiency and performance of the new reconstructor are demonstrated using the OCTOPUS, the official end-to-end simulation environment of the ESO for extremely large telescopes. For more specific simulations we also use the MOST toolbox. PMID:26906596

  10. The nature and geochemical role of density convection in the East European evaporite basin

    NASA Astrophysics Data System (ADS)

    Popov, V. G.; Abdrakhmanov, R. F.; Puchkov, V. N.

    2015-09-01

    The role of the gravitation factor in the formation of the hydrostratisphere in the East European evaporate basin is considered. The features of Paleozoic sedimentation are characterized, as are the mechanism and litho-hydrogeochemical effects of the density concentration convection of mother brines of the Low-Permian salt-bearing basin to the underlying terrigenous-carbonate Paleozoic and Proterozoic layers. It is shown that the convection processes resulted in the formation of multicomponent calcium chloride brines prevailing in the sedimentary layer of the basis; they also caused the metasomatic dolomitization of limestones with growth of their filtration capacity.

  11. Time-dependent density functional theory study of UV/vis spectra of natural styrylpyrones.

    PubMed

    Anouar, El Hassane; Weber, Jean-Frédéric F

    2013-11-01

    Natural styrylpyrones isolated from fungi are known for various biological activities including antioxidant activity by scavenging free radicals. UV/vis spectra play an important role in elucidating chemical structures of these compounds via identification of chromophore units. With the aim of predicting the UV/vis spectra of a series of natural styrylpyrones, we tested TD-DFT, CIS and ZINDO methods in gas and in PCM solvent. The results showed that the individual or combined B3P86 and B3LYP hybrid functionals are suitable to predict the maximum wavelength absorption bands (λmax) for styrylpyrones. The structure property relationship (SPR) study emphasized the role of (i) structural parameters (e.g., hydrogen bond and the length of conjugated double bonds) and (ii) electronic descriptors (e.g., ionization potential, electronic affinity, hardness and electrophilicity) in bathochromic and hypsochromic shifts of maximum wavelength absorption bands (λmax) of styrylpyrone derivatives. PMID:23880409

  12. The effect of heterogeneity on the character of density-driven natural convection of CO 2 overlying a brine layer

    NASA Astrophysics Data System (ADS)

    Farajzadeh, R.; Ranganathan, P.; Zitha, P. L. J.; Bruining, J.

    2011-03-01

    The efficiency of mixing in density-driven natural-convection is largely governed by the aquifer permeability, which is heterogeneous in practice. The character (fingering, stable mixing or channeling) of flow-driven mixing processes depends primarily on the permeability heterogeneity character of the aquifer, i.e., on its degree of permeability variance (Dykstra-Parsons coefficient) and the correlation length. Here we follow the ideas of Waggoner et al. (1992) [13] to identify different flow regimes of a density-driven natural convection flow by numerical simulation. Heterogeneous fields are generated with the spectral method of Shinozuka and Jan (1972) [13], because the method allows the use of power-law variograms. In this paper, we extended the classification of Waggoner et al. (1992) [13] for the natural convection phenomenon, which can be used as a tool in selecting optimal fields with maximum transfer rates of CO 2 into water. We observe from our simulations that the rate of mass transfer of CO 2 into water is higher for heterogeneous media.

  13. Does natural larval parasitism of Lobesia botrana (Lepidoptera: Tortricidae) vary between years, generation, density of the host and vine cultivar?

    PubMed

    Xuéreb, A; Thiéry, D

    2006-04-01

    Populations of European grapevine moth Lobesia botrana Denis & Schiffermüller and its larval parasitoids were studied for two consecutive years on an experimental insecticide-free vineyard in France planted with adjacent plots of five grape cultivars (Merlot, Cabernet Franc, Sauvignon, Cabernet Sauvignon and Sémillon) using a natural L. botrana population during the first year, and a natural population supplemented with artificially inoculated individuals during the second year. Levels of natural populations of larval parasitoids were measured by their parasitism rate. The ichneumonid Campoplex capitator Aubert was the most common species collected from L. botrana larvae. Its incidence was higher during the spring compared to summer. The overall parasitism rate found on the experimental vineyard varied from 23% in 2000 to 53% in 2001, and was mainly due to C. capitator. Parasitism was not affected by the grape cultivar on which the host developed but was positively correlated with the host density, per bunch or per stock, suggesting that among the five grape cultivars tested, C. capitator females probably do not discriminate between hosts feeding on different grape cultivars, but rather the densities of L. botrana larvae. PMID:16556330

  14. Development of a natural practice to adapt conservation goals to global change.

    PubMed

    Heller, Nicole E; Hobbs, Richard J

    2014-06-01

    Conservation goals at the start of the 21st century reflect a combination of contrasting ideas. Ideal nature is something that is historically intact but also futuristically flexible. Ideal nature is independent from humans, but also, because of the pervasiveness of human impacts, only able to reach expression through human management. These tensions emerge in current management rationales because scientists and managers are struggling to accommodate old and new scientific and cultural thinking, while also maintaining legal mandates from the past and commitments to preservation of individual species in particular places under the stresses of global change. Common management goals (such as integrity, wilderness, resilience), whether they are forward looking and focused on sustainability and change, or backward looking and focused on the persistence and restoration of historic states, tend to create essentialisms about how ecosystems should be. These essentialisms limit the options of managers to accommodate the dynamic, and often novel, response of ecosystems to global change. Essentialisms emerge because there is a tight conceptual coupling of place and historical species composition as an indicator of naturalness (e.g., normal, healthy, independent from humans). Given that change is increasingly the norm and ecosystems evolve in response, the focus on idealized ecosystem states is increasingly unwise and unattainable. To provide more open-ended goals, we propose greater attention be paid to the characteristics of management intervention. We suggest that the way we interact with other species in management and the extent to which those interactions reflect the interactions among other biotic organisms, and also reflect our conservation virtues (e.g., humility, respect), influences our ability to cultivate naturalness on the landscape. We call this goal a natural practice (NP) and propose it as a framework for prioritizing and formulating how, when, and where to

  15. Nature and Nurture of Early-Type Dwarf Galaxies in Low Density Environments

    NASA Astrophysics Data System (ADS)

    Grützbauch, R.; Annibali, F.; Rampazzo, R.; Bressan, A.; Zeilinger, W. W.

    We study stellar population parameters of a sample of 13 dwarf galaxies located in poor groups of galaxies using high resolution spectra observed with VIMOS at the ESO-VLT [Grützbauch et al., A&A 502, 473 (2009)]. LICK-indices were compared with Simple Stellar Population models to derive ages, metallicities and [α/Fe]-ratios. Comparing the dwarfs with a sample of giant ETGs residing in comparable environments we find that the dwarfs are on average younger, less metal-rich, and less enhanced in alpha-elements than giants. Age, Z, and [α/Fe] ratios are found to correlate both with velocity dispersion and with morphology. We also find possible evidence that low density environment (LDE) dwarfs experienced more prolonged star formation histories than Coma dwarfs, however, larger samples are needed to draw firm conclusions.

  16. Estimation of Vegetation Aerodynamic Roughness of Natural Regions Using Frontal Area Density Determined from Satellite Imagery

    NASA Technical Reports Server (NTRS)

    Jasinski, Michael F.; Crago, Richard

    1994-01-01

    Parameterizations of the frontal area index and canopy area index of natural or randomly distributed plants are developed, and applied to the estimation of local aerodynamic roughness using satellite imagery. The formulas are expressed in terms of the subpixel fractional vegetation cover and one non-dimensional geometric parameter that characterizes the plant's shape. Geometrically similar plants and Poisson distributed plant centers are assumed. An appropriate averaging technique to extend satellite pixel-scale estimates to larger scales is provided. ne parameterization is applied to the estimation of aerodynamic roughness using satellite imagery for a 2.3 sq km coniferous portion of the Landes Forest near Lubbon, France, during the 1986 HAPEX-Mobilhy Experiment. The canopy area index is estimated first for each pixel in the scene based on previous estimates of fractional cover obtained using Landsat Thematic Mapper imagery. Next, the results are incorporated into Raupach's (1992, 1994) analytical formulas for momentum roughness and zero-plane displacement height. The estimates compare reasonably well to reference values determined from measurements taken during the experiment and to published literature values. The approach offers the potential for estimating regionally variable, vegetation aerodynamic roughness lengths over natural regions using satellite imagery when there exists only limited knowledge of the vegetated surface.

  17. High natural gene expression variation in the reef-building coral Acropora millepora: potential for acclimative and adaptive plasticity

    PubMed Central

    2013-01-01

    Background Ecosystems worldwide are suffering the consequences of anthropogenic impact. The diverse ecosystem of coral reefs, for example, are globally threatened by increases in sea surface temperatures due to global warming. Studies to date have focused on determining genetic diversity, the sequence variability of genes in a species, as a proxy to estimate and predict the potential adaptive response of coral populations to environmental changes linked to climate changes. However, the examination of natural gene expression variation has received less attention. This variation has been implicated as an important factor in evolutionary processes, upon which natural selection can act. Results We acclimatized coral nubbins from six colonies of the reef-building coral Acropora millepora to a common garden in Heron Island (Great Barrier Reef, GBR) for a period of four weeks to remove any site-specific environmental effects on the physiology of the coral nubbins. By using a cDNA microarray platform, we detected a high level of gene expression variation, with 17% (488) of the unigenes differentially expressed across coral nubbins of the six colonies (jsFDR-corrected, p < 0.01). Among the main categories of biological processes found differentially expressed were transport, translation, response to stimulus, oxidation-reduction processes, and apoptosis. We found that the transcriptional profiles did not correspond to the genotype of the colony characterized using either an intron of the carbonic anhydrase gene or microsatellite loci markers. Conclusion Our results provide evidence of the high inter-colony variation in A. millepora at the transcriptomic level grown under a common garden and without a correspondence with genotypic identity. This finding brings to our attention the importance of taking into account natural variation between reef corals when assessing experimental gene expression differences. The high transcriptional variation detected in this study is

  18. Floral display size, conspecific density and florivory affect fruit set in natural populations of Phlox hirsuta, an endangered species

    PubMed Central

    Ruane, Lauren G.; Rotzin, Andrew T.; Congleton, Philip H.

    2014-01-01

    Background and Aims Natural variation in fruit and seed set may be explained by factors that affect the composition of pollen grains on stigmas. Self-incompatible species require compatible outcross pollen grains to produce seeds. The siring success of outcross pollen grains, however, can be hindered if self (or other incompatible) pollen grains co-occur on stigmas. This study identifies factors that determine fruit set in Phlox hirsuta, a self-sterile endangered species that is prone to self-pollination, and its associated fitness costs. Methods Multiple linear regressions were used to identify factors that explain variation in percentage fruit set within three of the five known populations of this endangered species. Florivorous beetle density, petal colour, floral display size, local conspecific density and pre-dispersal seed predation were quantified and their effects on the ability of flowers to produce fruits were assessed. Key Results In all three populations, percentage fruit set decreased as florivorous beetle density increased and as floral display size increased. The effect of floral display size on fruit set, however, often depended on the density of nearby conspecific plants. High local conspecific densities offset – even reversed – the negative effects of floral display size on percentage fruit set. Seed predation by mammals decreased fruit set in one population. Conclusions The results indicate that seed production in P. hirsuta can be maximized by selectively augmenting populations in areas containing isolated large plants, by reducing the population sizes of florivorous beetles and by excluding mammals that consume unripe fruits. PMID:24557879

  19. Recognition of Porphyromonas gingivalis Gingipain Epitopes by Natural IgM Binding to Malondialdehyde Modified Low-Density Lipoprotein

    PubMed Central

    Turunen, S. Pauliina; Kummu, Outi; Harila, Kirsi; Veneskoski, Marja; Soliymani, Rabah; Baumann, Marc; Pussinen, Pirkko J.; Hörkkö, Sohvi

    2012-01-01

    Objective Increased risk for atherosclerosis is associated with infectious diseases including periodontitis. Natural IgM antibodies recognize pathogen-associated molecular patterns on bacteria, and oxidized lipid and protein epitopes on low-density lipoprotein (LDL) and apoptotic cells. We aimed to identify epitopes on periodontal pathogen Porphyromonas gingivalis recognized by natural IgM binding to malondialdehyde (MDA) modified LDL. Methods and Results Mouse monoclonal IgM (MDmAb) specific for MDA-LDL recognized epitopes on P. gingivalis on flow cytometry and chemiluminescence immunoassays. Immunization of C57BL/6 mice with P. gingivalis induced IgM, but not IgG, immune response to MDA-LDL and apoptotic cells. Immunization of LDLR−/− mice with P. gingivalis induced IgM, but not IgG, immune response to MDA-LDL and diminished aortic lipid deposition. On Western blot MDmAb bound to P. gingivalis fragments identified as arginine-specific gingipain (Rgp) by mass spectrometry. Recombinant domains of Rgp produced in E. coli were devoid of phosphocholine epitopes but contained epitopes recognized by MDmAb and human serum IgM. Serum IgM levels to P. gingivalis were associated with anti-MDA-LDL levels in humans. Conclusion Gingipain of P. gingivalis is recognized by natural IgM and shares molecular identity with epitopes on MDA-LDL. These findings suggest a role for natural antibodies in the pathogenesis of two related inflammatory diseases, atherosclerosis and periodontitis. PMID:22496875

  20. Using the conservative nature of fresh leaf surface density to measure foliar area

    NASA Astrophysics Data System (ADS)

    Castillo, Omar S.; Zaragoza, Esther M.; Alvarado, Carlos J.; Barrera, Maria G.; Dasgupta-Schubert, Nabanita

    2014-10-01

    For a herbaceous species, the inverse of the fresh leaf surface density, the Hughes constant, is nearly conserved. We apply the Hughes constant to develop an absolute method of leafarea measurement that requires no regression fits, prior calibrations or oven-drying. The Hughes constant was determined in situ using a known geometry and weights of a sub-set obtained from the fresh leaves whose areas are desired. Subsequently, the leaf-areas (at any desired stratification level), were derived by utilizing the Hughes constant and the masses of the fresh leaves. The proof of concept was established for leaf-discs of the plants Mandevilla splendens and Spathiphyllum wallisii. The conservativeness of the Hughes constant over individual leaf-zones and different leaftypes from the leaves of each species was quantitatively validated. Using the globally averaged Hughes constant for each species, the leaf-area of these and additional co-species plants, were obtained. The leaf-area-measurement-by-mass was cross-checked with standard digital image analysis. There were no statistically significant differences between the leaf-area-measurement-by-mass and the digital image analysis measured leaf-areas and the linear correlation between the two methods was very good. Leaf-areameasurement- by-mass was found to be rapid and simple with accuracies comparable to the digital image analysis method. The greatly reduced cost of leaf-area-measurement-by-mass could be beneficial for small agri-businesses in developing countries.

  1. Natural Selection at the Brush-Border: Adaptations to Carbohydrate Diets in Humans and Other Mammals

    PubMed Central

    Pontremoli, Chiara; Mozzi, Alessandra; Forni, Diego; Cagliani, Rachele; Pozzoli, Uberto; Menozzi, Giorgia; Vertemara, Jacopo; Bresolin, Nereo; Clerici, Mario; Sironi, Manuela

    2015-01-01

    Dietary shifts can drive molecular evolution in mammals and a major transition in human history, the agricultural revolution, favored carbohydrate consumption. We investigated the evolutionary history of nine genes encoding brush-border proteins involved in carbohydrate digestion/absorption. Results indicated widespread adaptive evolution in mammals, with several branches experiencing episodic selection, particularly strong in bats. Many positively selected sites map to functional protein regions (e.g., within glucosidase catalytic crevices), with parallel evolution at SI (sucrase-isomaltase) and MGAM (maltase-glucoamylase). In human populations, five genes were targeted by positive selection acting on noncoding variants within regulatory elements. Analysis of ancient DNA samples indicated that most derived alleles were already present in the Paleolithic. Positively selected variants at SLC2A5 (fructose transporter) were an exception and possibly spread following the domestication of specific fruit crops. We conclude that agriculture determined no major selective event at carbohydrate metabolism genes in humans, with implications for susceptibility to metabolic disorders. PMID:26319403

  2. Investigations into the Nature of Halogen Bonding Including Symmetry Adapted Perturbation Theory Analyses

    SciTech Connect

    Riley, Kevin E.; Hobza, Pavel

    2008-01-12

    In recent years it has been recognized that, because of their unique properties, halogen bonds have tremendous potential in the development of new pharmaceutical compounds and materials. In this study we investigate the phenomenon of halogen bonding by carrying out ab initio calculations on the halomethane-formaldehyde complexes as well as the fluorine substituted FnH₃-nCX---OCH₂ dimers, where the halogen bonding halogens (X) are chlorine, bromine, and iodine. Coupled cluster (CCSD(T)/aug-cc-pVTZ) calculations indicate that the binding energies for these type of interactions lie in the range between -1.05 kcal/mol (H₃CCl---OCH₂) and -3.72 kcal/mol (F₃CI---OCH₂). One of the most important findings in this study is that, according to symmetry adapted perturbation theory (SAPT) analyses, halogen bonds are largely dependent on both electrostatic and dispersion type interactions. As the halogen atom involved in halogen bonding becomes larger the interaction strength for this type of interaction also gets larger and, interestingly, more electrostatic (and less dispersive) in character. Halogen bonding interactions also become stronger and more electrostatic upon substitution of (the very electronegative) fluorines onto the halomethane molecule.

  3. Performance Characterization of KAPAO, a Low-Cost Natural Guide Star Adaptive Optics Instrument

    NASA Astrophysics Data System (ADS)

    Long, Joseph; Choi, P. I.; Severson, S. A.; Littleton, E.; Badham, K.; Bolger, D.; Guerrero, C.; Ortega, F.; Wong, J.; Baranec, C.; Riddle, R. L.

    2014-01-01

    We present a software overview of KAPAO, an adaptive optics system designed for the Pomona College 1-meter telescope at Table Mountain Observatory. The instrument is currently in the commissioning phase and data presented here are from both in-lab and on-sky observations. In an effort to maximize on-sky performance, we have developed a suite of instrument-specific data analysis tools. This suite of tools aids in the alignment of the instrument's optics, and the optimization of on-sky performance. The analysis suite visualizes and extends the telemetry output by the Robo-AO control software. This includes visualization of deformable mirror and wavefront sensor telemetry and a Zernike decomposition of the residual wavefront error. We complement this with analysis tools for the science camera data. We model a synthetic PSF for the Table Mountain telescope to calibrate our Strehl measurements, and process image data cubes to track instrument performance over the course of an observation. By coupling WFS telemetry with science camera data we can use image sharpening techniques to account for non-common-path wavefront errors and improve image performance. Python packages for scientific computing, such as NumPy and Matplotlib, are employed to complement existing IDL code. A primary goal of this suite of software is to support the remote use of the system by a broad range of users that includes faculty and undergraduate students from the consortium of member campuses.

  4. Natural Selection at the Brush-Border: Adaptations to Carbohydrate Diets in Humans and Other Mammals.

    PubMed

    Pontremoli, Chiara; Mozzi, Alessandra; Forni, Diego; Cagliani, Rachele; Pozzoli, Uberto; Menozzi, Giorgia; Vertemara, Jacopo; Bresolin, Nereo; Clerici, Mario; Sironi, Manuela

    2015-09-01

    Dietary shifts can drive molecular evolution in mammals and a major transition in human history, the agricultural revolution, favored carbohydrate consumption. We investigated the evolutionary history of nine genes encoding brush-border proteins involved in carbohydrate digestion/absorption. Results indicated widespread adaptive evolution in mammals, with several branches experiencing episodic selection, particularly strong in bats. Many positively selected sites map to functional protein regions (e.g., within glucosidase catalytic crevices), with parallel evolution at SI (sucrase-isomaltase) and MGAM (maltase-glucoamylase). In human populations, five genes were targeted by positive selection acting on noncoding variants within regulatory elements. Analysis of ancient DNA samples indicated that most derived alleles were already present in the Paleolithic. Positively selected variants at SLC2A5 (fructose transporter) were an exception and possibly spread following the domestication of specific fruit crops. We conclude that agriculture determined no major selective event at carbohydrate metabolism genes in humans, with implications for susceptibility to metabolic disorders. PMID:26319403

  5. Hybrid Incompatibilities, Local Adaptation, and the Genomic Distribution of Natural Introgression between Species.

    PubMed

    Muirhead, Christina A; Presgraves, Daven C

    2016-02-01

    Under allopatric speciation, geographic barriers eliminate gene flow between eventual species at all loci in the genome simultaneously. There is increasing evidence, however, that speciation can be complex, with some loci experiencing gene flow during speciation or during bouts of secondary contact. In taxa with heteromorphic sex chromosomes-birds, butterflies, mammals, and Drosophila-the X (or Z) chromosome generally shows reduced levels of gene flow compared to autosomes. To investigate why, we develop population genetic models of secondary contact and gene flow at a neutral locus that is genetically linked to selected loci involved in hybrid incompatibilities and/or local adaptation. Using models that assume weak migration and strong selection, we compare gene flow at X-linked versus autosomal neutral loci as a function of linkage, dominance, sex-specific selection, and sex-specific recombination. For most cases, gene flow at neutral loci on the X is reduced relative to autosomes, as the greater efficacy of hemizygous selection in XY hybrids reduces the opportunity for neutral migrant alleles to escape their genetically linked, locally disfavored alleles via recombination. There are some circumstances, however, involving sex-limited selection and sex-limited recombination that allow neutral loci on the X to introgress more readily than those on autosomes. PMID:26807751

  6. Natural bond orbital analysis, electronic structure and vibrational spectral analysis of N-(4-hydroxyl phenyl) acetamide: A density functional theory

    NASA Astrophysics Data System (ADS)

    Govindasamy, P.; Gunasekaran, S.; Ramkumaar, G. R.

    2014-09-01

    The Fourier transform infrared (FT-IR) and FT-Raman spectra of N-(4-hydroxy phenyl) acetamide (N4HPA) of painkiller agent were recorded in the region 4000-450 cm-1 and 4000-50 cm-1 respectively. Density functional theory (DFT) has been used to calculate the optimized geometrical parameter, atomic charges, and vibrational wavenumbers and intensity of the vibrational bands. The computed vibrational wave numbers were compared with the FT-IR and FT-Raman experimental data. The computational calculations at DFT/B3LYP level with 6-31G(d,p), 6-31++G(d,p), 6-311G(d,p) and 6-311++G(d,p) basis sets. The complete vibrational assignments were performed on the basis of the potential energy distribution (PED) of the vibrational modes calculated using Vibrational energy distribution analysis (VEDA 4) program. The oscillator’s strength calculated by TD-DFT and N4HPA is approach complement with the experimental findings. The NMR chemical shifts 13C and 1H were recorded and calculated using the gauge independent atomic orbital (GIAO) method. The molecular electrostatic potential (MESP) and electron density surfaces of the molecule were constructed. The Natural charges and intermolecular contacts have been interpreted using Natural Bond orbital (NBO) analysis the HOMO-LUMO energy gap has been calculated. The thermodynamic properties like entropy, heat capacity and zero vibrational energy have been calculated.

  7. Using Natural Selection to Explore the Adaptive Potential of Chlamydomonas reinhardtii

    PubMed Central

    Price, Dana C.; Levitan, Orly; Boyd, Jeffrey; Bhattacharya, Debashish

    2014-01-01

    Improving feedstock is critical to facilitate the commercial utilization of algae, in particular in open pond systems where, due to the presence of competitors and pests, high algal growth rates and stress tolerance are beneficial. Here we raised laboratory cultures of the model alga Chlamydomonas reinhardtii under serial dilution to explore the potential of crop improvement using natural selection. The alga was evolved for 1,880 generations in liquid medium under continuous light (EL population). At the end of the experiment, EL cells had a growth rate that was 35% greater than the progenitor population (PL). The removal of acetate from the medium demonstrated that EL growth enhancement largely relied on efficient usage of this organic carbon source. Genome re-sequencing uncovered 1,937 polymorphic DNA regions in the EL population with 149 single nucleotide polymorphisms resulting in amino acid substitutions. Transcriptome analysis showed, in the EL population, significant up regulation of genes involved in protein synthesis, the cell cycle and cellular respiration, whereas the DNA repair pathway and photosynthesis were down regulated. Like other algae, EL cells accumulated neutral lipids under nitrogen depletion. Our work demonstrates transcriptome and genome-wide impacts of natural selection on algal cells and points to a useful strategy for strain improvement. PMID:24658261

  8. Limits to the thermal tolerance of corals adapted to a highly fluctuating, naturally extreme temperature environment

    PubMed Central

    Schoepf, Verena; Stat, Michael; Falter, James L.; McCulloch, Malcolm T.

    2015-01-01

    Naturally extreme temperature environments can provide important insights into the processes underlying coral thermal tolerance. We determined the bleaching resistance of Acropora aspera and Dipsastraea sp. from both intertidal and subtidal environments of the naturally extreme Kimberley region in northwest Australia. Here tides of up to 10 m can cause aerial exposure of corals and temperatures as high as 37 °C that fluctuate daily by up to 7 °C. Control corals were maintained at ambient nearshore temperatures which varied diurnally by 4-5 °C, while treatment corals were exposed to similar diurnal variations and heat stress corresponding to ~20 degree heating days. All corals hosted Symbiodinium clade C independent of treatment or origin. Detailed physiological measurements showed that these corals were nevertheless highly sensitive to daily average temperatures exceeding their maximum monthly mean of ~31 °C by 1 °C for only a few days. Generally, Acropora was much more susceptible to bleaching than Dipsastraea and experienced up to 75% mortality, whereas all Dipsastraea survived. Furthermore, subtidal corals, which originated from a more thermally stable environment compared to intertidal corals, were more susceptible to bleaching. This demonstrates that while highly fluctuating temperatures enhance coral resilience to thermal stress, they do not provide immunity to extreme heat stress events. PMID:26627576

  9. Limits to the thermal tolerance of corals adapted to a highly fluctuating, naturally extreme temperature environment.

    PubMed

    Schoepf, Verena; Stat, Michael; Falter, James L; McCulloch, Malcolm T

    2015-01-01

    Naturally extreme temperature environments can provide important insights into the processes underlying coral thermal tolerance. We determined the bleaching resistance of Acropora aspera and Dipsastraea sp. from both intertidal and subtidal environments of the naturally extreme Kimberley region in northwest Australia. Here tides of up to 10 m can cause aerial exposure of corals and temperatures as high as 37 °C that fluctuate daily by up to 7 °C. Control corals were maintained at ambient nearshore temperatures which varied diurnally by 4-5 °C, while treatment corals were exposed to similar diurnal variations and heat stress corresponding to ~20 degree heating days. All corals hosted Symbiodinium clade C independent of treatment or origin. Detailed physiological measurements showed that these corals were nevertheless highly sensitive to daily average temperatures exceeding their maximum monthly mean of ~31 °C by 1 °C for only a few days. Generally, Acropora was much more susceptible to bleaching than Dipsastraea and experienced up to 75% mortality, whereas all Dipsastraea survived. Furthermore, subtidal corals, which originated from a more thermally stable environment compared to intertidal corals, were more susceptible to bleaching. This demonstrates that while highly fluctuating temperatures enhance coral resilience to thermal stress, they do not provide immunity to extreme heat stress events. PMID:26627576

  10. Limits to the thermal tolerance of corals adapted to a highly fluctuating, naturally extreme temperature environment

    NASA Astrophysics Data System (ADS)

    Schoepf, Verena; Stat, Michael; Falter, James L.; McCulloch, Malcolm T.

    2015-12-01

    Naturally extreme temperature environments can provide important insights into the processes underlying coral thermal tolerance. We determined the bleaching resistance of Acropora aspera and Dipsastraea sp. from both intertidal and subtidal environments of the naturally extreme Kimberley region in northwest Australia. Here tides of up to 10 m can cause aerial exposure of corals and temperatures as high as 37 °C that fluctuate daily by up to 7 °C. Control corals were maintained at ambient nearshore temperatures which varied diurnally by 4-5 °C, while treatment corals were exposed to similar diurnal variations and heat stress corresponding to ~20 degree heating days. All corals hosted Symbiodinium clade C independent of treatment or origin. Detailed physiological measurements showed that these corals were nevertheless highly sensitive to daily average temperatures exceeding their maximum monthly mean of ~31 °C by 1 °C for only a few days. Generally, Acropora was much more susceptible to bleaching than Dipsastraea and experienced up to 75% mortality, whereas all Dipsastraea survived. Furthermore, subtidal corals, which originated from a more thermally stable environment compared to intertidal corals, were more susceptible to bleaching. This demonstrates that while highly fluctuating temperatures enhance coral resilience to thermal stress, they do not provide immunity to extreme heat stress events.

  11. [Adaptive reactions of dehydrogenation processes in root voles during additional impacts of the physical nature].

    PubMed

    Kudiasheva, A G; Taskaev, A I

    2011-01-01

    Variations of the dehydrogenation enzyme activity (succinate dehydrogenase, pyruvate dehydrogenase, lactate dehydrogenase) in the heart muscle, liver and brain of root voles (Microtus oeconomus Pall.) and their progeny associated with additional stress effects (chronic low-level gamma-irradiation, short-term exposure to cold) have been studied. Root voles (parents) were caught in the areas with a normal and high-level natural radioactivity in the Republic of Komi. It has been revealed that the direction of shifts of the dehydrogenation enzyme activity in response to the factors of the physical nature is determined by the initial level of the oxidation process in tissues of root voles and their progeny that haven't been subjected to these actions. The reaction of root voles and their progeny (1-3 generations) from the radium zone has lower reserve functional possibilities in relation to the additional exposure as compared with the animals from the control zone. In some cases, chronic low-level irradiation and short-term cooling lead to leveling of differences between groups of animals which initially varied from each other in biochemical indexes. PMID:22279768

  12. Local density effects on individual production are dynamic: insights from natural stands of a perennial savanna grass.

    PubMed

    Zimmermann, Julia; Higgins, Steven I; Grimm, Volker; Hoffmann, John; Linstädter, Anja

    2015-08-01

    Perennial grasses are a dominant component of grasslands, and provide important ecosystem services. However, most knowledge of grasslands' functioning and production comes from plot-level studies, and drivers of individual-level production remain poorly explored. Extrapolation from existing experiments is hampered by the fact that these are mostly concentrated on even-aged cohorts, and/or on the early stages of a plant's life cycle. Here we explored how local density regulates individual production in mono-specific natural grassland, focusing on adult individuals of a perennial savanna grass (Stipagrostis uniplumis). We found individual production to increase with individuals' size, but to decrease with neighbour abundance. A metric of neighbour abundance that considered size was superior to a metric based solely on the number of individuals. This finding is particularly important for studying competitive effects in natural populations, where plants are normally not even-sized. The inferred competition kernel, i.e. the function describing how competitive strength varies with spatial distance from a target plant, was hump-shaped, indicating strongest intraspecific competition at intermediate distances (10-30 cm). The spatial signature of competitive effects changed with time since fire; peak effects moved successively away from the target plant. Our results suggest that inferred competition kernels of long-lived plant populations may have shapes that differ from exponential or sigmoidal decreases. More generally, results underline that competition among neighbouring plants is dynamic. Studies that address density-dependent and density-independent (fire-related) population dynamics of perennial grasses in their fire-prone environment may thus shed new light on the functioning and production of grasslands. PMID:25790804

  13. A new equation of state for better liquid density prediction of natural gas systems

    NASA Astrophysics Data System (ADS)

    Nwankwo, Princess C.

    Equations of state formulations, modifications and applications have remained active research areas since the success of van der Waal's equation in 1873. The need for better reservoir fluid modeling and characterization is of great importance to petroleum engineers who deal with thermodynamic related properties of petroleum fluids at every stage of the petroleum "life span" from its drilling, to production through the wellbore, to transportation, metering and storage. Equations of state methods are far less expensive (in terms of material cost and time) than laboratory or experimental forages and the results are interestingly not too far removed from the limits of acceptable accuracy. In most cases, the degree of accuracy obtained, by using various EOS's, though not appreciable, have been acceptable when considering the gain in time. The possibility of obtaining an equation of state which though simple in form and in use, could have the potential of further narrowing the present existing bias between experimentally determined and popular EOS estimated results spurred the interest that resulted in this study. This research study had as its chief objective, to develop a new equation of state that would more efficiently capture the thermodynamic properties of gas condensate fluids, especially the liquid phase density, which is the major weakness of other established and popular cubic equations of state. The set objective was satisfied by a new semi analytical cubic three parameter equation of state, derived by the modification of the attraction term contribution to pressure of the van der Waal EOS without compromising either structural simplicity or accuracy of estimating other vapor liquid equilibria properties. The application of new EOS to single and multi-component light hydrocarbon fluids recorded far lower error values than does the popular two parameter, Peng-Robinson's (PR) and three parameter Patel-Teja's (PT) equations of state. Furthermore, this research

  14. Selection and adaptation to high plant density in the Iowa Stiff Stalk synthetic maize (Zea mays L.) population

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The plant density at which Zea mays L. hybrids achieve maximum grain yield has increased throughout the hybrid era while grain yield on a per plant basis has increased little. Changes in plant traits including grain yield, moisture, test weight, and stalk and root lodging have been well characterize...

  15. Human APOBEC3 Induced Mutation of Human Immunodeficiency Virus Type-1 Contributes to Adaptation and Evolution in Natural Infection

    PubMed Central

    Kim, Eun-Young; Lorenzo-Redondo, Ramon; Little, Susan J.; Chung, Yoon-Seok; Phalora, Prabhjeet K.; Maljkovic Berry, Irina; Archer, John; Penugonda, Sudhir; Fischer, Will; Richman, Douglas D.; Bhattacharya, Tanmoy; Malim, Michael H.; Wolinsky, Steven M.

    2014-01-01

    Human APOBEC3 proteins are cytidine deaminases that contribute broadly to innate immunity through the control of exogenous retrovirus replication and endogenous retroelement retrotransposition. As an intrinsic antiretroviral defense mechanism, APOBEC3 proteins induce extensive guanosine-to-adenosine (G-to-A) mutagenesis and inhibit synthesis of nascent human immunodeficiency virus-type 1 (HIV-1) cDNA. Human APOBEC3 proteins have additionally been proposed to induce infrequent, potentially non-lethal G-to-A mutations that make subtle contributions to sequence diversification of the viral genome and adaptation though acquisition of beneficial mutations. Using single-cycle HIV-1 infections in culture and highly parallel DNA sequencing, we defined trinucleotide contexts of the edited sites for APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H. We then compared these APOBEC3 editing contexts with the patterns of G-to-A mutations in HIV-1 DNA in cells obtained sequentially from ten patients with primary HIV-1 infection. Viral substitutions were highest in the preferred trinucleotide contexts of the edited sites for the APOBEC3 deaminases. Consistent with the effects of immune selection, amino acid changes accumulated at the APOBEC3 editing contexts located within human leukocyte antigen (HLA)-appropriate epitopes that are known or predicted to enable peptide binding. Thus, APOBEC3 activity may induce mutations that influence the genetic diversity and adaptation of the HIV-1 population in natural infection. PMID:25080100

  16. Tip-tilt reconstruction with a single dim natural guide star in multiconjugate adaptive optics with laser guide stars

    NASA Astrophysics Data System (ADS)

    Femenã­A, Bruno

    2005-12-01

    A solution to the problem of detecting the tip-tilt modes in multiconjugate adaptive optics (MCAO) with laser guide stars (LGS) is presented. This solution requires the presence of only a single relatively dim natural guide star (NGS) within the reconstructed field of view (FoV). The dim NGS is used for the reconstruction of the tip-tilt modes on the entire FoV, while the tomographic reconstruction of second-order and higher-order modes is made possible by having an LGS constellation with LGSs at different heights. Due to the relatively low brightness required for the tip-tilt NGS and the large corrected FoV (as compared with the case of conventional adaptive optics) the presented solution provides a means to achieve near-diffraction-limited performance of a 10-m-class telescope in the near infrared over a large portion of the sky. Sky coverage calculations assuming median seeing conditions indicate that this technique could be applied to 75% (95%) of the sky, achieving corrections with an average Strehl ratio -0.42(-0.33) in the 2.2 μm K band across the 1.5 - reconstructed FoV.

  17. Molecular interaction between natural IgG and ficolin - mechanistic insights on adaptive-innate immune crosstalk

    NASA Astrophysics Data System (ADS)

    Panda, Saswati; Zhang, Jing; Yang, Lifeng; Anand, Ganesh S.; Ding, Jeak L.

    2014-01-01

    Recently, we found that natural IgG (nIgG; a non-specific immunoglobulin of adaptive immunity) is not quiescent, but plays a crucial role in immediate immune defense by collaborating with ficolin (an innate immune protein). However, how the nIgG and ficolin interplay and what factors control the complex formation during infection is unknown. Here, we found that mild acidosis and hypocalcaemia induced by infection- inflammation condition increased the nIgG:ficolin complex formation. Hydrogen-deuterium exchange mass spectrometry delineated the binding interfaces to the CH2-CH3 region of nIgG Fc and P-subdomain of ficolin FBG domain. Infection condition exposes novel binding sites. Site-directed mutagenesis and surface plasmon resonance analyses of peptides, derived from nIgG and ficolin, defined the interacting residues between the proteins. These results provide mechanistic insights on the interaction between two molecules representing the adaptive and innate immune pathways, prompting potential development of immunomodulatory/prophylactic peptides tunable to prevailing infection conditions.

  18. KAPAO first light: the design, construction and operation of a low-cost natural guide star adaptive optics system

    NASA Astrophysics Data System (ADS)

    Severson, Scott A.; Choi, Philip I.; Badham, Katherine E.; Bolger, Dalton; Contreras, Daniel S.; Gilbreth, Blaine N.; Guerrero, Christian; Littleton, Erik; Long, Joseph; McGonigle, Lorcan P.; Morrison, William A.; Ortega, Fernando; Rudy, Alex R.; Wong, Jonathan R.; Spjut, Erik; Baranec, Christoph; Riddle, Reed

    2014-07-01

    We present the instrument design and first light observations of KAPAO, a natural guide star adaptive optics (AO) system for the Pomona College Table Mountain Observatory (TMO) 1-meter telescope. The KAPAO system has dual science channels with visible and near-infrared cameras, a Shack-Hartmann wavefront sensor, and a commercially available 140-actuator MEMS deformable mirror. The pupil relays are two pairs of custom off-axis parabolas and the control system is based on a version of the Robo-AO control software. The AO system and telescope are remotely operable, and KAPAO is designed to share the Cassegrain focus with the existing TMO polarimeter. We discuss the extensive integration of undergraduate students in the program including the multiple senior theses/capstones and summer assistantships amongst our partner institutions. This material is based upon work supported by the National Science Foundation under Grant No. 0960343.

  19. Mechanical adaptability of the Bouligand-type structure in natural dermal armour.

    PubMed

    Zimmermann, Elizabeth A; Gludovatz, Bernd; Schaible, Eric; Dave, Neil K N; Yang, Wen; Meyers, Marc A; Ritchie, Robert O

    2013-01-01

    Arapaima gigas, a fresh water fish found in the Amazon Basin, resist predation by piranhas through the strength and toughness of their scales, which act as natural dermal armour. Arapaima scales consist of a hard, mineralized outer shell surrounding a more ductile core. This core region is composed of aligned mineralized collagen fibrils arranged in distinct lamellae. Here we show how the Bouligand-type (twisted plywood) arrangement of collagen fibril lamellae has a key role in developing their unique protective properties, by using in situ synchrotron small-angle X-ray scattering during mechanical tensile tests to observe deformation mechanisms in the fibrils. Specifically, the Bouligand-type structure allows the lamellae to reorient in response to the loading environment; remarkably, most lamellae reorient towards the tensile axis and deform in tension through stretching/sliding mechanisms, whereas other lamellae sympathetically rotate away from the tensile axis and compress, thereby enhancing the scale's ductility and toughness to prevent fracture. PMID:24129554

  20. Mechanical adaptability of the Bouligand-type structure in natural dermal armour

    NASA Astrophysics Data System (ADS)

    Zimmermann, Elizabeth A.; Gludovatz, Bernd; Schaible, Eric; Dave, Neil K. N.; Yang, Wen; Meyers, Marc A.; Ritchie, Robert O.

    2013-10-01

    Arapaima gigas, a fresh water fish found in the Amazon Basin, resist predation by piranhas through the strength and toughness of their scales, which act as natural dermal armour. Arapaima scales consist of a hard, mineralized outer shell surrounding a more ductile core. This core region is composed of aligned mineralized collagen fibrils arranged in distinct lamellae. Here we show how the Bouligand-type (twisted plywood) arrangement of collagen fibril lamellae has a key role in developing their unique protective properties, by using in situ synchrotron small-angle X-ray scattering during mechanical tensile tests to observe deformation mechanisms in the fibrils. Specifically, the Bouligand-type structure allows the lamellae to reorient in response to the loading environment; remarkably, most lamellae reorient towards the tensile axis and deform in tension through stretching/sliding mechanisms, whereas other lamellae sympathetically rotate away from the tensile axis and compress, thereby enhancing the scale’s ductility and toughness to prevent fracture.

  1. The assessment of natural flood management measures as a climate change adaptation option through land use scenarios

    NASA Astrophysics Data System (ADS)

    Iacob, Oana; Rowan, John; Brown, Iain; Ellis, Chris

    2014-05-01

    Climate change is one of the most pressing issues facing civil society. Greater variability and more frequent extremes of temperature and precipitation will result in increased flood risk and corresponding social, economic and environmental impacts. Complementing more traditional structurally-based engineering interventions an important additional adaptation strategy is through natural flood management (NFM) measures utilising natural soil, wetland and groundwater storage at the catchment scale to attenuate runoff generation and downstream flooding. Such schemes have multiple co-benefits including improved water quality, biodiversity and amenity and so contribute to greater resilience to uncertain climate futures. As a case-study of a more integrated approach to land use planning we here consider the policy target of the Scottish Government to expand woodland in Scotland by 100,000 ha by 2025 from the current 3 000 ha/year. In this paper we examine runoff response under different woodland expansion scenarios using climate projections obtained from the UK Climate Projections (UKCP09). Woodland creation has recognised potential as a NFM measure, but locating this new planting is constrained by physical and cultural constraints. Land use choices in the future will also strongly reflect emergent socio-economic contexts, here assessed through scenario analysis. The distributed hydrological model WaSiM-ETH was utilised for the analysis using the case-study of the Tarland catchment, a tributary of the River Dee. Terrain data were obtained on a 50 m grid and the model calibrated using meteorological and river gauge data from 2005 to 2007 following a manual and an automatic calibration process. This novel approach highlights that land use change should be carefully managed for planned benefits and to avoid unintended consequences, such as changing the timing of tributary flood responses. Whilst woodland expansion may only provide modest gains in flood reductions the co

  2. The vibrational problem solution in natural coordinates with the application of ab initio methods and the functional density theory (DFT-methods)

    NASA Astrophysics Data System (ADS)

    Novoselova, Anna V.; Chernavina, Mariya L.; Berezin, Kirill V.; Berezin, Valentin I.

    2015-03-01

    This article describes the algorithm and the creation of programs for the input process automate the scaling factors of quantum mechanical force fields calculated in the natural coordinates using ab initio methods and the density functional theory (DFT-methods).

  3. Following a natural experiment of guideline adaptation and early implementation: a mixed-methods study of facilitation

    PubMed Central

    2012-01-01

    Background Facilitation is emerging as an important strategy in the uptake of evidence. However, it is not entirely clear from a practical perspective how facilitation occurs to help move research evidence into nursing practice. The Canadian Partnership Against Cancer, also known as the 'Partnership,' is a Pan-Canadian initiative supporting knowledge translation activity for improved care through guideline use. In this case-series study, five self-identified groups volunteered to use a systematic methodology to adapt existing clinical practice guidelines for Canadian use. With 'Partnership' support, local and external facilitators provided assistance for groups to begin the process by adapting the guidelines and planning for implementation. Methods To gain a more comprehensive understanding of the nature of facilitation, we conducted a mixed-methods study. Specifically, we examined the role and skills of individuals actively engaged in facilitation as well as the actual facilitation activities occurring within the 'Partnership.' The study was driven by and builds upon a focused literature review published in 2010 that examined facilitation as a role and process in achieving evidence-based practice in nursing. An audit tool outlining 46 discrete facilitation activities based on results of this review was used to examine the facilitation noted in the documents (emails, meeting minutes, field notes) of three nursing-related cases participating in the 'Partnership' case-series study. To further examine the concept, six facilitators were interviewed about their practical experiences. The case-audit data were analyzed through a simple content analysis and triangulated with participant responses from the focus group interview to understand what occurred as these cases undertook guideline adaptation. Results The analysis of the three cases revealed that almost all of the 46 discrete, practical facilitation activities from the literature were evidenced. Additionally, case

  4. Broken-symmetry-adapted Green function theory of condensed matter systems: Towards a vector spin-density-functional theory

    NASA Astrophysics Data System (ADS)

    Rajagopal, A. K.; Mochena, Mogus

    2000-12-01

    The group-theory framework developed by Fukutome for a systematic analysis of the various broken-symmetry types of Hartree-Fock solution exhibiting spin structures is here extended to the general many-body context using spinor Green function formalism for describing magnetic systems. Consequences of this theory are discussed for examining the magnetism of itinerant electrons in nanometric systems of current interest as well as bulk systems where a vector spin-density form is required, by specializing our work to spin-density-functional formalism. We also formulate the linear-response theory for such a system and compare and contrast our results with the recent results obtained for localized electron systems. The various phenomenological treatments of itinerant magnetic systems are here unified in this group-theoretical description. We apply this theory to the one-band Hubbard model to illustrate the usefulness of this approach.

  5. Spatial variation in osteon population density at the human femoral midshaft: histomorphometric adaptations to habitual load environment.

    PubMed

    Gocha, Timothy P; Agnew, Amanda M

    2016-05-01

    Intracortical remodeling, and the osteons it produces, is one aspect of the bone microstructure that is influenced by and, in turn, can influence its mechanical properties. Previous research examining the spatial distribution of intracortical remodeling density across the femoral midshaft has been limited to either considering only small regions of the cortex or, when looking at the entirety of the cortex, considering only a single individual. This study examined the spatial distribution of all remodeling events (intact osteons, fragmentary osteons, and resorptive bays) across the entirety of the femoral midshaft in a sample of 30 modern cadaveric donors. The sample consisted of 15 males and 15 females, aged 21-97 years at time of death. Using geographic information systems software, the femoral cortex was subdivided radially into thirds and circumferentially into octants, and the spatial location of all remodeling events was marked. Density maps and calculation of osteon population density in cortical regions of interest revealed that remodeling density is typically highest in the periosteal third of the bone, particularly in the lateral and anterolateral regions of the cortex. Due to modeling drift, this area of the midshaft femur has some of the youngest primary tissue, which consequently reveals that the lateral and anterolateral regions of the femoral midshaft have higher remodeling rates than elsewhere in the cortex. This is likely the result of tension/shear forces and/or greater strain magnitudes acting upon the anterolateral femur, which results in a greater amount of microdamage in need of repair than is seen in the medial and posterior regions of the femoral midshaft, which are more subject to compressive forces and/or lesser strain magnitudes. PMID:26708961

  6. Chronic intermittent ethanol exposure and withdrawal leads to adaptations in nucleus accumbens core postsynaptic density proteome and dendritic spines.

    PubMed

    Uys, Joachim D; McGuier, Natalie S; Gass, Justin T; Griffin, William C; Ball, Lauren E; Mulholland, Patrick J

    2016-05-01

    Alcohol use disorder is a chronic relapsing brain disease characterized by the loss of ability to control alcohol (ethanol) intake despite knowledge of detrimental health or personal consequences. Clinical and pre-clinical models provide strong evidence for chronic ethanol-associated alterations in glutamatergic signaling and impaired synaptic plasticity in the nucleus accumbens (NAc). However, the neural mechanisms that contribute to aberrant glutamatergic signaling in ethanol-dependent individuals in this critical brain structure remain unknown. Using an unbiased proteomic approach, we investigated the effects of chronic intermittent ethanol (CIE) exposure on neuroadaptations in postsynaptic density (PSD)-enriched proteins in the NAc of ethanol-dependent mice. Compared with controls, CIE exposure significantly changed expression levels of 50 proteins in the PSD-enriched fraction. Systems biology and functional annotation analyses demonstrated that the dysregulated proteins are expressed at tetrapartite synapses and critically regulate cellular morphology. To confirm this latter finding, the density and morphology of dendritic spines were examined in the NAc core of ethanol-dependent mice. We found that CIE exposure and withdrawal differentially altered dendrite diameter and dendritic spine density and morphology. Through the use of quantitative proteomics and functional annotation, these series of experiments demonstrate that ethanol dependence produces neuroadaptations in proteins that modify dendritic spine morphology. In addition, these studies identified novel PSD-related proteins that contribute to the neurobiological mechanisms of ethanol dependence that drive maladaptive structural plasticity of NAc neurons. PMID:25787124

  7. Irradiation-resistance conferred by superoxide dismutase: possible adaptive role of a natural polymorphism in Drosophila melanogaster.

    PubMed Central

    Peng, T X; Moya, A; Ayala, F J

    1986-01-01

    The toxic effects of ionizing radiation to DNA are thought to be due to the generation of the superoxide radical, 02-. Superoxide dismutase (SOD), which scavenges 02-., has been invoked as a protecting enzyme against ionizing radiation in viruses, bacteria, mammalian cells in culture, and live mice. We now demonstrate that SOD is involved in the resistance of Drosophila melanogaster against irradiation. The protection is greatest when flies carry the S form of the enzyme (which exhibits highest in vitro specific activity), intermediate when they carry the F form of the enzyme, and lowest when they are homozygous for N, an allele that reduces the amount of the enzyme to 3.5% of the normal level. Natural selection experiments show that the fitness of the high-activity S allele is increased in an irradiated population relative to the nonirradiated control. These results point towards a possible adaptive function of the S/F polymorphism found in natural populations of D. melanogaster. PMID:3080745

  8. The nature of organic carbon in density-fractionated sediments in the Sacramento-San Joaquin River Delta (California)

    NASA Astrophysics Data System (ADS)

    Wakeham, S. G.; Canuel, E. A.

    2016-02-01

    Rivers are the primary means by which sediments and carbon are transported from the terrestrial biosphere to the oceans but gaps remain in our understanding of carbon associations from source to sink. Bed sediments from the Sacramento-San Joaquin River Delta (CA) were fractionated according to density and analyzed for sediment mass distribution, elemental (C and N) composition, mineral surface area, and stable carbon and radiocarbon isotope compositions of organic carbon (OC) and fatty acids to evaluate the nature of organic carbon in river sediments. OC was unevenly distributed among density fractions. Mass and OC were in general concentrated in mesodensity (1.6-2.0 and 2.0-2.5 g cm-3) fractions, comprising 84.0 ± 1.3 % of total sediment mass and 80.8 ± 13.3 % of total OC (TOC). Low-density (< 1.6 g cm-3) material, although rich in OC (34.0 ± 2.0 % OC) due to woody debris, constituted only 17.3 ± 12.8 % of TOC. High-density (> 2.5 g cm-3) organic-poor, mineral-rich material made-up 13.7 ± 1.4 % of sediment mass and 2.0 ± 0.9 % of TOC. Stable carbon isotope compositions of sedimentary OC were relatively uniform across bulk and density fractions (δ13C -27.4 ± 0.5 ‰). Radiocarbon content varied from Δ14C values of -382 (radiocarbon age 3800 yr BP) to +94 ‰ (modern) indicating a mix of young and old OC. Fatty acids were used to further constrain the origins of sedimentary OC. Short-chain n-C14-n-C18 fatty acids of algal origin were depleted in 13C (δ13C -37.5 to -35.2 ‰) but were enriched in 14C (Δ14C > 0) compared to long-chain n-C24-n-C28 acids of vascular plant origins with higher δ13C (-33.0 to -31.0 ‰) but variable Δ14C values (-180 and 61 ‰). These data demonstrate the potentially complex source and age distributions found within river sediments and provide insights about sediment and organic matter supply to the Delta.

  9. The nature of organic carbon in density-fractionated sediments in the Sacramento-San Joaquin River Delta (California)

    NASA Astrophysics Data System (ADS)

    Wakeham, S. G.; Canuel, E. A.

    2015-10-01

    Rivers are the primary means by which sediments and carbon are transported from the terrestrial biosphere to the oceans but gaps remain in our understanding of carbon associations from source to sink. Bed sediments from the Sacramento-San Joaquin River Delta (CA) were fractionated according to density and analyzed for sediment mass distribution, elemental (C and N) composition, mineral surface area, and stable carbon and radiocarbon isotope compositions of organic carbon (OC) and fatty acids to evaluate the nature of organic carbon in river sediments. OC was unevenly distributed among density fractions. Mass and TOC were in general concentrated in mesodensity (1.6-2.0 and 2.0-2.5 g cm-3) fractions, comprising 84.0 ± 1.3 % of total sediment mass and 80.8 ± 13.3 % of total OC (TOC). Low density (< 1.6 g cm-3) material, although rich in OC (34.0 ± 2.0 % OC) due to woody debris, constituted only 17.3 ± 12.8 % of TOC. High density (> 2.5 g cm-3) organic-poor, mineral material made-up 13.7 ± 1.4 % of sediment mass and 2.0 ± 0.9 % of TOC. Stable carbon isotope compositions of sedimentary OC were relatively uniform across bulk and density fractions (δ13C -27.4 ± 0.5 ‰). Radiocarbon content varied from Δ14C values of -382 (radiocarbon age 3800 yr BP) to +94 ‰ (modern) indicating a~mix of young and pre-aged OC. Fatty acids were used to further constrain the origins of sedimentary OC. Short-chain n-C14-n-C18 fatty acids of algal origin were depleted in δ13C (δ13C -37.5 to -35.2 ‰) but were enriched in 14C (Δ14C > 0) compared to long-chain n-C24-n-C28 acids of vascular plant origins with higher δ13C (-33.0 to -31.0 ‰) but variable Δ14C values (-180 and 61 ‰). These data demonstrate the potentially complex source and age distributions found within river sediments and provide insights about sediment and organic matter supply to the Sacramento-San Joaquin River Delta.

  10. Elevated Periimplantation Uterine Natural Killer Cell Density in Human Endometrium Is Associated With Impaired Corticosteroid Signaling in Decidualizing Stromal Cells

    PubMed Central

    Kuroda, Keiji; Venkatakrishnan, Radha; James, Sean; Šućurović, Sandra; Mulac-Jericevic, Biserka; Lucas, Emma S.; Takeda, Satoru; Shmygol, Anatoly; Brosens, Jan J.

    2013-01-01

    Background: Decidualizing human endometrial stromal cells (HESCs) profoundly up-regulate 11β-hydroxysteroid dehydrogenase type 1 (11βHSD1), the enzyme that converts inert cortisone to active cortisol. We postulated that the induction of a cortisol gradient upon decidualization of the periimplantation endometrium may impact on the uterine natural killer (uNK) cell population and on local expression of corticosteroid-dependent target genes. Methods: Midluteal endometrial biopsies (n = 55) were processed for uNK cell (CD56) analysis and primary HESC cultures. The cultures remained either untreated or were decidualized for 4 or 8 days. A tissue microarray was constructed from endometria with normal (n = 18) and elevated uNK cell (n = 18) scores. An abnormal uNK cell test was defined as greater than 5% CD56+ cells in the subluminal stroma. Results: Increased uNK cell density was associated with lower endometrial expression of 11βHSD1 and mineralocorticoid receptor (MR) but not glucocorticoid receptor in vivo. Elevated uNK cell density also corresponded to impaired induction of key decidual markers (11βHSD1, prolactin, and insulin-like growth factor binding protein-1) and MR-dependent enzymes (dehydrogenase/reductase member 3 and retinol saturase) in differentiating HESC cultures. Increased uNK cell density in vivo was not associated with increased in vitro expression of either IL-15 or IL-11, two cytokines implicated in uNK cell regulation. Conclusions: Elevated levels of uNK cells in the stroma underlying the surface epithelium are associated with inadequate cortisol biosynthesis by resident decidualizing cells and suboptimal induction of key MR-dependent enzymes involved in lipid biogenesis and the retinoid transport pathway. Our observations suggest that uNK cell testing identifies those women at risk of reproductive failure due to relative uterine cortisol deficiency. PMID:24025400

  11. An Atlas-Based Electron Density Mapping Method for Magnetic Resonance Imaging (MRI)-Alone Treatment Planning and Adaptive MRI-Based Prostate Radiation Therapy

    SciTech Connect

    Dowling, Jason A.; Lambert, Jonathan; Parker, Joel; Salvado, Olivier; Fripp, Jurgen; Capp, Anne; Wratten, Chris; Denham, James W.; Greer, Peter B.

    2012-05-01

    Purpose: Prostate radiation therapy dose planning directly on magnetic resonance imaging (MRI) scans would reduce costs and uncertainties due to multimodality image registration. Adaptive planning using a combined MRI-linear accelerator approach will also require dose calculations to be performed using MRI data. The aim of this work was to develop an atlas-based method to map realistic electron densities to MRI scans for dose calculations and digitally reconstructed radiograph (DRR) generation. Methods and Materials: Whole-pelvis MRI and CT scan data were collected from 39 prostate patients. Scans from 2 patients showed significantly different anatomy from that of the remaining patient population, and these patients were excluded. A whole-pelvis MRI atlas was generated based on the manually delineated MRI scans. In addition, a conjugate electron-density atlas was generated from the coregistered computed tomography (CT)-MRI scans. Pseudo-CT scans for each patient were automatically generated by global and nonrigid registration of the MRI atlas to the patient MRI scan, followed by application of the same transformations to the electron-density atlas. Comparisons were made between organ segmentations by using the Dice similarity coefficient (DSC) and point dose calculations for 26 patients on planning CT and pseudo-CT scans. Results: The agreement between pseudo-CT and planning CT was quantified by differences in the point dose at isocenter and distance to agreement in corresponding voxels. Dose differences were found to be less than 2%. Chi-squared values indicated that the planning CT and pseudo-CT dose distributions were equivalent. No significant differences (p > 0.9) were found between CT and pseudo-CT Hounsfield units for organs of interest. Mean {+-} standard deviation DSC scores for the atlas-based segmentation of the pelvic bones were 0.79 {+-} 0.12, 0.70 {+-} 0.14 for the prostate, 0.64 {+-} 0.16 for the bladder, and 0.63 {+-} 0.16 for the rectum

  12. Host-Specific Parvovirus Evolution in Nature Is Recapitulated by In Vitro Adaptation to Different Carnivore Species

    PubMed Central

    Allison, Andrew B.; Kohler, Dennis J.; Ortega, Alicia; Hoover, Elizabeth A.; Grove, Daniel M.; Holmes, Edward C.; Parrish, Colin R.

    2014-01-01

    Canine parvovirus (CPV) emerged as a new pandemic pathogen of dogs in the 1970s and is closely related to feline panleukopenia virus (FPV), a parvovirus of cats and related carnivores. Although both viruses have wide host ranges, analysis of viral sequences recovered from different wild carnivore species, as shown here, demonstrated that >95% were derived from CPV-like viruses, suggesting that CPV is dominant in sylvatic cycles. Many viral sequences showed host-specific mutations in their capsid proteins, which were often close to sites known to control binding to the transferrin receptor (TfR), the host receptor for these carnivore parvoviruses, and which exhibited frequent parallel evolution. To further examine the process of host adaptation, we passaged parvoviruses with alternative backgrounds in cells from different carnivore hosts. Specific mutations were selected in several viruses and these differed depending on both the background of the virus and the host cells in which they were passaged. Strikingly, these in vitro mutations recapitulated many specific changes seen in viruses from natural populations, strongly suggesting they are host adaptive, and which were shown to result in fitness advantages over their parental virus. Comparison of the sequences of the transferrin receptors of the different carnivore species demonstrated that many mutations occurred in and around the apical domain where the virus binds, indicating that viral variants were likely selected through their fit to receptor structures. Some of the viruses accumulated high levels of variation upon passage in alternative hosts, while others could infect multiple different hosts with no or only a few additional mutations. Overall, these studies demonstrate that the evolutionary history of a virus, including how long it has been circulating and in which hosts, as well as its phylogenetic background, has a profound effect on determining viral host range. PMID:25375184

  13. Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors.

    PubMed

    Kelly, Linda W; Williams, Gareth J; Barott, Katie L; Carlson, Craig A; Dinsdale, Elizabeth A; Edwards, Robert A; Haas, Andreas F; Haynes, Matthew; Lim, Yan Wei; McDole, Tracey; Nelson, Craig E; Sala, Enric; Sandin, Stuart A; Smith, Jennifer E; Vermeij, Mark J A; Youle, Merry; Rohwer, Forest

    2014-07-15

    Holobionts are species-specific associations between macro- and microorganisms. On coral reefs, the benthic coverage of coral and algal holobionts varies due to natural and anthropogenic forcings. Different benthic macroorganisms are predicted to have specific microbiomes. In contrast, local environmental factors are predicted to select for specific metabolic pathways in microbes. To reconcile these two predictions, we hypothesized that adaptation of microbiomes to local conditions is facilitated by the horizontal transfer of genes responsible for specific metabolic capabilities. To test this hypothesis, microbial metagenomes were sequenced from 22 coral reefs at 11 Line Islands in the central Pacific that together span a wide range of biogeochemical and anthropogenic influences. Consistent with our hypothesis, the percent cover of major benthic functional groups significantly correlated with particular microbial taxa. Reefs with higher coral cover had a coral microbiome with higher abundances of Alphaproteobacteria (such as Rhodobacterales and Sphingomonadales), whereas microbiomes of algae-dominated reefs had higher abundances of Gammaproteobacteria (such as Alteromonadales, Pseudomonadales, and Vibrionales), Betaproteobacteria, and Bacteriodetes. In contrast to taxa, geography was the strongest predictor of microbial community metabolism. Microbial communities on reefs with higher nutrient availability (e.g., equatorial upwelling zones) were enriched in genes involved in nutrient-related metabolisms (e.g., nitrate and nitrite ammonification, Ton/Tol transport, etc.). On reefs further from the equator, microbes had more genes encoding chlorophyll biosynthesis and photosystems I/II. These results support the hypothesis that core microbiomes are determined by holobiont macroorganisms, and that those core taxa adapt to local conditions by selecting for advantageous metabolic genes. PMID:24982156

  14. Host-specific parvovirus evolution in nature is recapitulated by in vitro adaptation to different carnivore species.

    PubMed

    Allison, Andrew B; Kohler, Dennis J; Ortega, Alicia; Hoover, Elizabeth A; Grove, Daniel M; Holmes, Edward C; Parrish, Colin R

    2014-11-01

    Canine parvovirus (CPV) emerged as a new pandemic pathogen of dogs in the 1970s and is closely related to feline panleukopenia virus (FPV), a parvovirus of cats and related carnivores. Although both viruses have wide host ranges, analysis of viral sequences recovered from different wild carnivore species, as shown here, demonstrated that>95% were derived from CPV-like viruses, suggesting that CPV is dominant in sylvatic cycles. Many viral sequences showed host-specific mutations in their capsid proteins, which were often close to sites known to control binding to the transferrin receptor (TfR), the host receptor for these carnivore parvoviruses, and which exhibited frequent parallel evolution. To further examine the process of host adaptation, we passaged parvoviruses with alternative backgrounds in cells from different carnivore hosts. Specific mutations were selected in several viruses and these differed depending on both the background of the virus and the host cells in which they were passaged. Strikingly, these in vitro mutations recapitulated many specific changes seen in viruses from natural populations, strongly suggesting they are host adaptive, and which were shown to result in fitness advantages over their parental virus. Comparison of the sequences of the transferrin receptors of the different carnivore species demonstrated that many mutations occurred in and around the apical domain where the virus binds, indicating that viral variants were likely selected through their fit to receptor structures. Some of the viruses accumulated high levels of variation upon passage in alternative hosts, while others could infect multiple different hosts with no or only a few additional mutations. Overall, these studies demonstrate that the evolutionary history of a virus, including how long it has been circulating and in which hosts, as well as its phylogenetic background, has a profound effect on determining viral host range. PMID:25375184

  15. Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors

    PubMed Central

    Kelly, Linda W.; Williams, Gareth J.; Barott, Katie L.; Carlson, Craig A.; Dinsdale, Elizabeth A.; Edwards, Robert A.; Haas, Andreas F.; Haynes, Matthew; Lim, Yan Wei; McDole, Tracey; Nelson, Craig E.; Sala, Enric; Sandin, Stuart A.; Smith, Jennifer E.; Vermeij, Mark J. A.; Youle, Merry; Rohwer, Forest

    2014-01-01

    Holobionts are species-specific associations between macro- and microorganisms. On coral reefs, the benthic coverage of coral and algal holobionts varies due to natural and anthropogenic forcings. Different benthic macroorganisms are predicted to have specific microbiomes. In contrast, local environmental factors are predicted to select for specific metabolic pathways in microbes. To reconcile these two predictions, we hypothesized that adaptation of microbiomes to local conditions is facilitated by the horizontal transfer of genes responsible for specific metabolic capabilities. To test this hypothesis, microbial metagenomes were sequenced from 22 coral reefs at 11 Line Islands in the central Pacific that together span a wide range of biogeochemical and anthropogenic influences. Consistent with our hypothesis, the percent cover of major benthic functional groups significantly correlated with particular microbial taxa. Reefs with higher coral cover had a coral microbiome with higher abundances of Alphaproteobacteria (such as Rhodobacterales and Sphingomonadales), whereas microbiomes of algae-dominated reefs had higher abundances of Gammaproteobacteria (such as Alteromonadales, Pseudomonadales, and Vibrionales), Betaproteobacteria, and Bacteriodetes. In contrast to taxa, geography was the strongest predictor of microbial community metabolism. Microbial communities on reefs with higher nutrient availability (e.g., equatorial upwelling zones) were enriched in genes involved in nutrient-related metabolisms (e.g., nitrate and nitrite ammonification, Ton/Tol transport, etc.). On reefs further from the equator, microbes had more genes encoding chlorophyll biosynthesis and photosystems I/II. These results support the hypothesis that core microbiomes are determined by holobiont macroorganisms, and that those core taxa adapt to local conditions by selecting for advantageous metabolic genes. PMID:24982156

  16. Natural resource mitigation, adaptation and research needs related to climate change in the Great Basin and Mojave Desert

    USGS Publications Warehouse

    Hughson, Debra L.; Busch, David E.; Davis, Scott; Finn, Sean P.; Caicco, Steve; Verburg, Paul S.J.

    2011-01-01

    This report synthesizes the knowledge, opinions, and concerns of many Federal and State land managers, scientists, stakeholders, and partners from a workshop, held at the University of Nevada, Las Vegas, on April 20-22, 2010. Land managers, research scientists, and resource specialists identified common concerns regarding the potential effects of climate change on public lands and natural resources in the Great Basin and Mojave Desert and developed recommendations for mitigation, adaptation, and research needs. Water and, conversely, the effects of drought emerged as a common theme in all breakout sessions on terrestrial and aquatic species at risk, managing across boundaries, monitoring, and ecosystem services. Climate change models for the southwestern deserts predict general warming and drying with increasing precipitation variability year to year. Scientists noted that under these changing conditions the past may no longer be a guide to the future in which managers envision increasing conflicts between human water uses and sustaining ecosystems. Increasing environmental stress also is expected as a consequence of shifting ecosystem boundaries and species distributions, expansion of non-native species, and decoupling of biotic mutualisms, leading to increasingly unstable biologic communities. Managers uniformly expressed a desire to work across management and agency boundaries at a landscape scale but conceded that conflicting agency missions and budgetary constraints often impede collaboration. More and better science is needed to cope with the effects of climate change but, perhaps even more important is the application of science to management issues using the methods of adaptive management based on long-term monitoring to assess the merits of management actions. Access to data is essential for science-based land management. Basic inventories, spatial databases, baseline condition assessments, data quality assurance, and data sharing were identified as top

  17. A fast tree-based method for estimating column densities in adaptive mesh refinement codes. Influence of UV radiation field on the structure of molecular clouds

    NASA Astrophysics Data System (ADS)

    Valdivia, Valeska; Hennebelle, Patrick

    2014-11-01

    Context. Ultraviolet radiation plays a crucial role in molecular clouds. Radiation and matter are tightly coupled and their interplay influences the physical and chemical properties of gas. In particular, modeling the radiation propagation requires calculating column densities, which can be numerically expensive in high-resolution multidimensional simulations. Aims: Developing fast methods for estimating column densities is mandatory if we are interested in the dynamical influence of the radiative transfer. In particular, we focus on the effect of the UV screening on the dynamics and on the statistical properties of molecular clouds. Methods: We have developed a tree-based method for a fast estimate of column densities, implemented in the adaptive mesh refinement code RAMSES. We performed numerical simulations using this method in order to analyze the influence of the screening on the clump formation. Results: We find that the accuracy for the extinction of the tree-based method is better than 10%, while the relative error for the column density can be much more. We describe the implementation of a method based on precalculating the geometrical terms that noticeably reduces the calculation time. To study the influence of the screening on the statistical properties of molecular clouds we present the probability distribution function of gas and the associated temperature per density bin and the mass spectra for different density thresholds. Conclusions: The tree-based method is fast and accurate enough to be used during numerical simulations since no communication is needed between CPUs when using a fully threaded tree. It is then suitable to parallel computing. We show that the screening for far UV radiation mainly affects the dense gas, thereby favoring low temperatures and affecting the fragmentation. We show that when we include the screening, more structures are formed with higher densities in comparison to the case that does not include this effect. We

  18. Estimation of breast percent density in raw and processed full field digital mammography images via adaptive fuzzy c-means clustering and support vector machine segmentation

    SciTech Connect

    Keller, Brad M.; Nathan, Diane L.; Wang Yan; Zheng Yuanjie; Gee, James C.; Conant, Emily F.; Kontos, Despina

    2012-08-15

    Purpose: The amount of fibroglandular tissue content in the breast as estimated mammographically, commonly referred to as breast percent density (PD%), is one of the most significant risk factors for developing breast cancer. Approaches to quantify breast density commonly focus on either semiautomated methods or visual assessment, both of which are highly subjective. Furthermore, most studies published to date investigating computer-aided assessment of breast PD% have been performed using digitized screen-film mammograms, while digital mammography is increasingly replacing screen-film mammography in breast cancer screening protocols. Digital mammography imaging generates two types of images for analysis, raw (i.e., 'FOR PROCESSING') and vendor postprocessed (i.e., 'FOR PRESENTATION'), of which postprocessed images are commonly used in clinical practice. Development of an algorithm which effectively estimates breast PD% in both raw and postprocessed digital mammography images would be beneficial in terms of direct clinical application and retrospective analysis. Methods: This work proposes a new algorithm for fully automated quantification of breast PD% based on adaptive multiclass fuzzy c-means (FCM) clustering and support vector machine (SVM) classification, optimized for the imaging characteristics of both raw and processed digital mammography images as well as for individual patient and image characteristics. Our algorithm first delineates the breast region within the mammogram via an automated thresholding scheme to identify background air followed by a straight line Hough transform to extract the pectoral muscle region. The algorithm then applies adaptive FCM clustering based on an optimal number of clusters derived from image properties of the specific mammogram to subdivide the breast into regions of similar gray-level intensity. Finally, a SVM classifier is trained to identify which clusters within the breast tissue are likely fibroglandular, which are then

  19. Estimation of breast percent density in raw and processed full field digital mammography images via adaptive fuzzy c-means clustering and support vector machine segmentation

    PubMed Central

    Keller, Brad M.; Nathan, Diane L.; Wang, Yan; Zheng, Yuanjie; Gee, James C.; Conant, Emily F.; Kontos, Despina

    2012-01-01

    Purpose: The amount of fibroglandular tissue content in the breast as estimated mammographically, commonly referred to as breast percent density (PD%), is one of the most significant risk factors for developing breast cancer. Approaches to quantify breast density commonly focus on either semiautomated methods or visual assessment, both of which are highly subjective. Furthermore, most studies published to date investigating computer-aided assessment of breast PD% have been performed using digitized screen-film mammograms, while digital mammography is increasingly replacing screen-film mammography in breast cancer screening protocols. Digital mammography imaging generates two types of images for analysis, raw (i.e., “FOR PROCESSING”) and vendor postprocessed (i.e., “FOR PRESENTATION”), of which postprocessed images are commonly used in clinical practice. Development of an algorithm which effectively estimates breast PD% in both raw and postprocessed digital mammography images would be beneficial in terms of direct clinical application and retrospective analysis. Methods: This work proposes a new algorithm for fully automated quantification of breast PD% based on adaptive multiclass fuzzy c-means (FCM) clustering and support vector machine (SVM) classification, optimized for the imaging characteristics of both raw and processed digital mammography images as well as for individual patient and image characteristics. Our algorithm first delineates the breast region within the mammogram via an automated thresholding scheme to identify background air followed by a straight line Hough transform to extract the pectoral muscle region. The algorithm then applies adaptive FCM clustering based on an optimal number of clusters derived from image properties of the specific mammogram to subdivide the breast into regions of similar gray-level intensity. Finally, a SVM classifier is trained to identify which clusters within the breast tissue are likely fibroglandular, which

  20. Measuring cone density in a Japanese macaque (Macaca fuscata) model of age-related macular degeneration with commercially available adaptive optics.

    PubMed

    Pennesi, Mark E; Garg, Anupam K; Feng, Shu; Michaels, Keith V; Smith, Travis B; Fay, Jonathan D; Weiss, Alison R; Renner, Laurie M; Hurst, Sawan; McGill, Trevor J; Cornea, Anda; Rittenhouse, Kay D; Sperling, Marvin; Fruebis, Joachim; Neuringer, Martha

    2014-01-01

    The aim of this study was to assess the feasibility of using a commercially available high-resolution adaptive optics (AO) camera to image the cone mosaic in Japanese macaques (Macaca fuscata) with dominantly inherited drusen. The macaques examined develop drusen closely resembling those seen in humans with age-related macular degeneration (AMD). For each animal, we acquired and processed images from the AO camera, montaged the results into a composite image, applied custom cone-counting software to detect individual cone photoreceptors, and created a cone density map of the macular region. We conclude that flood-illuminated AO provides a promising method of visualizing the cone mosaic in nonhuman primates. Future studies will quantify the longitudinal change in the cone mosaic and its relationship to the severity of drusen in these animals. PMID:24664712

  1. Marine microbes rapidly adapt to consume ethane, propane, and butane within the dissolved hydrocarbon plume of a natural seep

    NASA Astrophysics Data System (ADS)

    Mendes, Stephanie D.; Redmond, Molly C.; Voigritter, Karl; Perez, Christian; Scarlett, Rachel; Valentine, David L.

    2015-03-01

    Simple hydrocarbon gases containing two to four carbons (ethane, propane, and butane) are among the most abundant compounds present in petroleum reservoirs, and are introduced into the ocean through natural seepage and industrial discharge. Yet little is known about the bacterial consumption of these compounds in ocean waters. To assess the timing by which microbes metabolize these gases, we conducted a three-phase study that tested and applied a radiotracer-based method to quantify the oxidation rates of ethane, propane, and butane in fresh seawater samples. Phase 1 involved the synthesis of tritiated ethane, propane, and butane using Grignard reagents and tritiated water. Phase 2 was a systematic assessment of experimental conditions, wherein the indigenous microbial community was found to rapidly oxidize ethane, propane, and butane. Phase 3 was the application of this tritium method near the Coal Oil Point seeps, offshore California. Spatial and temporal patterns of ethane, propane, and butane oxidation down current from the hydrocarbon seeps demonstrated that >99% of these gases are metabolized within 1.3 days following initial exposure. The oxidation of ethane outpaced oxidation of propane and butane with patterns indicating the microbial community responded to these gases by rapid adaptation or growth. Methane oxidation responded the slowest in plume waters. Estimates based on the observed metabolic rates and carbon mass balance suggest that ethane, propane, and butane-consuming microorganisms may transiently account for a majority of the total microbial community in these impacted waters.

  2. Metabolic Noise, Vestigial Metabolites or the Raw Material of Ecological Adaptation? Opportunitistic Enzymes, Catalytic Promiscuity and the Evolution of chemodiversity in Nature (2010 JGI User Meeting)

    ScienceCinema

    Noel, Joseph

    2011-04-25

    Joseph Noel from the Salk Institute on "Metabolic Noise, Vestigial Metabolites or the Raw Material of Ecological Adaptation? Enzymes, Catalytic Promiscuity and the Evolution of Chemodiversity in Nature" on March 26, 2010 at the 5th Annual DOE JGI User Meeting

  3. Metabolic Noise, Vestigial Metabolites or the Raw Material of Ecological Adaptation? Opportunitistic Enzymes, Catalytic Promiscuity and the Evolution of chemodiversity in Nature (2010 JGI User Meeting)

    SciTech Connect

    Noel, Joseph

    2010-03-26

    Joseph Noel from the Salk Institute on "Metabolic Noise, Vestigial Metabolites or the Raw Material of Ecological Adaptation? Enzymes, Catalytic Promiscuity and the Evolution of Chemodiversity in Nature" on March 26, 2010 at the 5th Annual DOE JGI User Meeting

  4. Multicomponent training program with weight-bearing exercises elicits favorable bone density, muscle strength, and balance adaptations in older women.

    PubMed

    Marques, Elisa A; Mota, Jorge; Machado, Leandro; Sousa, Filipa; Coelho, Margarida; Moreira, Pedro; Carvalho, Joana

    2011-02-01

    Physical exercise is advised as a preventive and therapeutic strategy against aging-induced bone weakness. In this study we examined the effects of 8-month multicomponent training with weight-bearing exercises on different risk factors of falling, including muscle strength, balance, agility, and bone mineral density (BMD) in older women. Participants were randomly assigned to either an exercise-training group (ET, n = 30) or a control group (CON, n = 30). Twenty-seven subjects in the ET group and 22 in the CON group completed the study. Training was performed twice a week and was designed to load bones with intermittent and multidirectional compressive forces and to improve physical function. Outcome measures included lumbar spine and proximal femoral BMD (by dual X-ray absorptiometry), muscle strength, balance, handgrip strength, walking performance, fat mass, and anthropometric data. Potential confounding variables included dietary intake, accelerometer-based physical activity, and molecularly defined lactase nonpersistence. After 8 months, the ET group decreased percent fat mass and improved handgrip strength, postural sway, strength on knee flexion at 180°/s, and BMD at the femoral neck (+2.8%). Both groups decreased waist circumference and improved dynamic balance, chair stand performance, strength on knee extension for the right leg at 180°/s, and knee flexion for both legs at 60°/s. No associations were found between lactase nonpersistence and BMD changes. Data suggest that 8 months of moderate-impact weight-bearing and multicomponent exercises reduces the potential risk factors for falls and related fractures in older women. PMID:21113584

  5. Adaptive Localization of Focus Point Regions via Random Patch Probabilistic Density from Whole-Slide, Ki-67-Stained Brain Tumor Tissue

    PubMed Central

    Alomari, Yazan M.; MdZin, Reena Rahayu

    2015-01-01

    Analysis of whole-slide tissue for digital pathology images has been clinically approved to provide a second opinion to pathologists. Localization of focus points from Ki-67-stained histopathology whole-slide tissue microscopic images is considered the first step in the process of proliferation rate estimation. Pathologists use eye pooling or eagle-view techniques to localize the highly stained cell-concentrated regions from the whole slide under microscope, which is called focus-point regions. This procedure leads to a high variety of interpersonal observations and time consuming, tedious work and causes inaccurate findings. The localization of focus-point regions can be addressed as a clustering problem. This paper aims to automate the localization of focus-point regions from whole-slide images using the random patch probabilistic density method. Unlike other clustering methods, random patch probabilistic density method can adaptively localize focus-point regions without predetermining the number of clusters. The proposed method was compared with the k-means and fuzzy c-means clustering methods. Our proposed method achieves a good performance, when the results were evaluated by three expert pathologists. The proposed method achieves an average false-positive rate of 0.84% for the focus-point region localization error. Moreover, regarding RPPD used to localize tissue from whole-slide images, 228 whole-slide images have been tested; 97.3% localization accuracy was achieved. PMID:25793010

  6. Adaptive localization of focus point regions via random patch probabilistic density from whole-slide, Ki-67-stained brain tumor tissue.

    PubMed

    Alomari, Yazan M; Sheikh Abdullah, Siti Norul Huda; MdZin, Reena Rahayu; Omar, Khairuddin

    2015-01-01

    Analysis of whole-slide tissue for digital pathology images has been clinically approved to provide a second opinion to pathologists. Localization of focus points from Ki-67-stained histopathology whole-slide tissue microscopic images is considered the first step in the process of proliferation rate estimation. Pathologists use eye pooling or eagle-view techniques to localize the highly stained cell-concentrated regions from the whole slide under microscope, which is called focus-point regions. This procedure leads to a high variety of interpersonal observations and time consuming, tedious work and causes inaccurate findings. The localization of focus-point regions can be addressed as a clustering problem. This paper aims to automate the localization of focus-point regions from whole-slide images using the random patch probabilistic density method. Unlike other clustering methods, random patch probabilistic density method can adaptively localize focus-point regions without predetermining the number of clusters. The proposed method was compared with the k-means and fuzzy c-means clustering methods. Our proposed method achieves a good performance, when the results were evaluated by three expert pathologists. The proposed method achieves an average false-positive rate of 0.84% for the focus-point region localization error. Moreover, regarding RPPD used to localize tissue from whole-slide images, 228 whole-slide images have been tested; 97.3% localization accuracy was achieved. PMID:25793010

  7. Effects of Climate Change on Natural and Regulated Flood Risks in the Skagit River Basin and Prospects for Adaptation

    NASA Astrophysics Data System (ADS)

    LEE, S.; Hamlet, A. F.

    2011-12-01

    Based on global climate model (GCM) scenarios from the Intergovernmental Panel on Climate Change Fourth Assessment Report (IPCC AR4) and subsequent hydrologic modeling studies for the Pacific Northwest, the impacts of climate change on flooding in Western Washington are likely to be substantial. Many rivers draining to Puget Sound show timing shifts of peak flows from spring to winter and increases in the simulated natural 100-year flood (Q100) of 20-30% by the mid-21st century. A regional climate model (RCM) scenario, which provides greatly improved representation of mountain topography and important feedback mechanisms, is also used in this study. Preliminary results based on a RCM scenario (Echam5 A1B) for the 2050s also show substantial increases in future flood risk in many Pacific Northwest River basins. In comparison with GCM scenarios, a RCM scenario shows more apparent timing shifts of peak flows from spring to fall/winter. To assess the combined effects of increasing natural flood risks and dam operations that determine impacts to regulated flow, a new integrated daily time step reservoir operations model was built for the Skagit River Basin. The model simulates current operating policies for historical flow conditions and for projected flow for the 2040s and 2080s associated with the Echam5 A1B scenario (a global climate model scenario which approximates the average conditions simulated by all models). By simulating alternative reservoir operating policies that provide increased flood storage and starting flood evacuation one month earlier, prospects for the adaptation are considered. Preliminary results from daily time step reservoir operations modeling (based on a single climate change scenario) suggest that the regulated 100-year flood will increase substantially in the future in comparison with historical baselines (20% by the 2040s and 24% by the 2080s). Proposed increases in flood storage are simulated to decrease the magnitude of the regulated 100

  8. Rapid adaptive divergence of life-history traits in response to abiotic stress within a natural population of a parthenogenetic nematode

    PubMed Central

    Doroszuk, Agnieszka; Wojewodzic, Marcin W; Kammenga, Jan E

    2006-01-01

    Sexual reproduction is acknowledged to facilitate adaptation to novel environments while asexual eukaryotes are often regarded as having low adaptive potential. This view has been challenged in a number of studies, but the adaptive potential of asexual populations in the field is poorly documented. We investigated the response of natural populations of the parthenogenetic nematode Acrobeloides nanus to imposed divergent selective pressures. For this purpose, we employed a replicated evolution experiment in the field. After 20 years of evolution under abiotic stress and control conditions, life-history traits were assessed in reaction norm- and reciprocal transplant experiments. Both these experiments indicated adaptive divergence within the population of A. nanus. Namely, the transplant experiment demonstrated that in the stressed soil environment, body growth rate was more reduced in the nematodes originating from the control treatment. In the reaction norm experiment, survival and reproduction were higher under test conditions corresponding to the native environment of the nematodes. The differences in the analysed traits are discussed in the context of life-history theory. Overall, our results strongly support high adaptive potential of A. nanus and suggest that population structure and distribution of asexual species is shaped by local adaptation events. PMID:17002946

  9. Natural and adaptive IgM antibodies in the recognition of tumor-associated antigens of breast cancer (Review)

    PubMed Central

    DÍAZ-ZARAGOZA, MARIANA; HERNÁNDEZ-ÁVILA, RICARDO; VIEDMA-RODRÍGUEZ, RUBÍ; ARENAS-ARANDA, DIEGO; OSTOA-SALOMA, PEDRO

    2015-01-01

    For early detection of cancer, education and screening are important, but the most critical factor is the development of early diagnostic tools. Methods that recognize the warning signs of cancer and take prompt action lead to an early diagnosis; simple tests can identify individuals in a healthy population who have the disease but have not developed symptoms. Early detection of cancer is significant and is one of the most promising approaches by which to reduce the growing cancer burden and guide curative treatment. The early diagnosis of patients with breast cancer is challenging, since it is the most common cancer in women worldwide. Despite the advent of mammography in screening for breast cancer, low-resource, low-cost alternative tools must be implemented to complement mammography findings. IgM is part of the first line of defense of an organism and is responsible for recognizing and eliminating infectious particles and removing transformed cells. Most studies on breast cancer have focused on the development of IgG-like molecules as biomarkers or as a treatment for the advanced stages of cancer, but autoantibodies (IgM) and tumor-associated antigens (proteins or carbohydrates with aberrant structures) have not been examined as early diagnostic tools for breast cancer. The present review summarizes the function of natural and adaptive IgM in eliminating cancer cells in the early stages of pathology and their value as early diagnostic tools. IgM, as a component of the immune system, is being used to identify tumor-associated antigens and tumor-associated carbohydrate antigens. PMID:26133558

  10. Adaptive management of invasive pests in natural protected areas: the case of Matsucoccus feytaudi in Central Italy.

    PubMed

    Sciarretta, A; Marziali, L; Squarcini, M; Marianelli, L; Benassai, D; Logli, F; Roversi, P F

    2016-02-01

    Invasive species are a significant threat to affected ecosystems, having serious environmental, economic and social impacts. The maritime pine bast scale, Matsucoccus feytaudi Ducasse (Hemiptera: Matsucoccidae), causes serious damage to Pinus pinaster forests in SE France, Corsica and Italy where it has been introduced. This study illustrates the adaptive management plan implemented in the Migliarino, San Rossore, Massaciuccoli Regional Natural Park in Tuscany, Italy, where M. feytaudi arrived in 2004, leading to the decay of local P. pinaster stands. The management programme, aimed at slowing the establishment and growth of M. feytaudi, was carried out in the main sector of the park, Tenuta di San Rossore, to retard the destruction of the P. pinaster coastal strip protecting the more internal woodland from sea salt and to allow replacement of P. pinaster trees with a more stable broad-leaved wood. The combined use of mass trapping and silvicultural interventions, applied in a targeted manner according to distribution maps of pest captures and damage, helped to delay forest destruction compared with a nearby unmanaged area of the park Tenuta di Tombolo. Although M. feytaudi continued to spread during the management period, the populations remained at low levels for 6 years, showing a marked increase in 2012. During this period, the P. pinaster stands were reduced from 320 to 249 ha. The final result of this ongoing gradual conversion process will be transformation of the P. pinaster forest into Holm oak woods and Mediterranean shrub land, while P. pinaster will survive as clusters or blocks of trees. PMID:26521882

  11. Motivation and drives in bottom-up developments in natural hazards management: multiple-use of adaptation strategies in Austria

    NASA Astrophysics Data System (ADS)

    Thaler, Thomas; Fuchs, Sven

    2015-04-01

    Losses from extreme hydrological events, such as recently experienced in Europe have focused the attention of policymakers as well as researchers on vulnerability to natural hazards. In parallel, the context of changing flood risks under climate and societal change is driving transformation in the role of the state in responsibility sharing and individual responsibilities for risk management and precaution. The new policy agenda enhances the responsibilities of local authorities and private citizens in hazard management and reduces the role of central governments. Within the objective is to place added responsibility on local organisations and citizens to determine locally-based strategies for risk reduction. A major challenge of modelling adaptation is to represent the complexity of coupled human-environmental systems and particularly the feedback loops between environmental dynamics and human decision-making processes on different scales. This paper focuses on bottom-up initiatives to flood risk management which are, by definition, different from the mainstream. These initiatives are clearly influenced (positively or negatively) by a number of factors, where the combination of these interdependences can create specific conditions that alter the opportunity for effective governance arrangements in a local scheme approach. In total, this study identified six general drivers which encourage the implementation of flood storages, such as direct relation to recent major flood frequency and history, the initiative of individual stakeholders (promoters), political pressures from outside (e.g. business companies, private households) and a strong solidarity attitude of municipalities and the stakeholders involved. Although partnership approach may be seen as an 'optimal' solution for flood risk management, in practice there are many limitations and barriers in establishing these collaborations and making them effective (especially in the long term) with the consequences

  12. Variation in rod and cone density from the fovea to the mid-periphery in healthy human retinas using adaptive optics scanning laser ophthalmoscopy.

    PubMed

    Wells-Gray, E M; Choi, S S; Bries, A; Doble, N

    2016-08-01

    PurposeTo characterize the rod and cone photoreceptor mosaic at retinal locations spanning the central 60° in vivo using adaptive optics scanning laser ophthalmoscopy (AO-SLO) in healthy human eyes.MethodsAO-SLO images (0.7 × 0.9°) were acquired at 680 nm from 14 locations from 30° nasal retina (NR) to 30° temporal retina (TR) in 5 subjects. Registered averaged images were used to measure rod and cone density and spacing within 60 × 60 μm regions of interest. Voronoi analysis was performed to examine packing geometry at all locations.ResultsAverage peak cone density near the fovea was 164 000±24 000 cones/mm(2) and decreased to 6700±1500 and 5400±700 cones/mm(2) at 30° NR and 30° TR, respectively. Cone-to-cone spacing increased from 2.7±0.2 μm at the fovea to 14.6±1.4 μm at 30° NR and 16.3±0.7 μm at 30° TR. Rod density peaked at 25° NR (124 000±20 000 rods/mm(2)) and 20° TR (120 000±12 000 rods/mm(2)) and decreased at higher eccentricities. Center-to-center rod spacing was lowest nasally at 25° (2.1±0.1 μm). Temporally, rod spacing was lowest at 20° (2.2±0.1 μm) before increasing to 2.3±0.1 μm at 30° TR.ConclusionsBoth rod and cone densities showed good agreement with histology and prior AO-SLO studies. The results demonstrate the ability to image at higher retinal eccentricities than reported previously. This has clinical importance in diseases that initially affect the peripheral retina such as retinitis pigmentosa. PMID:27229708

  13. NOTE: Cone beam computerized tomography: the effect of calibration of the Hounsfield unit number to electron density on dose calculation accuracy for adaptive radiation therapy

    NASA Astrophysics Data System (ADS)

    Hatton, Joan; McCurdy, Boyd; Greer, Peter B.

    2009-08-01

    The availability of cone beam computerized tomography (CBCT) images at the time of treatment has opened possibilities for dose calculations representing the delivered dose for adaptive radiation therapy. A significant component in the accuracy of dose calculation is the calibration of the Hounsfield unit (HU) number to electron density (ED). The aim of this work is to assess the impact of HU to ED calibration phantom insert composition and phantom volume on dose calculation accuracy for CBCT. CBCT HU to ED calibration curves for different commercial phantoms were measured and compared. The effect of the scattering volume of the phantom on the HU to ED calibration was examined as a function of phantom length and radial diameter. The resulting calibration curves were used at the treatment planning system to calculate doses for geometrically simple phantoms and a pelvic anatomical phantom to compare against measured doses. Three-dimensional dose distributions for the pelvis phantom were calculated using the HU to ED curves and compared using Chi comparisons. The HU to ED calibration curves for the commercial phantoms diverge at densities greater than that of water, depending on the elemental composition of the phantom insert. The effect of adding scatter material longitudinally, increasing the phantom length from 5 cm to 26 cm, was found to be up to 260 HU numbers for the high-density insert. The change in the HU value, by increasing the diameter of the phantom from 18 to 40 cm, was found to be up to 1200 HU for the high-density insert. The effect of phantom diameter on the HU to ED curve can lead to dose differences for 6 MV and 18 MV x-rays under bone inhomogeneities of up to 20% in extreme cases. These results show significant dosimetric differences when using a calibration phantom with materials which are not tissue equivalent. More importantly, the amount of scattering material used with the HU to ED calibration phantom has a significant effect on the dosimetric

  14. The Relationship Between Perceptions of Wilderness Character and Attitudes Toward Management Intervention to Adapt Biophysical Resources to a Changing Climate and Nature Restoration at Sequoia and Kings Canyon National Parks.

    PubMed

    Watson, Alan; Martin, Steve; Christensen, Neal; Fauth, Gregg; Williams, Dan

    2015-09-01

    In a recent national survey of federal wilderness managers, respondents identified the high priority need for scientific information about public attitudes toward biophysical intervention to adapt to climate change and attitudes of the public toward restoration of natural conditions. In a survey of visitors to one National Park wilderness in California, visitors revealed that they largely do not support biophysical intervention in wilderness to mitigate the effects of climate change, but broad support for activities that restore natural conditions exists. In an attempt to understand how these attitudes vary among visitors, it was found that those visitors who most value naturalness aspects of wilderness character also most positively support restoration and are most negative toward climate change intervention practices. More information about visitor-defined wilderness character attributes is needed and strategic planning to guide intervention decisions and restoration should be a priority. In this study, it was found that wilderness character is largely defined by visitors based on its wildness attributes, which include natural sounds, low density of people, pure water, clean air, and the presence of humans substantially unnoticeable. PMID:25910871

  15. The Relationship Between Perceptions of Wilderness Character and Attitudes Toward Management Intervention to Adapt Biophysical Resources to a Changing Climate and Nature Restoration at Sequoia and Kings Canyon National Parks

    NASA Astrophysics Data System (ADS)

    Watson, Alan; Martin, Steve; Christensen, Neal; Fauth, Gregg; Williams, Dan

    2015-09-01

    In a recent national survey of federal wilderness managers, respondents identified the high priority need for scientific information about public attitudes toward biophysical intervention to adapt to climate change and attitudes of the public toward restoration of natural conditions. In a survey of visitors to one National Park wilderness in California, visitors revealed that they largely do not support biophysical intervention in wilderness to mitigate the effects of climate change, but broad support for activities that restore natural conditions exists. In an attempt to understand how these attitudes vary among visitors, it was found that those visitors who most value naturalness aspects of wilderness character also most positively support restoration and are most negative toward climate change intervention practices. More information about visitor-defined wilderness character attributes is needed and strategic planning to guide intervention decisions and restoration should be a priority. In this study, it was found that wilderness character is largely defined by visitors based on its wildness attributes, which include natural sounds, low density of people, pure water, clean air, and the presence of humans substantially unnoticeable.

  16. Adaptation in Practice: How Managers of Nature Conservation Areas in Eastern England are Responding to Climate Change

    NASA Astrophysics Data System (ADS)

    Macgregor, Nicholas A.; van Dijk, Nikki

    2014-10-01

    Although good general principles for climate change adaptation in conservation have been developed, it is proving a challenge to translate them into more detailed recommendations for action. To improve our understanding of what adaptation might involve in practice, we investigated how the managers of conservation areas in eastern England are considering climate change. We used a written questionnaire and semi-structured interviews to collect information from managers of a range of different conservation areas. Topics investigated include the impacts of climate change perceived to be of the greatest importance; adaptation goals being set; management actions being carried out to achieve these goals; sources of information used; and perceived barriers to taking action. We identified major themes and issues that were apparent across the sites studied. Specifically, we found ways in which adaptation had been informed by past experience; different strategies relating to whether to accept or resist change; approaches for coping with more variable conditions; ways of taking a large-scale approach and managing sites as networks; some practical examples of aspects of adaptive management; and examples of the role that other sectors can play in both constraining and increasing a conservation area's capacity to adapt. We discuss the relevance of these findings to the growing discussion in conservation about identifying adaptation pathways for different conservation areas and a potential progression from a focus on resilience and incremental change to embracing "transformation." Though adaptation will be place-specific, we believe these findings provide useful lessons for future action in both England and other countries.

  17. Adaptation in practice: how managers of nature conservation areas in eastern england are responding to climate change.

    PubMed

    Macgregor, Nicholas A; van Dijk, Nikki

    2014-10-01

    Although good general principles for climate change adaptation in conservation have been developed, it is proving a challenge to translate them into more detailed recommendations for action. To improve our understanding of what adaptation might involve in practice, we investigated how the managers of conservation areas in eastern England are considering climate change. We used a written questionnaire and semi-structured interviews to collect information from managers of a range of different conservation areas. Topics investigated include the impacts of climate change perceived to be of the greatest importance; adaptation goals being set; management actions being carried out to achieve these goals; sources of information used; and perceived barriers to taking action. We identified major themes and issues that were apparent across the sites studied. Specifically, we found ways in which adaptation had been informed by past experience; different strategies relating to whether to accept or resist change; approaches for coping with more variable conditions; ways of taking a large-scale approach and managing sites as networks; some practical examples of aspects of adaptive management; and examples of the role that other sectors can play in both constraining and increasing a conservation area's capacity to adapt. We discuss the relevance of these findings to the growing discussion in conservation about identifying adaptation pathways for different conservation areas and a potential progression from a focus on resilience and incremental change to embracing "transformation." Though adaptation will be place-specific, we believe these findings provide useful lessons for future action in both England and other countries. PMID:24647625

  18. Critical Role of CD2 Co-stimulation in Adaptive Natural Killer Cell Responses Revealed in NKG2C-Deficient Humans

    PubMed Central

    Liu, Lisa L.; Landskron, Johannes; Ask, Eivind H.; Enqvist, Monika; Sohlberg, Ebba; Traherne, James A.; Hammer, Quirin; Goodridge, Jodie P.; Larsson, Stella; Jayaraman, Jyothi; Oei, Vincent Y.S.; Schaffer, Marie; Taskén, Kjetil; Ljunggren, Hans-Gustaf; Romagnani, Chiara; Trowsdale, John; Malmberg, Karl-Johan; Béziat, Vivien

    2016-01-01

    Summary Infection by human cytomegalovirus (HCMV) leads to NKG2C-driven expansion of adaptive natural killer (NK) cells, contributing to host defense. However, approximately 4% of all humans carry a homozygous deletion of the gene that encodes NKG2C (NKG2C−/−). Assessment of NK cell repertoires in 60 NKG2C−/− donors revealed a broad range of NK cell populations displaying characteristic footprints of adaptive NK cells, including a terminally differentiated phenotype, functional reprogramming, and epigenetic remodeling of the interferon (IFN)-γ promoter. We found that both NKG2C− and NKG2C+ adaptive NK cells expressed high levels of CD2, which synergistically enhanced ERK and S6RP phosphorylation following CD16 ligation. Notably, CD2 co-stimulation was critical for the ability of adaptive NK cells to respond to antibody-coated target cells. These results reveal an unexpected redundancy in the human NK cell response to HCMV and suggest that CD2 provides “signal 2” in antibody-driven adaptive NK cell responses. PMID:27117418

  19. Critical Role of CD2 Co-stimulation in Adaptive Natural Killer Cell Responses Revealed in NKG2C-Deficient Humans.

    PubMed

    Liu, Lisa L; Landskron, Johannes; Ask, Eivind H; Enqvist, Monika; Sohlberg, Ebba; Traherne, James A; Hammer, Quirin; Goodridge, Jodie P; Larsson, Stella; Jayaraman, Jyothi; Oei, Vincent Y S; Schaffer, Marie; Taskén, Kjetil; Ljunggren, Hans-Gustaf; Romagnani, Chiara; Trowsdale, John; Malmberg, Karl-Johan; Béziat, Vivien

    2016-05-01

    Infection by human cytomegalovirus (HCMV) leads to NKG2C-driven expansion of adaptive natural killer (NK) cells, contributing to host defense. However, approximately 4% of all humans carry a homozygous deletion of the gene that encodes NKG2C (NKG2C(-/-)). Assessment of NK cell repertoires in 60 NKG2C(-/-) donors revealed a broad range of NK cell populations displaying characteristic footprints of adaptive NK cells, including a terminally differentiated phenotype, functional reprogramming, and epigenetic remodeling of the interferon (IFN)-γ promoter. We found that both NKG2C(-) and NKG2C(+) adaptive NK cells expressed high levels of CD2, which synergistically enhanced ERK and S6RP phosphorylation following CD16 ligation. Notably, CD2 co-stimulation was critical for the ability of adaptive NK cells to respond to antibody-coated target cells. These results reveal an unexpected redundancy in the human NK cell response to HCMV and suggest that CD2 provides "signal 2" in antibody-driven adaptive NK cell responses. PMID:27117418

  20. Symmetry-adapted perturbation theory with Kohn-Sham orbitals using non-empirically tuned, long-range-corrected density functionals

    SciTech Connect

    Lao, Ka Un; Herbert, John M.

    2014-01-28

    The performance of second-order symmetry-adapted perturbation theory (SAPT) calculations using Kohn-Sham (KS) orbitals is evaluated against benchmark results for intermolecular interactions. Unlike previous studies of this “SAPT(KS)” methodology, the present study uses non-empirically tuned long-range corrected (LRC) functionals for the monomers. The proper v{sub xc} (r)→0 asymptotic limit is achieved by tuning the range separation parameter in order to satisfy the condition that the highest occupied KS energy level equals minus the molecule's ionization energy, for each monomer unit. Tests for He{sub 2}, Ne{sub 2}, and the S22 and S66 data sets reveal that this condition is important for accurate prediction of the non-dispersion components of the energy, although errors in SAPT(KS) dispersion energies remain unacceptably large. In conjunction with an empirical dispersion potential, however, the SAPT(KS) method affords good results for S22 and S66, and also accurately predicts the whole potential energy curve for the sandwich isomer of the benzene dimer. Tuned LRC functionals represent an attractive alternative to other asymptotic corrections that have been employed in density-functional-based SAPT calculations, and we recommend the use of tuned LRC functionals in both coupled-perturbed SAPT(DFT) calculations and dispersion-corrected SAPT(KS) calculations.

  1. Thoracic and lumbar vertebral bone mineral density changes in a natural occurring dog model of diffuse idiopathic skeletal hyperostosis.

    PubMed

    De Decker, Steven; Lam, Richard; Packer, Rowena M A; Gielen, Ingrid M V L; Volk, Holger A

    2015-01-01

    Ankylosing spinal disorders can be associated with alterations in vertebral bone mineral density (BMD). There is however controversy about vertebral BMD in patients wuse idiopathic skeletal hyperostosis (DISH). DISH in Boxer dogs has been considered a natural occurring disease model for DISH in people. The purpose of this study was to compare vertebral BMD between Boxers with and without DISH. Fifty-nine Boxers with (n=30) or without (n=29) DISH that underwent computed tomography were included. Vertebral BMD was calculated for each thoracic and lumbar vertebra by using an earlier reported and validated protocol. For each vertebral body, a region of interest was drawn on the axial computed tomographic images at three separate locations: immediately inferior to the superior end plate, in the middle of the vertebral body, and superior to the inferior end plate. Values from the three axial slices were averaged to give a mean Hounsfield Unit value for each vertebral body. Univariate statistical analysis was performed to identify factors to be included in a multivariate model. The multivariate model including all dogs demonstrated that vertebral DISH status (Coefficient 24.63; 95% CI 16.07 to 33.19; p <0.001), lumbar vertebrae (Coefficient -17.25; 95% CI -23.42 to -11.09; p < 0.01), and to a lesser extent higher age (Coefficient -0.56; 95% CI -1.07 to -0.05; p = 0.03) were significant predictors for vertebral BMD. When the multivariate model was repeated using only dogs with DISH, vertebral DISH status (Coefficient 20.67; 95% CI, 10.98 to 30.37; p < 0.001) and lumbar anatomical region (Coefficient -38.24; 95% CI, -47.75 to -28.73; p < 0.001) were again predictors for vertebral BMD but age was not. The results of this study indicate that DISH can be associated with decreased vertebral BMD. Further studies are necessary to evaluate the clinical importance and pathophysiology of this finding. PMID:25898128

  2. Nature of the Fe(4)/(2) center in KTaO3 : A density functional theory study

    NASA Astrophysics Data System (ADS)

    Trueba, A.; García-Fernández, P.; García-Lastra, J. M.; Barriuso, M. T.; Aramburu, J. A.; Moreno, M.

    2008-08-01

    This work is aimed at clearing out the nature of the axial Fe(4)/(2) center detected by electron-paramagnetic resonance in iron-doped KTaO3 for which two different models have been put forward. While some authors ascribe such a center to a Fe+ impurity at a K+ site, although suffering an off-center motion along ⟨001⟩ directions, other groups propose that the Fe(4)/(2) center involves a Fe5+ ion at a Ta5+ site, which later also undergoes an off-center shift along a principal direction of the KTaO3 lattice. Seeking to clarify this puzzling situation, the possible off-center shift of both Fe5+ and Fe+ impurities in KTaO3 is explored in this work by means of density functional calculations. As a salient feature it is shown that there is a huge barrier that prevents the motion of Fe5+ against one of the closest O2- anions. The case of Fe+ at a K+ site is more complex as the energy difference (10Dq) between the lower-lying eg ( ˜x2-y2 , 3z2-r2 ) and t2g ( ˜xy , xz , yz ) Oh levels is found to be equal to only -0.038eV , and thus several states as a function of the displacement coordinate ZFe have to be explored in order to determine what is the actual ground state and the associated equilibrium coordinate ZFe0 . The ground state is found to correspond to the b1(x2-y2)1 a1(3z2-r2)2 b2(xy)2 e(xz,yz)2 C4v configuration with spin S=3/2 and ZFe0=90pm , thus involving a significant off-center motion from the K+ site, which is found to be accompanied by a small ligand relaxation. As a salient feature this ground state is different from that derived constraining Fe+ at the K+ site. The present calculations also reproduce the experimental feature g⊥-g0>g∥-g0 observed for the Fe(4)/(2) center. An analysis of first-excited states at equilibrium allows one to understand this fingerprint in a simple way.

  3. Thoracic and Lumbar Vertebral Bone Mineral Density Changes in a Natural Occurring Dog Model of Diffuse Idiopathic Skeletal Hyperostosis

    PubMed Central

    De Decker, Steven; Lam, Richard; Packer, Rowena M. A.; Gielen, Ingrid M. V. L.; Volk, Holger A.

    2015-01-01

    Ankylosing spinal disorders can be associated with alterations in vertebral bone mineral density (BMD). There is however controversy about vertebral BMD in patients wuse idiopathic skeletal hyperostosis (DISH). DISH in Boxer dogs has been considered a natural occurring disease model for DISH in people. The purpose of this study was to compare vertebral BMD between Boxers with and without DISH. Fifty-nine Boxers with (n=30) or without (n=29) DISH that underwent computed tomography were included. Vertebral BMD was calculated for each thoracic and lumbar vertebra by using an earlier reported and validated protocol. For each vertebral body, a region of interest was drawn on the axial computed tomographic images at three separate locations: immediately inferior to the superior end plate, in the middle of the vertebral body, and superior to the inferior end plate. Values from the three axial slices were averaged to give a mean Hounsfield Unit value for each vertebral body. Univariate statistical analysis was performed to identify factors to be included in a multivariate model. The multivariate model including all dogs demonstrated that vertebral DISH status (Coefficient 24.63; 95% CI 16.07 to 33.19; p <0.001), lumbar vertebrae (Coefficient -17.25; 95% CI -23.42 to -11.09; p < 0.01), and to a lesser extent higher age (Coefficient -0.56; 95% CI -1.07 to -0.05; p = 0.03) were significant predictors for vertebral BMD. When the multivariate model was repeated using only dogs with DISH, vertebral DISH status (Coefficient 20.67; 95% CI, 10.98 to 30.37; p < 0.001) and lumbar anatomical region (Coefficient -38.24; 95% CI, -47.75 to -28.73; p < 0.001) were again predictors for vertebral BMD but age was not. The results of this study indicate that DISH can be associated with decreased vertebral BMD. Further studies are necessary to evaluate the clinical importance and pathophysiology of this finding. PMID:25898128

  4. Correction for ‘artificial’ electron disequilibrium due to cone-beam CT density errors: implications for on-line adaptive stereotactic body radiation therapy of lung

    NASA Astrophysics Data System (ADS)

    Disher, Brandon; Hajdok, George; Wang, An; Craig, Jeff; Gaede, Stewart; Battista, Jerry J.

    2013-06-01

    Cone-beam computed tomography (CBCT) has rapidly become a clinically useful imaging modality for image-guided radiation therapy. Unfortunately, CBCT images of the thorax are susceptible to artefacts due to scattered photons, beam hardening, lag in data acquisition, and respiratory motion during a slow scan. These limitations cause dose errors when CBCT image data are used directly in dose computations for on-line, dose adaptive radiation therapy (DART). The purpose of this work is to assess the magnitude of errors in CBCT numbers (HU), and determine the resultant effects on derived tissue density and computed dose accuracy for stereotactic body radiation therapy (SBRT) of lung cancer. Planning CT (PCT) images of three lung patients were acquired using a Philips multi-slice helical CT simulator, while CBCT images were obtained with a Varian On-Board Imaging system. To account for erroneous CBCT data, three practical correction techniques were tested: (1) conversion of CBCT numbers to electron density using phantoms, (2) replacement of individual CBCT pixel values with bulk CT numbers, averaged from PCT images for tissue regions, and (3) limited replacement of CBCT lung pixels values (LCT) likely to produce artificial lateral electron disequilibrium. For each corrected CBCT data set, lung SBRT dose distributions were computed for a 6 MV volume modulated arc therapy (VMAT) technique within the Philips Pinnacle treatment planning system. The reference prescription dose was set such that 95% of the planning target volume (PTV) received at least 54 Gy (i.e. D95). Further, we used the relative depth dose factor as an a priori index to predict the effects of incorrect low tissue density on computed lung dose in regions of severe electron disequilibrium. CT number profiles from co-registered CBCT and PCT patient lung images revealed many reduced lung pixel values in CBCT data, with some pixels corresponding to vacuum (-1000 HU). Similarly, CBCT data in a plastic lung

  5. Correction for 'artificial' electron disequilibrium due to cone-beam CT density errors: implications for on-line adaptive stereotactic body radiation therapy of lung.

    PubMed

    Disher, Brandon; Hajdok, George; Wang, An; Craig, Jeff; Gaede, Stewart; Battista, Jerry J

    2013-06-21

    Cone-beam computed tomography (CBCT) has rapidly become a clinically useful imaging modality for image-guided radiation therapy. Unfortunately, CBCT images of the thorax are susceptible to artefacts due to scattered photons, beam hardening, lag in data acquisition, and respiratory motion during a slow scan. These limitations cause dose errors when CBCT image data are used directly in dose computations for on-line, dose adaptive radiation therapy (DART). The purpose of this work is to assess the magnitude of errors in CBCT numbers (HU), and determine the resultant effects on derived tissue density and computed dose accuracy for stereotactic body radiation therapy (SBRT) of lung cancer. Planning CT (PCT) images of three lung patients were acquired using a Philips multi-slice helical CT simulator, while CBCT images were obtained with a Varian On-Board Imaging system. To account for erroneous CBCT data, three practical correction techniques were tested: (1) conversion of CBCT numbers to electron density using phantoms, (2) replacement of individual CBCT pixel values with bulk CT numbers, averaged from PCT images for tissue regions, and (3) limited replacement of CBCT lung pixels values (LCT) likely to produce artificial lateral electron disequilibrium. For each corrected CBCT data set, lung SBRT dose distributions were computed for a 6 MV volume modulated arc therapy (VMAT) technique within the Philips Pinnacle treatment planning system. The reference prescription dose was set such that 95% of the planning target volume (PTV) received at least 54 Gy (i.e. D95). Further, we used the relative depth dose factor as an a priori index to predict the effects of incorrect low tissue density on computed lung dose in regions of severe electron disequilibrium. CT number profiles from co-registered CBCT and PCT patient lung images revealed many reduced lung pixel values in CBCT data, with some pixels corresponding to vacuum (-1000 HU). Similarly, CBCT data in a plastic lung

  6. Study of static and dynamic first hyperpolarizabilities using time-dependent density functional quadratic response theory with local contribution and natural bond orbital analysis.

    PubMed

    Ye, Aijun; Autschbach, Jochen

    2006-12-21

    We apply time-dependent density-functional quadratic response theory to investigate the static and dynamic second-order polarizabilities (first hyperpolarizability) beta. A new implementation using Slater-type basis functions, numerical integration, and density fitting techniques is reported. The second order coupled perturbed Kohn-Sham equations are solved and the second-order perturbed charge density is obtained. It is useful to highlight atomic and bond contributions to understand the relation between molecular structure and properties. Four moderately sized molecules (para-nitroaniline and derivatives thereof) are investigated to assess the accuracy of the time-dependent density-functional theory computations and to investigate the distribution of the second-order charge density as well as the "beta density." Our results highlight the contributions from atoms and bonds on different functional groups to the total value of beta with Mulliken-type and natural bond orbital (NBO) analyses, and demonstrate in some cases how contributions from a particular bond may be identified easily by visual inspection of the beta density. In addition, the position of side group substitution on carbon-carbon bonds significantly affects the hyperpolarizability. A contribution analysis as performed here might be helpful for the design of new materials with desired properties. PMID:17190541

  7. Fat utilization during exercise: adaptation to a fat-rich diet increases utilization of plasma fatty acids and very low density lipoprotein-triacylglycerol in humans

    PubMed Central

    Helge, Jørn W; Watt, Peter W; Richter, Erik A; Rennie, Michael J; Kiens, Bente

    2001-01-01

    This study was carried out to test the hypothesis that the greater fat oxidation observed during exercise after adaptation to a high-fat diet is due to an increased uptake of fat originating from the bloodstream. Of 13 male untrained subjects, seven consumed a fat-rich diet (62% fat, 21% carbohydrate) and six consumed a carbohydrate-rich diet (20% fat, 65% carbohydrate). After 7 weeks of training and diet, 60 min of bicycle exercise was performed at 68 ± 1% of maximum oxygen uptake. During exercise [1-13C]palmitate was infused, arterial and venous femoral blood samples were collected, and blood flow was determined by the thermodilution technique. Muscle biopsy samples were taken from the vastus lateralis muscle before and after exercise. During exercise, the respiratory exchange ratio was significantly lower in subjects consuming the fat-rich diet (0.86 ± 0.01, mean ±s.e.m.) than in those consuming the carbohydrate-rich diet (0.93 ± 0.02). The leg fatty acid (FA) uptake (183 ± 37 vs. 105 ± 28 μmol min−1) and very low density lipoprotein-triacylglycerol (VLDL-TG) uptake (132 ± 26 vs. 16 ± 21 μmol min−1) were both higher (each P < 0.05) in the subjects consuming the fat-rich diet. Whole-body plasma FA oxidation (determined by comparison of 13CO2 production and blood palmitate labelling) was 55-65% of total lipid oxidation, and was higher after the fat-rich diet than after the carbohydrate-rich diet (13.5 ± 1.2 vs. 8.9 ± 1.1 μmol min−1 kg−1; P < 0.05). Muscle glycogen breakdown was significantly lower in the subjects taking the fat-rich diet than those taking the carbohydrate-rich diet (2.6 ± 0.5 vs. 4.8 ± 0.5 mmol (kg dry weight)−1 min−1, respectively; P < 0.05), whereas leg glucose uptake was similar (1.07 ± 0.13 vs. 1.15 ± 0.13 mmol min−1). In conclusion, plasma VLDL-TG appears to be an important substrate source during aerobic exercise, and in combination with the higher plasma FA uptake it accounts for the increased fat oxidation

  8. CheMPS2: A free open-source spin-adapted implementation of the density matrix renormalization group for ab initio quantum chemistry

    NASA Astrophysics Data System (ADS)

    Wouters, Sebastian; Poelmans, Ward; Ayers, Paul W.; Van Neck, Dimitri

    2014-06-01

    The density matrix renormalization group (DMRG) has become an indispensable numerical tool to find exact eigenstates of finite-size quantum systems with strong correlation. In the fields of condensed matter, nuclear structure and molecular electronic structure, it has significantly extended the system sizes that can be handled compared to full configuration interaction, without losing numerical accuracy. For quantum chemistry (QC), the most efficient implementations of DMRG require the incorporation of particle number, spin and point group symmetries in the underlying matrix product state (MPS) ansatz, as well as the use of so-called complementary operators. The symmetries introduce a sparse block structure in the MPS ansatz and in the intermediary contracted tensors. If a symmetry is non-abelian, the Wigner-Eckart theorem allows to factorize a tensor into a Clebsch-Gordan coefficient and a reduced tensor. In addition, the fermion signs have to be carefully tracked. Because of these challenges, implementing DMRG efficiently for QC is not straightforward. Efficient and freely available implementations are therefore highly desired. In this work we present CheMPS2, our free open-source spin-adapted implementation of DMRG for ab initio QC. Around CheMPS2, we have implemented the augmented Hessian Newton-Raphson complete active space self-consistent field method, with exact Hessian. The bond dissociation curves of the 12 lowest states of the carbon dimer were obtained at the DMRG(28 orbitals, 12 electrons, DSU(2) = 2500)/cc-pVDZ level of theory. The contribution of 1 s core correlation to the X1Σg+ bond dissociation curve of the carbon dimer was estimated by comparing energies at the DMRG(36o, 12e, DSU(2) = 2500)/cc-pCVDZ and DMRG-SCF(34o, 8e, DSU(2) = 2500)/cc-pCVDZ levels of theory.

  9. Natural variation and the capacity to adapt to ocean acidification in the keystone sea urchin Strongylocentrotus purpuratus.

    PubMed

    Kelly, Morgan W; Padilla-Gamiño, Jacqueline L; Hofmann, Gretchen E

    2013-08-01

    A rapidly growing body of literature documents the potential negative effects of CO2 -driven ocean acidification (OA) on marine organisms. However, nearly all this work has focused on the effects of future conditions on modern populations, neglecting the role of adaptation. Rapid evolution can alter demographic responses to environmental change, ultimately affecting the likelihood of population persistence, but the capacity for adaptation will differ among populations and species. Here, we measure the capacity of the ecologically important purple sea urchin Strongylocentrotus purpuratus to adapt to OA, using a breeding experiment to estimate additive genetic variance for larval size (an important component of fitness) under future high-pCO2 /low-pH conditions. Although larvae reared under future conditions were smaller than those reared under present-day conditions, we show that there is also abundant genetic variation for body size under elevated pCO2 , indicating that this trait can evolve. The observed heritability of size was 0.40 ± 0.32 (95% CI) under low pCO2 , and 0.50 ± 0.30 under high-pCO2 conditions. Accounting for the observed genetic variation in models of future larval size and demographic rates substantially alters projections of performance for this species in the future ocean. Importantly, our model shows that after incorporating the effects of adaptation, the OA-driven decrease in population growth rate is up to 50% smaller, than that predicted by the 'no-adaptation' scenario. Adults used in the experiment were collected from two sites on the coast of the Northeast Pacific that are characterized by different pH regimes, as measured by autonomous sensors. Comparing results between sites, we also found subtle differences in larval size under high-pCO2 rearing conditions, consistent with local adaptation to carbonate chemistry in the field. These results suggest that spatially varying selection may help to maintain genetic variation necessary

  10. Detection of haptoglobin in the high-density lipoprotein and the very high-density lipoprotein fractions from sera of calves with experimental pneumonia and cows with naturally occurring fatty liver.

    PubMed

    Katoh, N; Nakagawa, H

    1999-02-01

    In addition to the lipoprotein-deficient d > 1.25 fraction, haptoglobin was detected in the high-density lipoprotein (HDL) and the very high-density lipoprotein (VHDL) fractions from sera of calves with experimental pneumonia and cows with naturally occurring fatty liver. It was not found in the chylomicrons, very low-density lipoprotein and low-density lipoprotein fractions. Washing of the HDL fraction did not decrease the haptoglobin concentration. Transferrin and immunoglobulin G were immunoblotted to examine the possibility of contamination of the lipoprotein fractions by the d > 1.25 fraction. The two serum proteins were detected only in the d > 1.25 fraction, not in any lipoprotein fractions. The distribution pattern of haptoglobin in the lipoprotein fractions was distinct from that of serum albumin. Concentrations of haptoglobin in the HDL fractions from pneumonic sera were largely proportional to those in whole sera. Cholesteryl ester concentrations were decreased in sera from calves with pneumonia, as in cows with fatty liver. A protein immunologically related to hemoglobin was also detected in particular in the VHDL fractions from sera of both groups. These results suggest that haptoglobin or a complex with the hemoglobin-like protein may have a role or roles related to the lipid metabolism. PMID:10081748

  11. Genome-Wide Association Study in Arabidopsis thaliana of Natural Variation in Seed Oil Melting Point: A Widespread Adaptive Trait in Plants.

    PubMed

    Branham, Sandra E; Wright, Sara J; Reba, Aaron; Morrison, Ginnie D; Linder, C Randal

    2016-05-01

    Seed oil melting point is an adaptive, quantitative trait determined by the relative proportions of the fatty acids that compose the oil. Micro- and macro-evolutionary evidence suggests selection has changed the melting point of seed oils to covary with germination temperatures because of a trade-off between total energy stores and the rate of energy acquisition during germination under competition. The seed oil compositions of 391 natural accessions of Arabidopsis thaliana, grown under common-garden conditions, were used to assess whether seed oil melting point within a species varied with germination temperature. In support of the adaptive explanation, long-term monthly spring and fall field temperatures of the accession collection sites significantly predicted their seed oil melting points. In addition, a genome-wide association study (GWAS) was performed to determine which genes were most likely responsible for the natural variation in seed oil melting point. The GWAS found a single highly significant association within the coding region of FAD2, which encodes a fatty acid desaturase central to the oil biosynthesis pathway. In a separate analysis of 15 a priori oil synthesis candidate genes, 2 (FAD2 and FATB) were located near significant SNPs associated with seed oil melting point. These results comport with others' molecular work showing that lines with alterations in these genes affect seed oil melting point as expected. Our results suggest natural selection has acted on a small number of loci to alter a quantitative trait in response to local environmental conditions. PMID:26865732

  12. Natural gas leak location with K-L divergence-based adaptive selection of Ensemble Local Mean Decomposition components and high-order ambiguity function

    NASA Astrophysics Data System (ADS)

    Sun, Jiedi; Xiao, Qiyang; Wen, Jiangtao; Zhang, Ying

    2015-07-01

    In this study, a time-delay estimation method based on Ensemble Local Mean Decomposition (ELMD) method and high-order ambiguity function (HAF) is proposed for locating natural gas pipeline leaks. The leakage signals were decomposed using ELMD, and numerous production functions (PFs) were obtained. An adaptive selection method based on Kullback-Leibler (K-L) divergence was proposed to process these PF components and choose the characteristic PFs that contain most of the leakage information. The HAF was employed to analyze the instantaneous parameters of the characteristic PFs and calculate the difference in arrival time of characteristic frequencies. From the time difference and the signal propagation speed, the natural gas pipeline leakage location can be determined. The experiment results show that the proposed method can locate leaks with higher accuracy than cross-correlation method.

  13. When climate change is a fact! Adaptive strategies for drinking water production in a changing natural environment.

    PubMed

    Meuleman, A F M; Cirkel, G; Zwolsman, G J J

    2007-01-01

    Climate change increases water system dynamics through temperature changes, changes in precipitation patterns, evaporation, and water quality and water storage in ice packs. Water system dependent economical stakeholders, such as drinking water companies in the Netherlands, have to cope with consequences of climate change, e.g. floods and water shortages in river systems, upcoming of brackish ground water, salt water intrusion, increasing peak demands and microbiological activity due to temperature rise. In the past decades, however, both water systems and drinking water production have become more and more inflexible; water systems have been heavily regulated aiming at maximum security and economic functions and the drinking water supply in the Netherlands has grown into an inflexible, but cheap and reliable, system. At a water catchment scale, flexibility and adaptation are solutions to overcome climate change related consequences. Flexible adaptive strategies for drinking water production comprise new sources for drinking water production, application of storage concepts in the short term, and a redesign of large centralized systems, including flexible treatment plants, in the long term. Transition to flexible concepts will take decades because investment depreciation periods of assets are long. These strategies must be based on thorough knowledge of current assets to seize opportunities for change. PMID:17851214

  14. Genome-wide amplifications caused by chromosomal rearrangements play a major role in the adaptive evolution of natural yeast.

    PubMed Central

    Infante, Juan J; Dombek, Kenneth M; Rebordinos, Laureana; Cantoral, Jesús M; Young, Elton T

    2003-01-01

    The relative importance of gross chromosomal rearrangements to adaptive evolution has not been precisely defined. The Saccharomyces cerevisiae flor yeast strains offer significant advantages for the study of molecular evolution since they have recently evolved to a high degree of specialization in a very restrictive environment. Using DNA microarray technology, we have compared the genomes of two prominent variants of S. cerevisiae flor yeast strains. The strains differ from one another in the DNA copy number of 116 genomic regions that comprise 38% of the genome. In most cases, these regions are amplicons flanked by repeated sequences or other recombination hotspots previously described as regions where double-strand breaks occur. The presence of genes that confer specific characteristics to the flor yeast within the amplicons supports the role of chromosomal rearrangements as a major mechanism of adaptive evolution in S. cerevisiae. We propose that nonallelic interactions are enhanced by ethanol- and acetaldehyde-induced double-strand breaks in the chromosomal DNA, which are repaired by pathways that yield gross chromosomal rearrangements. This mechanism of chromosomal evolution could also account for the sexual isolation shown among the flor yeast. PMID:14704163

  15. Keeping wetlands wet in the western United States: adaptations to drought in agriculture-dominated human-natural systems.

    PubMed

    Downard, Rebekah; Endter-Wada, Joanna

    2013-12-15

    Water is critical to protecting wetlands in arid regions, especially in agriculture-dominated watersheds. This comparative case study analyzes three federal wildlife refuges in the Bear River Basin of the U.S. West where refuge managers secured water supplies by adapting to their local environmental context and their refuge's relationship to agriculture in being either irrigation-dependent, reservoir-adjacent or diked-delta wetlands. We found that each refuge's position confers different opportunities for securing a water supply and entails unique management challenges linked to agricultural water uses. Acquiring contextually-appropriate water rights portfolios was important for protecting these arid region wetlands and was accomplished through various strategies. Once acquired, water is managed to buffer wetlands against fluctuations caused by a dynamic climate and agricultural demands, especially during droughts. Management plans are responsive to needs of neighboring water users and values of the public at large. Such context-specific adaptations will be critical as the West faces climate change and population growth that threaten wetlands and agricultural systems to which they are linked. PMID:24211568

  16. Structural changes in the low-density polyethylene/natural rubber composites in the aqueous and soil media

    NASA Astrophysics Data System (ADS)

    Mastalygina, Elena E.; Varyan, Ivetta A.; Kolesnikova, Natalya N.; Popov, Anatoly A.

    2016-05-01

    The novel biodegradable materials based on polyethylene with different content of natural rubber have been developed. In this paper the regularities of changes in structure and properties of the composites under the influence of biological and non-biological factors have been investigated. High levels of biodegradability and satisfied mechanical properties of biocomposites, as well as the significant modification of the polyethylene crystalline phase in the composites affected by moisture and environmental factors have been determined.

  17. Density functional theory studies of structural properties, energies and natural band orbital for two new aluminate compounds

    NASA Astrophysics Data System (ADS)

    Sahebalzamani, Hajar; Ghammamy, Shahriare; Mehrani, Kheyrollah; Jahandide, Shahram; Salimi, Farshid

    2012-05-01

    Two new aluminate compounds was prepared by the reaction of AlCl3 with KX (X = SCN-, CN-) in a 1:1 mole ratio. In these salts the aluminum atom is surrounded by three chlorine atoms and a ligand (X = SCN-, CN-). In AlCl3SCN anion, the SCN coordinates to the Al through sulfur and AlCl3CN anion the CN- coordinates to the Al center through carbon. The molecular geometry, vibrational frequencies, energies and natural bond orbital (NBO) in the ground state are calculated by using the DFT (B3LYP) methods with 6-311G* basis sets. The geometries and normal modes of vibrations obtained from B3LYP calculations are in good agreement with the experimentally observed data.

  18. Neural adaptation and perceptual learning using a portable real-time cochlear implant simulator in natural environments.

    PubMed

    Smalt, Christopher J; Talavage, Thomas M; Pisoni, David B; Svirsky, Mario A

    2011-01-01

    A portable real-time speech processor that implements an acoustic simulation model of a cochlear implant (CI) has been developed on the Apple iPhone / iPod Touch to permit testing and experimentation under extended exposure in real-world environments. This simulator allows for both a variable number of noise band channels and electrode insertion depth. Utilizing this portable CI simulator, we tested perceptual learning in normal hearing listeners by measuring word and sentence comprehension behaviorally before and after 2 weeks of exposure. To evaluate changes in neural activation related to adaptation to transformed speech, fMRI was also conducted. Differences in brain activation after training occurred in the inferior frontal gyrus and areas related to language processing. A 15-20% improvement in word and sentence comprehension of cochlear implant simulated speech was also observed. These results demonstrate the effectiveness of a portable CI simulator as a research tool and provide new information about the physiological changes that accompany perceptual learning of degraded auditory input. PMID:22254517

  19. The signature of fine scale local adaptation in Atlantic salmon revealed from common garden experiments in nature

    PubMed Central

    O'Toole, Ciar L; Reed, Thomas E; Bailie, Deborah; Bradley, Caroline; Cotter, Deirdre; Coughlan, Jamie; Cross, Tom; Dillane, Eileen; McEvoy, Sarah; Ó Maoiléidigh, Niall; Prodöhl, Paulo; Rogan, Ger; McGinnity, Philip

    2015-01-01

    Understanding the extent, scale and genetic basis of local adaptation (LA) is important for conservation and management. Its relevance in salmonids at microgeographic scales, where dispersal (and hence potential gene flow) can be substantial, has however been questioned. Here, we compare the fitness of communally reared offspring of local and foreign Atlantic salmon Salmo salar from adjacent Irish rivers and reciprocal F1 hybrid crosses between them, in the wild ‘home’ environment of the local population. Experimental groups did not differ in wild smolt output but a catastrophic flood event may have limited our ability to detect freshwater performance differences, which were evident in a previous study. Foreign parr exhibited higher, and hybrids intermediate, emigration rates from the natal stream relative to local parr, consistent with genetically based behavioural differences. Adult return rates were lower for the foreign compared to the local group. Overall lifetime success of foreigners and hybrids relative to locals was estimated at 31% and 40% (mean of both hybrid groups), respectively. The results imply a genetic basis to fitness differences among populations separated by only 50 km, driven largely by variation in smolt to adult return rates. Hence even if supplementary stocking programs obtain broodstock from neighbouring rivers, the risk of extrinsic outbreeding depression may be high. PMID:26495041

  20. The signature of fine scale local adaptation in Atlantic salmon revealed from common garden experiments in nature.

    PubMed

    O'Toole, Ciar L; Reed, Thomas E; Bailie, Deborah; Bradley, Caroline; Cotter, Deirdre; Coughlan, Jamie; Cross, Tom; Dillane, Eileen; McEvoy, Sarah; Ó Maoiléidigh, Niall; Prodöhl, Paulo; Rogan, Ger; McGinnity, Philip

    2015-10-01

    Understanding the extent, scale and genetic basis of local adaptation (LA) is important for conservation and management. Its relevance in salmonids at microgeographic scales, where dispersal (and hence potential gene flow) can be substantial, has however been questioned. Here, we compare the fitness of communally reared offspring of local and foreign Atlantic salmon Salmo salar from adjacent Irish rivers and reciprocal F1 hybrid crosses between them, in the wild 'home' environment of the local population. Experimental groups did not differ in wild smolt output but a catastrophic flood event may have limited our ability to detect freshwater performance differences, which were evident in a previous study. Foreign parr exhibited higher, and hybrids intermediate, emigration rates from the natal stream relative to local parr, consistent with genetically based behavioural differences. Adult return rates were lower for the foreign compared to the local group. Overall lifetime success of foreigners and hybrids relative to locals was estimated at 31% and 40% (mean of both hybrid groups), respectively. The results imply a genetic basis to fitness differences among populations separated by only 50 km, driven largely by variation in smolt to adult return rates. Hence even if supplementary stocking programs obtain broodstock from neighbouring rivers, the risk of extrinsic outbreeding depression may be high. PMID:26495041

  1. Natural alleles of a proteasome α2 subunit gene contribute to thermotolerance and adaptation of African rice.

    PubMed

    Li, Xin-Min; Chao, Dai-Yin; Wu, Yuan; Huang, Xuehui; Chen, Ke; Cui, Long-Gang; Su, Lei; Ye, Wang-Wei; Chen, Hao; Chen, Hua-Chang; Dong, Nai-Qian; Guo, Tao; Shi, Min; Feng, Qi; Zhang, Peng; Han, Bin; Shan, Jun-Xiang; Gao, Ji-Ping; Lin, Hong-Xuan

    2015-07-01

    Global warming threatens many aspects of human life, for example, by reducing crop yields. Breeding heat-tolerant crops using genes conferring thermotolerance is a fundamental way to help deal with this challenge. Here we identify a major quantitative trait locus (QTL) for thermotolerance in African rice (Oryza glaberrima), Thermo-tolerance 1 (TT1), which encodes an α2 subunit of the 26S proteasome involved in the degradation of ubiquitinated proteins. Ubiquitylome analysis indicated that OgTT1 protects cells from heat stress through more efficient elimination of cytotoxic denatured proteins and more effective maintenance of heat-response processes than achieved with OsTT1. Variation in TT1 has been selected for on the basis of climatic temperature and has had an important role in local adaptation during rice evolution. In addition, we found that overexpression of OgTT1 was associated with markedly enhanced thermotolerance in rice, Arabidopsis and Festuca elata. This discovery may lead to an increase in crop security in the face of the ongoing threat of global warming. PMID:25985140

  2. Neural Adaptation and Perceptual Learning using a Portable Real-Time Cochlear Implant Simulator in Natural Environments

    PubMed Central

    Smalt, Christopher J.; Talavage, Thomas M.; Pisoni, David B.; Svirsky, Mario A.

    2013-01-01

    A portable real-time speech processor that implements an acoustic simulation model of a cochlear implant (CI) has been developed on the Apple iPhone/iPod Touch to permit testing and experimentation under extended exposure in real-world environments. This simulator allows for both a variable number of noise band channels and electrode insertion depth. Utilizing this portable CI simulator, we tested perceptual learning in normal hearing listeners by measuring word and sentence comprehension behaviorally before and after 2 weeks of exposure. To evaluate changes in neural activation related to adaptation to transformed speech, fMRI was also conducted. Differences in brain activation after training occurred in the inferior frontal gyrus and areas related to language processing. A 15–20% improvement in word and sentence comprehension of cochlear implant simulated speech was also observed. These results demonstrate the effectiveness of a portable CI simulator as a research tool and provide new information about the physiological changes that accompany perceptual learning of degraded auditory input. PMID:22254517

  3. Multiferroic nature of intrinsic point defects in BiFeO3: A hybrid Hartree-Fock density functional study

    NASA Astrophysics Data System (ADS)

    Shimada, Takahiro; Matsui, Takahiro; Xu, Tao; Arisue, Kou; Zhang, Yajun; Wang, Jie; Kitamura, Takayuki

    2016-05-01

    To achieve a fundamental understanding of the multiferroic behavior and electronic properties of intrinsic vacancies in BiFe O3 , here we performed first-principles calculations based on hybrid Hartree-Fock density functional theories, which can accurately describe defect electronic structures. Oxygen vacancies, which behave as deep donors with high concentrations under oxygen-poor conditions, reduce the magnetic moments at neighboring Fe ions in the neutral state, while charged oxygen vacancies induce additional ferroelectric polarizations. Cation vacancies, on the other hand, are likely to form under oxygen-rich conditions and result in multiferroic properties distinct from those induced by oxygen vacancies. Bi vacancies act as triple-shallow acceptors and strongly suppress spontaneous polarization regardless of charge states, while Fe vacancies locally interfere with both electric and spin polarization and are thus regarded as multiferroic singular points in BiFe O3 . A rich variety of the multiferroic behavior of vacancies can be systematically understood from the localized/delocalized features of defect states, and the different formation conditions for vacancies provide a strategy to tailor the multiferroic properties of BiFe O3 through control of the concentration and charge states of vacancies.

  4. Nature of charge density waves and superconductivity in 1 T -TaSe2 -xTex

    NASA Astrophysics Data System (ADS)

    Liu, Y.; Shao, D. F.; Li, L. J.; Lu, W. J.; Zhu, X. D.; Tong, P.; Xiao, R. C.; Ling, L. S.; Xi, C. Y.; Pi, L.; Tian, H. F.; Yang, H. X.; Li, J. Q.; Song, W. H.; Zhu, X. B.; Sun, Y. P.

    2016-07-01

    Transition-metal dichalcogenides (TMDs) M X2 (M =Ti,Nb,Ta;X =S,Se,Te) exhibit a rich set of charge density wave (CDW) orders, which usually coexist and/or compete with superconductivity. The mechanisms of CDWs and superconductivity in TMDs are still under debate. Here we perform an investigation on a typical TMD system, 1 T -TaSe2 -xTex (0 ≤x ≤2 ). Doping-induced disordered distribution of Se/Te suppresses CDWs in 1 T -TaSe2. A domelike superconducting phase with the maximum Tconset of 2.5 K was observed near CDWs. The superconducting volume is very small inside the CDW phase and becomes very large instantly when the CDW phase is fully suppressed. The observations can be understood based on the strong q -dependent electron-phonon coupling-induced periodic-lattice-distortion (PLD) mechanism of CDWs. The volume variation of superconductivity implies the emergence of domain walls in the suppressing process of CDWs. Our concluded scenario makes a fundamental understanding about CDWs and related superconductivity in TMDs.

  5. Influence of environmental information in natural scenes and the effects of motion adaptation on a fly motion-sensitive neuron during simulated flight

    PubMed Central

    Ullrich, Thomas W.; Kern, Roland; Egelhaaf, Martin

    2015-01-01

    ABSTRACT Gaining information about the spatial layout of natural scenes is a challenging task that flies need to solve, especially when moving at high velocities. A group of motion sensitive cells in the lobula plate of flies is supposed to represent information about self-motion as well as the environment. Relevant environmental features might be the nearness of structures, influencing retinal velocity during translational self-motion, and the brightness contrast. We recorded the responses of the H1 cell, an individually identifiable lobula plate tangential cell, during stimulation with image sequences, simulating translational motion through natural sceneries with a variety of differing depth structures. A correlation was found between the average nearness of environmental structures within large parts of the cell's receptive field and its response across a variety of scenes, but no correlation was found between the brightness contrast of the stimuli and the cell response. As a consequence of motion adaptation resulting from repeated translation through the environment, the time-dependent response modulations induced by the spatial structure of the environment were increased relatively to the background activity of the cell. These results support the hypothesis that some lobula plate tangential cells do not only serve as sensors of self-motion, but also as a part of a neural system that processes information about the spatial layout of natural scenes. PMID:25505148

  6. Reviewing molecular adaptations of Lyme borreliosis spirochetes in the context of reproductive fitness in natural transmission cycles

    PubMed Central

    Tsao, Jean I.

    2009-01-01

    Lyme borreliosis (LB) is caused by a group of pathogenic spirochetes – most often Borrelia burgdorferi, B. afzelii, and B. garinii – that are vectored by hard ticks in the Ixodes ricinus-persulcatus complex, which feed on a variety of mammals, birds, and lizards. Although LB is one of the best-studied vector-borne zoonoses, the annual incidence in North America and Europe leads other vector-borne diseases and continues to increase. What factors make the LB system so successful, and how can researchers hope to reduce disease risk – either through vaccinating humans or reducing the risk of contacting infected ticks in nature? Discoveries of molecular interactions involved in the transmission of LB spirochetes have accelerated recently, revealing complex interactions among the spirochete-tick-vertebrate triad. These interactions involve multiple, and often redundant, pathways that reflect the evolution of general and specific mechanisms by which the spirochetes survive and reproduce. Previous reviews have focused on the molecular interactions or population biology of the system. Here molecular interactions among the LB spirochete, its vector, and vertebrate hosts are reviewed in the context of natural maintenance cycles, which represent the ecological and evolutionary contexts that shape these interactions. This holistic system approach may help researchers develop additional testable hypotheses about transmission processes, interpret laboratory results, and guide development of future LB control measures and management. PMID:19368764

  7. Reviewing molecular adaptations of Lyme borreliosis spirochetes in the context of reproductive fitness in natural transmission cycles.

    PubMed

    Tsao, Jean I

    2009-01-01

    Lyme borreliosis (LB) is caused by a group of pathogenic spirochetes - most often Borrelia burgdorferi, B. afzelii, and B. garinii - that are vectored by hard ticks in the Ixodes ricinus-persulcatus complex, which feed on a variety of mammals, birds, and lizards. Although LB is one of the best-studied vector-borne zoonoses, the annual incidence in North America and Europe leads other vector-borne diseases and continues to increase. What factors make the LB system so successful, and how can researchers hope to reduce disease risk - either through vaccinating humans or reducing the risk of contacting infected ticks in nature? Discoveries of molecular interactions involved in the transmission of LB spirochetes have accelerated recently, revealing complex interactions among the spirochete-tick-vertebrate triad. These interactions involve multiple, and often redundant, pathways that reflect the evolution of general and specific mechanisms by which the spirochetes survive and reproduce. Previous reviews have focused on the molecular interactions or population biology of the system. Here molecular interactions among the LB spirochete, its vector, and vertebrate hosts are reviewed in the context of natural maintenance cycles, which represent the ecological and evolutionary contexts that shape these interactions. This holistic system approach may help researchers develop additional testable hypotheses about transmission processes, interpret laboratory results, and guide development of future LB control measures and management. PMID:19368764

  8. Microscale Adaptation of In Vitro Transcription/Translation for High-Throughput Screening of Natural Product Extract Libraries

    PubMed Central

    Lowell, Andrew N.; Santoro, Nicholas; Swaney, Steven M.; McQuade, Thomas J.; Schultz, Pamela J.; Larsen, Martha J.; Sherman, David H.

    2016-01-01

    Novel antimicrobials that effectively inhibit bacterial growth are essential to fight the growing threat of antibiotic resistance. A promising target is the bacterial ribosome, a 2.5 MDa organelle susceptible to several biorthogonal modes of action used by different classes of antibiotics. To promote the discovery of unique inhibitors, we have miniaturized a coupled transcription/translation assay using E. coli and applied it to screen a natural product library of ∼30 000 extracts. We significantly reduced the scale of the assay to 2 μL in a 1536-well plate format and decreased the effective concentration of costly reagents. The improved assay returned 1327 hits (4.6% hit rate) with %CV and Z′ values of 8.5% and 0.74, respectively. This assay represents a significant advance in molecular screening, both in miniaturization and its application to a natural product extract library, and we intend to apply it to a broad array of pathogenic microbes in the search for novel anti-infective agents. PMID:26147927

  9. Vibrational spectra, molecular structure, natural bond orbital, first order hyperpolarizability, thermodynamic analysis and normal coordinate analysis of Salicylaldehyde p-methylphenylthiosemicarbazone by density functional method.

    PubMed

    Porchelvi, E Elamurugu; Muthu, S

    2015-01-01

    The thiosemicarbazone compound, Salicylaldehyde p-methylphenylthiosemicarbazone (abbreviated as SMPTSC) was synthesized and characterized by FTIR, FT-Raman and UV. Density functional (DFT) calculations have been carried out for the title compound by performing DFT level of theory using B3LYP/6-31++G(d,p) basis set. The molecular geometry and vibrational frequencies were calculated and compared with the experimental data. The detailed interpretation of the vibrational spectra has been carried out with aid of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology. The electronic dipole moment (μD) and the first hyperpolarizability (βtot) values of the investigated molecule were computed using density functional theory (DFT/B3LYP) with 6-311++G(d,p) basis set. The stability and charge delocalization of the molecule was studied by natural bond orbital (NBO) analysis. Thearomaticities of the phenyl rings were studied using the standard harmonic oscillator model of aromaticity (HOMA) index. Mulliken population analysis on atomic charges is also calculated. The molecule orbital contributions are studied by density of energy states (DOSs). PMID:25033238

  10. Density-dependent regulation of fecundity in Syngamus trachea infrapopulations in semi-naturally occurring ring-necked pheasants (Phasianus colchicus) and wild Carrion Crows (Corvus corone).

    PubMed

    Gethings, O J; Sage, R B; Leather, S R

    2016-05-01

    Previous work has highlighted increased opportunities for the transmission of Syngamus trachea within pheasant release pens, due in part to high levels of environmental contamination around communal areas. Despite this, the distribution of adult worms within their definitive hosts is not significantly different from predicted distributions under Taylor's power law. Therefore, density-dependent processes are probably acting to regulate S. trachea population dynamics. Patterns of nematode fecundity were investigated in a semi-naturally occurring population of ring-necked pheasants (Phasianus colchicus) and a wild population of carrion crows (Corvus carone). Worm length was a reliable indicator of nematode fecundity, and a negative association between mean worm length and mean worm burden was identified within both the species. The stunting of worms at greater parasite densities was present in both immunologically naïve and previously exposed pheasants, so is unlikely to be a function of age-dependent acquired immunity. Interestingly, the effect of parasite crowding in the crow population explained more of the variation in mean worm length, apparently driven by a greater mean worm burden when compared with pheasants. The findings of the present study suggest that fecundity is a function of parasite density, i.e. parasite-mediated competition and not host-mediated heterogeneities in immunocompetence. PMID:26932519

  11. What kind of memory has evolution wrought? Introductory article for the special issue of memory: adaptive memory: the emergence and nature of proximate mechanisms.

    PubMed

    Otgaar, Henry; Howe, Mark L

    2014-01-01

    It is without question that our memory system evolved through a process of natural selection. However, basic research into the evolutionary foundations of memory has begun in earnest only recently. This is quite peculiar as the majority, perhaps even all, of memory research relates to whether memory is adaptive or not. In this Special Issue of Memory we have assembled a variety of papers that represent the cutting edge in research on the evolution of memory. These papers are centred on issues about the ultimate and proximate explanations of memory, the development of the adaptive functions of memory, as well as the positive consequences that arise from the current evolutionary form that our memory has taken. In this introductory article we briefly outline these different areas and indicate why they are vital for a more complete theory of memory. Further we argue that, by adopting a more applied stance in the area of the evolution of memory, one of the many future directions in this field could be a new branch of psychology that addresses questions in evolutionary legal psychology. PMID:23731185

  12. Towards adaptive management of the natural capital: Disentangling trade-offs among marine activities and seagrass meadows.

    PubMed

    Bas Ventín, Leticia; de Souza Troncoso, Jesús; Villasante, Sebastián

    2015-12-15

    This paper investigates the ecological, social and institutional dimensions of the synergies and trade-offs between seagrasses and human activities operating in the Natura 2000 protected site of San Simón Bay (Galicia, NW Spain). By means of a multidisciplinary approach that brings together the development of a biological inventory combined with participatory mapping processes we get key spatial and contextual understanding regarding how, where and why marine users interact with seagrasses and how seagrasses are considered in policy making. The results highlight the fisheries' reliance on seagrass meadows and the controversial links with shellfisheries. The study also reveals unresolved conflicts among those management plans that promote the protection of natural values and those responsible for the exploitation of marine resources. We conclude that the adoption of pre-planning bottom-up participatory processes is crucial for the design of realistic strategies where both seagrasses and human activities were considered as a couple system. PMID:26589639

  13. Metabolic adaptation and in situ attenuation of chlorinated ethenes by naturally occurring microorganisms in a fractured dolomite aquifer near Niagara Falls, New York

    USGS Publications Warehouse

    Yager, R.M.; Bilotta, S.E.; Mann, C.L.; Madsen, E.L.

    1997-01-01

    A combination of hydrogeological, geochemical, and microbiological methods was used to document the biotransformation of trichloroethene (TCE) to ethene, a completely dechlorinated and environmentally benign compound, by naturally occurring microorganisms within a fractured dolomite aquifer. Analyses of groundwater samples showed that three microbially produced TCE breakdown products (cis-1,2-dichloroethene, vinyl chloride, and ethene) were present in the contaminant plume. Hydrogen (H2) concentrations in groundwater indicated that iron reduction was the predominant terminal electron-accepting process in the most contaminated geologic zone of the site. Laboratory microcosms prepared with groundwater demonstrated complete sequential dechlorination of TCE to ethene. Microcosm assays also revealed that reductive dechlorination activity was present in waters from the center but not from the periphery of the contaminant plume. This dechlorination activity indicated that naturally occurring microorganisms have adapted to utilize chlorinated ethenes and suggested that dehalorespiring rather than cometabolic, microbial processes were the cause of the dechlorination. The addition of pulverized dolomite to microcosms enhanced the rate of reductive dechlorination, suggesting that hydrocarbons in the dolomite aquifer may serve as electron donors to drive microbially mediated reductive dechlorination reactions. Biodegradation of the chlorinated ethenes appears to contribute significantly to decontamination of the site.A combination of hydrogeological, geochemical, and microbiological methods was used to document the biotransformation of trichloroethene (TCE) to ethene, a completely dechlorinated and environmentally benign compound, by naturally occurring microorganisms within a fractured dolomite aquifer. Analyses of groundwater samples showed that three microbially produced TCE breakdown products (cis-1,2-dichloroethene, vinyl chloride, and ethene) were present in the

  14. Application of thermodynamic modelling to natural mantle xenoliths: examples of density variations and pressure-temperature evolution of the lithospheric mantle

    NASA Astrophysics Data System (ADS)

    Ziberna, L.; Klemme, S.

    2016-02-01

    In this paper, we show how the results of phase equilibria calculations in different mantle compositions can be reconciled with the evidence from natural mantle samples. We present data on the response of bulk rock density to pressure (P), temperature (T) and compositional changes in the lithospheric mantle and obtain constraints on the P-T evolution recorded by mantle xenoliths. To do this, we examine the mantle xenolith suite from the Quaternary alkali basalts of Pali-Aike, Patagonia, using phase equilibria calculation in six representative compositions. The calculations were done subsolidus and in volatile-free conditions. Our results show that the density change related to the spinel peridotite to garnet peridotite transition is not sharp and strongly depends on the bulk composition. In a depleted mantle composition, this transition is not reflected in the density profile, while in a fertile mantle it leads to a relative increase in density with respect to more depleted compositions. In mantle sections characterized by hot geothermal gradients (~70 mW/m2), the spinel-garnet transition may overlap with the lithosphere-asthenosphere boundary. Phase equilibria calculations in peridotitic compositions representative of the Pali-Aike mantle were also used to constrain the origin and evolution of the mantle xenoliths. Our results indicate that the mineral modes and compositions, and the mineral zonation reported for the low-temperature peridotites (spinel and spinel + garnet harzburgites and lherzolites), are linked to a cooling event in the mantle which occurred long before the eruption of the host basalts. In addition, our phase equilibria calculations show that kelyphitic rims around garnets, as those observed in the high-temperature garnet peridotites from Pali-Aike, can be explained simply by decompression and do not require additional metasomatic fluid or melt.

  15. Adaptation as organism design

    PubMed Central

    Gardner, Andy

    2009-01-01

    The problem of adaptation is to explain the apparent design of organisms. Darwin solved this problem with the theory of natural selection. However, population geneticists, whose responsibility it is to formalize evolutionary theory, have long neglected the link between natural selection and organismal design. Here, I review the major historical developments in theory of organismal adaptation, clarifying what adaptation is and what it is not, and I point out future avenues for research. PMID:19793739

  16. Nature of organo-mineral particles across density fractions in a volcanic-ash soil: air-drying and sonication effect

    NASA Astrophysics Data System (ADS)

    Wagai, R.; Kajiura, M.; Shirato, Y.; Uchida, M.

    2011-12-01

    Interactions of plant- and microbially-derived organic matter with mineral phases exert significant controls on the stabilization of organic matter (OM) as well as other biogeochemical processes in soil. Density fractionation techniques have been successful in distinguishing soil organo-mineral particles of different degrees of microbial alteration, turnover rate of C, mineral associations. A major methodological difference among the density fractionation studies is the choice of sample pre-treatment. Presence or absence of sonication to disrupt and disperse soil particles and aggregates is a particularly important choice which could significantly alter the nature and distribution of organo-mineral particle and thus the resultant elemental concentration in each density fraction. Soil moisture condition (air-dry vs. field-moist) may also have strong impact especially for soils rich in Fe oxides/hydroxides and/or poorly-crystalline minerals that are prone for (possibly irreversible) aggregation. We thus tested these two effects on the concentration and distribution of C, N, and extractable phases of Fe and Al (by pyrophosphate and acid oxalate) across six density fractions (from <1.6 to >2.5 g/cm^3) using a surface-horizon of volcanic-ash soil which contained large amounts of poorly-crystalline minerals and organo-metal complexes. Compared to field-moist sample, air-drying had little effects on the elemental concentration or distribution across the fractions. In contrast, sonication on air-dried sample at each density cutoff during fractionation process caused significant changes. In addition to well-known increase in low-density material due to the liberation of plant detritus upon aggregate disruption, we found clear increase in C, N, and metals in 2.0-2.3 g/cm^3 fraction, which was largely compensated by the reduction in 1.8-2.0 g/cm^3 and, to a less extent, 2.3-2.5 g/cm^3 particles. Overall, sonication led to the redistribution of C and N by 15-20% and that of

  17. Response of fish communities to cropland density and natural environmental setting in the Eastern Highland Rim Ecoregion of the lower Tennessee River basin, Alabama and Tennessee, 1999

    USGS Publications Warehouse

    Powell, Jeffrey R.

    2003-01-01

    Response of fish communities to cropland density and natural environmental setting were evaluated at 20 streams in the Eastern Highland Rim Ecoregion of the lower Tennessee River Basin during the spring of 1999. Sites were selected to represent a gradient of cropland densities in basins draining about 30 to 100 square miles. Fish communities were sampled by using a combination of seining and electrofishing techniques. A total of 10,550 individual fish, representing 63 species and 15 families, were collected during the study and included the families Cyprinidae (minnows), 18 species; Percidae (perch and darters), 12 species; and Centrarchidae (sunfish), 12 species. Assessments of environmental characteristics, including instream and terrestrial data and land-cover data, were conducted for each site. Instream measurements, such as depth, velocity, substrate type, and embeddedness, were recorded at 3 points across 11 equidistant transects at each site. Terrestrial measurements, such as bank angle, canopy angle, and canopy closure percentage, were made along the stream bank and midchannel areas. Water-quality data collected included pH, dissolved oxygen, specific conductivity, water temperature, nutrients, and fecal-indicator bacteria. Substrate embeddedness was the only variable correlated with both cropland density and fish communities (as characterized by ordination scores and several community level metrics). Multivariate and nonparametric correlation techniques were used to evaluate fish-community responses to physical and chemical factors associated with a cropland-density gradient, where the gradient was defined as the percentage of the basin in row crops. Principal component analysis and correspondence analysis suggest that the Eastern Highland Rim Ecoregion is composed of three subgroups of sites based on inherent physical and biological differences. Data for the subgroup containing the largest number of sites were then re-analyzed, revealing that several

  18. Viability and adaptation potential of indigenous microorganisms from natural gas field fluids in high pressure incubations with supercritical CO2.

    PubMed

    Frerichs, Janin; Rakoczy, Jana; Ostertag-Henning, Christian; Krüger, Martin

    2014-01-21

    Carbon Capture and Storage (CCS) is currently under debate as large-scale solution to globally reduce emissions of the greenhouse gas CO2. Depleted gas or oil reservoirs and saline aquifers are considered as suitable reservoirs providing sufficient storage capacity. We investigated the influence of high CO2 concentrations on the indigenous bacterial population in the saline formation fluids of a natural gas field. Bacterial community changes were closely examined at elevated CO2 concentrations under near in situ pressures and temperatures. Conditions in the high pressure reactor systems simulated reservoir fluids i) close to the CO2 injection point, i.e. saturated with CO2, and ii) at the outer boundaries of the CO2 dissolution gradient. During the incubations with CO2, total cell numbers remained relatively stable, but no microbial sulfate reduction activity was detected. After CO2 release and subsequent transfer of the fluids, an actively sulfate-respiring community was re-established. The predominance of spore-forming Clostridiales provided evidence for the resilience of this taxon against the bactericidal effects of supercritical (sc)CO2. To ensure the long-term safety and injectivity, the viability of fermentative and sulfate-reducing bacteria has to be considered in the selection, design, and operation of CCS sites. PMID:24320192

  19. The BOY NAMED SUE Quantitative Trait Locus Confers Increased Meiotic Stability to an Adapted Natural Allopolyploid of Arabidopsis[C][W][OPEN

    PubMed Central

    Henry, Isabelle M.; Dilkes, Brian P.; Tyagi, Anand; Gao, Jian; Christensen, Brian; Comai, Luca

    2014-01-01

    Whole-genome duplication resulting from polyploidy is ubiquitous in the evolutionary history of plant species. Yet, polyploids must overcome the meiotic challenge of pairing, recombining, and segregating more than two sets of chromosomes. Using genomic sequencing of synthetic and natural allopolyploids of Arabidopsis thaliana and Arabidopsis arenosa, we determined that dosage variation and chromosomal translocations consistent with homoeologous pairing were more frequent in the synthetic allopolyploids. To test the role of structural chromosomal differentiation versus genetic regulation of meiotic pairing, we performed sequenced-based, high-density genetic mapping in F2 hybrids between synthetic and natural lines. This F2 population displayed frequent dosage variation and deleterious homoeologous recombination. The genetic map derived from this population provided no indication of structural evolution of the genome of the natural allopolyploid Arabidopsis suecica, compared with its predicted parents. The F2 population displayed variation in meiotic regularity and pollen viability that correlated with a single quantitative trait locus, which we named BOY NAMED SUE, and whose beneficial allele was contributed by A. suecica. This demonstrates that an additive, gain-of-function allele contributes to meiotic stability and fertility in a recently established allopolyploid and provides an Arabidopsis system to decipher evolutionary and molecular mechanisms of meiotic regularity in polyploids. PMID:24464296

  20. C and N Content in Density Fractions of Whole Soil and Soil Size Fraction Under Cacao Agroforestry Systems and Natural Forest in Bahia, Brazil

    NASA Astrophysics Data System (ADS)

    Rita, Joice Cleide O.; Gama-Rodrigues, Emanuela Forestieri; Gama-Rodrigues, Antonio Carlos; Polidoro, Jose Carlos; Machado, Regina Cele R.; Baligar, Virupax C.

    2011-07-01

    Agroforestry systems (AFSs) have an important role in capturing above and below ground soil carbon and play a dominant role in mitigation of atmospheric CO2. Attempts has been made here to identify soil organic matter fractions in the cacao-AFSs that have different susceptibility to microbial decomposition and further represent the basis of understanding soil C dynamics. The objective of this study was to characterize the organic matter density fractions and soil size fractions in soils of two types of cacao agroforestry systems and to compare with an adjacent natural forest in Bahia, Brazil. The land-use systems studied were: (1) a 30-year-old stand of natural forest with cacao (cacao cabruca), (2) a 30-year-old stand of cacao with Erythrina glauca as shade trees (cacao + erythrina), and (3) an adjacent natural forest without cacao. Soil samples were collected from 0-10 cm depth layer in reddish-yellow Oxisols. Soil samples was separated by wet sieving into five fraction-size classes (>2000 μm, 1000-2000 μm, 250-1000 μm, 53-250 μm, and <53 μm). C and N accumulated in to the light (free- and intra-aggregate density fractions) and heavy fractions of whole soil and soil size fraction were determined. Soil size fraction obtained in cacao AFS soils consisted mainly (65 %) of mega-aggregates (>2000 μm) mixed with macroaggregates (32-34%), and microaggregates (1-1.3%). Soil organic carbon (SOC) and total N content increased with increasing soil size fraction in all land-use systems. Organic C-to-total N ratio was higher in the macroaggregate than in the microaggregate. In general, in natural forest and cacao cabruca the contribution of C and N in the light and heavy fractions was similar. However, in cacao + erythrina the heavy fraction was the most common and contributed 67% of C and 63% of N. Finding of this study shows that the majority of C and N in all three systems studied are found in macroaggregates, particularly in the 250-1000 μm size aggregate class

  1. Selection and adaptation to high plant density in the Iowa Stiff Stalk synthetic maize (Zea mays L.) population: II. Plant morphology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The plant density at which Zea mays L. hybrids achieve maximum grain yield has increased throughout the hybrid era while grain yield on a per plant basis has increased little. Changes in plant characteristics including flag leaf angle, anthesis-silking interval (ASI), plant height, tassel branch num...

  2. Climate change adaptation strategies and mitigation policies

    NASA Astrophysics Data System (ADS)

    García Fernández, Cristina

    2015-04-01

    The pace of climate change and the consequent warming of the Earth's surface is increasing vulnerability and decreasing adaptive capacity. Achieving a successful adaptation depends on the development of technology, institutional organization, financing availability and the exchange of information. Populations living in arid and semi-arid zones, low-lying coastal areas, land with water shortages or at risk of overflow or small islands are particularly vulnerable to climate change. Due to increasing population density in sensitive areas, some regions have become more vulnerable to events such as storms, floods and droughts, like the river basins and coastal plains. Human activities have fragmented and increased the vulnerability of ecosystems, which limit both, their natural adaptation and the effectiveness of the measures adopted. Adaptation means to carry out the necessary modifications for society to adapt to new climatic conditions in order to reduce their vulnerability to climate change. Adaptive capacity is the ability of a system to adjust to climate change (including climate variability and extremes) and to moderate potential damages, to take advantage of opportunities or face the consequences. Adaptation reduces the adverse impacts of climate change and enhance beneficial impacts, but will not prevent substantial cost that are produced by all damages. The performances require adaptation actions. These are defined and implemented at national, regional or local levels since many of the impacts and vulnerabilities depend on the particular economic, geographic and social circumstances of each country or region. We will present some adaptation strategies at national and local level and revise some cases of its implementation in several vulnerable areas. However, adaptation to climate change must be closely related to mitigation policies because the degree of change planned in different climatic variables is a function of the concentration levels that are achieved

  3. Natural Selection Causes Adaptive Genetic Resistance in Wild Emmer Wheat against Powdery Mildew at “Evolution Canyon” Microsite, Mt. Carmel, Israel

    PubMed Central

    Yin, Huayan; Ben-Abu, Yuval; Wang, Hongwei; Li, Anfei; Nevo, Eviatar; Kong, Lingrang

    2015-01-01

    Background “Evolution Canyon” (ECI) at Lower Nahal Oren, Mount Carmel, Israel, is an optimal natural microscale model for unraveling evolution in action highlighting the basic evolutionary processes of adaptation and speciation. A major model organism in ECI is wild emmer, Triticum dicoccoides, the progenitor of cultivated wheat, which displays dramatic interslope adaptive and speciational divergence on the tropical-xeric “African” slope (AS) and the temperate-mesic “European” slope (ES), separated on average by 250 m. Methods We examined 278 single sequence repeats (SSRs) and the phenotype diversity of the resistance to powdery mildew between the opposite slopes. Furthermore, 18 phenotypes on the AS and 20 phenotypes on the ES, were inoculated by both Bgt E09 and a mixture of powdery mildew races. Results In the experiment of genetic diversity, very little polymorphism was identified intra-slope in the accessions from both the AS or ES. By contrast, 148 pairs of SSR primers (53.23%) amplified polymorphic products between the phenotypes of AS and ES. There are some differences between the two wild emmer wheat genomes and the inter-slope SSR polymorphic products between genome A and B. Interestingly, all wild emmer types growing on the south-facing slope (SFS=AS) were susceptible to a composite of Blumeria graminis, while the ones growing on the north-facing slope (NFS=ES) were highly resistant to Blumeria graminis at both seedling and adult stages. Conclusion/Significance Remarkable inter-slope evolutionary divergent processes occur in wild emmer wheat, T. dicoccoides at EC I, despite the shot average distance of 250 meters. The AS, a dry and hot slope, did not develop resistance to powdery mildew, whereas the ES, a cool and humid slope, did develop resistance since the disease stress was strong there. This is a remarkable demonstration in host-pathogen interaction on how resistance develops when stress causes an adaptive result at a micro

  4. Characterization of a natural mouse monoclonal antibody recognizing epitopes shared by oxidized low-density lipoprotein and chaperonin 60 of Aggregatibacter actinomycetemcomitans.

    PubMed

    Wang, Chunguang; Kankaanpää, Jari; Kummu, Outi; Turunen, S Pauliina; Akhi, Ramin; Bergmann, Ulrich; Pussinen, Pirkko; Remes, Anne M; Hörkkö, Sohvi

    2016-06-01

    Natural antibodies are predominantly antibodies of the IgM isotype present in the circulation of all vertebrates that have not been previously exposed to exogenous antigens. They are often directed against highly conserved epitopes and bind to ligands of varying chemical composition with low affinity. In this study we cloned and characterized a natural mouse monoclonal IgM antibody selected by binding to malondialdehyde acetaldehyde epitopes on low-density lipoprotein (LDL). Interestingly, the IgM antibody cross-reacted with Aggregatibacter actinomycetemcomitans (Aa) bacteria, a key pathogenic microbe in periodontitis reported to be associated with risk factor for atherosclerosis, thus being named as Aa_Mab. It is more intriguing that the binding molecule of Aa to Aa_Mab IgM was found to be Aa chaperonin 60 or HSP60, a member of heat-shock protein family, behaving not only as a chaperone for correct protein folding but also as a powerful virulence factor of the bacteria for inducing bone resorption and as a putative pathogenic factor in atherosclerosis. The findings will highlight the question of whether molecular mimicry between pathogen components and oxidized LDL could lead to atheroprotective immune activity, and also would be of great importance in potential application of immune response-based preventive and therapeutic strategies against atherosclerosis and periodontal disease. PMID:26786003

  5. Carbon storage potential in size-density fractions from semi-natural grassland ecosystems with different productivities over varying soil depths.

    PubMed

    Breulmann, Marc; Boettger, Tatjana; Buscot, François; Gruendling, Ralf; Schulz, Elke

    2016-03-01

    Researchers have increasingly recognised a profound need for more information on SOC stocks in the soil and the factors governing their stability and dynamics. Many questions still remain unanswered about the interplay between changes in plant communities and the extent to which changes in aboveground productivity affect the carbon dynamics in soils through changes in its quantity and quality. Therefore, the main aim of this research was to examine the SOC accumulation potential of semi-natural grasslands of different productivities and determine the distribution of SOM fractions over varying soil depth intervals (0-10, 10-20, 20-30 30-50 50-80 and 80+cm). SOM fractionation was considered as a relative measure of stability to separate SOM associated with clay minerals from SOM of specific light densities less than 2 g cm(-3) (size-density fractionation). Two clay-associated fractions (CF1, <1 μm; and CF2, 1-2 μm) and two light fractions (LF1, <1.8 g cm(-3); and LF2, 1.8-2.0 g cm(-3)) were separated. The stability of these fractions was characterised by their carbon hot water extractability (CHWE) and stable carbon isotope composition. In the semi-natural grasslands studied, most OC was stored in the top 30 cm, where turnover is rapid. Effects of low productivity grasslands became only significantly apparent when fractional OC contributions of total SOM was considered (CF1 and LF1). In deeper soil depths OC was largely attributed to the CF1 fraction of low productivity grasslands. We suggest that the majority of OM in deeper soil depth intervals is microbially-derived, as evidenced by decreasing C/N ratios and decreasing δ(13)C values. The hot water extraction and natural δ(13)C abundance, employed here allowed the characterisation of SOM stabilisation properties, however how climatic changes affect the fate of OM within different soil depth intervals is still unknown. PMID:26745290

  6. Structure and function of cytochrome P450S in insect adaptation to natural and synthetic toxins: insights gained from molecular modeling.

    PubMed

    Schuler, Mary A; Berenbaum, May R

    2013-09-01

    Over evolutionary time, insect herbivores have adapted to the presence of natural toxins and more recently to synthetic insecticides in or on the plants they consume. Biochemical analyses and molecular modeling of the cytochrome P450 monooxygenases (P450s) that metabolize these compounds have provided insight into the many variations affecting their catalytic activity. Phylogenetically distinct P450s may metabolize similar substrates, and phylogenetically similar P450s may metabolize different substrates; as well, some P450s process broad arrays of both phytochemicals and synthetic insecticides, while closely related P450s are restricted to a narrow range of phytochemicals. Mapped on the predicted three-dimensional structures of insect P450s developed from available mammalian P450 crystal structures, differences in multiple regions of the insect proteins reveal the evolutionary processes occurring as P450 genes have duplicated and diverged. Analyses of site-directed mutants in select lepidopteran and dipteran P450s demonstrate that slight changes in the catalytic site, the putative product release channel, and the proximal surface (interacting with electron transfer partners such as cytochrome P450 reductase and cytochrome b5) yield pronounced activity differences. Additionally, changes in the catalytic site and in the linker region preceding the proline-hinge influence P450 folding. With predicted structures available for many mammalian P450s involved in metabolism of xenobiotics, it is possible to record allelic variation relative to catalytically important regions in the overall P450 structure and to predict functionally critical differences. Together with information on the relative levels of allelic variant transcripts, comprehensive characterization of the mechanisms that modulate metabolism of natural and synthetic xenobiotics in insects can yield insights into plant-insect coevolution and into novel approaches for chemical pest management. PMID:24036972

  7. Is It Possible To Obtain Coupled Cluster Quality Energies at near Density Functional Theory Cost? Domain-Based Local Pair Natural Orbital Coupled Cluster vs Modern Density Functional Theory.

    PubMed

    Liakos, Dimitrios G; Neese, Frank

    2015-09-01

    The recently developed domain-based local pair natural orbital coupled cluster theory with single, double, and perturbative triple excitations (DLPNO-CCSD(T)) delivers results that are closely approaching those of the parent canonical coupled cluster method at a small fraction of the computational cost. A recent extended benchmark study established that, depending on the three main truncation thresholds, it is possible to approach the canonical CCSD(T) results within 1 kJ (default setting, TightPNO), 1 kcal/mol (default setting, NormalPNO), and 2-3 kcal (default setting, LoosePNO). Although thresholds for calculations with TightPNO are 2-4 times slower than those based on NormalPNO thresholds, they are still many orders of magnitude faster than canonical CCSD(T) calculations, even for small and medium sized molecules where there is little locality. The computational effort for the coupled cluster step scales nearly linearly with system size. Since, in many instances, the coupled cluster step in DLPNO-CCSD(T) is cheaper or at least not much more expensive than the preceding Hartree-Fock calculation, it is useful to compare the method against modern density functional theory (DFT), which requires an effort comparable to that of Hartree-Fock theory (at least if Hartree-Fock exchange is part of the functional definition). Double hybrid density functionals (DHDF's) even require a MP2-like step. The purpose of this article is to evaluate the cost vs accuracy ratio of DLPNO-CCSD(T) against modern DFT (including the PBE, B3LYP, M06-2X, B2PLYP, and B2GP-PLYP functionals and, where applicable, their van der Waals corrected counterparts). To eliminate any possible bias in favor of DLPNO-CCSD(T), we have chosen established benchmark sets that were specifically proposed for evaluating DFT functionals. It is demonstrated that DLPNO-CCSD(T) with any of the three default thresholds is more accurate than any of the DFT functionals. Furthermore, using the aug-cc-pVTZ basis set and

  8. Comparative characterization of two marine alginate lyases from Zobellia galactanivorans reveals distinct modes of action and exquisite adaptation to their natural substrate.

    PubMed

    Thomas, François; Lundqvist, Lena C E; Jam, Murielle; Jeudy, Alexandra; Barbeyron, Tristan; Sandström, Corine; Michel, Gurvan; Czjzek, Mirjam

    2013-08-01

    Cell walls of brown algae are complex supramolecular assemblies containing various original, sulfated, and carboxylated polysaccharides. Among these, the major marine polysaccharide component, alginate, represents an important biomass that is successfully turned over by the heterotrophic marine bacteria. In the marine flavobacterium Zobellia galactanivorans, the catabolism and uptake of alginate are encoded by operon structures that resemble the typical Bacteroidetes polysaccharide utilization locus. The genome of Z. galactanivorans contains seven putative alginate lyase genes, five of which are localized within two clusters comprising additional carbohydrate-related genes. This study reports on the detailed biochemical and structural characterization of two of these. We demonstrate here that AlyA1PL7 is an endolytic guluronate lyase, and AlyA5 cleaves unsaturated units, α-L-guluronate or β-D-manuronate residues, at the nonreducing end of oligo-alginates in an exolytic fashion. Despite a common jelly roll-fold, these striking differences of the mode of action are explained by a distinct active site topology, an open cleft in AlyA1(PL7), whereas AlyA5 displays a pocket topology due to the presence of additional loops partially obstructing the catalytic groove. Finally, in contrast to PL7 alginate lyases from terrestrial bacteria, both enzymes proceed according to a calcium-dependent mechanism suggesting an exquisite adaptation to their natural substrate in the context of brown algal cell walls. PMID:23782694

  9. A Resource for Eliciting Student Alternative Conceptions: Examining the Adaptability of a Concept Inventory for Natural Selection at the Secondary School Level

    NASA Astrophysics Data System (ADS)

    Lucero, Margaret M.; Petrosino, Anthony J.

    2016-07-01

    The Conceptual Inventory of Natural Selection (CINS) is an example of a research-based instrument that assesses conceptual understanding in an area that contains well-documented alternative conceptions. Much of the CINS's use and original validation has been relegated to undergraduate settings, but the information learned from student responses on the CINS can also potentially be a useful resource for teachers at the secondary level. Because of its structure, the CINS can have a role in eliciting alternative conceptions and induce deeper conceptual understanding by having student ideas leveraged during instruction. In a first step toward this goal, the present study further investigated the CINS's internal properties by having it administered to a group (n = 339) of students among four different biology teachers at a predominantly Latino, economically disadvantaged high school. In addition, incidences of the concept inventory's use among the teachers' practices were collected for support of its adaptability at the secondary level. Despite the teachers' initial enthusiasm for the CINS's use as an assessment tool in the present study, results from a principal components analysis demonstrate inconsistencies between the original and present validations. Results also reveal how the teachers think CINS items may be revised for future use among secondary student populations.

  10. Adaptation to Ephemeral Habitat May Overcome Natural Barriers and Severe Habitat Fragmentation in a Fire-Dependent Species, the Bachman's Sparrow (Peucaea aestivalis)

    PubMed Central

    Cerame, Blain; Cox, James A.; Brumfield, Robb T.; Tucker, James W.; Taylor, Sabrina S.

    2014-01-01

    Bachman's Sparrow (Peucaea aestivalis) is a fire-dependent species that has undergone range-wide population declines in recent decades. We examined genetic diversity in Bachman's Sparrows to determine whether natural barriers have led to distinct population units and to assess the effect of anthropogenic habitat loss and fragmentation. Genetic diversity was examined across the geographic range by genotyping 226 individuals at 18 microsatellite loci and sequencing 48 individuals at mitochondrial and nuclear genes. Multiple analyses consistently demonstrated little genetic structure and high levels of genetic variation, suggesting that populations are panmictic. Based on these genetic data, separate management units/subspecies designations or translocations to promote gene flow among fragmented populations do not appear to be necessary. Panmixia in Bachman's Sparrow may be a consequence of an historical range expansion and retraction. Alternatively, high vagility in Bachman's Sparrow may be an adaptation to the ephemeral, fire-mediated habitat that this species prefers. In recent times, high vagility also appears to have offset inbreeding and loss of genetic diversity in highly fragmented habitat. PMID:25180939

  11. Communication: Spin densities within a unitary group based spin-adapted open-shell coupled-cluster theory: Analytic evaluation of isotropic hyperfine-coupling constants for the combinatoric open-shell coupled-cluster scheme

    SciTech Connect

    Datta, Dipayan Gauss, Jürgen

    2015-07-07

    We report analytical calculations of isotropic hyperfine-coupling constants in radicals using a spin-adapted open-shell coupled-cluster theory, namely, the unitary group based combinatoric open-shell coupled-cluster (COSCC) approach within the singles and doubles approximation. A scheme for the evaluation of the one-particle spin-density matrix required in these calculations is outlined within the spin-free formulation of the COSCC approach. In this scheme, the one-particle spin-density matrix for an open-shell state with spin S and M{sub S} = + S is expressed in terms of the one- and two-particle spin-free (charge) density matrices obtained from the Lagrangian formulation that is used for calculating the analytic first derivatives of the energy. Benchmark calculations are presented for NO, NCO, CH{sub 2}CN, and two conjugated π-radicals, viz., allyl and 1-pyrrolyl in order to demonstrate the performance of the proposed scheme.

  12. A transported probability density function/photon Monte Carlo method for high-temperature oxy-natural gas combustion with spectral gas and wall radiation

    NASA Astrophysics Data System (ADS)

    Zhao, X. Y.; Haworth, D. C.; Ren, T.; Modest, M. F.

    2013-04-01

    A computational fluid dynamics model for high-temperature oxy-natural gas combustion is developed and exercised. The model features detailed gas-phase chemistry and radiation treatments (a photon Monte Carlo method with line-by-line spectral resolution for gas and wall radiation - PMC/LBL) and a transported probability density function (PDF) method to account for turbulent fluctuations in composition and temperature. The model is first validated for a 0.8 MW oxy-natural gas furnace, and the level of agreement between model and experiment is found to be at least as good as any that has been published earlier. Next, simulations are performed with systematic model variations to provide insight into the roles of individual physical processes and their interplay in high-temperature oxy-fuel combustion. This includes variations in the chemical mechanism and the radiation model, and comparisons of results obtained with versus without the PDF method to isolate and quantify the effects of turbulence-chemistry interactions and turbulence-radiation interactions. In this combustion environment, it is found to be important to account for the interconversion of CO and CO2, and radiation plays a dominant role. The PMC/LBL model allows the effects of molecular gas radiation and wall radiation to be clearly separated and quantified. Radiation and chemistry are tightly coupled through the temperature, and correct temperature prediction is required for correct prediction of the CO/CO2 ratio. Turbulence-chemistry interactions influence the computed flame structure and mean CO levels. Strong local effects of turbulence-radiation interactions are found in the flame, but the net influence of TRI on computed mean temperature and species profiles is small. The ultimate goal of this research is to simulate high-temperature oxy-coal combustion, where accurate treatments of chemistry, radiation and turbulence-chemistry-particle-radiation interactions will be even more important.

  13. Tracking the Emergence of Host-Specific Simian Immunodeficiency Virus env and nef Populations Reveals nef Early Adaptation and Convergent Evolution in Brain of Naturally Progressing Rhesus Macaques

    PubMed Central

    Lamers, Susanna L.; Nolan, David J.; Rife, Brittany D.; Fogel, Gary B.; McGrath, Michael S.; Burdo, Tricia H.; Autissier, Patrick; Williams, Kenneth C.; Goodenow, Maureen M.

    2015-01-01

    ABSTRACT While a clear understanding of the events leading to successful establishment of host-specific viral populations and productive infection in the central nervous system (CNS) has not yet been reached, the simian immunodeficiency virus (SIV)-infected rhesus macaque provides a powerful model for the study of human immunodeficiency virus (HIV) intrahost evolution and neuropathogenesis. The evolution of the gp120 and nef genes, which encode two key proteins required for the establishment and maintenance of infection, was assessed in macaques that were intravenously inoculated with the same viral swarm and allowed to naturally progress to simian AIDS and potential SIV-associated encephalitis (SIVE). Longitudinal plasma samples and immune markers were monitored until terminal illness. Single-genome sequencing was employed to amplify full-length env through nef transcripts from plasma over time and from brain tissues at necropsy. nef sequences diverged from the founder virus faster than gp120 diverged. Host-specific sequence populations were detected in nef (∼92 days) before they were detected in gp120 (∼182 days). At necropsy, similar brain nef sequences were found in different macaques, indicating convergent evolution, while gp120 brain sequences remained largely host specific. Molecular clock and selection analyses showed weaker clock-like behavior and stronger selection pressure in nef than in gp120, with the strongest nef selection in the macaque with SIVE. Rapid nef diversification, occurring prior to gp120 diversification, indicates that early adaptation of nef in the new host is essential for successful infection. Moreover, the convergent evolution of nef sequences in the CNS suggests a significant role for nef in establishing neurotropic strains. IMPORTANCE The SIV-infected rhesus macaque model closely resembles HIV-1 immunopathogenesis, neuropathogenesis, and disease progression in humans. Macaques were intravenously infected with identical viral

  14. The Limits to Adaptation; A Systems Approach

    EPA Science Inventory

    The Limits to Adaptation: A Systems Approach. The ability to adapt to climate change is delineated by capacity thresholds, after which climate damages begin to overwhelm the adaptation response. Such thresholds depend upon physical properties (natural processes and engineering...

  15. The genomics of adaptation.

    PubMed

    Radwan, Jacek; Babik, Wiesław

    2012-12-22

    The amount and nature of genetic variation available to natural selection affect the rate, course and outcome of evolution. Consequently, the study of the genetic basis of adaptive evolutionary change has occupied biologists for decades, but progress has been hampered by the lack of resolution and the absence of a genome-level perspective. Technological advances in recent years should now allow us to answer many long-standing questions about the nature of adaptation. The data gathered so far are beginning to challenge some widespread views of the way in which natural selection operates at the genomic level. Papers in this Special Feature of Proceedings of the Royal Society B illustrate various aspects of the broad field of adaptation genomics. This introductory article sets up a context and, on the basis of a few selected examples, discusses how genomic data can advance our understanding of the process of adaptation. PMID:23097510

  16. Adaptive Management of Ecosystems

    EPA Science Inventory

    Adaptive management is an approach to natural resource management that emphasizes learning through management. As such, management may be treated as experiment, with replication, or management may be conducted in an iterative manner. Although the concept has resonated with many...

  17. Effects of natural and artificial selection on survival of columnar cacti seedlings: the role of adaptation to xeric and mesic environments

    PubMed Central

    Guillén, Susana; Terrazas, Teresa; Casas, Alejandro

    2015-01-01

    Escontria chiotilla, Polaskia chichipe, and Stenocereus pruinosus are species of Mexican columnar cacti that are economically important because of their edible fruits. These species are managed by gathering fruits from the wild, silvicultural management in agroforestry systems, and cultivation in home gardens. Previous studies reported that artificial selection favored individuals that produced larger fruits, which indirectly led to the production of larger seeds and seedlings, with possible effects on survival. We hypothesized that seedlings from managed populations would be larger but more susceptible to xeric conditions than those from wild populations. We evaluated the effects of artificial and natural selection on seedling survival of the three species in wild and managed populations, which were managed with low and high intensity, respectively. We tested seedling performance in gradients of shade (0, 40, and 80%) and humidity (low and high). A GLM of seedling survival showed significant differences among species, shade, and humidity treatments, with each species having environmental requirements associated with their particular adaptations. High humidity decreased seedling survival of all species, and high solar radiation decreased survival of S. pruinosus and P. chichipe. The effect of management type was significant only in S. pruinosus. Significant differences in the initial growth of seedlings among species were detected with ANOVA. In optimal conditions, the hypocotyl and the cotyledons decreased in size and the epicotyl grew, whereas under stress, these structures remained unchanged. The optimum conditions of shade and humidity varied among species and management types. The seedlings of S. pruinosus were the largest and the most susceptible, but in all species, seedlings from managed populations were more susceptible to environmental conditions. Thus, artificial selection influenced the susceptibility of these cacti to xeric environments. PMID

  18. Evaluation of total effective dose due to certain environmentally placed naturally occurring radioactive materials using a procedural adaptation of RESRAD code.

    PubMed

    Beauvais, Z S; Thompson, K H; Kearfott, K J

    2009-07-01

    Due to a recent upward trend in the price of uranium and subsequent increased interest in uranium mining, accurate modeling of baseline dose from environmental sources of radioactivity is of increasing interest. Residual radioactivity model and code (RESRAD) is a program used to model environmental movement and calculate the dose due to the inhalation, ingestion, and exposure to radioactive materials following a placement. This paper presents a novel use of RESRAD for the calculation of dose from non-enhanced, or ancient, naturally occurring radioactive material (NORM). In order to use RESRAD to calculate the total effective dose (TED) due to ancient NORM, a procedural adaptation was developed to negate the effects of time progressive distribution of radioactive materials. A dose due to United States' average concentrations of uranium, actinium, and thorium series radionuclides was then calculated. For adults exposed in a residential setting and assumed to eat significant amounts of food grown in NORM concentrated areas, the annual dose due to national average NORM concentrations was 0.935 mSv y(-1). A set of environmental dose factors were calculated for simple estimation of dose from uranium, thorium, and actinium series radionuclides for various age groups and exposure scenarios as a function of elemental uranium and thorium activity concentrations in groundwater and soil. The values of these factors for uranium were lowest for an adult exposed in an industrial setting: 0.00476 microSv kg Bq(-1) y(-1) for soil and 0.00596 microSv m(3) Bq(-1) y(-1) for water (assuming a 1:1 234U:238U activity ratio in water). The uranium factors were highest for infants exposed in a residential setting and assumed to ingest food grown onsite: 34.8 microSv kg Bq(-1) y(-1) in soil and 13.0 microSv m(3) Bq(-1) y(-1) in water. PMID:19509509

  19. Regulation of Emotions in Socially Challenging Learning Situations: An Instrument to Measure the Adaptive and Social Nature of the Regulation Process

    ERIC Educational Resources Information Center

    Jarvenoja, Hanna; Volet, Simone; Jarvela, Sanna

    2013-01-01

    Self-regulated learning (SRL) research has conventionally relied on measures, which treat SRL as an aptitude. To study self-regulation and motivation in learning contexts as an ongoing adaptive process, situation-specific methods are needed in addition to static measures. This article presents an "Adaptive Instrument for Regulation of Emotions"…

  20. Nature of halogen bonding. A study based on the topological analysis of the Laplacian of the electron charge density and an energy decomposition analysis.

    PubMed

    Duarte, Darío J R; Sosa, Gladis L; Peruchena, Nélida M

    2013-05-01

    In this work we investigate the nature of the Cl···N interactions in complexes formed between substituted ammonium [NHn(X3-n) (with n = 0, 1, 2, 3 and X = -CH3, -F] as Lewis bases and F-Cl molecule as Lewis acid. They have been chosen as a study case due to the wide range of variation of their binding energies, BEs. Møller-Plesset [MP2/6-311++G(2d,2p)] calculations show that the BEs for this set of complexes lie in the range from 1.27 kcal/mol (in F-Cl···NF3) to 27.62 kcal/mol [in F-Cl···N(CH3)3]. The intermolecular distribution of the electronic charge density and their L(r) = -¼∇(2)ρ(r) function have been investigated within the framework of the atoms in molecules (AIM) theory. The intermolecular interaction energy decomposition has also been analyzed using the reduced variational space (RVS) method. The topological analysis of the L(r) function reveals that the local topological properties measured at the (3,+1) critical point [in L(r) topology] are good descriptors of the strength of the halogen bonding interactions. The results obtained from energy decomposition analysis indicate that electrostatic interactions play a key role in these halogen bonding interactions. These results allow us to establish that, when the halogen atom is bonded to a group with high electron-withdrawing capacity, the electrostatic interaction between the electron cloud of the Lewis base and the halogen atom unprotected nucleus of the Lewis acid produces the formation and determines the geometry of the halogen bonded complexes. In addition, a good linear relationship has been established between: the natural logarithm of the BEs and the electrostatic interaction energy between electron charge distribution of N atom and nucleus of Cl atom, denoted as V e-n(N,Cl) within the AIM theory. PMID:23076553

  1. Toward panchromatic organic functional molecules: density functional theory study on the nature of the broad UV-Vis-NIR spectra of substituted tetra(azulene)porphyrins.

    PubMed

    Qi, Dongdong; Zhang, Lijuan; Jiang, Jianzhuang

    2012-09-01

    To achieve full solar spectrum absorption of organic dyes for organic solar cells and organic solar antenna collectors, a series of tetra(azulene)porphyrin derivatives including H₂(TAzP), H₂(α-F₄TAzP), H₂(β-F₄TAzP), H₂(γ-F₄TAzP), H₂(δ-F₄TAzP), H₂(ɛ-F₄TAzP), H₂(ζ-F₄TAzP), H₂[α-(NH₂)₄TAzP], H₂[β-(NH₂)₄TAzP], H₂[γ-(NH₂)₄TAzP], H₂[δ-(NH₂)₄TAzP], H₂[ɛ-(NH₂)₄TAzP], and H₂[ζ-(NH₂)₄TAzP] were designed and their electronic absorption spectra were systematically studied on the basis of TDDFT calculations. The nature of the broad and intense electronic absorptions of H₂(TAzP) in the range of 500-1450 nm is clearly revealed. In addition, different types of π→π* electronic transitions associated with different absorption bands are revealed to correspond to different electron density moving direction between peripherally-fused ten electron-π-conjugated azulene units and the central eighteen electron-π-conjugated porphyrin core. Introduction of electron-donating groups onto the periphery of H₂(TAzP) macrocycle is revealed to be able to lead to novel NIR dyes such as H₂[α-(NH₂)₄TAzP] and H₂[ɛ-(NH₂)₄TAzP] with regulated UV-Vis-NIR absorption bands covering the full solar spectrum in the range of 300-2500 nm. In addition, the basic designing rules for panchromatic organic functional molecules based on tetrapyrrole derivatives are proposed together with the suggestions in experiments, including low molecular symmetry and narrow gap between HOMO and LUMO/LUMO+1, which will be helpful toward the design and synthesis of new panchromatic organic functional molecules. PMID:23085169

  2. Technology transfer for adaptation

    NASA Astrophysics Data System (ADS)

    Biagini, Bonizella; Kuhl, Laura; Gallagher, Kelly Sims; Ortiz, Claudia

    2014-09-01

    Technology alone will not be able to solve adaptation challenges, but it is likely to play an important role. As a result of the role of technology in adaptation and the importance of international collaboration for climate change, technology transfer for adaptation is a critical but understudied issue. Through an analysis of Global Environment Facility-managed adaptation projects, we find there is significantly more technology transfer occurring in adaptation projects than might be expected given the pessimistic rhetoric surrounding technology transfer for adaptation. Most projects focused on demonstration and early deployment/niche formation for existing technologies rather than earlier stages of innovation, which is understandable considering the pilot nature of the projects. Key challenges for the transfer process, including technology selection and appropriateness under climate change, markets and access to technology, and diffusion strategies are discussed in more detail.

  3. Saltwater spray as an agent of natural selection: no evidence of local adaptation within a coastal population of Triplasis purpurea (Poaceae).

    PubMed

    Cheplick, Gregory P; White, Timothy P

    2002-04-01

    An ability to tolerate airborne saltwater spray is critical for plant populations in coastal environments. The opportunity for continued microevolution for improved salt tolerance can exist if there is variation in the response of genetic families to saltwater spray. Our objective was to determine whether or not there was differentiation among subpopulations near (15 m) and far (80 m) from shore and among families within subpopulations in relation to the effects of salt spray on life history traits in a population of the dunegrass Triplasis purpurea. In this annual, most seeds are matured in cleistogamous spikelets on axillary, leaf-sheath enclosed panicles and show poor dispersal capacity. Plants were reared in the greenhouse from seeds of 13 and 11 families from the near and far subpopulations, respectively. Fifty percent of plants in a family were subjected to 6 seawater sprays/wk, resulting in weekly salt deposition of 213 μg/cm(2); the others were sprayed with distilled water. Data were recorded on life span, tiller numbers, root and shoot dry mass, and seed production. There was no effect of subpopulation on any measured trait and, hence, no evidence for local adaptation to salt spray. Final tiller numbers, but not dry mass or seed production, were reduced by salt spray. However, for most traits there were significant family (within subpopulation) effects, indicating genetic substructuring. Life span and mean seed mass showed a significant family by treatment interaction, indicating genetic variation in phenotypic responses to salt spray. Life span and mean seed mass were reduced by salt spray in some, but not all, families. Path analysis revealed that an increase in life span or tiller number indirectly increased seed production via direct effects on vegetative mass. For this relatively salt-tolerant T. purpurea population on the south shore of Staten Island, New York, USA, salt sprays may not be a significant agent of natural selection. However, there are

  4. Study of settlement distribution pattern in the Kolkheti lowland (Black Sea coast of Georgia) starting from early Bronze Age - natural and human influence and adaptation to landscape evolution

    NASA Astrophysics Data System (ADS)

    Elashvili, Mikheil; Akhvlediani, Dimitri; Navrozashvili, Levan; Sukhishvili, Lasha; Kirkitadze, Giorgi; Kelterbaum, Daniel; Laermans, Hannes

    2015-04-01

    During the past decades the question of a changing environment/nature became crucial. Actually we are trying to understand its nature or to predict future changes and their possible effects represent the main goals of many interdisciplinary studies. Therefore, the study of paleoenvironmental changes delivers key information for a better understanding of the whole process and especially the influence of these changes on human society. The selected research topic is dictated by the fact that the Colchis lowland played an important role in the history of old societies (countries and empires). Especially the interaction between developing human societies under the pressure of a changing environment are most interesting in this context. The Kolkheti valley and the Black Sea shore represent a region involved in many global historical events, starting from the Myth of Argonauts and followed by the ancient greek colonization, the Kingdom of Pontus ending at the Roman and Byzantine empires. River Phasis (present Rioni) was an important segment in trade way between the Mediterranean and India and the East in general. In addition it is the area of the "lost or vanished" city of Phasis, an ancient and early medieval city, founded in the 7th or 6th century BC as a colony of the Milesian Greeks at the mouth of the river Phasis, near the modern-day seaport Poti. Considering the local history of Georgia, this is the area of formation of the Kolkhys (Colchis) culture in late bronze-early iron periods, forming Colchis and later on the Lazika kingdoms. It is important to note that the archaeology and geomorphology of the seashore of Georgia is rather scarcely studied (mainly in the 1970s during soviet era). It is quite clear that the history of the region will not be deciphered without the reconstruction of the paleo and historical environment. The study based on an ongoing collaboration between the University of Cologne and the Ilia State University. Actually, geomorphological and

  5. Uncertainty in adaptive capacity

    NASA Astrophysics Data System (ADS)

    Adger, W. Neil; Vincent, Katharine

    2005-03-01

    The capacity to adapt is a critical element of the process of adaptation: it is the vector of resources that represent the asset base from which adaptation actions can be made. Adaptive capacity can in theory be identified and measured at various scales, from the individual to the nation. The assessment of uncertainty within such measures comes from the contested knowledge domain and theories surrounding the nature of the determinants of adaptive capacity and the human action of adaptation. While generic adaptive capacity at the national level, for example, is often postulated as being dependent on health, governance and political rights, and literacy, and economic well-being, the determinants of these variables at national levels are not widely understood. We outline the nature of this uncertainty for the major elements of adaptive capacity and illustrate these issues with the example of a social vulnerability index for countries in Africa. To cite this article: W.N. Adger, K. Vincent, C. R. Geoscience 337 (2005).

  6. Adaptive Natural Killer Cell and Killer Cell Immunoglobulin-Like Receptor-Expressing T Cell Responses are Induced by Cytomegalovirus and Are Associated with Protection against Cytomegalovirus Reactivation after Allogeneic Donor Hematopoietic Cell Transplantation.

    PubMed

    Davis, Zachary B; Cooley, Sarah A; Cichocki, Frank; Felices, Martin; Wangen, Rose; Luo, Xianghua; DeFor, Todd E; Bryceson, Yenan T; Diamond, Don J; Brunstein, Claudio; Blazar, Bruce R; Wagner, John E; Weisdorf, Daniel J; Horowitz, Amir; Guethlein, Lisbeth A; Parham, Peter; Verneris, Michael R; Miller, Jeffrey S

    2015-09-01

    Cytomegalovirus (CMV) reactivates in >30% of CMV-seropositive patients after allogeneic hematopoietic cell transplantation (HCT). Previously, we reported an increase of natural killer (NK) cells expressing NKG2C, CD57, and inhibitory killer cell immunoglobulin-like receptors (KIRs) in response to CMV reactivation after HCT. These NK cells persist after the resolution of infection and display "adaptive" or memory properties. Despite these findings, the differential impact of persistent/inactive versus reactivated CMV on NK versus T cell maturation after HCT from different graft sources has not been defined. We compared the phenotype of NK and T cells from 292 recipients of allogeneic sibling (n = 118) or umbilical cord blood (UCB; n = 174) grafts based on recipient pretransplantation CMV serostatus and post-HCT CMV reactivation. This cohort was utilized to evaluate CMV-dependent increases in KIR-expressing NK cells exhibiting an adaptive phenotype (NKG2C(+)CD57(+)). Compared with CMV-seronegative recipients, those who reactivated CMV had the highest adaptive cell frequencies, whereas intermediate frequencies were observed in CMV-seropositive recipients harboring persistent/nonreplicating CMV. The same effect was observed in T cells and CD56(+) T cells. These adaptive lymphocyte subsets were increased in CMV-seropositive recipients of sibling but not UCB grafts and were correlated with lower rates of CMV reactivation (sibling 33% versus UCB 51%; P < .01). These data suggest that persistent/nonreplicating recipient CMV induces rapid production of adaptive NK and T cells from mature cells from sibling but not UCB grafts. These adaptive lymphocytes are associated with protection from CMV reactivation. PMID:26055301

  7. Evolution of adaptation mechanisms: Adaptation energy, stress, and oscillating death.

    PubMed

    Gorban, Alexander N; Tyukina, Tatiana A; Smirnova, Elena V; Pokidysheva, Lyudmila I

    2016-09-21

    In 1938, Selye proposed the notion of adaptation energy and published 'Experimental evidence supporting the conception of adaptation energy.' Adaptation of an animal to different factors appears as the spending of one resource. Adaptation energy is a hypothetical extensive quantity spent for adaptation. This term causes much debate when one takes it literally, as a physical quantity, i.e. a sort of energy. The controversial points of view impede the systematic use of the notion of adaptation energy despite experimental evidence. Nevertheless, the response to many harmful factors often has general non-specific form and we suggest that the mechanisms of physiological adaptation admit a very general and nonspecific description. We aim to demonstrate that Selye׳s adaptation energy is the cornerstone of the top-down approach to modelling of non-specific adaptation processes. We analyze Selye׳s axioms of adaptation energy together with Goldstone׳s modifications and propose a series of models for interpretation of these axioms. Adaptation energy is considered as an internal coordinate on the 'dominant path' in the model of adaptation. The phenomena of 'oscillating death' and 'oscillating remission' are predicted on the base of the dynamical models of adaptation. Natural selection plays a key role in the evolution of mechanisms of physiological adaptation. We use the fitness optimization approach to study of the distribution of resources for neutralization of harmful factors, during adaptation to a multifactor environment, and analyze the optimal strategies for different systems of factors. PMID:26801872

  8. Adaptations, exaptations, and spandrels.

    PubMed

    Buss, D M; Haselton, M G; Shackelford, T K; Bleske, A L; Wakefield, J C

    1998-05-01

    Adaptation and natural selection are central concepts in the emerging science of evolutionary psychology. Natural selection is the only known causal process capable of producing complex functional organic mechanisms. These adaptations, along with their incidental by-products and a residue of noise, comprise all forms of life. Recently, S. J. Gould (1991) proposed that exaptations and spandrels may be more important than adaptations for evolutionary psychology. These refer to features that did not originally arise for their current use but rather were co-opted for new purposes. He suggested that many important phenomena--such as art, language, commerce, and war--although evolutionary in origin, are incidental spandrels of the large human brain. The authors outline the conceptual and evidentiary standards that apply to adaptations, exaptations, and spandrels and discuss the relative utility of these concepts for psychological science. PMID:9612136

  9. Genome-wide association study in arabidopsis thaliana of natural variation in seed oil melting point, a widespread adaptive trait in plants

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Seed oil melting point is an adaptive, quantitative trait determined by the relative proportions of the fatty acids that compose the oil. Micro- and macro-evolutionary evidence suggests selection has changed the melting point of seed oils to co-vary with germination temperatures because of a trade-o...

  10. "Do You Know Actimel?" The Adaptive Nature of Dialogic Teacher-Led Discussions in the CLIL Science Classroom: A Case Study

    ERIC Educational Resources Information Center

    Escobar Urmeneta, Cristina; Evnitskaya, Natalia

    2014-01-01

    This interpretive case study is framed within recent sociocultural conceptualisations of learning. It draws on research on teacher-led classroom discussions, and investigates the conversational intricacies through which "dialogicity" is accomplished in adaptive ways in one content and language integrated learning (CLIL) science…

  11. Patterns of host-parasite adaptation in three populations of monarch butterflies infected with a naturally occurring protozoan disease: virulence, resistance, and tolerance.

    PubMed

    Sternberg, Eleanore D; Li, Hui; Wang, Rebecca; Gowler, Camden; de Roode, Jacobus C

    2013-12-01

    Many studies have used host-parasite systems to study local adaptation, but few of these studies have found unequivocal evidence for adaptation. One potential reason is that most studies have focused on limited measures of host and parasite fitness that are generally assumed to be under negative frequency-dependent selection. We have used reciprocal cross-infection experiments to test for local adaptation in Hawaiian, south Floridian, and eastern North American populations of monarch butterflies and their protozoan parasites. Sympatric host-parasite combinations did not result in greater host or parasite fitness, as would be expected under coevolutionary dynamics driven by negative frequency-dependent selection. Instead, we found that Hawaiian hosts were more resistant and carried more infective and virulent parasites, which is consistent with theoretical predictions for virulence evolution and coevolutionary arms race dynamics. We also found that Hawaiian hosts were more tolerant, particularly of Hawaiian parasites, indicating that increased resistance does not preclude increased tolerance within a population and that hosts may be more tolerant of local parasites. We did not find a similar pattern in the south Floridian or eastern populations, possibly because host-parasite adaptation occurs within the context of a greater ecological community. PMID:24231547

  12. Dynamical Adaptation in Photoreceptors

    PubMed Central

    Clark, Damon A.; Benichou, Raphael; Meister, Markus; Azeredo da Silveira, Rava

    2013-01-01

    Adaptation is at the heart of sensation and nowhere is it more salient than in early visual processing. Light adaptation in photoreceptors is doubly dynamical: it depends upon the temporal structure of the input and it affects the temporal structure of the response. We introduce a non-linear dynamical adaptation model of photoreceptors. It is simple enough that it can be solved exactly and simulated with ease; analytical and numerical approaches combined provide both intuition on the behavior of dynamical adaptation and quantitative results to be compared with data. Yet the model is rich enough to capture intricate phenomenology. First, we show that it reproduces the known phenomenology of light response and short-term adaptation. Second, we present new recordings and demonstrate that the model reproduces cone response with great precision. Third, we derive a number of predictions on the response of photoreceptors to sophisticated stimuli such as periodic inputs, various forms of flickering inputs, and natural inputs. In particular, we demonstrate that photoreceptors undergo rapid adaptation of response gain and time scale, over ∼ 300 ms—i. e., over the time scale of the response itself—and we confirm this prediction with data. For natural inputs, this fast adaptation can modulate the response gain more than tenfold and is hence physiologically relevant. PMID:24244119

  13. Natural selection of adaptive mutations in non-structural genes increases trans-encapsidation of hepatitis C virus replicons lacking envelope protein genes.

    PubMed

    Fournier, Carole; Helle, François; Descamps, Véronique; Morel, Virginie; François, Catherine; Dedeurwaerder, Sarah; Wychowski, Czeslaw; Duverlie, Gilles; Castelain, Sandrine

    2013-05-01

    A trans-packaging system for hepatitis C virus (HCV) replicons lacking envelope glycoproteins was developed. The replicons were efficiently encapsidated into infectious particles after expression in trans of homologous HCV envelope proteins under the control of an adenoviral vector. Interestingly, expression in trans of core or core, p7 and NS2 with envelope proteins did not enhance trans-encapsidation. Expression of heterologous envelope proteins, in the presence or absence of heterologous core, p7 and NS2, did not rescue single-round infectious particle production. To increase the titre of homologous, single-round infectious particles in our system, successive cycles of trans-encapsidation and infection were performed. Four cycles resulted in a 100-fold increase in the yield of particles. Sequence analysis revealed a total of 16 potential adaptive mutations in two independent experiments. Except for a core mutation in one experiment, all the mutations were located in non-structural regions mainly in NS5A (four in domain III and two near the junction with the NS5B gene). Reverse genetics studies suggested that D2437A and S2443T adaptive mutations, which are located at the NS5A-B cleavage site did not affect viral replication, but enhanced the single-round infectious particles assembly only in trans-encapsidation model. In conclusion, our trans-encapsidation system enables the production of HCV single-round infectious particles. This system is adaptable and can positively select variants. The adapted variants promote trans-encapsidation and should constitute a valuable tool in the development of replicon-based HCV vaccines. PMID:23288424

  14. Theory of psychological adaptive modes.

    PubMed

    Lehti, Juha

    2016-05-01

    When an individual is facing a stressor and normal stress-response mechanism cannot guarantee sufficient adaptation, special emotional states, adaptive modes, are activated (for example a depressive reaction). Adaptive modes are involuntary states of mind, they are of comprehensive nature, they interfere with normal functioning, and they cannot be repressed or controlled the same way as many emotions. Their transformational nature differentiates them from other emotional states. The object of the adaptive mode is to optimize the problem-solving abilities according to the situation that has provoked the mode. Cognitions and emotions during the adaptive mode are different than in a normal mental state. These altered cognitions and emotional reactions guide the individual to use the correct coping skills in order to deal with the stressor. Successful adaptation will cause the adaptive mode to fade off since the adaptive mode is no longer necessary, and the process as a whole will lead to raised well-being. However, if the adaptation process is inadequate, then the transformation period is prolonged, and the adaptive mode will turn into a dysfunctional state. Many psychiatric disorders are such maladaptive processes. The maladaptive processes can be turned into functional ones by using adaptive skills that are used in functional adaptive processes. PMID:27063089

  15. Transformational adaptation when incremental adaptations to climate change are insufficient

    PubMed Central

    Kates, Robert W.; Travis, William R.; Wilbanks, Thomas J.

    2012-01-01

    All human–environment systems adapt to climate and its natural variation. Adaptation to human-induced change in climate has largely been envisioned as increments of these adaptations intended to avoid disruptions of systems at their current locations. In some places, for some systems, however, vulnerabilities and risks may be so sizeable that they require transformational rather than incremental adaptations. Three classes of transformational adaptations are those that are adopted at a much larger scale, that are truly new to a particular region or resource system, and that transform places and shift locations. We illustrate these with examples drawn from Africa, Europe, and North America. Two conditions set the stage for transformational adaptation to climate change: large vulnerability in certain regions, populations, or resource systems; and severe climate change that overwhelms even robust human use systems. However, anticipatory transformational adaptation may be difficult to implement because of uncertainties about climate change risks and adaptation benefits, the high costs of transformational actions, and institutional and behavioral actions that tend to maintain existing resource systems and policies. Implementing transformational adaptation requires effort to initiate it and then to sustain the effort over time. In initiating transformational adaptation focusing events and multiple stresses are important, combined with local leadership. In sustaining transformational adaptation, it seems likely that supportive social contexts and the availability of acceptable options and resources for actions are key enabling factors. Early steps would include incorporating transformation adaptation into risk management and initiating research to expand the menu of innovative transformational adaptations. PMID:22509036

  16. Adaptive SPECT

    PubMed Central

    Barrett, Harrison H.; Furenlid, Lars R.; Freed, Melanie; Hesterman, Jacob Y.; Kupinski, Matthew A.; Clarkson, Eric; Whitaker, Meredith K.

    2008-01-01

    Adaptive imaging systems alter their data-acquisition configuration or protocol in response to the image information received. An adaptive pinhole single-photon emission computed tomography (SPECT) system might acquire an initial scout image to obtain preliminary information about the radiotracer distribution and then adjust the configuration or sizes of the pinholes, the magnifications, or the projection angles in order to improve performance. This paper briefly describes two small-animal SPECT systems that allow this flexibility and then presents a framework for evaluating adaptive systems in general, and adaptive SPECT systems in particular. The evaluation is in terms of the performance of linear observers on detection or estimation tasks. Expressions are derived for the ideal linear (Hotelling) observer and the ideal linear (Wiener) estimator with adaptive imaging. Detailed expressions for the performance figures of merit are given, and possible adaptation rules are discussed. PMID:18541485

  17. The Limits to Adaptation: A Systems Approach

    EPA Science Inventory

    The ability to adapt to climate change is delineated by capacity thresholds, after which climate damages begin to overwhelm the adaptation response. Such thresholds depend upon physical properties (natural processes and engineering parameters), resource constraints (expressed th...

  18. A holistic strategy for adaptive land management

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Adaptive management is widely applied to natural resources management. Adaptive management can be generally defined as an iterative decision-making process that incorporates formulation of management objectives, actions designed to address these objectives, monitoring of results, and repeated adapta...

  19. Toward optimizing the delivery and use of climate science for natural resource management: lessons learned from recent adaptation efforts in the southwestern U.S.

    NASA Astrophysics Data System (ADS)

    Enquist, C.

    2014-12-01

    Within the past decade, a wealth of federal, state, and NGO-driven initiatives has emerged across managed landscapes in the United States with the goal of facilitating a coordinated response to rapidly changing climate and environmental conditions. In addition to acquisition and translation of the latest climate science, climate vulnerability assessment and scenario planning at multiple spatial and temporal scales are typically major components of such broad adaptation efforts. Numerous approaches for conducting this work have emerged in recent years and have culminated in general guidance and trainings for resource professionals that are specifically designed to help practitioners face the challenges of climate change. In particular, early engagement of stakeholders across multiple jurisdictions is particularly critical to cultivate buy-in and other enabling conditions for moving the science to on-the-ground action. I report on a suite of adaptation efforts in the southwestern US and interior Rockies, highlighting processes used, actions taken, lessons learned, and recommended next steps to facilitate achieving desired management outcomes. This includes a discussion of current efforts to optimize funding for actionable climate science, formalize science-management collaborations, and facilitate new investments in approaches for strategic climate-informed monitoring and evaluation.

  20. Exploring the Nature of the Intention, Meaning and Perception Process of the Neuro-occupation Model to Understand Adaptation to Change.

    PubMed

    Derakhshanrad, Seyed Alireza; Piven, Emily; Hosseini, Seyed Ali; Shahboulaghi, Farahnaz Mohammadi; Nazeran, Homer; Rassafiani, Mehdi

    2016-03-01

    The theoretical model of neuro-occupation, intention, meaning and perception, sought to describe the symbiotic relationship between occupation and the brain, as a chaotic, self-organized, complex system. Lack of evidence has limited its applicability to practice. The aim of this study was to track the postulates of the model within the daily experiences of subjects. Structured matrices were created for content analysis, using a qualitative multiple-case-study design, typically used for testing models. An underpinning principle of the model, defined a circular causality feedback process, which was confirmed as described through tracing the repetitive processes within the lived experience of two Iranian men. The process suggested that continual adaptation occurred in lives interrupted by cerebrovascular accident, which enabled the subjects to return to expression of meaning through purposeful occupation and continually re-shaped their perceptions. The primary limitation of this study was that it was the earliest attempt to test the model and to substantiate the process by comparing the similarities and differences between too few subjects. Future research should identify the same process in more subjects and validate a practical assessment tool for clients. These findings may inform practitioners about intentional use of occupational challenges to elicit adaptive behaviours in clients. PMID:26234718

  1. An adaptive contextual quantum language model

    NASA Astrophysics Data System (ADS)

    Li, Jingfei; Zhang, Peng; Song, Dawei; Hou, Yuexian

    2016-08-01

    User interactions in search system represent a rich source of implicit knowledge about the user's cognitive state and information need that continuously evolves over time. Despite massive efforts that have been made to exploiting and incorporating this implicit knowledge in information retrieval, it is still a challenge to effectively capture the term dependencies and the user's dynamic information need (reflected by query modifications) in the context of user interaction. To tackle these issues, motivated by the recent Quantum Language Model (QLM), we develop a QLM based retrieval model for session search, which naturally incorporates the complex term dependencies occurring in user's historical queries and clicked documents with density matrices. In order to capture the dynamic information within users' search session, we propose a density matrix transformation framework and further develop an adaptive QLM ranking model. Extensive comparative experiments show the effectiveness of our session quantum language models.

  2. Adaptation of a commercially available 200 kW natural gas fuel cell power plant for operation on a hydrogen rich gas stream

    SciTech Connect

    Maston, V.A.

    1997-12-01

    International Fuel Cells (IFC) has designed a hydrogen fueled fuel cell power plant based on a modification of its standard natural gas fueled PC25{trademark} C fuel cell power plant. The natural gas fueled PC25 C is a 200 kW, fuel cell power plant that is commercially available. The program to accomplish the fuel change involved deleting the natural gas processing elements, designing a new fuel pretreatment subsystem, modifying the water and thermal management subsystem, developing a hydrogen burner to combust unconsumed hydrogen, and modifying the control system. Additionally, the required modifications to the manufacturing and assembly procedures necessary to allow the hydrogen fueled power plant to be manufactured in conjunction with the on-going production of the standard PC25 C power plants were identified. This work establishes the design and manufacturing plan for the 200 kW hydrogen fueled PC25 power plant.

  3. Computational chemistry of natural products: a comparison of the chemical reactivity of isonaringin calculated with the M06 family of density functionals.

    PubMed

    Glossman-Mitnik, Daniel

    2014-07-01

    The M06 family of density functionals has been assessed for the calculation of the molecular structure and properties of the Isonaringin flavonoid that can be an interesting material for dye-sensitized solar cells (DSSC). The chemical reactivity descriptors have been calculated through chemical reactivity theory within DFT (CR-DFT). The active sites for nucleophilic and electrophilic attacks have been chosen by relating them to the Fukui function indices and the dual descriptor f ((2))(r). A comparison between the descriptors calculated through vertical energy values and those arising from the Janak's theorem approximation have been performed in order to check for the validity of the last procedure. PMID:24992989

  4. Adapting to the Environment.

    ERIC Educational Resources Information Center

    Kovach, Amy L.

    2003-01-01

    Presents an activity on natural selection and how the peppered moth's adaptive values for their colors changed during the Industrial Revolution in Manchester, England, influencing their survival and ultimately affecting the survival of their offspring. Includes activity objectives. (Author/KHR)

  5. Adapting Bulls to Florida

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The adaptation of bulls used for natural breeding purposes to the Gulf Coast region of the United States including all of Florida is an important topic. Nearly 40% of the U.S. cow/calf population resides in the Gulf Coast and Southeast. Thus, as A.I. is relatively rare, the number of bulls used for ...

  6. Thiol dependent NF-κB suppression and inhibition of T-cell mediated adaptive immune responses by a naturally occurring steroidal lactone Withaferin A.

    PubMed

    Gambhir, Lokesh; Checker, Rahul; Sharma, Deepak; Thoh, M; Patil, Anand; Degani, M; Gota, Vikram; Sandur, Santosh K

    2015-12-01

    Withaferin A (WA), a steroidal lactone isolated from ayurvedic medicinal plant Withania somnifera, was shown to inhibit tumor growth by inducing oxidative stress and suppressing NF-κB pathway. However, its effect on T-cell mediated adaptive immune responses and the underlying mechanism has not been investigated. Since both T-cell responses and NF-κB pathway are known to be redox sensitive, the present study was undertaken to elucidate the effect of WA on adaptive immune responses in vitro and in vivo. WA inhibited mitogen induced T-cell and B-cell proliferation in vitro without inducing any cell death. It inhibited upregulation of T-cell (CD25, CD69, CD71 and CD54) and B-cell (CD80, CD86 and MHC-II) activation markers and secretion of Th1 and Th2 cytokines. WA induced oxidative stress by increasing the basal ROS levels and the immunosuppressive effects of WA were abrogated only by thiol anti-oxidants. The redox modulatory effects of WA in T-cells were attributed to its ability to directly interact with free thiols. WA inhibited NF-κB nuclear translocation in lymphocytes and prevented the direct binding of nuclear NF-κB to its consensus sequence. MALDI-TOF analysis using a synthetic NF-κB-p50 peptide containing Cys-62 residue suggested that WA can modify the cysteine residue of NF-κB. The pharmacokinetic studies for WA were also carried out and in vivo efficacy of WA was studied using mouse model of Graft-versus-host disease. In conclusion, WA is a potent inhibitor of T-cell responses and acts via a novel thiol dependent mechanism and inhibition of NF-κB pathway. PMID:26408225

  7. LATITUDINAL ADAPTATION OF SWITCHGRASS POPULATIONS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Switchgrass (Panicum virgatum L.) is a widely adapted warm-season perennial that has considerable potential as a biofuel crop. Broad species adaptation, natural selection, and photoperiodism have combined to create considerable ecotypic differentiation in switchgrass. The objective of this study w...

  8. Adaptive Femtosecond Quantum Control

    NASA Astrophysics Data System (ADS)

    Gerber, Gustav

    2003-03-01

    Obtaining active control over the dynamics of quantum-mechanical systems is a fascinating perspective in modern physics. A promising tool for this purpose is available with femtosecond laser technologies. The intrinsically broad spectral distribution and the phase function of femtosecond laser pulses can be specifically manipulated by pulse shapers to drive molecular systems coherently into the desired reaction pathways [1]. The approach of adaptive femtosecond quantum control follows the suggestion of Judson and Rabitz [2], in which a computer-controlled pulse shaper is used in combination with a learning algorithm [3] and direct feedback from the experiment to achieve coherent control over quantum-mechanical processes in an automated fashion, without requiring any model for the system's response. This technique can be applied to the control of gas-phase photodissociation processes [4]. Different bond-cleaving reactions can be preferentially selected, resulting in chemically different products. Prior knowledge about molecular Hamiltonians or reaction mechanisms is not required in this automated control loop, and this scheme works for complex systems. Adaptive pulse-shaping techniques can be transferred to the control of photoprocesses in the liquid phase as well, motivated by the wish to achieve control at particle densities high enough for (bimolecular) synthetic-chemical applications. Chemically selective molecular excitation is achieved by many-parameter adaptive quantum control [5], despite the failure of typical single-parameter approaches (such as wavelength control, intensity control, or linear chirp control). This experiment demonstrates that photoprocesses in two different molecular species can be controlled simultaneously. Applications are envisioned in bimolecular reaction control where specific educt molecules could selectively be "activated" for purposes of chemical synthesis. A new technological development further increases the possibilities and

  9. Hydropower, adaptive management, and Biodiversity

    NASA Astrophysics Data System (ADS)

    Wieringa, Mark J.; Morton, Anthony G.

    1996-11-01

    Adaptive management is a policy framework within which an iterative process of decision making is followed based on the observed responses to and effectiveness of previous decisions. The use of adaptive management allows science-based research and monitoring of natural resource and ecological community responses, in conjunction with societal values and goals, to guide decisions concerning man's activities. The adaptive management process has been proposed for application to hydropower operations at Glen Canyon Dam on the Colorado River, a situation that requires complex balancing of natural resources requirements and competing human uses. This example is representative of the general increase in public interest in the operation of hydropower facilities and possible effects on downstream natural resources and of the growing conflicts between uses and users of river-based resources. This paper describes the adaptive management process, using the Glen Canyon Dam example, and discusses ways to make the process work effectively in managing downstream natural resources and biodiversity.

  10. Density Visualization

    ERIC Educational Resources Information Center

    Keiter, Richard L.; Puzey, Whitney L.; Blitz, Erin A.

    2006-01-01

    Metal rods of high purity for many elements are now commercially available and may be used to construct a display of relative densities. We have constructed a display with nine metal rods (Mg, Al, Ti, V, Fe, Cu, Ag, Pb, and W) of equal mass whose densities vary from 1.74 to 19.3 g cm[superscript -3]. The relative densities of the metals may be…

  11. Land use Effects on Storage, Stability and Structure of Organic Carbon in Soil Density Fractions Revealed by 13C Natural Abundance and CPMAS 13C NMR

    NASA Astrophysics Data System (ADS)

    Flessa, H.; Helfrich, M.; John, B.; Yamashita, T.; Ludwig, B.

    2004-12-01

    The type of land use and soil cultivation are important factors controlling organic carbon storage (SOC) in soils and they can also influence the relative importance, the structure, and the stability of different SOC pools. The objectives of our study were: i) to quantify the SOC stocks in different density fractions (mineral-associated soil organic matter > 2 g cm-3 (Mineral-SOM), free particulate organic matter < 1.6 g cm-3 (free POM), light occluded particulate organic matter < 1.6 g cm-3 (occluded POM<1.6) and dense occluded particulate organic matter 1.6 to 2.0 g cm-3 (occluded POM1.6-2.0)) of silty soils under different land use (spruce forest, grassland, maize, wheat), ii) to determine the structure of these SOC fractions by CPMAS 13C NMR spectroscopy, and iii) to analyse the stability of these SOC fractions in the maize soil on the basis of the stable isotope composition of SOC. The SOC concentration in the A horizon increased in the order wheat (12.7 g kg-1) < maize (13.0 g kg-1) < grassland (24.5 g kg-1) < spruce (40.5 g kg-1). The major part (86-91%) of the SOC was associated with the heavy mineral fraction at the grassland, maize and wheat site. In the A horizon of the spruce soil, the particulate organic matter accounted for 52% of the total SOC content. The chemical structure of the soil organic matter (SOM) was influenced by litter quality, the intensity of litter decomposition and the related production and storage of microbially-derived substances. SOM of the acid forest soil was characterized by large amounts of POM with a high content of spruce litter-derived alkyl C. In the biologically more active grassland and maize soil, litter-derived POM was decomposed more rapidly and SOC stocks were dominated by mineral-associated SOM which contained greater proportions of aryl and carbonyl C. The cultivation of the grassland soil induced enhanced mineralization of POM and in particular of mineral-associated SOM. The faster SOC turnover was associated

  12. Measuring opportunity for natural selection: Adaptation among two linguistically cognate tribes inhabiting two eco-situations of North-East India

    PubMed Central

    Sarma, Maitreyee

    2013-01-01

    BACKGROUND: Numerous literature on the migration of Mishings point out to the fact that the Mishing and the Minyong are two culturally and linguistically cognate tribes that co-existed in the same ecology in the hills of Arunachal Pradesh. The Mishing tribe after migration, now inhabits flood-prone areas of Brahmaputra valley of Assam. AIM: The study aims to measure the adaptation process of these two cognate tribes inhabiting two different ecologies at present: Hills and plains by calculating the index of selection intensity by Crow’s and Johnston and Kensinger’s formulae. MATERIALS AND METHODS: The reproductive histories of 77 Mishing mothers of completed fertility inhabiting a flood affected village of Assam and 74 Minyong mothers inhabiting a hilly village of Arunachal Pradesh are selected. RESULTS AND DISCUSSION: The Minyongs show higher average fertility than the Mishings. The proportion of embryonic death is higher, and child death is lower among the Mishings (0.1661; 0.1623) than the Minyongs (0.1319; 0.2238). The index of selection due to mortality component is contributing more toward the total index of selection in both the tribes. CONCLUSION: The contribution of mortality component is sizeable to the total selection like many other tribes of North-East India. Higher proportion of embryonic deaths among the Mishings infers that the causes are mostly biological whereas, the higher proportion of child deaths among the Minyongs infers that the causes are mostly socio-cultural. PMID:24019616

  13. Density and wave function analysis of actinide complexes: What can fuzzy atom, atoms-in-molecules, Mulliken, Löwdin, and natural population analysis tell us?

    NASA Astrophysics Data System (ADS)

    Clark, Aurora E.; Sonnenberg, Jason L.; Hay, P. Jeffrey; Martin, Richard L.

    2004-08-01

    Recent advances in computational methods have made it possible to calculate the wave functions for a wide variety of simple actinide complexes. Equally important is the ability to analyze the information contained therein and produce a chemically meaningful understanding of the electronic structure. Yet the performance of the most common wave function analyses for the calculation of atomic charge and bond order has not been thoroughly investigated for actinide systems. This is particularly relevant because the calculation of charge and bond order even in transition metal complexes is known to be fraught with difficulty. Here we use Mulliken, Löwdin, natural population analysis, atoms-in-molecules (AIM), and fuzzy atom techniques to determine the charges and bond orders of UO22+, PuO22+, UO2, UO2Cl42-, UO2(CO)52+, UO2(CO)42+, UO2(CN)53-, UO2(CN)42-, UO2(OH)53-, and UO2(OH)42-. This series exhibits a clear experimental and computational trend in bond lengths and vibrational frequencies. The results indicate that Mulliken and Löwdin populations and bond orders are unreliable for the actinyls. Natural population analysis performs well after modification of the partitioning of atomic orbitals to include the 6d in the valence space. The AIM topological partitioning is insensitive to the electron donating ability of the equatorial ligands and the relative atomic volume of the formally U(VI) center is counterintuitively larger than that of O2- in the UO22+ core. Lastly, the calibrated fuzzy atom method yields reasonable bond orders for the actinyls at significantly reduced computational cost relative to the AIM analysis.

  14. Nature of the empty states and signature of the charge density wave instability and upper Peierls transition of TTF-TCNQ by temperature-dependent NEXAFS spectroscopy

    NASA Astrophysics Data System (ADS)

    Chernenkaya, Alisa; Medjanik, Katerina; Nagel, Peter; Merz, Michael; Schuppler, Stefan; Canadell, Enric; Pouget, Jean-Paul; Schönhense, Gerd

    2015-01-01

    The electronic structure of TTF-TCNQ was studied by near-edge X-ray absorption fine structure (NEXAFS) spectroscopy in order to detect a spectroscopic signature of the phase transitions, especially that occurring at 54 K, which is related to a Peierls gap opening on the TCNQ stacks. All unoccupied TCNQ orbitals predicted by first-principles calculations and, in particular the pair σ ∗( π( a g , b 3 u )), located in the cyano groups, are clearly resolved in our experimental data. The latter orbital was observed for the first time in our NEXAFS spectra. The temperature dependence of NEXAFS peak intensities gives evidence of a subtle modification of the electronic structure when the charge density wave (CDW) fluctuations develop as the Peierls transition of the TCNQ stacks is approached from higher temperatures. These changes are explained on the basis of the charge transfer, the shape of the lower empty TCNQ molecular orbitals and the deformation of TCNQ during the pre-transitional CDW fluctuations. Finally the data suggest that the internal stack deformation consisting in a substantial out of plane displacement of the central ring with respect to the cyano-groups allows to gain C α -C α bonding energy which helps the stabilization of the Peierls transition on the TCNQ stack.

  15. Aging and dark adaptation.

    PubMed

    Jackson, G R; Owsley, C; McGwin, G

    1999-11-01

    Older adults have serious difficulty seeing under low illumination and at night, even in the absence of ocular disease. Optical changes in the aged eye, such as pupillary miosis and increased lens density, cannot account for the severity of this problem, and little is known about its neural basis. Dark adaptation functions were measured on 94 adults ranging in age from the 20s to the 80s to assess the rate of rod-mediated sensitivity recovery after exposure to a 98% bleach. Fundus photography and a grading scale were used to characterize macular health in subjects over age 49 in order to control for macular disease. Thresholds for each subject were corrected for lens density based on individual estimates, and pupil diameter was controlled. Results indicated that during human aging there is a dramatic slowing in rod-mediated dark adaptation that can be attributed to delayed rhodopsin regeneration. During the second component of the rod-mediated phase of dark adaptation, the rate of sensitivity recovery decreased 0.02 log unit/min per decade, and the time constant of rhodopsin regeneration increased 8.4 s/decade. The amount of time to reach within 0.3 log units of baseline scotopic sensitivity increased 2.76 min/decade. These aging-related changes in rod-mediated dark adaptation may contribute to night vision problems commonly experienced by the elderly. PMID:10748929

  16. Natural gradient learning algorithms for RBF networks.

    PubMed

    Zhao, Junsheng; Wei, Haikun; Zhang, Chi; Li, Weiling; Guo, Weili; Zhang, Kanjian

    2015-02-01

    Radial basis function (RBF) networks are one of the most widely used models for function approximation and classification. There are many strange behaviors in the learning process of RBF networks, such as slow learning speed and the existence of the plateaus. The natural gradient learning method can overcome these disadvantages effectively. It can accelerate the dynamics of learning and avoid plateaus. In this letter, we assume that the probability density function (pdf) of the input and the activation function are gaussian. First, we introduce natural gradient learning to the RBF networks and give the explicit forms of the Fisher information matrix and its inverse. Second, since it is difficult to calculate the Fisher information matrix and its inverse when the numbers of the hidden units and the dimensions of the input are large, we introduce the adaptive method to the natural gradient learning algorithms. Finally, we give an explicit form of the adaptive natural gradient learning algorithm and compare it to the conventional gradient descent method. Simulations show that the proposed adaptive natural gradient method, which can avoid the plateaus effectively, has a good performance when RBF networks are used for nonlinear functions approximation. PMID:25380332

  17. Learning and Domain Adaptation

    NASA Astrophysics Data System (ADS)

    Mansour, Yishay

    Domain adaptation is a fundamental learning problem where one wishes to use labeled data from one or several source domains to learn a hypothesis performing well on a different, yet related, domain for which no labeled data is available. This generalization across domains is a very significant challenge for many machine learning applications and arises in a variety of natural settings, including NLP tasks (document classification, sentiment analysis, etc.), speech recognition (speakers and noise or environment adaptation) and face recognition (different lighting conditions, different population composition).

  18. Verification of Adaptive Systems

    SciTech Connect

    Pullum, Laura L; Cui, Xiaohui; Vassev, Emil; Hinchey, Mike; Rouff, Christopher; Buskens, Richard

    2012-01-01

    Adaptive systems are critical for future space and other unmanned and intelligent systems. Verification of these systems is also critical for their use in systems with potential harm to human life or with large financial investments. Due to their nondeterministic nature and extremely large state space, current methods for verification of software systems are not adequate to provide a high level of assurance for them. The combination of stabilization science, high performance computing simulations, compositional verification and traditional verification techniques, plus operational monitors, provides a complete approach to verification and deployment of adaptive systems that has not been used before. This paper gives an overview of this approach.

  19. SELEX_DB: a database on in vitro selected oligomers adapted for recognizing natural sites and for analyzing both SNPs and site-directed mutagenesis data.

    PubMed

    Ponomarenko, Julia V; Orlova, Galina V; Frolov, Anatoly S; Gelfand, Mikhail S; Ponomarenko, Mikhail P

    2002-01-01

    SELEX_DB is an online resource containing both the experimental data on in vitro selected DNA/RNA oligomers (aptamers) and the applets for recognition of these oligomers. Since in vitro experimental data are evidently system-dependent, the new release of the SELEX_DB has been supplemented by the database SYSTEM storing the experimental design. In addition, the recognition applet package, SELEX_TOOLS, applying in vitro selected data to annotation of the genome DNA, is accompanied by the cross-validation test database CROSS_TEST discriminating the sites (natural or other) related to in vitro selected sites out of random DNA. By cross-validation testing, we have unexpectedly observed that the recognition accuracy increases with the growth of homology between the training and test sets of protein binding sequences. For natural sites, the recognition accuracy was lower than that for the nearest protein homologs and higher than that for distant homologs and non-homologous proteins binding the common site. The current SELEX_DB release is available at http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/. PMID:11752291

  20. Adaptation in Collaborative Governance Regimes

    NASA Astrophysics Data System (ADS)

    Emerson, Kirk; Gerlak, Andrea K.

    2014-10-01

    Adaptation and the adaptive capacity of human and environmental systems have been of central concern to natural and social science scholars, many of whom characterize and promote the need for collaborative cross-boundary systems that are seen as flexible and adaptive by definition. Researchers who study collaborative governance systems in the public administration, planning and policy literature have paid less attention to adaptive capacity specifically and institutional adaptation in general. This paper bridges the two literatures and finds four common dimensions of capacity, including structural arrangements, leadership, knowledge and learning, and resources. In this paper, we focus on institutional adaptation in the context of collaborative governance regimes and try to clarify and distinguish collaborative capacity from adaptive capacity and their contributions to adaptive action. We posit further that collaborative capacities generate associated adaptive capacities thereby enabling institutional adaptation within collaborative governance regimes. We develop these distinctions and linkages between collaborative and adaptive capacities with the help of an illustrative case study in watershed management within the National Estuary Program.

  1. Adaptation in collaborative governance regimes.

    PubMed

    Emerson, Kirk; Gerlak, Andrea K

    2014-10-01

    Adaptation and the adaptive capacity of human and environmental systems have been of central concern to natural and social science scholars, many of whom characterize and promote the need for collaborative cross-boundary systems that are seen as flexible and adaptive by definition. Researchers who study collaborative governance systems in the public administration, planning and policy literature have paid less attention to adaptive capacity specifically and institutional adaptation in general. This paper bridges the two literatures and finds four common dimensions of capacity, including structural arrangements, leadership, knowledge and learning, and resources. In this paper, we focus on institutional adaptation in the context of collaborative governance regimes and try to clarify and distinguish collaborative capacity from adaptive capacity and their contributions to adaptive action. We posit further that collaborative capacities generate associated adaptive capacities thereby enabling institutional adaptation within collaborative governance regimes. We develop these distinctions and linkages between collaborative and adaptive capacities with the help of an illustrative case study in watershed management within the National Estuary Program. PMID:25073764

  2. The Adaptive Change of HLA-DRB1 Allele Frequencies Caused by Natural Selection in a Mongolian Population That Migrated to the South of China

    PubMed Central

    Sun, Hao; Yang, Zhaoqing; Lin, Keqin; Liu, Shuyuan; Huang, Kai; Wang, Xiuyun; Chu, Jiayou; Huang, Xiaoqin

    2015-01-01

    Pathogen-driven balancing selection determines the richness of human leukocyte antigen (HLA) alleles. Changes in the pathogen spectrum may cause corresponding changes in HLA loci. Approximately 700 years ago, a Mongolian population moved from the north of China to the Yunnan region in the south of China. The pathogen spectrum in the south of China differs from that in the north. In this study, changes in the HLA genes in the Yunnan Mongolian population, as well as the underlying mechanism, were investigated. A sequence-based typing method (SBT) was used to genotype HLA-DRB1 in 470 individuals from two Mongolian populations and another five ethnic groups. Meanwhile, 10 autosomal short tandem repeats (STRs) were genotyped to assess the influence of genetic background on HLA-DRB1 frequencies. The frequencies of certain alleles changed significantly in the Mongolian population that migrated to Yunnan. For example, DRB1*12:02:01 increased from 6.1% to 35.4%. STR analysis excluded the possibility of a recent bottleneck and indicated that 50% of the genetic consistency between northern and southern Mongolians; Tajima's D value for HLA-DRB1 exon2 and dN/dS analysis showed that the HLA-DRB1 genes in both Mongolian populations were under balancing selection. However, the sites under natural selection changed. We proposed that the dramatically change of HLA frequencies in southern Mongolian was caused by a combination of inter-population gene flow and natural selection. Certain diseases specific to the south of China, such as malaria, may be the driving force behind the enhanced DRB1*12:02:01 frequency. PMID:26230582

  3. Nature vs. nurture in the low-density environment: structure and evolution of early-type dwarf galaxies in poor groups

    NASA Astrophysics Data System (ADS)

    Annibali, F.; Grützbauch, R.; Rampazzo, R.; Bressan, A.; Zeilinger, W. W.

    2011-04-01

    We present the stellar population properties of 13 dwarf galaxies residing in poor groups (low-density environment, LDE) observed with VIMOS at VLT. Ages, metallicities, and [α/Fe] ratios were derived within an r < re/2 aperture from the Lick indices Hβ, Mgb, Fe5270, and Fe5335 through comparison with our simple stellar population (SSP) models that account for variable [α/Fe] ratios. For a fiducial subsample of 10 early-type dwarfs, we derived median values and scatters around the medians of 5.7 ± 4.4 Gyr, -0.26 ± 0.28, and -0.04 ± 0.33 for age, log Z/Z⊙, and [α/Fe] , respectively. For a selection of bright early-type galaxies (ETGs) from an earlier sample residing in a comparable environment, we derive median values of 9.8 ± 4.1 Gyr, 0.06 ± 0.16, and 0.18 ± 0.13 for the same stellar population parameters. It follows that dwarfs are on average younger, less metal rich, and less enhanced in the α-elements than giants, in agreement with the extrapolation to the low-mass regime of the scaling relations derived for giant ETGs. From the total (dwarf + giant) sample, we find that age ∝ σ0.39 ± 0.22, Z ∝ σ0.80 ± 0.16, and α/Fe ∝ σ0.42 ± 0.22. We also find correlations with morphology, in the sense that the metallicity and the [α/Fe] ratio increase with the Sersic index n or with the bulge-to-total light fraction B/T. The presence of a strong morphology-[α/Fe] relation appears to contradict the possible evolution along the Hubble sequence from low B/T (low n) to high B/T (high n) galaxies. We also investigate the role played by environment by comparing the properties of our LDE dwarfs with those of Coma red passive dwarfs from the literature. We find possible evidence that LDE dwarfs experienced more prolonged star formations than Coma dwarfs, however larger data samples are needed to draw firmer conclusions. Based on observations obtained at the European Southern Observatory, La Silla, Chile.

  4. The nature of chemical bonding in actinide and lanthanide ferrocyanides determined by X-ray absorption spectroscopy and density functional theory.

    PubMed

    Dumas, Thomas; Guillaumont, Dominique; Fillaux, Clara; Scheinost, Andreas; Moisy, Philippe; Petit, Sébastien; Shuh, David K; Tyliszczak, Tolek; Den Auwer, Christophe

    2016-01-28

    The electronic properties of actinide cations are of fundamental interest to describe intramolecular interactions and chemical bonding in the context of nuclear waste reprocessing or direct storage. The 5f and 6d orbitals are the first partially or totally vacant states in these elements, and the nature of the actinide ligand bonds is related to their ability to overlap with ligand orbitals. Because of its chemical and orbital selectivities, X-ray absorption spectroscopy (XAS) is an effective probe of actinide species frontier orbitals and for understanding actinide cation reactivity toward chelating ligands. The soft X-ray probes of the light elements provide better resolution than actinide L3-edges to obtain electronic information from the ligand. Thus coupling simulations to experimental soft X-ray spectral measurements and complementary quantum chemical calculations yields quantitative information on chemical bonding. In this study, soft X-ray XAS at the K-edges of C and N, and the L2,3-edges of Fe was used to investigate the electronic structures of the well-known ferrocyanide complexes K4Fe(II)(CN)6, thorium hexacyanoferrate Th(IV)Fe(II)(CN)6, and neodymium hexacyanoferrate KNd(III)Fe(II)(CN)6. The soft X-ray spectra were simulated based on quantum chemical calculations. Our results highlight the orbital overlapping effects and atomic effective charges in the Fe(II)(CN)6 building block. In addition to providing a detailed description of the electronic structure of the ferrocyanide complex (K4Fe(II)(CN)6), the results strongly contribute to confirming the actinide 5f and 6d orbital oddity in comparison to lanthanide 4f and 5d. PMID:26733312

  5. Bone Density

    MedlinePlus

    ... bone health. It compares your bone density, or mass, to that of a healthy person who is ... Whether your osteoporosis treatment is working Low bone mass that is not low enough to be osteoporosis ...

  6. Classifying climate change adaptation frameworks

    NASA Astrophysics Data System (ADS)

    Armstrong, Jennifer

    2014-05-01

    Complex socio-ecological demographics are factors that must be considered when addressing adaptation to the potential effects of climate change. As such, a suite of deployable climate change adaptation frameworks is necessary. Multiple frameworks that are required to communicate the risks of climate change and facilitate adaptation. Three principal adaptation frameworks have emerged from the literature; Scenario - Led (SL), Vulnerability - Led (VL) and Decision - Centric (DC). This study aims to identify to what extent these adaptation frameworks; either, planned or deployed are used in a neighbourhood vulnerable to climate change. This work presents a criterion that may be used as a tool for identifying the hallmarks of adaptation frameworks and thus enabling categorisation of projects. The study focussed on the coastal zone surrounding the Sizewell nuclear power plant in Suffolk in the UK. An online survey was conducted identifying climate change adaptation projects operating in the study area. This inventory was analysed to identify the hallmarks of each adaptation project; Levels of dependency on climate model information, Metrics/units of analysis utilised, Level of demographic knowledge, Level of stakeholder engagement, Adaptation implementation strategies and Scale of adaptation implementation. The study found that climate change adaptation projects could be categorised, based on the hallmarks identified, in accordance with the published literature. As such, the criterion may be used to establish the matrix of adaptation frameworks present in a given area. A comprehensive summary of the nature of adaptation frameworks in operation in a locality provides a platform for further comparative analysis. Such analysis, enabled by the criterion, may aid the selection of appropriate frameworks enhancing the efficacy of climate change adaptation.

  7. Maximum Likelihood Wavelet Density Estimation With Applications to Image and Shape Matching

    PubMed Central

    Peter, Adrian M.; Rangarajan, Anand

    2010-01-01

    Density estimation for observational data plays an integral role in a broad spectrum of applications, e.g., statistical data analysis and information-theoretic image registration. Of late, wavelet-based density estimators have gained in popularity due to their ability to approximate a large class of functions, adapting well to difficult situations such as when densities exhibit abrupt changes. The decision to work with wavelet density estimators brings along with it theoretical considerations (e.g., non-negativity, integrability) and empirical issues (e.g., computation of basis coefficients) that must be addressed in order to obtain a bona fide density. In this paper, we present a new method to accurately estimate a non-negative density which directly addresses many of the problems in practical wavelet density estimation. We cast the estimation procedure in a maximum likelihood framework which estimates the square root of the density p, allowing us to obtain the natural non-negative density representation (p)2. Analysis of this method will bring to light a remarkable theoretical connection with the Fisher information of the density and, consequently, lead to an efficient constrained optimization procedure to estimate the wavelet coefficients. We illustrate the effectiveness of the algorithm by evaluating its performance on mutual information-based image registration, shape point set alignment, and empirical comparisons to known densities. The present method is also compared to fixed and variable bandwidth kernel density estimators. PMID:18390355

  8. Coastal Climate Change Education, Mitigation, and Adaptation in the Natural and Built Environments: Progress of the Coastal Areas Climate Change Education Partnership

    NASA Astrophysics Data System (ADS)

    Feldman, A.; Herman, B.; Vernaza-Hernández, V.; Ryan, J. G.; Muller-Karger, F. E.; Gilbes, F.

    2011-12-01

    The Coastal Area Climate Change Education (CACCE) Partnership, funded by the National Science Foundation, seeks to develop new ways to educate citizens about global climate change. The core themes are sea level rise and impacts of climate change in the southeastern United States and the Caribbean Sea. CACCE focuses on helping partners, educators, students, and the general public gain a fundamental and working understanding of the interrelation among the natural environment, built environment, and social aspects in the context of climate change in coastal regions. To this end, CACCE's objectives reported here include: 1) defining the current state of awareness, perceptions, and literacy about the impacts of climate change; and 2) testing a model of transdisciplinary research and learning as a means of training a new generation of climate professionals. Objective one is met in part by CACCE survey efforts that reveal Florida and Puerto Rico secondary science teachers hold many non-scientific views about climate change and climate change science and provide inadequate instruction about climate change. Associated with objective two are five Multiple Outcome Interdisciplinary Research and Learning (MOIRL) pilot projects underway in schools in Florida and Puerto Rico. In the CACCE Partnership the stakeholders include: students (K-16 and graduate); teachers and education researchers; informal science educators; scientists and engineers; business and industry; policy makers; and community members. CACCE combines interdisciplinary research with action research and community-based participatory research in a way that is best described as "transdisciplinary". Learning occurs in all spheres of interactions among stakeholders as they engage in scientific, educational, community and business activities through their legitimate peripheral participation in research communities of practice. We will describe the process of seeking and building partnerships, and call for a dialogue

  9. Adaptive Development

    NASA Technical Reports Server (NTRS)

    2005-01-01

    The goal of this research is to develop and demonstrate innovative adaptive seal technologies that can lead to dramatic improvements in engine performance, life, range, and emissions, and enhance operability for next generation gas turbine engines. This work is concentrated on the development of self-adaptive clearance control systems for gas turbine engines. Researchers have targeted the high-pressure turbine (HPT) blade tip seal location for following reasons: Current active clearance control (ACC) systems (e.g., thermal case-cooling schemes) cannot respond to blade tip clearance changes due to mechanical, thermal, and aerodynamic loads. As such they are prone to wear due to the required tight running clearances during operation. Blade tip seal wear (increased clearances) reduces engine efficiency, performance, and service life. Adaptive sealing technology research has inherent impact on all envisioned 21st century propulsion systems (e.g. distributed vectored, hybrid and electric drive propulsion concepts).

  10. Low Bone Density

    MedlinePlus

    ... Density Exam/Testing › Low Bone Density Low Bone Density Low bone density is when your bone density ... people with normal bone density. Detecting Low Bone Density A bone density test will determine whether you ...

  11. Adaptive Optics with Sodium Laser Guide Stars

    NASA Astrophysics Data System (ADS)

    Lloyd-Hart, M.; Angel, J. R. P.; Jacobsen, B.; Wittman, D.; McCarthy, D.; Martinez, T.

    1994-12-01

    Adaptive optics requires a reference source of light in the sky to measure wavefront aberration introduced by atmospheric turbulence. Natural stars are ideal for this purpose, but the density of bright stars is not sufficient to provide complete sky coverage. The problem can be overcome with an artificial beacon generated from resonant backscattering off mesospheric sodium atoms exited by a low-power laser tuned to the D2 resonance. Recent experiments at the Multiple Mirror Telescope (MMT) have demonstrated for the first time that an adaptive optics system using a sodium laser guide beacon can be used to improve the imaging quality of the telescope. A beacon of mv = 10.4 was used to control the relative image motion between two of the six apertures of the MMT, while a natural star was used to measure the absolute tilt. A factor of two improvement in the K-band Strehl ratio was measured, and the resolution improved from 0(\\?.58) to 0(\\?.41) . The experiment demonstrated all the features needed for correction of telescopes of 6.5 to 8-m diameter to the diffraction limit in the near infrared with a single sodium laser beacon.

  12. The adaptation challenge in the Arctic

    NASA Astrophysics Data System (ADS)

    Ford, James D.; McDowell, Graham; Pearce, Tristan

    2015-12-01

    It is commonly asserted that human communities in the Arctic are highly vulnerable to climate change, with the magnitude of projected impacts limiting their ability to adapt. At the same time, an increasing number of field studies demonstrate significant adaptive capacity. Given this paradox, we review climate change adaptation, resilience and vulnerability research to identify and characterize the nature and magnitude of the adaptation challenge facing the Arctic. We find that the challenge of adaptation in the Arctic is formidable, but suggest that drivers of vulnerability and barriers to adaptation can be overcome, avoided or reduced by individual and collective efforts across scales for many, if not all, climate change risks.

  13. Adapting Animals.

    ERIC Educational Resources Information Center

    Wedman, John; Wedman, Judy

    1985-01-01

    The "Animals" program found on the Apple II and IIe system master disk can be adapted for use in the mathematics classroom. Instructions for making the necessary changes and suggestions for using it in lessons related to geometric shapes are provided. (JN)

  14. Adaptive Thresholds

    SciTech Connect

    Bremer, P. -T.

    2014-08-26

    ADAPT is a topological analysis code that allow to compute local threshold, in particular relevance based thresholds for features defined in scalar fields. The initial target application is vortex detection but the software is more generally applicable to all threshold based feature definitions.

  15. Adaptive homeostasis.

    PubMed

    Davies, Kelvin J A

    2016-06-01

    Homeostasis is a central pillar of modern Physiology. The term homeostasis was invented by Walter Bradford Cannon in an attempt to extend and codify the principle of 'milieu intérieur,' or a constant interior bodily environment, that had previously been postulated by Claude Bernard. Clearly, 'milieu intérieur' and homeostasis have served us well for over a century. Nevertheless, research on signal transduction systems that regulate gene expression, or that cause biochemical alterations to existing enzymes, in response to external and internal stimuli, makes it clear that biological systems are continuously making short-term adaptations both to set-points, and to the range of 'normal' capacity. These transient adaptations typically occur in response to relatively mild changes in conditions, to programs of exercise training, or to sub-toxic, non-damaging levels of chemical agents; thus, the terms hormesis, heterostasis, and allostasis are not accurate descriptors. Therefore, an operational adjustment to our understanding of homeostasis suggests that the modified term, Adaptive Homeostasis, may be useful especially in studies of stress, toxicology, disease, and aging. Adaptive Homeostasis may be defined as follows: 'The transient expansion or contraction of the homeostatic range in response to exposure to sub-toxic, non-damaging, signaling molecules or events, or the removal or cessation of such molecules or events.' PMID:27112802

  16. Natural Gas Emergencies

    MedlinePlus

    ... by the Cass (ND) and Clay (MN) Emergency Planning Partnerships. Adapted with funding provided by Fargo Cass Public Health through the Cities Readiness Initiative (CRI) English – Natural Gas Emergencies - Last ...

  17. Adaptive manifold learning.

    PubMed

    Zhang, Zhenyue; Wang, Jing; Zha, Hongyuan

    2012-02-01

    Manifold learning algorithms seek to find a low-dimensional parameterization of high-dimensional data. They heavily rely on the notion of what can be considered as local, how accurately the manifold can be approximated locally, and, last but not least, how the local structures can be patched together to produce the global parameterization. In this paper, we develop algorithms that address two key issues in manifold learning: 1) the adaptive selection of the local neighborhood sizes when imposing a connectivity structure on the given set of high-dimensional data points and 2) the adaptive bias reduction in the local low-dimensional embedding by accounting for the variations in the curvature of the manifold as well as its interplay with the sampling density of the data set. We demonstrate the effectiveness of our methods for improving the performance of manifold learning algorithms using both synthetic and real-world data sets. PMID:21670485

  18. Connector adapter

    NASA Technical Reports Server (NTRS)

    Hacker, Scott C. (Inventor); Dean, Richard J. (Inventor); Burge, Scott W. (Inventor); Dartez, Toby W. (Inventor)

    2007-01-01

    An adapter for installing a connector to a terminal post, wherein the connector is attached to a cable, is presented. In an embodiment, the adapter is comprised of an elongated collet member having a longitudinal axis comprised of a first collet member end, a second collet member end, an outer collet member surface, and an inner collet member surface. The inner collet member surface at the first collet member end is used to engage the connector. The outer collet member surface at the first collet member end is tapered for a predetermined first length at a predetermined taper angle. The collet includes a longitudinal slot that extends along the longitudinal axis initiating at the first collet member end for a predetermined second length. The first collet member end is formed of a predetermined number of sections segregated by a predetermined number of channels and the longitudinal slot.

  19. The challenge of adaptive structures

    NASA Astrophysics Data System (ADS)

    Breitbach, E. J.; Wimmel, R.

    Future lightweight design in space structure technology has to pay more attention to vibration suppression, to position control, or, more generally, to structure-inherent adaptability. These properties are often called "intelligent" or "smart", ignoring the fact that only creatures can have mental abilities. Having adaptation mechanisms for every dynamic process, living nature indeed teaches us that it is inexpedient if technical structural systems dispense with adaptability. Vibration and stability phenomena are making performance restrictions in space systems more and more evident. The DLR project ARES (Actively Reacting Flexible Structures) intends to overcome these limitations by developing a new class of technical systems. The ARES concept essentially consists of two new technologies: new kinds of integrated sensors and actuators working as components lying in the structural load path, and adaptive controllers consisting of digital filters which are adaptive in that they react against changing environmental influences as well as changes within the structure itself.

  20. Evolutionary genetics of plant adaptation

    PubMed Central

    Anderson, Jill T.; Willis, John H.; Mitchell-Olds, Thomas

    2011-01-01

    Plants provide unique opportunities to study the mechanistic basis and evolutionary processes of adaptation to diverse environmental conditions. Complementary laboratory and field experiments are important for testing hypothesis reflecting long term ecological and evolutionary history. For example, these approaches can infer whether local adaptation results from genetic tradeoffs (antagonistic pleiotropy), where native alleles are best adapted to local conditions, or if local adaptation is caused by conditional neutrality at many loci, where alleles show fitness differences in one environment, but not in the contrasting environment. Ecological genetics in natural populations of perennial or outcrossing plants also may differ substantially from model systems. In this review of the evolutionary genetics of plant adaptation, we emphasize the importance of field studies for understanding the evolutionary dynamics of model and non-model systems, highlight a key life history trait (flowering time), and discuss emerging conservation issues. PMID:21550682

  1. Adaptive sampler

    DOEpatents

    Watson, Bobby L.; Aeby, Ian

    1982-01-01

    An adaptive data compression device for compressing data having variable frequency content, including a plurality of digital filters for analyzing the content of the data over a plurality of frequency regions, a memory, and a control logic circuit for generating a variable rate memory clock corresponding to the analyzed frequency content of the data in the frequency region and for clocking the data into the memory in response to the variable rate memory clock.

  2. Adaptive sampler

    DOEpatents

    Watson, B.L.; Aeby, I.

    1980-08-26

    An adaptive data compression device for compressing data is described. The device has a frequency content, including a plurality of digital filters for analyzing the content of the data over a plurality of frequency regions, a memory, and a control logic circuit for generating a variable rate memory clock corresponding to the analyzed frequency content of the data in the frequency region and for clocking the data into the memory in response to the variable rate memory clock.

  3. Adaptive antennas

    NASA Astrophysics Data System (ADS)

    Barton, P.

    1987-04-01

    The basic principles of adaptive antennas are outlined in terms of the Wiener-Hopf expression for maximizing signal to noise ratio in an arbitrary noise environment; the analogy with generalized matched filter theory provides a useful aid to understanding. For many applications, there is insufficient information to achieve the above solution and thus non-optimum constrained null steering algorithms are also described, together with a summary of methods for preventing wanted signals being nulled by the adaptive system. The three generic approaches to adaptive weight control are discussed; correlation steepest descent, weight perturbation and direct solutions based on sample matrix conversion. The tradeoffs between hardware complexity and performance in terms of null depth and convergence rate are outlined. The sidelobe cancellor technique is described. Performance variation with jammer power and angular distribution is summarized and the key performance limitations identified. The configuration and performance characteristics of both multiple beam and phase scan array antennas are covered, with a brief discussion of performance factors.

  4. Adaptive node techniques for Maxwell's equations

    SciTech Connect

    Hewett, D W

    2000-04-01

    The computational mesh in numerical simulation provides a framework on which to monitor the spatial dependence of function and their derivatives. Spatial mesh is therefore essential to the ability to integrate systems in time without loss of fidelity. Several philosophies have emerged to provide such fidelity (Eulerian, Lagrangian, Arbitrary Lagrangian Eulerian ALE, Adaptive Mesh Refinement AMR, and adaptive node generation/deletion). Regardless of the type of mesh, a major difficulty is in setting up the initial mesh. Clearly a high density of grid points is essential in regions of high geometric complexity and/or regions of intense, energetic activity. For some problems, mesh generation is such a crucial part of the problem that it can take as much computational effort as the run itself, and these tasks are now taking weeks of massively parallel CPU time. Mesh generation is no less crucial to electromagnetic calculations. In fact EM problem set up can be even more challenging without the clues given by fluid motion in hydrodynamic systems. When the mesh is advected with the fluid (Lagrangian), mesh points naturally congregate in regions of high activity. Similarly in AMR algorithms, strong gradients in the fluid flow are one of the triggers for mesh refinement. In the hyperbolic Maxwell's equations without advection, mesh point placement/motion is not so intuitive. In fixed geometry systems, it at least feasible to finely mesh high leverage, geometrically challenged areas. For other systems, where the action takes place far from the boundaries and, likely, changes position in time, the options are limited to either using a high resolution (expensive) mesh in all regions that could require such resolution or adaptively generating nodes to resolve the physics as it evolves. The authors have developed a new time of adaptive node technique for Maxwell's equations to deal with this set of issues.

  5. Perceptual adaptation in the use of night vision goggles

    NASA Technical Reports Server (NTRS)

    Durgin, Frank H.; Proffitt, Dennis R.

    1992-01-01

    The image intensification (I sup 2) systems studied for this report were the biocular AN/PVS-7(NVG) and the binocular AN/AVS-6(ANVIS). Both are quite impressive for purposes of revealing the structure of the environment in a fairly straightforward way in extremely low-light conditions. But these systems represent an unusual viewing medium. The perceptual information available through I sup 2 systems is different in a variety of ways from the typical input of everyday vision, and extensive training and practice is required for optimal use. Using this sort of system involves a kind of perceptual skill learning, but is may also involve visual adaptations that are not simply an extension of normal vision. For example, the visual noise evident in the goggles in very low-light conditions results in unusual statistical properties in visual input. Because we had recently discovered a strong and enduring aftereffect of perceived texture density which seemed to be sensitive to precisely the sorts of statistical distortions introduced by I sup 2 systems, it occurred to use that visual noise of this sort might be a very adapting stimulus for texture density and produce an aftereffect that extended into normal vision once the goggles were removed. We have not found any experimental evidence that I sup 2 systems produce texture density aftereffects. The nature of the texture density aftereffect is briefly explained, followed by an accounting of our studies of I sup 2 systems and our most recent work on the texture density aftereffect. A test for spatial frequency adaptation after exposure to NVG's is also reported, as is a study of perceived depth from motion (motion parallax) while wearing the biocular goggles. We conclude with a summary of our findings.

  6. Periodic Density Functional Theory Solver using Multiresolution Analysis with MADNESS

    NASA Astrophysics Data System (ADS)

    Harrison, Robert; Thornton, William

    2011-03-01

    We describe the first implementation of the all-electron Kohn-Sham density functional periodic solver (DFT) using multi-wavelets and fast integral equations using MADNESS (multiresolution adaptive numerical environment for scientific simulation; http://code.google.com/p/m-a-d-n-e-s-s). The multiresolution nature of a multi-wavelet basis allows for fast computation with guaranteed precision. By reformulating the Kohn-Sham eigenvalue equation into the Lippmann-Schwinger equation, we can avoid using the derivative operator which allows better control of overall precision for the all-electron problem. Other highlights include the development of periodic integral operators with low-rank separation, an adaptable model potential for nuclear potential, and an implementation for Hartree Fock exchange. This work was supported by NSF project OCI-0904972 and made use of resources at the Center for Computational Sciences at Oak Ridge National Laboratory under contract DE-AC05-00OR22725.

  7. Negative Ion Density Fronts

    SciTech Connect

    Igor Kaganovich

    2000-12-18

    Negative ions tend to stratify in electronegative plasmas with hot electrons (electron temperature Te much larger than ion temperature Ti, Te > Ti ). The boundary separating a plasma containing negative ions, and a plasma, without negative ions, is usually thin, so that the negative ion density falls rapidly to zero-forming a negative ion density front. We review theoretical, experimental and numerical results giving the spatio-temporal evolution of negative ion density fronts during plasma ignition, the steady state, and extinction (afterglow). During plasma ignition, negative ion fronts are the result of the break of smooth plasma density profiles during nonlinear convection. In a steady-state plasma, the fronts are boundary layers with steepening of ion density profiles due to nonlinear convection also. But during plasma extinction, the ion fronts are of a completely different nature. Negative ions diffuse freely in the plasma core (no convection), whereas the negative ion front propagates towards the chamber walls with a nearly constant velocity. The concept of fronts turns out to be very effective in analysis of plasma density profile evolution in strongly non-isothermal plasmas.

  8. Coupled adaptive complex networks

    NASA Astrophysics Data System (ADS)

    Shai, S.; Dobson, S.

    2013-04-01

    Adaptive networks, which combine topological evolution of the network with dynamics on the network, are ubiquitous across disciplines. Examples include technical distribution networks such as road networks and the internet, natural and biological networks, and social science networks. These networks often interact with or depend upon other networks, resulting in coupled adaptive networks. In this paper we study susceptible-infected-susceptible (SIS) epidemic dynamics on coupled adaptive networks, where susceptible nodes are able to avoid contact with infected nodes by rewiring their intranetwork connections. However, infected nodes can pass the disease through internetwork connections, which do not change with time: The dependencies between the coupled networks remain constant. We develop an analytical formalism for these systems and validate it using extensive numerical simulation. We find that stability is increased by increasing the number of internetwork links, in the sense that the range of parameters over which both endemic and healthy states coexist (both states are reachable depending on the initial conditions) becomes smaller. Finally, we find a new stable state that does not appear in the case of a single adaptive network but only in the case of weakly coupled networks, in which the infection is endemic in one network but neither becomes endemic nor dies out in the other. Instead, it persists only at the nodes that are coupled to nodes in the other network through internetwork links. We speculate on the implications of these findings.

  9. Teaching About Adaptation: Why Evolutionary History Matters

    NASA Astrophysics Data System (ADS)

    Kampourakis, Kostas

    2013-02-01

    Adaptation is one of the central concepts in evolutionary theory, which nonetheless has been given different definitions. Some scholars support a historical definition of adaptation, considering it as a trait that is the outcome of natural selection, whereas others support an ahistorical definition, considering it as a trait that contributes to the survival and reproduction of its possessors. Finally, adaptation has been defined as a process, as well. Consequently, two questions arise: the first is a philosophical one and focuses on what adaptation actually is; the second is a pedagogical one and focuses on what science teachers and educators should teach about it. In this article, the various definitions of adaptation are discussed and their uses in some textbooks are presented. It is suggested that, given elementary students' intuitions about purpose and design in nature and secondary students' teleological explanations for the origin of adaptations, any definition of adaptation as a trait should include some information about its evolutionary history.

  10. Density estimators in particle hydrodynamics. DTFE versus regular SPH

    NASA Astrophysics Data System (ADS)

    Pelupessy, F. I.; Schaap, W. E.; van de Weygaert, R.

    2003-05-01

    We present the results of a study comparing density maps reconstructed by the Delaunay Tessellation Field Estimator (DTFE) and by regular SPH kernel-based techniques. The density maps are constructed from the outcome of an SPH particle hydrodynamics simulation of a multiphase interstellar medium. The comparison between the two methods clearly demonstrates the superior performance of the DTFE with respect to conventional SPH methods, in particular at locations where SPH appears to fail. Filamentary and sheetlike structures form telling examples. The DTFE is a fully self-adaptive technique for reconstructing continuous density fields from discrete particle distributions, and is based upon the corresponding Delaunay tessellation. Its principal asset is its complete independence of arbitrary smoothing functions and parameters specifying the properties of these. As a result it manages to faithfully reproduce the anisotropies of the local particle distribution and through its adaptive and local nature proves to be optimally suited for uncovering the full structural richness in the density distribution. Through the improvement in local density estimates, calculations invoking the DTFE will yield a much better representation of physical processes which depend on density. This will be crucial in the case of feedback processes, which play a major role in galaxy and star formation. The presented results form an encouraging step towards the application and insertion of the DTFE in astrophysical hydrocodes. We describe an outline for the construction of a particle hydrodynamics code in which the DTFE replaces kernel-based methods. Further discussion addresses the issue and possibilities for a moving grid-based hydrocode invoking the DTFE, and Delaunay tessellations, in an attempt to combine the virtues of the Eulerian and Lagrangian approaches.

  11. Reconceptualizing Family Adaptation to Developmental Delay.

    PubMed

    Pedersen, Anita L; Crnic, Keith A; Baker, Bruce L; Blacher, Jan

    2015-07-01

    This study explores accurate conceptualization of the adaptation construct in families of children with developmental delay aged 3 to 8 years. Parents' self-reported measures of adaptation and observed dyadic relationship variables were examined. Confirmatory factor analysis and longitudinal growth modeling were used to evaluate the nature of adaptational processes. Results indicate that adaptational processes vary across adaptation index, child developmental level, and parent gender. Adaptation indices did not load onto a single construct at any time point. Several adaptational processes remained stable across time, although others showed linear or quadratic change. The findings of the current study indicate that it is time for a change in how adaptation is conceived for families of children with developmental delay. PMID:26161471

  12. Nature of the bonding in the AuNgX (Ng = Ar, Kr, Xe; X = F, Cl, Br, I) molecules. Topological study on electron density and the electron localization function (ELF).

    PubMed

    Makarewicz, Emilia; Gordon, Agnieszka J; Berski, Slawomir

    2015-03-19

    Topological analysis of the electron localization function (ELF) has been carried out for the AuNgX (Ng = Ar, Kr, Xe; X = F, Cl, Br, I) molecules using the wave function approximated by the CCSD, MP2, and DFT(B3LYP, M062X) methods including zero-order regular approximation (ZORA). In the Ng-F bond, the bonding disynaptic attractor V(Ng,F) is missing; therefore, there are no signs of the covalent binding. The nature of the Au-Ng bond depends on the computational method used. Analysis of the ELF carried out for the AuArF and AuXeF molecules, with the wave function approximated by the CCSD and MP2 methods, shows the V(Au,Ng) attractor possibly corresponding to a partially covalent binding between the gold and noble gas atom. However, its very small basin population (<1e) and a very large value of the variance of the basin population suggest that the Au-Ng bond has a very delocalized character. Such bond nature may be related to the charge shift concept with a resonance of the Au(-+)NgX, Au(+-)NgX hybrids. The weakest Au-Ng bond, in terms of the smallest amount of electron density for the V(Au,Ng) basin, is found for the AuKrF molecule with the CCSD method (0.13e). The MP2 method, however, does not yield any V(Au, Ng) population; hence, the covalent Au-Kr bond is not confirmed. Because the V(Au,Ng) attractor is also not observed with the DFT method, the proper characterization of the Au-Ng bond requires proper description of correlation effects. Additional studies on the Au2 and [AuXe](+) molecules, performed at the CCSD and B3LYP levels, exhibit no V(Au,Au) and V(Au,Xe) bonding basins either. PMID:25266645

  13. Promoting intestinal adaptation by nutrition and medication.

    PubMed

    Neelis, E G; Olieman, J F; Hulst, J M; de Koning, B A E; Wijnen, R M H; Rings, E H H M

    2016-04-01

    The ultimate goal in the treatment of short bowel syndrome is to wean patients off parenteral nutrition, by promoting intestinal adaptation. Intestinal adaptation is the natural compensatory process that occurs after small bowel resection. Stimulating the remaining bowel with enteral nutrition can enhance this process. Additionally, medication can be used to either reduce factors that complicate the adaptation process or to stimulate intestinal adaptation, such as antisecretory drugs and several growth factors. The aim of this review was to provide an overview of the best nutritional strategies and medication that best promote intestinal adaptation. PMID:27086889

  14. Adaptive management of watersheds and related resources

    USGS Publications Warehouse

    Williams, Byron K.

    2009-01-01

    The concept of learning about natural resources through the practice of management has been around for several decades and by now is associated with the term adaptive management. The objectives of this paper are to offer a framework for adaptive management that includes an operational definition, a description of conditions in which it can be usefully applied, and a systematic approach to its application. Adaptive decisionmaking is described as iterative, learning-based management in two phases, each with its own mechanisms for feedback and adaptation. The linkages between traditional experimental science and adaptive management are discussed.

  15. Adaptive building skin structures

    NASA Astrophysics Data System (ADS)

    Del Grosso, A. E.; Basso, P.

    2010-12-01

    The concept of adaptive and morphing structures has gained considerable attention in the recent years in many fields of engineering. In civil engineering very few practical applications are reported to date however. Non-conventional structural concepts like deployable, inflatable and morphing structures may indeed provide innovative solutions to some of the problems that the construction industry is being called to face. To give some examples, searches for low-energy consumption or even energy-harvesting green buildings are amongst such problems. This paper first presents a review of the above problems and technologies, which shows how the solution to these problems requires a multidisciplinary approach, involving the integration of architectural and engineering disciplines. The discussion continues with the presentation of a possible application of two adaptive and dynamically morphing structures which are proposed for the realization of an acoustic envelope. The core of the two applications is the use of a novel optimization process which leads the search for optimal solutions by means of an evolutionary technique while the compatibility of the resulting configurations of the adaptive envelope is ensured by the virtual force density method.

  16. The ectodysplasin pathway: from diseases to adaptations.

    PubMed

    Sadier, Alexa; Viriot, Laurent; Pantalacci, Sophie; Laudet, Vincent

    2014-01-01

    The ectodysplasin (EDA) pathway, which is active during the development of ectodermal organs, including teeth, hairs, feathers, and mammary glands, and which is crucial for fine-tuning the developmental network controlling the number, size, and density of these structures, was discovered by studying human patients affected by anhidrotic/hypohidrotic ectodermal dysplasia. It comprises three main gene products: EDA, a ligand that belongs to the tumor necrosis factor (TNF)-α family, EDAR, a receptor related to the TNFα receptors, and EDARADD, a specific adaptor. This core pathway relies on downstream NF-κB pathway activation to regulate target genes. The pathway has recently been found to be associated with specific adaptations in natural populations: the magnitude of armor plates in sticklebacks and the hair structure in Asian human populations. Thus, despite its role in human disease, the EDA pathway is a 'hopeful pathway' that could allow adaptive changes in ectodermal appendages which, as specialized interfaces with the environment, are considered hot-spots of morphological evolution. PMID:24070496

  17. NFIRAOS: TMT narrow field near-infrared facility adaptive optics

    NASA Astrophysics Data System (ADS)

    Herriot, Glen; Hickson, Paul; Ellerbroek, B. L.; Andersen, D. A.; Davidge, T.; Erickson, D. A.; Powell, I. P.; Clare, R.; Gilles, L.; Boyer, C.; Smith, M.; Saddlemyer, L.; Véran, J.-P.

    2006-06-01

    Although many of the instruments planned for the TMT (Thirty Meter Telescope) have their own closely-coupled adaptive optics systems, TMT will also have a facility Adaptive Optics (AO) system, NFIRAOS, feeding three instruments on the Nasmyth platform. This Narrow-Field Infrared Adaptive Optics System, employs conventional deformable mirrors with large diameters of about 300 mm. The requirements for NFIRAOS include 1.0-2.5 microns wavelength range, 30 arcsecond diameter science field of view (FOV), excellent sky coverage, and diffraction-limited atmospheric turbulence compensation (specified at 133 nm RMS including residual telescope and science instrument errors.) The reference design for NFIRAOS includes six sodium laser guide stars over a 70 arcsecond FOV, and multiple infrared tip/tilt sensors and a natural guide star focus sensor within instruments. Larger telescopes require greater deformable mirror (DM) stroke. Although initially NFIRAOS will correct a 10 arcsecond science field, it uses two deformable mirrors in series, partly to provide sufficient stroke for atmospheric correction over the 30 m telescope aperture, but mainly to improve sky coverage by sharpening near-IR natural guide stars over a 2 arcminute diameter "technical" field. The planned upgrade to full performance includes replacing the ground-conjugated DM with a higher actuator density, and using a deformable telescope secondary mirror as a "woofer." NFIRAOS feeds three live instruments: a near-Infrared integral field Imaging spectrograph, a near-infrared echelle spectrograph, and after upgrading NFIRAOS to full multi-conjugation, a wide field (30 arcsecond) infrared camera.

  18. Adaptive encoding in the visual pathway.

    PubMed

    Lesica, Nicholas A; Boloori, Alireza S; Stanley, Garrett B

    2003-02-01

    In a natural setting, the mean luminance and contrast of the light within a visual neuron's receptive field are constantly changing as the eyes saccade across complex scenes. Adaptive mechanisms modulate filtering properties of the early visual pathway in response to these variations, allowing the system to maintain differential sensitivity to nonstationary stimuli. An adaptive variant of the reverse correlation technique is used to characterize these changes during single trials. Properties of the adaptive reverse correlation algorithm were investigated via simulation. Analysis of data collected from the mammalian visual system demonstrates the ability to continuously track adaptive changes in the encoding scheme. The adaptive estimation approach provides a framework for characterizing the role of adaptation in natural scene viewing. PMID:12613554

  19. Adapting and Writing Language Lessons.

    ERIC Educational Resources Information Center

    Stevick, Earl W.

    The dual purpose of this book is to set forth guidelines for appreciating the kinds of instructional materials available for the uncommonly taught languages and to suggest an approach to writing new materials which will be as adaptable as possible. Of principal concern are considerations relating to: (1) the nature of language teaching, (2) the…

  20. Adapted Minds and Evolved Schools

    ERIC Educational Resources Information Center

    Keil, Frank C.

    2008-01-01

    Evolutionary psychology raises questions about how cognitive adaptations might be related to the emergence of formal schooling. Is there a special role for natural domains of cognition such as folk physics, folk psychology and folk biology? These domains may vary from small fragments of reasoning to large integrated systems. This heterogeneity…

  1. Hydropower, adaptive management, and biodiversity

    SciTech Connect

    Wieringa, M.J.; Morton, A.G.

    1996-11-01

    Adaptive management is a policy framework within which an iterative process of decision making is allowed based on the observed responses to and effectiveness of previous decisions. The use of adaptive management allows science-based research and monitoring of natural resource and ecological community responses, in conjunction with societal values and goals, to guide decisions concerning man`s activities. The adaptive management process has been proposed for application to hydropower operations at Glen Canyon Dam on the Colorado River, a situation that requires complex balancing of natural resources requirements and competing human uses. This example is representative of the general increase in public interest in the operation of hydropower facilities and possible effects on downstream natural resources and of the growing conflicts between uses and users of river-based resources. This paper describes the adaptive management process, using the Glen Canyon Dam example, and discusses ways to make the process work effectively in managing downstream natural resources and biodiversity. 10 refs., 2 figs.

  2. Density Fluctuations in Liquid Water

    NASA Astrophysics Data System (ADS)

    English, Niall J.; Tse, John S.

    2011-01-01

    The density distributions and fluctuations in grids of varying size in liquid water at ambient pressure, both above the freezing point and in the supercooled state, are analyzed from the trajectories obtained from large-scale molecular dynamics simulations. It is found that the occurrence of low- and high-density regions (LDL and HDL) is transient and their respective residence times are dependent on the size of the simulated system. The spatial extent of density-density correlation is found to be within 7 Å or less. The temporal existence of LDL and HDL arises as a result of natural density fluctuations of an equilibrium system. The density of bulk water at ambient conditions is homogenous.

  3. Adaptation of Maize to Temperate Climates: Mid-Density Genome-Wide Association Genetics and Diversity Patterns Reveal Key Genomic Regions, with a Major Contribution of the Vgt2 (ZCN8) Locus

    PubMed Central

    Bouchet, Sophie; Servin, Bertrand; Bertin, Pascal; Madur, Delphine; Combes, Valérie; Dumas, Fabrice; Brunel, Dominique; Laborde, Jacques; Charcosset, Alain; Nicolas, Stéphane

    2013-01-01

    The migration of maize from tropical to temperate climates was accompanied by a dramatic evolution in flowering time. To gain insight into the genetic architecture of this adaptive trait, we conducted a 50K SNP-based genome-wide association and diversity investigation on a panel of tropical and temperate American and European representatives. Eighteen genomic regions were associated with flowering time. The number of early alleles cumulated along these regions was highly correlated with flowering time. Polymorphism in the vicinity of the ZCN8 gene, which is the closest maize homologue to Arabidopsis major flowering time (FT) gene, had the strongest effect. This polymorphism is in the vicinity of the causal factor of Vgt2 QTL. Diversity was lower, whereas differentiation and LD were higher for associated loci compared to the rest of the genome, which is consistent with selection acting on flowering time during maize migration. Selection tests also revealed supplementary loci that were highly differentiated among groups and not associated with flowering time in our panel, whereas they were in other linkage-based studies. This suggests that allele fixation led to a lack of statistical power when structure and relatedness were taken into account in a linear mixed model. Complementary designs and analysis methods are necessary to unravel the architecture of complex traits. Based on linkage disequilibrium (LD) estimates corrected for population structure, we concluded that the number of SNPs genotyped should be at least doubled to capture all QTLs contributing to the genetic architecture of polygenic traits in this panel. These results show that maize flowering time is controlled by numerous QTLs of small additive effect and that strong polygenic selection occurred under cool climatic conditions. They should contribute to more efficient genomic predictions of flowering time and facilitate the dissemination of diverse maize genetic resources under a wide range of

  4. Teaching about Adaptation: Why Evolutionary History Matters

    ERIC Educational Resources Information Center

    Kampourakis, Kostas

    2013-01-01

    Adaptation is one of the central concepts in evolutionary theory, which nonetheless has been given different definitions. Some scholars support a historical definition of adaptation, considering it as a trait that is the outcome of natural selection, whereas others support an ahistorical definition, considering it as a trait that contributes to…

  5. Population Genomics of Human Adaptation.

    PubMed

    Lachance, Joseph; Tishkoff, Sarah A

    2013-11-01

    Recent advances in genotyping technologies have facilitated genome-wide scans for natural selection. Identification of targets of natural selection will shed light on processes of human adaptation and evolution and could be important for identifying variation that influences both normal human phenotypic variation as well as disease susceptibility. Here we focus on studies of natural selection in modern humans who originated ~200,000 years go in Africa and migrated across the globe ~50,000 - 100,000 years ago. Movement into new environments, as well as changes in culture and technology including plant and animal domestication, resulted in local adaptation to diverse environments. We summarize statistical approaches for detecting targets of natural selection and for distinguishing the effects of demographic history from natural selection. On a genome-wide scale, immune-related genes appear to be major targets of positive selection. Genes associated with reproduction and fertility also appear to be fast evolving. Additional examples of recent human adaptation include genes associated with lactase persistence, eccrine glands, and response to hypoxia. Lastly, we emphasize the need to supplement scans of selection with functional studies to demonstrate the physiologic impact of candidate loci. PMID:25383060

  6. Population Genomics of Human Adaptation

    PubMed Central

    Lachance, Joseph; Tishkoff, Sarah A.

    2014-01-01

    Recent advances in genotyping technologies have facilitated genome-wide scans for natural selection. Identification of targets of natural selection will shed light on processes of human adaptation and evolution and could be important for identifying variation that influences both normal human phenotypic variation as well as disease susceptibility. Here we focus on studies of natural selection in modern humans who originated ~200,000 years go in Africa and migrated across the globe ~50,000 – 100,000 years ago. Movement into new environments, as well as changes in culture and technology including plant and animal domestication, resulted in local adaptation to diverse environments. We summarize statistical approaches for detecting targets of natural selection and for distinguishing the effects of demographic history from natural selection. On a genome-wide scale, immune-related genes appear to be major targets of positive selection. Genes associated with reproduction and fertility also appear to be fast evolving. Additional examples of recent human adaptation include genes associated with lactase persistence, eccrine glands, and response to hypoxia. Lastly, we emphasize the need to supplement scans of selection with functional studies to demonstrate the physiologic impact of candidate loci. PMID:25383060

  7. Coevolution of information processing and topology in hierarchical adaptive random Boolean networks

    NASA Astrophysics Data System (ADS)

    Górski, Piotr J.; Czaplicka, Agnieszka; Hołyst, Janusz A.

    2016-02-01

    Random Boolean Networks (RBNs) are frequently used for modeling complex systems driven by information processing, e.g. for gene regulatory networks (GRNs). Here we propose a hierarchical adaptive random Boolean Network (HARBN) as a system consisting of distinct adaptive RBNs (ARBNs) - subnetworks - connected by a set of permanent interlinks. We investigate mean node information, mean edge information as well as mean node degree. Information measures and internal subnetworks topology of HARBN coevolve and reach steady-states that are specific for a given network structure. The main natural feature of ARBNs, i.e. their adaptability, is preserved in HARBNs and they evolve towards critical configurations which is documented by power law distributions of network attractor lengths. The mean information processed by a single node or a single link increases with the number of interlinks added to the system. The mean length of network attractors and the mean steady-state connectivity possess minima for certain specific values of the quotient between the density of interlinks and the density of all links in networks. It means that the modular network displays extremal values of its observables when subnetworks are connected with a density a few times lower than a mean density of all links.

  8. Adaptive oxide electronics: A review

    NASA Astrophysics Data System (ADS)

    Ha, Sieu D.; Ramanathan, Shriram

    2011-10-01

    Novel information processing techniques are being actively explored to overcome fundamental limitations associated with CMOS scaling. A new paradigm of adaptive electronic devices is emerging that may reshape the frontiers of electronics and enable new modalities. Creating systems that can learn and adapt to various inputs has generally been a complex algorithm problem in information science, albeit with wide-ranging and powerful applications from medical diagnosis to control systems. Recent work in oxide electronics suggests that it may be plausible to implement such systems at the device level, thereby drastically increasing computational density and power efficiency and expanding the potential for electronics beyond Boolean computation. Intriguing possibilities of adaptive electronics include fabrication of devices that mimic human brain functionality: the strengthening and weakening of synapses emulated by electrically, magnetically, thermally, or optically tunable properties of materials.In this review, we detail materials and device physics studies on functional metal oxides that may be utilized for adaptive electronics. It has been shown that properties, such as resistivity, polarization, and magnetization, of many oxides can be modified electrically in a non-volatile manner, suggesting that these materials respond to electrical stimulus similarly as a neural synapse. We discuss what device characteristics will likely be relevant for integration into adaptive platforms and then survey a variety of oxides with respect to these properties, such as, but not limited to, TaOx, SrTiO3, and Bi4-xLaxTi3O12. The physical mechanisms in each case are detailed and analyzed within the framework of adaptive electronics. We then review theoretically formulated and current experimentally realized adaptive devices with functional oxides, such as self-programmable logic and neuromorphic circuits. Finally, we speculate on what advances in materials physics and engineering may

  9. Adaptive wavelets and relativistic magnetohydrodynamics

    NASA Astrophysics Data System (ADS)

    Hirschmann, Eric; Neilsen, David; Anderson, Matthe; Debuhr, Jackson; Zhang, Bo

    2016-03-01

    We present a method for integrating the relativistic magnetohydrodynamics equations using iterated interpolating wavelets. Such provide an adaptive implementation for simulations in multidimensions. A measure of the local approximation error for the solution is provided by the wavelet coefficients. They place collocation points in locations naturally adapted to the flow while providing expected conservation. We present demanding 1D and 2D tests includingthe Kelvin-Helmholtz instability and the Rayleigh-Taylor instability. Finally, we consider an outgoing blast wave that models a GRB outflow.

  10. ADAPTATION AND ADAPTABILITY, THE BELLEFAIRE FOLLOWUP STUDY.

    ERIC Educational Resources Information Center

    ALLERHAND, MELVIN E.; AND OTHERS

    A RESEARCH TEAM STUDIED INFLUENCES, ADAPTATION, AND ADAPTABILITY IN 50 POORLY ADAPTING BOYS AT BELLEFAIRE, A REGIONAL CHILD CARE CENTER FOR EMOTIONALLY DISTURBED CHILDREN. THE TEAM ATTEMPTED TO GAUGE THE SUCCESS OF THE RESIDENTIAL TREATMENT CENTER IN TERMS OF THE PSYCHOLOGICAL PATTERNS AND ROLE PERFORMANCES OF THE BOYS DURING INDIVIDUAL CASEWORK…

  11. Density variations and anomalies in palladium compacts

    SciTech Connect

    Back, D.; Jones, T.; Ransick, M.; Walburg, T.; Werkmeister, D.

    1992-05-14

    Low-density compacts of palladium powder have relative densities of about 30{plus_minus}10% TD. The variations in density are of concern for operations such as chemical/hydrogen pump systems because heat, mass, and momentum transport properties can be affected. Variations in density result from the inherent nature and interacting forces of UASA compaction of powder in cylinders. In addition to these expected variations, discontinuous density anomalies, such as cracks or high density ridges, are also found. An anomaly of particular concern was found to resemble a ``steer`s head.`` it is a symmetrical region of low density located at or near the center of a compact. Typically, this region is surrounded by a band of high density, compacted palladium that sometimes exceeds the density of the surrounding compact matrix by a factor of three. This report examines these density variations and anomalies both theoretically and empirically.

  12. Density variations and anomalies in palladium compacts

    SciTech Connect

    Back, D.; Jones, T.; Ransick, M.; Walburg, T.; Werkmeister, D.

    1992-05-14

    Low-density compacts of palladium powder have relative densities of about 30{plus minus}10% TD. The variations in density are of concern for operations such as chemical/hydrogen pump systems because heat, mass, and momentum transport properties can be affected. Variations in density result from the inherent nature and interacting forces of UASA compaction of powder in cylinders. In addition to these expected variations, discontinuous density anomalies, such as cracks or high density ridges, are also found. An anomaly of particular concern was found to resemble a steer's head.'' it is a symmetrical region of low density located at or near the center of a compact. Typically, this region is surrounded by a band of high density, compacted palladium that sometimes exceeds the density of the surrounding compact matrix by a factor of three. This report examines these density variations and anomalies both theoretically and empirically.

  13. Man and SuperNature. Lecture 12, September 27, 1946

    ERIC Educational Resources Information Center

    Montessori, Maria

    2015-01-01

    "Man and SuperNature" is a lyrical chapter in the 1946 London course following the emergence of Cosmic Education in Kodaikanal, India. Montessori contrasts the adaptation required of animals for their survival to conscious human adaptation. Animals exist and adapt to nature, but man can alter nature and change the environment.…

  14. Adaptation pathways of global wheat production: Importance of strategic adaptation to climate change

    NASA Astrophysics Data System (ADS)

    Tanaka, Akemi; Takahashi, Kiyoshi; Masutomi, Yuji; Hanasaki, Naota; Hijioka, Yasuaki; Shiogama, Hideo; Yamanaka, Yasuhiro

    2015-09-01

    Agricultural adaptation is necessary to reduce the negative impacts of climate change on crop yields and to maintain food production. However, few studies have assessed the course of adaptation along with the progress of climate change in each of the current major food producing countries. Adaptation pathways, which describe the temporal sequences of adaptations, are helpful for illustrating the timing and intensity of the adaptation required. Here we present adaptation pathways in the current major wheat-producing countries, based on sequential introduction of the minimum adaptation measures necessary to maintain current wheat yields through the 21st century. We considered two adaptation options: (i) expanding irrigation infrastructure; and (ii) switching crop varieties and developing new heat-tolerant varieties. We find that the adaptation pathways differ markedly among the countries. The adaptation pathways are sensitive to both the climate model uncertainty and natural variability of the climate system, and the degree of sensitivity differs among countries. Finally, the negative impacts of climate change could be moderated by implementing adaptations steadily according to forecasts of the necessary future adaptations, as compared to missing the appropriate timing to implement adaptations.

  15. Adaptation pathways of global wheat production: Importance of strategic adaptation to climate change.

    PubMed

    Tanaka, Akemi; Takahashi, Kiyoshi; Masutomi, Yuji; Hanasaki, Naota; Hijioka, Yasuaki; Shiogama, Hideo; Yamanaka, Yasuhiro

    2015-01-01

    Agricultural adaptation is necessary to reduce the negative impacts of climate change on crop yields and to maintain food production. However, few studies have assessed the course of adaptation along with the progress of climate change in each of the current major food producing countries. Adaptation pathways, which describe the temporal sequences of adaptations, are helpful for illustrating the timing and intensity of the adaptation required. Here we present adaptation pathways in the current major wheat-producing countries, based on sequential introduction of the minimum adaptation measures necessary to maintain current wheat yields through the 21st century. We considered two adaptation options: (i) expanding irrigation infrastructure; and (ii) switching crop varieties and developing new heat-tolerant varieties. We find that the adaptation pathways differ markedly among the countries. The adaptation pathways are sensitive to both the climate model uncertainty and natural variability of the climate system, and the degree of sensitivity differs among countries. Finally, the negative impacts of climate change could be moderated by implementing adaptations steadily according to forecasts of the necessary future adaptations, as compared to missing the appropriate timing to implement adaptations. PMID:26373877

  16. Device for determining frost depth and density

    NASA Technical Reports Server (NTRS)

    Huneidi, F.

    1983-01-01

    A hand held device having a forward open window portion adapted to be pushed downwardly into the frost on a surface, and a rear container portion adapted to receive the frost removed from the window area are described. A graph on a side of the container enables an observer to determine the density of the frost from certain measurements noted. The depth of the frost is noted from calibrated lines on the sides of the open window portion.

  17. Adaptive Image Denoising by Mixture Adaptation.

    PubMed

    Luo, Enming; Chan, Stanley H; Nguyen, Truong Q

    2016-10-01

    We propose an adaptive learning procedure to learn patch-based image priors for image denoising. The new algorithm, called the expectation-maximization (EM) adaptation, takes a generic prior learned from a generic external database and adapts it to the noisy image to generate a specific prior. Different from existing methods that combine internal and external statistics in ad hoc ways, the proposed algorithm is rigorously derived from a Bayesian hyper-prior perspective. There are two contributions of this paper. First, we provide full derivation of the EM adaptation algorithm and demonstrate methods to improve the computational complexity. Second, in the absence of the latent clean image, we show how EM adaptation can be modified based on pre-filtering. The experimental results show that the proposed adaptation algorithm yields consistently better denoising results than the one without adaptation and is superior to several state-of-the-art algorithms. PMID:27416593

  18. Adaptive Sampling in Hierarchical Simulation

    SciTech Connect

    Knap, J; Barton, N R; Hornung, R D; Arsenlis, A; Becker, R; Jefferson, D R

    2007-07-09

    We propose an adaptive sampling methodology for hierarchical multi-scale simulation. The method utilizes a moving kriging interpolation to significantly reduce the number of evaluations of finer-scale response functions to provide essential constitutive information to a coarser-scale simulation model. The underlying interpolation scheme is unstructured and adaptive to handle the transient nature of a simulation. To handle the dynamic construction and searching of a potentially large set of finer-scale response data, we employ a dynamic metric tree database. We study the performance of our adaptive sampling methodology for a two-level multi-scale model involving a coarse-scale finite element simulation and a finer-scale crystal plasticity based constitutive law.

  19. Imaging an Adapted Dentoalveolar Complex

    PubMed Central

    Herber, Ralf-Peter; Fong, Justine; Lucas, Seth A.; Ho, Sunita P.

    2012-01-01

    Adaptation of a rat dentoalveolar complex was illustrated using various imaging modalities. Micro-X-ray computed tomography for 3D modeling, combined with complementary techniques, including image processing, scanning electron microscopy, fluorochrome labeling, conventional histology (H&E, TRAP), and immunohistochemistry (RANKL, OPN) elucidated the dynamic nature of bone, the periodontal ligament-space, and cementum in the rat periodontium. Tomography and electron microscopy illustrated structural adaptation of calcified tissues at a higher resolution. Ongoing biomineralization was analyzed using fluorochrome labeling, and by evaluating attenuation profiles using virtual sections from 3D tomographies. Osteoclastic distribution as a function of anatomical location was illustrated by combining histology, immunohistochemistry, and tomography. While tomography and SEM provided past resorption-related events, future adaptive changes were deduced by identifying matrix biomolecules using immunohistochemistry. Thus, a dynamic picture of the dentoalveolar complex in rats was illustrated. PMID:22567314

  20. Adaptation, aging, and genomic information

    PubMed Central

    Rose, Michael R.

    2009-01-01

    Aging is not simply an accumulation of damage or inappropriate higher-order signaling, though it does secondarily involve both of these subsidiary mechanisms. Rather, aging occurs because of the extensive absence of adaptive genomic information required for survival to, and function at, later adult ages, due to the declining forces of natural selection during adult life. This absence of information then secondarily leads to misallocations and damage at every level of biological organization. But the primary problem is a failure of adaptation at later ages. Contemporary proposals concerning means by which human aging can be ended or cured which are based on simple signaling or damage theories will thus reliably fail. Strategies based on reverse-engineering age-extended adaptation using experimental evolution and genomics offer the prospect of systematically greater success. PMID:20157529

  1. Development of Underwater Laser Scaling Adapter

    NASA Astrophysics Data System (ADS)

    Bluss, Kaspars

    2012-12-01

    In this paper the developed laser scaling adapter is presented. The scaling adapter is equipped with a twin laser unit where the two parallel laser beams are projected onto any target giving an exact indication of scale. The body of the laser scaling adapter is made of Teflon, the density of which is approximately two times the water density. The development involved multiple challenges - numerical hydrodynamic calculations for choosing an appropriate shape which would reduce the effects of turbulence, an accurate sealing of the power supply and the laser diodes, and others. The precision is estimated by the partial derivation method. Both experimental and theoretical data conclude the overall precision error to be in the 1% margin. This paper presents the development steps of such an underwater laser scaling adapter for a remotely operated vehicle (ROV).

  2. A holistic strategy for adaptive land management

    USGS Publications Warehouse

    Herrick, Jeffrey E.; Duniway, Michael C.; Pyke, David A.; Bestelmeyer, Brandon T.; Wills, Skye A.; Brown, Joel R.; Karl, Jason W.; Havstad, Kris M.

    2012-01-01

    Adaptive management is widely applied to natural resources management (Holling 1973; Walters and Holling 1990). Adaptive management can be generally defined as an iterative decision-making process that incorporates formulation of management objectives, actions designed to address these objectives, monitoring of results, and repeated adaptation of management until desired results are achieved (Brown and MacLeod 1996; Savory and Butterfield 1999). However, adaptive management is often criticized because very few projects ever complete more than one cycle, resulting in little adaptation and little knowledge gain (Lee 1999; Walters 2007). One significant criticism is that adaptive management is often used as a justification for undertaking actions with uncertain outcomes or as a surrogate for the development of specific, measurable indicators and monitoring programs (Lee 1999; Ruhl 2007).

  3. Genotype by environment interaction for plant density response in maize

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Increased adaptation to high plant density has been an important factor in improvements in grain yield in maize. Despite extensive public literature on variation in plant density response among maize varieties, almost no public information is available on environmental effects on plant density respo...

  4. Adaptive Responses Limited by Intrinsic Noise

    PubMed Central

    Shankar, Prabhat; Nishikawa, Masatoshi; Shibata, Tatsuo

    2015-01-01

    Sensory systems have mechanisms to respond to the external environment and adapt to them. Such adaptive responses are effective for a wide dynamic range of sensing and perception of temporal change in stimulus. However, noise generated by the adaptation system itself as well as extrinsic noise in sensory inputs may impose a limit on the ability of adaptation systems. The relation between response and noise is well understood for equilibrium systems in the form of fluctuation response relation. However, the relation for nonequilibrium systems, including adaptive systems, are poorly understood. Here, we systematically explore such a relation between response and fluctuation in adaptation systems. We study the two network motifs, incoherent feedforward loops (iFFL) and negative feedback loops (nFBL), that can achieve perfect adaptation. We find that the response magnitude in adaption systems is limited by its intrinsic noise, implying that higher response would have higher noise component as well. Comparing the relation of response and noise in iFFL and nFBL, we show that whereas iFFL exhibits adaptation over a wider parameter range, nFBL offers higher response to noise ratio than iFFL. We also identify the condition that yields the upper limit of response for both network motifs. These results may explain the reason of why nFBL seems to be more abundant in nature for the implementation of adaption systems. PMID:26305221

  5. Adaptive Objectness for Object Tracking

    NASA Astrophysics Data System (ADS)

    Liang, Pengpeng; Pang, Yu; Liao, Chunyuan; Mei, Xue; Ling, Haibin

    2016-07-01

    Object tracking is a long standing problem in vision. While great efforts have been spent to improve tracking performance, a simple yet reliable prior knowledge is left unexploited: the target object in tracking must be an object other than non-object. The recently proposed and popularized objectness measure provides a natural way to model such prior in visual tracking. Thus motivated, in this paper we propose to adapt objectness for visual object tracking. Instead of directly applying an existing objectness measure that is generic and handles various objects and environments, we adapt it to be compatible to the specific tracking sequence and object. More specifically, we use the newly proposed BING objectness as the base, and then train an object-adaptive objectness for each tracking task. The training is implemented by using an adaptive support vector machine that integrates information from the specific tracking target into the BING measure. We emphasize that the benefit of the proposed adaptive objectness, named ADOBING, is generic. To show this, we combine ADOBING with seven top performed trackers in recent evaluations. We run the ADOBING-enhanced trackers with their base trackers on two popular benchmarks, the CVPR2013 benchmark (50 sequences) and the Princeton Tracking Benchmark (100 sequences). On both benchmarks, our methods not only consistently improve the base trackers, but also achieve the best known performances. Noting that the way we integrate objectness in visual tracking is generic and straightforward, we expect even more improvement by using tracker-specific objectness.

  6. Visual adaptation and face perception

    PubMed Central

    Webster, Michael A.; MacLeod, Donald I. A.

    2011-01-01

    The appearance of faces can be strongly affected by the characteristics of faces viewed previously. These perceptual after-effects reflect processes of sensory adaptation that are found throughout the visual system, but which have been considered only relatively recently in the context of higher level perceptual judgements. In this review, we explore the consequences of adaptation for human face perception, and the implications of adaptation for understanding the neural-coding schemes underlying the visual representation of faces. The properties of face after-effects suggest that they, in part, reflect response changes at high and possibly face-specific levels of visual processing. Yet, the form of the after-effects and the norm-based codes that they point to show many parallels with the adaptations and functional organization that are thought to underlie the encoding of perceptual attributes like colour. The nature and basis for human colour vision have been studied extensively, and we draw on ideas and principles that have been developed to account for norms and normalization in colour vision to consider potential similarities and differences in the representation and adaptation of faces. PMID:21536555

  7. Natural killer cells: remembrances of things past.

    PubMed

    Raulet, David H

    2009-04-14

    Recent work has revealed that natural killer cells exhibit a form of memory, previously considered an exclusive property of adaptive immunity. While protective, natural killer cell memory is probably hazier and more fleeting than T cell memory. PMID:19368874

  8. Habituation of visual adaptation

    PubMed Central

    Dong, Xue; Gao, Yi; Lv, Lili; Bao, Min

    2016-01-01

    Our sensory system adjusts its function driven by both shorter-term (e.g. adaptation) and longer-term (e.g. learning) experiences. Most past adaptation literature focuses on short-term adaptation. Only recently researchers have begun to investigate how adaptation changes over a span of days. This question is important, since in real life many environmental changes stretch over multiple days or longer. However, the answer to the question remains largely unclear. Here we addressed this issue by tracking perceptual bias (also known as aftereffect) induced by motion or contrast adaptation across multiple daily adaptation sessions. Aftereffects were measured every day after adaptation, which corresponded to the degree of adaptation on each day. For passively viewed adapters, repeated adaptation attenuated aftereffects. Once adapters were presented with an attentional task, aftereffects could either reduce for easy tasks, or initially show an increase followed by a later decrease for demanding tasks. Quantitative analysis of the decay rates in contrast adaptation showed that repeated exposure of the adapter appeared to be equivalent to adaptation to a weaker stimulus. These results suggest that both attention and a non-attentional habituation-like mechanism jointly determine how adaptation develops across multiple daily sessions. PMID:26739917

  9. Habituation of visual adaptation.

    PubMed

    Dong, Xue; Gao, Yi; Lv, Lili; Bao, Min

    2016-01-01

    Our sensory system adjusts its function driven by both shorter-term (e.g. adaptation) and longer-term (e.g. learning) experiences. Most past adaptation literature focuses on short-term adaptation. Only recently researchers have begun to investigate how adaptation changes over a span of days. This question is important, since in real life many environmental changes stretch over multiple days or longer. However, the answer to the question remains largely unclear. Here we addressed this issue by tracking perceptual bias (also known as aftereffect) induced by motion or contrast adaptation across multiple daily adaptation sessions. Aftereffects were measured every day after adaptation, which corresponded to the degree of adaptation on each day. For passively viewed adapters, repeated adaptation attenuated aftereffects. Once adapters were presented with an attentional task, aftereffects could either reduce for easy tasks, or initially show an increase followed by a later decrease for demanding tasks. Quantitative analysis of the decay rates in contrast adaptation showed that repeated exposure of the adapter appeared to be equivalent to adaptation to a weaker stimulus. These results suggest that both attention and a non-attentional habituation-like mechanism jointly determine how adaptation develops across multiple daily sessions. PMID:26739917

  10. Conditions and limitations on learning in the adaptive management of mallard harvests

    USGS Publications Warehouse

    Johnson, F.A.; Kendall, W.L.; Dubovsky, J.A.

    2002-01-01

    In 1995, the United States Fish and Wildlife Service adopted a protocol for the adaptive management of waterfowl hunting regulations (AHM) to help reduce uncertainty about the magnitude of sustainable harvests. To date, the AHM process has focused principally on the midcontinent population of mallards (Anas platyrhynchos), whose dynamics are described by 4 alternative models. Collectively, these models express uncertainty (or disagreement) about whether harvest is an additive or a compensatory form of mortality and whether the reproductive process is weakly or strongly density-dependent. Each model is associated with a probability or 'weight,' which describes its relative ability to predict changes in population size. These Bayesian probabilities are updated annually using a comparison of population size predicted under each model with that observed by a monitoring program. The current AHM process is passively adaptive, in the sense that there is no a priori consideration of how harvest decisions might affect discrimination among models. We contrast this approach with an actively adaptive approach, in which harvest decisions are used in part to produce the learning needed to increase long-term management performance. Our investigation suggests that the passive approach is expected to perform nearly as well as an optimal actively adaptive approach, particularly considering the nature of the model set, management objectives and constraints, and current regulatory alternatives. We offer some comments about the nature of the biological hypotheses being tested and describe some of the inherent limitations on learning in the AHM process.

  11. Accurate ab Initio Spin Densities

    PubMed Central

    2012-01-01

    We present an approach for the calculation of spin density distributions for molecules that require very large active spaces for a qualitatively correct description of their electronic structure. Our approach is based on the density-matrix renormalization group (DMRG) algorithm to calculate the spin density matrix elements as a basic quantity for the spatially resolved spin density distribution. The spin density matrix elements are directly determined from the second-quantized elementary operators optimized by the DMRG algorithm. As an analytic convergence criterion for the spin density distribution, we employ our recently developed sampling-reconstruction scheme [J. Chem. Phys.2011, 134, 224101] to build an accurate complete-active-space configuration-interaction (CASCI) wave function from the optimized matrix product states. The spin density matrix elements can then also be determined as an expectation value employing the reconstructed wave function expansion. Furthermore, the explicit reconstruction of a CASCI-type wave function provides insight into chemically interesting features of the molecule under study such as the distribution of α and β electrons in terms of Slater determinants, CI coefficients, and natural orbitals. The methodology is applied to an iron nitrosyl complex which we have identified as a challenging system for standard approaches [J. Chem. Theory Comput.2011, 7, 2740]. PMID:22707921

  12. Oblique dust density waves

    NASA Astrophysics Data System (ADS)

    Piel, Alexander; Arp, Oliver; Menzel, Kristoffer; Klindworth, Markus

    2007-11-01

    We report on experimental observations of dust density waves in a complex (dusty) plasma under microgravity. The plasma is produced in a radio-frequency parallel-plate discharge (argon, p=15Pa, U=65Vpp). Different sizes of dust particles were used (3.4 μm and 6.4μm diameter). The low-frequency (f 11Hz) dust density waves are naturally unstable modes, which are driven by the ion flow in the plasma. Surprisingly, the wave propagation direction is aligned with the ion flow direction in the bulk plasma but becomes oblique at the boundary of the dust cloud with an inclination of 60^o with respect to the plasma boundary. The experimental results are compared with a kinetic model in the electrostatic approximation [1] and a fluid model [2]. Moreover, the role of dust surface waves is discussed. [1] M. Rosenberg, J. Vac. Sci. Technol. A 14, 631 (1996) [2] A. Piel et al, Phys. Rev. Lett. 97, 205009 (2006)

  13. Expressing Adaptation Strategies Using Adaptation Patterns

    ERIC Educational Resources Information Center

    Zemirline, N.; Bourda, Y.; Reynaud, C.

    2012-01-01

    Today, there is a real challenge to enable personalized access to information. Several systems have been proposed to address this challenge including Adaptive Hypermedia Systems (AHSs). However, the specification of adaptation strategies remains a difficult task for creators of such systems. In this paper, we consider the problem of the definition…

  14. Molecular evolution and thermal adaptation

    NASA Astrophysics Data System (ADS)

    Chen, Peiqiu

    2011-12-01

    In this thesis, we address problems in molecular evolution, thermal adaptation, and the kinetics of adaptation of bacteria and viruses to elevated environmental temperatures. We use a nearly neutral fitness model where the replication speed of an organism is proportional to the copy number of folded proteins. Our model reproduces the distribution of stabilities of natural proteins in excellent agreement with experiment. We find that species with high mutation rates tend to have less stable proteins compared to species with low mutation rate. We found that a broad distribution of protein stabilities observed in the model and in experiment is the key determinant of thermal response for viruses and bacteria. Our results explain most of the earlier experimental observations: striking asymmetry of thermal response curves, the absence of evolutionary trade-off which was expected but not found in experiments, correlation between denaturation temperature for several protein families and the Optimal Growth Temperature (OGT) of their carrier organisms, and proximity of bacterial or viral OGTs to their evolutionary temperatures. Our theory quantitatively and with high accuracy described thermal response curves for 35 bacterial species. The model also addresses the key to adaptation is in weak-link genes (WLG), which encode least thermodynamically stable essential proteins in the proteome. We observe, as in experiment, a two-stage adaptation process. The first stage is a Luria-Delbruck type of selection, whereby rare WLG alleles, whose proteins are more stable than WLG proteins of the majority of the population (either due to standing genetic variation or due to an early acquired mutation), rapidly rise to fixation. The second stage constitutes subsequent slow accumulation of mutations in an adapted population. As adaptation progresses, selection regime changes from positive to neutral: Selection coefficient of beneficial mutations scales as a negative power of number of

  15. Parallel Density-Based Clustering for Discovery of Ionospheric Phenomena

    NASA Astrophysics Data System (ADS)

    Pankratius, V.; Gowanlock, M.; Blair, D. M.

    2015-12-01

    Ionospheric total electron content maps derived from global networks of dual-frequency GPS receivers can reveal a plethora of ionospheric features in real-time and are key to space weather studies and natural hazard monitoring. However, growing data volumes from expanding sensor networks are making manual exploratory studies challenging. As the community is heading towards Big Data ionospheric science, automation and Computer-Aided Discovery become indispensable tools for scientists. One problem of machine learning methods is that they require domain-specific adaptations in order to be effective and useful for scientists. Addressing this problem, our Computer-Aided Discovery approach allows scientists to express various physical models as well as perturbation ranges for parameters. The search space is explored through an automated system and parallel processing of batched workloads, which finds corresponding matches and similarities in empirical data. We discuss density-based clustering as a particular method we employ in this process. Specifically, we adapt Density-Based Spatial Clustering of Applications with Noise (DBSCAN). This algorithm groups geospatial data points based on density. Clusters of points can be of arbitrary shape, and the number of clusters is not predetermined by the algorithm; only two input parameters need to be specified: (1) a distance threshold, (2) a minimum number of points within that threshold. We discuss an implementation of DBSCAN for batched workloads that is amenable to parallelization on manycore architectures such as Intel's Xeon Phi accelerator with 60+ general-purpose cores. This manycore parallelization can cluster large volumes of ionospheric total electronic content data quickly. Potential applications for cluster detection include the visualization, tracing, and examination of traveling ionospheric disturbances or other propagating phenomena. Acknowledgments. We acknowledge support from NSF ACI-1442997 (PI V. Pankratius).

  16. Variational method for adaptive grid generation

    SciTech Connect

    Brackbill, J.U.

    1983-01-01

    A variational method for generating adaptive meshes is described. Functionals measuring smoothness, skewness, orientation, and the Jacobian are minimized to generate a mapping from a rectilinear domain in natural coordinate to an arbitrary domain in physical coordinates. From the mapping, a mesh is easily constructed. In using the method to adaptively zone computational problems, as few as one third the number of mesh points are required in each coordinate direction compared with a uniformly zoned mesh.

  17. Dynamic adaptivity of "smart" piezoelectric structures

    NASA Astrophysics Data System (ADS)

    Tzou, Horn-Sen; Zhong, Jianping P.

    1990-10-01

    Active smart" space and machine structures with adaptive dynamic characteristics have long been interested in a variety of high-performance systems, e.g., flexible robots, flexible space structures, "smart" machines, etc. In this paper, an active adaptive structure made of piezoelectric materials is proposed and evaluated. The structural adaptivity is achieved by a voltage feedback (open or closed loops) utilizing the converse piezoelectric effect. A mathematical model is proposed and the electrodynamic equations of motion and the generalized boundary conditions of a generic piezoelectric shell subjected to mechanical and electrical excitations are derived using Hamilton's principle and the linear piezoelectric theory. The dynamic adaptivity of the structure is introduced using a feedback control system. The theory is demonstrated in a case study in which the structural adaptivity (natural frequency) is investigated.

  18. NFIRAOS: TMT facility adaptive optics with conventional DMs

    NASA Astrophysics Data System (ADS)

    Herriot, Glen; Hickson, Paul; Ellerbroek, B. L.; Andersen, David A.; Davidge, T.; Erickson, D. A.; Powell, I. P.; Clare, R.; Smith, M.; Saddlemyer, L.; Veran, J.-P.

    2005-08-01

    Although many of the instruments planned for the TMT (Thirty Meter Telescope) have their own closely-coupled adaptive optics systems, TMT will also have a facility Adaptive Optics (AO) system feeding three instruments on the Nasmyth platform. For this Narrow-Field Infrared Adaptive Optics System, NFIRAOS (pronounced nefarious), the TMT project considered two architectures. One, described in this paper, employs conventional deformable mirrors with large diameters of about 300 mm and this is the reference design adopted by the TMT project. An alternative design based on MEMS was also studied, and is being presented separately in this conference. The requirements for NFIRAOS include 0.8-5 microns wavelength range, 30 arcsecond diameter output field of view (FOV), excellent sky coverage, and diffraction- limited atmospheric turbulence compensation (specified at 133 nm RMS including residual telescope and science instrument errors.) The reference design for NFIRAOS includes multiple sodium laser guide stars over a 70 arcsecond FOV, and an infrared tip/tilt/focus/astigmatism natural guide star sensor within instruments. Larger telescopes require greater deformable mirror (DM) stroke. Although initially NFIRAOS will correct a 10 arcsecond science field, it uses two deformable mirrors in series, partly to provide sufficient stroke for atmospheric correction over the 30 m telescope aperture, but mainly to partially correct a 2 arcminute diameter "technical" field to sharpen near-IR natural guide stars and improve sky coverage. The planned upgrade to full performance includes replacing the groundconjugated DM with a higher actuator density, and using a deformable telescope secondary mirror as a "woofer." NFIRAOS incorporates an instrument rotator and selection of three live instruments: a near-Infrared integral field Imaging spectrograph, a near-infrared echelle spectrograph, and after upgrading NFIRAOS to full multi-conjugation, a wide field (30 arcsecond) infrared camera.

  19. Adaptive Evolution of Synthetic Cooperating Communities Improves Growth Performance

    PubMed Central

    Zhang, Xiaolin; Reed, Jennifer L.

    2014-01-01

    Symbiotic interactions between organisms are important for human health and biotechnological applications. Microbial mutualism is a widespread phenomenon and is important in maintaining natural microbial communities. Although cooperative interactions are prevalent in nature, little is known about the processes that allow their initial establishment, govern population dynamics and affect evolutionary processes. To investigate cooperative interactions between bacteria, we constructed, characterized, and adaptively evolved a synthetic community comprised of leucine and lysine Escherichia coli auxotrophs. The co-culture can grow in glucose minimal medium only if the two auxotrophs exchange essential metabolites — lysine and leucine (or its precursors). Our experiments showed that a viable co-culture using these two auxotrophs could be established and adaptively evolved to increase growth rates (by ∼3 fold) and optical densities. While independently evolved co-cultures achieved similar improvements in growth, they took different evolutionary trajectories leading to different community compositions. Experiments with individual isolates from these evolved co-cultures showed that changes in both the leucine and lysine auxotrophs improved growth of the co-culture. Interestingly, while evolved isolates increased growth of co-cultures, they exhibited decreased growth in mono-culture (in the presence of leucine or lysine). A genome-scale metabolic model of the co-culture was also constructed and used to investigate the effects of amino acid (leucine or lysine) release and uptake rates on growth and composition of the co-culture. When the metabolic model was constrained by the estimated leucine and lysine release rates, the model predictions agreed well with experimental growth rates and composition measurements. While this study and others have focused on cooperative interactions amongst community members, the adaptive evolution of communities with other types of

  20. An adaptive paradigm for human space settlement

    NASA Astrophysics Data System (ADS)

    Smith, Cameron M.

    2016-02-01

    Because permanent space settlement will be multigenerational it will have to be viable on ecological timescales so far unfamiliar to those planning space exploration. Long-term viability will require evolutionary and adaptive planning. Adaptations in the natural world provide many lessons for such planning, but implementing these lessons will require a new, evolutionary paradigm for envisioning and carrying out Earth-independent space settlement. I describe some of these adaptive lessons and propose some cognitive shifts required to implement them in a genuinely evolutionary approach to human space settlement.

  1. A genetic basis of variation in eccrine sweat gland and hair follicle density

    PubMed Central

    Kamberov, Yana G.; Karlsson, Elinor K.; Kamberova, Gerda L.; Lieberman, Daniel E.; Sabeti, Pardis C.; Morgan, Bruce A.; Tabin, Clifford J.

    2015-01-01

    Among the unique features of humans, one of the most salient is the ability to effectively cool the body during extreme prolonged activity through the evapotranspiration of water on the skin’s surface. The evolution of this novel physiological ability required a dramatic increase in the density and distribution of eccrine sweat glands relative to other mammals and a concomitant reduction of body hair cover. Elucidation of the genetic underpinnings for these adaptive changes is confounded by a lack of knowledge about how eccrine gland fate and density are specified during development. Moreover, although reciprocal changes in hair cover and eccrine gland density are required for efficient thermoregulation, it is unclear if these changes are linked by a common genetic regulation. To identify pathways controlling the relative patterning of eccrine glands and hair follicles, we exploited natural variation in the density of these organs between different strains of mice. Quantitative trait locus mapping identified a large region on mouse Chromosome 1 that controls both hair and eccrine gland densities. Differential and allelic expression analysis of the genes within this interval coupled with subsequent functional studies demonstrated that the level of En1 activity directs the relative numbers of eccrine glands and hair follicles. These findings implicate En1 as a newly identified and reciprocal determinant of hair follicle and eccrine gland density and identify a pathway that could have contributed to the evolution of the unique features of human skin. PMID:26195765

  2. A genetic basis of variation in eccrine sweat gland and hair follicle density.

    PubMed

    Kamberov, Yana G; Karlsson, Elinor K; Kamberova, Gerda L; Lieberman, Daniel E; Sabeti, Pardis C; Morgan, Bruce A; Tabin, Clifford J

    2015-08-11

    Among the unique features of humans, one of the most salient is the ability to effectively cool the body during extreme prolonged activity through the evapotranspiration of water on the skin's surface. The evolution of this novel physiological ability required a dramatic increase in the density and distribution of eccrine sweat glands relative to other mammals and a concomitant reduction of body hair cover. Elucidation of the genetic underpinnings for these adaptive changes is confounded by a lack of knowledge about how eccrine gland fate and density are specified during development. Moreover, although reciprocal changes in hair cover and eccrine gland density are required for efficient thermoregulation, it is unclear if these changes are linked by a common genetic regulation. To identify pathways controlling the relative patterning of eccrine glands and hair follicles, we exploited natural variation in the density of these organs between different strains of mice. Quantitative trait locus mapping identified a large region on mouse Chromosome 1 that controls both hair and eccrine gland densities. Differential and allelic expression analysis of the genes within this interval coupled with subsequent functional studies demonstrated that the level of En1 activity directs the relative numbers of eccrine glands and hair follicles. These findings implicate En1 as a newly identified and reciprocal determinant of hair follicle and eccrine gland density and identify a pathway that could have contributed to the evolution of the unique features of human skin. PMID:26195765

  3. Deleterious Passengers in Adapting Populations

    PubMed Central

    Good, Benjamin H.; Desai, Michael M.

    2014-01-01

    Most new mutations are deleterious and are eventually eliminated by natural selection. But in an adapting population, the rapid amplification of beneficial mutations can hinder the removal of deleterious variants in nearby regions of the genome, altering the patterns of sequence evolution. Here, we analyze the interactions between beneficial “driver” mutations and linked deleterious “passengers” during the course of adaptation. We derive analytical expressions for the substitution rate of a deleterious mutation as a function of its fitness cost, as well as the reduction in the beneficial substitution rate due to the genetic load of the passengers. We find that the fate of each deleterious mutation varies dramatically with the rate and spectrum of beneficial mutations and the deleterious substitution rate depends nonmonotonically on the population size and the rate of adaptation. By quantifying this dependence, our results allow us to estimate which deleterious mutations will be likely to fix and how many of these mutations must arise before the progress of adaptation is significantly reduced. PMID:25194161

  4. Evaluation of Natural Resource Interventions

    ERIC Educational Resources Information Center

    Rowe, Andy

    2012-01-01

    This article provides a frame for evaluation of natural resource interventions, which necessarily involves both human and natural systems. Two-system evaluands require us to adapt evaluation methods for comparison and attribution and to address differences in time and space occurring across the systems as well as potentially very different values…

  5. An Adaptable Metric Shapes Perceptual Space.

    PubMed

    Hisakata, Rumi; Nishida, Shin'ya; Johnston, Alan

    2016-07-25

    How do we derive a sense of the separation of points in the world within a space-variant visual system? Visual directions are thought to be coded directly by a process referred to as local sign, in which a neuron acts as a labeled line for the perceived direction associated with its activation [1, 2]. The separations of visual directions, however, are not given, nor are they directly related to the separations of signals on the receptive surface or in the brain, which are modified by retinal and cortical magnification, respectively [3]. To represent the separation of directions veridically, the corresponding neural signals need to be scaled in some way. We considered this scaling process may be influenced by adaptation. Here, we describe a novel adaptation paradigm, which can alter both apparent spatial separation and size. We measured the perceived separation of two dots and the size of geometric figures after adaptation to random dot patterns. We show that adapting to high-density texture not only increases the apparent sparseness (average element separation) of a lower-density pattern, as expected [4], but paradoxically, it reduces the apparent separation of dot pairs and induces apparent shrinkage of geometric form. This demonstrates for the first time a contrary linkage between perceived density and perceived extent. Separation and size appear to be expressed relative to a variable spatial metric whose properties, while not directly observable, are revealed by reductions in both apparent size and texture density. PMID:27426520

  6. Structural bistability in quasi-hard-discs under adaptive circular confinement

    NASA Astrophysics Data System (ADS)

    Williams, Ian; Oguz, Erdal C.; Bartlett, Paul; Loewen, Hartmut; Royall, C. Patrick

    2014-03-01

    The behaviour of materials under spatial confinement is dramatically different from that in the bulk. The exact nature of behavioural modification in confined systems is strongly dependent on the boundary enclosing the system with soft walls inducing different phenomena than similar hard walls. Here we present a quasi-two-dimensional colloidal model system confined by an adaptive circular boundary defined using holographic optical tweezers. The adaptive boundary is deformable, enabling mechanical measurements of pressure and leading to the observation of a novel structural bistability between concentric particle layering and locally hexagonal configurations at high density. These findings are reproduced in analogous Monte Carlo simulations. Additionally, shearing the confined system drives the this bistability resulting in the observation of a novel oscillatory state characterised by periodically self-similar structural organisation. Under varying conditions, both shear melted and rigid-body-like flow behaviour is observed.

  7. Plant adaptation to drought stress

    PubMed Central

    Basu, Supratim; Ramegowda, Venkategowda; Kumar, Anuj; Pereira, Andy

    2016-01-01

    Plants in their natural habitats adapt to drought stress in the environment through a variety of mechanisms, ranging from transient responses to low soil moisture to major survival mechanisms of escape by early flowering in absence of seasonal rainfall. However, crop plants selected by humans to yield products such as grain, vegetable, or fruit in favorable environments with high inputs of water and fertilizer are expected to yield an economic product in response to inputs. Crop plants selected for their economic yield need to survive drought stress through mechanisms that maintain crop yield. Studies on model plants for their survival under stress do not, therefore, always translate to yield of crop plants under stress, and different aspects of drought stress response need to be emphasized. The crop plant model rice ( Oryza sativa) is used here as an example to highlight mechanisms and genes for adaptation of crop plants to drought stress. PMID:27441087

  8. Adaptation and irreversibility in microevolution

    NASA Astrophysics Data System (ADS)

    Bo, Stefano; Mazzolini, Andrea; Celani, Antonio

    2014-12-01

    Within the framework of population genetics we consider the evolution of an asexual haploid population under the effect of a rapidly varying natural selection (microevolution). We focus on the case in which the environment exerting selection changes stochastically. We derive the effective genotype and fitness dynamics on the slower timescales at which the relevant genetic modifications take place. We find that, despite the fast environmental switches, the population manages to adapt on the fast timescales yielding a finite positive contribution to the fitness. However, such contribution is balanced by the continuous loss in fitness due to the varying selection so that the statistics of the global fitness can be described neglecting the details of the fast environmental process. The occurrence of adaptation on fast timescales would be undetectable if one were to consider only the effective genotype and fitness dynamics on the slow timescales. We therefore propose an experimental observable to detect it.

  9. Evolutionary Adaptations to Dietary Changes

    PubMed Central

    Luca, F.; Perry, G.H.; Di Rienzo, A.

    2014-01-01

    Through cultural innovation and changes in habitat and ecology, there have been a number of major dietary shifts in human evolution, including meat eating, cooking, and those associated with plant and animal domestication. The identification of signatures of adaptations to such dietary changes in the genome of extant primates (including humans) may shed light not only on the evolutionary history of our species, but also on the mechanisms that underlie common metabolic diseases in modern human populations. In this review, we provide a brief overview of the major dietary shifts that occurred during hominin evolution, and we discuss the methods and approaches used to identify signals of natural selection in patterns of sequence variation. We then review the results of studies aimed at detecting the genetic loci that played a major role in dietary adaptations and conclude by outlining the potential of future studies in this area. PMID:20420525

  10. Evolutionary adaptations to dietary changes.

    PubMed

    Luca, F; Perry, G H; Di Rienzo, A

    2010-08-21

    Through cultural innovation and changes in habitat and ecology, there have been a number of major dietary shifts in human evolution, including meat eating, cooking, and those associated with plant and animal domestication. The identification of signatures of adaptations to such dietary changes in the genome of extant primates (including humans) may shed light not only on the evolutionary history of our species, but also on the mechanisms that underlie common metabolic diseases in modern human populations. In this review, we provide a brief overview of the major dietary shifts that occurred during hominin evolution, and we discuss the methods and approaches used to identify signals of natural selection in patterns of sequence variation. We then review the results of studies aimed at detecting the genetic loci that played a major role in dietary adaptations and conclude by outlining the potential of future studies in this area. PMID:20420525

  11. Quorum sensing influences growth and photosynthetic membrane production in high-cell-density cultivations of Rhodospirillum rubrum

    PubMed Central

    2013-01-01

    Background The facultative anoxygenic photosynthetic bacterium Rhodospirillum rubrum exhibits versatile metabolic activity allowing the adaptation to rapidly changing growth conditions in its natural habitat, the microaerobic and anoxic zones of stagnant waters. The microaerobic growth mode is of special interest as it allows the high-level expression of photosynthetic membranes when grown on succinate and fructose in the dark, which could significantly simplify the industrial production of compounds associated with PM formation. However, recently we showed that PM synthesis is no longer inducible when R. rubrum cultures are grown to high cell densities under aerobic conditions. In addition a reduction of the growth rate and the continued accumulation of precursor molecules for bacteriochlorophyll synthesis were observed under high cell densities conditions. Results In the present work, we demonstrate that the cell density-dependent effects are reversible if the culture supernatant is replaced by fresh medium. We identified six N-acylhomoserine lactones and show that four of them are produced in varying amounts according to the growth phase and the applied growth conditions. Further, we demonstrate that N-acylhomoserine lactones and tetrapyrrole compounds released into the growth medium affect the growth rate and PM expression in high cell density cultures. Conclusions In summary, we provide evidence that R. rubrum possesses a Lux-type quorum sensing system which influences the biosynthesis of PM and the growth rate and is thus likely to be involved in the phenotypes of high cell density cultures and the rapid adaptation to changing environmental conditions. PMID:23927486

  12. Urban behavioural adaptation.

    PubMed

    Garroway, Colin J; Sheldon, Ben C

    2013-07-01

    A large and growing proportion of the world is impacted directly by human activities; among the most extreme of these is the spread of urban environments. Environmental change associated with urbanization represents a potentially potent source of selection. While urban environments generally have lowered biodiversity, some clades seem to thrive in urban settings. For example, many members of the bird family Turdidae, known as the ‘truethrushes’ and the blackbird Turdus merula (Fig. 1) in particular, are familiar urban species. Indeed, the colonization of urban environments by blackbirds has become a textbook case study for our understanding of the many ways a wild species can deal with urbanization. In this issue, Mueller et al. (Molecular Ecology, 00, 2013, 00) add to that story by beginning to address the genetic nature of behavioural adaptation of blackbirds colonizing urban areas. They do this by testing for divergence between paired urban and rural samples at a suite of candidate genes with hypothesized effects on behaviours thought to be important for the colonization of urban environments.They find evidence for consistent patterns of divergence at an exonic microsatellite associated with the SERT gene. SERT has a number of hypothesized behavioural effects, including harm avoidance, which may be associated with tolerating the hustle and bustle of urban environments. This is among the first evidence that behavioural differences between urban and rural environments have a genetic basis and this work suggests that urban environments can in some cases exert homogeneous selection pressures. PMID:23967452

  13. Adaptive management for a turbulent future.

    PubMed

    Allen, Craig R; Fontaine, Joseph J; Pope, Kevin L; Garmestani, Ahjond S

    2011-05-01

    The challenges that face humanity today differ from the past because as the scale of human influence has increased, our biggest challenges have become global in nature, and formerly local problems that could be addressed by shifting populations or switching resources, now aggregate (i.e., "scale up") limiting potential management options. Adaptive management is an approach to natural resource management that emphasizes learning through management based on the philosophy that knowledge is incomplete and much of what we think we know is actually wrong. Adaptive management has explicit structure, including careful elucidation of goals, identification of alternative management objectives and hypotheses of causation, and procedures for the collection of data followed by evaluation and reiteration. It is evident that adaptive management has matured, but it has also reached a crossroads. Practitioners and scientists have developed adaptive management and structured decision making techniques, and mathematicians have developed methods to reduce the uncertainties encountered in resource management, yet there continues to be misapplication of the method and misunderstanding of its purpose. Ironically, the confusion over the term "adaptive management" may stem from the flexibility inherent in the approach, which has resulted in multiple interpretations of "adaptive management" that fall along a continuum of complexity and a priori design. Adaptive management is not a panacea for the navigation of 'wicked problems' as it does not produce easy answers, and is only appropriate in a subset of natural resource management problems where both uncertainty and controllability are high. Nonetheless, the conceptual underpinnings of adaptive management are simple; there will always be inherent uncertainty and unpredictability in the dynamics and behavior of complex social-ecological systems, but management decisions must still be made, and whenever possible, we should incorporate

  14. Adaptive Management for a Turbulent Future

    USGS Publications Warehouse

    Allen, Craig R.; Fontaine, Joseph J.; Pope, Kevin L.; Garmestani, Ahjond S.

    2011-01-01

    The challenges that face humanity today differ from the past because as the scale of human influence has increased, our biggest challenges have become global in nature, and formerly local problems that could be addressed by shifting populations or switching resources, now aggregate (i.e., "scale up") limiting potential management options. Adaptive management is an approach to natural resource management that emphasizes learning through management based on the philosophy that knowledge is incomplete and much of what we think we know is actually wrong. Adaptive management has explicit structure, including careful elucidation of goals, identification of alternative management objectives and hypotheses of causation, and procedures for the collection of data followed by evaluation and reiteration. It is evident that adaptive management has matured, but it has also reached a crossroads. Practitioners and scientists have developed adaptive management and structured decision making techniques, and mathematicians have developed methods to reduce the uncertainties encountered in resource management, yet there continues to be misapplication of the method and misunderstanding of its purpose. Ironically, the confusion over the term "adaptive management" may stem from the flexibility inherent in the approach, which has resulted in multiple interpretations of "adaptive management" that fall along a continuum of complexity and a priori design. Adaptive management is not a panacea for the navigation of 'wicked problems' as it does not produce easy answers, and is only appropriate in a subset of natural resource management problems where both uncertainty and controllability are high. Nonetheless, the conceptual underpinnings of adaptive management are simple; there will always be inherent uncertainty and unpredictability in the dynamics and behavior of complex social-ecological systems, but management decisions must still be made, and whenever possible, we should incorporate

  15. Adaptive management for a turbulent future

    USGS Publications Warehouse

    Allen, C.R.; Fontaine, J.J.; Pope, K.L.; Garmestani, A.S.

    2011-01-01

    The challenges that face humanity today differ from the past because as the scale of human influence has increased, our biggest challenges have become global in nature, and formerly local problems that could be addressed by shifting populations or switching resources, now aggregate (i.e., "scale up") limiting potential management options. Adaptive management is an approach to natural resource management that emphasizes learning through management based on the philosophy that knowledge is incomplete and much of what we think we know is actually wrong. Adaptive management has explicit structure, including careful elucidation of goals, identification of alternative management objectives and hypotheses of causation, and procedures for the collection of data followed by evaluation and reiteration. It is evident that adaptive management has matured, but it has also reached a crossroads. Practitioners and scientists have developed adaptive management and structured decision making techniques, and mathematicians have developed methods to reduce the uncertainties encountered in resource management, yet there continues to be misapplication of the method and misunderstanding of its purpose. Ironically, the confusion over the term "adaptive management" may stem from the flexibility inherent in the approach, which has resulted in multiple interpretations of "adaptive management" that fall along a continuum of complexity and a priori design. Adaptive management is not a panacea for the navigation of 'wicked problems' as it does not produce easy answers, and is only appropriate in a subset of natural resource management problems where both uncertainty and controllability are high. Nonetheless, the conceptual underpinnings of adaptive management are simple; there will always be inherent uncertainty and unpredictability in the dynamics and behavior of complex social-ecological systems, but management decisions must still be made, and whenever possible, we should incorporate

  16. Hydrological silviculture effects in a natural Quercus ilex forest

    NASA Astrophysics Data System (ADS)

    González-Sanchis, María; del Campo, Antonio; Bautista, Inma; Lidón, Antonio; García, Alberto; Llull, Cristina

    2013-04-01

    Mediterranean forests play a key role in the hydrological cycle regulation. On the one hand, its presence decreases the soil water evaporation, increasing the water availability. However, on the other hand, the forest density reduces the precipitation that reaches the soil, where an excessive forest density could induce water scarcity problems, at the forest itself as well as at the whole catchment. Hence, there should be an equilibrium that protects the soil from excessive evaporation at the same time that reduces the forest water interception. This equilibrium can be reached by means of the Adaptative Forest Management (AFM). AFM aims to adapt the forest to water availability by means of an artificial regulation of the forest structure and density. Hence, areas under water scarcity situations, such as the Mediterranean region, might require this AFM to optimize the hydrological cycle under normal and future global change conditions. The present study enhances the relevance of the hydrological silviculture in Mediterranean regions. A natural Mediterranean oak forest, whose density appears to be decreasing the hydrological contribution to the catchment, was selected. The forest is located in a typical Mediterranean area, at the headwaters of Rambla Espadilla catchment, within the public forest La Hunde, Valencia (NE Spain). Two contiguous plots, control and treatment, of 1800 m2 area respectively were selected. The orientation (NO), slope (30 %) and forest density (861 tree per ha) were the same for both plots. Treatment plot was thinned following the forest nursery requirements, reducing the forest density from 861 to 414 tree per ha. Control plot was not thinned. Then, the thinning effects into the hydrological cycle were characterized by means of comparing throughfall, stemflow, soil moisture and transpiration, of control and treatment plots.

  17. Cold adaptation in marine organisms.

    PubMed

    Johnston, I A

    1990-01-30

    Animals from polar seas exhibit numerous so called resistance adaptations that serve to maintain homeostasis at low temperature and prevent lethal freezing injury. Specialization to temperatures at or below 0 degrees C is associated with an inability to survive at temperatures above 3-8 degrees C. Polar fish synthesize various types of glycoproteins or peptides to lower the freezing point of most extracellular fluid compartments in a non-colligative manner. Antifreeze production is seasonal in boreal species and is often initiated by environmental cues other than low temperature, particularly short day lengths. Most of the adaptations that enable intertidal invertebrates to survive freezing are associated with their ability to withstand ariel exposure. Unique adaptations for freezing avoidance include the synthesis of low molecular mass ice-nucleating proteins that control and induce extracellular ice-formation. Marine poikilotherms also exhibit a range of capacity adaptations that increase the rate of some physiological processes so as to partially compensate for the effects of low temperature. However, the rate of embryonic development in a diverse range of marine organisms shows no evidence of temperature compensation. This results in a significant lengthening of the time from fertilization to hatching in polar, relative to temperate, species. Some aspects of the physiology of polar marine species, such as low metabolic and slow growth rates, probably result from a combination of low temperature and other factors such as the highly seasonal nature of food supplies. Although neuromuscular function shows a partial capacity adaptation in Antarctic fish, maximum swimming speeds are lower than for temperate and tropical species, particularly for early stages in the life history. PMID:1969650

  18. Density-dependent adjustment of inducible defenses

    PubMed Central

    Tollrian, Ralph; Duggen, Sonja; Weiss, Linda C.; Laforsch, Christian; Kopp, Michael

    2015-01-01

    Predation is a major factor driving evolution, and organisms have evolved adaptations increasing their survival chances. However, most defenses incur trade-offs between benefits and costs. Many organisms save costs by employing inducible defenses as responses to fluctuating predation risk. The level of defense often increases with predator densities. However, individual predation risk should not only depend on predator density but also on the density of conspecifics. If the predator has a saturating functional response one would predict a negative correlation between prey density and individual predation risk and hence defense expression. Here, we tested this hypothesis using six model systems, covering a taxonomic range from protozoa to rotifers and crustaceans. In all six systems, we found that the level of defense expression increased with predator density but decreased with prey density. In one of our systems, i.e. in Daphnia, we further show that the response to prey density is triggered by a chemical cue released by conspecifics and congeners. Our results indicate that organisms adjust the degree of defense to the acute predation risk, rather than merely to predators’ densities. Our study suggests that density-dependent defense expression reflects accurate predation-risk assessment and is a general principle in many inducible-defense systems. PMID:26235428

  19. Organizational Adaptation and Higher Education.

    ERIC Educational Resources Information Center

    Cameron, Kim S.

    1984-01-01

    Organizational adaptation and types of adaptation needed in academe in the future are reviewed and major conceptual approaches to organizational adaptation are presented. The probable environment that institutions will face in the future that will require adaptation is discussed. (MLW)

  20. Fine-scale temporal adaptation within a salmonid population: mechanism and consequences.

    PubMed

    Gharrett, Anthony J; Joyce, John; Smoker, William W

    2013-09-01

    We demonstrate a clear example of local adaptation of seasonal timing of spawning and embryo development. The consequence is a population of pink salmon that is segmented into spawning groups that use the same limited habitat. We synthesize published observations with results of new analyses to demonstrate that genetic variation of these traits results in survival differentials related to that variation, and that density-dependent embryo mortality and seasonally variable juvenile mortality are a mechanism of selection. Most examples of local adaptation in natural systems depend on observed correlations between environments and fitness traits, but do not fully demonstrate local adaptation: that the trait is genetically determined, exhibits different fitness in common environments or across different environments, and its variation is mechanistically connected to fitness differences. The geographic or temporal scales of local adaptation often remain obscure. Here, we show that heritable, fine-scale differences of timing of reproductive migration in a pink salmon (Oncorhynchus gorbuscha) resulted in temporal structure that persisted several generations; the differences enable a density-dependent population to pack more spawners into limited spawning habitat, that is, enhance its fitness. A balanced trade-off of survivals results because embryos from early-migrating fish have a lower freshwater survival (harsh early physical conditions and disturbance by late spawners), but emigrant fry from late-migrating fish have lower marine survivals (timing of their vernal emergence into the estuarine environment). Such fine-scale local adaptations increase the genetic portfolio of the populations and may provide a buffer against the impacts of climate change. PMID:23980763

  1. Density perturbation theory

    SciTech Connect

    Palenik, Mark C.; Dunlap, Brett I.

    2015-07-28

    Despite the fundamental importance of electron density in density functional theory, perturbations are still usually dealt with using Hartree-Fock-like orbital equations known as coupled-perturbed Kohn-Sham (CPKS). As an alternative, we develop a perturbation theory that solves for the perturbed density directly, removing the need for CPKS. This replaces CPKS with a true Hohenberg-Kohn density perturbation theory. In CPKS, the perturbed density is found in the basis of products of occupied and virtual orbitals, which becomes ever more over-complete as the size of the orbital basis set increases. In our method, the perturbation to the density is expanded in terms of a series of density basis functions and found directly. It is possible to solve for the density in such a way that it makes the total energy stationary even if the density basis is incomplete.

  2. A mesh density study for application to large deformation rolling process evaluations

    SciTech Connect

    Martin, J.A.

    1997-12-01

    When addressing large deformation through an elastic-plastic analysis the mesh density is paramount in determining the accuracy of the solution. However, given the nonlinear nature of the problem, a highly-refined mesh will generally require a prohibitive amount of computer resources. This paper addresses finite element mesh optimization studies considering accuracy of results and computer resource needs as applied to large deformation rolling processes. In particular, the simulation of the thread rolling manufacturing process is considered using the MARC software package and a Cray C90 supercomputer. Both mesh density and adaptive meshing on final results for both indentation of a rigid body to a specified depth and contact rolling along a predetermined length are evaluated.

  3. Origins of adaptive immunity.

    PubMed

    Liongue, Clifford; John, Liza B; Ward, Alister

    2011-01-01

    Adaptive immunity, involving distinctive antibody- and cell-mediated responses to specific antigens based on "memory" of previous exposure, is a hallmark of higher vertebrates. It has been argued that adaptive immunity arose rapidly, as articulated in the "big bang theory" surrounding its origins, which stresses the importance of coincident whole-genome duplications. Through a close examination of the key molecules and molecular processes underpinning adaptive immunity, this review suggests a less-extreme model, in which adaptive immunity emerged as part of longer evolutionary journey. Clearly, whole-genome duplications provided additional raw genetic materials that were vital to the emergence of adaptive immunity, but a variety of other genetic events were also required to generate some of the key molecules, whereas others were preexisting and simply co-opted into adaptive immunity. PMID:21395512

  4. Parallel Anisotropic Tetrahedral Adaptation

    NASA Technical Reports Server (NTRS)

    Park, Michael A.; Darmofal, David L.

    2008-01-01

    An adaptive method that robustly produces high aspect ratio tetrahedra to a general 3D metric specification without introducing hybrid semi-structured regions is presented. The elemental operators and higher-level logic is described with their respective domain-decomposed parallelizations. An anisotropic tetrahedral grid adaptation scheme is demonstrated for 1000-1 stretching for a simple cube geometry. This form of adaptation is applicable to more complex domain boundaries via a cut-cell approach as demonstrated by a parallel 3D supersonic simulation of a complex fighter aircraft. To avoid the assumptions and approximations required to form a metric to specify adaptation, an approach is introduced that directly evaluates interpolation error. The grid is adapted to reduce and equidistribute this interpolation error calculation without the use of an intervening anisotropic metric. Direct interpolation error adaptation is illustrated for 1D and 3D domains.

  5. Gravitational adaptation of animals

    NASA Technical Reports Server (NTRS)

    Smith, A. H.; Burton, R. R.

    1982-01-01

    The effect of gravitational adaptation is studied in a group of five Leghorn cocks which had become physiologically adapted to 2 G after 162 days of centrifugation. After this period of adaptation, they are periodically exposed to a 2 G field, accompanied by five previously unexposed hatch-mates, and the degree of retained acceleration adaptation is estimated from the decrease in lymphocyte frequency after 24 hr at 2 G. Results show that the previously adapted birds exhibit an 84% greater lymphopenia than the unexposed birds, and that the lymphocyte frequency does not decrease to a level below that found at the end of 162 days at 2 G. In addition, the capacity for adaptation to chronic acceleration is found to be highly heritable. An acceleration tolerant strain of birds shows lesser mortality during chronic acceleration, particularly in intermediate fields, although the result of acceleration selection is largely quantitative (a greater number of survivors) rather than qualitative (behavioral or physiological changes).

  6. Direction Selectivity Mediated by Adaptation in the Owl's Inferior Colliculus

    PubMed Central

    Peña, José Luis

    2013-01-01

    Motion direction is a crucial cue for predicting future states in natural scenes. In the auditory system, the mechanisms that confer direction selectivity to neurons are not well understood. Neither is it known whether sound motion is encoded independently of stationary sound location. Here we investigated these questions in neurons of the owl's external nucleus of the inferior colliculus, where auditory space is represented in a map. Using a high-density speaker array, we show that the preferred direction and the degree of direction selectivity can be predicted by response adaptation to sounds moving over asymmetric spatial receptive fields. At the population level, we found that preference for sounds moving toward frontal space increased with eccentricity in spatial tuning. This distribution was consistent with larger receptive-field asymmetry in neurons tuned to more peripheral auditory space. A model of suppression based on spatiotemporal summation predicted the observations. Thus, response adaptation and receptive-field shape can explain direction selectivity to acoustic motion and an orderly distribution of preferred direction. PMID:24305813

  7. Phase Adaptation and Correction by Adaptive Optics

    NASA Astrophysics Data System (ADS)

    Tiziani, Hans J.

    2010-04-01

    Adaptive optical elements and systems for imaging or laser beam propagation are used for some time in particular in astronomy, where the image quality is degraded by atmospheric turbulence. In astronomical telescopes a deformable mirror is frequently used to compensate wavefront-errors due to deformations of the large mirror, vibrations as well as turbulence and hence to increase the image quality. In the last few years interesting elements like Spatial Light Modulators, SLM's, such as photorefractive crystals, liquid crystals and micro mirrors and membrane mirrors were introduced. The development of liquid crystals and micro mirrors was driven by data projectors as consumer products. They contain typically a matrix of individually addressable pixels of liquid crystals and flip mirrors respectively or more recently piston mirrors for special applications. Pixel sizes are in the order of a few microns and therefore also appropriate as active diffractive elements in digital holography or miniature masks. Although liquid crystals are mainly optimized for intensity modulation; they can be used for phase modulation. Adaptive optics is a technology for beam shaping and wavefront adaptation. The application of spatial light modulators for wavefront adaptation and correction and defect analysis as well as sensing will be discussed. Dynamic digital holograms are generated with liquid crystal devices (LCD) and used for wavefront correction as well as for beam shaping and phase manipulation, for instance. Furthermore, adaptive optics is very useful to extend the measuring range of wavefront sensors and for the wavefront adaptation in order to measure and compare the shape of high precision aspherical surfaces.

  8. Visual adaptation to thin and fat bodies transfers across identity.

    PubMed

    Hummel, Dennis; Rudolf, Anne K; Untch, Karl-Heinz; Grabhorn, Ralph; Mohr, Harald M

    2012-01-01

    Visual perception is highly variable and can be influenced by the surrounding world. Previous research has revealed that body perception can be biased due to adaptation to thin or fat body shapes. The aim of the present study was to show that adaptation to certain body shapes and the resulting perceptual biases transfer across different identities of adaptation and test stimuli. We designed two similar adaptation experiments in which healthy female participants adapted to pictures of either thin or fat bodies and subsequently compared more or less distorted pictures of their own body to their actual body shape. In the first experiment (n = 16) the same identity was used as adaptation and test stimuli (i.e. pictures of the participant's own body) while in the second experiment (n = 16) we used pictures of unfamiliar thin or fat bodies as adaptation stimuli. We found comparable adaptation effects in both experiments: After adaptation to a thin body, participants rated a thinner than actual body picture to be the most realistic and vice versa. We therefore assume that adaptation to certain body shapes transfers across different identities. These results raise the questions of whether some type of natural adaptation occurs in everyday life. Natural and predominant exposure to certain bodily features like body shape--especially the thin ideal in Western societies--could bias perception for these features. In this regard, further research might shed light on aspects of body dissatisfaction and the development of body image disturbances in terms of eating disorders. PMID:22905232

  9. The Nature of Natural Hazards Communication (Invited)

    NASA Astrophysics Data System (ADS)

    Kontar, Y. Y.

    2013-12-01

    of risk governance and increase the awareness of practitioners and decision-makers to the need to adopt proactive policies, leading to a more integrated, participative, and adaptive governance that can respond more efficiently to the increasing uncertainty resulting from escalating natural hazards risk exposure.

  10. Human adaptation to smog

    SciTech Connect

    Evans, G.W. Jacobs, S.V.; Frager, N.B.

    1982-10-01

    This study examined the health effects of human adaptation to photochemical smog. A group of recent arrivals to the Los Angeles air basin were compared to long-term residents of the basin. Evidence for adaptation included greater irritation and respiratory problems among the recent arrivals and desensitization among the long-term residents in their judgments of the severity of the smog problem to their health. There was no evidence for biochemical adaptation as measured by hemoglobin response to oxidant challenge. The results were discussed in terms of psychological adaption to chronic environmental stressors.

  11. Adaptive parallel logic networks

    NASA Technical Reports Server (NTRS)

    Martinez, Tony R.; Vidal, Jacques J.

    1988-01-01

    Adaptive, self-organizing concurrent systems (ASOCS) that combine self-organization with massive parallelism for such applications as adaptive logic devices, robotics, process control, and system malfunction management, are presently discussed. In ASOCS, an adaptive network composed of many simple computing elements operating in combinational and asynchronous fashion is used and problems are specified by presenting if-then rules to the system in the form of Boolean conjunctions. During data processing, which is a different operational phase from adaptation, the network acts as a parallel hardware circuit.

  12. Quantifying the Adaptive Cycle

    PubMed Central

    Angeler, David G.; Allen, Craig R.; Garmestani, Ahjond S.; Gunderson, Lance H.; Hjerne, Olle; Winder, Monika

    2015-01-01

    The adaptive cycle was proposed as a conceptual model to portray patterns of change in complex systems. Despite the model having potential for elucidating change across systems, it has been used mainly as a metaphor, describing system dynamics qualitatively. We use a quantitative approach for testing premises (reorganisation, conservatism, adaptation) in the adaptive cycle, using Baltic Sea phytoplankton communities as an example of such complex system dynamics. Phytoplankton organizes in recurring spring and summer blooms, a well-established paradigm in planktology and succession theory, with characteristic temporal trajectories during blooms that may be consistent with adaptive cycle phases. We used long-term (1994–2011) data and multivariate analysis of community structure to assess key components of the adaptive cycle. Specifically, we tested predictions about: reorganisation: spring and summer blooms comprise distinct community states; conservatism: community trajectories during individual adaptive cycles are conservative; and adaptation: phytoplankton species during blooms change in the long term. All predictions were supported by our analyses. Results suggest that traditional ecological paradigms such as phytoplankton successional models have potential for moving the adaptive cycle from a metaphor to a framework that can improve our understanding how complex systems organize and reorganize following collapse. Quantifying reorganization, conservatism and adaptation provides opportunities to cope with the intricacies and uncertainties associated with fast ecological change, driven by shifting system controls. Ultimately, combining traditional ecological paradigms with heuristics of complex system dynamics using quantitative approaches may help refine ecological theory and improve our understanding of the resilience of ecosystems. PMID:26716453

  13. Decentralized adaptive control

    NASA Technical Reports Server (NTRS)

    Oh, B. J.; Jamshidi, M.; Seraji, H.

    1988-01-01

    A decentralized adaptive control is proposed to stabilize and track the nonlinear, interconnected subsystems with unknown parameters. The adaptation of the controller gain is derived by using model reference adaptive control theory based on Lyapunov's direct method. The adaptive gains consist of sigma, proportional, and integral combination of the measured and reference values of the corresponding subsystem. The proposed control is applied to the joint control of a two-link robot manipulator, and the performance in computer simulation corresponds with what is expected in theoretical development.

  14. A Dastardly Density Deed.

    ERIC Educational Resources Information Center

    Shaw, Mike

    2003-01-01

    Integrates story telling into a science activity on the density of liquids in order to increase student interest. Shows the relationship between mass and volume ratio and how they determine density. Includes teacher notes. (YDS)

  15. Direct Density Derivative Estimation.

    PubMed

    Sasaki, Hiroaki; Noh, Yung-Kyun; Niu, Gang; Sugiyama, Masashi

    2016-06-01

    Estimating the derivatives of probability density functions is an essential step in statistical data analysis. A naive approach to estimate the derivatives is to first perform density estimation and then compute its derivatives. However, this approach can be unreliable because a good density estimator does not necessarily mean a good density derivative estimator. To cope with this problem, in this letter, we propose a novel method that directly estimates density derivatives without going through density estimation. The proposed method provides computationally efficient estimation for the derivatives of any order on multidimensional data with a hyperparameter tuning method and achieves the optimal parametric convergence rate. We further discuss an extension of the proposed method by applying regularized multitask learning and a general framework for density derivative estimation based on Bregman divergences. Applications of the proposed method to nonparametric Kullback-Leibler divergence approximation and bandwidth matrix selection in kernel density estimation are also explored. PMID:27140943

  16. Adaptation and optimization of biological transport networks.

    PubMed

    Hu, Dan; Cai, David

    2013-09-27

    It has been hypothesized that topological structures of biological transport networks are consequences of energy optimization. Motivated by experimental observation, we propose that adaptation dynamics may underlie this optimization. In contrast to the global nature of optimization, our adaptation dynamics responds only to local information and can naturally incorporate fluctuations in flow distributions. The adaptation dynamics minimizes the global energy consumption to produce optimal networks, which may possess hierarchical loop structures in the presence of strong fluctuations in flow distribution. We further show that there may exist a new phase transition as there is a critical open probability of sinks, above which there are only trees for network structures whereas below which loops begin to emerge. PMID:24116821

  17. Neural Adaptation Effects in Conceptual Processing

    PubMed Central

    Marino, Barbara F. M.; Borghi, Anna M.; Gemmi, Luca; Cacciari, Cristina; Riggio, Lucia

    2015-01-01

    We investigated the conceptual processing of nouns referring to objects characterized by a highly typical color and orientation. We used a go/no-go task in which we asked participants to categorize each noun as referring or not to natural entities (e.g., animals) after a selective adaptation of color-edge neurons in the posterior LV4 region of the visual cortex was induced by means of a McCollough effect procedure. This manipulation affected categorization: the green-vertical adaptation led to slower responses than the green-horizontal adaptation, regardless of the specific color and orientation of the to-be-categorized noun. This result suggests that the conceptual processing of natural entities may entail the activation of modality-specific neural channels with weights proportional to the reliability of the signals produced by these channels during actual perception. This finding is discussed with reference to the debate about the grounded cognition view. PMID:26264031

  18. Information geometric density estimation

    NASA Astrophysics Data System (ADS)

    Sun, Ke; Marchand-Maillet, Stéphane

    2015-01-01

    We investigate kernel density estimation where the kernel function varies from point to point. Density estimation in the input space means to find a set of coordinates on a statistical manifold. This novel perspective helps to combine efforts from information geometry and machine learning to spawn a family of density estimators. We present example models with simulations. We discuss the principle and theory of such density estimation.

  19. Rapid Adaptation of a Daphnia magna Population to Metal Stress Is Associated with Heterozygote Excess.

    PubMed

    Hochmuth, Jennifer D; De Meester, Luc; Pereira, Cecília M S; Janssen, Colin R; De Schamphelaere, Karel A C

    2015-08-01

    Although natural populations can harbor evolutionary potential to adapt genetically to chemical stress, it is often thought that natural selection leads to a general reduction of genetic diversity and involves costs. Here, a 10 week microevolution experiment was conducted with a genetically diverse and representative sample of one natural Daphnia magna population that was exposed to copper and zinc. Both Cu- and Zn-selected populations developed a significantly higher metal tolerance (i.e., genetic adaptation), indicated by higher reproduction probabilities of clonal lines in Cu and Zn exposures than observed for the original and control populations. The complete recovery of the population densities after 10 weeks of Zn selection (following an initial decrease of 74%) illustrates an example of evolutionary rescue. Microsatellite genotyping revealed a decrease in clonal diversity but no change in allelic richness, and showed an excess in heterozygosity in the Cu- and Zn-selected populations compared to the control and original populations. The excess heterozygosity in metal-selected populations that we observed has important consequences for risk assessment, as it contributes to the maintenance of a higher allelic diversity under multigenerational chemical exposure. This study is, to our knowledge, the first report of an increase in heterozygosity following multigenerational exposure to metal stress, despite a decline in clonal diversity. In a follow-up study with the Zn-selected populations, we observed no effect of Zn selection on the tolerance to heat and cyanobacteria. However, we observed higher tolerance to Cd in the Zn-selected than in the original and control populations if the 20% effective concentration of Cd was considered (cross-tolerance). Our results suggest only limited costs of adaptation but future research is needed to evaluate the adaptive potential of metal-selected populations to novel stressors and to determine to what extent increased