Science.gov

Sample records for lake constance phylogeny

  1. Lake Constance

    Atmospheric Science Data Center

    2013-04-17

    ... Swiss shores of Lake Constance at the town of Rorschach. Eutrophication, or the process of nutrient enrichment, is rapidly accelerated ... of the value of Lake Constance, efforts to mitigate eutrophication were initiated in the 1970's. MISR was built and is managed ...

  2. Seasonal variation of solitary wave properties in Lake Constance

    NASA Astrophysics Data System (ADS)

    Preusse, M.; Freistühler, H.; Peeters, F.

    2012-04-01

    The properties of internal solitary waves (ISWs) depend on the stratification of the water body. In most climatic regions the stratification in lakes and oceans varies during the year, and hence the properties of the ISWs can also be expected to change over the seasons. On the basis of a long-term temperature time series recorded over 6 years, this paper investigates seasonal changes in the characteristic properties of ISWs in Lake Überlingen, a subbasin of Lake Constance. A large number of ISWs with amplitudes ranging from 3 m to 30 m were identified. More than 15% of the leading ISWs of a wave train were associated with density inversions, often indicating shear instabilities or trapped cores. For all waves the propagation depth and the value of a nonlinearity index nlp providing the degree of nonlinearity were determined, propagation depth being the rest height of the isotherm undergoing maximum displacement and nlp the ratio between wave amplitude and propagation depth. The index nlp was found to be a good parameter for predicting the occurrence of inversions. The statistical analysis of the wave properties derived from the observations revealed that the degree of nonlinearity of the ISWs changes with season. Complementary to the statistical analysis, the seasonally averaged ISW properties were compared with wave prototypes obtained numerically from the Dubreil-Jacotin-Long (DJL) and the stratified Korteweg-deVries (KdV) models. The simulations indicate that the typical stratification and its seasonal variation are responsible for the degree and the seasonality of nonlinearity of the ISWs.

  3. ["Constanze": a trinational project on avian influenza in wild birds at Lake Constance].

    PubMed

    Brunhart, I; Baumer, A; Reist, M; Stärk, K; Griot, C

    2010-11-01

    When highly pathogenic avian influenza H5N1 (HPAI H5N1) arrived at Lake Constance in February 2006, little was known about its ecology and epidemiology in wild birds. In order to prevent virus transmission from wild birds to poultry, the adjacent countries initiated the tri-national, interdisciplinary research program «Constanze» to investigate avian influenza infections in water birds at Lake Constance. In collaboration with government agencies scientists examined the prevalence of AI virus in the region of Lake Constance for a period of 33 months, compared the effectiveness of different surveillance methods and analysed the migration behaviour of water birds. Although virus introduction from regions as far as the Ural Mountains seemed possible based on the migration behaviour of certain species, no influenza A viruses of the highly pathogenic subtype H5N1 (HPAIV) was found. However, influenza A viruses of different low pathogenic subtypes were isolated in 2.2 % of the sampled birds (swabs). Of the different surveillance methods utilised in the program the sampling of so called sentinel birds was particularly efficient. PMID:21043024

  4. Seasonal and habitat-related distribution pattern of Synechococcus genotypes in Lake Constance.

    PubMed

    Becker, Sven; Richl, Petra; Ernst, Anneliese

    2007-10-01

    The abundance and distribution of Synechococcus spp. in the autotrophic picoplankton of Lake Constance, were followed in the pelagic and littoral habitat by qPCR over 2 years. One genotype, represented by isolated phycoerythrin-rich strain BO 8807, showed a seasonal distribution pattern in both habitats. Before a stable thermal stratification, the maximum of both the Synechococcus population and genotype BO 8807 occurred at 15 or 20 m water depth in the pelagic habitat. During the summer stratification, when the absolute abundance of all Synechococcus spp. was highest above 15 m, the absolute and relative abundance of genotype BO 8807 was maximal at 20 m. These results indicate that Synechococcus spp. or single genotypes are present in deep maxima in Lake Constance. The in situ dynamics of genotype BO 8807 is consistent with the observation that isolated strain BO 8807 requires higher phosphate concentrations for maximum growth rates than a strain from the same phylogenetic cluster that dominates the pelagic summer population. In contrast to these findings, low genome numbers of phycocyanin-rich genotype BO 8805 were found temporarily only in both the littoral and pelagic plankton. Microscopy revealed that PC-rich cells in general occurred preferentially in the littoral habitat. We discuss our results with respect to the versatility of picocyanobacteria of the evolutionary lineage VI of cyanobacteria, and a habitat-related distribution pattern of Synechococcus genotypes. PMID:17825073

  5. Underflows in Lake Constance - Numerical Modeling, Instrumental Observations and Sediment Data

    NASA Astrophysics Data System (ADS)

    Eder, Magdalena; Wessels, Martin; Dare, Julian

    2014-05-01

    A torrential rain event in the western Alps in August 2005 caused high flood flows in the rivers Alpine Rhine and Bregenzer Ache which are the main tributaries into Lake Constance. The discharge of the Alpine Rhine reached 2200 m³/s, which is little below a centennial flood event. Discharge of the Bregenzer Ache was estimated to 1350 m³/s which statistically occurs every 100 yr but with a 1000 yr frequency in selected smaller tributaries. The high concentration of suspended solids in the fluvial water increased its density and created an underflow with considerable influence on the lake's hydrodynamics and water quality. Consequences within the lake were directly registered by a mooring (equipped with thermistor chain, sediment trap, current meter, oxygen sensor). Spatial data of the path and form of suspended matter cloud within the lake were gathered using echo sounder and probe measurements (turbidity, temperature, salinity). An underflow with a temperature of 14°C flew with 1.4 km/h some 20 km into the lake. Several days after the event, the fluvial sediments were detected as increased turbidity at the drinking water outtakes around the lake. Sediment cores recovered from the lake bottom show the distribution pattern of the sediments while sidescan data give a picture from proximal sediment structures originating from this event. Further, we modelled this underflow using the three dimensional hydrodynamic and water quality model ELCOM-CAEDYM. The suspended solids module of the model accounts for the impact of the sediment load on water density. Settling is considered using Stokes Law, and resuspension can also be included. The simulation of the August 2005 flood event and comparison with measured data impressively showed the ability to reproduce the most important effects of the flood flow on the lake. Comparative simulations with and without consideration of the coriolis effect indicate an influence of the coriolis force on the flow path of the density

  6. Dust transport and palaeoclimate during the Oldest Dryas in Central Europe - implications from varves (Lake Constance)

    SciTech Connect

    Niessen, F.; Lister, G.; Giovanoli, F.

    1992-10-01

    This paper evaluates evidence for seasonal loess deposits in peri-Alpine Lake Constance at the end of the last Glacial (Oldest Dryas chronozone). The sedimentology of laminated couplets comprising yellow and grey silts evaluates the couplets as varves comprising alternations of loess and glacial silt and clay. The laminae, less than 1 mm thick, include from bottom to top: (1) a matrix of well-sorted, non-graded fine yellow silt with sand-size intraclasts, (2) coarsening-upward grey silt with a cap of fining-upward silt to clay. This is typical and reflects summer and winter deposits (silt and clay, respectively). The authors propose that the lack of grading and the matrix supported fabric is indicative of aeolian transport and interpret the yellow laminae as loess deposits. Volcanic glass intraclasts in the loess layers are probably derived from volcanic terrain to the west of the lake, indicating an easterly palaeowind direction. Deposition of loess in the lake occurred regularly at the beginning of each annual cycle, suggesting the palaeowinds were associated with winter and/or spring conditions. Two transport scenarios are suggested to explain the sand grains scattered in this deep-water lacustrine record. 1. The grains may have been transported as bedload over the annual winter ice-cover of the lake under moderate wind strengths, frozen into the ice, and released for deposition during spring melt. 2. The sand grains were blown directly out onto the lake water by very strong winds during spring. The first scenario is contrary to the general view that loess was transported during summer, and that loess deposits thus reflect summer conditions only. Loess input to the lake shows a transitional decrease after ca. 14.3 kyr BP and cessation at ca. 14 kyr BP, probably as a result of a change of wind behaviour, increased humidity and/or vegetational changes during the Oldest Dryas in central Europe. 62 refs., 8 figs.

  7. Genetic diversity and distribution of periphytic Synechococcus spp. in biofilms and picoplankton of Lake Constance.

    PubMed

    Becker, Sven; Singh, Arvind Kumar; Postius, Christine; Böger, Peter; Ernst, Anneliese

    2004-08-01

    In various water depths of the littoral zone of Lake Constance (Bodensee) cyanobacteria of the Synechococcus-type were isolated from biofilms (periphyton) on three natural substrates and an artificial one (unglazed tiles). From one tile three strains of phycoerythrin (PE)-rich Synechococcus spp. were isolated, the first examples of these organisms in the epibenthos. Phylogenetic inference based on the 16S-23S rRNA intergenic spacer (ITS-1) assigned all periphytic isolates to two clusters of the picophytoplankton clade (evolutionary lineage VI of cyanobacteria). The sequence divergence in the ITS-1 was used to design specific PCR primers to allow direct, culture-independent detection and quantification of isolated Synechococcus strains in natural periphytic and pelagic samples. Denaturing gradient gel electrophoresis (DGGE) analysis revealed depth-related differences of Synechococcus spp. distribution on tiles placed in the littoral zone. Synechococcus genotypes were observed which occurred in both the periphyton (on tiles) and in the pelagic picoplankton. A strain with one of these genotypes, Synechococcus sp. BO 8805, was isolated from the pelagic zone in 1988. Its genotype was found on tiles that had been exposed at different water depths in the littoral zone in spring and autumn of the year 2000. Quantitative analysis with a genotype-specific TaqMan probe and real-time Taq nuclease assays (TNA) confirmed its presence in the pelagic zone, although appearance of this and related genotypes was highly irregular and exhibited strong differences between consecutive years. Our results show that the ability to form significant subpopulations in pelagic and periphytic communities exists in three out of four phylogenetic clusters of Synechococcus spp. in Lake Constance. This versatility may be a key feature in the ubiquity of the evolutionary lineage VI of cyanobacteria. PMID:19712413

  8. Spatially explicit exposure assessment for small streams in catchments of the orchard growing region `Lake Constance

    NASA Astrophysics Data System (ADS)

    Golla, B.; Bach, M.; Krumpe, J.

    2009-04-01

    1. Introduction Small streams differ greatly from the standardised water body used in the context of aquatic risk assessment for the regulation of plant protection products in Germany. The standard water body is static, with a depth of 0.3 m and a width of 1.0 m. No dilution or water replacement takes place. Spray drift happens always in direction to the water body. There is no variability in drift deposition rate (90th percentile spray drift deposition values [2]). There is no spray drift filtering by vegetation. The application takes place directly adjacent to the water body. In order to establish a more realistic risk assessment procedure the Federal Office for Consumer Protection and Food Safety (BVL) and the Federal Environment Agency (UBA) aggreed to replace deterministic assumptions with data distributions and spatially explicit data and introduce probabilistic methods [3, 4, 5]. To consider the spatial and temporal variability in the exposure situations of small streams the hydraulic and morphological characteristics of catchments need to be described as well as the spatial distribution of fields treated with pesticides. As small streams are the dominant type of water body in most German orchard regions, we use the growing region Lake Constance as pilot region. 2. Materials and methods During field surveys we derive basic morphological parameters for small streams in the Lake Constance region. The mean water width/depth ratio is 13 with a mean depth of 0.12 m. The average residence time is 5.6 s/m (n=87) [1]. Orchards are mostly located in the upper parts of the catchments. Based on an authoritative dataset on rivers and streams of Germany (ATKIS DLM25) we constructed a directed network topology for the Lake Constance region. The gradient of the riverbed is calculated for river stretches of > 500 m length. The network for the pilot region consists of 2000 km rivers and streams. 500 km stream length are located within a distance of 150 m to orchards. Within

  9. Impact of submerged aquatic macrophytes on 3-dim current systems and hydrodynamic transport processes in Lake Constance

    NASA Astrophysics Data System (ADS)

    Wolf, Thomas; Lüddeke, Frauke; Thiange, Christophe

    2015-04-01

    According to the assessment criteria of the European water framework directive Lake Constance is having a good water quality. Nevertheless upcoming criteria using environmental quality measures show that there are still problems with respect to micropollutants. In fact, we observe significantly enhanced concentrations of micropollutants close to river mouths and in the areas of shallow water zones within Lake Constance compared to deep water concentrations. These findings are caused by river water plumes which can flow over distances of kilometers in the lake without being diluted or mixed only weakly with the surrounding lake water body. Besides, in the area of interest exist large populations of submerged aquatic macrophytes (SAM). There is only little knowledge, how these influence the distribution and transport processes of micropollutants. In order to assess the impact and distribution of river water plumes in different areas of the lake we implemented a 3-dim hydrodynamic model using DELFT3D-FLOW on a locally refined numerical grid which enables to cover different process scales of the distribution of river water bodies ranging from a few meters up to basin wide scales in the order of a few kilometers. We used numerical tracers (conservative and non-conservative) in order to quantify the impact of different abstract substance classes which are distinguished by their decay rates. In order to asses the influence of SAM populations on current field and transport processes we used a special simulation technique - the trachytope concept. The results of our 3-dim hydrodynamic model showed significantly changed current velocities, residence times and age of water parameters within the SAM areas compared to the control simulation without SAM. By simulating the propagation of coliform bacteria using numerical tracers with spatially and temporarily variable decay rates, we found complex impact pattern of the SAM on the distribution of these potentially harmful

  10. Role of pressure, temperature, salinity, lithology, and structure in hydrocarbon accumulation in Constance Bayou, Deep Lake, and southeast Little Pecan Lake Fields, Cameron Parish, Louisiana

    SciTech Connect

    Harrison, F.W. III

    1980-01-01

    Pressure, temperature, salinity, lithology, and structural studies indicate that hydrocarbons in Deep Lake, Constance Bayou, and Little Pecan Lake Fields, were generated in the shale beds of the hard geopressured zone and migrated upward along major growth faults. The hydrocarbons were originally dissolved in hot fresh pore water and came out of solution in the overlying low temperature and pressure zones, accumulating in the sand beds of the first structural traps encountered. By examining regional cross sections and anomaly maps, fluid escape routes taken by the hot pore water containing dissolved hydrocarbons can be identified. Areas below which a vertical flush of hot fresh pore water from the hard geopressured zone has occurred have 3 identifying characteristics: low fluid pressures, high formation water salinity values, and presence of residual high pressure areas. These areas are considered to be highly prospective places to search for hydrocarbon accumulations.

  11. Pb isotopes in sediments of Lake Constance, Central Europe constrain the heavy metal pathways and the pollution history of the catchment, the lake and the regional atmosphere

    SciTech Connect

    Kober, B.; Wessels, M.; Bollhoefer, A.; Mangini

    1999-05-01

    Pb isotope ratios and Pb concentrations of well-dated sediments of Lake Constance, Central Europe have been analyzed using thermal ion mass spectrometry. Sequential extraction studies indicated isotope homogeneity of the leachable Pb components within the investigated layers. Since the middle of the 19th century a significant anthropogenic Pb component appeared in the lake sediments, and rapidly approaches concentration levels similar to that of the geogenic Pb background (20 ppm) at the beginning of the 20th century. Anthropogenic Pb was predominantly transferred to the lake sediments via the atmosphere. Pb sources were coal combustion, industrial ore processing and leaded gasoline. The flux of a fluvial Pb component to the lake sediments, additive to atmospheric Pb deposition, peaked in about 1960. This flux is attributed to (re)mobilization of Pb from polluted parts of the lake catchment, and indicates the change of catchment soils from a pollution sink to a heavy metal source. The strong reduction of anthropogenic Pb in the uppermost lake sediments since the 1960s has been caused by advances of environmental protection. The lake sediments record the changing fluxes and the isotope composition of the deposited aeolian Pb pollution. During the 20th century aeolian Pb fluxes to the lake sediments were in the range of 1--4 {micro}g/cm{sup 2}/a. During peak emission periods of gasoline Pb to the atmosphere (1960--1990) the aerosol Pb isotope composition was rather constant ({sup 206}Pb/{sup 207}Pb: 1.12--1.13) and probably a mixture of Canadian and Australian with Russian and Central European Pb types. Aeolian Pb isotope and Pb flux trends in the lake sediments as a whole agree well with the trends found in Alpine glaciers (Doering et al., 1997a,b) and in ombrotrophic peat bogs of Switzerland (Shotyk et al., 1996). However, different industrial Pb components were deposited in the archives of aeolian pollution during the early 20th century.

  12. Multi-level approach for the integrated assessment of polar organic micropollutants in an international lake catchment: the example of Lake Constance.

    PubMed

    Moschet, Christoph; Götz, Christian; Longrée, Philipp; Hollender, Juliane; Singer, Heinz

    2013-07-01

    Polar organic micropollutants (MPs) can have ecotoxicological effects on aquatic ecosystems and their occurrence in drinking water is a threat to public health. An extensive exposure assessment of MPs in large river and lake catchments is a necessary but challenging proposition for researchers and regulators. To get a complete picture of MP exposure in a large catchment, we employed a novel integrated strategy including MP measurement in the international catchment of Lake Constance and mass-flux modeling. A comprehensive screening of 252 MPs in the lake water by high-resolution mass spectrometry was used to identify the most commonly present MPs for the study site. It was found that the wastewater borne MPs diclofenac, carbamazepine, sulfamethoxazole, acesulfame, sucralose, benzotriazole, and methylbenzotriazole accounted for the most frequent and prominent findings. The concentration pattern of these compounds in the catchment was calculated based on regionalized inputs from wastewater treatment plants (WWTPs) and substance specific elimination rates. In 52, 8, and 3 of the 112 investigated river locations the concentration exceeded the predicted no-effect levels for diclofenac, sulfamethoxazole and carbamazepine, respectively. By coupling the catchment and lake model the effect of future trends in usage as well as possible mitigation options were evaluated for the tributaries and the lake. The upgrade of the major WWTPs in the catchment with a postozonation step would lead to a load reduction between 32% and 52% for all substances except for sucralose (10%). PMID:23441970

  13. Water Quality Monitoring for Lake Constance with a Physically Based Algorithm for MERIS Data

    PubMed Central

    Odermatt, Daniel; Heege, Thomas; Nieke, Jens; Kneubühler, Mathias; Itten, Klaus

    2008-01-01

    A physically based algorithm is used for automatic processing of MERIS level 1B full resolution data. The algorithm is originally used with input variables for optimization with different sensors (i.e. channel recalibration and weighting), aquatic regions (i.e. specific inherent optical properties) or atmospheric conditions (i.e. aerosol models). For operational use, however, a lake-specific parameterization is required, representing an approximation of the spatio-temporal variation in atmospheric and hydrooptic conditions, and accounting for sensor properties. The algorithm performs atmospheric correction with a LUT for at-sensor radiance, and a downhill simplex inversion of chl-a, sm and y from subsurface irradiance reflectance. These outputs are enhanced by a selective filter, which makes use of the retrieval residuals. Regular chl-a sampling measurements by the Lake's protection authority coinciding with MERIS acquisitions were used for parameterization, training and validation.

  14. Methane release from sediment seeps to the atmosphere is counteracted by highly active Methylococcaceae in the water column of deep oligotrophic Lake Constance.

    PubMed

    Bornemann, Maren; Bussmann, Ingeborg; Tichy, Lucas; Deutzmann, Jörg; Schink, Bernhard; Pester, Michael

    2016-08-01

    Methane emissions from freshwater environments contribute substantially to global warming but are under strong control of aerobic methane-oxidizing bacteria. Recently discovered methane seeps (pockmarks) in freshwater lake sediments have the potential to bypass this control by their strong outgassing activity. Whether this is counteracted by pelagic methanotrophs is not well understood yet. We used a (3)H-CH4-radiotracer technique and pmoA-based molecular approaches to assess the activity, abundance and community structure of pelagic methanotrophs above active pockmarks in deep oligotrophic Lake Constance. Above profundal pockmarks, methane oxidation rates (up to 458 nmol CH4 l(-1) d(-1)) exceeded those of the surrounding water column by two orders of magnitude and coincided with maximum methanotroph abundances of 0.6% of the microbial community. Phylogenetic analysis indicated a dominance of members of the Methylococcaceae in the water column of both, pockmark and reference sites, with most of the retrieved sequences being associated with a water-column specific clade. Communities at pockmark and reference locations also differed in parts, which was likely caused by entrainment of sediment-hosted methanotrophs at pockmark sites. Our results show that the release of seep-derived methane to the atmosphere is counteracted by a distinct methanotrophic community with a pronounced activity throughout bottom waters. PMID:27267930

  15. First evidence for postzygotic reproductive isolation between two populations of Eurasian perch (Perca fluviatilis L.) within Lake Constance

    PubMed Central

    Behrmann-Godel, Jasminca; Gerlach, Gabriele

    2008-01-01

    Background The evolution of reproductive traits, such as hybrid incompatibility (postzygotic isolation) and species recognition (prezygotic isolation), have shown their key role in speciation. Theoretical modeling has recently predicted that close linkage between genes controlling pre- and postzygotic reproductive isolation could accelerate the conditions for speciation. Postzygotic isolation could develop during the sympatric speciation process contributing to the divergence of populations. Using hybrid fitness as a measure of postzygotic reproductive isolation, we empirically studied population divergence in perch (Perca fluviatilis L.) from two genetically divergent populations within a lake. Results During spawning time of perch we artificially created parental offspring and F1 hybrids of the two populations and studied fertilization rate and hatching success under laboratory conditions. The combined fitness measure (product of fertilization rate and hatching success) of F1 hybrids was significantly reduced compared to offspring from within population crosses. Conclusion Our results suggest intrinsic genetic incompatibility between the two populations and indicate that population divergence between two populations of perch inhabiting the same lake may indeed be promoted by postzygotic isolation. PMID:18218080

  16. Rethinking Colour Constancy.

    PubMed

    Logvinenko, Alexander D; Funt, Brian; Mirzaei, Hamidreza; Tokunaga, Rumi

    2015-01-01

    Colour constancy needs to be reconsidered in light of the limits imposed by metamer mismatching. Metamer mismatching refers to the fact that two objects reflecting metameric light under one illumination may reflect non-metameric light under a second; so two objects appearing as having the same colour under one illuminant can appear as having different colours under a second. Yet since Helmholtz, object colour has generally been believed to remain relatively constant. The deviations from colour constancy registered in experiments are usually thought to be small enough that they do not contradict the notion of colour constancy. However, it is important to determine how the deviations from colour constancy relate to the limits metamer mismatching imposes on constancy. Hence, we calculated metamer mismatching's effect for the 20 Munsell papers and 8 pairs of illuminants employed in the colour constancy study by Logvinenko and Tokunaga and found it to be so extensive that the two notions-metamer mismatching and colour constancy-must be mutually exclusive. In particular, the notion of colour constancy leads to some paradoxical phenomena such as the possibility of 20 objects having the same colour under chromatic light dispersing into a hue circle of colours under neutral light. Thus, colour constancy refers to a phenomenon, which because of metamer mismatching, simply cannot exist. Moreover, it obscures the really important visual phenomenon; namely, the alteration of object colours induced by illumination change. We show that colour is not an independent, intrinsic attribute of an object, but rather an attribute of an object/light pair, and then define a concept of material colour in terms of equivalence classes of such object/light pairs. We suggest that studying the shift in material colour under a change in illuminant will be more fruitful than pursuing colour constancy's false premise that colour is an intrinsic attribute of an object. PMID:26356217

  17. Rethinking Colour Constancy

    PubMed Central

    Logvinenko, Alexander D.; Funt, Brian; Mirzaei, Hamidreza; Tokunaga, Rumi

    2015-01-01

    Colour constancy needs to be reconsidered in light of the limits imposed by metamer mismatching. Metamer mismatching refers to the fact that two objects reflecting metameric light under one illumination may reflect non-metameric light under a second; so two objects appearing as having the same colour under one illuminant can appear as having different colours under a second. Yet since Helmholtz, object colour has generally been believed to remain relatively constant. The deviations from colour constancy registered in experiments are usually thought to be small enough that they do not contradict the notion of colour constancy. However, it is important to determine how the deviations from colour constancy relate to the limits metamer mismatching imposes on constancy. Hence, we calculated metamer mismatching’s effect for the 20 Munsell papers and 8 pairs of illuminants employed in the colour constancy study by Logvinenko and Tokunaga and found it to be so extensive that the two notions—metamer mismatching and colour constancy—must be mutually exclusive. In particular, the notion of colour constancy leads to some paradoxical phenomena such as the possibility of 20 objects having the same colour under chromatic light dispersing into a hue circle of colours under neutral light. Thus, colour constancy refers to a phenomenon, which because of metamer mismatching, simply cannot exist. Moreover, it obscures the really important visual phenomenon; namely, the alteration of object colours induced by illumination change. We show that colour is not an independent, intrinsic attribute of an object, but rather an attribute of an object/light pair, and then define a concept of material colour in terms of equivalence classes of such object/light pairs. We suggest that studying the shift in material colour under a change in illuminant will be more fruitful than pursuing colour constancy’s false premise that colour is an intrinsic attribute of an object. PMID:26356217

  18. Colour constancy in insects.

    PubMed

    Chittka, Lars; Faruq, Samia; Skorupski, Peter; Werner, Annette

    2014-06-01

    Colour constancy is the perceptual phenomenon that the colour of an object appears largely unchanged, even if the spectral composition of the illuminating light changes. Colour constancy has been found in all insect species so far tested. Especially the pollinating insects offer a remarkable opportunity to study the ecological significance of colour constancy since they spend much of their adult lives identifying and choosing between colour targets (flowers) under continuously changing ambient lighting conditions. In bees, whose colour vision is best studied among the insects, the compensation provided by colour constancy is only partial and its efficiency depends on the area of colour space. There is no evidence for complete 'discounting' of the illuminant in bees, and the spectral composition of the light can itself be used as adaptive information. In patchy illumination, bees adjust their spatial foraging to minimise transitions between variously illuminated zones. Modelling allows the quantification of the adaptive benefits of various colour constancy mechanisms in the economy of nature. We also discuss the neural mechanisms and cognitive operations that might underpin colour constancy in insects. PMID:24647930

  19. Stereoscopic depth constancy.

    PubMed

    Guan, Phillip; Banks, Martin S

    2016-06-19

    Depth constancy is the ability to perceive a fixed depth interval in the world as constant despite changes in viewing distance and the spatial scale of depth variation. It is well known that the spatial frequency of depth variation has a large effect on threshold. In the first experiment, we determined that the visual system compensates for this differential sensitivity when the change in disparity is suprathreshold, thereby attaining constancy similar to contrast constancy in the luminance domain. In a second experiment, we examined the ability to perceive constant depth when the spatial frequency and viewing distance both changed. To attain constancy in this situation, the visual system has to estimate distance. We investigated this ability when vergence, accommodation and vertical disparity are all presented accurately and therefore provided veridical information about viewing distance. We found that constancy is nearly complete across changes in viewing distance. Depth constancy is most complete when the scale of the depth relief is constant in the world rather than when it is constant in angular units at the retina. These results bear on the efficacy of algorithms for creating stereo content.This article is part of the themed issue 'Vision in our three-dimensional world'. PMID:27269596

  20. Stereoscopic depth constancy

    PubMed Central

    Guan, Phillip

    2016-01-01

    Depth constancy is the ability to perceive a fixed depth interval in the world as constant despite changes in viewing distance and the spatial scale of depth variation. It is well known that the spatial frequency of depth variation has a large effect on threshold. In the first experiment, we determined that the visual system compensates for this differential sensitivity when the change in disparity is suprathreshold, thereby attaining constancy similar to contrast constancy in the luminance domain. In a second experiment, we examined the ability to perceive constant depth when the spatial frequency and viewing distance both changed. To attain constancy in this situation, the visual system has to estimate distance. We investigated this ability when vergence, accommodation and vertical disparity are all presented accurately and therefore provided veridical information about viewing distance. We found that constancy is nearly complete across changes in viewing distance. Depth constancy is most complete when the scale of the depth relief is constant in the world rather than when it is constant in angular units at the retina. These results bear on the efficacy of algorithms for creating stereo content. This article is part of the themed issue ‘Vision in our three-dimensional world’. PMID:27269596

  1. Auditory color constancy

    NASA Astrophysics Data System (ADS)

    Kluender, Keith R.; Kiefte, Michael

    2003-10-01

    It is both true and efficient that sensorineural systems respond to change and little else. Perceptual systems do not record absolute level be it loudness, pitch, brightness, or color. This fact has been demonstrated in every sensory domain. For example, the visual system is remarkable at maintaining color constancy over widely varying illumination such as sunlight and varieties of artificial light (incandescent, fluorescent, etc.) for which spectra reflected from objects differ dramatically. Results will be reported for a series of experiments demonstrating how auditory systems similarly compensate for reliable characteristics of spectral shape in acoustic signals. Specifically, listeners' perception of vowel sounds, characterized by both local (e.g., formants) and broad (e.g., tilt) spectral composition, changes radically depending upon reliable spectral composition of precursor signals. These experiments have been conducted using a variety of precursor signals consisting of meaningful and time-reversed vocoded sentences, as well as novel nonspeech precursors consisting of multiple filter poles modulating sinusoidally across a source spectrum with specific local and broad spectral characteristics. Constancy across widely varying spectral compositions shares much in common with visual color constancy. However, auditory spectral constancy appears to be more effective than visual constancy in compensating for local spectral fluctuations. [Work supported by NIDCD DC-04072.

  2. Binaural Loudness Constancy.

    PubMed

    Culling, John F; Dare, Helen

    2016-01-01

    In binaural loudness summation, diotic presentation of a sound usually produces greater loudness than monaural presentation. However, experiments using loudspeaker presentation with and without earplugs find that magnitude estimates of loudness are little altered by the earplug, suggesting a form of loudness constancy. We explored the significance of controlling stimulation of the second ear using meatal occlusion as opposed to the deactivation of one earphone. We measured the point of subjective loudness equality (PSLE) for monaural vs. binaural presentation using an adaptive technique for both speech and noise. These stimuli were presented in a reverberant room over a loudspeaker to the right of the listener, or over lightweight headphones. Using the headphones, stimuli were either presented dry, or matched to those of the loudspeaker by convolution with impulse responses measured from the loudspeaker to the listener position, using an acoustic manikin. The headphone response was also compensated. Using the loudspeaker, monaural presentation was achieved by instructing the listener to block the left ear with a finger. Near perfect binaural loudness constancy was observed using loudspeaker presentation, while there was a summation effect of 3-6 dB for both headphone conditions. However, only partial constancy was observed when meatal occlusion was simulated. These results suggest that there may be contributions to binaural loudness constancy from residual low frequencies at the occluded ear as well as a cognitive element, which is activated by the knowledge that one ear is occluded. PMID:27080647

  3. Phylogenies of microcystin-producing cyanobacteria in the lower Laurentian Great Lakes suggest extensive genetic connectivity.

    PubMed

    Davis, Timothy W; Watson, Susan B; Rozmarynowycz, Mark J; Ciborowski, Jan J H; McKay, Robert Michael; Bullerjahn, George S

    2014-01-01

    Lake St. Clair is the smallest lake in the Laurentian Great Lakes system. MODIS satellite imagery suggests that high algal biomass events have occurred annually along the southern shore during late summer. In this study, we evaluated these events and tested the hypothesis that summer bloom material derived from Lake St. Clair may enter Lake Erie via the Detroit River and represent an overlooked source of potentially toxic Microcystis biomass to the western basin of Lake Erie. We conducted a seasonally and spatially resolved study carried out in the summer of 2013. Our goals were to: 1) track the development of the 2013 summer south-east shore bloom 2) conduct a spatial survey to characterize the extent of toxicity, taxonomic diversity of the total phytoplankton population and the phylogenetic diversity of potential MC-producing cyanobacteria (Microcystis, Planktothrix and Anabaena) during a high biomass event, and 3) compare the strains of potential MC-producers in Lake St. Clair with strains from Lake Erie and Lake Ontario. Our results demonstrated a clear predominance of cyanobacteria during a late August bloom event, primarily dominated by Microcystis, which we traced along the Lake St. Clair coastline downstream to the Detroit River's outflow at Lake Erie. Microcystin levels exceeded the Province of Ontario Drinking Water Quality Standard (1.5 µg L(-1)) for safe drinking water at most sites, reaching up to five times this level in some areas. Microcystis was the predominant microcystin producer, and all toxic Microcystis strains found in Lake St. Clair were genetically similar to toxic Microcystis strains found in lakes Erie and Ontario. These findings suggest extensive genetic connectivity among the three systems. PMID:25207941

  4. Phylogenies of Microcystin-Producing Cyanobacteria in the Lower Laurentian Great Lakes Suggest Extensive Genetic Connectivity

    PubMed Central

    Davis, Timothy W.; Watson, Susan B.; Rozmarynowycz, Mark J.; Ciborowski, Jan J. H.; McKay, Robert Michael; Bullerjahn, George S.

    2014-01-01

    Lake St. Clair is the smallest lake in the Laurentian Great Lakes system. MODIS satellite imagery suggests that high algal biomass events have occurred annually along the southern shore during late summer. In this study, we evaluated these events and tested the hypothesis that summer bloom material derived from Lake St. Clair may enter Lake Erie via the Detroit River and represent an overlooked source of potentially toxic Microcystis biomass to the western basin of Lake Erie. We conducted a seasonally and spatially resolved study carried out in the summer of 2013. Our goals were to: 1) track the development of the 2013 summer south-east shore bloom 2) conduct a spatial survey to characterize the extent of toxicity, taxonomic diversity of the total phytoplankton population and the phylogenetic diversity of potential MC-producing cyanobacteria (Microcystis, Planktothrix and Anabaena) during a high biomass event, and 3) compare the strains of potential MC-producers in Lake St. Clair with strains from Lake Erie and Lake Ontario. Our results demonstrated a clear predominance of cyanobacteria during a late August bloom event, primarily dominated by Microcystis, which we traced along the Lake St. Clair coastline downstream to the Detroit River's outflow at Lake Erie. Microcystin levels exceeded the Province of Ontario Drinking Water Quality Standard (1.5 µg L−1) for safe drinking water at most sites, reaching up to five times this level in some areas. Microcystis was the predominant microcystin producer, and all toxic Microcystis strains found in Lake St. Clair were genetically similar to toxic Microcystis strains found in lakes Erie and Ontario. These findings suggest extensive genetic connectivity among the three systems. PMID:25207941

  5. Flower constancy in insect pollinators

    PubMed Central

    Ratnieks, Francis L.W.

    2011-01-01

    As first noted by Aristotle in honeybee workers, many insect pollinators show a preference to visit flowers of just one species during a foraging trip. This “flower constancy” probably benefits plants, because pollen is more likely to be deposited on conspecific stigmas. But it is less clear why insects should ignore rewarding alternative flowers. Many researchers have argued that flower constancy is caused by constraints imposed by insect nervous systems rather than because flower constancy is itself an efficient foraging method. We argue that this view is unsatisfactory because it both fails to explain why foragers flexibly adjust the degree of flower constancy and does not explain why foragers of closely related species show different degrees of constancy. While limitations of the nervous system exist and are likely to influence flower constancy to some degree, the observed behavioural flexibility suggests that flower constancy is a successful foraging strategy given the insect’s own information about different foraging options. PMID:22446521

  6. Origin and Phylogeny of Microbes Living in Permanent Antarctic Lake Ice.

    PubMed

    Gordon, D. A.; Priscu, J.; Giovannoni, S.

    2000-04-01

    A BSTRACTThe phylogenetic diversity of bacteria and cyanobacteria colonizing sediment particles in the permanent ice cover of an Antarctic lake was characterized by analyses of 16S rRNA genes amplified from environmental DNA. Samples of mineral particles were collected from a depth of 2.5 m in the 4-m-thick ice cover of Lake Bonney, McMurdo Dry Valleys, Antarctica. A rRNA gene clone library of 198 clones was made and characterized by sequencing and oligonucleotide probe hybridization. The library was dominated by representatives of the cyanobacteria, proteobacteria, and Planctomycetales, but also contained diverse clones representing many other microbial groups, including the Acidobacterium/Holophaga division, the Green Non-Sulfur division, and the Actinobacteria. Six oligonucleotide probes were made for the most abundant clades recovered in the library. To determine whether the ice microbial community might originate from wind dispersal of the algal mats found elsewhere in Taylor Valley, the probes were hybridized to 16S rDNAs amplified from three samples of terrestrial cyanobacterial mats collected at nearby sites, as well as to bacterial 16S rDNAs from the lake ice community. The results demonstrate the presence of a diverse microbial community dominated by cyanobacteria in the lake ice, and also show that the dominant members of the lake ice microbial community are found in terrestrial mats elsewhere in the area. The lake ice microbial community appears to be dominated by organisms that are not uniquely adapted to the lake ice ecosystem, but instead are species that originate elsewhere in the surrounding region and opportunistically colonize the unusual habitat provided by the sediments suspended in lake ice. PMID:12035096

  7. Synaesthesia and colour constancy.

    PubMed

    Erskine, Holly; Mattingley, Jason B; Arnold, Derek H

    2013-04-01

    Grapheme-colour synaesthesia is an atypical condition characterized by the perception of colours when reading achromatic text. We investigated the level of colour processing responsible for these experiences. To do so, we tapped a central characteristic of colour perception. In different lighting conditions the same wavelength of light can prompt the perception of different colours. This helps humans recognize distinctive coloured objects despite changes in illumination. We wanted to see if synaesthetic colours were generated at a neural locus that was susceptible to colour constancy analyses. We used colour matching and naming tasks to examine interactions between simulated coloured illuminants and synaesthetic colours. Neither synaesthetic colour matching or naming was impacted. This contrasted with non-synaesthetic control participants, who performed the colour-matching task with graphemes physically coloured to mimic synaesthesia. Our data suggest that synaesthetic colour signals are not generated at lower-levels of colour processing, but are introduced at higher levels of analysis and are therefore not impacted by the processes responsible for perceptual constancy. PMID:22487049

  8. Surveys, simulation and single-cell assays relate function and phylogeny in a lake ecosystem.

    PubMed

    Preheim, Sarah P; Olesen, Scott W; Spencer, Sarah J; Materna, Arne; Varadharajan, Charuleka; Blackburn, Matthew; Friedman, Jonathan; Rodríguez, Jorge; Hemond, Harold; Alm, Eric J

    2016-01-01

    Much remains unknown about what drives microbial community structure and diversity. Highly structured environments might offer clues. For example, it may be possible to identify metabolically similar species as groups of organisms that correlate spatially with the geochemical processes they carry out. Here, we use a 16S ribosomal RNA gene survey in a lake that has chemical gradients across its depth to identify groups of spatially correlated but phylogenetically diverse organisms. Some groups had distributions across depth that aligned with the distributions of metabolic processes predicted by a biogeochemical model, suggesting that these groups performed biogeochemical functions. A single-cell genetic assay showed, however, that the groups associated with one biogeochemical process, sulfate reduction, contained only a few organisms that have the genes required to reduce sulfate. These results raise the possibility that some of these spatially correlated groups are consortia of phylogenetically diverse and metabolically different microbes that cooperate to carry out geochemical functions. PMID:27562262

  9. Invertebrates as indicators for chemical stress in sewage-influenced stream systems: toxic and endocrine effects in gammarids and reactions at the community level in two tributaries of Lake Constance, Schussen and Argen.

    PubMed

    Peschke, Katharina; Geburzi, Jonas; Köhler, Heinz-R; Wurm, Karl; Triebskorn, Rita

    2014-08-01

    The present study investigates the impact of releases from waste water treatment plants and storm water overflow basins on gammarids and other macrozoobenthos. The study relates to a recent upgrading of a waste water treatment plant (Langwiese) at the Schussen river, an important tributary to Lake Constance. Samples were taken at different sites at the Schussen river upstream and downstream of a storm water overflow basin and the waste water treatment plant Langwiese and, in parallel, at the Argen river, a less polluted reference stream. We assessed the influence of water quality on the distribution of macrozoobenthos and on the health of gammarid populations by a variety of ecotoxicological methods including biomarkers prior to the expansion of the waste water treatment plant. Through histopathological studies, the impact of parasites on host tissue health was evaluated. Analyses of heat shock protein (hsp70) levels allowed us to draw conclusions about the proteotoxicity-related stress status of the organisms. Furthermore, gammarid populations from all sites were investigated in respect to sex ratio, parasitism rate, and fecundity. Macrozoobenthos community integrity was determined by means of the saprobic index and the abundance as well as by the number of taxa. In gammarids, the sex ratio was significantly shifted towards females, fecundity was significantly decreased, and the hsp70 level was significantly increased downstream of the waste water treatment plant Langwiese, compared to the upstream sampling site. Similarly, these effects could be detected downstream of three small storm water overflow basins. In the macrozoobenthos communities, the abundance of taxa, the number of taxa, the number of ephemeroptera, plecoptera, and trichoptera taxa (EPT-taxa), and the number of sensitive taxa decreased downstream of the storm water overflow basin Mariatal as well as downstream of the waste water treatment plant Langwiese. Our study showed, that waste water

  10. Adaptive Color Constancy Using Faces.

    PubMed

    Bianco, Simone; Schettini, Raimondo

    2014-08-01

    In this work we design an adaptive color constancy algorithm that, exploiting the skin regions found in faces, is able to estimate and correct the scene illumination. The algorithm automatically switches from global to spatially varying color correction on the basis of the illuminant estimations on the different faces detected in the image. An extensive comparison with both global and local color constancy algorithms is carried out to validate the effectiveness of the proposed algorithm in terms of both statistical and perceptual significance on a large heterogeneous data set of RAW images containing faces. PMID:26353334

  11. Lightness Constancy in Surface Visualization.

    PubMed

    Szafir, Danielle Albers; Sarikaya, Alper; Gleicher, Michael

    2016-09-01

    Color is a common channel for displaying data in surface visualization, but is affected by the shadows and shading used to convey surface depth and shape. Understanding encoded data in the context of surface structure is critical for effective analysis in a variety of domains, such as in molecular biology. In the physical world, lightness constancy allows people to accurately perceive shadowed colors; however, its effectiveness in complex synthetic environments such as surface visualizations is not well understood. We report a series of crowdsourced and laboratory studies that confirm the existence of lightness constancy effects for molecular surface visualizations using ambient occlusion. We provide empirical evidence of how common visualization design decisions can impact viewers' abilities to accurately identify encoded surface colors. These findings suggest that lightness constancy aids in understanding color encodings in surface visualization and reveal a correlation between visualization techniques that improve color interpretation in shadow and those that enhance perceptions of surface depth. These results collectively suggest that understanding constancy in practice can inform effective visualization design. PMID:26584495

  12. Gender Constancy and Television Viewing.

    ERIC Educational Resources Information Center

    Luecke-Aleksa, Diane; And Others

    1995-01-01

    Explored gender constancy's interaction with television viewing, using videotapes of television viewing and viewing diaries for 5-year olds. Gender-constant boys focused on more male characters and watched more action and sports programs than preconstant boys. Gender-constant girls viewed more action programming than preconstant girls. Acquisition…

  13. Constructing Phylogenies.

    ERIC Educational Resources Information Center

    Bilardello, Nicholas; Valdes, Linda

    1998-01-01

    Introduces a method for constructing phylogenies using molecular traits and elementary graph theory. Discusses analyzing molecular data and using weighted graphs, minimum-weight spanning trees, and rooted cube phylogenies to display the data. (DDR)

  14. Color constancy in Japanese animation

    NASA Astrophysics Data System (ADS)

    Ichihara, Yasuyo G.

    2006-01-01

    In this study, we measure the colors used in a Japanese Animations. The result can be seen on CIE-xy color spaces. It clearly shows that the color system is not a natural appearance system but an imagined and artistic appearance system. Color constancy of human vision can tell the difference in skin and hair colors between under moonlight and day light. Human brain generates a match to the memorized color of an object from daylight viewing conditions to the color of the object in different viewing conditions. For example, Japanese people always perceive the color of the Rising Sun in the Japanese flag as red even in a different viewing condition such as under moonlight. Color images captured by a camera cannot present those human perceptions. However, Japanese colorists in Animation succeeded in painting the effects of color constancy not only under moonlight but also added the memory matching colors. They aim to create a greater impact on viewer's perceptions by using the effect of the memory matching colors. In this paper, we propose the Imagined Japanese Animation Color System. This system in art is currently a subject of research in Japan. Its importance is that it could also provide an explanation on how human brain perceives the same color under different viewing conditions.

  15. Flower Constancy, Insect Psychology, and Plant Evolution

    NASA Astrophysics Data System (ADS)

    Chittka, Lars; Thomson, James D.; Waser, Nickolas M.

    Individuals of some species of pollinating insects tend to restrict their visits to only a few of the available plant species, in the process bypassing valuable food sources. The question of why this flower constancy exists is a rich and important one with implications for the organization of natural communities of plants, floral evolution, and our understanding of the learning processes involved in finding food. Some scientists have assumed that flower constancy is adaptive per se. Others argued that constancy occurs because memory capacity for floral features in insects is limited, but attempts to identify the limitations often remained rather simplistic. We elucidate now different sensory and motor memories from natural foraging tasks are stored and retrieved, using concepts from modern learning science and visual search, and conclude that flower constancy is likely to have multiple causes. Possible constraints favoring constancy are interference sensitivity of short-term memory, and temporal limitations on retrieving information from long-term memory as rapidly as from short-term memory, but further empirical evidence is needed to substantiate these possibilities. In addition, retrieving memories may be slower and more prone to errors when there are several options than when an insect copes with only a single task. In addition to memory limitations, we also point out alternative explanations for flower constancy. We then consider the way in which floral parameters, such as interplant distances, nectar rewards, flower morphology, and floral color (as seen through bees' eyes) affect constancy. Finally, we discuss the implications of pollinator constancy for plant evolution. To date there is no evidence that flowers have diverged to favor constancy, although the appropriate tests may not have yet been conducted. However, there is good evidence against the notion that pollinator constancy is involved in speciation or maintenance of plant species integrity.

  16. A tribal level phylogeny of Lake Tanganyika cichlid fishes based on a genomic multi-marker approach.

    PubMed

    Meyer, Britta S; Matschiner, Michael; Salzburger, Walter

    2015-02-01

    The species-flocks of cichlid fishes in the East African Great Lakes Victoria, Malawi and Tanganyika constitute the most diverse extant adaptive radiations in vertebrates. Lake Tanganyika, the oldest of the lakes, harbors the morphologically and genetically most diverse assemblage of cichlids and contains the highest number of endemic cichlid genera of all African lakes. Based on morphological grounds, the Tanganyikan cichlid species have been grouped into 12-16 distinct lineages, so-called tribes. While the monophyly of most of the tribes is well established, the phylogenetic relationships among the tribes remain largely elusive. Here, we present a new tribal level phylogenetic hypothesis for the cichlid fishes of Lake Tanganyika that is based on the so far largest set of nuclear markers and a total alignment length of close to 18kb. Using next-generation amplicon sequencing with the 454 pyrosequencing technology, we compiled a dataset consisting of 42 nuclear loci in 45 East African cichlid species, which we subjected to maximum likelihood and Bayesian inference phylogenetic analyses. We analyzed the entire concatenated dataset and each marker individually, and performed a Bayesian concordance analysis and gene tree discordance tests. Overall, we find strong support for a position of the Oreochromini, Boulengerochromini, Bathybatini and Trematocarini outside of a clade combining the substrate spawning Lamprologini and the mouthbrooding tribes of the 'H-lineage', which are both strongly supported to be monophyletic. The Eretmodini are firmly placed within the 'H-lineage', as sister-group to the most species-rich tribe of cichlids, the Haplochromini. The phylogenetic relationships at the base of the 'H-lineage' received less support, which is likely due to high speciation rates in the early phase of the radiation. Discordance among gene trees and marker sets further suggests the occurrence of past hybridization and/or incomplete lineage sorting in the cichlid

  17. Lightness constancy and illumination discounting.

    PubMed

    Logvinenko, Alexander D; Tokunaga, Rumi

    2011-08-01

    Contrary to the implication of the term "lightness constancy", asymmetric lightness matching has never been found to be perfect unless the scene is highly articulated (i.e., contains a number of different reflectances). Also, lightness constancy has been found to vary for different observers, and an effect of instruction (lightness vs. brightness) has been reported. The elusiveness of lightness constancy presents a great challenge to visual science; we revisit these issues in the following experiment, which involved 44 observers in total. The stimuli consisted of a large sheet of black paper with a rectangular spotlight projected onto the lower half and 40 squares of various shades of grey printed on the upper half. The luminance ratio at the edge of the spotlight was 25, while that of the squares varied from 2 to 16. Three different instructions were given to observers: They were asked to find a square in the upper half that (i) looked as if it was made of the same paper as that on which the spotlight fell (lightness match), (ii) had the same luminance contrast as the spotlight edge (contrast match), or (iii) had the same brightness as the spotlight (brightness match). Observers made 10 matches of each of the three types. Great interindividual variability was found for all three types of matches. In particular, the individual Brunswik ratios were found to vary over a broad range (from .47 to .85). That is, lightness matches were found to be far from veridical. Contrast matches were also found to be inaccurate, being on average, underestimated by a factor of 3.4. Articulation was found to essentially affect not only lightness, but contrast and brightness matches as well. No difference was found between the lightness and luminance contrast matches. While the brightness matches significantly differed from the other matches, the difference was small. Furthermore, the brightness matches were found to be subject to the same interindividual variability and the same

  18. White constancy method for mobile displays

    NASA Astrophysics Data System (ADS)

    Yum, Ji Young; Park, Hyun Hee; Jang, Seul Ki; Lee, Jae Hyang; Kim, Jong Ho; Yi, Ji Young; Lee, Min Woo

    2014-03-01

    In these days, consumer's needs for image quality of mobile devices are increasing as smartphone is widely used. For example, colors may be perceived differently when displayed contents under different illuminants. Displayed white in incandescent lamp is perceived as bluish, while same content in LED light is perceived as yellowish. When changed in perceived white under illuminant environment, image quality would be degraded. Objective of the proposed white constancy method is restricted to maintain consistent output colors regardless of the illuminants utilized. Human visual experiments are performed to analyze viewers'perceptual constancy. Participants are asked to choose the displayed white in a variety of illuminants. Relationship between the illuminants and the selected colors with white are modeled by mapping function based on the results of human visual experiments. White constancy values for image control are determined on the predesigned functions. Experimental results indicate that propsed method yields better image quality by keeping the display white.

  19. Color constancy by characterization of illumination chromaticity

    NASA Astrophysics Data System (ADS)

    Nikkanen, Jarno T.

    2011-05-01

    Computational color constancy algorithms play a key role in achieving desired color reproduction in digital cameras. Failure to estimate illumination chromaticity correctly will result in invalid overall colour cast in the image that will be easily detected by human observers. A new algorithm is presented for computational color constancy. Low computational complexity and low memory requirement make the algorithm suitable for resource-limited camera devices, such as consumer digital cameras and camera phones. Operation of the algorithm relies on characterization of the range of possible illumination chromaticities in terms of camera sensor response. The fact that only illumination chromaticity is characterized instead of the full color gamut, for example, increases robustness against variations in sensor characteristics and against failure of diagonal model of illumination change. Multiple databases are used in order to demonstrate the good performance of the algorithm in comparison to the state-of-the-art color constancy algorithms.

  20. Color constancy influenced by unnatural spatial structure.

    PubMed

    Mizokami, Yoko; Yaguchi, Hirohisa

    2014-04-01

    The recognition of spatial structures is important for color constancy because we cannot identify an object's color under different illuminations without knowing which space it is in and how that space is illuminated. To show the importance of the natural structure of environments on color constancy, we investigated the way in which color appearance was affected by unnatural viewing conditions in which a spatial structure was distorted. Observers judged the color of a test patch placed in the center of a small room illuminated by white or reddish lights, as well as two rooms illuminated by white and reddish light, respectively. In the natural viewing condition, an observer saw the room(s) through a viewing window, whereas in an unnatural viewing condition, the scene structure was scrambled by a kaleidoscope-type viewing box. Results of single room condition with one illuminant color showed little difference in color constancy between the two viewing conditions. However, it decreased in the two-rooms condition with a more complex arrangement of space and illumination. The patch's appearance under the unnatural viewing condition was more influenced by simultaneous contrast than its appearance under the natural viewing condition. It also appears that color appearance under white illumination is more stable compared to that under reddish illumination. These findings suggest that natural spatial structure plays an important role for color constancy in a complex environment. PMID:24695167

  1. Improving dermoscopy image classification using color constancy.

    PubMed

    Barata, Catarina; Celebi, M Emre; Marques, Jorge S

    2015-05-01

    Robustness is one of the most important characteristics of computer-aided diagnosis systems designed for dermoscopy images. However, it is difficult to ensure this characteristic if the systems operate with multisource images acquired under different setups. Changes in the illumination and acquisition devices alter the color of images and often reduce the performance of the systems. Thus, it is important to normalize the colors of dermoscopy images before training and testing any system. In this paper, we investigate four color constancy algorithms: Gray World, max-RGB, Shades of Gray, and General Gray World. Our results show that color constancy improves the classification of multisource images, increasing the sensitivity of a bag-of-features system from 71.0% to 79.7% and the specificity from 55.2% to 76% using only 1-D RGB histograms as features. PMID:25073179

  2. Constance mirror program: Progress and plans

    NASA Astrophysics Data System (ADS)

    Klinkowstein, R. E.; Mauel, M. E.; Irby, J. H.; Smullin, L. D.; Voldman, S. H.

    1981-03-01

    The current state of the mechanics of the Constance II experiment, the physics results gathered, the motivation background, and future plans for the Constance II experiment are reviewed. Several improvements have been made and several experimental investigations have been completed. These include the construction/installation/testing of: (1) liquid-nitrogen cooled, Ioffe bars installed, (2) a diverter coil (3) the 100 kW ICRF generator, (4) the data acquisition system, and (5) the optimum hot-iron operation of the machine with Titanium and pulsed-gas plasma guns. Measurements were made of the density, temperature, and radius of the plasma. Ion-cyclotron fluctuations were observed, their bandwidth measured, and data collected demonstrating resonance heating. New X-ray diagnostics were designed and purchased, and progress on the Thomson scattering was made. Finally, a new hot cathode gun was designed and constructed.

  3. Constance mirror program: Progress and plans

    NASA Technical Reports Server (NTRS)

    Klinkowstein, R. E.; Mauel, M. E.; Irby, J. H.; Smullin, L. D.; Voldman, S. H.

    1981-01-01

    The current state of the mechanics of the Constance II experiment, the physics results gathered, the motivation background, and future plans for the Constance II experiment are reviewed. Several improvements have been made and several experimental investigations have been completed. These include the construction/installation/testing of: (1) liquid-nitrogen cooled, Ioffe bars installed, (2) a diverter coil (3) the 100 kW ICRF generator, (4) the data acquisition system, and (5) the optimum hot-iron operation of the machine with Titanium and pulsed-gas plasma guns. Measurements were made of the density, temperature, and radius of the plasma. Ion-cyclotron fluctuations were observed, their bandwidth measured, and data collected demonstrating resonance heating. New X-ray diagnostics were designed and purchased, and progress on the Thomson scattering was made. Finally, a new hot cathode gun was designed and constructed.

  4. Reflectance, illumination, and appearance in color constancy.

    PubMed

    McCann, John J; Parraman, Carinna; Rizzi, Alessandro

    2014-01-01

    We studied color constancy using a pair of identical 3-D Color Mondrian displays. We viewed one 3-D Mondrian in nearly uniform illumination, and the other in directional, nonuniform illumination. We used the three dimensional structures to modulate the light falling on the painted surfaces. The 3-D structures in the displays were a matching set of wooden blocks. Across Mondrian displays, each corresponding facet had the same paint on its surface. We used only 6 chromatic, and 5 achromatic paints applied to 104 block facets. The 3-D blocks add shadows and multiple reflections not found in flat Mondrians. Both 3-D Mondrians were viewed simultaneously, side-by-side. We used two techniques to measure correlation of appearance with surface reflectance. First, observers made magnitude estimates of changes in the appearances of identical reflectances. Second, an author painted a watercolor of the 3-D Mondrians. The watercolor's reflectances quantified the changes in appearances. While constancy generalizations about illumination and reflectance hold for flat Mondrians, they do not for 3-D Mondrians. A constant paint does not exhibit perfect color constancy, but rather shows significant shifts in lightness, hue and chroma in response to the structure in the nonuniform illumination. Color appearance depends on the spatial information in both the illumination and the reflectances of objects. The spatial information of the quanta catch from the array of retinal receptors generates sensations that have variable correlation with surface reflectance. Models of appearance in humans need to calculate the departures from perfect constancy measured here. This article provides a dataset of measurements of color appearances for computational models of sensation. PMID:24478738

  5. Reflectance, illumination, and appearance in color constancy

    PubMed Central

    McCann, John J.; Parraman, Carinna; Rizzi, Alessandro

    2013-01-01

    We studied color constancy using a pair of identical 3-D Color Mondrian displays. We viewed one 3-D Mondrian in nearly uniform illumination, and the other in directional, nonuniform illumination. We used the three dimensional structures to modulate the light falling on the painted surfaces. The 3-D structures in the displays were a matching set of wooden blocks. Across Mondrian displays, each corresponding facet had the same paint on its surface. We used only 6 chromatic, and 5 achromatic paints applied to 104 block facets. The 3-D blocks add shadows and multiple reflections not found in flat Mondrians. Both 3-D Mondrians were viewed simultaneously, side-by-side. We used two techniques to measure correlation of appearance with surface reflectance. First, observers made magnitude estimates of changes in the appearances of identical reflectances. Second, an author painted a watercolor of the 3-D Mondrians. The watercolor's reflectances quantified the changes in appearances. While constancy generalizations about illumination and reflectance hold for flat Mondrians, they do not for 3-D Mondrians. A constant paint does not exhibit perfect color constancy, but rather shows significant shifts in lightness, hue and chroma in response to the structure in the nonuniform illumination. Color appearance depends on the spatial information in both the illumination and the reflectances of objects. The spatial information of the quanta catch from the array of retinal receptors generates sensations that have variable correlation with surface reflectance. Models of appearance in humans need to calculate the departures from perfect constancy measured here. This article provides a dataset of measurements of color appearances for computational models of sensation. PMID:24478738

  6. Color Constancy Using Double-Opponency.

    PubMed

    Gao, Shao-Bing; Yang, Kai-Fu; Li, Chao-Yi; Li, Yong-Jie

    2015-10-01

    The double-opponent (DO) color-sensitive cells in the primary visual cortex (V1) of the human visual system (HVS) have long been recognized as the physiological basis of color constancy. In this work we propose a new color constancy model by imitating the functional properties of the HVS from the single-opponent (SO) cells in the retina to the DO cells in V1 and the possible neurons in the higher visual cortexes. The idea behind the proposed double-opponency based color constancy (DOCC) model originates from the substantial observation that the color distribution of the responses of DO cells to the color-biased images coincides well with the vector denoting the light source color. Then the illuminant color is easily estimated by pooling the responses of DO cells in separate channels in LMS space with the pooling mechanism of sum or max. Extensive evaluations on three commonly used datasets, including the test with the dataset dependent optimal parameters, as well as the intra- and inter-dataset cross validation, show that our physiologically inspired DOCC model can produce quite competitive results in comparison to the state-of-the-art approaches, but with a relative simple implementation and without requiring fine-tuning of the method for each different dataset. PMID:26353182

  7. Pre-constancy Vision in Infants.

    PubMed

    Yang, Jiale; Kanazawa, So; Yamaguchi, Masami K; Motoyoshi, Isamu

    2015-12-21

    Our visual system can easily estimate the constant color and material of external objects despite dynamic changes in the retinal image across viewpoints and illuminations in natural scenes. It is commonly believed that this high-level visual function, called "perceptual constancy," is acquired through postnatal learning [1], building upon low-level functions that have developed earlier, such as image discrimination. However, we demonstrate here that before developing perceptual constancy, 3- to 4-month-old infants have a striking ability to discriminate slight image changes due to illumination that are not salient for adults. These young infants lose this ability after 5 months of age and then develop an ability to perceive distal surface properties (glossy or matte) at 7-8 months of age. Moreover, we identify the transition period between these two functions at 5-6 months of age, wherein infants show difficulty in both image and surface discrimination. These findings support the notion that acquiring perceptual constancy leads to a loss of sensitivity to variant information, which is negligible for constant surface material perception. We suggest that the immature visual system may initially directly access local image features and then develops a complementary constant neural representation of the properties of an object. PMID:26671667

  8. Lake

    ERIC Educational Resources Information Center

    Wien, Carol Anne

    2008-01-01

    The lake is blue black and deep. It is a glaciated finger lake, clawed out of rock when ice retracted across Nova Scotia in a northerly direction during the last ice age. The lake is narrow, a little over a mile long, and deep, 90 to 190 feet in places according to local lore, off the charts in others. The author loves to swim there, with a sense…

  9. A Retinal Mechanism Inspired Color Constancy Model.

    PubMed

    Zhang, Xian-Shi; Gao, Shao-Bing; Li, Ruo-Xuan; Du, Xin-Yu; Li, Chao-Yi; Li, Yong-Jie

    2016-03-01

    In this paper, we propose a novel model for the computational color constancy, inspired by the amazing ability of the human vision system (HVS) to perceive the color of objects largely constant as the light source color changes. The proposed model imitates the color processing mechanisms in the specific level of the retina, the first stage of the HVS, from the adaptation emerging in the layers of cone photoreceptors and horizontal cells (HCs) to the color-opponent mechanism and disinhibition effect of the non-classical receptive field in the layer of retinal ganglion cells (RGCs). In particular, HC modulation provides a global color correction with cone-specific lateral gain control, and the following RGCs refine the processing with iterative adaptation until all the three opponent channels reach their stable states (i.e., obtain stable outputs). Instead of explicitly estimating the scene illuminant(s), such as most existing algorithms, our model directly removes the effect of scene illuminant. Evaluations on four commonly used color constancy data sets show that the proposed model produces competitive results in comparison with the state-of-the-art methods for the scenes under either single or multiple illuminants. The results indicate that single opponency, especially the disinhibitory effect emerging in the receptive field's subunit-structured surround of RGCs, plays an important role in removing scene illuminant(s) by inherently distinguishing the spatial structures of surfaces from extensive illuminant(s). PMID:26766375

  10. Color constancy in a naturalistic, goal-directed task.

    PubMed

    Radonjic, Ana; Cottaris, Nicolas P; Brainard, David H

    2015-01-01

    In daily life, we use color information to select objects that will best serve a particular goal (e.g., pick the best-tasting fruit or avoid spoiled food). This is challenging when judgments must be made across changes in illumination as the spectrum reflected from an object to the eye varies with the illumination. Color constancy mechanisms serve to partially stabilize object color appearance across illumination changes, but whether and to what degree constancy supports accurate cross-illumination object selection is not well understood. To get closer to understanding how constancy operates in real-life tasks, we developed a paradigm in which subjects engage in a goal-directed task for which color is instrumental. Specifically, in each trial, subjects re-created an arrangement of colored blocks (the model) across a change in illumination. By analyzing the re-creations, we were able to infer and quantify the degree of color constancy that mediated subjects' performance. In Experiments 1 and 2, we used our paradigm to characterize constancy for two different sets of block reflectances, two different illuminant changes, and two different groups of subjects. On average, constancy was good in our naturalistic task, but it varied considerably across subjects. In Experiment 3, we tested whether varying scene complexity and the validity of local contrast as a cue to the illumination change modulated constancy. Increasing complexity did not lead to improved constancy; silencing local contrast significantly reduced constancy. Our results establish a novel goal-directed task that enables us to approach color constancy as it emerges in real life. PMID:26381834

  11. Color constancy in a naturalistic, goal-directed task

    PubMed Central

    Radonjić, Ana; Cottaris, Nicolas P.; Brainard, David H.

    2015-01-01

    In daily life, we use color information to select objects that will best serve a particular goal (e.g., pick the best-tasting fruit or avoid spoiled food). This is challenging when judgments must be made across changes in illumination as the spectrum reflected from an object to the eye varies with the illumination. Color constancy mechanisms serve to partially stabilize object color appearance across illumination changes, but whether and to what degree constancy supports accurate cross-illumination object selection is not well understood. To get closer to understanding how constancy operates in real-life tasks, we developed a paradigm in which subjects engage in a goal-directed task for which color is instrumental. Specifically, in each trial, subjects re-created an arrangement of colored blocks (the model) across a change in illumination. By analyzing the re-creations, we were able to infer and quantify the degree of color constancy that mediated subjects' performance. In Experiments 1 and 2, we used our paradigm to characterize constancy for two different sets of block reflectances, two different illuminant changes, and two different groups of subjects. On average, constancy was good in our naturalistic task, but it varied considerably across subjects. In Experiment 3, we tested whether varying scene complexity and the validity of local contrast as a cue to the illumination change modulated constancy. Increasing complexity did not lead to improved constancy; silencing local contrast significantly reduced constancy. Our results establish a novel goal-directed task that enables us to approach color constancy as it emerges in real life. PMID:26381834

  12. Color constancy supports cross-illumination color selection.

    PubMed

    Radonjić, Ana; Cottaris, Nicolas P; Brainard, David H

    2015-01-01

    We rely on color to select objects as the targets of our actions (e.g., the freshest fish, the ripest fruit). To be useful for selection, color must provide accurate guidance about object identity across changes in illumination. Although the visual system partially stabilizes object color appearance across illumination changes, how such color constancy supports object selection is not understood. To study how constancy operates in real-life tasks, we developed a novel paradigm in which subjects selected which of two test objects presented under a test illumination appeared closer in color to a target object presented under a standard illumination. From subjects' choices, we inferred a selection-based match for the target via a variant of maximum likelihood difference scaling, and used it to quantify constancy. Selection-based constancy was good when measured using naturalistic stimuli, but was dramatically reduced when the stimuli were simplified, indicating that a naturalistic stimulus context is critical for good constancy. Overall, our results suggest that color supports accurate object selection across illumination changes when both stimuli and task match how color is used in real life. We compared our selection-based constancy results with data obtained using a classic asymmetric matching task and found that the adjustment-based matches predicted selection well for our stimuli and instructions, indicating that the appearance literature provides useful guidance for the emerging study of constancy in natural tasks. PMID:26024460

  13. Color constancy supports cross-illumination color selection

    PubMed Central

    Radonjić, Ana; Cottaris, Nicolas P.; Brainard, David H.

    2015-01-01

    We rely on color to select objects as the targets of our actions (e.g., the freshest fish, the ripest fruit). To be useful for selection, color must provide accurate guidance about object identity across changes in illumination. Although the visual system partially stabilizes object color appearance across illumination changes, how such color constancy supports object selection is not understood. To study how constancy operates in real-life tasks, we developed a novel paradigm in which subjects selected which of two test objects presented under a test illumination appeared closer in color to a target object presented under a standard illumination. From subjects' choices, we inferred a selection-based match for the target via a variant of maximum likelihood difference scaling, and used it to quantify constancy. Selection-based constancy was good when measured using naturalistic stimuli, but was dramatically reduced when the stimuli were simplified, indicating that a naturalistic stimulus context is critical for good constancy. Overall, our results suggest that color supports accurate object selection across illumination changes when both stimuli and task match how color is used in real life. We compared our selection-based constancy results with data obtained using a classic asymmetric matching task and found that the adjustment-based matches predicted selection well for our stimuli and instructions, indicating that the appearance literature provides useful guidance for the emerging study of constancy in natural tasks. PMID:26024460

  14. Scene Context Dependency of Pattern Constancy of Time Series Imagery

    NASA Technical Reports Server (NTRS)

    Woodell, Glenn A.; Jobson, Daniel J.; Rahman, Zia-ur

    2008-01-01

    A fundamental element of future generic pattern recognition technology is the ability to extract similar patterns for the same scene despite wide ranging extraneous variables, including lighting, turbidity, sensor exposure variations, and signal noise. In the process of demonstrating pattern constancy of this kind for retinex/visual servo (RVS) image enhancement processing, we found that the pattern constancy performance depended somewhat on scene content. Most notably, the scene topography and, in particular, the scale and extent of the topography in an image, affects the pattern constancy the most. This paper will explore these effects in more depth and present experimental data from several time series tests. These results further quantify the impact of topography on pattern constancy. Despite this residual inconstancy, the results of overall pattern constancy testing support the idea that RVS image processing can be a universal front-end for generic visual pattern recognition. While the effects on pattern constancy were significant, the RVS processing still does achieve a high degree of pattern constancy over a wide spectrum of scene content diversity, and wide ranging extraneousness variations in lighting, turbidity, and sensor exposure.

  15. Open problems in color constancy: discussion.

    PubMed

    van Trigt, C

    2014-02-01

    This paper discusses a number of open problems in color constancy theory whose correct solution is a prerequisite for the theory of the phenomenon. Solutions employing suitable visually meaningful versus physically meaningful basis functions (principal components) are examined. In the former case the starting point is an estimate of the first derivative of the reflectance (illuminant), essential for defining color, instead of an estimate of the reflectance (illuminant), as in the latter. Conceptual consequences are discussed. Mathematical and physical constraints are identified. We compare the results of theories that do or do not ignore them. The following questions are considered. (1) Do unique solutions of the estimation problem exist everywhere in the object-color solid belonging to the illuminant? (2) Are they physically meaningful, i.e., at least nonnegative? (3) Are they representative for reflectance and spectral distribution functions? (4) What role plays metamerism? PMID:24562033

  16. Extending "color constancy" outside the visible region.

    PubMed

    Ratnasingam, Sivalogeswaran; Collins, Steve; Hernández-Andrés, Javier

    2011-04-01

    In this paper, the results of an investigation of the possibility of extending "color constancy" to obtain illuminant-invariant reflectance features from data in the near-ultraviolet (UV) and near-infrared (IR) wavelength regions are reported. These features are obtained by extending a blackbody-model-based color constancy algorithm proposed by Ratnasingam and Collins [J. Opt. Soc. Am. A27, 286 (2010)] to these additional wavelengths. Ratnasingam and Collins applied the model-based algorithm in the visible region to extract two illuminant-invariant features related to the wavelength-dependent reflectance of a surface from the responses of four sensors. In this paper, this model-based algorithm is extended to extract two illuminant-invariant reflectance features from the responses of sensors that cover the visible and either the near-UV or near-IR wavelength. In this investigation, test reflectance data sets are generated using the goodness-fitness coefficient (GFC). The appropriateness of the GFC for generating the test data sets is demonstrated by comparing the results obtained with these data with those obtained from data sets generated using the CIELab distance. Results based upon the GFC are then presented that suggest that the model-based algorithm can extract useful features from data from the visible and near-IR wavelengths. Finally, results are presented that show that, although the spectrum of daylight in the near UV is very different from a blackbody spectrum, the algorithm can be modified to extract useful features from visible and near-UV wavelengths. PMID:21478947

  17. Spectral sharpening of color sensors: diagonal color constancy and beyond.

    PubMed

    Vazquez-Corral, Javier; Bertalmío, Marcelo

    2014-01-01

    It has now been 20 years since the seminal work by Finlayson et al. on the use of spectral sharpening of sensors to achieve diagonal color constancy. Spectral sharpening is still used today by numerous researchers for different goals unrelated to the original goal of diagonal color constancy e.g., multispectral processing, shadow removal, location of unique hues. This paper reviews the idea of spectral sharpening through the lens of what is known today in color constancy, describes the different methods used for obtaining a set of sharpening sensors and presents an overview of the many different uses that have been found for spectral sharpening over the years. PMID:24577523

  18. Spectral Sharpening of Color Sensors: Diagonal Color Constancy and Beyond

    PubMed Central

    Vazquez-Corral, Javier; Bertalmío, Marcelo

    2014-01-01

    It has now been 20 years since the seminal work by Finlayson et al. on the use of spectral sharpening of sensors to achieve diagonal color constancy. Spectral sharpening is still used today by numerous researchers for different goals unrelated to the original goal of diagonal color constancy e.g., multispectral processing, shadow removal, location of unique hues. This paper reviews the idea of spectral sharpening through the lens of what is known today in color constancy, describes the different methods used for obtaining a set of sharpening sensors and presents an overview of the many different uses that have been found for spectral sharpening over the years. PMID:24577523

  19. The nature of instructional effects in color constancy.

    PubMed

    Radonjić, Ana; Brainard, David H

    2016-06-01

    The instructions subjects receive can have a large effect on experimentally measured color constancy, but the nature of these effects and how their existence should inform our understanding of color perception remains unclear. We used a factorial design to measure how instructional effects on constancy vary with experimental task and stimulus set. In each of 2 experiments, we employed both a classic adjustment-based asymmetric matching task and a novel color selection task. Four groups of naive subjects were instructed to make adjustments/selections based on (a) color (neutral instructions); (b) the light reaching the eye (physical spectrum instructions); (c) the actual surface reflectance of an object (objective reflectance instructions); or (d) the apparent surface reflectance of an object (apparent reflectance instructions). Across the 2 experiments we varied the naturalness of the stimuli. We find clear interactions between instructions, task, and stimuli. With simplified stimuli (Experiment 1), instructional effects were large and the data revealed 2 instruction-dependent patterns. In 1 (neutral and physical spectrum instructions) constancy was low, intersubject variability was also low, and adjustment-based and selection-based constancy were in agreement. In the other (reflectance instructions) constancy was high, intersubject variability was large, adjustment-based constancy deviated from selection-based constancy and for some subjects selection-based constancy increased across sessions. Similar patterns held for naturalistic stimuli (Experiment 2), although instructional effects were smaller. We interpret these 2 patterns as signatures of distinct task strategies-1 is perceptual, with judgments based primarily on the perceptual representation of color; the other involves explicit instruction-driven reasoning. (PsycINFO Database Record PMID:26727021

  20. Color constancy for an unseen surface.

    PubMed

    Norman, Liam J; Akins, Kathleen; Heywood, Charles A; Kentridge, Robert W

    2014-12-01

    The illumination of a scene strongly affects our perception of objects in that scene, e.g., the pages of a book illuminated by candlelight will appear quite yellow relative to other types of artificial illuminants. Yet at the same time, the reader still judges the pages as white, their surface color unaffected by the interplay of paper and illuminant. It has been shown empirically that we can indeed report two quite different interpretations of "color": one is dependent on the constant surface spectral reflectance of an object (surface color) and the other on the power of light of different wavelengths reflected from that object (reflected color). How then are these two representations related? The common view, dating from Aristotle, is that our experience of surface color is derived from reflected color or, in more familiar terms, that color perception follows from color sensation. By definition, color constancy requires that vision "discounts the illuminant"; thus, it seems reasonable that vision begins with the color of objects as they naively appear and that we infer from their appearances their surface color. Here, we question this classic view. We use metacontrast-masked priming and, by presenting the unseen prime and the visible mask under different illuminants, dissociate two ways in which the prime matched the mask: in surface color or in reflected color. We find that priming of the mask occurs when it matches the prime in surface color, not reflected color. It follows that color perception can arise without prior color sensation. PMID:25456450

  1. Crater Lake: blue through time

    USGS Publications Warehouse

    Larson, Gary L.; Buktenica, Mark; Collier, Robert

    2003-01-01

    Blue is the color of constancy, hence the term true blue. The unearthly blueness of Crater Lake reflects its pristine character and gives scientists a focal point for studying human impacts on aquatic environments over long periods of time. Scientists with the U.S. Geological Survey (USGS), National Park Service, and Oregon State University have systematically studied the lake for the last two decades. Long-term monitoring of this lake is a priority of Crater Lake National Park and will continue far into the future.

  2. Chromatic settings and the structural color constancy index.

    PubMed

    Roca-Vila, Jordi; Parraga, C Alejandro; Vanrell, Maria

    2013-01-01

    Color constancy is usually measured by achromatic setting, asymmetric matching, or color naming paradigms, whose results are interpreted in terms of indexes and models that arguably do not capture the full complexity of the phenomenon. Here we propose a new paradigm, chromatic setting, which allows a more comprehensive characterization of color constancy through the measurement of multiple points in color space under immersive adaptation. We demonstrated its feasibility by assessing the consistency of subjects' responses over time. The paradigm was applied to two-dimensional (2-D) Mondrian stimuli under three different illuminants, and the results were used to fit a set of linear color constancy models. The use of multiple colors improved the precision of more complex linear models compared to the popular diagonal model computed from gray. Our results show that a diagonal plus translation matrix that models mechanisms other than cone gain might be best suited to explain the phenomenon. Additionally, we calculated a number of color constancy indices for several points in color space, and our results suggest that interrelations among colors are not as uniform as previously believed. To account for this variability, we developed a new structural color constancy index that takes into account the magnitude and orientation of the chromatic shift in addition to the interrelations among colors and memory effects. PMID:23479473

  3. Accommodation and size-constancy of virtual objects.

    PubMed

    Kenyon, Robert V; Phenany, Moses; Sandin, Daniel; Defanti, Thomas

    2008-02-01

    Accommodation has been suspected as a contributor to size illusions in virtual environments (VE) due to the lack of appropriate accommodative stimuli in a VE for the objects displayed. Previous experiments examining size-constancy in VE have shown that monocular cues to depth that accompany the object are a major contributor to correct size perception. When these accompanying cues are removed perceived size varied with the object's distance from the subject, i.e., visual angle. If accommodation were the dominant mechanism contributing to a visual angle response [due to its action to keep physical objects clear] in this condition, an open-loop accommodation viewing condition might restore size-constancy to this condition. Pinhole apertures were used to open-loop accommodation and examine if size-constancy might be restored when few accompanying monocular cues to depth were present. Visual angle performance when viewing a low cue environment was found with and without the use of the pinhole apertures. Thus, these results signify that accommodation does not play a dominate role in the loss of size-constancy in sparse visual environments often used in VE. These results suggest that size-constancy is driven by the inclusion of the remaining monocular cues to depth in VE as it is in the physical world. PMID:18066664

  4. Life/Work Planning: Change and Constancy in the World of Work.

    ERIC Educational Resources Information Center

    Bolles, Richard N.

    1983-01-01

    To plan for our future we must consider both change and constancy, but most futurists today pay insufficient attention to constancy. As individuals plan their lives, they must assess their desire for change or constancy in geography, goals, special knowledge, people environments, working conditions, salary, and transferable skills. (IS)

  5. "God Made Me a Girl": Sex-Category Constancy Judgments and Explanations Revisited.

    ERIC Educational Resources Information Center

    Szkrybalo, Joel; Ruble, Diane N.

    1999-01-01

    Studied children's sex-category constancy judgments and accompanying explanations over three years. Found that constancy improvements were linked to explanations based on operational reasoning. Lower constancy scores were linked to explanations emphasizing gender-role norms and external appearances. Judgment-explanation relationships were stronger…

  6. Sensory, computational and cognitive components of human colour constancy

    PubMed Central

    Smithson, H.E

    2005-01-01

    When the illumination on a scene changes, so do the visual signals elicited by that scene. In spite of these changes, the objects within a scene tend to remain constant in their apparent colour. We start this review by discussing the psychophysical procedures that have been used to quantify colour constancy. The transformation imposed on the visual signals by a change in illumination dictates what the visual system must ‘undo’ to achieve constancy. The problem is mathematically underdetermined, and can be solved only by exploiting regularities of the visual world. The last decade has seen a substantial increase in our knowledge of such regularities as technical advances have made it possible to make empirical measurements of large numbers of environmental scenes and illuminants. This review provides a taxonomy of models of human colour constancy based first on the assumptions they make about how the inverse transformation might be simplified, and second, on how the parameters of the inverse transformation might be set by elements of a complex scene. Candidate algorithms for human colour constancy are represented graphically and pictorially, and the availability and utility of an accurate estimate of the illuminant is discussed. Throughout this review, we consider both the information that is, in principle, available and empirical assessments of what information the visual system actually uses. In the final section we discuss where in our visual systems these computations might be implemented. PMID:16147525

  7. Gender Constancy and Same-Sex Imitation: A Developmental Study.

    ERIC Educational Resources Information Center

    Perloff, Richard M.

    1982-01-01

    Fifty-one preschool children were interviewed individually to assess awareness of gender constancy and choice of same-sex models. Differences emerged between high and low gender-constant children when they were given a choice between imitating a same-sex model performing a relatively unpleasant task and imitating an opposite-sex model enacting a…

  8. Constance Mellon's "Library Anxiety": An Appreciation and a Critique

    ERIC Educational Resources Information Center

    Gremmels, Gillian S.

    2015-01-01

    In this article, the author recollects her memories reading Constance A. Mellon's article, "Library Anxiety: A Grounded Theory and Its Development," when it appeared in the March 1986 issue of "College & Research Libraries." She was a reference librarian at at DePauw University in Indiana at the time, helping students…

  9. Constance D'Arcy Mackay: A Historiographical Perspective.

    ERIC Educational Resources Information Center

    van de Water, Manon

    1995-01-01

    States that Constance D'Arcy Mackay was instrumental in defining the genre of children's theater in the early 20th century. Discusses her career highlights. Concludes that Mackay played a pivotal role in the "making" of the history of children's theater in the United States, and that while little of her personal history is known, her theories are…

  10. Exemplar-Based Color Constancy and Multiple Illumination.

    PubMed

    Joze, Hamid Reza Vaezi; Drew, Mark S

    2014-05-01

    Exemplar-based learning or, equally, nearest neighbor methods have recently gained interest from researchers in a variety of computer science domains because of the prevalence of large amounts of accessible data and storage capacity. In computer vision, these types of technique have been successful in several problems such as scene recognition, shape matching, image parsing, character recognition, and object detection. Applying the concept of exemplar-based learning to the problem of color constancy seems odd at first glance since, in the first place, similar nearest neighbor images are not usually affected by precisely similar illuminants and, in the second place, gathering a dataset consisting of all possible real-world images, including indoor and outdoor scenes and for all possible illuminant colors and intensities, is indeed impossible. In this paper, we instead focus on surfaces in the image and address the color constancy problem by unsupervised learning of an appropriate model for each training surface in training images. We find nearest neighbor models for each surface in a test image and estimate its illumination based on comparing the statistics of pixels belonging to nearest neighbor surfaces and the target surface. The final illumination estimation results from combining these estimated illuminants over surfaces to generate a unique estimate. We show that it performs very well, for standard datasets, compared to current color constancy algorithms, including when learning based on one image dataset is applied to tests from a different dataset. The proposed method has the advantage of overcoming multi-illuminant situations, which is not possible for most current methods since they assume the color of the illuminant is constant all over the image. We show a technique to overcome the multiple illuminant situation using the proposed method and test our technique on images with two distinct sources of illumination using a multiple-illuminant color constancy

  11. Depth perception in the framework of General Object Constancy.

    PubMed

    Qian, Jiehui; Petrov, Yury

    2013-01-01

    Size constancy is a well-known example of perceptual stabilization accounting for the effect of viewing distance on retinal image size. In a recent study (Qian & Petrov, 2012), we demonstrated a similar stabilization mechanism for contrast perception and suggested that the brain accounts for effects of perceived distance on various other object features in a similar way, a hypothesis that we called General Object Constancy. Here we report a new illusion of depth further supporting this hypothesis. Pairs of disks moved across the screen in a pattern of radial optic flow. A pair comprised a small black disk floating in front of a large white disk, creating the percept of a pencil tip viewed head on. As these "pencils" moved away, they appeared to grow in contrast, in diameter, and also appeared to be getting "sharper." The contrast and size illusions replicated our previous findings, while the depth gradient (sharpness) illusion revealed a depth constancy phenomenon. We discovered that depth and size constancies were related, e.g., the two illusions were strongly correlated across observers. Whereas the illusory diameter increase could not be canceled by any degree of depth modulation, decreasing the diameter of the "pencils" during optic flow motion (thus increasing their disparity gradient) weakened the illusory depth gradient increase. This paradoxical result, as well as our other results, is explained by the General Object Constancy model: Besides using the same scaling factor to account for size, contrast, and depth variations with distance, the brain uses the apparent object size to additionally scale contrast and depth signals. PMID:24023274

  12. Building a Twig Phylogeny

    ERIC Educational Resources Information Center

    Flinn, Kathryn M.

    2015-01-01

    In this classroom activity, students build a phylogeny for woody plant species based on the morphology of their twigs. Using any available twigs, students can practice the process of cladistics to test evolutionary hypotheses for real organisms. They identify homologous characters, determine polarity through outgroup comparison, and construct a…

  13. Color constancy using 3D scene geometry derived from a single image.

    PubMed

    Elfiky, Noha; Gevers, Theo; Gijsenij, Arjan; Gonzalez, Jordi

    2014-09-01

    The aim of color constancy is to remove the effect of the color of the light source. As color constancy is inherently an ill-posed problem, most of the existing color constancy algorithms are based on specific imaging assumptions (e.g., gray-world and white patch assumption). In this paper, 3D geometry models are used to determine which color constancy method to use for the different geometrical regions (depth/layer) found in images. The aim is to classify images into stages (rough 3D geometry models). According to stage models, images are divided into stage regions using hard and soft segmentation. After that, the best color constancy methods are selected for each geometry depth. To this end, we propose a method to combine color constancy algorithms by investigating the relation between depth, local image statistics, and color constancy. Image statistics are then exploited per depth to select the proper color constancy method. Our approach opens the possibility to estimate multiple illuminations by distinguishing nearby light source from distant illuminations. Experiments on state-of-the-art data sets show that the proposed algorithm outperforms state-of-the-art single color constancy algorithms with an improvement of almost 50% of median angular error. When using a perfect classifier (i.e, all of the test images are correctly classified into stages); the performance of the proposed method achieves an improvement of 52% of the median angular error compared with the best-performing single color constancy algorithm. PMID:25051548

  14. Constructing computer virus phylogenies

    SciTech Connect

    Goldberg, L.A.; Goldberg, P.W.; Phillips, C.A.; Sorkin, G.B.

    1996-03-01

    There has been much recent algorithmic work on the problem of reconstructing the evolutionary history of biological species. Computer virus specialists are interested in finding the evolutionary history of computer viruses--a virus is often written using code fragments from one or more other viruses, which are its immediate ancestors. A phylogeny for a collection of computer viruses is a directed acyclic graph whose nodes are the viruses and whose edges map ancestors to descendants and satisfy the property that each code fragment is ``invented`` only once. To provide a simple explanation for the data, we consider the problem of constructing such a phylogeny with a minimal number of edges. In general, this optimization problem cannot be solved in quasi-polynomial time unless NQP=QP; we present positive and negative results for associated approximated problems. When tree solutions exist, they can be constructed and randomly sampled in polynomial time.

  15. Color constancy - A method for recovering surface spectral reflectance

    NASA Technical Reports Server (NTRS)

    Maloney, L. T.; Wandell, B. A.

    1986-01-01

    An algorithm has been developed for estimating the surface reflectance functions of objects in a scene with incomplete knowledge of the spectral power distribution of the ambient light. An image processing system employing this algorithm can assign colors that are constant despite changes in the lighting of the scene; this capability is essential to correct color rendering in photography, TV, and in the construction of artificial visual systems for robotics. Attention is given to the way in which constraints on lights and surfaces in the environment make color-constancy possible for a visual system, and the algorithm's implications for human color vision are discussed.

  16. The Development of Sex-Gender Constancy Among Children in Four Cultures.

    ERIC Educational Resources Information Center

    Munroe, Ruth H.; Munroe, Robert L.

    The study examines the acquisition of gender constancy in children as it relates to cultural, socioenvironmental, or individual differences. Gender constancy refers to the stages from simple identification of biological sex of self and others, to the understanding that one's sex is stable over time, and to comprehension of one's sex as consistent…

  17. An Experimental Test of the Effects of Gender Constancy on Sex Typing

    ERIC Educational Resources Information Center

    Arthur, Andrea E.; Bigler, Rebecca S.; Ruble, Diane N.

    2009-01-01

    This study provides an experimental test of the hypothesis that level of gender constancy understanding affects children's sex typing. Preschool-age children (N = 62, mean age = 47 months) were randomly assigned to experimental lessons that taught that biological traits (including gender) are either fixed (pro-constancy condition) or mutable…

  18. Hippopotamus and whale phylogeny.

    PubMed

    Geisler, Jonathan H; Theodor, Jessica M

    2009-03-19

    Thewissen et al. describe new fossils from India that apparently support a phylogeny that places Cetacea (that is, whales, dolphins, porpoises) as the sister group to the extinct family Raoellidae, and Hippopotamidae as more closely related to pigs and peccaries (that is, Suina) than to cetaceans. However, our reanalysis of a modified version of the data set they used differs in retaining molecular characters and demonstrates that Hippopotamidae is the closest extant family to Cetacea and that raoellids are the closest extinct group, consistent with previous phylogenetic studies. This topology supports the view that the aquatic adaptations in hippopotamids and cetaceans are inherited from their common ancestor. PMID:19295550

  19. Color constancy in 3D-2D face recognition

    NASA Astrophysics Data System (ADS)

    Meyer, Manuel; Riess, Christian; Angelopoulou, Elli; Evangelopoulos, Georgios; Kakadiaris, Ioannis A.

    2013-05-01

    Face is one of the most popular biometric modalities. However, up to now, color is rarely actively used in face recognition. Yet, it is well-known that when a person recognizes a face, color cues can become as important as shape, especially when combined with the ability of people to identify the color of objects independent of illuminant color variations. In this paper, we examine the feasibility and effect of explicitly embedding illuminant color information in face recognition systems. We empirically examine the theoretical maximum gain of including known illuminant color to a 3D-2D face recognition system. We also investigate the impact of using computational color constancy methods for estimating the illuminant color, which is then incorporated into the face recognition framework. Our experiments show that under close-to-ideal illumination estimates, one can improve face recognition rates by 16%. When the illuminant color is algorithmically estimated, the improvement is approximately 5%. These results suggest that color constancy has a positive impact on face recognition, but the accuracy of the illuminant color estimate has a considerable effect on its benefits.

  20. The Development of Gender Constancy in Early Childhood and Its Relation to Time Comprehension and False-Belief Understanding

    ERIC Educational Resources Information Center

    Zmyj, Norbert; Bischof-Köhler, Doris

    2015-01-01

    What is the developmental course of children's gender constancy? Do other cognitive abilities such as time comprehension and false-belief understanding foster gender constancy and the subcomponents gender stability and gender consistency? We examined the development of gender constancy and its relation to time comprehension and false-belief…

  1. Constancy and diversity in the flavivirus fusion peptide

    PubMed Central

    Seligman, Stephen J

    2008-01-01

    Background Flaviviruses include the mosquito-borne dengue, Japanese encephalitis, yellow fever and West Nile and the tick-borne encephalitis viruses. They are responsible for considerable world-wide morbidity and mortality. Viral entry is mediated by a conserved fusion peptide containing 16 amino acids located in domain II of the envelope protein E. Highly orchestrated conformational changes initiated by exposure to acidic pH accompany the fusion process and are important factors limiting amino acid changes in the fusion peptide that still permit fusion with host cell membranes in both arthropod and vertebrate hosts. The cell-fusing related agents, growing only in mosquitoes or insect cell lines, possess a different homologous peptide. Results Analysis of 46 named flaviviruses deposited in the Entrez Nucleotides database extended the constancy in the canonical fusion peptide sequences of mosquito-borne, tick-borne and viruses with no known vector to include more recently-sequenced viruses. The mosquito-borne signature amino acid, G104, was also found in flaviviruses with no known vector and with the cell-fusion related viruses. Despite the constancy in the canonical sequences in pathogenic flaviviruses, mutations were surprisingly frequent with a 27% prevalence of nonsynonymous mutations in yellow fever virus fusion peptide sequences, and 0 to 7.4% prevalence in the others. Six of seven yellow fever patients whose virus had fusion peptide mutations died. In the cell-fusing related agents, not enough sequences have been deposited to estimate reliably the prevalence of fusion peptide mutations. However, the canonical sequences homologous to the fusion peptide and the pattern of disulfide linkages in protein E differed significantly from the other flaviviruses. Conclusion The constancy of the canonical fusion peptide sequences in the arthropod-borne flaviviruses contrasts with the high prevalence of mutations in most individual viruses. The discrepancy may be the

  2. Quantitative studies of animal colour constancy: using the chicken as model.

    PubMed

    Olsson, Peter; Wilby, David; Kelber, Almut

    2016-05-11

    Colour constancy is the capacity of visual systems to keep colour perception constant despite changes in the illumination spectrum. Colour constancy has been tested extensively in humans and has also been described in many animals. In humans, colour constancy is often studied quantitatively, but besides humans, this has only been done for the goldfish and the honeybee. In this study, we quantified colour constancy in the chicken by training the birds in a colour discrimination task and testing them in changed illumination spectra to find the largest illumination change in which they were able to remain colour-constant. We used the receptor noise limited model for animal colour vision to quantify the illumination changes, and found that colour constancy performance depended on the difference between the colours used in the discrimination task, the training procedure and the time the chickens were allowed to adapt to a new illumination before making a choice. We analysed literature data on goldfish and honeybee colour constancy with the same method and found that chickens can compensate for larger illumination changes than both. We suggest that future studies on colour constancy in non-human animals could use a similar approach to allow for comparison between species and populations. PMID:27170714

  3. Monitoring linear accelerator output constancy using the PTW Linacheck.

    PubMed

    McDermott, Garry M; Buckle, Andrew H

    2011-01-01

    The PTW-Linacheck was assessed for its ability to monitor linear accelerator radiation output constancy. The key issues that were considered were the setup for daily output measurements, e.g., requirements for build-up and backscatter material, and the reproducibility and linearity of the device with linear accelerator output. An appropriate measurement setup includes a 10 × 10 cm field at 100 cm FSD, 5 cm backscatter, and no added build-up for 4 MeV electron beams, 1 cm added build-up for 6-16 MeV electron beams and 5 cm added build-up for 6-15 MV photon beams. Using this measurement setup, the dose linearity and short-term reproducibility were acceptable; however, the Linacheck should be recalibrated on a monthly basis to ensure acceptable long-term reproducibility. PMID:20346645

  4. Speed Constancy or Only Slowness: What Drives the Kappa Effect

    PubMed Central

    Chen, Youguo; Zhang, Bangwu; Kording, Konrad Paul

    2016-01-01

    In the Kappa effect, two visual stimuli are given, and their spatial distance affects their perceived temporal interval. The classical model assumes constant speed while a competing Bayesian model assumes a slow speed prior. The two models are based on different assumptions about the statistical structure of the environment. Here we introduce a new visual experiment to distinguish between these models. When fit to the data, both the two models replicated human response, but the slowness model makes better behavioral predictions than the speed constancy model, and the estimated constant speed is close to the absolute threshold of speed. Our findings suggest that the Kappa effect appears to be due to slow speeds, and also modulated by spatial variance. PMID:27100097

  5. Monitoring Linear Accelerator Output Constancy Using the PTW Linacheck

    SciTech Connect

    McDermott, Garry M.; Buckle, Andrew H.

    2011-04-01

    The PTW-Linacheck was assessed for its ability to monitor linear accelerator radiation output constancy. The key issues that were considered were the setup for daily output measurements, e.g., requirements for build-up and backscatter material, and the reproducibility and linearity of the device with linear accelerator output. An appropriate measurement setup includes a 10 x 10 cm field at 100 cm FSD, 5 cm backscatter, and no added build-up for 4 MeV electron beams, 1 cm added build-up for 6-16 MeV electron beams and 5 cm added build-up for 6-15 MV photon beams. Using this measurement setup, the dose linearity and short-term reproducibility were acceptable; however, the Linacheck should be recalibrated on a monthly basis to ensure acceptable long-term reproducibility.

  6. The intensity dependent spread model and color constancy

    NASA Technical Reports Server (NTRS)

    Kurrasch, Ellie

    1990-01-01

    Odetics is investigating the use of the intensity dependent spread (IDS) model for determining color constancy. Object segmentation is performed effortlessly by the human visual systems, but creating computer vision that takes an image as input and performs object identification on the basis of color has some difficulties. The unknown aspects of the light illuminating a scene in space or anywhere can seriously interfere with the use of color for object identification. The color of an image depends not only on the physical characteristics of the object, but also on the wavelength composition of the incident illumination. IDS processing provides the extraction of edges and of reflectance changes across edges, independent of variations in scene illumination. IDS depends solely on the ratio of the reflectances on the two sides of the edge. Researchers are in the process of using IDS to recover the reflectance image.

  7. TARA and constance B mirror confinement experiments and theory

    SciTech Connect

    Post, R.S.; Gerver, M.; Kesner, J.; Irby, J.H.; Lane, B.G.; Mauel, M.E.; McVey, B.D.; Ram, A.; Sevillano, E.; Smatlak, D.L.

    1984-01-01

    The axisymmetric TARA central cell has been heated using aperture and double half turn ICRF antennas to produce stable plasma with ..beta.. less than or equal to 0.2%. Parameters suitable for startup of thermal barriers with n = 3.5 x 10/sup 12//cm/sup 3/ and Ti/sub perpendiculer/ approx. 30 eV have been reached. Hot electron plasmas with ..beta.. less than or equal to 15% are obtained in the TARA and Constance quadrupoles. Electron cyclotron instabilities are analyzed. A new scheme for single frequency drift pumping with stochasticity by ICRF is proposed. ICRF modulated at the electron bounce frequency is shown to yield stochastic parallel electron heating for thermal barriers.

  8. Generalized Enhanced Multivariance Product Representation for Data Partitioning: Constancy Level

    SciTech Connect

    Tunga, M. Alper; Demiralp, Metin

    2011-09-14

    Enhanced Multivariance Product Representation (EMPR) method is used to represent multivariate functions in terms of less-variate structures. The EMPR method extends the HDMR expansion by inserting some additional support functions to increase the quality of the approximants obtained for dominantly or purely multiplicative analytical structures. This work aims to develop the generalized form of the EMPR method to be used in multivariate data partitioning approaches. For this purpose, the Generalized HDMR philosophy is taken into consideration to construct the details of the Generalized EMPR at constancy level as the introductory steps and encouraging results are obtained in data partitioning problems by using our new method. In addition, to examine this performance, a number of numerical implementations with concluding remarks are given at the end of this paper.

  9. Electron-cyclotron heating in the Constance 2 mirror experiment

    SciTech Connect

    Mauel, Michael E.

    1982-09-01

    Electron cyclotron heating of a highly-ionized plasma in mirror geometry is investigated. The experimental diagnosis of the electron energy distribution and the comparison of the results of this diagnosis with a two dimensional, time-dependent Fokker-Planck simulation are accomplished in four steps. (1) First, the power balance of the heated and unheated Constance 2 plasma is analyzed experimentally. It is concluded that the heated electrons escape the mirror at a rate dominated by a combination of the influx of cool electrons from outside the mirror and the increased loss rate of the ions. (2) The microwave parameters at the resonance zones are then calculated by cold-plasma ray tracing. High N/sub parallel/ waves are launched and for these waves, strong first-pass absorption is predicted. The absorption strength is qualitatively checked in the experiment by surrounding the plasma with non-reflecting liners. (3) A simplified quasilinear theory including the effect of N/sub parallel/ is developed to model the electrons. An analytic expression is derived for the RF-induced pump-out of the magnetically-confined warm electrons. Results of the Fokker-Planck simulations show the development of the electron energy distribution for several plasma conditions and verify the scaling of the analytic expression for RF-induced diffusion into the loss cone. (4) Sample x-ray and endloss data are presented, and the overall comparison between the simulation and experiment is discussed. The x-ray signals indicate that, for greater RF power, the hot electrondensity increases more rapidly than its temperature. The time history of the endloss data, illustrating RF-enhancement, suggests the predicted scaling for warm-electron pump-out. Finally, a comparison between the measured and predicted energy distribution shows that the bulk, warm and hot components of the heated Constance 2 electrons are indeed reproduced by the simulation.

  10. Color constancy demonstrated in a photographic picture by means of a D-up viewer

    NASA Astrophysics Data System (ADS)

    Phuangsuwan, Chanprapha; Ikeda, Mitsuo; Katemake, Pichayada

    2013-01-01

    According to the recognized visual space of illumination concept, space perception is essential for color constancy. It should be possible to experience the color constancy in a picture if we perceive a three-dimensional space in the picture. A dimension-up (D-up) viewer was constructed to perceive a space for a picture. An experimental room illuminated by various color lights was used as the reference scene and the subject determined a picture in which the color impression was matched to that of the room by selecting from 13 different colored pictures of the room. The picture with the color nearest to the color of the room was selected with the D-up viewer implying the existence of color constancy in the picture. When subjects observed a picture in a normal way the picture of the room illuminated in white was selected regardless of the actual room illumination color, confirming no color constancy in the picture.

  11. Phylogeny of filamentous ascomycetes

    NASA Astrophysics Data System (ADS)

    Lumbsch, H. T.

    Phylogenetic studies of higher ascomycetes are enhanced by the introduction of molecular markers. Most studies employed sequences of the SSU rRNA gene, but recently data from additional genes (RPB2, LSU rRNA) have become available. Several groups defined by their ascoma-type, such as Pyrenomycetes, are supported while others, like the Discomycetes, appear to be paraphyletic. The Pezizales with operculate asci are basal to other eu-ascomycetes, while other Discomycetes appear to be derived eu-ascomycetes. The re-evaluation of classical characters using molecular data is discussed using three examples. Ascus types are often regarded as being of major importance in ascomycete systematics, but prototunicate asci were found to be of poor taxonomic value, since ascomycetes with prototunicate asci are polyphyletic. The independence of the Agyriales, assumed from their morphological characters, is supported by sequence data but the relationship to supposed sister groups remains dubious. The phylogeny of ascolocularous fungi and their circumscription requires further study. While a circumscription based on bitunicate asci can be rejected, it remains unclear whether fungi with ascolocularous ascoma development represent a monophyletic entity.

  12. Phylogeny of African cichlid fishes as revealed by molecular markers.

    PubMed

    Mayer, W E; Tichy, H; Klein, J

    1998-06-01

    The species flocks of cichlid fish in the three great East African Lakes, Victoria, Malawi, and Tanganyika, have arisen in each lake by explosive adaptive radiation. Various questions concerning their phylogeny have not yet been answered. In particular, the identity of the ancestral founder species and the monophyletic origin of the haplochromine cichlids from the East African lakes have not been established conclusively. In the present study, we used the anonymous nuclear DNA marker DXTU1 as a step towards answering these questions. A 280 bp-fragment of the DXTU1 locus was amplified by the polymerase chain reaction from East African lacustrine species, the East African riverine cichlid species Haplochromis bloyeti, H. burtoni and H. sparsidens, and other African cichlids. Sequencing revealed several indels and substitutions that were used as cladistically informative markers to support a phylogenetic tree constructed by the neighbor-joining method. The topology, although not supported by high bootstrap values, corresponds well to the geographical distribution and previous classification of the cichlids. Markers could be defined that: (i) differentiate East African from West African cichlids; (ii) distinguish the riverine and Lake Victoria/Malawi haplochromines from Lake Tanganyika cichlids; and (iii) indicate the existence of a monophyletic Lake Victoria cichlid superflock which includes haplochromines from satellite lakes and East African rivers. In order to resolve further the relationship of East African riverine and lacustrine species, mtDNA cytochrome b and control region segments were sequenced. The mtDNA-based trees support the notion of the monophyly of the Lake Victoria superflock but are ambiguous with respect to the phylogenetic position of the Lake Malawi flock. PMID:9675872

  13. Chromatic illumination discrimination ability reveals that human colour constancy is optimised for blue daylight illuminations.

    PubMed

    Pearce, Bradley; Crichton, Stuart; Mackiewicz, Michal; Finlayson, Graham D; Hurlbert, Anya

    2014-01-01

    The phenomenon of colour constancy in human visual perception keeps surface colours constant, despite changes in their reflected light due to changing illumination. Although colour constancy has evolved under a constrained subset of illuminations, it is unknown whether its underlying mechanisms, thought to involve multiple components from retina to cortex, are optimised for particular environmental variations. Here we demonstrate a new method for investigating colour constancy using illumination matching in real scenes which, unlike previous methods using surface matching and simulated scenes, allows testing of multiple, real illuminations. We use real scenes consisting of solid familiar or unfamiliar objects against uniform or variegated backgrounds and compare discrimination performance for typical illuminations from the daylight chromaticity locus (approximately blue-yellow) and atypical spectra from an orthogonal locus (approximately red-green, at correlated colour temperature 6700 K), all produced in real time by a 10-channel LED illuminator. We find that discrimination of illumination changes is poorer along the daylight locus than the atypical locus, and is poorest particularly for bluer illumination changes, demonstrating conversely that surface colour constancy is best for blue daylight illuminations. Illumination discrimination is also enhanced, and therefore colour constancy diminished, for uniform backgrounds, irrespective of the object type. These results are not explained by statistical properties of the scene signal changes at the retinal level. We conclude that high-level mechanisms of colour constancy are biased for the blue daylight illuminations and variegated backgrounds to which the human visual system has typically been exposed. PMID:24586299

  14. Chromatic Illumination Discrimination Ability Reveals that Human Colour Constancy Is Optimised for Blue Daylight Illuminations

    PubMed Central

    Pearce, Bradley; Crichton, Stuart; Mackiewicz, Michal; Finlayson, Graham D.; Hurlbert, Anya

    2014-01-01

    The phenomenon of colour constancy in human visual perception keeps surface colours constant, despite changes in their reflected light due to changing illumination. Although colour constancy has evolved under a constrained subset of illuminations, it is unknown whether its underlying mechanisms, thought to involve multiple components from retina to cortex, are optimised for particular environmental variations. Here we demonstrate a new method for investigating colour constancy using illumination matching in real scenes which, unlike previous methods using surface matching and simulated scenes, allows testing of multiple, real illuminations. We use real scenes consisting of solid familiar or unfamiliar objects against uniform or variegated backgrounds and compare discrimination performance for typical illuminations from the daylight chromaticity locus (approximately blue-yellow) and atypical spectra from an orthogonal locus (approximately red-green, at correlated colour temperature 6700 K), all produced in real time by a 10-channel LED illuminator. We find that discrimination of illumination changes is poorer along the daylight locus than the atypical locus, and is poorest particularly for bluer illumination changes, demonstrating conversely that surface colour constancy is best for blue daylight illuminations. Illumination discrimination is also enhanced, and therefore colour constancy diminished, for uniform backgrounds, irrespective of the object type. These results are not explained by statistical properties of the scene signal changes at the retinal level. We conclude that high-level mechanisms of colour constancy are biased for the blue daylight illuminations and variegated backgrounds to which the human visual system has typically been exposed. PMID:24586299

  15. Repeated Lake-Stream Divergence in Stickleback Life History within a Central European Lake Basin

    PubMed Central

    Moser, Dario; Roesti, Marius; Berner, Daniel

    2012-01-01

    Life history divergence between populations inhabiting ecologically distinct habitats might be a potent source of reproductive isolation, but has received little attention in the context of speciation. We here test for life history divergence between threespine stickleback inhabiting Lake Constance (Central Europe) and multiple tributary streams. Otolith analysis shows that lake fish generally reproduce at two years of age, while their conspecifics in all streams have shifted to a primarily annual life cycle. This divergence is paralleled by a striking and consistent reduction in body size and fecundity in stream fish relative to lake fish. Stomach content analysis suggests that life history divergence might reflect a genetic or plastic response to pelagic versus benthic foraging modes in the lake and the streams. Microsatellite and mitochondrial markers further reveal that life history shifts in the different streams have occurred independently following the colonization by Lake Constance stickleback, and indicate the presence of strong barriers to gene flow across at least some of the lake-stream habitat transitions. Given that body size is known to strongly influence stickleback mating behavior, these barriers might well be related to life history divergence. PMID:23226528

  16. Colour constancy across the life span: evidence for compensatory mechanisms.

    PubMed

    Wuerger, Sophie

    2013-01-01

    It is well known that the peripheral visual system declines with age: the yellowing of the lens causes a selective reduction of short-wavelength light and sensitivity losses occur in the cone receptor mechanisms. At the same time, our subjective experience of colour does not change with age. The main purpose of this large-scale study (n = 185) covering a wide age range of colour-normal observers (18-75 years of age) was to assess the extent to which the human visual system is able to compensate for the changes in the optical media and at which level of processing this compensation is likely to occur. We report two main results: (1) Supra-threshold parafoveal colour perception remains largely unaffected by the age-related changes in the optical media (yellowing of the lens) whereas our ability to discriminate between small colour differences is compromised with an increase in age. (2) Significant changes in colour appearance are only found for unique green settings under daylight viewing condition which is consistent with the idea that the yellow-blue mechanism is most affected by an increase in age due to selective attenuation of short-wavelength light. The data on the invariance of hue perception, in conjunction with the age-related decline in chromatic sensitivity, provides evidence for compensatory mechanisms that enable colour-normal human observers a large degree of colour constancy across the life span. These compensatory mechanisms are likely to originate at cortical sites. PMID:23667689

  17. ON THE CONSTANCY OF THE SOLAR RADIUS. III

    SciTech Connect

    Bush, R. I.; Emilio, M.; Kuhn, J. R. E-mail: memilio@uepg.b

    2010-06-20

    The Michelson Doppler Imager on board the Solar and Heliospheric Observatory satellite has operated for over a sunspot cycle. This instrument is now relatively well understood and provides a nearly continuous record of the solar radius in combination with previously developed algorithms. Because these data are obtained from above Earth's atmosphere, they are uniquely sensitive to possible long-term changes of the Sun's size. We report here on the first homogeneous, highly precise, and complete solar-cycle measurement of the Sun's radius variability. Our results show that any intrinsic changes in the solar radius that are synchronous with the sunspot cycle must be smaller than 23 mas peak to peak. In addition, we find that the average solar radius must not be changing (on average) by more than 1.2 mas yr{sup -1}. If ground- and space-based measurements are both correct, the pervasive difference between the constancy of the solar radius seen from space and the apparent ground-based solar astrometric variability can only be accounted for by long-term changes in the terrestrial atmosphere.

  18. The effect of exposure on MaxRGB color constancy

    NASA Astrophysics Data System (ADS)

    Funt, Brian; Shi, Lilong

    2010-02-01

    The performance of the MaxRGB illumination-estimation method for color constancy and automatic white balancing has been reported in the literature as being mediocre at best; however, MaxRGB has usually been tested on images of only 8-bits per channel. The question arises as to whether the method itself is inadequate, or rather whether it has simply been tested on data of inadequate dynamic range. To address this question, a database of sets of exposure-bracketed images was created. The image sets include exposures ranging from very underexposed to slightly overexposed. The color of the scene illumination was determined by taking an extra image of the scene containing 4 Gretag Macbeth mini Colorcheckers placed at an angle to one another. MaxRGB was then run on the images of increasing exposure. The results clearly show that its performance drops dramatically when the 14-bit exposure range of the Nikon D700 camera is exceeded, thereby resulting in clipping of high values. For those images exposed such that no clipping occurs, the median error in MaxRGB's estimate of the color of the scene illumination is found to be relatively small.

  19. Surface-illuminant ambiguity and color constancy: effects of scene complexity and depth cues.

    PubMed

    Kraft, James M; Maloney, Shannon I; Brainard, David H

    2002-01-01

    Two experiments were conducted to study how scene complexity and cues to depth affect human color constancy. Specifically, two levels of scene complexity were compared. The low-complexity scene contained two walls with the same surface reflectance and a test patch which provided no information about the illuminant. In addition to the surfaces visible in the low-complexity scene, the high-complexity scene contained two rectangular solid objects and 24 paper samples with diverse surface reflectances. Observers viewed illuminated objects in an experimental chamber and adjusted the test patch until it appeared achromatic. Achromatic settings made tinder two different illuminants were used to compute an index that quantified the degree of constancy. Two experiments were conducted: one in which observers viewed the stimuli directly, and one in which they viewed the scenes through an optical system that reduced cues to depth. In each experiment, constancy was assessed for two conditions. In the valid-cue condition, many cues provided valid information about the illuminant change. In the invalid-cue condition, some image cues provided invalid information. Four broad conclusions are drawn from the data: (a) constancy is generally better in the valid-cue condition than in the invalid-cue condition: (b) for the stimulus configuration used, increasing image complexity has little effect in the valid-cue condition but leads to increased constancy in the invalid-cue condition; (c) for the stimulus configuration used, reducing cues to depth has little effect for either constancy condition: and (d) there is moderate individual variation in the degree of constancy exhibited, particularly in the degree to which the complexity manipulation affects performance. PMID:11922136

  20. Chlorine-36 dating of saline sediments: Preliminary results from Searles Lake, California

    USGS Publications Warehouse

    Phillips, F.M.; Smith, G.I.; Bentley, H.W.; Elmore, D.; Gove, H.E.

    1983-01-01

    Measurements have been made of the ratios of chlorine-36 to chlorine in five halite samples from Searles Lake sediments, previously dated by carbon-14, thorium-230, and magnetostratigraphic techniques. The ages calculated from the chlorine ratios are generally concordant with those from the other methods, implying the constancy of the chlorine input ratio over the last million years.

  1. The effects of surface gloss and roughness on color constancy for real 3-D objects.

    PubMed

    Granzier, Jeroen J M; Vergne, Romain; Gegenfurtner, Karl R

    2014-01-01

    Color constancy denotes the phenomenon that the appearance of an object remains fairly stable under changes in illumination and background color. Most of what we know about color constancy comes from experiments using flat, matte surfaces placed on a single plane under diffuse illumination simulated on a computer monitor. Here we investigate whether material properties (glossiness and roughness) have an effect on color constancy for real objects. Subjects matched the color and brightness of cylinders (painted red, green, or blue) illuminated by simulated daylight (D65) or by a reddish light with a Munsell color book illuminated by a tungsten lamp. The cylinders were either glossy or matte and either smooth or rough. The object was placed in front of a black background or a colored checkerboard. We found that color constancy was significantly higher for the glossy objects compared to the matte objects, and higher for the smooth objects compared to the rough objects. This was independent of the background. We conclude that material properties like glossiness and roughness can have significant effects on color constancy. PMID:24563527

  2. Effects of memory colour on colour constancy for unknown coloured objects

    PubMed Central

    Granzier, Jeroen J M; Gegenfurtner, Karl R

    2012-01-01

    The perception of an object's colour remains constant despite large variations in the chromaticity of the illumination—colour constancy. Hering suggested that memory colours, the typical colours of objects, could help in estimating the illuminant's colour and therefore be an important factor in establishing colour constancy. Here we test whether the presence of objects with diagnostical colours (fruits, vegetables, etc) within a scene influence colour constancy for unknown coloured objects in the scene. Subjects matched one of four Munsell papers placed in a scene illuminated under either a reddish or a greenish lamp with the Munsell book of colour illuminated by a neutral lamp. The Munsell papers were embedded in four different scenes—one scene containing diagnostically coloured objects, one scene containing incongruent coloured objects, a third scene with geometrical objects of the same colour as the diagnostically coloured objects, and one scene containing non-diagnostically coloured objects (eg, a yellow coffee mug). All objects were placed against a black background. Colour constancy was on average significantly higher for the scene containing the diagnostically coloured objects compared with the other scenes tested. We conclude that the colours of familiar objects help in obtaining colour constancy for unknown objects. PMID:23145282

  3. Research on color constancy computation based on YCbCr color space and gray surface

    NASA Astrophysics Data System (ADS)

    Wang, Hong; Yang, Jianfeng; Xue, Bin; Yan, Xingtao; Liang, Xiaofen

    2014-11-01

    Color constancy is of important for many computer vision applications, such as image classification, color object recognition, object tracking and so on. But unlike the human visual system, imaging device cannot be able to compute color constant descriptors which do not vary with the color of the illuminant, so solving color constancy problem is necessary. In the calculation of color constancy, illuminant estimation is the key. Because grey surfaces can perfectly reflect the color of the scene illumination, many methods have been proposed to identify grey surfaces to estimate the illuminant. But they either rely on the camera's parameters, lacking universality, or work inaccurate in worse conditions. In order to solve these problems, in this paper, an iterative method is proposed. The quality of the proposed method is tested and compared to the previous color constancy methods on the Macbeth Chart and two data sets of synthetic and real images. Through MATLAB simulation, experimental pictures and quantitative data for performance evaluation were gotten. The simulated results show that the proposed algorithm is accurate and efficient in identification of the grey surfaces, even in worse condition. And it performs well in color constancy computation on both synthetic and real images.

  4. No Measured Effect of a Familiar Contextual Object on Color Constancy.

    PubMed

    Kanematsu, Erika; Brainard, David H

    2014-08-01

    Some familiar objects have a typical color, such as the yellow of a banana. The presence of such objects in a scene is a potential cue to the scene illumination, since the light reflected from them should on average be consistent with their typical surface reflectance. Although there are many studies on how the identity of an object affects how its color is perceived, little is known about whether the presence of a familiar object in a scene helps the visual system stabilize the color appearance of other objects with respect to changes in illumination. We used a successive color matching procedure in three experiments designed to address this question. Across the experiments we studied a total of 6 subjects (2 in Experiment 1, 3 in Experiment 2, and 4 in Experiment 3) with partial overlap of subjects between experiments. We compared measured color constancy across conditions in which a familiar object cue to the illuminant was available with conditions in which such a cue was not present. Overall, our results do not reveal a reliable improvement in color constancy with the addition of a familiar object to a scene. An analysis of the experimental power of our data suggests that if there is such an effect, it is small: less than approximately a change of 0.09 in a constancy index where an absence of constancy corresponds to an index value of 0 and perfect constancy corresponds to an index value of 1. PMID:25313267

  5. No Measured Effect of a Familiar Contextual Object on Color Constancy

    PubMed Central

    Kanematsu, Erika; Brainard, David H.

    2013-01-01

    Some familiar objects have a typical color, such as the yellow of a banana. The presence of such objects in a scene is a potential cue to the scene illumination, since the light reflected from them should on average be consistent with their typical surface reflectance. Although there are many studies on how the identity of an object affects how its color is perceived, little is known about whether the presence of a familiar object in a scene helps the visual system stabilize the color appearance of other objects with respect to changes in illumination. We used a successive color matching procedure in three experiments designed to address this question. Across the experiments we studied a total of 6 subjects (2 in Experiment 1, 3 in Experiment 2, and 4 in Experiment 3) with partial overlap of subjects between experiments. We compared measured color constancy across conditions in which a familiar object cue to the illuminant was available with conditions in which such a cue was not present. Overall, our results do not reveal a reliable improvement in color constancy with the addition of a familiar object to a scene. An analysis of the experimental power of our data suggests that if there is such an effect, it is small: less than approximately a change of 0.09 in a constancy index where an absence of constancy corresponds to an index value of 0 and perfect constancy corresponds to an index value of 1. PMID:25313267

  6. Demonstration of color constancy in photographs by two techniques: Stereoscope and D-up viewer

    NASA Astrophysics Data System (ADS)

    Phuangsuwan, Chanprapha; Ikeda, Mitsuo; Shinoda, Hiroyuki

    2014-11-01

    When we look, under daylight, at a scene in a photograph taken under an incandescent lamp, it appears very reddish, showing that color constancy is not maintained. According to the recognized visual space of illumination (RVSI) concept, color constancy should exist in a photograph if one can perceive three dimensions in it. This prediction was confirmed by applying two viewing techniques to perceive a 3D space in a 2D photograph: a stereoscope viewed with two eyes and a D-up viewer viewed with one eye. A wide range of illumination color was investigated, covering range from vivid blue through to vivid orange, and the color constancy index became larger with the 3D perception than with the 2D perception of the photographs produced by the two techniques.

  7. Determination of Sectional Constancy of Organic Coal-Water Fuel Compositions

    NASA Astrophysics Data System (ADS)

    Dmitrienko, Margarita A.; Nyashina, Galina S.; Strizhak, Pavel A.

    2016-02-01

    To use widespreadly the waste of coals and oils processing in the great and the small-scale power generation, the key parameter, which is sectional constancy of promising organic coal-water fuels (OCWF), was studied. The compo-sitions of OCWF from brown and bituminous coals, filter cakes, used motor, turbine and dielectrical oils, water-oil emul-sion and special wetting agent (plasticizer) were investigated. Two modes of preparation were considered. They are with homogenizer and cavitator. It was established that the constancy did not exceed 5-7 days for the compositions of OCWF with brown coals, and 12-15 days for that compositions with bituminous coals and filter cakes. The injection of used oils in a composition of OCWF led to increase in viscosity of fuel compositions and their sectional constancy.

  8. Brunswik ratios: a ratio scale for comparative analyses of size constancy data from different experiments.

    PubMed

    Smith, O W; Smith, P C; Zimmermann, R R; Geist, C

    1977-12-01

    The literature on visual size constancy implicitly assumes that the perceived size of any dimension of a thing is evidence of how well (a) any other dimension of the thing will be perceived and (b) any visible dimension of any other thing will be perceived under comparable conditions of perception. For tests of these assumptions Brunswik ratios (1956) are described as a common conceptual and numerical basis, a ratio scale, for testing statistically for differences among or the equivalence of two or more sets of data from different experiments on visual size constancy. PMID:604909

  9. Iterative color constancy with temporal filtering for an image sequence with no relative motion between the camera and the scene.

    PubMed

    Simão, Josemar; Jörg Andreas Schneebeli, Hans; Vassallo, Raquel Frizera

    2015-11-01

    Color constancy is the ability to perceive the color of a surface as invariant even under changing illumination. In outdoor applications, such as mobile robot navigation or surveillance, the lack of this ability harms the segmentation, tracking, and object recognition tasks. The main approaches for color constancy are generally targeted to static images and intend to estimate the scene illuminant color from the images. We present an iterative color constancy method with temporal filtering applied to image sequences in which reference colors are estimated from previous corrected images. Furthermore, two strategies to sample colors from the images are tested. The proposed method has been tested using image sequences with no relative movement between the scene and the camera. It also has been compared with known color constancy algorithms such as gray-world, max-RGB, and gray-edge. In most cases, the iterative color constancy method achieved better results than the other approaches. PMID:26560917

  10. Phylogeny and diversification of bryophytes.

    PubMed

    Shaw, Jonathan; Renzaglia, Karen

    2004-10-01

    The bryophytes comprise three phyla of embryophytes that are well established to occupy the first nodes among extant lineages in the land-plant tree of life. The three bryophyte groups (hornworts, liverworts, mosses) may not form a monophyletic clade, but they share life history features including dominant free-living gametophytes and matrotrophic monosporangiate sporophytes. Because of their unique vegetative and reproductive innovations and their critical position in embryophyte phylogeny, studies of bryophytes are crucial to understanding the evolution of land plant morphology and genomes. This review focuses on phylogenetic relationships within each of the three divisions of bryophytes and relates morphological diversity to new insights about those relationships. Most previous work has been on the mosses, but progress on understanding the phylogeny of hornworts and liverworts is advancing at a rapid pace. Multilocus multigenome studies have been successful at resolving deep relationships within the mosses and liverworts, whereas single-gene analyses have advanced understanding of hornwort evolution. PMID:21652309

  11. Support Values for Genome Phylogenies

    PubMed Central

    Klötzl, Fabian; Haubold, Bernhard

    2016-01-01

    We have recently developed a distance metric for efficiently estimating the number of substitutions per site between unaligned genome sequences. These substitution rates are called “anchor distances” and can be used for phylogeny reconstruction. Most phylogenies come with bootstrap support values, which are computed by resampling with replacement columns of homologous residues from the original alignment. Unfortunately, this method cannot be applied to anchor distances, as they are based on approximate pairwise local alignments rather than the full multiple sequence alignment necessary for the classical bootstrap. We explore two alternatives: pairwise bootstrap and quartet analysis, which we compare to classical bootstrap. With simulated sequences and 53 human primate mitochondrial genomes, pairwise bootstrap gives better results than quartet analysis. However, when applied to 29 E. coli genomes, quartet analysis comes closer to the classical bootstrap. PMID:26959064

  12. High-Performance Phylogeny Reconstruction

    SciTech Connect

    Tiffani L. Williams

    2004-11-10

    Under the Alfred P. Sloan Fellowship in Computational Biology, I have been afforded the opportunity to study phylogenetics--one of the most important and exciting disciplines in computational biology. A phylogeny depicts an evolutionary relationship among a set of organisms (or taxa). Typically, a phylogeny is represented by a binary tree, where modern organisms are placed at the leaves and ancestral organisms occupy internal nodes, with the edges of the tree denoting evolutionary relationships. The task of phylogenetics is to infer this tree from observations upon present-day organisms. Reconstructing phylogenies is a major component of modern research programs in many areas of biology and medicine, but it is enormously expensive. The most commonly used techniques attempt to solve NP-hard problems such as maximum likelihood and maximum parsimony, typically by bounded searches through an exponentially-sized tree-space. For example, there are over 13 billion possible trees for 13 organisms. Phylogenetic heuristics that quickly analyze large amounts of data accurately will revolutionize the biological field. This final report highlights my activities in phylogenetics during the two-year postdoctoral period at the University of New Mexico under Prof. Bernard Moret. Specifically, this report reports my scientific, community and professional activities as an Alfred P. Sloan Postdoctoral Fellow in Computational Biology.

  13. Spatial and temporal aspects of chromatic adaptation and their functional significance for colour constancy.

    PubMed

    Werner, Annette

    2014-11-01

    Illumination in natural scenes changes at multiple temporal and spatial scales: slow changes in global illumination occur in the course of a day, and we encounter fast and localised illumination changes when visually exploring the non-uniform light field of three-dimensional scenes; in addition, very long-term chromatic variations may come from the environment, like for example seasonal changes. In this context, I consider the temporal and spatial properties of chromatic adaptation and discuss their functional significance for colour constancy in three-dimensional scenes. A process of fast spatial tuning in chromatic adaptation is proposed as a possible sensory mechanism for linking colour constancy to the spatial structure of a scene. The observed middlewavelength selectivity of this process is particularly suitable for adaptation to the mean chromaticity and the compensation of interreflections in natural scenes. Two types of sensory colour constancy are distinguished, based on the functional differences of their temporal and spatial scales: a slow type, operating at a global scale for the compensation of the ambient illumination; and a fast colour constancy, which is locally restricted and well suited to compensate region-specific variations in the light field of three dimensional scenes. PMID:25449338

  14. Morphological Constancy in Spelling: A Comparison of Children with Dyslexia and Typically Developing Children

    ERIC Educational Resources Information Center

    Bourassa, Derrick C.; Treiman, Rebecca

    2008-01-01

    The spellings of many English words follow a principle of morphological constancy. For example, "musician" includes the c of "music", even though the pronunciation of this letter changes. With other words, such as "explanation" and "explain", the spellings of morphemes are not retained when affixes are added. We asked whether children with…

  15. A Neural Model of Distance-Dependent Percept of Object Size Constancy

    PubMed Central

    Qian, Jiehui; Yazdanbakhsh, Arash

    2015-01-01

    Size constancy is one of the well-known visual phenomena that demonstrates perceptual stability to account for the effect of viewing distance on retinal image size. Although theories involving distance scaling to achieve size constancy have flourished based on psychophysical studies, its underlying neural mechanisms remain unknown. Single cell recordings show that distance-dependent size tuned cells are common along the ventral stream, originating from V1, V2, and V4 leading to IT. In addition, recent research employing fMRI demonstrates that an object’s perceived size, associated with its perceived egocentric distance, modulates its retinotopic representation in V1. These results suggest that V1 contributes to size constancy, and its activity is possibly regulated by feedback of distance information from other brain areas. Here, we propose a neural model based on these findings. First, we construct an egocentric distance map in LIP by integrating horizontal disparity and vergence through gain-modulated MT neurons. Second, LIP neurons send modulatory feedback of distance information to size tuned cells in V1, resulting in a spread of V1 cortical activity. This process provides V1 with distance-dependent size representations. The model supports that size constancy is preserved by scaling retinal image size to compensate for changes in perceived distance, and suggests a possible neural circuit capable of implementing this process. PMID:26132106

  16. The role of size constancy for the integration of local elements into a global shape

    PubMed Central

    Rennig, Johannes; Karnath, Hans-Otto; Huberle, Elisabeth

    2013-01-01

    Visual perception depends on the visual context and is likely to be influenced by size constancy, which predicts a size and distance invariant perception of objects. However, size constancy can also result in optical illusions that allow the manipulation of the perceived size. We thus asked whether the integration of local elements into a global object can be influenced by manipulations of the visual context and size constancy? A set of stimuli was applied in healthy individuals that took advantage of the “Kanizsa” illusion, in which three circles with open wedges oriented toward a center point are placed to form an illusionary perception of a triangle. In addition, a 3D-perspective view was implemented in which the global target (“Kanizsa” triangle) was placed in combination with several distractor circles either in a close or a distant position. Subjects were engaged in a global recognition task on the location of the “Kanizsa” triangle. Global recognition of “Kanizsa” triangles improved with a decreasing length of the illusory contour. Interestingly, recognition of “Kanizsa” triangles decreased when they were perceived as if they were located further away. We conclude that the integration of local elements into a global object is dependent on the visual context and dominated by size constancy. PMID:23840187

  17. A Neural Model of Distance-Dependent Percept of Object Size Constancy.

    PubMed

    Qian, Jiehui; Yazdanbakhsh, Arash

    2015-01-01

    Size constancy is one of the well-known visual phenomena that demonstrates perceptual stability to account for the effect of viewing distance on retinal image size. Although theories involving distance scaling to achieve size constancy have flourished based on psychophysical studies, its underlying neural mechanisms remain unknown. Single cell recordings show that distance-dependent size tuned cells are common along the ventral stream, originating from V1, V2, and V4 leading to IT. In addition, recent research employing fMRI demonstrates that an object's perceived size, associated with its perceived egocentric distance, modulates its retinotopic representation in V1. These results suggest that V1 contributes to size constancy, and its activity is possibly regulated by feedback of distance information from other brain areas. Here, we propose a neural model based on these findings. First, we construct an egocentric distance map in LIP by integrating horizontal disparity and vergence through gain-modulated MT neurons. Second, LIP neurons send modulatory feedback of distance information to size tuned cells in V1, resulting in a spread of V1 cortical activity. This process provides V1 with distance-dependent size representations. The model supports that size constancy is preserved by scaling retinal image size to compensate for changes in perceived distance, and suggests a possible neural circuit capable of implementing this process. PMID:26132106

  18. Constance "Connie" Hanf (1917-2002): The Mentor and the Model

    ERIC Educational Resources Information Center

    Reitman, David; McMahon, Robert J.

    2013-01-01

    This article provides an account of the impact of Constance Hanf, Ph.D., developer of the well-known two-stage parent training model that bears her name. Past colleagues, interns, postdoctoral students, and undergraduate trainees reflect on their experiences with Dr. Hanf and comment on her influence on their careers, as well as the impact of the…

  19. The Relation between Gender Labelling and Gender Constancy in Preschool Children.

    ERIC Educational Resources Information Center

    Zucker, Kenneth J.; Yoannidis, Tom

    The relationship between preschool children's level of gender understanding and their ability to identify gender-linked attributes was examined. Participants were 26 3-year-old and 30 4-year-old children who were administered a single-cue gender labelling task, Slaby and Frey's (1975) gender constancy test, and the Peabody Picture Vocabulary Test.…

  20. Restructuring Philadelphia's Neighborhood High Schools: A Conversation with Constance Clayton and Michelle Fine.

    ERIC Educational Resources Information Center

    Schwartz, Robert

    1994-01-01

    This interview with Constance Clayton, superintendent of the Philadelphia (Pennsylvania) public schools, and Michelle Fine, professor of psychology and consultant, discusses the Philadelphia Schools Collaborative, a nonprofit organization established to lead the restructuring of the city's high schools. Central to the effort is the concept of…

  1. Surface color perception under two illuminants: the second illuminant reduces color constancy

    NASA Technical Reports Server (NTRS)

    Yang, Joong Nam; Shevell, Steven K.

    2003-01-01

    This study investigates color perception in a scene with two different illuminants. The two illuminants, in opposite corners, simultaneously shine on a (simulated) scene with an opaque dividing wall, which controls how much of the scene is illuminated by each source. In the first experiment, the height of the dividing wall was varied. This changed the amount of each illuminant reaching objects on the opposite side of the wall. Results showed that the degree of color constancy decreased when a region on one side of the wall had cues to both illuminants, suggesting that cues from the second illuminant are detrimental to color constancy. In a later experiment, color constancy was found to improve when the specular highlight cues from the second illuminant were altered to be consistent with the first illuminant. This corroborates the influence of specular highlights in surface color perception, and suggests that the reduced color constancy in the first experiment is due to the inconsistent, though physically correct, cues from the two illuminants.

  2. Right Temporal Cortex is Critical for Utilization of Melodic Contextual Cues in a Pitch Constancy Task

    ERIC Educational Resources Information Center

    Warrier, Catherine M.; Zatorre, Robert J.

    2004-01-01

    Pitch constancy, perceiving the same pitch from tones with differing spectral shapes, requires one to extract the fundamental frequency from two sets of harmonics and compare them. We previously showed this difficult task to be easier when tonal context is present, presumably because the context creates a tonal reference point from which to judge…

  3. Revisiting the Principle of Relative Constancy: Consumer Mass Media Expenditures in Belgium.

    ERIC Educational Resources Information Center

    Dupagne, Michel; Green, R. Jeffery

    1996-01-01

    Proposes two new econometric models for testing the principle of relative constancy (PRC). Reports on regression and cointegration analyses conducted with Belgian mass media expenditure data from 1953-91. Suggests that alternative mass media expenditure models should be developed because PRC lacks of economic foundation and sound empirical…

  4. CONSTANCY OF THE RELATION BETWEEN FLOC SIZE AND DENSITY IN SAN FRANCISCO BAY

    EPA Science Inventory

    Ganju, N.K., D.H. Schoellhamer, M.C. Murrell, J.W. Gartner and S.A. Wright. In press. Constancy of the Relation Between Floc Size and Density in San Francisco Bay. In: INTERCOH 2003: Proceedings of the 7th International Conference on Nearshore and Estuarine Cohesive Sediment Tran...

  5. The Development of Language Constancy: Attention to Native versus Nonnative Accents

    ERIC Educational Resources Information Center

    Kitamura, Christine; Panneton, Robin; Best, Catherine T.

    2013-01-01

    The time frame for infants' acquisition of language constancy was probed, using the phonetic variation in a rarely heard accent (South African English) or a frequently heard accent (American English). A total of 156 Australian infants were tested. Six-month-olds looked longer to Australian English than less commonly heard South African…

  6. Lake Life.

    ERIC Educational Resources Information Center

    Ohrn, Deborah Gore, Ed.

    1993-01-01

    This quarterly publication of the State Historical Society of Iowa features articles and activities for elementary school students. This summer issue focuses on the topic of lake life. The issue includes the following features: (1) "Where the Lakes Are Map"; (2) "Letter from the Lake"; (3) "Lake People"; (4) "Spirit Lake"; (5) "Lake Manawa"; (6)…

  7. Phylogeny and subgeneric taxonomy of Aspergillus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The phylogeny of the genus Aspergillus and its teleomorphs is discussed based on multilocus sequence data. DNA sequence analysis was used to formulate a nucleotide sequence framework of the genus and to analyze character changes in relationship to the phylogeny hypothesized from the DNA sequence an...

  8. Phylogeny of major intrinsic proteins.

    PubMed

    Danielson, Jonas A H; Johanson, Urban

    2010-01-01

    Major intrinsic proteins (MIPs) form a large superfamily of proteins that can be divided into different subfamilies and groups according to phylogenetic analyses. Plants encode more MIPs than o ther organisms and se ven subfamilies have been defined, whereofthe Nodulin26-like major intrinsic proteins (NIPs) have been shown to permeate metalloids. In this chapter we review the phylogeny of MIPs in general and especially of the plant MIPs. We also identify bacterial NIP-like MIPs and discuss the evolutionary implications of this finding regarding the origin and ancestral transport specificity of the NIPs. PMID:20666221

  9. Advances in estimating the climate sensibility of a large lake using scenario simulations

    NASA Astrophysics Data System (ADS)

    Eder, M. M.; Schlabing, D.; Frassl, M. A.; Rinke, K.; Bárdossy, A.

    2012-04-01

    The vertical mixing behaviour of large deep lakes as e.g. Lake Constance is reflecting the long-term meteorological conditions and therefore is likely to be sensible to climate change. Today, Lake Constance does not mix completely every year, but only once in 2-3 years, which leads to the typical saw-tooth pattern in the deep water temperature. Whether complete mixing does occur is not only depending on the meteorological conditions in the respective winter period, but also on the thermal conditions in the lake and hence on the meteorological conditions in the preceding years. The lake's response to climate change thus depends on the temperature increase itself as well as on its gradient and on the inter-annual variability of the meteorological variables. Last year we showed first steps towards a model system to evaluate possible effects of climate change on Lake Constance: The Vector-Autoregressive Weathergenerator VG produces time series of meteorological data, which are used as boundary conditions for the 3D hydrodynamic lake model ELCOM (Centre of Water Research, University of Western Australia). As VG gives the opportunity to change mean and variability of selected variables, "What if?" - scenarios for process understanding can be performed. The time scales of variability turned out to be a critical point in the artificial time series for modelling the hydrodynamics of Lake Constance, as the big water body integrates over time and thus the hydrodynamics overlook the variability of air temperature on short time scales. Therefore, VG was developed further, especially with respect to the time scales of variability. While for heat input, the time scale of several days to weeks seems to be more important, wind and, when biology is modelled, short-wave radiation should be given at a sub-daily timestep. Besides producing user-defined scenario time-series, VG can also be used to stochastical downscale output of global climate model IPCC scenarios for lake modelling

  10. Eumetazoan Cryptochrome Phylogeny and Evolution

    PubMed Central

    Haug, Marion F.; Gesemann, Matthias; Lazović, Viktor; Neuhauss, Stephan C.F.

    2015-01-01

    Cryptochromes (Crys) are light sensing receptors that are present in all eukaryotes. They mainly absorb light in the UV/blue spectrum. The extant Crys consist of two subfamilies, which are descendants of photolyases but are now involved in the regulation of circadian rhythms. So far, knowledge about the evolution, phylogeny, and expression of cry genes is still scarce. The inclusion of cry sequences from a wide range of bilaterian species allowed us to analyze their phylogeny in detail, identifying six major Cry subgroups. Selective gene inactivations and stabilizations in multiple chordate as well as arthropod lineages suggest several sub- and/or neofunctionalization events. An expression study performed in zebrafish, the model organism harboring the largest amount of crys, showed indeed only partially overlapping expression of paralogous mRNA, supporting gene sub- and/or neofunctionalization. Moreover, the daily cry expression in the adult zebrafish retina indicated varying oscillation patterns in different cell types. Our extensive phylogenetic analysis provides for the first time an overview of cry evolutionary history. Although several, especially parasitic or blind species, have lost all cry genes, crustaceans have retained up to three crys, teleosts possess up to seven, and tetrapods up to four crys. The broad and cyclic expression pattern of all cry transcripts in zebrafish retinal layers implies an involvement in retinal circadian processes and supports the hypothesis of several autonomous circadian clocks present in the vertebrate retina. PMID:25601102

  11. The phylogeny of amphibian metamorphosis.

    PubMed

    Reiss, John O

    2002-01-01

    Frogs have one of the most extreme metamorphoses among vertebrates. How did this metamorphosis evolve? By combining the methods previously proposed by Mabee and Humphries (1993) and Velhagen (1997), I develop a phylogenetic method suited for rigorous analysis of this question. In a preliminary analysis using 12 transformation sequence characters and 36 associated event sequence characters, all drawn from the osteology of the skull, the evolution of metamorphosis is traced on an assumed phylogeny. This phylogeny has lissamphibians (frogs, salamanders, and caecilians) monophyletic, with frogs the sister group of salamanders. Successive outgroups used are temnospondyls and discosauriscids, both of which are fossil groups for which ontogenetic data are available. In the reconstruction of character evolution, an unambiguous change (synapomorphy) along the branch leading to lissamphibians is a delay in the lengthening of the maxilla until metamorphosis, in accordance with my previous suggestion (Reiss, 1996). However, widening of the interpterygoid vacuity does not appear as a synapomophy of lissamphibians, due to variation in the character states in the outgroups. From a more theoretical perspective, the reconstructed evolution of amphibian metamorphosis involves examples of heterochrony, through the shift of ancestral premetamorphic events to the metamorphic period, caenogenesis, through the origin of new larval features, and terminal addition, through the origin of new adult features. Other changes don't readily fit these categories. This preliminary study provides evidence that metamorphic changes in frogs arose as further modifications of changes unique to lissamphibians, as well as a new method by which such questions can be examined. PMID:16351859

  12. Reconciling molecular phylogenies with the fossil record.

    PubMed

    Morlon, Hélène; Parsons, Todd L; Plotkin, Joshua B

    2011-09-27

    Historical patterns of species diversity inferred from phylogenies typically contradict the direct evidence found in the fossil record. According to the fossil record, species frequently go extinct, and many clades experience periods of dramatic diversity loss. However, most analyses of molecular phylogenies fail to identify any periods of declining diversity, and they typically infer low levels of extinction. This striking inconsistency between phylogenies and fossils limits our understanding of macroevolution, and it undermines our confidence in phylogenetic inference. Here, we show that realistic extinction rates and diversity trajectories can be inferred from molecular phylogenies. To make this inference, we derive an analytic expression for the likelihood of a phylogeny that accommodates scenarios of declining diversity, time-variable rates, and incomplete sampling; we show that this likelihood expression reliably detects periods of diversity loss using simulation. We then study the cetaceans (whales, dolphins, and porpoises), a group for which standard phylogenetic inferences are strikingly inconsistent with fossil data. When the cetacean phylogeny is considered as a whole, recently radiating clades, such as the Balaneopteridae, Delphinidae, Phocoenidae, and Ziphiidae, mask the signal of extinctions. However, when isolating these groups, we infer diversity dynamics that are consistent with the fossil record. These results reconcile molecular phylogenies with fossil data, and they suggest that most extant cetaceans arose from four recent radiations, with a few additional species arising from clades that have been in decline over the last ~10 Myr. PMID:21930899

  13. Reconciling molecular phylogenies with the fossil record

    PubMed Central

    Morlon, Hélène; Parsons, Todd L.; Plotkin, Joshua B.

    2011-01-01

    Historical patterns of species diversity inferred from phylogenies typically contradict the direct evidence found in the fossil record. According to the fossil record, species frequently go extinct, and many clades experience periods of dramatic diversity loss. However, most analyses of molecular phylogenies fail to identify any periods of declining diversity, and they typically infer low levels of extinction. This striking inconsistency between phylogenies and fossils limits our understanding of macroevolution, and it undermines our confidence in phylogenetic inference. Here, we show that realistic extinction rates and diversity trajectories can be inferred from molecular phylogenies. To make this inference, we derive an analytic expression for the likelihood of a phylogeny that accommodates scenarios of declining diversity, time-variable rates, and incomplete sampling; we show that this likelihood expression reliably detects periods of diversity loss using simulation. We then study the cetaceans (whales, dolphins, and porpoises), a group for which standard phylogenetic inferences are strikingly inconsistent with fossil data. When the cetacean phylogeny is considered as a whole, recently radiating clades, such as the Balaneopteridae, Delphinidae, Phocoenidae, and Ziphiidae, mask the signal of extinctions. However, when isolating these groups, we infer diversity dynamics that are consistent with the fossil record. These results reconcile molecular phylogenies with fossil data, and they suggest that most extant cetaceans arose from four recent radiations, with a few additional species arising from clades that have been in decline over the last ∼10 Myr. PMID:21930899

  14. The biological significance of color constancy: an agent-based model with bees foraging from flowers under varied illumination.

    PubMed

    Faruq, Samia; McOwan, Peter W; Chittka, Lars

    2013-01-01

    The perceived color of an object depends on its spectral reflectance and the spectral composition of the illuminant. Thus when the illumination changes, the light reflected from the object also varies. This would result in a different color sensation if no color constancy mechanism is put in place-that is, the ability to form consistent representation of colors across various illuminants and background scenes. We explore the quantitative benefits of various color constancy algorithms in an agent-based model of foraging bees, where agents select flower color based on reward. Each simulation is based on 100 "meadows" with five randomly selected flower species with empirically determined spectral reflectance properties, and each flower species is associated with realistic distributions of nectar rewards. Simulated foraging bees memorize the colors of flowers that they have experienced as most rewarding, and their task is to discriminate against other flower colors with lower rewards, even in the face of changing illumination conditions. We compared the performance of von Kries, White Patch, and Gray World constancy models with (hypothetical) bees with perfect color constancy, and color-blind bees. A bee equipped with trichromatic color vision but no color constancy performed only ∼20% better than a color-blind bee (relative to a maximum improvement at 100% for perfect color constancy), whereas the most powerful recovery of reflectance in the face of changing illumination was generated by a combination of von Kries photoreceptor adaptation and a White Patch calibration (∼30% improvement relative to a bee without color constancy). However, none of the tested algorithms generated perfect color constancy. PMID:23962735

  15. Transparent layer constancy under changes in illumination color: Does task matter?

    PubMed

    Faul, Franz; Falkenberg, Charlotte

    2015-11-01

    If the perceived transmittances of transparent objects are matched across illuminants, only incomplete constancy is found. This implies that physically identical objects may appear different. Nevertheless, it was reported in the literature that subjects could almost perfectly identify such objects across illuminants, even if a transparency impression was suppressed by violating geometric transparency conditions. A potential interpretation of these findings is that (a) identification and matching rely on different criteria and processes and that (b) identification is solely based on low-level color information. We here present evidence against these hypotheses. Our results show that the best match, that is, the transparent object under the test illuminant that appears most similar to the standard, is also the preferred object in the identification task. Furthermore, we found that the degree of constancy increases in both tasks, if figural cues support a transparency impression and the accompanying color scission. We discuss the relation between matching and identification suggested by these findings. PMID:26409045

  16. Morphological constancy in spelling: a comparison of children with dyslexia and typically developing children.

    PubMed

    Bourassa, Derrick C; Treiman, Rebecca

    2008-08-01

    The spellings of many English words follow a principle of morphological constancy. For example, musician includes the c of music, even though the pronunciation of this letter changes. With other words, such as explanation and explain, the spellings of morphemes are not retained when affixes are added. We asked whether children with dyslexia use root morphemes to aid their spelling of morphologically complex words. If so, they should sometimes produce misspellings such as 'explaination' for explanation. Our results suggest that children with dyslexia adhere to the principle of morphological constancy to the same extent as typically developing younger children of the same spelling level. In this and other ways, the spellings of older dyslexic children are remarkably similar to those of typical younger children. PMID:18720405

  17. Color constancy in a scene with bright colors that do not have a fully natural surface appearance.

    PubMed

    Fukuda, Kazuho; Uchikawa, Keiji

    2014-04-01

    Theoretical and experimental approaches have proposed that color constancy involves a correction related to some average of stimulation over the scene, and some of the studies showed that the average gives greater weight to surrounding bright colors. However, in a natural scene, high-luminance elements do not necessarily carry information about the scene illuminant when the luminance is too high for it to appear as a natural object color. The question is how a surrounding color's appearance mode influences its contribution to the degree of color constancy. Here the stimuli were simple geometric patterns, and the luminance of surrounding colors was tested over the range beyond the luminosity threshold. Observers performed perceptual achromatic setting on the test patch in order to measure the degree of color constancy and evaluated the surrounding bright colors' appearance mode. Broadly, our results support the assumption that the visual system counts only the colors in the object-color appearance for color constancy. However, detailed analysis indicated that surrounding colors without a fully natural object-color appearance had some sort of influence on color constancy. Consideration of this contribution of unnatural object color might be important for precise modeling of human color constancy. PMID:24695177

  18. SU-E-T-257: Output Constancy: Reducing Measurement Variations in a Large Practice Group

    SciTech Connect

    Hedrick, K; Fitzgerald, T; Miller, R

    2014-06-01

    Purpose: To standardize output constancy check procedures in a large medical physics practice group covering multiple sites, in order to identify and reduce small systematic errors caused by differences in equipment and the procedures of multiple physicists. Methods: A standardized machine output constancy check for both photons and electrons was instituted within the practice group in 2010. After conducting annual TG-51 measurements in water and adjusting the linac to deliver 1.00 cGy/MU at Dmax, an acrylic phantom (comparable at all sites) and PTW farmer ion chamber are used to obtain monthly output constancy reference readings. From the collected charge reading, measurements of air pressure and temperature, and chamber Ndw and Pelec, a value we call the Kacrylic factor is determined, relating the chamber reading in acrylic to the dose in water with standard set-up conditions. This procedure easily allows for multiple equipment combinations to be used at any site. The Kacrylic factors and output results from all sites and machines are logged monthly in a central database and used to monitor trends in calibration and output. Results: The practice group consists of 19 sites, currently with 34 Varian and 8 Elekta linacs (24 Varian and 5 Elekta linacs in 2010). Over the past three years, the standard deviation of Kacrylic factors measured on all machines decreased by 20% for photons and high energy electrons as systematic errors were found and reduced. Low energy electrons showed very little change in the distribution of Kacrylic values. Small errors in linac beam data were found by investigating outlier Kacrylic values. Conclusion: While the use of acrylic phantoms introduces an additional source of error through small differences in depth and effective depth, the new standardized procedure eliminates potential sources of error from using many different phantoms and results in more consistent output constancy measurements.

  19. Color constancy of color-deficient observers under illuminations defined by individual color discrimination ellipsoids.

    PubMed

    Ma, Ruiqing; Kawamoto, Ken-Ichiro; Shinomori, Keizo

    2016-03-01

    We explored the color constancy mechanisms of color-deficient observers under red, green, blue, and yellow illuminations. The red and green illuminations were defined individually by the longer axis of the color discrimination ellipsoid measured by the Cambridge Colour Test. Four dichromats (3 protanopes and 1 deuteranope), two anomalous trichromats (2 deuteranomalous observers), and five color-normal observers were asked to complete the color constancy task by making a simultaneous paper match under asymmetrical illuminations in haploscopic view on a monitor. The von Kries adaptation model was applied to estimate the cone responses. The model fits showed that for all color-deficient observers under all illuminations, the adjustment of the S-cone response or blue-yellow chromatically opponent responses modeled with the simple assumption of cone deletion in a certain type (S-M, S-L or S-(L+M)) was consistent with the principle of the von Kries model. The degree of adaptation was similar to that of color-normal observers. The results indicate that the color constancy of color-deficient observers is mediated by the simplified blue-yellow color system with a von Kries-type adaptation effect, even in the case of brightness match, as well as by a possible cone-level adaptation to the S-cone when the illumination produces a strong S-cone stimulation, such as blue illumination. PMID:26974935

  20. Effects of surrounding stimulus properties on color constancy based on luminance balance.

    PubMed

    Morimoto, Takuma; Fukuda, Kazuho; Uchikawa, Keiji

    2016-03-01

    The visual system needs to discount the influence of an illuminant to achieve color constancy. Uchikawa et al. [J. Opt. Soc. Am. A29, A133 (2012) showed that the luminance-balance change of surfaces in a scene contributes to illuminant estimation; however, its effect was substantially less than the chromaticity change. We conduct three experiments to reinforce the previous findings and investigate possible factors that can influence the effect of luminance balance. Experimental results replicate the previous finding; i.e., luminance balance makes a small, but significant, contribution to illuminant estimation. We find that stimulus dimensionality affects neither the degree of color constancy nor the effect of luminance balance. Unlike chromaticity-based color constancy, chromatic variation does not influence the effect of luminance balance. It is shown that luminance-balance-based estimation of an illuminant performs better for scenes with reddish or bluish surfaces. This suggests that the visual system exploits the optimal color distribution for illuminant estimation [J. Opt. Soc. Am. A 29, A133(2012)]. PMID:26974926

  1. Genome downsizing and karyotype constancy in diploid and polyploid congeners: a model of genome size variation

    PubMed Central

    Poggio, Lidia; Realini, María Florencia; Fourastié, María Florencia; García, Ana María; González, Graciela Esther

    2014-01-01

    Evolutionary chromosome change involves significant variation in DNA amount in diploids and genome downsizing in polyploids. Genome size and karyotype parameters of Hippeastrum species with different ploidy level were analysed. In Hippeastrum, polyploid species show less DNA content per basic genome than diploid species. The rate of variation is lower at higher ploidy levels. All the species have a basic number x = 11 and bimodal karyotypes. The basic karyotypes consist of four short metacentric chromosomes and seven large chromosomes (submetacentric and subtelocentric). The bimodal karyotype is preserved maintaining the relative proportions of members of the haploid chromosome set, even in the presence of genome downsizing. The constancy of the karyotype is maintained because changes in DNA amount are proportional to the length of the whole-chromosome complement and vary independently in the long and short sets of chromosomes. This karyotype constancy in taxa of Hippeastrum with different genome size and ploidy level indicates that the distribution of extra DNA within the complement is not at random and suggests the presence of mechanisms selecting for constancy, or against changes, in karyotype morphology. PMID:24969503

  2. Temporal-envelope constancy of speech in rooms and the perceptual weighting of frequency bands.

    PubMed

    Watkins, Anthony J; Raimond, Andrew P; Makin, Simon J

    2011-11-01

    Three experiments measured constancy in speech perception, using natural-speech messages or noise-band vocoder versions of them. The eight vocoder-bands had equally log-spaced center-frequencies and the shapes of corresponding "auditory" filters. Consequently, the bands had the temporal envelopes that arise in these auditory filters when the speech is played. The "sir" or "stir" test-words were distinguished by degrees of amplitude modulation, and played in the context; "next you'll get _ to click on." Listeners identified test-words appropriately, even in the vocoder conditions where the speech had a "noise-like" quality. Constancy was assessed by comparing the identification of test-words with low or high levels of room reflections across conditions where the context had either a low or a high level of reflections. Constancy was obtained with both the natural and the vocoded speech, indicating that the effect arises through temporal-envelope processing. Two further experiments assessed perceptual weighting of the different bands, both in the test word and in the context. The resulting weighting functions both increase monotonically with frequency, following the spectral characteristics of the test-word's [s]. It is suggested that these two weighting functions are similar because they both come about through the perceptual grouping of the test-word's bands. PMID:22087906

  3. Coding polymorphism for phylogeny reconstruction.

    PubMed

    Kornet, D J; Turner, H

    1999-06-01

    The methodology of coding polymorphic taxa has received limited attention to date. A search of the taxonomic literature revealed seven types of coding methods. Apart from ignoring polymorphic characters (sometimes called the fixed-only method), two main categories can be distinguished: methods that identify the start of a new character state with the origin of an evolutionary novelty, and methods that identify the new state with the fixation of a novelty. The methods of the first category introduce soft reversals, yielding signals that support cladograms incompatible with true phylogenies. We conclude that coding the plesiomorphy is the method to be preferred, unless the ancestral state is unknown, in which case coding as ambiguous is recommended. This holds for coding polymorphism in species as well as in supraspecific taxa. In this light we remark on methods proposed by previous authors. PMID:12066713

  4. Ontogeny and phylogeny of language

    PubMed Central

    Yang, Charles

    2013-01-01

    How did language evolve? A popular approach points to the similarities between the ontogeny and phylogeny of language. Young children’s language and nonhuman primates’ signing both appear formulaic with limited syntactic combinations, thereby suggesting a degree of continuity in their cognitive abilities. To evaluate the validity of this approach, as well as to develop a quantitative benchmark to assess children’s language development, I propose a formal analysis that characterizes the statistical profile of grammatical rules. I show that very young children’s language is consistent with a productive grammar rather than memorization of specific word combinations from caregivers’ speech. Furthermore, I provide a statistically rigorous demonstration that the sign use of Nim Chimpsky, the chimpanzee who was taught American Sign Language, does not show the expected productivity of a rule-based grammar. Implications for theories of language acquisition and evolution are discussed. PMID:23576720

  5. Untangling the phylogeny of amoeboid protists.

    PubMed

    Pawlowski, Jan; Burki, Fabien

    2009-01-01

    The amoebae and amoeboid protists form a large and diverse assemblage of eukaryotes characterized by various types of pseudopodia. For convenience, the traditional morphology-based classification grouped them together in a macrotaxon named Sarcodina. Molecular phylogenies contributed to the dismantlement of this assemblage, placing the majority of sarcodinids into two new supergroups: Amoebozoa and Rhizaria. In this review, we describe the taxonomic composition of both supergroups and present their small subunit rDNA-based phylogeny. We comment on the advantages and weaknesses of these phylogenies and emphasize the necessity of taxon-rich multigene datasets to resolve phylogenetic relationships within Amoebozoa and Rhizaria. We show the importance of environmental sequencing as a way of increasing taxon sampling in these supergroups. Finally, we highlight the interest of Amoebozoa and Rhizaria for understanding eukaryotic evolution and suggest that resolving their phylogenies will be among the main challenges for future phylogenomic analyses. PMID:19335771

  6. Reconstructing the prior probabilities of allelic phylogenies.

    PubMed Central

    Golding, G Brian

    2002-01-01

    In general when a phylogeny is reconstructed from DNA or protein sequence data, it makes use only of the probabilities of obtaining some phylogeny given a collection of data. It is also possible to determine the prior probabilities of different phylogenies. This information can be of use in analyzing the biological causes for the observed divergence of sampled taxa. Unusually "rare" topologies for a given data set may be indicative of different biological forces acting. A recursive algorithm is presented that calculates the prior probabilities of a phylogeny for different allelic samples and for different phylogenies. This method is a straightforward extension of Ewens' sample distribution. The probability of obtaining each possible sample according to Ewens' distribution is further subdivided into each of the possible phylogenetic topologies. These probabilities depend not only on the identity of the alleles and on 4N(mu) (four times the effective population size times the neutral mutation rate) but also on the phylogenetic relationships among the alleles. Illustrations of the algorithm are given to demonstrate how different phylogenies are favored under different conditions. PMID:12072482

  7. Phylogeny of the Genus Flavivirus

    PubMed Central

    Kuno, Goro; Chang, Gwong-Jen J.; Tsuchiya, K. Richard; Karabatsos, Nick; Cropp, C. Bruce

    1998-01-01

    We undertook a comprehensive phylogenetic study to establish the genetic relationship among the viruses of the genus Flavivirus and to compare the classification based on molecular phylogeny with the existing serologic method. By using a combination of quantitative definitions (bootstrap support level and the pairwise nucleotide sequence identity), the viruses could be classified into clusters, clades, and species. Our phylogenetic study revealed for the first time that from the putative ancestor two branches, non-vector and vector-borne virus clusters, evolved and from the latter cluster emerged tick-borne and mosquito-borne virus clusters. Provided that the theory of arthropod association being an acquired trait was correct, pairwise nucleotide sequence identity among these three clusters provided supporting data for a possibility that the non-vector cluster evolved first, followed by the separation of tick-borne and mosquito-borne virus clusters in that order. Clades established in our study correlated significantly with existing antigenic complexes. We also resolved many of the past taxonomic problems by establishing phylogenetic relationships of the antigenically unclassified viruses with the well-established viruses and by identifying synonymous viruses. PMID:9420202

  8. Alveolate phylogeny inferred using concatenated ribosomal proteins.

    PubMed

    Bachvaroff, Tsvetan R; Handy, Sara M; Place, Allen R; Delwiche, Charles F

    2011-01-01

    Dinoflagellates and apicomplexans are a strongly supported monophyletic group in rDNA phylogenies, although this phylogeny is not without controversy, particularly between the two groups. Here we use concatenated protein-coding genes from expressed sequence tags or genomic data to construct phylogenies including "typical" dinophycean dinoflagellates, a parasitic syndinian dinoflagellate, Amoebophrya sp., and two related species, Oxyrrhis marina, and Perkinsus marinus. Seventeen genes encoding proteins associated with the ribosome were selected for phylogenetic analysis. The dataset was limited for the most part by data availability from the dinoflagellates. Forty-five taxa from four major lineages were used: the heterokont outgroup, ciliates, dinoflagellates, and apicomplexans. Amoebophrya sp. was included in this phylogeny as a sole representative of the enigmatic marine alveolate or syndinian lineage. The atypical dinoflagellate O. marina, usually excluded from rDNA analyses due to long branches, was also included. The resulting phylogenies were well supported in concatenated analyses with only a few unstable or weakly supported branches; most features were consistent when different lineages were pruned from the tree or different genes were concatenated. The least stable branches involved the placement of Cryptosporidium spp. within the Apicomplexa and the relationships between P. marinus, Amoebophrya sp., and O. marina. Both bootstrap and approximately unbiased test results confirmed that P. marinus, Amoebophrya sp., O. marina, and the remaining dinoflagellates form a monophyletic lineage to the exclusion of Apicomplexa. PMID:21518081

  9. Recovering of weather degraded images based on RGB response ratio constancy.

    PubMed

    Luzón-González, Raúl; Nieves, Juan L; Romero, Javier

    2015-02-01

    Images captured under bad weather conditions suffer from poor contrast and visibility. These effects are noticeable for haze, mist, fog, or dust storms. We have proposed a recovering method for images captured for several adverse weather conditions based on the RGB response ratio constancy under illuminant changes. This algorithm improves the visibility, contrast, and color in degraded images with low computational times. We obtain results similar to those from previously published deweathering methods but with no prior information about the image content or atmospheric parameters needed. PMID:25967830

  10. Juvenile morphology in baleen whale phylogeny

    NASA Astrophysics Data System (ADS)

    Tsai, Cheng-Hsiu; Fordyce, R. Ewan

    2014-09-01

    Phylogenetic reconstructions are sensitive to the influence of ontogeny on morphology. Here, we use foetal/neonatal specimens of known species of living baleen whales (Cetacea: Mysticeti) to show how juvenile morphology of extant species affects phylogenetic placement of the species. In one clade (sei whale, Balaenopteridae), the juvenile is distant from the usual phylogenetic position of adults, but in the other clade (pygmy right whale, Cetotheriidae), the juvenile is close to the adult. Different heterochronic processes at work in the studied species have different influences on juvenile morphology and on phylogenetic placement. This study helps to understand the relationship between evolutionary processes and phylogenetic patterns in baleen whale evolution and, more in general, between phylogeny and ontogeny; likewise, this study provides a proxy how to interpret the phylogeny when fossils that are immature individuals are included. Juvenile individuals in the peramorphic acceleration clades would produce misleading phylogenies, whereas juvenile individuals in the paedomorphic neoteny clades should still provide reliable phylogenetic signals.

  11. Juvenile morphology in baleen whale phylogeny

    NASA Astrophysics Data System (ADS)

    Tsai, Cheng-Hsiu; Fordyce, R. Ewan

    2014-08-01

    Phylogenetic reconstructions are sensitive to the influence of ontogeny on morphology. Here, we use foetal/neonatal specimens of known species of living baleen whales (Cetacea: Mysticeti) to show how juvenile morphology of extant species affects phylogenetic placement of the species. In one clade (sei whale, Balaenopteridae), the juvenile is distant from the usual phylogenetic position of adults, but in the other clade (pygmy right whale, Cetotheriidae), the juvenile is close to the adult. Different heterochronic processes at work in the studied species have different influences on juvenile morphology and on phylogenetic placement. This study helps to understand the relationship between evolutionary processes and phylogenetic patterns in baleen whale evolution and, more in general, between phylogeny and ontogeny; likewise, this study provides a proxy how to interpret the phylogeny when fossils that are immature individuals are included. Juvenile individuals in the peramorphic acceleration clades would produce misleading phylogenies, whereas juvenile individuals in the paedomorphic neoteny clades should still provide reliable phylogenetic signals.

  12. Development of Phonological Constancy: 19-Month-Olds, but Not 15-Month-Olds, Identify Words in a Non-Native Regional Accent

    ERIC Educational Resources Information Center

    Mulak, Karen E.; Best, Catherine T.; Tyler, Michael D.; Kitamura, Christine; Irwin, Julia R.

    2013-01-01

    By 12 months, children grasp that a phonetic change to a word can change its identity ("phonological distinctiveness"). However, they must also grasp that some phonetic changes do "not" ("phonological constancy"). To test development of phonological constancy, sixteen 15-month-olds and sixteen 19-month-olds completed…

  13. Israeli Kindergarten Children's Gender Constancy for Others' Counter-Stereotypic Toy Play and Appearance: The Role of Sibling Gender and Relative Age

    ERIC Educational Resources Information Center

    Karniol, Rachel

    2009-01-01

    To test divergent theoretical predictions as to the impact of having a younger or older, same-sex sibling or opposite-sex sibling on other gender constancy, Israeli kindergarten children in two-child families responded to a gender constancy task in which a male and female picture target engaged in counter-stereotypic toy play and adopted…

  14. Ribosomal RNA: a key to phylogeny

    NASA Technical Reports Server (NTRS)

    Olsen, G. J.; Woese, C. R.

    1993-01-01

    As molecular phylogeny increasingly shapes our understanding of organismal relationships, no molecule has been applied to more questions than have ribosomal RNAs. We review this role of the rRNAs and some of the insights that have been gained from them. We also offer some of the practical considerations in extracting the phylogenetic information from the sequences. Finally, we stress the importance of comparing results from multiple molecules, both as a method for testing the overall reliability of the organismal phylogeny and as a method for more broadly exploring the history of the genome.

  15. Low levels of specularity support operational color constancy, particularly when surface and illumination geometry can be inferred.

    PubMed

    Lee, Robert J; Smithson, Hannah E

    2016-03-01

    We tested whether surface specularity alone supports operational color constancy-the ability to discriminate changes in illumination or reflectance. Observers viewed short animations of illuminant or reflectance changes in rendered scenes containing a single spherical surface and were asked to classify the change. Performance improved with increasing specularity, as predicted from regularities in chromatic statistics. Peak performance was impaired by spatial rearrangements of image pixels that disrupted the perception of illuminated surfaces but was maintained with increased surface complexity. The characteristic chromatic transformations that are available with nonzero specularity are useful for operational color constancy, particularly if accompanied by appropriate perceptual organization. PMID:26974938

  16. Low levels of specularity support operational color constancy, particularly when surface and illumination geometry can be inferred

    PubMed Central

    Lee, Robert J.; Smithson, Hannah E.

    2016-01-01

    We tested whether surface specularity alone supports operational color constancy – the ability to discriminate changes in illumination or reflectance. Observers viewed short animations of illuminant or reflectance changes in rendered scenes containing a single spherical surface, and were asked to classify the change. Performance improved with increasing specularity, as predicted from regularities in chromatic statistics. Peak performance was impaired by spatial rearrangements of image pixels that disrupted the perception of illuminated surfaces, but was maintained with increased surface complexity. The characteristic chromatic transformations that are available with non-zero specularity are useful for operational color constancy, particularly if accompanied by appropriate perceptual organisation. PMID:26974938

  17. Modelling colour constancy in fish: implications for vision and signalling in water.

    PubMed

    Wilkins, Lucas; Marshall, N Justin; Johnsen, Sönke; Osorio, D

    2016-06-15

    Colour vision and colour signals are important to aquatic animals, but light scattering and absorption by water distorts spectral stimuli. To investigate the performance of colour vision in water, and to suggest how photoreceptor spectral sensitivities and body colours might evolve for visual communication, we model the effects of changes in viewing distance and depth on the appearance of fish colours for three teleosts: a barracuda, Sphyraena helleri, which is dichromatic and two damselfishes, Chromis verater and Chromis hanui, which are trichromatic. We assume that photoreceptors light-adapt to the background, thereby implementing the von Kries transformation, which can largely account for observed colour constancy in humans and other animals, including fish. This transformation does not, however, compensate for light scattering over variable viewing distances, which in less than a metre seriously impairs dichromatic colour vision, and makes judgement of colour saturation unreliable for trichromats. The von Kries transformation does substantially offset colour shifts caused by changing depth, so that from depths of 0 to 30 m modelled colour changes (i.e. failures of colour constancy) are sometimes negligible. However, the magnitudes and directions of remaining changes are complex, depending upon the specific spectral sensitivities of the receptors and the reflectance spectra. This predicts that when judgement of colour is important, the spectra of signalling colours and photoreceptor spectral sensitivities should be evolutionarily linked, with the colours dependent on photoreceptor spectral sensitivities, and vice versa. PMID:27045090

  18. Experimental studies of instantaneous color constancy: dynamic color matching under rapid changes of illuminant

    NASA Astrophysics Data System (ADS)

    Barbur, John L.; de Cunha, Darryl; Williams, Cristyn B.; Plant, Gordon

    2002-06-01

    We have extended the experiments of McCann et al., (1976) by incorporating the Mondrian stimulus into a dynamic colour matching (DCM) technique that allows the subject to match accurately the colour of any test patch under sequential changes of illuminant. We have also studied how scattered light affects the measured instantaneous colour constancy (ICC) index. The results show that correction for forward light scatter in the eye can increase significantly the measured ICC index. The changes in the perceived colour of a central test stimulus as a result of surround illuminant changes was investigated in a number of successful binocular and dichoptic experiments. The contribution made by distant patches to ICC was found to be small with the immediate surround (i.e., less than 2 degree(s) separation) contributing over 50% of the constancy effect. A number of subjects with partial loss of ability to see and discriminate colours caused by damage to ventromedial pre-striate visual cortex were also investigated. In order to establish the site of ICC mechanisms, the dynamic colour matching technique was modified to make it suitable for studies in patients with unilateral damage to the primary visual cortex.

  19. Accurate moving cast shadow suppression based on local color constancy detection.

    PubMed

    Amato, Ariel; Mozerov, Mikhail G; Bagdanov, Andrew D; Gonzàlez, Jordi

    2011-10-01

    This paper describes a novel framework for detection and suppression of properly shadowed regions for most possible scenarios occurring in real video sequences. Our approach requires no prior knowledge about the scene, nor is it restricted to specific scene structures. Furthermore, the technique can detect both achromatic and chromatic shadows even in the presence of camouflage that occurs when foreground regions are very similar in color to shadowed regions. The method exploits local color constancy properties due to reflectance suppression over shadowed regions. To detect shadowed regions in a scene, the values of the background image are divided by values of the current frame in the RGB color space. We show how this luminance ratio can be used to identify segments with low gradient constancy, which in turn distinguish shadows from foreground. Experimental results on a collection of publicly available datasets illustrate the superior performance of our method compared with the most sophisticated, state-of-the-art shadow detection algorithms. These results show that our approach is robust and accurate over a broad range of shadow types and challenging video conditions. PMID:21435975

  20. Influence of gender constancy and social power on sex-linked modeling.

    PubMed

    Bussey, K; Bandura, A

    1984-12-01

    Competing predictions derived from cognitive-developmental theory and social learning theory concerning sex-linked modeling were tested. In cognitive-developmental theory, gender constancy is considered a necessary prerequisite for the emulation of same-sex models, whereas according to social learning theory, sex-role development is promoted through a vast system of social influences with modeling serving as a major conveyor of sex role information. In accord with social learning theory, even children at a lower level of gender conception emulated same-sex models in preference to opposite-sex ones. Level of gender constancy was associated with higher emulation of both male and female models rather than operating as a selective determinant of modeling. This finding corroborates modeling as a basic mechanism in the sex-typing process. In a second experiment we explored the limits of same-sex modeling by pitting social power against the force of collective modeling of different patterns of behavior by male and female models. Social power over activities and rewarding resources produced cross-sex modeling in boys, but not in girls. This unexpected pattern of cross-sex modeling is explained by the differential sex-typing pressures that exist for boys and girls and socialization experiences that heighten the attractiveness of social power for boys. PMID:6527216

  1. Auditory color constancy: calibration to reliable spectral properties across nonspeech context and targets.

    PubMed

    Stilp, Christian E; Alexander, Joshua M; Kiefte, Michael; Kluender, Keith R

    2010-02-01

    Brief experience with reliable spectral characteristics of a listening context can markedly alter perception of subsequent speech sounds, and parallels have been drawn between auditory compensation for listening context and visual color constancy. In order to better evaluate such an analogy, the generality of acoustic context effects for sounds with spectral-temporal compositions distinct from speech was investigated. Listeners identified nonspeech sounds-extensively edited samples produced by a French horn and a tenor saxophone-following either resynthesized speech or a short passage of music. Preceding contexts were "colored" by spectral envelope difference filters, which were created to emphasize differences between French horn and saxophone spectra. Listeners were more likely to report hearing a saxophone when the stimulus followed a context filtered to emphasize spectral characteristics of the French horn, and vice versa. Despite clear changes in apparent acoustic source, the auditory system calibrated to relatively predictable spectral characteristics of filtered context, differentially affecting perception of subsequent target nonspeech sounds. This calibration to listening context and relative indifference to acoustic sources operates much like visual color constancy, for which reliable properties of the spectrum of illumination are factored out of perception of color. PMID:20139460

  2. Dodging the cosmic curvature to probe the constancy of the speed of light

    NASA Astrophysics Data System (ADS)

    Cai, Rong-Gen; Guo, Zong-Kuan; Yang, Tao

    2016-08-01

    We develop a new model-independent method to probe the constancy of the speed of light c. In our method, the degeneracy between the cosmic curvature and the speed of light can be eliminated, which makes the test more natural and general. Combining the independent observations of Hubble parameter H(z) and luminosity distance dL(z), we use the model-independent smoothing technique, Gaussian processes, to reconstruct them and then detect variation of the speed of light. We find no signal of deviation from the present value of the speed of light c0. Moreover, to demonstrate the improvement in probing the constancy of the speed of light from future experiments, we produce a series of simulated data. The Dark Energy Survey will be able to detect Δc/c0 ~ 1% at ~ 1.5σ confidence level and Δc/c0 ~ 2% at ~ 3σ confidence level. If the errors are reduced to one-tenth of the expected DES ones, it can detect a Δc/c0 ~ 0.1% variation at ~ 2σ confidence level.

  3. A robust phylogeny among major lineages of the East African cichlids.

    PubMed

    Takahashi, Tetsumi; Sota, Teiji

    2016-07-01

    The huge monophyletic group of the East African cichlid radiations (EAR) consists of thousands of species belonging to 12-14 tribes; the number of tribes differs among studies. Many studies have inferred phylogenies of EAR tribes using various genetic markers. However, these phylogenies partly contradict one another and can have weak statistic support. In this study, we conducted maximum-likelihood (ML) phylogenetic analyses using restriction site-associated DNA (RAD) sequences and propose a new robust phylogenetic hypothesis among Lake Tanganyika cichlid fishes, which cover most EAR tribes. Data matrices can vary in size and contents depending on the strategies used to process RAD sequences. Therefore, we prepared 23 data matrices with various processing strategies. The ML phylogenies inferred from 15 large matrices (2.0×10(6) to 1.1×10(7) base pairs) resolved every tribe as a monophyletic group with 100% bootstrap support and shared the same topology regarding relationships among the tribes. Most nodes among the tribes were supported by 100% bootstrap values, and the bootstrap support for the other node varied among the 15 ML trees from 70% to 100%. These robust ML trees differ partly in topology from those in earlier studies, and these phylogenetic relationships have important implications for the tribal classification of EAR. PMID:27068840

  4. CONNECTICUT LAKES

    EPA Science Inventory

    This is a 1:24,000-scale datalayer of named lakes in Connecticut. It is a polygon Shapefile that includes all lakes that are named on the U.S. Geologicial Survey (USGS) 7½ minute topographic quadrangle maps that cover the State of Connecticut, plus other officially named lakes i...

  5. Lake Powell

    Atmospheric Science Data Center

    2014-05-15

    article title:  Lake Powell     View Larger Image ... (14.42 mb)   This true-color image over Lake Powell was acquired by Multi-angle Imaging SpectroRadiometer (MISR) in late March 2000. Lake Powell was formed with the construction of the Glen Canyon Dam in 1963, on the ...

  6. Lake Eyre

    Atmospheric Science Data Center

    2013-04-16

    ...   View Larger Image Lake Eyre is a large salt lake situated between two deserts in one of Australia's driest regions. ... the effect of sunglint at the nadir camera view angle. Dry, salt encrusted parts of the lake appear bright white or gray. Purple areas have ...

  7. Does phylogeny control U37K -temperature sensitivity? Implications for lacustrine alkenone paleothermometry

    NASA Astrophysics Data System (ADS)

    D'Andrea, William J.; Theroux, Susanna; Bradley, Raymond S.; Huang, Xiaohui

    2016-02-01

    Alkenone paleothermometry (via the U37K and U37K‧ indices) has long been used to reconstruct sea surface temperature and has more recently been proven effective in lacustrine settings. Genetic analyses indicate that there is a diversity of different alkenone-producing lacustrine haptophytes, and differences among U37K -temperature calibrations suggest that unique calibrations might be required to quantify past temperature variation from individual lakes. The only term necessary to quantify U37K -inferred temperature relative to a reference period (e.g., modern temperature 20th Century mean) is the slope of the calibration regression, the U37K -temperature sensitivity (i.e., the change in U37K per °C temperature change). Here, we bring together all of the existing U37K -temperature calibrations in order to compare the variability among U37K -temperature sensitivities. We also report a new in situ U37K -temperature calibration along with environmental genomic analysis based on the 18S rRNA gene of an alkenone producing haptophyte from lake Vikvatnet in Norway. We propose and test the hypothesis that U37K -temperature sensitivity is controlled by phylogeny and that this term can be used to quantify past temperature variation from lake sediments if the genetic identity of the lake's alkenone-producer is known. Using the existing calibration data sets, we determine four phylotype-specific U37K -temperature sensitivities for use in cases where in situ calibration is unavailable but the phylogeny of the alkenone producers is known.

  8. How metamer mismatching decreases as the number of colour mechanisms increases with implications for colour and lightness constancy.

    PubMed

    Logvinenko, Alexander D; Funt, Brian; Godau, Christoph

    2015-08-01

    Metamer mismatching has been previously found to impose serious limitations on colour constancy. The extent of metamer mismatching is shown here to be considerably smaller for trichromats than for dichromats, and maximal for monochromats. The implications for achromatic colour perception are discussed. PMID:26054251

  9. Messages for Educational Leadership: The Constance E. Clayton Lectures 1998-2007. Black Studies and Critical Thinking. Volume 34

    ERIC Educational Resources Information Center

    Slaughter-Defoe, Diana T., Ed.

    2012-01-01

    Urban education is an interdisciplinary field, characterized by introducing many perspectives to research pertaining to educational policy and to the practice of educating youth whose lives unfold in densely populated urban metropolitan areas. This book celebrates Constance Clayton's eleven-year tenure as superintendent of the School District of…

  10. Stereotype Knowledge, Flexibility, and Gender Constancy: Applications of Gender Schema Theory to Sex-Typing by Preschoolers.

    ERIC Educational Resources Information Center

    Carter, D. Bruce; And Others

    An investigation was made of relationships between children's understanding of gender constancy, their conceptions of sex-role stereotypes, their perceptions of similarities between themselves and other children, and their schematic processing of gender-relevant choices. Forty-nine children between 36 and 73 months of age participated in a…

  11. Constancy adding space extension for ODE sets with second degree multinomial right hand side functions

    NASA Astrophysics Data System (ADS)

    Gözükirmizi, Coşar; Demiralp, Metin

    2014-10-01

    Constancy adding space extension is a technique to convert ODE of the form ẋ(t) = F0+F1x(t)+F2x(t)⊗2 to form ṡ = G1s+G2P-1s⊗2. There are arbitrary parameters in the representation. These parameters may be utilized in such a way that G1 becomes a multiple of identity matrix. Then, using a function transformation it is possible to obtain the form ds˜(u)/du = G2P-1s˜(u)⊗2. Therefore, a new universal representation for ODEs with second degree multinomial right hand side functions is proposed. There are remaining arbitrary parameters of the space extension and this paper also focuses on how to choose them.

  12. Motion Vector Field Estimation Using Brightness Constancy Assumption and Epipolar Geometry Constraint

    NASA Astrophysics Data System (ADS)

    Hosseinyalamdary, S.; Yilmaz, A.

    2014-11-01

    In most Photogrammetry and computer vision tasks, finding the corresponding points among images is required. Among many, the Lucas-Kanade optical flow estimation has been employed for tracking interest points as well as motion vector field estimation. This paper uses the IMU measurements to reconstruct the epipolar geometry and it integrates the epipolar geometry constraint with the brightness constancy assumption in the Lucas-Kanade method. The proposed method has been tested using the KITTI dataset. The results show the improvement in motion vector field estimation in comparison to the Lucas-Kanade optical flow estimation. The same approach has been used in the KLT tracker and it has been shown that using epipolar geometry constraint can improve the KLT tracker. It is recommended that the epipolar geometry constraint is used in advanced variational optical flow estimation methods.

  13. Apparent size contrasts of retinal images and size constancy as determinants of the moon illusion.

    PubMed

    Smith, O W; Smith, P C; Geist, C C; Zimmermann, R R

    1978-06-01

    Kaufman and Rock (1962) and Rock and Kaufman (1962) concluded that the moon illusion is a function of and attributable to apparent distance. They also reported a large framing effect as an exception. Analysis of the effect suggests two components which can account for the illusion independently of apparent distance. These are apparent size contrasts of visual images of discriminable features or objects of the earth with the moon's image and size constancy of the features or objects plus the interactions of the two. Apparent distances to horizons are always a consequence of the necessary conditions for the illusion. They are related to the illusion but are not a determinant of it. PMID:673635

  14. [Research on developping the spectral dataset for Dunhuang typical colors based on color constancy].

    PubMed

    Liu, Qiang; Wan, Xiao-Xia; Liu, Zhen; Li, Chan; Liang, Jin-Xing

    2013-11-01

    The present paper aims at developping a method to reasonably set up the typical spectral color dataset for different kinds of Chinese cultural heritage in color rendering process. The world famous wall paintings dating from more than 1700 years ago in Dunhuang Mogao Grottoes was taken as typical case in this research. In order to maintain the color constancy during the color rendering workflow of Dunhuang culture relics, a chromatic adaptation based method for developping the spectral dataset of typical colors for those wall paintings was proposed from the view point of human vision perception ability. Under the help and guidance of researchers in the art-research institution and protection-research institution of Dunhuang Academy and according to the existing research achievement of Dunhuang Research in the past years, 48 typical known Dunhuang pigments were chosen and 240 representative color samples were made with reflective spectral ranging from 360 to 750 nm was acquired by a spectrometer. In order to find the typical colors of the above mentioned color samples, the original dataset was devided into several subgroups by clustering analysis. The grouping number, together with the most typical samples for each subgroup which made up the firstly built typical color dataset, was determined by wilcoxon signed rank test according to the color inconstancy index comprehensively calculated under 6 typical illuminating conditions. Considering the completeness of gamut of Dunhuang wall paintings, 8 complementary colors was determined and finally the typical spectral color dataset was built up which contains 100 representative spectral colors. The analytical calculating results show that the median color inconstancy index of the built dataset in 99% confidence level by wilcoxon signed rank test was 3.28 and the 100 colors are distributing in the whole gamut uniformly, which ensures that this dataset can provide reasonable reference for choosing the color with highest

  15. Verification of a novel method for tube voltage constancy measurement of orthovoltage x-ray irradiators

    SciTech Connect

    Wang, Chu; Belley, Matthew D.; Chao, Nelson J.; Dewhirst, Mark W.; Yoshizumi, Terry

    2014-08-15

    Purpose: For orthovoltage x-ray irradiators, the tube voltage is one of the most fundamental system parameters as this directly relates to the dosimetry in radiation biology studies; however, to the best of our knowledge, there is no commercial portable quality assurance (QA) tool to directly test the constancy of the tube voltage greater than 160 kV. The purpose of this study is to establish the Beam Quality Index (BQI), a quantity strongly correlated to the tube voltage, as an alternative parameter for the verification of the tube voltage as part of the QA program of orthovoltage x-ray irradiators. Methods: A multipurpose QA meter and its associated data acquisition software were used to customize the measurement parameters to measure the BQI and collect its time-plot. BQI measurements were performed at 320 kV with four filtration levels on three orthovoltage x-ray irradiators of the same model, one of which had been recently energy-calibrated at the factory. Results: For each of the four filtration levels, the measured BQI values were in good agreement (<5%) between the three irradiators. BQI showed filtration-specificity, possibly due to the difference in beam quality. Conclusions: The BQI has been verified as a feasible alternative for monitoring the constancy of the tube voltage for orthovoltage irradiators. The time-plot of BQI offers information on the behavior of beam energy at different phases of the irradiation time line. In addition, this would provide power supply performance characteristics from initial ramp-up to plateau, and finally, the sharp drop-off at the end of the exposure.

  16. Verification of a novel method for tube voltage constancy measurement of orthovoltage x-ray irradiators

    PubMed Central

    Wang, Chu; Belley, Matthew D.; Chao, Nelson J.; Dewhirst, Mark W.; Yoshizumi, Terry

    2014-01-01

    Purpose: For orthovoltage x-ray irradiators, the tube voltage is one of the most fundamental system parameters as this directly relates to the dosimetry in radiation biology studies; however, to the best of our knowledge, there is no commercial portable quality assurance (QA) tool to directly test the constancy of the tube voltage greater than 160 kV. The purpose of this study is to establish the Beam Quality Index (BQI), a quantity strongly correlated to the tube voltage, as an alternative parameter for the verification of the tube voltage as part of the QA program of orthovoltage x-ray irradiators. Methods: A multipurpose QA meter and its associated data acquisition software were used to customize the measurement parameters to measure the BQI and collect its time-plot. BQI measurements were performed at 320 kV with four filtration levels on three orthovoltage x-ray irradiators of the same model, one of which had been recently energy-calibrated at the factory. Results: For each of the four filtration levels, the measured BQI values were in good agreement (<5%) between the three irradiators. BQI showed filtration-specificity, possibly due to the difference in beam quality. Conclusions: The BQI has been verified as a feasible alternative for monitoring the constancy of the tube voltage for orthovoltage irradiators. The time-plot of BQI offers information on the behavior of beam energy at different phases of the irradiation time line. In addition, this would provide power supply performance characteristics from initial ramp-up to plateau, and finally, the sharp drop-off at the end of the exposure. PMID:25086562

  17. Taxonomic triage and the poverty of phylogeny.

    PubMed Central

    Wheeler, Quentin D

    2004-01-01

    Revisionary taxonomy is frequently dismissed as merely descriptive, which belies its strong intellectual content and hypothesis-driven nature. Funding for taxonomy is inadequate and largely diverted to studies of phylogeny that neither improve classifications nor nomenclature. Phylogenetic classifications are optimal for storing and predicting information, but phylogeny divorced from taxonomy is ephemeral and erodes the accuracy and information content of the language of biology. Taxonomic revisions and monographs are efficient, high-throughput species hypothesis-testing devices that are ideal for the World Wide Web. Taxonomic knowledge remains essential to credible biological research and is made urgent by the biodiversity crisis. Theoretical and technological advances and threats of mass species extinctions indicate that this is the time for a renaissance in taxonomy. Clarity of vision and courage of purpose are needed from individual taxonomists and natural history museums to bring about this evolution of taxonomy into the information age. PMID:15253345

  18. A Molecular Phylogeny of Living Primates

    PubMed Central

    Perelman, Polina; Johnson, Warren E.; Roos, Christian; Seuánez, Hector N.; Horvath, Julie E.; Moreira, Miguel A. M.; Kessing, Bailey; Pontius, Joan; Roelke, Melody; Rumpler, Yves; Schneider, Maria Paula C.; Silva, Artur; O'Brien, Stephen J.; Pecon-Slattery, Jill

    2011-01-01

    Comparative genomic analyses of primates offer considerable potential to define and understand the processes that mold, shape, and transform the human genome. However, primate taxonomy is both complex and controversial, with marginal unifying consensus of the evolutionary hierarchy of extant primate species. Here we provide new genomic sequence (∼8 Mb) from 186 primates representing 61 (∼90%) of the described genera, and we include outgroup species from Dermoptera, Scandentia, and Lagomorpha. The resultant phylogeny is exceptionally robust and illuminates events in primate evolution from ancient to recent, clarifying numerous taxonomic controversies and providing new data on human evolution. Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered. Our resolution of the primate phylogeny provides an essential evolutionary framework with far-reaching applications including: human selection and adaptation, global emergence of zoonotic diseases, mammalian comparative genomics, primate taxonomy, and conservation of endangered species. PMID:21436896

  19. Mammalian phylogeny reveals recent diversification rate shifts.

    PubMed

    Stadler, Tanja

    2011-04-12

    Phylogenetic trees of present-day species allow investigation of the rate of evolution that led to the present-day diversity. A recent analysis of the mammalian phylogeny challenged the view of explosive mammalian evolution after the Cretaceous-Tertiary (K/T) boundary (65 Mya). However, due to lack of appropriate methods, the diversification (speciation minus extinction) rates in the more recent past of mammalian evolution could not be determined. In this paper, I provide a method that reveals that the tempo of mammalian evolution did not change until ∼ 33 Mya. This constant period was followed by a peak of diversification rates between 33 and 30 Mya. Thereafter, diversification rates remained high and constant until 8.55 Mya. Diversification rates declined significantly at 8.55 and 3.35 Mya. Investigation of mammalian subgroups (marsupials, placentals, and the six largest placental subgroups) reveals that the diversification rate peak at 33-30 Mya is mainly driven by rodents, cetartiodactyla, and marsupials. The recent diversification rate decrease is significant for all analyzed subgroups but eulipotyphla, cetartiodactyla, and primates. My likelihood approach is not limited to mammalian evolution. It provides a robust framework to infer diversification rate changes and mass extinction events in phylogenies, reconstructed from, e.g., present-day species or virus data. In particular, the method is very robust toward noise and uncertainty in the phylogeny and can account for incomplete taxon sampling. PMID:21444816

  20. Phylogeny and evolution of RNA structure.

    PubMed

    Gesell, Tanja; Schuster, Peter

    2014-01-01

    Darwin's conviction that all living beings on Earth are related and the graph of relatedness is tree-shaped has been essentially confirmed by phylogenetic reconstruction first from morphology and later from data obtained by molecular sequencing. Limitations of the phylogenetic tree concept were recognized as more and more sequence information became available. The other path-breaking idea of Darwin, natural selection of fitter variants in populations, is cast into simple mathematical form and extended to mutation-selection dynamics. In this form the theory is directly applicable to RNA evolution in vitro and to virus evolution. Phylogeny and population dynamics of RNA provide complementary insights into evolution and the interplay between the two concepts will be pursued throughout this chapter. The two strategies for understanding evolution are ultimately related through the central paradigm of structural biology: sequence ⇒ structure ⇒ function. We elaborate on the state of the art in modeling both phylogeny and evolution of RNA driven by reproduction and mutation. Thereby the focus will be laid on models for phylogenetic sequence evolution as well as evolution and design of RNA structures with selected examples and notes on simulation methods. In the perspectives an attempt is made to combine molecular structure, population dynamics, and phylogeny in modeling evolution. PMID:24639167

  1. Development of phonological constancy: 19-month-olds, but not 15-month-olds, identify words in a non-native regional accent

    PubMed Central

    Mulak, Karen E.; Best, Catherine T.; Tyler, Michael D.; Kitamura, Christine; Irwin, Julia R.

    2014-01-01

    By 12 months, children grasp that a phonetic change to a word can change its identity (phonological distinctiveness). However, they must also grasp that some phonetic changes do not (phonological constancy). To test development of phonological constancy, 16 15-month-olds and 16 19-month-olds completed an eye-tracking task that tracked their gaze to named versus unnamed images for familiar words spoken in their native (Australian) and an unfamiliar non-native (Jamaican) regional accent of English. Both groups looked longer at named than unnamed images for Australian pronunciations, but only 19-month-olds did so for Jamaican pronunciations, indicating that phonological constancy emerges by 19 months. Vocabulary size predicted 15-month-olds' identifications for the Jamaican pronunciations, suggesting vocabulary growth is a viable predictor for phonological constancy development. PMID:23521607

  2. Development of phonological constancy: 19-month-olds, but not 15-month-olds, identify words in a non-native regional accent.

    PubMed

    Mulak, Karen E; Best, Catherine T; Tyler, Michael D; Kitamura, Christine; Irwin, Julia R

    2013-01-01

    By 12 months, children grasp that a phonetic change to a word can change its identity (phonological distinctiveness). However, they must also grasp that some phonetic changes do not (phonological constancy). To test development of phonological constancy, sixteen 15-month-olds and sixteen 19-month-olds completed an eye-tracking task that tracked their gaze to named versus unnamed images for familiar words spoken in their native (Australian) and an unfamiliar non-native (Jamaican) regional accent of English. Both groups looked longer at named than unnamed images for Australian pronunciations, but only 19-month-olds did so for Jamaican pronunciations, indicating that phonological constancy emerges by 19 months. Vocabulary size predicted 15-month-olds' identifications for the Jamaican pronunciations, suggesting vocabulary growth is a viable predictor for phonological constancy development. PMID:23521607

  3. LAKE FORK

    EPA Science Inventory

    The Lake Fork of the Arkansas River Watershed has been adversely affected through mining, water diversion and storage projects, grazing, logging, and other human influences over the past 120 years. It is the goals of the LFWWG to improve the health of Lake fork by addressing th...

  4. Hot electron plasma equilibrium and stability in the Constance B mirror experiment

    SciTech Connect

    Chen, Xing

    1988-04-01

    An experimental study of the equilibrium and macroscopic stability property of an electron cyclotron resonance heating (ECRH) generated plasma in a minimum-B mirror is presented. The Constance B mirror is a single cell quadrupole magnetic mirror in which high beta (..beta.. less than or equal to 0.3) hot electron plasmas (T/sub e/approx. =400 keV) are created with up to 4 kW of ECRH power. The plasma equilibrium profile is hollow and resembles the baseball seam geometry of the magnet which provides the confining magnetic field. This configuration coincides with the drift orbit of deeply trapped particles. The on-axis hollowness of the hot electron density profile is 50 /+-/ 10%, and the pressure profile is at least as hollow as, if not more than, the hot electron density profile. The hollow plasma equilibrium is macroscopically stable and generated in all the experimental conditions in which the machine has been operated. The hollowness of the plasma pressure profile is not limited by the marginal stability condition. Small macroscopic plasma fluctuations in the range of the hot electron curvature drift frequency sometimes occur but their growth rate is small (..omega../sub i//..omega../sub r/ less than or equal to 10/sup -2/) and saturate at very low level (deltaB//bar B/ less than or equal to 10/sup -3/). Particle drift reversal is predicted to occur for the model pressure profile which best fits the experimental data under the typical operating conditions. No strong instability is observed when the plasma is near the drift reversal parameter regime, despite a theoretical prediction of instability under such conditions. The experiment shows that the cold electron population has no stabilizing effect to the hot electrons, which disagrees with current hot electron stability theories and results of previous maximum-B experiments. A theoretical analysis using MHD theory shows that the compressibility can stabilize a plasma with a hollowness of 20--30% in the

  5. Retrospective analysis of linear accelerator output constancy checks using process control techniques.

    PubMed

    Sanghangthum, Taweap; Suriyapee, Sivalee; Srisatit, Somyot; Pawlicki, Todd

    2013-01-01

    Shewhart control charts have previously been suggested as a process control tool for use in routine linear accelerator (linac) output verifications. However, a comprehensive approach to process control has not been investigated for linac output verifications. The purpose of this work is to investigate a comprehensive process control approach to linac output constancy quality assurance (QA). The RBA-3 dose constancy check was used to verify outputs of photon beams and electron beams delivered by a Varian Clinac 21EX linac. The data were collected during 2009 to 2010. Shewhart-type control charts, exponentially weighted moving average (EWMA) charts, and capability indices were applied to these processes. The Shewhart-type individuals chart (X-chart) was used and the number of data points used to calculate the control limits was varied. The parameters tested for the EWMA charts (smoothing parameter (λ) and the control limit width (L)) were λ = 0.05, L = 2.492; λ = 0.10, L = 2.703; and λ = 0.20, L = 2.860, as well as the number of points used to estimate the initial process mean and variation. Lastly, the number of in-control data points used to determine process capability (C(p)) and acceptability (C(pk)) were investigated, comparing the first in-control run to the longest in-control run of the process data. C(p) and C(pk) values greater than 1.0 were considered acceptable. The 95% confidence intervals were reported. The X-charts detected systematic errors (e.g., device setup errors). In-control run lengths on the X-charts varied from 5 to 30 output measurements (about one to seven months). EWMA charts showed in-control runs ranging from 9 to 33 output measurements (about two to eight months). The C(p) and C(pk) ratios are higher than 1.0 for all energies, except 12 and 20 MeV. However, 10 MV and 6, 9, and 16 MeV were in question when considering the 95% confidence limits. The X-chart should be calculated using 8-12 data points. For EWMA chart, using 4 data points

  6. Trial of a proposed protocol for constancy control of digital mammography systems

    SciTech Connect

    Pedersen, Kristin; Landmark, Ingrid Dypvik

    2009-12-15

    Purpose: Evaluate the utility of tests in a proposed protocol for constancy control of digital mammography systems. Methods: The protocol contained tests for image acquisition, mechanical function and safety, monitors and printers, and viewing conditions. Nine sites with digital systems from four equipment manufacturers were recruited. Dedicated PMMA test objects and Excel spreadsheets were developed. Quantitative measurements were done on processed images for systems where these images were the ones most readily available. For daily assessment of the automatic exposure control system, a homogeneous PMMA phantom was exposed under clinical conditions. The mAs and signal to noise ratio (SNR) were recorded, the deviation from a target value calculated, and the resulting image inspected for artifacts. For thickness tracking, the signal difference to noise ratio obtained for three thicknesses was calculated. Detector uniformity was assessed through comparison of SNR values for regions of interest in the center and corners of an image of a homogeneous test object. Mechanical function and safety control included a compression test, a checklist for mechanical aspects, and control of field alignment. Monitor performance was evaluated by visual inspection of the AAPM TG 18 QC test image [E. Samei et al., ''Assessment of display performance for medical imaging systems,'' Task Group 18 (Madison, WI, April 2005)]. Results: For quantitative parameters, target values and tolerance limits were established. Test results exceeding the limits were registered. Most systems exhibited stable mAs values, indicating that the tolerance limit of {+-}10% was readily achievable. The SNR also showed little variation, indicating that the tolerance limit of {+-}20% was too wide. At one site, a defective grid caused artifacts that were visible in the test images. The monitor controls proved more difficult to implement due to both difficulties importing and displaying the test image, and the

  7. Detection of IMRT delivery errors based on a simple constancy check of transit dose by using an EPID

    NASA Astrophysics Data System (ADS)

    Baek, Tae Seong; Chung, Eun Ji; Son, Jaeman; Yoon, Myonggeun

    2015-11-01

    Beam delivery errors during intensity modulated radiotherapy (IMRT) were detected based on a simple constancy check of the transit dose by using an electronic portal imaging device (EPID). Twenty-one IMRT plans were selected from various treatment sites, and the transit doses during treatment were measured by using an EPID. Transit doses were measured 11 times for each course of treatment, and the constancy check was based on gamma index (3%/3 mm) comparisons between a reference dose map (the first measured transit dose) and test dose maps (the following ten measured dose maps). In a simulation using an anthropomorphic phantom, the average passing rate of the tested transit dose was 100% for three representative treatment sites (head & neck, chest, and pelvis), indicating that IMRT was highly constant for normal beam delivery. The average passing rate of the transit dose for 1224 IMRT fields from 21 actual patients was 97.6% ± 2.5%, with the lower rate possibly being due to inaccuracies of patient positioning or anatomic changes. An EPIDbased simple constancy check may provide information about IMRT beam delivery errors during treatment.

  8. Edge-moment-based color constancy using illumination-coherent regularized regression.

    PubMed

    Wu, Meng; Luo, Kai; Dang, Jianjun; Zhou, Jun

    2015-09-01

    Considering no previous literature reveals the effectiveness of image similarity coherent with corresponding illuminant in color constancy, we propose an edge-moment-based algorithm using regularized regression in an illumination-coherent space in a divide-and-conquer way. To represent the scene images, we adopt color edge moments which are then projected into an illumination-coherent space using canonical correlation analysis (CCA). Further, a mixture of Gaussians (MoG) model is exploited to construct consistent subspaces, in each of which an iterative l2-norm regularized regression is used to learn the correlation between edge moments and illuminants. In the testing phase, estimations from each subspace are fused in a soft way according to the posterior possibility of the test image caused by the MoG. Extensive experiments on the standard datasets including the intra- and inter-dataset evaluations show that our approach outperforms the state-of-the-art algorithms. PMID:26367440

  9. Recent results from the Tara tandem mirror and Constance-B mirror

    SciTech Connect

    Post, R.S.; Brau, K.; Casey, J.; Chen, X.; Coleman, J.; Garner, R.; Golovato, S.; Gerver, M.; Goodman, D.; Guss, W.

    1986-11-01

    The Tara tandem mirror program has studied anchor and ponderomotive stabilization, axicell plugging with ECH and ICRF, sloshing ion buildup in the axicells, and halo formation and stabilization by an axisymmetric divertor. Central cell plasma parameters achieved by midplane fueling and slow wave ICRF heating from a local magnetic hill are ..beta.. = 1.2%, n/sub e/ = 3 x 10/sup 12/ cm/sup -3/. The plasma is stabilized both by anchor ion ..beta.. and by ponderomotive stabilization with the central cell ICRF in combination with a magnetic divertor, realizing a completely axisymmetric configuration. Anchor ICRF creates non-Boltzman potential plugging of central cell ions. Neutral beam injection establishes a sloshing ion distribution for a cold dense central cell stream; the hot ion confinement is classical and dominated by electron drag. Axicell ECH plugging experiments lead to near total reduction in endloss, but also to a decrease in the central cell density, indicating increased radial losses. Single-ended ECH plugging shows no increase in opposite endloss. Single-ended plugging with axicell ICRF produces 50% reduction in ion endloss, with about half of the reflected ions observed in the opposite endloss. In the Constance-B quadrupole mirror the hot electron pressure profile is peaked off-axis and has the shape of a baseball seam.

  10. Synaptic depression in conjunction with A-current channels promote phase constancy in a rhythmic network.

    PubMed

    Greenberg, Idan; Manor, Yair

    2005-02-01

    In many central pattern generators, pairs of neurons maintain an approximately fixed phase despite large changes in the frequency. The mechanisms underlying phase maintenance are not clear. Previous theoretical work suggested that inhibitory synapses that show short-term depression could play a critical role in this respect. In this work we examine how the interaction between synaptic depression and the kinetics of a transient potassium (A-like) current could be advantageous for phase constancy in a rhythmic network. To demonstrate the mechanism in the context of a realistic central pattern generator, we constructed a detailed model of the crustacean pyloric circuit. The frequency of the rhythm was modified by changing the level of a ligand-activated current in one of the pyloric neurons. We examined how the time difference of firing activities between two selected neurons in this circuit is affected by synaptic depression, A-current, and a combination of the two. We tuned the parameters of the model such that with synaptic depression alone, or A-current alone, phase was not maintained between these two neurons. However, when these two components came together, they acted synergistically to maintain the phase across a wide range of cycle periods. This suggests that synaptic depression may be necessary to allow an A-current to delay a postsynaptic neuron in a frequency-dependent manner, such that phase invariance is ensured. PMID:15356180

  11. Julius Caesar Scaliger on plant generation and the question of species constancy.

    PubMed

    Blank, Andreas

    2010-01-01

    The sixteenth-century physician and philosopher Julius Caesar Scaliger combines the view that living beings are individuated by a single substantial form with the view that the constituents of the organic body retain their identity due to the continued existence and operation of their own substantial forms. This essay investigates the implications of Scaliger's account of subordinate and dominant substantial forms for the question of the constancy of biological species. According to Scaliger, biological mutability involves not only change on the ontological level of accidents but, in some cases, also change on the level of substantial forms. While he shares the received view that substantial forms themselves cannot undergo change, he maintains that relations of domination and subordination between substantial forms can undergo change. He uses his theory of how such changes can occur to explain cases of revertible plant degeneration. Moreover, in his view plants that belong to previously unknown biological species can emerge from changes in the relations between the many forms contained in plant seeds. PMID:20695395

  12. Constancy of the relation between floc size and density in San Francisco Bay

    USGS Publications Warehouse

    Ganju, N.K.; Schoellhamer, D.H.; Murrell, M.C.; Gartner, J.W.; Wright, S.A.

    2007-01-01

    The size and density of fine-sediment aggregates, or flocs, govern their transport and depositional properties. While the mass and volume concentrations of flocs can be measured directly or by optical methods, they must be determined simultaneously to gain an accurate density measurement. Results are presented from a tidal cycle study in San Francisco Bay, where mass concentration was determined directly, and volume concentration was measured in 32 logarithmically spaced size bins by laser-diffraction methods. The relation between floc size and density is investigated assuming a constant primary particle size and fractal floc dimension. This relation is validated with measurements from several sites throughout San Francisco Bay. The constancy of this relation implies a uniform primary particle size throughout the Bay, as well as uniform aggregation/disaggregation mechanisms (which modify fractal dimension). The exception to the relation is identified during near-bed measurements, when advected flocs mix with recently resuspended flocs from the bed, which typically have a higher fractal dimension than suspended flocs. The constant relation for suspended flocs simplifies monitoring and numerical modeling of suspended sediment in San Francisco Bay. ?? 2007 Elsevier B.V. All rights reserved.

  13. Chromosomal phylogeny and evolution of gibbons (Hylobatidae).

    PubMed

    Müller, Stefan; Hollatz, Melanie; Wienberg, Johannes

    2003-11-01

    Although human and gibbons are classified in the same primate superfamily (Hominoidae), their karyotypes differ by extensive chromosome reshuffling. To date, there is still limited understanding of the events that shaped extant gibbon karyotypes. Further, the phylogeny and evolution of the twelve or more extant gibbon species (lesser apes, Hylobatidae) is poorly understood, and conflicting phylogenies have been published. We present a comprehensive analysis of gibbon chromosome rearrangements and a phylogenetic reconstruction of the four recognized subgenera based on molecular cytogenetics data. We have used two different approaches to interpret our data: (1) a cladistic reconstruction based on the identification of ancestral versus derived chromosome forms observed in extant gibbon species; (2) an approach in which adjacent homologous segments that have been changed by translocations and intra-chromosomal rearrangements are treated as discrete characters in a parsimony analysis (PAUP). The orangutan serves as an "outgroup", since it has a karyotype that is supposed to be most similar to the ancestral form of all humans and apes. Both approaches place the subgenus Bunopithecus as the most basal group of the Hylobatidae, followed by Hylobates, with Symphalangus and Nomascus as the last to diverge. Since most chromosome rearrangements observed in gibbons are either ancestral to all four subgenera or specific for individual species and only a few common derived rearrangements at subsequent branching points have been recorded, all extant gibbons may have diverged within relatively short evolutionary time. In general, chromosomal rearrangements produce changes that should be considered as unique landmarks at the divergence nodes. Thus, molecular cytogenetics could be an important tool to elucidate phylogenies in other species in which speciation may have occurred over very short evolutionary time with not enough genetic (DNA sequence) and other biological divergence to

  14. Detecting Macroevolutionary Self-Destruction from Phylogenies.

    PubMed

    Bromham, Lindell; Hua, Xia; Cardillo, Marcel

    2016-01-01

    Phylogenetic analyses have lent support to the concept of lineage selection: that biological lineages can have heritable traits that influence their capacity to persist and diversify, and thereby affect their representation in biodiversity. While many discussions have focused on "positive" lineage selection, where stably heritable properties of lineages enhance their diversification rate, there are also intriguing examples that seem to represent "negative" lineage selection, where traits reduce the likelihood that a lineage will persist or speciate. In this article, we test whether a particular pattern of negative lineage selection is detectable from the distributions of the trait on a phylogeny. "Self-destructive" traits are those that arise often but then disappear again because they confer either a raised extinction rate or they are prone to a high rate of trait loss. For such a trait, the reconstructed origins will tend to be dispersed across the tips of the phylogeny, rather than defining large clades of related lineages that all share the trait. We examine the utility of four possible measures of "tippiness" as potential indicators of macroevolutionary self-destruction, applying them to phylogenies on which trait evolution has been simulated under different combinations of parameters for speciation, extinction, trait gain, and trait loss. We use an efficient simulation approach that starts with the required number of tips with and without the trait and uses a model to work "backwards" to construct different possible trees that result in that set of tips. We then apply these methods to a number of case studies: salt tolerance in grasses, color polymorphism in birds of prey, and selfing in nightshades. We find that the relative age of species, measured from tip length, can indicate a reduced speciation rate but does not identify traits that increase the extinction rate or the trait loss rate. We show that it is possible to detect cases of macroevolutionary self

  15. Explaining evolution via constrained persistent perfect phylogeny

    PubMed Central

    2014-01-01

    Background The perfect phylogeny is an often used model in phylogenetics since it provides an efficient basic procedure for representing the evolution of genomic binary characters in several frameworks, such as for example in haplotype inference. The model, which is conceptually the simplest, is based on the infinite sites assumption, that is no character can mutate more than once in the whole tree. A main open problem regarding the model is finding generalizations that retain the computational tractability of the original model but are more flexible in modeling biological data when the infinite site assumption is violated because of e.g. back mutations. A special case of back mutations that has been considered in the study of the evolution of protein domains (where a domain is acquired and then lost) is persistency, that is the fact that a character is allowed to return back to the ancestral state. In this model characters can be gained and lost at most once. In this paper we consider the computational problem of explaining binary data by the Persistent Perfect Phylogeny model (referred as PPP) and for this purpose we investigate the problem of reconstructing an evolution where some constraints are imposed on the paths of the tree. Results We define a natural generalization of the PPP problem obtained by requiring that for some pairs (character, species), neither the species nor any of its ancestors can have the character. In other words, some characters cannot be persistent for some species. This new problem is called Constrained PPP (CPPP). Based on a graph formulation of the CPPP problem, we are able to provide a polynomial time solution for the CPPP problem for matrices whose conflict graph has no edges. Using this result, we develop a parameterized algorithm for solving the CPPP problem where the parameter is the number of characters. Conclusions A preliminary experimental analysis shows that the constrained persistent perfect phylogeny model allows to

  16. [Phylogeny and divergence time estimation of Schizothoracinae fishes in Xinjiang].

    PubMed

    Ayelhan, Haysa; Guo, Yan; Meng, Wei; Yang, Tianyan; Ma, Yanwu

    2014-10-01

    Based on combined data of mitochondrial COI, ND4 and 16S RNA genes, molecular phylogeny of 4 genera, 10 species or subspecies of Schizothoracinae fishes distributed in Xinjiang were analyzed. The molecular clock was calibrated by divergence time of Cyprininae and geological segregation event between the upper Yellow River and Qinghai Lake. Divergence time of Schizothoracinae fishes was calculated, and its relationship with the major geological events and the climate changes in surrounding areas of Tarim Basin was discussed. The results showed that genus Aspiorhynchus did not form an independent clade, but clustered with Schizothorax biddulphi and S. irregularis. Kimura 2-parameter model was used to calculate the genetic distance of COI gene, the genetic distance between genus Aspiorhynchus and Schizothorax did not reach genus level, and Aspiorhynchus laticeps might be a specialized species of genus Schizothorax. Cluster analysis showed a different result with morphological classification method, and it did not support the subgenus division of Schizothorax fishes. Divergence of two groups of primitive Schizothoracinae (8.18Ma) and divergence of Gymnodiptychus dybowskii and Diptychus maculates (7.67Ma) occurred in late Miocene, which might be related with the separation of Kunlun Mountain and north Tianshan Mountain River system that was caused by the uplift of Qinghai-Tibet Plateau and Tianshan Mountain, and the aridification of Tarim Basin. The terrain of Tarim Basin that was affected by Quaternary Himalayan movement was high in west but low in east, as a result, Lop Nor became the center of surrounding mountain rivers in Tarim Basin, which shaped the distribution pattern of genus Schizothorax. PMID:25406249

  17. Molecular phylogeny of tintinnid ciliates (Tintinnida, Ciliophora).

    PubMed

    Bachy, Charles; Gómez, Fernando; López-García, Purificación; Dolan, John R; Moreira, David

    2012-11-01

    We investigated the phylogeny of tintinnids (Ciliophora, Tintinnida) with 62 new SSU-rDNA sequences from single cells of 32 marine and freshwater species in 20 genera, including the first SSU-rDNA sequences for Amphorides, Climacocylis, Codonaria, Cyttarocylis, Parundella, Petalotricha, Undella and Xystonella, and 23 ITS sequences of 17 species in 15 genera. SSU-rDNA phylogenies suggested a basal position for Eutintinnus, distant to other Tintinnidae. We propose Eutintinnidae fam. nov. for this divergent genus, keeping the family Tintinnidae for Amphorellopsis, Amphorides and Steenstrupiella. Tintinnopsis species branched in at least two separate groups and, unexpectedly, Climacocylis branched among Tintinnopsis sensu stricto species. Tintinnopsis does not belong to the family Codonellidae, which is restricted to Codonella, Codonaria, and also Dictyocysta (formerly in the family Dictyocystidae). The oceanic genus Undella branched close to an undescribed freshwater species. Metacylis, Rhabdonella and Cyttarocylis formed a well supported clade with several Tintinnopsis species at a basal position. Petalotricha ampulla and Cyttarocylis cassis SSU-rDNA and ITS sequences were identical or almost identical. Therefore, we propose Cyttarocylis ampulla comb. nov. for them. Intensive use of single-cell isolation and sequencing revealed unexpected complexity in the evolutionary history of these relatively well-studied ciliates. Notably, the diversity of freshwater forms suggests multiple marine-freshwater invasions. PMID:22321440

  18. Mitochondrial phylogeny and systematics of baboons (Papio).

    PubMed

    Newman, Timothy K; Jolly, Clifford J; Rogers, Jeffrey

    2004-05-01

    Baboons (Papio, s.s.) comprise a series of parapatric allotaxa (subspecies or closely related species) widely distributed in sub-Saharan Africa. Despite extensive studies of their ecology, morphology, and behavior, disagreement about their phylogenetic relationships continues, as expressed in the current coexistence of at least three major, competing taxonomic treatments. To help resolve this situation, we sequenced approximately 900 bases of mitochondrial DNA of 40 individuals from five of the widely recognized "major" allotaxa. Total sequence diversity (>5%) is high compared to most primate species. Major mitochondrial clades correspond to recognized allotaxa, with the important exception that haplotypes from yellow and olive baboons form a single, monophyletic clade within which the two allotaxa do not comprise mutually exclusive clusters. The major clades fall unambiguously into the pattern: (chacma (Guinea (hamadryas (yellow + olive)))). This phylogeny does not support taxonomies that oppose hamadryas to all other baboons ("desert" vs. "savanna"), but is compatible with the view that all definable allotaxa should be recognized as coordinates, either as "phylogenetic" species or "biological" subspecies. The close relationship and unsegregated distribution of haplotypes from Kenyan and Tanzanian yellow and olive baboons are unexplained, but may reflect introgression across the documented hybrid zone. The overall phylogeny, when combined with paleontological data, suggests a southern African origin for extant Papio baboons, with all extant lineages sharing a common mitochondrial ancestor at approximately 1.8 Ma. PMID:15085544

  19. Phylogeny, host-parasite relationship and zoogeography

    PubMed Central

    1999-01-01

    Phylogeny is the evolutionary history of a group or the lineage of organisms and is reconstructed based on morphological, molecular and other characteristics. The genealogical relationship of a group of taxa is often expressed as a phylogenetic tree. The difficulty in categorizing the phylogeny is mainly due to the existence of frequent homoplasies that deceive observers. At the present time, cladistic analysis is believed to be one of the most effective methods of reconstructing a phylogenetic tree. Excellent computer program software for phylogenetic analysis is available. As an example, cladistic analysis was applied for nematode genera of the family Acuariidae, and the phylogenetic tree formed was compared with the system used currently. Nematodes in the genera Nippostrongylus and Heligmonoides were also analyzed, and the validity of the reconstructed phylogenetic trees was observed from a zoogeographical point of view. Some of the theories of parasite evolution were briefly reviewed as well. Coevolution of parasites and humans was discussed with special reference to the evolutionary relationship between Enterobius and primates. PMID:10634036

  20. Progress in nemertean biology: development and phylogeny.

    PubMed

    Turbeville, J M

    2002-07-01

    This paper reviews progress in developmental biology and phylogeny of the Nemertea, a common but poorly studied spiralian taxon of considerable ecological and evolutionary significance. Analyses of reproductive biology (including calcium dynamics during fertilization and oocyte maturation), larval morphology and development and developmental genetics have significantly extended our knowledge of spiralian developmental biology. Developmental genetics studies have in addition provided characters useful for reconstructing metazoan phylogeny. Reinvestigation of the cell lineage of Cerebratulus lacteus using fluorescent tracers revealed that endomesoderm forms from the 4d cell as in other spiralians and that ectomesoderm is derived from the 3a and 3b cells as in annelids, echiurans and molluscs. Studies examining blastomere specification show that cell fates are established precociously in direct developers and later in indirect developers. Morphological characters used to estimate the phylogenetic position of nemerteans are critically re-evaluated, and cladistic analyses of morphology reveal that conflicting hypotheses of nemertean relationships result because of different provisional homology statements. Analyses that include disputed homology statements (1, gliointerstitial cell system 2, coelomic circulatory system) suggest that nemerteans form the sister taxon to the coelomate spiralian taxa rather than the sister taxon to Platyhelminthes. Analyses of small subunit rRNA (18S rDNA) sequences alone or in combination with morphological characters support the inclusion of the nemerteans in a spiralian coelomate clade nested within a more inclusive lophotrochozoan clade. Ongoing evaluation of nemertean relationships with mitochondrial gene rearrangements and other molecular characters is discussed. PMID:21708766

  1. ON THE CONSTANCY OF THE ELECTRON TEMPERATURE IN THE EXPANDING CORONA THROUGHOUT SOLAR CYCLE 23

    SciTech Connect

    Habbal, Shadia Rifai; Morgan, Huw; Druckmueller, Miloslav; Ding, Adalbert

    2010-03-10

    A recent analysis of Fe emission lines observed during the total solar eclipses of 2006 March 29 and 2008 August 1 established the first empirical link between the electron temperature in the expanding corona and Fe charge states measured in interplanetary space. In this Letter, we use this link to infer this temperature throughout solar cycle 23 from in situ charge state measurements from the Solar Wind Ion Composition Spectrometer (SWICS) on the Advanced Composition Explorer (ACE) and on Ulysses. The distribution of the SWICS/ACE Fe charge states, which span cycle 23 from 1998 to 2009, is skewed with a peak centered on Fe{sup 8+}, Fe{sup 9+}, and Fe{sup 10+} and a tail spanning Fe{sup 12+} to Fe{sup 20+}. An iterative process based on this distribution and on the Fe ion fraction as a function of electron temperature yields a narrow peak at 1.1 x 10{sup 6} K. The tail in the measured charge state distribution is attributed to the sporadic release of material hotter than 2 x 10{sup 6} K from closed magnetic structures within the bulges of streamers. The Fe Ulysses charge state measurements between 1992 and 1997 from cycle 22 peaked at Fe{sup 11+}, indicative of a slightly higher temperature of 1.5 x 10{sup 6} K. The relative constancy of the electron temperature in the expanding corona throughout solar cycle 23 points to the presence of an unknown mechanism regulating the energy input to electrons in the acceleration region of the solar wind at all latitudes during this cycle.

  2. On the Basis of Synaptic Integration Constancy during Growth of a Neuronal Circuit

    PubMed Central

    De-La-Rosa Tovar, Adriana; Mishra, Prashant K.; De-Miguel, Francisco F.

    2016-01-01

    We studied how a neuronal circuit composed of two neuron types connected by chemical and electrical synapses maintains constant its integrative capacities as neurons grow. For this we combined electrophysiological experiments with mathematical modeling in pairs of electrically-coupled Retzius neurons from postnatal to adult leeches. The electrically-coupled dendrites of both Retzius neurons receive a common chemical input, which produces excitatory postsynaptic potentials (EPSPs) with varying amplitudes. Each EPSP spreads to the soma, but also crosses the electrical synapse to arrive at the soma of the coupled neuron. The leak of synaptic current across the electrical synapse reduces the amplitude of the EPSPs in proportion to the coupling ratio. In addition, summation of EPSPs generated in both neurons generates the baseline action potentials of these serotonergic neurons. To study how integration is adjusted as neurons grow, we first studied the characteristics of the chemical and electrical connections onto the coupled dendrites of neuron pairs with soma diameters ranging from 21 to 75 μm. Then by feeding a mathematical model with the neuronal voltage responses to pseudorandom noise currents we obtained the values of the coupling ratio, the membrane resistance of the soma (rm) and dendrites (rdend), the space constant (λ) and the characteristic dendritic length (L = l/λ). We found that the EPSPs recorded from the somata were similar regardless on the neuron size. However, the amplitude of the EPSPs and the firing frequency of the neurons were inversely proportional to the coupling ratio of the neuron pair, which also was independent from the neuronal size. This data indicated that the integrative constancy relied on the passive membrane properties. We show that the growth of Retzius neurons was compensated by increasing the membrane resistance of the dendrites and therefore the λ value. By solely increasing the dendrite resistance this circuit maintains

  3. On the Basis of Synaptic Integration Constancy during Growth of a Neuronal Circuit.

    PubMed

    De-La-Rosa Tovar, Adriana; Mishra, Prashant K; De-Miguel, Francisco F

    2016-01-01

    We studied how a neuronal circuit composed of two neuron types connected by chemical and electrical synapses maintains constant its integrative capacities as neurons grow. For this we combined electrophysiological experiments with mathematical modeling in pairs of electrically-coupled Retzius neurons from postnatal to adult leeches. The electrically-coupled dendrites of both Retzius neurons receive a common chemical input, which produces excitatory postsynaptic potentials (EPSPs) with varying amplitudes. Each EPSP spreads to the soma, but also crosses the electrical synapse to arrive at the soma of the coupled neuron. The leak of synaptic current across the electrical synapse reduces the amplitude of the EPSPs in proportion to the coupling ratio. In addition, summation of EPSPs generated in both neurons generates the baseline action potentials of these serotonergic neurons. To study how integration is adjusted as neurons grow, we first studied the characteristics of the chemical and electrical connections onto the coupled dendrites of neuron pairs with soma diameters ranging from 21 to 75 μm. Then by feeding a mathematical model with the neuronal voltage responses to pseudorandom noise currents we obtained the values of the coupling ratio, the membrane resistance of the soma (rm ) and dendrites (r dend), the space constant (λ) and the characteristic dendritic length (L = l/λ). We found that the EPSPs recorded from the somata were similar regardless on the neuron size. However, the amplitude of the EPSPs and the firing frequency of the neurons were inversely proportional to the coupling ratio of the neuron pair, which also was independent from the neuronal size. This data indicated that the integrative constancy relied on the passive membrane properties. We show that the growth of Retzius neurons was compensated by increasing the membrane resistance of the dendrites and therefore the λ value. By solely increasing the dendrite resistance this circuit maintains

  4. [In-phantom dosimetric measurements as quality control for brachytherapy: System check and constancy check].

    PubMed

    Kollefrath, Michael; Bruggmoser, Gregor; Nanko, Norbert; Gainey, Mark

    2015-06-01

    In brachytherapy dosimetric measurements are difficult due to the inherent dose-inhomogenieties. Typically in routine clincal practice only the nominal dose rate is determined for computer controlled afterloading systems. The region of interest lies close to the source when measuring the spatial dose distribution. In this region small errors in the postioning of the detector, and its finite size, lead to large measurement uncertainties that exacerbate the routine dosimetric control of the system in the clinic. The size of the measurement chamber, its energy dependence, and the directional dependence of the measurement apparatus are the factors which have a significant influence on dosimetry. Although ionisation chambers are relatively large, they are employed since similar chambers are commonly found on clincal brachytherapy units. The dose is determined using DIN 6800 [11] since DIN 6809-2 [12], which deals with dosimetry in brachytherapy, is antiquated and is currently in the process of revision. Further information regarding dosimetry for brachytherapy can be found in textbooks [1] and [2]. The measurements for this work were performed with a HDR (High-Dose-Rate) (192)Ir source, type mHDR V2, and a Microselectron Afterloader V2 both from Nucletron/Elekta. In this work two dosimetric procedures are presented which, despite the aforemention difficulties, should assist in performing checks of the proper operation of the system. The first is a system check that measures the dose distribution along a line and is to be performed when first bringing the afterloader into operation, or after significant changes to the system. The other is a dosimetric constancy check, which with little effort can be performed monhtly or weekly. It simultaneously verifies the positioning of the source at two positions, the functionality of the system clock and the automatic re-calculation of the source activity. PMID:25791738

  5. Lake Powell

    NASA Technical Reports Server (NTRS)

    2007-01-01

    The white ring around Lake Powell tells the story. The surface is down 98 feet. This is critical, because Powell, Lake Mead, and other lakes along the Colorado River provide water for millions of people in five states. We are in the eighth year of a drought on the Colorado River. This year was the driest year ever reported in Southern California, and there is a severe drought in Northern California, down to less than 30-percent of snow pack. This ASTER image of part of Lake Powell was acquired in 2001. The gray area depicts the shrunken, reduced 2007 lake extent compared to the extended, larger black area in 2001.

    The image covers an area of 24 x 30 km, and is centered near 37.1 degrees north latitude, 111.3 degrees west longitude.

    The U.S. science team is located at NASA's Jet Propulsion Laboratory, Pasadena, Calif. The Terra mission is part of NASA's Science Mission Directorate.

  6. A Guide to the Natural History of Freshwater Lake Bacteria†

    PubMed Central

    Newton, Ryan J.; Jones, Stuart E.; Eiler, Alexander; McMahon, Katherine D.; Bertilsson, Stefan

    2011-01-01

    Summary: Freshwater bacteria are at the hub of biogeochemical cycles and control water quality in lakes. Despite this, little is known about the identity and ecology of functionally significant lake bacteria. Molecular studies have identified many abundant lake bacteria, but there is a large variation in the taxonomic or phylogenetic breadths among the methods used for this exploration. Because of this, an inconsistent and overlapping naming structure has developed for freshwater bacteria, creating a significant obstacle to identifying coherent ecological traits among these groups. A discourse that unites the field is sorely needed. Here we present a new freshwater lake phylogeny constructed from all published 16S rRNA gene sequences from lake epilimnia and propose a unifying vocabulary to discuss freshwater taxa. With this new vocabulary in place, we review the current information on the ecology, ecophysiology, and distribution of lake bacteria and highlight newly identified phylotypes. In the second part of our review, we conduct meta-analyses on the compiled data, identifying distribution patterns for bacterial phylotypes among biomes and across environmental gradients in lakes. We conclude by emphasizing the role that this review can play in providing a coherent framework for future studies. PMID:21372319

  7. Climate Change and its Potential Consequences to the Thermodynamics of an Alpine Lake

    NASA Astrophysics Data System (ADS)

    Fink, G.

    2012-04-01

    The characteristics of mixing processes as well as duration, frequency, and stability of an alpine lake's stratification are strongly coupled to the local climate conditions. These physical processes then again define the way in which life - from bacteria to human being - develops in this environment. Hence, probably economic and cultural lake uses are affected by climate change. Studies discovered reactions of lake physics due to global warming in central Europe in measured time series. The question is: What changes in alpine lake's thermodynamic processes do we have to expect in the next decades? This question is directed at first to general lake properties like water temperature, metalimnion depth, and heat balance and their behavior in space and time. Secondly, there is a need for information about mixing processes in these monomictic lakes. Mixing is important for the distribution of e.g. nutrients and oxygen. Thus, it is necessary to know how mixing intensity changes under likely future climate conditions. For this purpose three representative lakes were selected: Lake Constance (international), Lago di Viverone (Italy), and Woerthersee (Austria). For each lake a 1dv hydrodynamic model was built up, calibrated with an evolutionary algorithm, and finally validated. The model's source code is in an experimental state and it was provided by Deltares (Netherlands). During calibration the calculated mean monthly temperatures in different depths were compared to measurements. Then, based upon measured meteorological data "what if"-scenarios of air temperature, wind speed, cloud cover and relative humidity were developed by changing the mean value or by removing the old trend and adding a new one. When driving the model with this broad range of meteorology the result is a sensitivity study. This allows the determination of the lake's sensitivity e.g. regarding mixing intensity on changing climate, in a way that is independent from rough regional climate projections

  8. Partitional Classification: A Complement to Phylogeny

    PubMed Central

    Salomon, Marc; Dassy, Bruno

    2016-01-01

    The tree of life is currently an active object of research, though next to vertical gene transmission non vertical gene transfers proved to play a significant role in the evolutionary process. To overcome this difficulty, trees of life are now constructed from genes hypothesized vital, on the assumption that these are all transmitted vertically. This view has been challenged. As a frame for this discussion, we developed a partitional taxonomical system clustering taxa at a high taxonomical rank. Our analysis (1) selects RNase P RNA sequences of bacterial, archaeal, and eucaryal genera from genetic databases, (2) submits the sequences, aligned, to k-medoid analysis to obtain clusters, (3) establishes the correspondence between clusters and taxa, (4) constructs from the taxa a new type of taxon, the genetic community (GC), and (5) classifies the GCs: Archaea–Eukaryotes contrastingly different from the six others, all bacterial. The GCs would be the broadest frame to carry out the phylogenies. PMID:27346943

  9. New culturing studies of various haptophyte algae: The role of phylogeny on the alkenone paleothermometer

    NASA Astrophysics Data System (ADS)

    Walker Karega, I. I.; D'Andrea, W. J.; Juhl, A. R.

    2015-12-01

    Alkenone paleothermometry (via the Uk37and UK'37 indices) is widely used to reconstruct sea surface temperature and, more recently, lake water temperature. Genetic analyses indicate that there is a diversity of different alkenone-producing lacustrine haptophytes, and differences among UK37-temperature calibrations suggest that unique calibrations might be required to quantify past temperature variation from individual lakes. The only term needed to quantify UK37-inferred temperature relative to a reference period (e.g., modern temperature, or 20th Century mean temperature) is the slope of the calibration regression: UK37-temperature sensitivity (i.e., the change in UK37 per °C temperature change). Here, we present new data developed by culturing four different species of alkenone-producing haptophyte algae across a range of temperatures (6-30 °C) and light levels (20-200 mE). The simultaneous culture of four distinct species allows direct comparison of the absolute quantities of alkenones and alkenoates, as well as other lipids, produced by different species of haptophytes under identical environmental conditions. Our results indicate that algal growth rate, when controlled by light intensity, has no impact on values. As expected, we find that growth temperature controls both the degree of alkenone unsaturation and the relative production of alkenones vs. alkenoates in all four species. Importantly, comparison of the four UK37-temperature calibrations resulting from our experiments with preexisting calibrations supports the hypothesis that UK37-temperature sensitivity is controlled by phylogeny. Therefore, even in the absence of a site-specific calibration, this term can be used to quantify past temperature variation from lake sediments if the genetic identity of the lake's alkenone-producer is known.

  10. Archaebacterial phylogeny: perspectives on the urkingdoms

    NASA Technical Reports Server (NTRS)

    Woese, C. R.; Olsen, G. J.

    1986-01-01

    Comparisons of complete 16S ribosomal RNA sequences have been used to confirm, refine and extend earlier concepts of archaebacterial phylogeny. The archaebacteria fall naturally into two major branches or divisions, I--the sulfur-dependent thermophilic archaebacteria, and II--the methanogenic archaebacteria and their relatives. Division I comprises a relatively closely related and phenotypically homogeneous collection of thermophilic sulfur-dependent species--encompassing the genera Sulfolobus, Thermoproteus, Pyrodictium and Desulfurococcus. The organisms of Division II, however, form a less compact grouping phylogenetically, and are also more diverse in phenotype. All three of the (major) methanogen groups are found in Division II, as are the extreme halophiles and two types of thermoacidophiles, Thermoplasma acidophilum and Thermococcus celer. This last species branches sufficiently deeply in the Division II line that it might be considered to represent a separate, third Division. However, both the extreme halophiles and Tp. acidophilum branch within the cluster of methanogens. The extreme halophiles are specifically related to the Methanomicrobiales, to the exclusion of both the Methanococcales and the Methanobacteriales. Tp. acidophilum is peripherally related to the halophile-Methanomicrobiales group. By 16S rRNA sequence measure the archaebacteria constitute a phylogenetically coherent grouping (clade), which excludes both the eubacteria and the eukaryotes--a conclusion that is supported by other sequence evidence as well. Alternative proposals for archaebacterial phylogeny, not based upon sequence evidence, are discussed and evaluated. In particular, proposals to rename (reclassify) various subgroups of the archaebacteria as new kingdoms are found wanting, for both their lack of proper experimental support and the taxonomic confusion they introduce.

  11. Homology and phylogeny and their automated inference

    NASA Astrophysics Data System (ADS)

    Fuellen, Georg

    2008-06-01

    The analysis of the ever-increasing amount of biological and biomedical data can be pushed forward by comparing the data within and among species. For example, an integrative analysis of data from the genome sequencing projects for various species traces the evolution of the genomes and identifies conserved and innovative parts. Here, I review the foundations and advantages of this “historical” approach and evaluate recent attempts at automating such analyses. Biological data is comparable if a common origin exists (homology), as is the case for members of a gene family originating via duplication of an ancestral gene. If the family has relatives in other species, we can assume that the ancestral gene was present in the ancestral species from which all the other species evolved. In particular, describing the relationships among the duplicated biological sequences found in the various species is often possible by a phylogeny, which is more informative than homology statements. Detecting and elaborating on common origins may answer how certain biological sequences developed, and predict what sequences are in a particular species and what their function is. Such knowledge transfer from sequences in one species to the homologous sequences of the other is based on the principle of ‘my closest relative looks and behaves like I do’, often referred to as ‘guilt by association’. To enable knowledge transfer on a large scale, several automated ‘phylogenomics pipelines’ have been developed in recent years, and seven of these will be described and compared. Overall, the examples in this review demonstrate that homology and phylogeny analyses, done on a large (and automated) scale, can give insights into function in biology and biomedicine.

  12. Phylogeny and forelimb disparity in waterbirds.

    PubMed

    Wang, Xia; Clarke, Julia A

    2014-10-01

    Previous work has shown that the relative proportions of wing components (i.e., humerus, ulna, carpometacarpus) in birds are related to function and ecology, but these have rarely been investigated in a phylogenetic context. Waterbirds including "Pelecaniformes," Ciconiiformes, Procellariiformes, Sphenisciformes, and Gaviiformes form a highly supported clade and developed a great diversity of wing forms and foraging ecologies. In this study, forelimb disparity in the waterbird clade was assessed in a phylogenetic context. Phylogenetic signal was assessed via Pagel's lambda, Blomberg's K, and permutation tests. We find that different waterbird clades are clearly separated based on forelimb component proportions, which are significantly correlated with phylogeny but not with flight style. Most of the traditional contents of "Pelecaniformes" (e.g., pelicans, cormorants, and boobies) cluster with Ciconiiformes (herons and storks) and occupy a reduced morphospace. These taxa are closely related phylogenetically but exhibit a wide range of ecologies and flight styles. Procellariiformes (e.g., petrels, albatross, and shearwaters) occupy a wide range of morphospace, characterized primarily by variation in the relative length of carpometacarpus and ulna. Gaviiformes (loons) surprisingly occupy a wing morphospace closest to diving petrels and penguins. Whether this result may reflect wing proportions plesiomorphic for the waterbird clade or a functional signal is unclear. A Bayesian approach detecting significant rate shifts across phylogeny recovered two such shifts. At the base of the two sister clades Sphenisciformes + Procellariiformes, a shift to an increase evolutionary rate of change is inferred for the ulna and carpometacarpus. Thus, changes in wing shape begin prior to the loss of flight in the wing-propelled diving clade. Several shifts to slower rate of change are recovered within stem penguins. PMID:24989899

  13. A MOLECULAR PHYLOGENY FOR THE PROTOSTRONGYLIDAE (NEMATODA: METASTRONGYLINA)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Protostrongylids, a putative monophyletic group among the lungworms (Metastrongylina: Metastrongyloidea), are economically important pathogens infecting domestic and free-ranging ungulate and leporid hosts throughout the world. Here, we reconstruct a molecular phylogeny based on ribosomal DNA (28S) ...

  14. Target recognitions in multiple-camera closed-circuit television using color constancy

    NASA Astrophysics Data System (ADS)

    Soori, Umair; Yuen, Peter; Han, Ji Wen; Ibrahim, Izzati; Chen, Wentao; Hong, Kan; Merfort, Christian; James, David; Richardson, Mark

    2013-04-01

    People tracking in crowded scenes from closed-circuit television (CCTV) footage has been a popular and challenging task in computer vision. Due to the limited spatial resolution in the CCTV footage, the color of people's dress may offer an alternative feature for their recognition and tracking. However, there are many factors, such as variable illumination conditions, viewing angles, and camera calibration, that may induce illusive modification of intrinsic color signatures of the target. Our objective is to recognize and track targets in multiple camera views using color as the detection feature, and to understand if a color constancy (CC) approach may help to reduce these color illusions due to illumination and camera artifacts and thereby improve target recognition performance. We have tested a number of CC algorithms using various color descriptors to assess the efficiency of target recognition from a real multicamera Imagery Library for Intelligent Detection Systems (i-LIDS) data set. Various classifiers have been used for target detection, and the figure of merit to assess the efficiency of target recognition is achieved through the area under the receiver operating characteristics (AUROC). We have proposed two modifications of luminance-based CC algorithms: one with a color transfer mechanism and the other using a pixel-wise sigmoid function for an adaptive dynamic range compression, a method termed enhanced luminance reflectance CC (ELRCC). We found that both algorithms improve the efficiency of target recognitions substantially better than that of the raw data without CC treatment, and in some cases the ELRCC improves target tracking by over 100% within the AUROC assessment metric. The performance of the ELRCC has been assessed over 10 selected targets from three different camera views of the i-LIDS footage, and the averaged target recognition efficiency over all these targets is found to be improved by about 54% in AUROC after the data are processed by

  15. Inferring the Origin of Metastases from Cancer Phylogenies.

    PubMed

    Hong, Woo Suk; Shpak, Max; Townsend, Jeffrey P

    2015-10-01

    Determining the evolutionary history of metastases is a key problem in cancer biology. Several recent studies have presented inferences regarding the origin of metastases based on phylogenies of cancer lineages. Many of these studies have concluded that the observed monophyly of metastatic subclones favored metastasis-to-metastasis spread ("a metastatic cascade" rather than parallel metastases from the primary tumor). In this article, we argue that identifying a monophyletic clade of metastatic subclones does not provide sufficient evidence to unequivocally establish a history of metastatic cascades. In the absence of a complete phylogeny of the subclones within the primary tumor, a scenario of parallel metastatic events from the primary tumor is an equally plausible interpretation. Future phylogenetic studies on the origin of metastases should obtain a complete phylogeny of subclones within the primary tumor. This complete phylogeny may be obtainable by ultra-deep sequencing and phasing of large sections or by targeted sequencing of many small, spatially heterogeneous sections, followed by phylogenetic reconstruction using well-established molecular evolutionary models. In addition to resolving the evolutionary history of metastases, a complete phylogeny of subclones within the primary tumor facilitates the identification of driver mutations by application of phylogeny-based tests of natural selection. PMID:26260528

  16. The shape of mammalian phylogeny: patterns, processes and scales

    PubMed Central

    Purvis, Andy; Fritz, Susanne A.; Rodríguez, Jesús; Harvey, Paul H.; Grenyer, Richard

    2011-01-01

    Mammalian phylogeny is far too asymmetric for all contemporaneous lineages to have had equal chances of diversifying. We consider this asymmetry or imbalance from four perspectives. First, we infer a minimal set of ‘regime changes’—points at which net diversification rate has changed—identifying 15 significant radiations and 12 clades that may be ‘downshifts’. We next show that mammalian phylogeny is similar in shape to a large set of published phylogenies of other vertebrate, arthropod and plant groups, suggesting that many clades may diversify under a largely shared set of ‘rules’. Third, we simulate six simple macroevolutionary models, showing that those where speciation slows down as geographical or niche space is filled, produce more realistic phylogenies than do models involving key innovations. Lastly, an analysis of the spatial scaling of imbalance shows that the phylogeny of species within an assemblage, ecoregion or larger area always tends to be more unbalanced than expected from the phylogeny of species at the next more inclusive spatial scale. We conclude with a verbal model of mammalian macroevolution, which emphasizes the importance to diversification of accessing new regions of geographical or niche space. PMID:21807729

  17. Phylogeny of the Paracalanidae Giesbrecht, 1888 (Crustacea: Copepoda: Calanoida).

    PubMed

    Cornils, Astrid; Blanco-Bercial, Leocadio

    2013-12-01

    The Paracalanidae are ecologically-important marine planktonic copepods that occur in the epipelagic zone in temperate and tropical waters. They are often the dominant taxon - in terms of biomass and abundance - in continental shelf regions. As primary consumers, they form a vital link in the pelagic food web between primary producers and higher trophic levels. Despite the ecological importance of the taxon, evolutionary and systematic relationships within the family remain largely unknown. A multigene phylogeny including 24 species, including representatives for all seven genera, was determined based on two nuclear genes, small-subunit (18S) ribosomal RNA and Histone 3 (H3) and one mitochondrial gene, cytochrome c oxidase subunit I (COI). The molecular phylogeny was well supported by Maximum likelihood and Bayesian inference analysis; all genera were found to be monophyletic, except for Paracalanus, which was separated into two distinct clades: the Paracalanus aculeatus group and Paracalanus parvus group. The molecular phylogeny also confirmed previous findings that Mecynocera and Calocalanus are genera of the family Paracalanidae. For comparison, a morphological phylogeny was created for 35 paracalanid species based on 54 morphological characters derived from published descriptions. The morphological phylogeny did not resolve all genera as monophyletic and bootstrap support was not strong. Molecular and morphological phylogenies were not congruent in the positioning of Bestiolina and the Paracalanus species groups, possibly due to the lack of sufficient phylogenetically-informative morphological characters. PMID:23831457

  18. Conquest of the deep, old and cold: an exceptional limpet radiation in Lake Baikal.

    PubMed

    Stelbrink, Björn; Shirokaya, Alena A; Clewing, Catharina; Sitnikova, Tatiana Y; Prozorova, Larisa A; Albrecht, Christian

    2015-07-01

    Lake Baikal is the deepest, oldest and most speciose ancient lake in the world. The lake is characterized by high levels of molluscan species richness and endemicity, including the limpet family Acroloxidae with 25 endemic species. Members of this group generally inhabit the littoral zone, but have been recently found in the abyssal zone at hydrothermal vents and oil-seeps. Here, we use mitochondrial and nuclear data to provide a first molecular phylogeny of the Lake Baikal limpet radiation, and to date the beginning of intra-lacustrine diversification. Divergence time estimates suggest a considerably younger age for the species flock compared with lake age estimates, and the beginning of extensive diversification is possibly related to rapid deepening and cooling during rifting. Phylogenetic relationships and divergence time estimates do not clearly indicate when exactly the abyssal was colonized but suggest a timeframe coincident with the formation of the abyssal in the northern basin (Middle to Late Pleistocene). PMID:26202427

  19. Conquest of the deep, old and cold: an exceptional limpet radiation in Lake Baikal

    PubMed Central

    Stelbrink, Björn; Shirokaya, Alena A.; Clewing, Catharina; Sitnikova, Tatiana Y.; Prozorova, Larisa A.; Albrecht, Christian

    2015-01-01

    Lake Baikal is the deepest, oldest and most speciose ancient lake in the world. The lake is characterized by high levels of molluscan species richness and endemicity, including the limpet family Acroloxidae with 25 endemic species. Members of this group generally inhabit the littoral zone, but have been recently found in the abyssal zone at hydrothermal vents and oil-seeps. Here, we use mitochondrial and nuclear data to provide a first molecular phylogeny of the Lake Baikal limpet radiation, and to date the beginning of intra-lacustrine diversification. Divergence time estimates suggest a considerably younger age for the species flock compared with lake age estimates, and the beginning of extensive diversification is possibly related to rapid deepening and cooling during rifting. Phylogenetic relationships and divergence time estimates do not clearly indicate when exactly the abyssal was colonized but suggest a timeframe coincident with the formation of the abyssal in the northern basin (Middle to Late Pleistocene). PMID:26202427

  20. Visual discrimination of rotated 3D objects in Malawi cichlids (Pseudotropheus sp.): a first indication for form constancy in fishes.

    PubMed

    Schluessel, V; Kraniotakes, H; Bleckmann, H

    2014-03-01

    Fish move in a three-dimensional environment in which it is important to discriminate between stimuli varying in colour, size, and shape. It is also advantageous to be able to recognize the same structures or individuals when presented from different angles, such as back to front or front to side. This study assessed visual discrimination abilities of rotated three-dimensional objects in eight individuals of Pseudotropheus sp. using various plastic animal models. All models were displayed in two choice experiments. After successful training, fish were presented in a range of transfer tests with objects rotated in the same plane and in space by 45° and 90° to the side or to the front. In one experiment, models were additionally rotated by 180°, i.e., shown back to front. Fish showed quick associative learning and with only one exception successfully solved and finished all experimental tasks. These results provide first evidence for form constancy in this species and in fish in general. Furthermore, Pseudotropheus seemed to be able to categorize stimuli; a range of turtle and frog models were recognized independently of colour and minor shape variations. Form constancy and categorization abilities may be important for behaviours such as foraging, recognition of predators, and conspecifics as well as for orienting within habitats or territories. PMID:23982620

  1. Illuminant estimation for color constancy: why spatial-domain methods work and the role of the color distribution.

    PubMed

    Cheng, Dongliang; Prasad, Dilip K; Brown, Michael S

    2014-05-01

    Color constancy is a well-studied topic in color vision. Methods are generally categorized as (1) low-level statistical methods, (2) gamut-based methods, and (3) learning-based methods. In this work, we distinguish methods depending on whether they work directly from color values (i.e., color domain) or from values obtained from the image's spatial information (e.g., image gradients/frequencies). We show that spatial information does not provide any additional information that cannot be obtained directly from the color distribution and that the indirect aim of spatial-domain methods is to obtain large color differences for estimating the illumination direction. This finding allows us to develop a simple and efficient illumination estimation method that chooses bright and dark pixels using a projection distance in the color distribution and then applies principal component analysis to estimate the illumination direction. Our method gives state-of-the-art results on existing public color constancy datasets as well as on our newly collected dataset (NUS dataset) containing 1736 images from eight different high-end consumer cameras. PMID:24979637

  2. Biomass Size Spectra and Plankton Diversity in a Shallow Eutrophic Lake

    NASA Astrophysics Data System (ADS)

    Gaedke, Ursula; Seifried, Angelika; Adrian, Rita

    2004-01-01

    Biomass size spectra collate structural and functional attributes of plankton communities enabling standardised temporal and cross-system comparisons and may be rapidly obtained by automated particle counters. To examine how differences in plankton communities from highly eutrophic and more oligotrophic lakes are reflected in size spectra, a three-year time series of biomass size spectra was established for polymictic, eutrophic Lake Müggelsee, based on approximately weekly sampling and microscopic enumeration. The continuous but often bumpy size spectra reflected appropriately the seasonal and trophy-related variations in the plankton composition and growth conditions and the potential impact of daphnids on smaller plankton. We tested the hypothesis that more diverse plankton communities have smoother size spectra than impoverished ones. The spectra of Lake Müggelsee and other more or less eutrophic lakes covaried roughly with the functional diversity in total plankton composition but were unrelated to taxonomical diversity within the phyto- or mesozooplankton. The slopes of the normalised size spectra of Lake Müggelsee were generally more negative than -1, exhibited a recurrent seasonal pattern and were strongly correlated with crustacean biomass. In contrast to less eutrophic systems, slopes could not be used to quantify energy fluxes within the food web due to highly variable algal P/B ratios and frequently bumpy size distributions. The latter indicated stronger deviations from the ideal concept of a steady energy flow along the size gradient than found in e.g. large, mesotrophic Lake Constance. (

  3. Evolutionary History of Lake Tanganyika's Predatory Deepwater Cichlids

    PubMed Central

    Kirchberger, Paul C.; Sefc, Kristina M.; Sturmbauer, Christian; Koblmüller, Stephan

    2012-01-01

    Hybridization among littoral cichlid species in Lake Tanganyika was inferred in several molecular phylogenetic studies. The phenomenon is generally attributed to the lake level-induced shoreline and habitat changes. These allow for allopatric divergence of geographically fragmented populations alternating with locally restricted secondary contact and introgression between incompletely isolated taxa. In contrast, the deepwater habitat is characterized by weak geographic structure and a high potential for gene flow, which may explain the lower species richness of deepwater than littoral lineages. For the same reason, divergent deepwater lineages should have evolved strong intrinsic reproductive isolation already in the incipient stages of diversification, and, consequently, hybridization among established lineages should have been less frequent than in littoral lineages. We test this hypothesis in the endemic Lake Tanganyika deepwater cichlid tribe Bathybatini by comparing phylogenetic trees of Hemibates and Bathybates species obtained with nuclear multilocus AFLP data with a phylogeny based on mitochondrial sequences. Consistent with our hypothesis, largely congruent tree topologies and negative tests for introgression provided no evidence for introgressive hybridization between the deepwater taxa. Together, the nuclear and mitochondrial data established a well-supported phylogeny and suggested ecological segregation during speciation. PMID:22675652

  4. A Framework for Studying Emotions Across Phylogeny

    PubMed Central

    Anderson, David J.; Adolphs, Ralph

    2014-01-01

    Since the 19th century, there has been disagreement over the fundamental question of whether “emotions” are cause or consequence of their associated behaviors. This question of causation is most directly addressable in genetically tractable model organisms, including invertebrates such as Drosophila. Yet there is ongoing debate about whether such species even have “emotions,” since emotions are typically defined with reference to human behavior and neuroanatomy. Here we argue that emotional behaviors are a class of behaviors that express internal emotion states. These emotion states exhibit certain general functional and adaptive properties that apply across any specific human emotions like fear or anger, as well as across phylogeny. These general properties, which can be thought of as “emotion primitives”, can be modeled and studied in evolutionarily distant model organisms, allowing functional dissection of their mechanistic bases, and tests of their causal relationships to behavior. More generally, our approach aims not only at better integration of such studies in model organisms with studies of emotion in humans, but also suggests a revision of how emotion should be operationalized within psychology and psychiatry. PMID:24679535

  5. Bacterial phylogeny structures soil resistomes across habitats

    NASA Astrophysics Data System (ADS)

    Forsberg, Kevin J.; Patel, Sanket; Gibson, Molly K.; Lauber, Christian L.; Knight, Rob; Fierer, Noah; Dantas, Gautam

    2014-05-01

    Ancient and diverse antibiotic resistance genes (ARGs) have previously been identified from soil, including genes identical to those in human pathogens. Despite the apparent overlap between soil and clinical resistomes, factors influencing ARG composition in soil and their movement between genomes and habitats remain largely unknown. General metagenome functions often correlate with the underlying structure of bacterial communities. However, ARGs are proposed to be highly mobile, prompting speculation that resistomes may not correlate with phylogenetic signatures or ecological divisions. To investigate these relationships, we performed functional metagenomic selections for resistance to 18 antibiotics from 18 agricultural and grassland soils. The 2,895 ARGs we discovered were mostly new, and represent all major resistance mechanisms. We demonstrate that distinct soil types harbour distinct resistomes, and that the addition of nitrogen fertilizer strongly influenced soil ARG content. Resistome composition also correlated with microbial phylogenetic and taxonomic structure, both across and within soil types. Consistent with this strong correlation, mobility elements (genes responsible for horizontal gene transfer between bacteria such as transposases and integrases) syntenic with ARGs were rare in soil by comparison with sequenced pathogens, suggesting that ARGs may not transfer between soil bacteria as readily as is observed between human pathogens. Together, our results indicate that bacterial community composition is the primary determinant of soil ARG content, challenging previous hypotheses that horizontal gene transfer effectively decouples resistomes from phylogeny.

  6. A transcriptome approach to ecdysozoan phylogeny.

    PubMed

    Borner, Janus; Rehm, Peter; Schill, Ralph O; Ebersberger, Ingo; Burmester, Thorsten

    2014-11-01

    The monophyly of Ecdysozoa, which comprise molting phyla, has received strong support from several lines of evidence. However, the internal relationships of Ecdysozoa are still contended. We generated expressed sequence tags from a priapulid (penis worm), a kinorhynch (mud dragon), a tardigrade (water bear) and five chelicerate taxa by 454 transcriptome sequencing. A multigene alignment was assembled from 63 taxa, which comprised after matrix optimization 24,249 amino acid positions with high data density (2.6% gaps, 19.1% missing data). Phylogenetic analyses employing various models support the monophyly of Ecdysozoa. A clade combining Priapulida and Kinorhyncha (i.e. Scalidophora) was recovered as the earliest branch among Ecdysozoa. We conclude that Cycloneuralia, a taxon erected to combine Priapulida, Kinorhyncha and Nematoda (and others), are paraphyletic. Rather Arthropoda (including Onychophora) are allied with Nematoda and Tardigrada. Within Arthropoda, we found strong support for most clades, including monophyletic Mandibulata and Pancrustacea. The phylogeny within the Euchelicerata remained largely unresolved. There is conflicting evidence on the position of tardigrades: While Bayesian and maximum likelihood analyses of only slowly evolving genes recovered Tardigrada as a sister group to Arthropoda, analyses of the full data set, and of subsets containing genes evolving at fast and intermediate rates identified a clade of Tardigrada and Nematoda. Notably, the latter topology is also supported by the analyses of indel patterns. PMID:25124096

  7. Molecular epidemiology, phylogeny and evolution of Legionella.

    PubMed

    Khodr, A; Kay, E; Gomez-Valero, L; Ginevra, C; Doublet, P; Buchrieser, C; Jarraud, S

    2016-09-01

    Legionella are opportunistic pathogens that develop in aquatic environments where they multiply in protozoa. When infected aerosols reach the human respiratory tract they may accidentally infect the alveolar macrophages leading to a severe pneumonia called Legionnaires' disease (LD). The ability of Legionella to survive within host-cells is strictly dependent on the Dot/Icm Type 4 Secretion System that translocates a large repertoire of effectors into the host cell cytosol. Although Legionella is a large genus comprising nearly 60 species that are worldwide distributed, only about half of them have been involved in LD cases. Strikingly, the species Legionella pneumophila alone is responsible for 90% of all LD cases. The present review summarizes the molecular approaches that are used for L. pneumophila genotyping with a major focus on the contribution of whole genome sequencing (WGS) to the investigation of local L. pneumophila outbreaks and global epidemiology studies. We report the newest knowledge regarding the phylogeny and the evolution of Legionella and then focus on virulence evolution of those Legionella species that are known to have the capacity to infect humans. Finally, we discuss the evolutionary forces and adaptation mechanisms acting on the Dot/Icm system itself as well as the role of mobile genetic elements (MGE) encoding T4ASSs and of gene duplications in the evolution of Legionella and its adaptation to different hosts and lifestyles. PMID:27180896

  8. A retroposon analysis of Afrotherian phylogeny.

    PubMed

    Nishihara, Hidenori; Satta, Yoko; Nikaido, Masato; Thewissen, J G M; Stanhope, Michael J; Okada, Norihiro

    2005-09-01

    Recent comprehensive studies of DNA sequences support the monophyly of Afrotheria, comprising elephants, sirenians (dugongs and manatees), hyraxes, tenrecs, golden moles, aardvarks, and elephant shrews, as well as that of Paenungulata, comprising elephants, sirenians, and hyraxes. However, phylogenetic relationships among paenungulates, as well as among nonpaenungulates, have remained ambiguous. Here we applied an extensive retroposon analysis to these problems to support the monophyly of aardvarks, tenrecs, and golden moles, with elephant shrews as their sister group. Regarding phylogenetic relationships in Paenungulata, we could characterize only one informative locus, although we could isolate many insertions specific to each of three lineages, namely, Proboscidea, Sirenia, and Hyracoidea. These data prompted us to reexamine phylogenetic relationships among Paenungulata using 19 nuclear gene sequences resulting in three different analyses, namely, short interspersed element (SINE) insertions, nuclear sequence analyses, and morphological cladistics, supporting different respective phylogenies. We concluded that these three lineages diverged very rapidly in a very short evolutionary period, with the consequence that ancestral polymorphism present in the last common ancestor of Paenungulata results in such incongruence. Our results suggest the rapid fixation of many large-scale morphological synapomorphies for Tethytheria; implications of this in relation to the morphological evolution in Paenungulata are discussed. PMID:15930154

  9. Alu insertion loci and platyrrhine primate phylogeny.

    PubMed

    Ray, David A; Xing, Jinchuan; Hedges, Dale J; Hall, Michael A; Laborde, Meredith E; Anders, Bridget A; White, Brittany R; Stoilova, Nadica; Fowlkes, Justin D; Landry, Kate E; Chemnick, Leona G; Ryder, Oliver A; Batzer, Mark A

    2005-04-01

    Short INterspersed Elements (SINEs) make very useful phylogenetic markers because the integration of a particular element at a location in the genome is irreversible and of known polarity. These attributes make analysis of SINEs as phylogenetic characters an essentially homoplasy-free affair. Alu elements are primate-specific SINEs that make up a large portion of the human genome and are also widespread in other primates. Using a combination wet-bench and computational approach we recovered 190 Alu insertions, 183 of which are specific to the genomes of nine New World primates. We used these loci to investigate branching order and have produced a cladogram that supports a sister relationship between Atelidae (spider, woolly, and howler monkeys) and Cebidae (marmosets, tamarins, and owl monkeys) and then the joining of this two family clade to Pitheciidae (titi and saki monkeys). The data support these relationships with a homoplasy index of 0.00. In this study, we report one of the largest applications of SINE elements to phylogenetic analysis to date, and the results provide a robust molecular phylogeny for platyrrhine primates. PMID:15737586

  10. Primate jumping genes elucidate strepsirrhine phylogeny

    PubMed Central

    Roos, Christian; Schmitz, Jürgen; Zischler, Hans

    2004-01-01

    Transposable elements provide a highly informative marker system for analyzing evolutionary histories. To solve controversially discussed topics in strepsirrhine phylogeny, we characterized 61 loci containing short interspersed elements (SINEs) and determined the SINE presence–absence pattern at orthologous loci in a representative strepsirrhine panel. This SINE monolocus study was complemented by a Southern blot analysis tracing multiple loci of two different strepsirrhine specific SINEs. The results thereof were combined with phylogenetic trees reconstructed on the basis of complete mitochondrial cytochrome b sequences from all recognized strepsirrhine genera. Here we present evidence for (i) a sister group relationship of Malagasy Chiromyiformes and Lemuriformes, (ii) Lorisidae being a monophyletic sister clade to the Galagidae, and (iii) common ancestry of African and Asian lorisids. Based on these findings, we conclude that strepsirrhines originated in Africa and that Madagascar and Asia were colonized by respective single immigration events. In agreement with paleocontinental data, the molecular analyses suggest a crossing of the Mozambique channel by rafting between the late Cretaceous and the middle Eocene, whereas Asia was most likely colonized between the early Eocene and the middle Oligocene on a continental route. Furthermore, one SINE integration links the two Lemuriformes families, Lemuridae and Indriidae, indicating a common origin of diurnality or cathemerality and a later reversal to nocturnality by the indriid genus Avahi. PMID:15249661

  11. Dobrava-Belgrade virus: phylogeny, epidemiology, disease.

    PubMed

    Papa, Anna

    2012-08-01

    Dobrava-Belgrade virus (DOBV) is an Old World hantavirus that causes hemorrhagic fever with renal syndrome in humans. With a case fatality rate up to 12%, DOBV infection is the most life-threatening hantavirus disease in Europe. The virus was initially identified in the Balkans, but the discovery of new endemic foci have expanded its recognized geographic range. The recent description of novel genetic variants with different degrees of pathogenicity have complicated its taxonomic analysis. The original rodent host of DOBV is Apodemus flavicollis, however additional Apodemus species, such Apodemus agrarius and Apodemus ponticus, have been found to serve as hosts of the various DOBV genotypes. The complex evolution and genetic diversity of the virus are still under investigation. The present review aims to provide an update on the phylogeny of DOBV and the epidemiology of infection in rodents and humans; to describe the clinical characteristics of the disease; to present current knowledge about laboratory diagnosis, treatment and prevention; discuss the current state of the art in antiviral drug and vaccine development. PMID:22659378

  12. Molecular phylogeny of euthyneura (mollusca: gastropoda).

    PubMed

    Grande, Cristina; Templado, José; Cervera, J Lucas; Zardoya, Rafael

    2004-02-01

    A new phylogenetic hypothesis for Euthyneura is proposed based on the analysis of primary sequence data (mitochondrial cox1, trnV, rrnL, trnL(cun), trnA, trnP, nad6, and nad5 genes) and the phylogenetic utility of two rare genomic changes (the relative position of the mitochondrial trnP gene, and an insertion/deletion event in a conserved region of the mitochondrial Cox1 protein) is addressed. Both sources of phylogenetic information clearly rejected the monophyly of pulmonates, a group of gastropods well supported so far by morphological evidence. The marine basommatophoran pulmonate Siphonaria was placed within opisthobranchs and shared with them the insertion of a Glycine in the Cox 1 protein. The marine systellommatophoran pulmonate Onchidella was recovered at the base of the opisthobranch + Siphonaria clade. Opisthobranchs, Siphonaria, and Onchidella shared the relative position of the mitochondrial trnP gene between the mitochondrial trnA and nad6 genes. The land snails and slugs (stylommatophoran pulmonates) were recovered as an early split in the phylogeny of advanced gastropods. The monophyly of the Euthyneura (Opisthobranchia + Pulmonata) was rejected by the inclusion of the heterostrophan Pyramidella. PMID:14660702

  13. Molecular phylogeny of Triatomini (Hemiptera: Reduviidae: Triatominae)

    PubMed Central

    2014-01-01

    Background The Triatomini and Rhodniini (Hemiptera: Reduviidae) tribes include the most diverse Chagas disease vectors; however, the phylogenetic relationships within the tribes remain obscure. This study provides the most comprehensive phylogeny of Triatomini reported to date. Methods The relationships between all of the Triatomini genera and representatives of the three Rhodniini species groups were examined in a novel molecular phylogenetic analysis based on the following six molecular markers: the mitochondrial 16S; Cytochrome Oxidase I and II (COI and COII) and Cytochrome B (Cyt B); and the nuclear 18S and 28S. Results Our results show that the Rhodnius prolixus and R. pictipes groups are more closely related to each other than to the R. pallescens group. For Triatomini, we demonstrate that the large complexes within the paraphyletic Triatoma genus are closely associated with their geographical distribution. Additionally, we observe that the divergence within the spinolai and flavida complex clades are higher than in the other Triatoma complexes. Conclusions We propose that the spinolai and flavida complexes should be ranked under the genera Mepraia and Nesotriatoma. Finally, we conclude that a thorough morphological investigation of the paraphyletic genera Triatoma and Panstrongylus is required to accurately assign queries to natural genera. PMID:24685273

  14. Phylogeny of the Highly Divergent Echinosteliales (Amoebozoa).

    PubMed

    Kretzschmar, Martin; Kuhnt, Andreas; Bonkowski, Michael; Fiore-Donno, Anna Maria

    2016-07-01

    Myxomycetes or plasmodial slime molds are widespread and very common soil amoebae with the ability to form macroscopic fruiting bodies. Even if their phylogenetic position as a monophyletic group in Amoebozoa is well established, their internal relationships are still not entirely resolved. At the base of the most intensively studied dark-spored clade lies the order Echinosteliales, whose highly divergent small subunit ribosomal (18S) RNA genes represent a challenge for phylogenetic reconstructions. This is because they are characterized by unusually long variable helices of unknown secondary structure and a high inter- and infraspecific divergence. Current classification recognizes two families: the monogeneric Echinosteliaceae and the Clastodermataceae with the genera Barbeyella and Clastoderma. To better resolve the phylogeny of the Echinosteliales, we obtained three new small subunit ribosomal (18S) RNA gene sequences of Clastoderma and Echinostelium corynophorum. Our phylogenetic analyses suggested the polyphyly of the family Clastodermataceae, as Barbeyella was more closely related to Echinostelium arboreum than to Clastoderma, while Clastoderma debaryanum was the earliest branching clade in Echinosteliales. We also found that E. corynophorum was the closest relative of the enigmatic Semimorula liquescens, a stalkless-modified Echinosteliales. We discuss possible evolutionary pathways in dark-spored Myxomycetes and propose a taxonomic update. PMID:26663217

  15. Phylogeny of the gudgeons (Teleostei: Cyprinidae: Gobioninae).

    PubMed

    Tang, Kevin L; Agnew, Mary K; Chen, Wei-Jen; Vincent Hirt, M; Raley, Morgan E; Sado, Tetsuya; Schneider, Leah M; Yang, Lei; Bart, Henry L; He, Shunping; Liu, Huanzhang; Miya, Masaki; Saitoh, Kenji; Simons, Andrew M; Wood, Robert M; Mayden, Richard L

    2011-10-01

    The members of the cyprinid subfamily Gobioninae, commonly called gudgeons, form one of the most well-established assemblages in the family Cyprinidae. The subfamily is a species-rich group of fishes, these fishes display diverse life histories, appearances, and behavior. The phylogenetic relationships of Gobioninae are examined using sequence data from four loci: cytochrome b, cytochrome c oxidase I, opsin, and recombination activating gene 1. This investigation produced a data matrix of 4114 bp for 162 taxa that was analyzed using parsimony, maximum likelihood, and Bayesian inference methods. The phylogenies our analyses recovered corroborate recent studies on the group. The subfamily Gobioninae is monophyletic and composed of three major lineages. We find evidence for a Hemibarbus-Squalidus group, and the tribes Gobionini and Sarcocheilichthyini, with the Hemibarbus-Squalidus group sister to a clade of Gobionini-Sarcocheilichthyini. The Hemibarbus-Squalidus group includes those two genera; the tribe Sarcocheilichthyini includes Coreius, Coreoleuciscus, Gnathopogon, Gobiocypris, Ladislavia, Paracanthobrama, Pseudorasbora, Pseudopungtungia, Pungtungia, Rhinogobio, and Sarcocheilichthys; the tribe Gobionini includes Abbottina, Biwia, Gobio, Gobiobotia, Huigobio, Microphysogobio, Platysmacheilus, Pseudogobio, Romanogobio, Saurogobio, and Xenophysogobio. The monotypic Acanthogobio is placed into the synonymy of Gobio. We tentatively assign Belligobio to the Hemibarbus-Squalidus group and Mesogobio to Gobionini; Paraleucogobio and Parasqualidus remain incertae sedis. Based on the topologies presented, the evolution of swim bladder specializations, a distinctive feature among cyprinids, has occurred more than once within the subfamily. PMID:21672635

  16. Dating Phylogenies with Hybrid Local Molecular Clocks

    PubMed Central

    Aris-Brosou, Stéphane

    2007-01-01

    Background Because rates of evolution and species divergence times cannot be estimated directly from molecular data, all current dating methods require that specific assumptions be made before inferring any divergence time. These assumptions typically bear either on rates of molecular evolution (molecular clock hypothesis, local clocks models) or on both rates and times (penalized likelihood, Bayesian methods). However, most of these assumptions can affect estimated dates, oftentimes because they underestimate large amounts of rate change. Principal Findings A significant modification to a recently proposed ad hoc rate-smoothing algorithm is described, in which local molecular clocks are automatically placed on a phylogeny. This modification makes use of hybrid approaches that borrow from recent theoretical developments in microarray data analysis. An ad hoc integration of phylogenetic uncertainty under these local clock models is also described. The performance and accuracy of the new methods are evaluated by reanalyzing three published data sets. Conclusions It is shown that the new maximum likelihood hybrid methods can perform better than penalized likelihood and almost as well as uncorrelated Bayesian models. However, the new methods still tend to underestimate the actual amount of rate change. This work demonstrates the difficulty of estimating divergence times using local molecular clocks. PMID:17849008

  17. Migration of 137Cs in tributaries, lake water and sediment of Lago Maggiore (Italy, Switzerland) - analysis and comparison with Lago di Lugano and other lakes.

    PubMed

    Putyrskaya, Victoria; Klemt, Eckehard; Röllin, Stefan

    2009-01-01

    This paper describes the behaviour of 137Cs in Lago Maggiore and other pre-alpine lakes as a consequence of atmospheric nuclear weapons testing fallout and the fallout from the nuclear accident in Chernobyl. It presents data on the 137Cs distribution in tributaries, lake water, bottom sediments and reveals the role of (137)Cs as a marker of the sedimentation processes. The run-off of 137Cs from the watershed to the lake is described with a simple compartment model. Measurements of the activity concentration of (137)Cs in sediments are compared with the output of a model (diffusion-convection type) which describes the input of 137Cs into and its vertical distribution within the sediment. Varying sedimentation rates (0.05-0.90g(cm2y)(-1)) in Lago Maggiore are compared with data of other authors. Sedimentation rates and total distribution coefficients (of about 10(5) Lkg(-1)) in Lago Maggiore are discussed and compared with those of Lago di Lugano, Lake Constance, and Lake Vorsee. PMID:19019505

  18. Phylogeny of Cirsium spp. in North America: Host Specificity Does Not Follow Phylogeny

    PubMed Central

    Slotta, Tracey A. Bodo; Horvath, David P.; Foley, Michael E.

    2012-01-01

    Weedy invasive Cirsium spp. are widespread in temperate regions of North America and some of their biological control agents have attacked native Cirsium spp. A phylogenetic tree was developed from DNA sequences for the internal transcribed spacer and external transcribed spacer regions from native and non-native Great Plains Cirsium spp. and other thistles to determine if host specificity follows phylogeny. The monophyly of Cirsium spp. and Carduus within the tribe Cardinae was confirmed with native North American and European lineages of the Cirsium spp. examined. We did not detect interspecific hybridization between the introduced invasive and the native North American Cirsium spp. Selected host-biological control agent interactions were mapped onto the phylogenic tree derived by maximum likelihood analysis to examine the co-occurrence of known hosts with biological control agents. Within Cirsium-Cardueae, the insect biological control agents do not associate with host phylogenetic lines. Thus, more comprehensive testing of species in host-specificity trials, rather than relying on a single representative of a given clade may be necessary; because the assumption that host-specificity follows phylogeny does not necessarily hold. Since the assumption does not always hold, it will also be important to evaluate ecological factors to provide better cues for host specificity. PMID:27137640

  19. Investigation of Color Constancy in 4.5-Month-Old Infants under a Strict Control of Luminance Contrast for Individual Participants

    ERIC Educational Resources Information Center

    Yang, Jiale; Kanazawa, So; Yamaguchi, Masami K.; Kuriki, Ichiro

    2013-01-01

    The current study examined color constancy in infants using a familiarization paradigm. We first obtained isoluminance in each infant as defined by the minimum motion paradigm and used these data to control the luminance of stimuli in the main experiments. In the familiarization phase of the main experiment, two identical smiling face patterns…

  20. Interracial Contact and Racial Constancy: A Multi-Site Study of Racial Intergroup Bias in 3-5 Year Old Anglo-British Children

    ERIC Educational Resources Information Center

    Rutland, Adam; Cameron, Lindsey; Bennett, Laura; Ferrell, Jennifer

    2005-01-01

    This paper examined the influence of interracial contact and racial constancy on the racial intergroup bias of young Anglo-British children. This multi-site study was conducted in areas of Great Britain that varied in terms of racial diversity. The study also investigated whether preschool children express bias on positive, but not negative,…

  1. On simulated annealing phase transitions in phylogeny reconstruction.

    PubMed

    Strobl, Maximilian A R; Barker, Daniel

    2016-08-01

    Phylogeny reconstruction with global criteria is NP-complete or NP-hard, hence in general requires a heuristic search. We investigate the powerful, physically inspired, general-purpose heuristic simulated annealing, applied to phylogeny reconstruction. Simulated annealing mimics the physical process of annealing, where a liquid is gently cooled to form a crystal. During the search, periods of elevated specific heat occur, analogous to physical phase transitions. These simulated annealing phase transitions play a crucial role in the outcome of the search. Nevertheless, they have received comparably little attention, for phylogeny or other optimisation problems. We analyse simulated annealing phase transitions during searches for the optimal phylogenetic tree for 34 real-world multiple alignments. In the same way in which melting temperatures differ between materials, we observe distinct specific heat profiles for each input file. We propose this reflects differences in the search landscape and can serve as a measure for problem difficulty and for suitability of the algorithm's parameters. We discuss application in algorithmic optimisation and as a diagnostic to assess parameterisation before computationally costly, large phylogeny reconstructions are launched. Whilst the focus here lies on phylogeny reconstruction under maximum parsimony, it is plausible that our results are more widely applicable to optimisation procedures in science and industry. PMID:27150349

  2. Phylogeny of Porphyromonas gingivalis by Ribosomal Intergenic Spacer Region Analysis

    PubMed Central

    Rumpf, Robert W.; Griffen, Ann L.; Leys, Eugene J.

    2000-01-01

    Periodontitis has been associated with the presence of Porphyromonas gingivalis, and previous studies have shown phenotypic differences in the pathogenicities of strains of P. gingivalis. An accurate and comprehensive phylogeny of strains of P. gingivalis would be useful in determining if there is an evolutionary basis to pathogenicity in this species. Previous phylogenies of P. gingivalis strains based on random amplified polymorphic DNA (RAPD) analysis and multilocus enzyme electrophoresis (MLEE) show little agreement. While the 16S ribosomal gene is the standard for phylogenetic reconstruction among bacterial species, it is insufficiently variable for this purpose. In the present study, the phylogeny of P. gingivalis was constructed on the basis of the sequence of the most variable region of the ribosomal operon, the intergenic spacer region (ISR). Heteroduplex analysis of the ISR has been used to study the variability of P. gingivalis strains in periodontitis. In the present study, typing by heteroduplex analysis was compared to ISR sequence-based phylogeny and close agreement was observed. The two strains of P. gingivalis whose heteroduplex types are strongly associated with periodontitis were found to be closely related and were well separated from strains whose heteroduplex types are less strongly associated with disease, suggesting a relationship between pathogenicity and phylogeny. PMID:10790104

  3. Partitioning the Relative Importance of Phylogeny and Environmental Conditions on Phytoplankton Fatty Acids.

    PubMed

    Galloway, Aaron W E; Winder, Monika

    2015-01-01

    Essential fatty acids (EFA), which are primarily generated by phytoplankton, limit growth and reproduction in diverse heterotrophs. The biochemical composition of phytoplankton is well-known to be governed both by phylogeny and environmental conditions. Nutrients, light, salinity, and temperature all affect both phytoplankton growth and fatty acid composition. However, the relative importance of taxonomy and environment on algal fatty acid content has yet to be comparatively quantified, thus inhibiting predictions of changes to phytoplankton food quality in response to global environmental change. We compiled 1145 published marine and freshwater phytoplankton fatty acid profiles, consisting of 208 species from six major taxonomic groups, cultured in a wide range of environmental conditions, and used a multivariate distance-based linear model to quantify the total variation explained by each variable. Our results show that taxonomic group accounts for 3-4 times more variation in phytoplankton fatty acids than the most important growth condition variables. The results underscore that environmental conditions clearly affect phytoplankton fatty acid profiles, but also show that conditions account for relatively low variation compared to phylogeny. This suggests that the underlying mechanism determining basal food quality in aquatic habitats is primarily phytoplankton community composition, and allows for prediction of environmental-scale EFA dynamics based on phytoplankton community data. We used the compiled dataset to calculate seasonal dynamics of long-chain EFA (LCEFA; ≥C20 ɷ-3 and ɷ-6 polyunsaturated fatty acid) concentrations and ɷ-3:ɷ-6 EFA ratios in Lake Washington using a multi-decadal phytoplankton community time series. These analyses quantify temporal dynamics of algal-derived LCEFA and food quality in a freshwater ecosystem that has undergone large community changes as a result of shifting resource management practices, highlighting diatoms

  4. Partitioning the Relative Importance of Phylogeny and Environmental Conditions on Phytoplankton Fatty Acids

    PubMed Central

    Galloway, Aaron W. E.; Winder, Monika

    2015-01-01

    Essential fatty acids (EFA), which are primarily generated by phytoplankton, limit growth and reproduction in diverse heterotrophs. The biochemical composition of phytoplankton is well-known to be governed both by phylogeny and environmental conditions. Nutrients, light, salinity, and temperature all affect both phytoplankton growth and fatty acid composition. However, the relative importance of taxonomy and environment on algal fatty acid content has yet to be comparatively quantified, thus inhibiting predictions of changes to phytoplankton food quality in response to global environmental change. We compiled 1145 published marine and freshwater phytoplankton fatty acid profiles, consisting of 208 species from six major taxonomic groups, cultured in a wide range of environmental conditions, and used a multivariate distance-based linear model to quantify the total variation explained by each variable. Our results show that taxonomic group accounts for 3-4 times more variation in phytoplankton fatty acids than the most important growth condition variables. The results underscore that environmental conditions clearly affect phytoplankton fatty acid profiles, but also show that conditions account for relatively low variation compared to phylogeny. This suggests that the underlying mechanism determining basal food quality in aquatic habitats is primarily phytoplankton community composition, and allows for prediction of environmental-scale EFA dynamics based on phytoplankton community data. We used the compiled dataset to calculate seasonal dynamics of long-chain EFA (LCEFA; ≥C20 ɷ-3 and ɷ-6 polyunsaturated fatty acid) concentrations and ɷ-3:ɷ-6 EFA ratios in Lake Washington using a multi-decadal phytoplankton community time series. These analyses quantify temporal dynamics of algal-derived LCEFA and food quality in a freshwater ecosystem that has undergone large community changes as a result of shifting resource management practices, highlighting diatoms

  5. Local to regional scale industrial heavy metal pollution recorded in sediments of large freshwater lakes in central Europe (lakes Geneva and Lucerne) over the last centuries.

    PubMed

    Thevenon, Florian; Graham, Neil D; Chiaradia, Massimo; Arpagaus, Philippe; Wildi, Walter; Poté, John

    2011-12-15

    This research first focuses on the spatial and temporal patterns of heavy metals from contrasting environments (highly polluted to deepwater sites) of Lake Geneva. The mercury (Hg) and lead (Pb) records from two deepwater sites show that the heavy metal variations before the industrial period are primarily linked to natural weathering input of trace elements. By opposition, the discharge of industrial treated wastewaters into Vidy Bay of Lake Geneva during the second part of the 20th century, involved the sedimentation of highly metal-contaminated sediments in the area surrounding the WWTP outlet pipe discharge. Eventually, a new Pb isotope record of sediments from Lake Lucerne identifies the long-term increasing anthropogenic lead pollution after ca. 1500, probably due to the development of metallurgical activities during the High Middle Ages. These data furthermore allows to compare the recent anthropogenic sources of water pollution from three of the largest freshwater lakes of Western Europe (lakes Geneva, Lucerne, and Constance). High increases in Pb and Hg highlight the regional impact of industrial pollution after ca. 1750-1850, and the decrease of metal pollution in the 1980s due to the effects of remediation strategies such as the implementation of wastewater treatment plants (WWTPs). However, at all the studied sites, the recent metal concentrations remain higher than pre-industrial levels. Moreover, the local scale pollution data reveal two highly contaminated sites (>100 μg Pb/g dry weight sediment) by industrial activities, during the late-19th and early-20th centuries (Lake Lucerne) and during the second part of the 20th century (Vidy Bay of Lake Geneva). Overall, the regional scale pollution history inferred from the three large and deep perialpine lakes points out at the pollution of water systems by heavy metals during the last two centuries due to the discharge of industrial effluents. PMID:22047737

  6. Cosmic ray exposure ages of iron meteorites, complex irradiation and the constancy of cosmic ray flux in the past

    NASA Technical Reports Server (NTRS)

    Marti, K.; Lavielle, B.; Regnier, S.

    1984-01-01

    While previous calculations of potassium ages assumed a constant cosmic ray flux and a single stage (no change in size) exposure of iron meteorites, present calculations relaxed these constancy assumptions and the results reveal multistage irradiations for some 25% of the meteorites studied, implying multiple breakup in space. The distribution of exposure ages suggests several major collisions (based on chemical composition and structure), although the calibration of age scales is not yet complete. It is concluded that shielding-corrected (corrections which depend on size and position of sample) production rates are consistent for the age bracket of 300 to 900 years. These production rates differ in a systematic way from those calculated for present day fluxes of cosmic rays (such as obtained for the last few million years).

  7. [Summary of phylogeny in family Felidae of Carnivora].

    PubMed

    Wang, Jin-Feng; Zhang, Ya-Ping; Yu, Li

    2012-11-01

    Felidae (cats) is one of the strict carnivorous groups in the order Carnivora, many of which are most familiar and spectacular to us. They are the top predators in the world. Thirty-six of 37 living cat species are considered as either "endangered" or "threatened". The relationships among species of the family Felidae, which evolved recently and rapidly, are difficult to resolve, and have been the subject of debate. Construction of a reliable Felidae phylogeny will be of evolutionarily significance and conservation value. In this paper, we summarized phylogeny of Felidae, including cytological, morphological and molecular evidence, and pointed out the existing phylogenetic problems. This review is expected to guide future researches of Felidae phylogeny, and to lay a theoretic foundation for the protection of this animal group. PMID:23208134

  8. Diversity dynamics: molecular phylogenies need the fossil record.

    PubMed

    Quental, Tiago B; Marshall, Charles R

    2010-08-01

    Over the last two decades, new tools in the analysis of molecular phylogenies have enabled study of the diversification dynamics of living clades in the absence of information about extinct lineages. However, computer simulations and the fossil record show that the inability to access extinct lineages severely limits the inferences that can be drawn from molecular phylogenies. It appears that molecular phylogenies can tell us only when there have been changes in diversification rates, but are blind to the true diversity trajectories and rates of origination and extinction that have led to the species that are alive today. We need to embrace the fossil record if we want to fully understand the diversity dynamics of the living biota. PMID:20646780

  9. Molecular phylogeny and a taxonomic proposal for the genus Streptococcus.

    PubMed

    Póntigo, F; Moraga, M; Flores, S V

    2015-01-01

    Alternative phylogenies for the genus Streptococcus have been proposed due to uncertainty about the among-species group relationships. Here, we performed a phylogenetic analysis of the genus Streptococcus, considering all the species groups and also the genomic data accumulated by other studies. Seventy-five species were subjected to a Bayesian phylogenetic analysis using sequences from eight genes (16S rRNA, rpoB, sodA, tuf, rnpB, gyrB, dnaJ, and recN). On the basis of our results, we propose a new Phylogeny for the genus, with special emphasis on the inter-species group level. This new phylogeny differs from those suggested previously. From topological and evolutionary distance criteria, we propose that gordonii, pluranimalium, and sobrinus should be considered as new species groups, in addition to the currently recognized groups of mutans, bovis, pyogenic, suis, mitis, and salivarius. PMID:26400318

  10. Ontogeny tends to recapitulate phylogeny in digital organisms.

    PubMed

    Clune, Jeff; Pennock, Robert T; Ofria, Charles; Lenski, Richard E

    2012-09-01

    Biologists have long debated whether ontogeny recapitulates phylogeny and, if so, why. Two plausible explanations are that (i) changes to early developmental stages are selected against because they tend to disrupt later development and (ii) simpler structures often precede more complex ones in both ontogeny and phylogeny if the former serve as building blocks for the latter. It is difficult to test these hypotheses experimentally in natural systems, so we used a computational system that exhibits evolutionary dynamics. We observed that ontogeny does indeed recapitulate phylogeny; traits that arose earlier in a lineage's history also tended to be expressed earlier in the development of individuals. The relative complexity of traits contributed substantially to this correlation, but a significant tendency toward recapitulation remained even after accounting for trait complexity. This additional effect provides evidence that selection against developmental disruption also contributed to the conservation of early stages in development. PMID:22854085