Optical transitions in highly charged californium ions with high sensitivity to variation of the fine-structure constant.

PubMed

Berengut, J C; Dzuba, V A; Flambaum, V V; Ong, A

2012-08-17

We study electronic transitions in highly charged Cf ions that are within the frequency range of optical lasers and have very high sensitivity to potential variations in the fine-structure constant, α. The transitions are in the optical range despite the large ionization energies because they lie on the level crossing of the 5f and 6p valence orbitals in the thallium isoelectronic sequence. Cf(16+) is a particularly rich ion, having several narrow lines with properties that minimize certain systematic effects. Cf(16+) has very large nuclear charge and large ionization energy, resulting in the largest α sensitivity seen in atomic systems. The lines include positive and negative shifters.

Replica exchange molecular dynamics simulation of structure variation from α/4β-fold to 3α-fold protein.

PubMed

Lazim, Raudah; Mei, Ye; Zhang, Dawei

2012-03-01

Replica exchange molecular dynamics (REMD) simulation provides an efficient conformational sampling tool for the study of protein folding. In this study, we explore the mechanism directing the structure variation from α/4β-fold protein to 3α-fold protein after mutation by conducting REMD simulation on 42 replicas with temperatures ranging from 270 K to 710 K. The simulation began from a protein possessing the primary structure of GA88 but the tertiary structure of GB88, two G proteins with "high sequence identity." Albeit the large Cα-root mean square deviation (RMSD) of the folded protein (4.34 Å at 270 K and 4.75 Å at 304 K), a variation in tertiary structure was observed. Together with the analysis of secondary structure assignment, cluster analysis and principal component, it provides insights to the folding and unfolding pathway of 3α-fold protein and α/4β-fold protein respectively paving the way toward the understanding of the ongoings during conformational variation.

Observed large-scale structures and diabatic heating and drying profiles during TWP-ICE

DOE PAGES

Xie, Shaocheng; Hume, Timothy; Jakob, Christian; ...

2010-01-01

This study documents the characteristics of the large-scale structures and diabatic heating and drying profiles observed during the Tropical Warm Pool–International Cloud Experiment (TWP-ICE), which was conducted in January–February 2006 in Darwin during the northern Australian monsoon season. The examined profiles exhibit significant variations between four distinct synoptic regimes that were observed during the experiment. The active monsoon period is characterized by strong upward motion and large advective cooling and moistening throughout the entire troposphere, while the suppressed and clear periods are dominated by moderate midlevel subsidence and significant low- to midlevel drying through horizontal advection. The midlevel subsidence andmore » horizontal dry advection are largely responsible for the dry midtroposphere observed during the suppressed period and limit the growth of clouds to low levels. During the break period, upward motion and advective cooling and moistening located primarily at midlevels dominate together with weak advective warming and drying (mainly from horizontal advection) at low levels. The variations of the diabatic heating and drying profiles with the different regimes are closely associated with differences in the large-scale structures, cloud types, and rainfall rates between the regimes. Strong diabatic heating and drying are seen throughout the troposphere during the active monsoon period while they are moderate and only occur above 700 hPa during the break period. The diabatic heating and drying tend to have their maxima at low levels during the suppressed periods. Furthermore, the diurnal variations of these structures between monsoon systems, continental/coastal, and tropical inland-initiated convective systems are also examined.« less

Parameter identification of civil engineering structures

NASA Technical Reports Server (NTRS)

Juang, J. N.; Sun, C. T.

1980-01-01

This paper concerns the development of an identification method required in determining structural parameter variations for systems subjected to an extended exposure to the environment. The concept of structural identifiability of a large scale structural system in the absence of damping is presented. Three criteria are established indicating that a large number of system parameters (the coefficient parameters of the differential equations) can be identified by a few actuators and sensors. An eight-bay-fifteen-story frame structure is used as example. A simple model is employed for analyzing the dynamic response of the frame structure.

Matching OPC and masks on 300-mm lithography tools utilizing variable illumination settings

NASA Astrophysics Data System (ADS)

Palitzsch, Katrin; Kubis, Michael; Schroeder, Uwe P.; Schumacher, Karl; Frangen, Andreas

2004-05-01

CD control is crucial to maximize product yields on 300mm wafers. This is particularly true for DRAM frontend lithography layers, like gate level, and deep trench (capacitor) level. In the DRAM process, large areas of the chip are taken up by array structures, which are difficult to structure due to aggressive pitch requirements. Consequently, the lithography process is centered such that the array structures are printed on target. Optical proximity correction is applied to print gate level structures in the periphery circuitry on target. Only slight differences of the different Zernike terms can cause rather large variations of the proximity curves, resulting in a difference of isolated and semi-isolated lines printed on different tools. If the deviations are too large, tool specific OPC is needed. The same is true for deep trench level, where the length to width ratio of elongated contact-like structures is an important parameter to adjust the electrical properties of the chip. Again, masks with specific biases for tools with different Zernikes are needed to optimize product yield. Additionally, mask making contributes to the CD variation of the process. Theoretically, the CD deviation caused by an off-centered mask process can easily eat up the majority of the CD budget of a lithography process. In practice, masks are very often distributed intelligently among production tools, such that lens and mask effects cancel each other. However, only dose adjusting and mask allocation may still result in a high CD variation with large systematical contributions. By adjusting the illumination settings, we have successfully implemented a method to reduce CD variation on our advanced processes. Especially inner and outer sigma for annular illumination, and the numerical aperture, can be optimized to match mask and stepper properties. This process will be shown to overcome slight lens and mask differences effectively. The effects on lithography process windows have to be considered, nonetheless.

Influence of Hybrid Perovskite Fabrication Methods on Film Formation, Electronic Structure, and Solar Cell Performance

PubMed Central

Schnier, Tobias; Emara, Jennifer; Olthof, Selina; Meerholz, Klaus

2017-01-01

Hybrid organic/inorganic halide perovskites have lately been a topic of great interest in the field of solar cell applications, with the potential to achieve device efficiencies exceeding other thin film device technologies. Yet, large variations in device efficiency and basic physical properties are reported. This is due to unintentional variations during film processing, which have not been sufficiently investigated so far. We therefore conducted an extensive study of the morphology and electronic structure of a large number of CH3NH3PbI3 perovskite where we show how the preparation method as well as the mixing ratio of educts methylammonium iodide and lead(II) iodide impact properties like film formation, crystal structure, density of states, energy levels, and ultimately the solar cell performance. PMID:28287555

Climate and Edaphic Controls on Humid Tropical Forest Tree Height

NASA Astrophysics Data System (ADS)

Yang, Y.; Saatchi, S. S.; Xu, L.

2014-12-01

Uncertainty in the magnitude and spatial variations of forest carbon density in tropical regions is due to under sampling of forest structure from inventory plots and the lack of regional allometry to estimate the carbon density from structure. Here we quantify the variation of tropical forest structure by using more than 2.5 million measurements of canopy height from systematic sampling of Geoscience Laser Altimeter System (GLAS) satellite observations between 2004 to 2008 and examine the climate and edaphic variables influencing the variations. We used top canopy height of GLAS footprints (~ 0.25 ha) to grid the statistical mean and 90 percentile of samples at 0.5 degrees to capture the regional variability of large trees in tropics. GLAS heights were also aggregated based on a stratification of tropical regions using soil, elevation, and forest types. Both approaches provided consistent patterns of statistically dominant large trees and the least heterogeneity, both as strong drivers of distribution of high biomass forests. Statistical models accounting for spatial autocorrelation suggest that climate, soil and spatial features together can explain more than 60% of the variations in observed tree height information, while climate-only variables explains about one third of the first-order changes in tree height. Soil basics, including physical compositions such as clay and sand contents, chemical properties such as PH values and cation-exchange capacity, as well as biological variables such as organic matters, all present independent but statistically significant relationships to tree height variations. The results confirm other landscape and regional studies that soil fertility, geology and climate may jointly control a majority of the regional variations of forest structure in pan-tropics and influencing both biomass stocks and dynamics. Consequently, other factors such as biotic and disturbance regimes, not included in this study, may have less influence on regional variations but strongly mediate landscape and small-scale forest structure and dynamics.

Large Scale Ionospheric Response During March 17, 2013 Geomagnetic Storm: Reanalysis Based on Multiple Satellites Observations and TIEGCM Simulations

NASA Astrophysics Data System (ADS)

Yue, X.; Wang, W.; Schreiner, W. S.; Kuo, Y. H.; Lei, J.; Liu, J.; Burns, A. G.; Zhang, Y.; Zhang, S.

2015-12-01

Based on slant total electron content (TEC) observations made by ~10 satellites and ~450 ground IGS GNSS stations, we constructed a 4-D ionospheric electron density reanalysis during the March 17, 2013 geomagnetic storm. Four main large-scale ionospheric disturbances are identified from reanalysis: (1) The positive storm during the initial phase; (2) The SED (storm enhanced density) structure in both northern and southern hemisphere; (3) The large positive storm in main phase; (4) The significant negative storm in middle and low latitude during recovery phase. We then run the NCAR-TIEGCM model with Heelis electric potential empirical model as polar input. The TIEGCM can reproduce 3 of 4 large-scale structures (except SED) very well. We then further analyzed the altitudinal variations of these large-scale disturbances and found several interesting things, such as the altitude variation of SED, the rotation of positive/negative storm phase with local time. Those structures could not be identified clearly by traditional used data sources, which either has no gloval coverage or no vertical resolution. The drivers such as neutral wind/density and electric field from TIEGCM simulations are also analyzed to self-consistantly explain the identified disturbance features.

Simultaneous Study of Intake and In-Cylinder IC Engine Flow Fields to Provide an Insight into Intake Induced Cyclic Variations

NASA Astrophysics Data System (ADS)

Justham, T.; Jarvis, S.; Clarke, A.; Garner, C. P.; Hargrave, G. K.; Halliwell, N. A.

2006-07-01

Simultaneous intake and in-cylinder digital particle image velocimetry (DPIV) experimental data is presented for a motored spark ignition (SI) optical internal combustion (IC) engine. Two individual DPIV systems were employed to study the inter-relationship between the intake and in-cylinder flow fields at an engine speed of 1500 rpm. Results for the intake runner velocity field at the time of maximum intake valve lift are compared to incylinder velocity fields later in the same engine cycle. Relationships between flow structures within the runner and cylinder were seen to be strong during the intake stroke but less significant during compression. Cyclic variations within the intake runner were seen to affect the large scale bulk flow motion. The subsequent decay of the large scale motions into smaller scale turbulent structures during the compression stroke appear to reduce the relationship with the intake flow variations.

Rare variation facilitates inferences of fine-scale population structure in humans.

PubMed

O'Connor, Timothy D; Fu, Wenqing; Mychaleckyj, Josyf C; Logsdon, Benjamin; Auer, Paul; Carlson, Christopher S; Leal, Suzanne M; Smith, Joshua D; Rieder, Mark J; Bamshad, Michael J; Nickerson, Deborah A; Akey, Joshua M

2015-03-01

Understanding the genetic structure of human populations has important implications for the design and interpretation of disease mapping studies and reconstructing human evolutionary history. To date, inferences of human population structure have primarily been made with common variants. However, recent large-scale resequencing studies have shown an abundance of rare variation in humans, which may be particularly useful for making inferences of fine-scale population structure. To this end, we used an information theory framework and extensive coalescent simulations to rigorously quantify the informativeness of rare and common variation to detect signatures of fine-scale population structure. We show that rare variation affords unique insights into patterns of recent population structure. Furthermore, to empirically assess our theoretical findings, we analyzed high-coverage exome sequences in 6,515 European and African American individuals. As predicted, rare variants are more informative than common polymorphisms in revealing a distinct cluster of European-American individuals, and subsequent analyses demonstrate that these individuals are likely of Ashkenazi Jewish ancestry. Our results provide new insights into the population structure using rare variation, which will be an important factor to account for in rare variant association studies. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Space Technology 5 Multi-point Observations of Field-aligned Currents: Temporal Variability of Meso-Scale Structures

NASA Technical Reports Server (NTRS)

Le, Guan; Wang, Yongli; Slavin, James A.; Strangeway, Robert J.

2007-01-01

Space Technology 5 (ST5) is a three micro-satellite constellation deployed into a 300 x 4500 km, dawn-dusk, sun-synchronous polar orbit from March 22 to June 21, 2006, for technology validations. In this paper, we present a study of the temporal variability of field-aligned currents using multi-point magnetic field measurements from ST5. The data demonstrate that meso-scale current structures are commonly embedded within large-scale field-aligned current sheets. The meso-scale current structures are very dynamic with highly variable current density and/or polarity in time scales of - 10 min. They exhibit large temporal variations during both quiet and disturbed times in such time scales. On the other hand, the data also shown that the time scales for the currents to be relatively stable are approx. 1 min for meso-scale currents and approx. 10 min for large scale current sheets. These temporal features are obviously associated with dynamic variations of their particle carriers (mainly electrons) as they respond to the variations of the parallel electric field in auroral acceleration region. The characteristic time scales for the temporal variability of meso-scale field-aligned currents are found to be consistent with those of auroral parallel electric field.

Thermal control requirements for large space structures

NASA Technical Reports Server (NTRS)

Manoff, M.

1978-01-01

Performance capabilities and weight requirements of large space structure systems will be significantly influenced by thermal response characteristics. Analyses have been performed to determine temperature levels and gradients for structural configurations and elemental concepts proposed for advanced system applications ranging from relatively small, low-power communication antennas to extremely large, high-power Satellite Power Systems (SPS). Results are presented for selected platform configurations, candidate strut elements, and potential mission environments. The analyses also incorporate material and surface optical property variation. The results illustrate many of the thermal problems which may be encountered in the development of three systems.

Evidence of Dynamic Crustal Deformation in Tohoku, Japan, From Time-Varying Receiver Functions

NASA Astrophysics Data System (ADS)

Porritt, R. W.; Yoshioka, S.

2017-10-01

Temporal variation of crustal structure is key to our understanding of Earth processes on human timescales. Often, we expect that the most significant structural variations are caused by strong ground shaking associated with large earthquakes, and recent studies seem to confirm this. Here we test the possibility of using P receiver functions (PRF) to isolate structural variations over time. Synthetic receiver function tests indicate that structural variation could produce PRF changes on the same order of magnitude as random noise or contamination by local earthquakes. Nonetheless, we find significant variability in observed receiver functions over time at several stations located in northeastern Honshu. Immediately following the Tohoku-oki earthquake, we observe high PRF variation clustering spatially, especially in two regions near the beginning and end of the rupture plane. Due to the depth sensitivity of PRF and the timescales over which this variability is observed, we infer this effect is primarily due to fluid migration in volcanic regions and shear stress/strength reorganization. While the noise levels in PRF are high for this type of analysis, by sampling small data sets, the computational cost is lower than other methods, such as ambient noise, thereby making PRF a useful tool for estimating temporal variations in crustal structure.

Temporal genetic structure in a poecilogonous polychaete: the interplay of developmental mode and environmental stochasticity

PubMed Central

2014-01-01

Background Temporal variation in the genetic structure of populations can be caused by multiple factors, including natural selection, stochastic environmental variation, migration, or genetic drift. In benthic marine species, the developmental mode of larvae may indicate a possibility for temporal genetic variation: species with dispersive planktonic larvae are expected to be more likely to show temporal genetic variation than species with benthic or brooded non-dispersive larvae, due to differences in larval mortality and dispersal ability. We examined temporal genetic structure in populations of Pygospio elegans, a poecilogonous polychaete with within-species variation in developmental mode. P. elegans produces either planktonic, benthic, or intermediate larvae, varying both among and within populations, providing a within-species test of the generality of a relationship between temporal genetic variation and larval developmental mode. Results In contrast to our expectations, our microsatellite analyses of P. elegans revealed temporal genetic stability in the UK population with planktonic larvae, whereas there was variation indicative of drift in temporal samples of the populations from the Baltic Sea, which have predominantly benthic and intermediate larvae. We also detected temporal variation in relatedness within these populations. A large temporal shift in genetic structure was detected in a population from the Netherlands, having multiple developmental modes. This shift could have been caused by local extiction due to extreme environmental conditions and (re)colonization by planktonic larvae from neighboring populations. Conclusions In our study of P. elegans, temporal genetic variation appears to be due to not only larval developmental mode, but also the stochastic environment of adults. Large temporal genetic shifts may be more likely in marine intertidal habitats (e.g. North Sea and Wadden Sea) which are more prone to environmental stochasticity than the sub-tidal Baltic habitats. Sub-tidal and/or brackish (less saline) habitats may support smaller P. elegans populations and these may be more susceptible to the effects of random genetic drift. Moreover, higher frequencies of asexual reproduction and the benthic larval developmental mode in these populations leads to higher relatedness and contributes to drift. Our results indicate that a general relationship between larval developmental mode and temporal genetic variation may not exist. PMID:24447386

Temporal genetic structure in a poecilogonous polychaete: the interplay of developmental mode and environmental stochasticity.

PubMed

Kesäniemi, Jenni E; Mustonen, Marina; Boström, Christoffer; Hansen, Benni W; Knott, K Emily

2014-01-22

Temporal variation in the genetic structure of populations can be caused by multiple factors, including natural selection, stochastic environmental variation, migration, or genetic drift. In benthic marine species, the developmental mode of larvae may indicate a possibility for temporal genetic variation: species with dispersive planktonic larvae are expected to be more likely to show temporal genetic variation than species with benthic or brooded non-dispersive larvae, due to differences in larval mortality and dispersal ability. We examined temporal genetic structure in populations of Pygospio elegans, a poecilogonous polychaete with within-species variation in developmental mode. P. elegans produces either planktonic, benthic, or intermediate larvae, varying both among and within populations, providing a within-species test of the generality of a relationship between temporal genetic variation and larval developmental mode. In contrast to our expectations, our microsatellite analyses of P. elegans revealed temporal genetic stability in the UK population with planktonic larvae, whereas there was variation indicative of drift in temporal samples of the populations from the Baltic Sea, which have predominantly benthic and intermediate larvae. We also detected temporal variation in relatedness within these populations. A large temporal shift in genetic structure was detected in a population from the Netherlands, having multiple developmental modes. This shift could have been caused by local extiction due to extreme environmental conditions and (re)colonization by planktonic larvae from neighboring populations. In our study of P. elegans, temporal genetic variation appears to be due to not only larval developmental mode, but also the stochastic environment of adults. Large temporal genetic shifts may be more likely in marine intertidal habitats (e.g. North Sea and Wadden Sea) which are more prone to environmental stochasticity than the sub-tidal Baltic habitats. Sub-tidal and/or brackish (less saline) habitats may support smaller P. elegans populations and these may be more susceptible to the effects of random genetic drift. Moreover, higher frequencies of asexual reproduction and the benthic larval developmental mode in these populations leads to higher relatedness and contributes to drift. Our results indicate that a general relationship between larval developmental mode and temporal genetic variation may not exist.

The effect of structural changes on charge transfer states in a light-harvesting carotenoid-diaryl-porphyrin-C{sub 60} molecular triad

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

Olguin, Marco; Basurto, Luis; Zope, Rajendra R.

We present a detailed study of charge transfer (CT) excited states for a large number of configurations in a light-harvesting Carotenoid-diaryl-Porphyrin-C{sub 60} (CPC{sub 60}) molecular triad. The chain-like molecular triad undergoes photoinduced charge transfer process exhibiting a large excited state dipole moment, making it suitable for application to molecular-scale opto-electronic devices. An important consideration is that the structural flexibility of the CPC{sub 60} triad impacts its dynamics in solvents. Since experimentally measured dipole moments for the triad of ∼110 D and ∼160 D strongly indicate a range in structural variability in the excited state, studying the effect of structural changesmore » on the CT excited state energetics furthers the understanding of its charge transfer states. We have calculated the variation in the lowest CT excited state energies by performing a scan of possible variation in the structure of the triad. Some of these configurations were generated by incrementally scanning a 360° torsional (dihedral) twist at the C{sub 60}-porhyrin linkage and the porphyrin-carotenoid linkage. Additionally, five different CPC{sub 60} conformations were studied to determine the effect of pi-conjugation and particle-hole Coulombic attraction on the CT excitation energies. Our calculations show that configurational changes in the triad induces a variation of ∼0.6 eV in CT excited state energies in the gas-phase. The corresponding calculated excited state dipoles show a range of 47 D–188 D. The absorption spectra and density of states of these structures show little variation except for the structures where the porphyrin and aryl conjugation is changed.« less

Morphological and genetic analysis of four color morphs of bean leaf beetle, Cerotoma trifurcata (Coleoptera: Chrysomelidae)

USDA-ARS?s Scientific Manuscript database

Bean leaf beetle (BLB) exhibits a relatively large amount of morphological variation in terms of color but little is known about the underlying genetic structure and gene flow. Genetic variation among four color phenotypes of the BLB was analyzed using amplified fragment length polymorphisms (AFLP) ...

Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq.

PubMed

Barrick, Jeffrey E; Colburn, Geoffrey; Deatherage, Daniel E; Traverse, Charles C; Strand, Matthew D; Borges, Jordan J; Knoester, David B; Reba, Aaron; Meyer, Austin G

2014-11-29

Mutations that alter chromosomal structure play critical roles in evolution and disease, including in the origin of new lifestyles and pathogenic traits in microbes. Large-scale rearrangements in genomes are often mediated by recombination events involving new or existing copies of mobile genetic elements, recently duplicated genes, or other repetitive sequences. Most current software programs for predicting structural variation from short-read DNA resequencing data are intended primarily for use on human genomes. They typically disregard information in reads mapping to repeat sequences, and significant post-processing and manual examination of their output is often required to rule out false-positive predictions and precisely describe mutational events. We have implemented an algorithm for identifying structural variation from DNA resequencing data as part of the breseq computational pipeline for predicting mutations in haploid microbial genomes. Our method evaluates the support for new sequence junctions present in a clonal sample from split-read alignments to a reference genome, including matches to repeat sequences. Then, it uses a statistical model of read coverage evenness to accept or reject these predictions. Finally, breseq combines predictions of new junctions and deleted chromosomal regions to output biologically relevant descriptions of mutations and their effects on genes. We demonstrate the performance of breseq on simulated Escherichia coli genomes with deletions generating unique breakpoint sequences, new insertions of mobile genetic elements, and deletions mediated by mobile elements. Then, we reanalyze data from an E. coli K-12 mutation accumulation evolution experiment in which structural variation was not previously identified. Transposon insertions and large-scale chromosomal changes detected by breseq account for ~25% of spontaneous mutations in this strain. In all cases, we find that breseq is able to reliably predict structural variation with modest read-depth coverage of the reference genome (>40-fold). Using breseq to predict structural variation should be useful for studies of microbial epidemiology, experimental evolution, synthetic biology, and genetics when a reference genome for a closely related strain is available. In these cases, breseq can discover mutations that may be responsible for important or unintended changes in genomes that might otherwise go undetected.

The impact of disorder on charge transport in three dimensional quantum dot resonant tunneling structures

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

Puthen-Veettil, B., E-mail: b.puthen-veettil@unsw.edu.au; Patterson, R.; König, D.

Efficient iso-entropic energy filtering of electronic waves can be realized through nanostructures with three dimensional confinement, such as quantum dot resonant tunneling structures. Large-area deployment of such structures is useful for energy selective contacts but such configuration is susceptible to structural disorders. In this work, the transport properties of quantum-dot-based wide-area resonant tunneling structures, subject to realistic disorder mechanisms, are studied. Positional variations of the quantum dots are shown to reduce the resonant transmission peaks while size variations in the device are shown to reduce as well as broaden the peaks. Increased quantum dot size distribution also results in amore » peak shift to lower energy which is attributed to large dots dominating transmission. A decrease in barrier thickness reduces the relative peak height while the overall transmission increases dramatically due to lower “series resistance.” While any shift away from ideality can be intuitively expected to reduce the resonance peak, quantification allows better understanding of the tolerances required for fabricating structures based on resonant tunneling phenomena/.« less

The Relationship between Cranial Structure, Biomechanical Performance and Ecological Diversity in Varanoid Lizards

PubMed Central

McCurry, Matthew R.; Mahony, Michael; Clausen, Phillip D.; Quayle, Michelle R.; Walmsley, Christopher W.; Jessop, Tim S.; Wroe, Stephen; Richards, Heather; McHenry, Colin R.

2015-01-01

Skull structure is intimately associated with feeding ability in vertebrates, both in terms of specific performance measures and general ecological characteristics. This study quantitatively assessed variation in the shape of the cranium and mandible in varanoid lizards, and its relationship to structural performance (von Mises strain) and interspecific differences in feeding ecology. Geometric morphometric and linear morphometric analyses were used to evaluate morphological differences, and finite element analysis was used to quantify variation in structural performance (strain during simulated biting, shaking and pulling). This data was then integrated with ecological classes compiled from relevant scientific literature on each species in order to establish structure-function relationships. Finite element modelling results showed that variation in cranial morphology resulted in large differences in the magnitudes and locations of strain in biting, shaking and pulling load cases. Gracile species such as Varanus salvadorii displayed high strain levels during shaking, especially in the areas between the orbits. All models exhibit less strain during pull back loading compared to shake loading, even though a larger force was applied (pull =30N, shake = 20N). Relationships were identified between the morphology, performance, and ecology. Species that did not feed on hard prey clustered in the gracile region of cranial morphospace and exhibited significantly higher levels of strain during biting (P = 0.0106). Species that fed on large prey clustered in the elongate area of mandible morphospace. This relationship differs from those that have been identified in other taxonomic groups such as crocodiles and mammals. This difference may be due to a combination of the open ‘space-frame’ structure of the varanoid lizard skull, and the ‘pull back’ behaviour that some species use for processing large prey. PMID:26106889

Rebelling for a Reason: Protein Structural “Outliers”

PubMed Central

Arumugam, Gandhimathi; Nair, Anu G.; Hariharaputran, Sridhar; Ramanathan, Sowdhamini

2013-01-01

Analysis of structural variation in domain superfamilies can reveal constraints in protein evolution which aids protein structure prediction and classification. Structure-based sequence alignment of distantly related proteins, organized in PASS2 database, provides clues about structurally conserved regions among different functional families. Some superfamily members show large structural differences which are functionally relevant. This paper analyses the impact of structural divergence on function for multi-member superfamilies, selected from the PASS2 superfamily alignment database. Functional annotations within superfamilies, with structural outliers or ‘rebels’, are discussed in the context of structural variations. Overall, these data reinforce the idea that functional similarities cannot be extrapolated from mere structural conservation. The implication for fold-function prediction is that the functional annotations can only be inherited with very careful consideration, especially at low sequence identities. PMID:24073209

Aluminum tolerance in maize is associated with higher MATE1 gene copy number

PubMed Central

Maron, Lyza G.; Guimarães, Claudia T.; Kirst, Matias; Albert, Patrice S.; Birchler, James A.; Bradbury, Peter J.; Buckler, Edward S.; Coluccio, Alison E.; Danilova, Tatiana V.; Kudrna, David; Magalhaes, Jurandir V.; Piñeros, Miguel A.; Schatz, Michael C.; Wing, Rod A.; Kochian, Leon V.

2013-01-01

Genome structure variation, including copy number variation and presence/absence variation, comprises a large extent of maize genetic diversity; however, its effect on phenotypes remains largely unexplored. Here, we describe how copy number variation underlies a rare allele that contributes to maize aluminum (Al) tolerance. Al toxicity is the primary limitation for crop production on acid soils, which make up 50% of the world’s potentially arable lands. In a recombinant inbred line mapping population, copy number variation of the Al tolerance gene multidrug and toxic compound extrusion 1 (MATE1) is the basis for the quantitative trait locus of largest effect on phenotypic variation. This expansion in MATE1 copy number is associated with higher MATE1 expression, which in turn results in superior Al tolerance. The three MATE1 copies are identical and are part of a tandem triplication. Only three maize inbred lines carrying the three-copy allele were identified from maize and teosinte diversity panels, indicating that copy number variation for MATE1 is a rare, and quite likely recent, event. These maize lines with higher MATE1 copy number are also Al-tolerant, have high MATE1 expression, and originate from regions of highly acidic soils. Our findings show a role for copy number variation in the adaptation of maize to acidic soils in the tropics and suggest that genome structural changes may be a rapid evolutionary response to new environments. PMID:23479633

Large-scale structure in superfluid Chaplygin gas cosmology

NASA Astrophysics Data System (ADS)

Yang, Rongjia

2014-03-01

We investigate the growth of the large-scale structure in the superfluid Chaplygin gas (SCG) model. Both linear and nonlinear growth, such as σ8 and the skewness S3, are discussed. We find the growth factor of SCG reduces to the Einstein-de Sitter case at early times while it differs from the cosmological constant model (ΛCDM) case in the large a limit. We also find there will be more stricture growth on large scales in the SCG scenario than in ΛCDM and the variations of σ8 and S3 between SCG and ΛCDM cannot be discriminated.

Ionospheric response to 17 March 2013 geomagnetic storm identified by data assimilation result

NASA Astrophysics Data System (ADS)

Yue, Xinan; Zhao, Biqiang; Hu, Lianhuan; She, Chengli

2017-04-01

Based on slant total electron content (TEC) observations made by 10 satellites and 450 ground IGS GNSS stations, we constructed a 4-D ionospheric electron density reanalysis during the March 17, 2013 geomagnetic storm. Four main large-scale ionospheric disturbances are identified from reanalysis: (1) The positive storm during the initial phase; (2) The SED (storm enhanced density) structure in both northern and southern hemisphere; (3) The large positive storm in main phase; (4) The significant negative storm in middle and low latitude during recovery phase. We then run the NCAR-TIEGCM model with Heelis electric potential empirical model as polar input. The TIEGCM can reproduce 3 of 4 large-scale structures (except SED) very well. We then further analyzed the altitudinal variations of these large-scale disturbances and found several interesting things, such as the altitude variation of SED, the rotation of positive/negative storm phase with local time. Those structures could not be identified clearly by traditional used data sources, which either has no global coverage or no vertical resolution. The drivers such as neutral wind/density and electric field from TIEGCM simulations are also analyzed to self-consistently explain the identified disturbance features.

Patterns of variations in large pelagic fish: A comparative approach between the Indian and the Atlantic Oceans

NASA Astrophysics Data System (ADS)

Corbineau, A.; Rouyer, T.; Fromentin, J.-M.; Cazelles, B.; Fonteneau, A.; Ménard, F.

2010-07-01

Catch data of large pelagic fish such as tuna, swordfish and billfish are highly variable ranging from short to long term. Based on fisheries data, these time series are noisy and reflect mixed information on exploitation (targeting, strategy, fishing power), population dynamics (recruitment, growth, mortality, migration, etc.), and environmental forcing (local conditions or dominant climate patterns). In this work, we investigated patterns of variation of large pelagic fish (i.e. yellowfin tuna, bigeye tuna, swordfish and blue marlin) in Japanese longliners catch data from 1960 to 2004. We performed wavelet analyses on the yearly time series of each fish species in each biogeographic province of the tropical Indian and Atlantic Oceans. In addition, we carried out cross-wavelet analyses between these biological time series and a large-scale climatic index, i.e. the Southern Oscillation Index (SOI). Results showed that the biogeographic province was the most important factor structuring the patterns of variability of Japanese catch time series. Relationships between the SOI and the fish catches in the Indian and Atlantic Oceans also pointed out the role of climatic variability for structuring patterns of variation of catch time series. This work finally confirmed that Japanese longline CPUE data poorly reflect the underlying population dynamics of tunas.

Responses of infaunal populations to benthoscape structure and the potential importance of transition zones

USGS Publications Warehouse

Zajac, R.N.; Lewis, R.S.; Poppe, L.J.; Twichell, D.C.; Vozarik, J.; DiGiacomo-Cohen, M. L.

2003-01-01

Relationships between population abundance and seafloor landscape, or benthoscape, structure were examined for 16 infaunal taxa in eastern Long Island Sound. Based on analyses of a side-scan sonar mosaic, the 19.4-km2 study area was comprised of six distinct large-scale (> km2) benthoscape elements, with varying levels of mesoscale (km2-m2) and small-scale (2) physical and biological habitat heterogeneity. Transition zones among elements varied from ~50 to 200 m in width, comprised ~32% of the benthoscape, and added to overall benthoscape heterogeneity. Population abundances of nine taxa varied significantly among the large-scale elements. Most species were found at high abundances only in one benthoscape element, but three had several foci of elevated abundances. Analyses of population responses to habitat heterogeneity at different spatial scales indicated that abundances of eight taxa varied significantly among spatial scales, but the significant scales were mixed among these species. Relatively large residual variations suggest significant amounts of mesoscale spatial variation were unaccounted for, varying from ~1 km2 to several m2. Responses to transition zones were mixed as well. Abundances of nine taxa varied significantly among transition zones and interiors of benthoscape elements, most with elevated abundances in transition zones. Our results show that infaunal populations exhibit complex and spatially varying patterns of abundance in relation to benthoscape structure and suggest that mesoscale variation may be particularly critical in this regard. Also, transition zones among benthoscape features add considerably to this variation and may be ecological important areas in seafloor environments.

Measures of large-scale structure in the CfA redshift survey slices

NASA Technical Reports Server (NTRS)

De Lapparent, Valerie; Geller, Margaret J.; Huchra, John P.

1991-01-01

Variations of the counts-in-cells with cell size are used here to define two statistical measures of large-scale clustering in three 6 deg slices of the CfA redshift survey. A percolation criterion is used to estimate the filling factor which measures the fraction of the total volume in the survey occupied by the large-scale structures. For the full 18 deg slice of the CfA redshift survey, f is about 0.25 + or - 0.05. After removing groups with more than five members from two of the slices, variations of the counts in occupied cells with cell size have a power-law behavior with a slope beta about 2.2 on scales from 1-10/h Mpc. Application of both this statistic and the percolation analysis to simulations suggests that a network of two-dimensional structures is a better description of the geometry of the clustering in the CfA slices than a network of one-dimensional structures. Counts-in-cells are also used to estimate at 0.3 galaxy h-squared/Mpc the average galaxy surface density in sheets like the Great Wall.

Anatomical and morphological spine variation in Gymnocalycium kieslingii subsp. castaneum (Cactaceae).

PubMed

Gebauer, Roman; Řepka, Radomír; Šmudla, Radek; Mamoňová, Miroslava; Ďurkovič, Jaroslav

2016-01-01

Although spine variation within cacti species or populations is assumed to be large, the minimum sample size of different spine anatomical and morphological traits required for species description is less studied. There are studies where only 2 spines were used for taxonomical comparison amnog species. Therefore, the spine structure variation within areoles and individuals of one population of Gymnocalycium kieslingii subsp. castaneum (Ferrari) Slaba was analyzed. Fifteen plants were selected and from each plant one areole from the basal, middle and upper part of the plant body was sampled. A scanning electron microscopy was used for spine surface description and a light microscopy for measurements of spine width, thickness, cross-section area, fiber diameter and fiber cell wall thickness. The spine surface was more visible and damaged less in the upper part of the plant body than in the basal part. Large spine and fiber differences were found between upper and lower parts of the plant body, but also within single areoles. In general, the examined traits in the upper part had by 8-17% higher values than in the lower parts. The variation of spine and fiber traits within areoles was lower than the differences between individuals. The minimum sample size was largely influenced by the studied spine and fiber traits, ranging from 1 to 70 spines. The results provide pioneer information useful in spine sample collection in the field for taxonomical, biomechanical and structural studies. Nevertheless, similar studies should be carried out for other cacti species to make generalizations. The large spine and fiber variation within areoles observed in our study indicates a very complex spine morphogenesis.

Anatomical and morphological spine variation in Gymnocalycium kieslingii subsp. castaneum (Cactaceae)

PubMed Central

Gebauer, Roman; Řepka, Radomír; Šmudla, Radek; Mamoňová, Miroslava; Ďurkovič, Jaroslav

2016-01-01

Abstract Although spine variation within cacti species or populations is assumed to be large, the minimum sample size of different spine anatomical and morphological traits required for species description is less studied. There are studies where only 2 spines were used for taxonomical comparison amnog species. Therefore, the spine structure variation within areoles and individuals of one population of Gymnocalycium kieslingii subsp. castaneum (Ferrari) Slaba was analyzed. Fifteen plants were selected and from each plant one areole from the basal, middle and upper part of the plant body was sampled. A scanning electron microscopy was used for spine surface description and a light microscopy for measurements of spine width, thickness, cross-section area, fiber diameter and fiber cell wall thickness. The spine surface was more visible and damaged less in the upper part of the plant body than in the basal part. Large spine and fiber differences were found between upper and lower parts of the plant body, but also within single areoles. In general, the examined traits in the upper part had by 8–17% higher values than in the lower parts. The variation of spine and fiber traits within areoles was lower than the differences between individuals. The minimum sample size was largely influenced by the studied spine and fiber traits, ranging from 1 to 70 spines. The results provide pioneer information useful in spine sample collection in the field for taxonomical, biomechanical and structural studies. Nevertheless, similar studies should be carried out for other cacti species to make generalizations. The large spine and fiber variation within areoles observed in our study indicates a very complex spine morphogenesis. PMID:27698579

The Mysterious Bar of the Large Magellanic Cloud: What Is It?

NASA Astrophysics Data System (ADS)

Subramaniam, Annapurni; Subramanian, Smitha

2009-09-01

The bar of the Large Magellanic Cloud (LMC) is one of the prominent, but controversial, features regarding its location with respect to the disk of the LMC. In order to study the relative location of the bar with respect to the disk, we present the high-resolution map of the structure across the LMC. We used the reddening corrected mean magnitudes (I 0) of red clump (RC) stars from the OGLE III catalog to map the relative variation in distance (vertical structure) or variation in RC population across the LMC. The bar does not appear as an identifiable vertical feature in the map, as there is no difference in I 0 values between the bar and the disk regions. We conclude that the LMC bar is very much part of the disk (within 0.02 mag), located in the plane of the disk and not a separate component. We identify warps or variation in RC population with increase in radial distance.

Global properties of the plasma in the outer heliosphere. I - Large-scale structure and evolution

NASA Technical Reports Server (NTRS)

Barnes, A.; Mihalov, J. D.; Gazis, P. R.; Lazarus, A. J.; Belcher, J. W.; Gordon, G. S., Jr.; Mcnutt, R. L., Jr.

1992-01-01

Pioneers 10 and 11, and Voyager 2, have active plasma analyzers as they proceed through heliocentric distances of the order of 30-50 AU, facilitating comparative studies of the global character of the outer solar wind and its variation over the solar cycle. Careful study of these data show that wind ion temperature remains constant beyond 15 AU, and that there may be large-scale variations of temperature with celestial longitude and heliographic latitude. There has thus far been no indication of a heliospheric terminal shock.

Intra-plant floral variation in Cleome viscosa L. and its possible significance in breeding system.

PubMed

Saroop, Shveta; Kaul, Veenu

2015-07-01

Cleome viscosa L., an annual rainy season weed, is cosmopolitan in distribution. Two naturally growing populations of C. viscosa from Jammu, J & K, India have been studied for floral variation at an intra-plant level and its possible role in its life cycle. Plants of both the populations bear flowers which exhibit tremendous intra-plant variation in size (large and small) and sex (hermaphrodite, staminate and pistillate). The average number of flowers per plant varied significantly and so did their structural and functional details. Greater propensity, however, was towards hermaphroditism at both plant and flower levels. The large and small sized flowers differed in their morphology and reproductive features; the former were significantly larger than the latter. Anthesis, anther dehiscence and stigma receptivity were coupled in all flower types. This functional aspect along with the structural proximity between stamens at two lengths and pistil further facilitated self-pollination. However, conspicuous floral display attracted diverse pollinator fauna (Apis dorsata, Halictus albescens, Nomia curvipes and N. elliotii) which in turn mediated cross pollination. Nevertheless, each floral type contributed towards plant's fitness in its own way. Hermaphrodite flowers exhibited both self and cross pollination and assured survival by setting fruits and seeds with the large sized counterparts more productive. All these floral variations seemed to impart flexibility to the pollination system and provide fitness over the short flowering season.

Variational study on the vibrational level structure and vibrational level mixing of highly vibrationally excited S₀ D₂CO.

PubMed

Rashev, Svetoslav; Moule, David C; Rashev, Vladimir

2012-11-01

We perform converged high precision variational calculations to determine the frequencies of a large number of vibrational levels in S(0) D(2)CO, extending from low to very high excess vibrational energies. For the calculations we use our specific vibrational method (recently employed for studies on H(2)CO), consisting of a combination of a search/selection algorithm and a Lanczos iteration procedure. Using the same method we perform large scale converged calculations on the vibrational level spectral structure and fragmentation at selected highly excited overtone states, up to excess vibrational energies of ∼17,000 cm(-1), in order to study the characteristics of intramolecular vibrational redistribution (IVR), vibrational level density and mode selectivity. Copyright © 2012 Elsevier B.V. All rights reserved.

Dynamical structure factor of the J1-J2 Heisenberg model in one dimension: The variational Monte Carlo approach

NASA Astrophysics Data System (ADS)

Ferrari, Francesco; Parola, Alberto; Sorella, Sandro; Becca, Federico

2018-06-01

The dynamical spin structure factor is computed within a variational framework to study the one-dimensional J1-J2 Heisenberg model. Starting from Gutzwiller-projected fermionic wave functions, the low-energy spectrum is constructed from two-spinon excitations. The direct comparison with Lanczos calculations on small clusters demonstrates the excellent description of both gapless and gapped (dimerized) phases, including incommensurate structures for J2/J1>0.5 . Calculations on large clusters show how the intensity evolves when increasing the frustrating ratio and give an unprecedented accurate characterization of the dynamical properties of (nonintegrable) frustrated spin models.

Lateral Moho variations and the geometry of Main Himalayan Thrust beneath Nepal Himalayan orogen revealed by teleseismic receiver functions

NASA Astrophysics Data System (ADS)

He, Ping; Lei, Jianshe; Yuan, Xiaohui; Xu, Xiwei; Xu, Qiang; Liu, Zhikun; Mi, Qi; Zhou, Lianqing

2018-05-01

The lateral Moho variations and the geometry of the Main Himalayan Thrust under the Nepal Himalayan orogen are investigated to determine a new crustal model using a large number of high-quality receiver functions recorded by the HIMNT and HiCLIMB portable seismic networks. Our new model shows an evident and complicated lateral Moho depth variation of 8-16 km in the east-west direction, which is related to the surface tectonic features. These results suggest a non-uniformed crustal deformation, resulted from the splitting and/or tearing of the Indian plate during the northward subduction. Our migrated receiver function images illustrate a discernible ramp structure of the Main Himalayan Thrust with an abrupt downward bending close to the hypocenter of the 2015 Gorkha Mw 7.8 earthquake. The distribution of the aftershocks coincides with the present decollement structure. Integrating previous magnetotelluric soundings and tomographic results, our results suggest that the ramp-shaped structure within the Main Himalayan Thrust could enhance stress concentration leading to the nucleation of the large earthquake. Our new crustal model provides new clues to the formation of the Himalayan orogen.

Genetic structure of Culex erraticus populations across the Americas.

PubMed

Mendenhall, Ian H; Bahl, Justin; Blum, Michael J; Wesson, Dawn M

2012-05-01

Culex erraticus (Dyar & Knab) is a potential competent vector for several arboviruses such as Eastern and Venezuelan equine encephalitis viruses and West Nile virus. It therefore may play a role in the maintenance and spread of viral populations in areas of concern, including the United States where it occurs in >33 states. However, little information is available on potential barriers to movement across the species' distribution. Here, we analyze genetic variation among Cx. erraticus collected from Colombia, Guatemala, and nine locations in the United States to better understand population structure and connectivity. Comparative sequence analysis of the second internal transcribed spacer and mitochondrial NADH dehydrogenase genes identified two major lineages of sampled populations. One lineage represented the central and eastern United States, whereas the other corresponded to Central America, South America, and the western United States. Hierarchical analysis of genetic variation provided further evidence of regional population structure, although the majority of genetic variation was found to reside within populations, suggestive of large population sizes. Although significant physical barriers such as the Chihuahuan Desert probably constrain the spread of Cx. erraticus, large population sizes and connectivity within regions remain important risk factors that probably contribute to the movement of arboviruses within and between these regions.

Variational study on the vibrational level structure and IVR behavior of highly vibrationally excited S0 formaldehyde.

PubMed

Rashev, Svetoslav; Moule, David C

2012-02-15

We perform large scale converged variational vibrational calculations on S(0) formaldehyde up to very high excess vibrational energies (E(v)), E(v)∼17,000cm(-1), using our vibrational method, consisting of a specific search/selection/Lanczos iteration procedure. Using the same method we investigate the vibrational level structure and intramolecular vibrational redistribution (IVR) characteristics for various vibrational levels in this energy range in order to assess the onset of IVR. Copyright © 2011 Elsevier B.V. All rights reserved.

Enhanced laboratory sensitivity to variation of the fine-structure constant using highly charged ions.

PubMed

Berengut, J C; Dzuba, V A; Flambaum, V V

2010-09-17

We study atomic systems that are in the frequency range of optical atomic clocks and have enhanced sensitivity to potential time variation of the fine-structure constant α. The high sensitivity is due to coherent contributions from three factors: high nuclear charge Z, high ionization degree, and significant differences in the configuration composition of the states involved. Configuration crossing keeps the frequencies in the optical range despite the large ionization energies. We discuss a few promising examples that have the largest α sensitivities seen in atomic systems.

Impact of genetic variation on three dimensional structure and function of proteins

PubMed Central

Bhattacharya, Roshni; Rose, Peter W.; Burley, Stephen K.

2017-01-01

The Protein Data Bank (PDB; http://wwpdb.org) was established in 1971 as the first open access digital data resource in biology with seven protein structures as its initial holdings. The global PDB archive now contains more than 126,000 experimentally determined atomic level three-dimensional (3D) structures of biological macromolecules (proteins, DNA, RNA), all of which are freely accessible via the Internet. Knowledge of the 3D structure of the gene product can help in understanding its function and role in disease. Of particular interest in the PDB archive are proteins for which 3D structures of genetic variant proteins have been determined, thus revealing atomic-level structural differences caused by the variation at the DNA level. Herein, we present a systematic and qualitative analysis of such cases. We observe a wide range of structural and functional changes caused by single amino acid differences, including changes in enzyme activity, aggregation propensity, structural stability, binding, and dissociation, some in the context of large assemblies. Structural comparison of wild type and mutated proteins, when both are available, provide insights into atomic-level structural differences caused by the genetic variation. PMID:28296894

Nest size is predicted by female identity and the local environment in the blue tit (Cyanistes caeruleus), but is not related to the nest size of the genetic or foster mother

PubMed Central

Parker, Timothy H.; Griffith, Simon C.

2018-01-01

The potential for animals to respond to changing climates has sparked interest in intraspecific variation in avian nest structure since this may influence nest microclimate and protect eggs and offspring from inclement weather. However, there have been relatively few large-scale attempts to examine variation in nests or the determinates of individual variation in nest structure within populations. Using a set of mostly pre-registered analyses, we studied potential predictors of variation in the size of a large sample (803) of blue tit (Cyanistes caeruleus) nests across three breeding seasons at Wytham Woods, UK. While our pre-registered analyses found that individual females built very similar nests across years, there was no evidence in follow-up (post hoc) analyses that their nest size correlated to that of their genetic mother or, in a cross-fostering experiment, to the nest where they were reared. In further pre-registered analyses, spatial environmental variability explained nest size variability at relatively broad spatial scales, and especially strongly at the scale of individual nest boxes. Our study indicates that nest structure is a characteristic of individuals, but is not strongly heritable, indicating that it will not respond rapidly to selection. Explaining the within-individual and within-location repeatability we observed requires further study. PMID:29765658

Understanding the General Packing Rearrangements Required for Successful Template Based Modeling of Protein Structure from a CASP Experiment

PubMed Central

Day, Ryan; Joo, Hyun; Chavan, Archana; Lennox, Kristin P.; Chen, Ann; Dahl, David B.; Vannucci, Marina; Tsai, Jerry W.

2012-01-01

As an alternative to the common template based protein structure prediction methods based on main-chain position, a novel side-chain centric approach has been developed. Together with a Bayesian loop modeling procedure and a combination scoring function, the Stone Soup algorithm was applied to the CASP9 set of template based modeling targets. Although the method did not generate as large of perturbations to the template structures as necessary, the analysis of the results gives unique insights into the differences in packing between the target structures and their templates. Considerable variation in packing is found between target and template structures even when the structures are close, and this variation is found due to 2 and 3 body packing interactions. Outside the inherent restrictions in packing representation of the PDB, the first steps in correctly defining those regions of variable packing have been mapped primarily to local interactions, as the packing at the secondary and tertiary structure are largely conserved. Of the scoring functions used, a loop scoring function based on water structure exhibited some promise for discrimination. These results present a clear structural path for further development of a side-chain centered approach to template based modeling. PMID:23266765

Understanding the general packing rearrangements required for successful template based modeling of protein structure from a CASP experiment.

PubMed

Day, Ryan; Joo, Hyun; Chavan, Archana C; Lennox, Kristin P; Chen, Y Ann; Dahl, David B; Vannucci, Marina; Tsai, Jerry W

2013-02-01

As an alternative to the common template based protein structure prediction methods based on main-chain position, a novel side-chain centric approach has been developed. Together with a Bayesian loop modeling procedure and a combination scoring function, the Stone Soup algorithm was applied to the CASP9 set of template based modeling targets. Although the method did not generate as large of perturbations to the template structures as necessary, the analysis of the results gives unique insights into the differences in packing between the target structures and their templates. Considerable variation in packing is found between target and template structures even when the structures are close, and this variation is found due to 2 and 3 body packing interactions. Outside the inherent restrictions in packing representation of the PDB, the first steps in correctly defining those regions of variable packing have been mapped primarily to local interactions, as the packing at the secondary and tertiary structure are largely conserved. Of the scoring functions used, a loop scoring function based on water structure exhibited some promise for discrimination. These results present a clear structural path for further development of a side-chain centered approach to template based modeling. Copyright © 2012 Elsevier Ltd. All rights reserved.

Research and Theory on Predecision Processes.

DTIC Science & Technology

1983-11-30

probl -sm detection process.........,.,......3.2 A problem detection taxonomy..*.......................,......3.6 Examples of the taxonomy gained from...large, and can be managed . A hierarchical tree structure is also necessary for distinguishing minor variations of ideas from major variations. Second...construct a scenario that involves forming a company to manufacture and market widgets. Widgets catch on, and soon every household has one, and the

The Effects of Magnetic-Field Geometry on Longitudinal Oscillations of Solar Prominences: Cross-Sectional Area Variation for Thin Tubes

NASA Technical Reports Server (NTRS)

Luna, M.; Diaz, A. J.; Oliver, R.; Terradas, J.; Karpen, J.

2016-01-01

Solar prominences are subject to both field-aligned (longitudinal) and transverse oscillatory motions, as evidenced by an increasing number of observations. Large-amplitude longitudinal motions provide valuable information on the geometry of the filament channel magnetic structure that supports the cool prominence plasma against gravity. Our pendulum model, in which the restoring force is the gravity projected along the dipped field lines of the magnetic structure, best explains these oscillations. However, several factors can influence the longitudinal oscillations, potentially invalidating the pendulum model. Aims. The aim of this work is to study the influence of large-scale variations in the magnetic field strength along the field lines, i.e., variations of the cross-sectional area along the flux tubes supporting prominence threads. Methods. We studied the normal modes of several flux tube configurations, using linear perturbation analysis, to assess the influence of different geometrical parameters on the oscillation properties. Results. We found that the influence of the symmetric and asymmetric expansion factors on longitudinal oscillations is small.Conclusions. We conclude that the longitudinal oscillations are not significantly influenced by variations of the cross-section of the flux tubes, validating the pendulum model in this context.

A statistical approach to detection of copy number variations in PCR-enriched targeted sequencing data.

PubMed

Demidov, German; Simakova, Tamara; Vnuchkova, Julia; Bragin, Anton

2016-10-22

Multiplex polymerase chain reaction (PCR) is a common enrichment technique for targeted massive parallel sequencing (MPS) protocols. MPS is widely used in biomedical research and clinical diagnostics as the fast and accurate tool for the detection of short genetic variations. However, identification of larger variations such as structure variants and copy number variations (CNV) is still being a challenge for targeted MPS. Some approaches and tools for structural variants detection were proposed, but they have limitations and often require datasets of certain type, size and expected number of amplicons affected by CNVs. In the paper, we describe novel algorithm for high-resolution germinal CNV detection in the PCR-enriched targeted sequencing data and present accompanying tool. We have developed a machine learning algorithm for the detection of large duplications and deletions in the targeted sequencing data generated with PCR-based enrichment step. We have performed verification studies and established the algorithm's sensitivity and specificity. We have compared developed tool with other available methods applicable for the described data and revealed its higher performance. We showed that our method has high specificity and sensitivity for high-resolution copy number detection in targeted sequencing data using large cohort of samples.

The ecology of an adaptive radiation of three-spined stickleback from North Uist, Scotland.

PubMed

Magalhaes, Isabel S; D'Agostino, Daniele; Hohenlohe, Paul A; MacColl, Andrew D C

2016-09-01

There has been a large focus on the genetics of traits involved in adaptation, but knowledge of the environmental variables leading to adaptive changes is surprisingly poor. Combined use of environmental data with morphological and genomic data should allow us to understand the extent to which patterns of phenotypic and genetic diversity within a species can be explained by the structure of the environment. Here, we analyse the variation of populations of three-spined stickleback from 27 freshwater lakes on North Uist, Scotland, that vary greatly in their environment, to understand how environmental and genetic constraints contribute to phenotypic divergence. We collected 35 individuals per population and 30 abiotic and biotic environmental parameters to characterize variation across lakes and analyse phenotype-environment associations. Additionally, we used RAD sequencing to estimate the genetic relationships among a subset of these populations. We found a large amount of phenotypic variation among populations, most prominently in armour and spine traits. Despite large variation in the abiotic environment, namely in ion composition, depth and dissolved organic Carbon, more phenotypic variation was explained by the biotic variables (presence of predators and density of predator and competitors), than by associated abiotic variables. Genetic structure among populations was partly geographic, with closer populations being more similar. Altogether, our results suggest that differences in body shape among stickleback populations are the result of both canalized genetic and plastic responses to environmental factors, which shape fish morphology in a predictable direction regardless of their genetic starting point. © 2016 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Cloud and boundary layer structure over San Nicolas Island during FIRE

NASA Technical Reports Server (NTRS)

Albrecht, Bruce A.; Fairall, Christopher W.; Syrett, William J.; Schubert, Wayne H.; Snider, Jack B.

1990-01-01

The temporal evolution of the structure of the marine boundary layer and of the associated low-level clouds observed in the vicinity of the San Nicolas Island (SNI) is defined from data collected during the First ISCCP Regional Experiment (FIRE) Marine Stratocumulus Intense Field Observations (IFO) (July 1 to 19). Surface, radiosonde, and remote-sensing measurements are used for this analysis. Sounding from the Island and from the ship Point Sur, which was located approximately 100 km northwest of SNI, are used to define variations in the thermodynamic structure of the lower-troposphere on time scales of 12 hours and longer. Time-height sections of potential temperature and equivalent potential temperature clearly define large-scale variations in the height and the strength of the inversion and periods where the conditions for cloud-top entrainment instability (CTEI) are met. Well defined variations in the height and the strength of the inversion were associated with a Cataline Eddy that was present at various times during the experiment and with the passage of the remnants of a tropical cyclone on July 18. The large-scale variations in the mean thermodynamic structure at SNI correlate well with those observed from the Point Sur. Cloud characteristics are defined for 19 days of the experiment using data from a microwave radiometer, a cloud ceilometer, a sodar, and longwave and shortwave radiometers. The depth of the cloud layer is estimated by defining inversion heights from the sodar reflectivity and cloud-base heights from a laser ceilometer. The integrated liquid water obtained from NOAA's microwave radiometer is compared with the adiabatic liquid water content that is calculated by lifting a parcel adiabatically from cloud base. In addition, the cloud structure is characterized by the variability in cloud-base height and in the integrated liquid water.

Denitrification in a large river: consideration of geomorphic controls on microbial activity and community structure.

PubMed

Tatariw, Corianne; Chapman, Elise L; Sponseller, Ryan A; Mortazavi, Behzad; Edmonds, Jennifer W

2013-10-01

Ecological theory argues that the controls over ecosystem processes are structured hierarchically, with broader-scale drivers acting as constraints over the interactions and dynamics at nested levels of organization. In river ecosystems, these interactions may arise from broadscale variation in channel form that directly shapes benthic habitat structure and indirectly constrains resource supply and biological activity within individual reaches. To evaluate these interactions, we identified sediment characteristics, water chemistry, and denitrifier community structure as factors influencing benthic denitrification rates in a sixth-order river that flows through two physiographic provinces and the transitional zone between them, each with distinct geomorphological properties. We found that denitrification rates tracked spatial changes in sediment characteristics and varied seasonally with expected trends in stream primary production. Highest rates were observed during the spring and summer seasons in the physiographic province dominated by fine-grained sediments, illustrating how large-scale changes in river structure can constrain the location of denitrification hotspots. In addition, nirS and nirK community structure each responded differently to variation in channel form, possibly due to changes in dissolved oxygen and organic matter supply. This shift in denitrifier community structure coincident with higher rates of N removal via denitrification suggests that microbial community structure may influence biogeochemical processes.

GENETIC STRUCTURE OF NORWAY SPRUCE (PICEA ABIES): CONCORDANCE OF MORPHOLOGICAL AND ALLOZYMIC VARIATION.

PubMed

Lagercrantz, Ulf; Ryman, Nils

1990-02-01

This study describes the population structure of Norway spruce (Picea abies) as revealed by protein polymorphisms and morphological variation. Electrophoretically detectable genetic variability was examined at 22 protein loci in 70 populations from the natural range of the species in Europe. Like other conifers, Norway spruce exhibits a relatively large amount of genetic variability and little differentiation among populations. Sixteen polymorphic loci (73%) segregate for a total of 51 alleles, and average heterozygosity per population is 0.115. Approximately 5% of the total genetic diversity is explained by differences between populations (G ST = 0.052), and Nei's standard genetic distance is less than 0.04 in all cases. We suggest that the population structure largely reflects relatively recent historical events related to the last glaciation and that Norway spruce is still in a process of adaptation and differentiation. There is a clear geographic pattern in the variation of allele frequencies. A major part of the allelefrequency variation can be accounted for by a few synthetic variables (principal components), and 80% of the variation of the first principal component is "explained" by latitude and longitude. The central European populations are consistently depauperate of genetic variability, most likely as an effect of severe restrictions of population size during the last glaciation. The pattern of differentiation at protein loci is very similar to that observed for seven morphological traits examined. This similarity suggests that the same evolutionary forces have acted upon both sets of characters. © 1990 The Society for the Study of Evolution.

Large trench-parallel gravity variations predict seismogenic behavior in subduction zones.

PubMed

Song, Teh-Ru Alex; Simons, Mark

2003-08-01

We demonstrate that great earthquakes occur predominantly in regions with a strongly negative trench-parallel gravity anomaly (TPGA), whereas regions with strongly positive TPGA are relatively aseismic. These observations suggest that, over time scales up to at least 1 million years, spatial variations of seismogenic behavior within a given subduction zone are stationary and linked to the geological structure of the fore-arc. The correlations we observe are consistent with a model in which spatial variations in frictional properties on the plate interface control trench-parellel variations in fore-arc topography, gravity, and seismogenic behavior.

Time-dependent breakdown of fiber networks: Uncertainty of lifetime

NASA Astrophysics Data System (ADS)

Mattsson, Amanda; Uesaka, Tetsu

2017-05-01

Materials often fail when subjected to stresses over a prolonged period. The time to failure, also called the lifetime, is known to exhibit large variability of many materials, particularly brittle and quasibrittle materials. For example, a coefficient of variation reaches 100% or even more. Its distribution shape is highly skewed toward zero lifetime, implying a large number of premature failures. This behavior contrasts with that of normal strength, which shows a variation of only 4%-10% and a nearly bell-shaped distribution. The fundamental cause of this large and unique variability of lifetime is not well understood because of the complex interplay between stochastic processes taking place on the molecular level and the hierarchical and disordered structure of the material. We have constructed fiber network models, both regular and random, as a paradigm for general material structures. With such networks, we have performed Monte Carlo simulations of creep failure to establish explicit relationships among fiber characteristics, network structures, system size, and lifetime distribution. We found that fiber characteristics have large, sometimes dominating, influences on the lifetime variability of a network. Among the factors investigated, geometrical disorders of the network were found to be essential to explain the large variability and highly skewed shape of the lifetime distribution. With increasing network size, the distribution asymptotically approaches a double-exponential form. The implication of this result is that, so-called "infant mortality," which is often predicted by the Weibull approximation of the lifetime distribution, may not exist for a large system.

A multi-scale comparison of trait linkages to environmental and spatial variables in fish communities across a large freshwater lake.

PubMed

Strecker, Angela L; Casselman, John M; Fortin, Marie-Josée; Jackson, Donald A; Ridgway, Mark S; Abrams, Peter A; Shuter, Brian J

2011-07-01

Species present in communities are affected by the prevailing environmental conditions, and the traits that these species display may be sensitive indicators of community responses to environmental change. However, interpretation of community responses may be confounded by environmental variation at different spatial scales. Using a hierarchical approach, we assessed the spatial and temporal variation of traits in coastal fish communities in Lake Huron over a 5-year time period (2001-2005) in response to biotic and abiotic environmental factors. The association of environmental and spatial variables with trophic, life-history, and thermal traits at two spatial scales (regional basin-scale, local site-scale) was quantified using multivariate statistics and variation partitioning. We defined these two scales (regional, local) on which to measure variation and then applied this measurement framework identically in all 5 study years. With this framework, we found that there was no change in the spatial scales of fish community traits over the course of the study, although there were small inter-annual shifts in the importance of regional basin- and local site-scale variables in determining community trait composition (e.g., life-history, trophic, and thermal). The overriding effects of regional-scale variables may be related to inter-annual variation in average summer temperature. Additionally, drivers of fish community traits were highly variable among study years, with some years dominated by environmental variation and others dominated by spatially structured variation. The influence of spatial factors on trait composition was dynamic, which suggests that spatial patterns in fish communities over large landscapes are transient. Air temperature and vegetation were significant variables in most years, underscoring the importance of future climate change and shoreline development as drivers of fish community structure. Overall, a trait-based hierarchical framework may be a useful conservation tool, as it highlights the multi-scaled interactive effect of variables over a large landscape.

Spatial and temporal aspects of the genetic structure of Juniperus communis populations.

PubMed

Merwe, M V; Winfield, M O; Arnold, G M; Parker, J S

2000-04-01

Juniperus communis is a dioecious, wind pollinated shrub or small tree that produces 'berries' (female cones) containing a small number of seeds that are thought to be dispersed by birds. The expectation, therefore, would be that populations of Juniper are genetically diverse with little structuring between them. In Britain, the species has two main centres of distribution: a highland zone in the north and west, in which populations are still large and sexually reproducing, and a southern zone on chalk downlands in which populations are small and fragmented and individuals suffer from a decline in fertility. Thus, one would expect the large sexually viable populations in the north to exhibit high levels of within-population genetic variation, while the declining southern populations would be genetically depauperate. The analysis of amplified fragment length polymorphisms (AFLPs) was used to test this hypothesis. Surprisingly, all populations studied showed high levels of genetic variation although there was clear structuring between populations. On the basis of the geographical structuring of the populations it was hypothesized that J. communis colonized Britain via three separate routes.

Solar Wind Speed Structure in the Inner Corona at 3-12 Ro

NASA Technical Reports Server (NTRS)

Woo, Richard

1995-01-01

Estimates of solar wind speed obtained by Armstrong et al. [1986] based on 1983 VLA multiple-station intensity scintillation measurements inside 12 R(sub o) have been correlated with the electron density structure observed in white-light coronagraph measurements. The observed large- scale and apparently systematic speed variations are found to depend primarily on changes in heliographic latitude and longitude, which leads to the first results on large-scale speed structure in the acceleration region of the solar wind. Over an equatorial hole, solar wind speed is relatively steady, with peak-to-peak variations of 50 km/s and an average of 230 km/s. In contrast, the near-Sun flow speed across the streamer belt shows regular large-scale variations in the range of 100-300 km/s. Based on four groups of data, the gradient is 36 km/s per degree in heliocentric coordinates (corresponding to a rise of 260 km/s over a spatial distance on the Sun of two arcmin) with a standard deviation of 2.4 km/s per degree. The lowest speeds most likely coincide with the stalks of coronal streamers observed in white-light measurements. The detection of significant wind shear over the streamer belt is consistent with in situ and scintillation measurements showing that the density spectrum has a power-law form characteristic of fully developed turbulence over a much broader range of scales than in neighboring regions.

Regional-scale drivers of forest structure and function in northwestern Amazonia.

PubMed

Higgins, Mark A; Asner, Gregory P; Anderson, Christopher B; Martin, Roberta E; Knapp, David E; Tupayachi, Raul; Perez, Eneas; Elespuru, Nydia; Alonso, Alfonso

2015-01-01

Field studies in Amazonia have found a relationship at continental scales between soil fertility and broad trends in forest structure and function. Little is known at regional scales, however, about how discrete patterns in forest structure or functional attributes map onto underlying edaphic or geological patterns. We collected airborne LiDAR (Light Detection and Ranging) data and VSWIR (Visible to Shortwave Infrared) imaging spectroscopy measurements over 600 km2 of northwestern Amazonian lowland forests. We also established 83 inventories of plant species composition and soil properties, distributed between two widespread geological formations. Using these data, we mapped forest structure and canopy reflectance, and compared them to patterns in plant species composition, soils, and underlying geology. We found that variations in soils and species composition explained up to 70% of variation in canopy height, and corresponded to profound changes in forest vertical profiles. We further found that soils and plant species composition explained more than 90% of the variation in canopy reflectance as measured by imaging spectroscopy, indicating edaphic and compositional control of canopy chemical properties. We last found that soils explained between 30% and 70% of the variation in gap frequency in these forests, depending on the height threshold used to define gaps. Our findings indicate that a relatively small number of edaphic and compositional variables, corresponding to underlying geology, may be responsible for variations in canopy structure and chemistry over large expanses of Amazonian forest.

Conserving genomic variability in large mammals: Effect of population fluctuations and variance in male reproductive success on variability in Yellowstone bison

Treesearch

Andres Perez-Figueroa; Rick L. Wallen; Tiago Antao; Jason A. Coombs; Michael K. Schwartz; P. J. White; Gordon Luikart

2012-01-01

Loss of genetic variation through genetic drift can reduce population viability. However, relatively little is known about loss of variation caused by the combination of fluctuating population size and variance in reproductive success in age structured populations. We built an individual-based computer simulation model to examine how actual culling and hunting...

Human structural variation: mechanisms of chromosome rearrangements

PubMed Central

Weckselblatt, Brooke; Rudd, M. Katharine

2015-01-01

Chromosome structural variation (SV) is a normal part of variation in the human genome, but some classes of SV can cause neurodevelopmental disorders. Analysis of the DNA sequence at SV breakpoints can reveal mutational mechanisms and risk factors for chromosome rearrangement. Large-scale SV breakpoint studies have become possible recently owing to advances in next-generation sequencing (NGS) including whole-genome sequencing (WGS). These findings have shed light on complex forms of SV such as triplications, inverted duplications, insertional translocations, and chromothripsis. Sequence-level breakpoint data resolve SV structure and determine how genes are disrupted, fused, and/or misregulated by breakpoints. Recent improvements in breakpoint sequencing have also revealed non-allelic homologous recombination (NAHR) between paralogous long interspersed nuclear element (LINE) or human endogenous retrovirus (HERV) repeats as a cause of deletions, duplications, and translocations. This review covers the genomic organization of simple and complex constitutional SVs, as well as the molecular mechanisms of their formation. PMID:26209074

Multiscale structure of time series revealed by the monotony spectrum.

PubMed

Vamoş, Călin

2017-03-01

Observation of complex systems produces time series with specific dynamics at different time scales. The majority of the existing numerical methods for multiscale analysis first decompose the time series into several simpler components and the multiscale structure is given by the properties of their components. We present a numerical method which describes the multiscale structure of arbitrary time series without decomposing them. It is based on the monotony spectrum defined as the variation of the mean amplitude of the monotonic segments with respect to the mean local time scale during successive averagings of the time series, the local time scales being the durations of the monotonic segments. The maxima of the monotony spectrum indicate the time scales which dominate the variations of the time series. We show that the monotony spectrum can correctly analyze a diversity of artificial time series and can discriminate the existence of deterministic variations at large time scales from the random fluctuations. As an application we analyze the multifractal structure of some hydrological time series.

Variation in mangrove forest structure and sediment characteristics in Bocas del Toro, Panama

USGS Publications Warehouse

Lovelock, C.E.; Feller, Ilka C.; McKee, K.L.; Thompson, R.

2005-01-01

Mangrove forest structure and sediment characteristics were examined in the extensive mangroves of Bocas del Toro, Republic of Panama. Forest structure was characterized to determine if spatial vegetation patterns were repeated over the Bocas del Toro landscape. Using a series of permanent plots and transects we found that the forests of Bocas del Toro were dominated by Rhizophora mangle with very few individuals of Avicennia germinans and Laguncularia racemosa. Despite this low species diversity, there was large variation in forest structure and in edaphic conditions (salinity, concentration of available phosphorus, Eh and sulphide concentration). Aboveground biomass varied 20-fold, from 6.8 Mg ha-1 in dwarf forests to 194.3 Mg ha-1 in the forests fringing the land. But variation in forest structure was predictable across the intertidal zone. There was a strong tree height gradient from seaward fringe (mean tree height 3.9 m), decreasing in stature in the interior dwarf forests (mean tree height 0.7 m), and increasing in stature in forests adjacent to the terrestrial forest (mean tree height 4.1 m). The predictable variation in forest structure emerges due to the complex interactions among edaphic and plant factors. Identifying predictable patterns in forest structure will aid in scaling up the ecosystem services provided by mangrove forests in coastal landscapes. Copyright 2005 College of Arts and Sciences.

Space Technology 5 Multi-Point Observations of Temporal Variability of Field-Aligned Currents

NASA Technical Reports Server (NTRS)

Le, Guan; Wang, Yongli; Slavin, James A.; Strangeway, Robert J.

2008-01-01

Space Technology 5 (ST5) is a three micro-satellite constellation deployed into a 300 x 4500 km, dawn-dusk, sun-synchronous polar orbit from March 22 to June 21, 2006, for technology validations. In this paper, we present a study of the temporal variability of field-aligned currents using multi-point magnetic field measurements from ST5. The data demonstrate that meso-scale current structures are commonly embedded within large-scale field-aligned current sheets. The meso-scale current structures are very dynamic with highly variable current density and/or polarity in time scales of approximately 10 min. They exhibit large temporal variations during both quiet and disturbed times in such time scales. On the other hand, the data also shown that the time scales for the currents to be relatively stable are approximately 1 min for meso-scale currents and approximately 10 min for large scale current sheets. These temporal features are obviously associated with dynamic variations of their particle carriers (mainly electrons) as they respond to the variations of the parallel electric field in auroral acceleration region. The characteristic time scales for the temporal variability of meso-scale field-aligned currents are found to be consistent with those of auroral parallel electric field.

Space Technology 5 (ST-5) Observations of Field-Aligned Currents: Temporal Variability

NASA Technical Reports Server (NTRS)

Le, Guan

2010-01-01

Space Technology 5 (ST-5) is a three micro-satellite constellation deployed into a 300 x 4500 km, dawn-dusk, sun-synchronous polar orbit from March 22 to June 21, 2006, for technology validations. In this paper, we present a study of the temporal variability of field-aligned currents using multi-point magnetic field measurements from STS. The data demonstrate that masoscale current structures are commonly embedded within large-scale field-aligned current sheets. The meso-scale current structures are very dynamic with highly variable current density and/or polarity in time scales of about 10 min. They exhibit large temporal variations during both quiet and disturbed times in such time scales. On the other hand, the data also shown that the time scales for the currents to be relatively stable are about I min for meso-scale currents and about 10 min for large scale current sheets. These temporal features are obviously associated with dynamic variations of their particle carriers (mainly electrons) as they respond to the variations of the parallel electric field in auroral acceleration region. The characteristic time scales for the temporal variability of meso-scale field-aligned currents are found to be consistent with those of auroral parallel electric field.

Space Technology 5 (ST-5) Multipoint Observations of Temporal and Spatial Variability of Field-Aligned Currents

NASA Technical Reports Server (NTRS)

Le, Guan

2010-01-01

Space Technology 5 (ST-5) is a three micro-satellite constellation deployed into a 300 x 4500 km, dawn-dusk, sun-synchronous polar orbit from March 22 to June 21, 2006, for technology validations. In this paper, we present a study of the temporal variability of field-aligned currents using multi-point magnetic field measurements from ST5. The data demonstrate that mesoscale current structures are commonly embedded within large-scale field-aligned current sheets. The meso-scale current structures are very dynamic with highly variable current density and/or polarity in time scales of about 10 min. They exhibit large temporal variations during both quiet and disturbed times in such time scales. On the other hand, the data also shown that the time scales for the currents to be relatively stable are about 1 min for meso-scale currents and about 10 min for large scale current sheets. These temporal features are obviously associated with dynamic variations of their particle carriers (mainly electrons) as they respond to the variations of the parallel electric field in auroral acceleration region. The characteristic time scales for the temporal variability of meso-scale field-aligned currents are found to be consistent with those of auroral parallel electric field.

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

Kataria, T.; Showman, A. P.; Fortney, J. J.

We present three-dimensional atmospheric circulation models of GJ 1214b, a 2.7 Earth-radius, 6.5 Earth-mass super Earth detected by the MEarth survey. Here we explore the planet's circulation as a function of atmospheric metallicity and atmospheric composition, modeling atmospheres with a low mean molecular weight (MMW; i.e., H{sub 2}-dominated) and a high MMW (i.e., water- and CO{sub 2}-dominated). We find that atmospheres with a low MMW have strong day-night temperature variations at pressures above the infrared photosphere that lead to equatorial superrotation. For these atmospheres, the enhancement of atmospheric opacities with increasing metallicity lead to shallower atmospheric heating, larger day-night temperaturemore » variations, and hence stronger superrotation. In comparison, atmospheres with a high MMW have larger day-night and equator-to-pole temperature variations than low MMW atmospheres, but differences in opacity structure and energy budget lead to differences in jet structure. The circulation of a water-dominated atmosphere is dominated by equatorial superrotation, while the circulation of a CO{sub 2}-dominated atmosphere is instead dominated by high-latitude jets. By comparing emergent flux spectra and light curves for 50× solar and water-dominated compositions, we show that observations in emission can break the degeneracy in determining the atmospheric composition of GJ 1214b. The variation in opacity with wavelength for the water-dominated atmosphere leads to large phase variations within water bands and small phase variations outside of water bands. The 50× solar atmosphere, however, yields small variations within water bands and large phase variations at other characteristic wavelengths. These observations would be much less sensitive to clouds, condensates, and hazes than transit observations.« less

Insights into structural variations and genome rearrangements in prokaryotic genomes.

PubMed

Periwal, Vinita; Scaria, Vinod

2015-01-01

Structural variations (SVs) are genomic rearrangements that affect fairly large fragments of DNA. Most of the SVs such as inversions, deletions and translocations have been largely studied in context of genetic diseases in eukaryotes. However, recent studies demonstrate that genome rearrangements can also have profound impact on prokaryotic genomes, leading to altered cell phenotype. In contrast to single-nucleotide variations, SVs provide a much deeper insight into organization of bacterial genomes at a much better resolution. SVs can confer change in gene copy number, creation of new genes, altered gene expression and many other functional consequences. High-throughput technologies have now made it possible to explore SVs at a much refined resolution in bacterial genomes. Through this review, we aim to highlight the importance of the less explored field of SVs in prokaryotic genomes and their impact. We also discuss its potential applicability in the emerging fields of synthetic biology and genome engineering where targeted SVs could serve to create sophisticated and accurate genome editing. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

An extended algebraic variational multiscale-multigrid-multifractal method (XAVM4) for large-eddy simulation of turbulent two-phase flow

NASA Astrophysics Data System (ADS)

Rasthofer, U.; Wall, W. A.; Gravemeier, V.

2018-04-01

A novel and comprehensive computational method, referred to as the eXtended Algebraic Variational Multiscale-Multigrid-Multifractal Method (XAVM4), is proposed for large-eddy simulation of the particularly challenging problem of turbulent two-phase flow. The XAVM4 involves multifractal subgrid-scale modeling as well as a Nitsche-type extended finite element method as an approach for two-phase flow. The application of an advanced structural subgrid-scale modeling approach in conjunction with a sharp representation of the discontinuities at the interface between two bulk fluids promise high-fidelity large-eddy simulation of turbulent two-phase flow. The high potential of the XAVM4 is demonstrated for large-eddy simulation of turbulent two-phase bubbly channel flow, that is, turbulent channel flow carrying a single large bubble of the size of the channel half-width in this particular application.

Diversity and Assembling Processes of Bacterial Communities in Cryoconite Holes of a Karakoram Glacier.

PubMed

Ambrosini, Roberto; Musitelli, Federica; Navarra, Federico; Tagliaferri, Ilario; Gandolfi, Isabella; Bestetti, Giuseppina; Mayer, Christoph; Minora, Umberto; Azzoni, Roberto Sergio; Diolaiuti, Guglielmina; Smiraglia, Claudio; Franzetti, Andrea

2017-05-01

Cryoconite holes are small ponds that form on the surface of glaciers that contain a dark debris, the cryoconite, at the bottom and host active ecological communities. Differences in the structure of bacterial communities have been documented among Arctic and mountain glaciers, and among glaciers in different areas of the world. In this study, we investigated the structure of bacterial communities of cryoconite holes of Baltoro Glacier, a large (62 km in length and 524 km 2 of surface) glacier of the Karakoram, by high-throughput sequencing of the V5-V6 hypervariable regions of the 16S rRNA gene. We found that Betaproteobacteria dominated bacterial communities, with large abundance of genera Polaromonas, probably thanks to its highly versatile metabolism, and Limnohabitans, which may have been favoured by the presence of supraglacial lakes in the area where cryoconite holes were sampled. Variation in bacterial communities among different sampling areas of the glacier could be explained by divergent selective processes driven by variation in environmental conditions, particularly pH, which was the only environmental variable that significantly affected the structure of bacterial communities. This variability may be due to both temporal and spatial patterns of variation in environmental conditions.

Precise colocalization of interacting structural and pigmentary elements generates extensive color pattern variation in Phelsuma lizards

PubMed Central

2013-01-01

Background Color traits in animals play crucial roles in thermoregulation, photoprotection, camouflage, and visual communication, and are amenable to objective quantification and modeling. However, the extensive variation in non-melanic pigments and structural colors in squamate reptiles has been largely disregarded. Here, we used an integrated approach to investigate the morphological basis and physical mechanisms generating variation in color traits in tropical day geckos of the genus Phelsuma. Results Combining histology, optics, mass spectrometry, and UV and Raman spectroscopy, we found that the extensive variation in color patterns within and among Phelsuma species is generated by complex interactions between, on the one hand, chromatophores containing yellow/red pteridine pigments and, on the other hand, iridophores producing structural color by constructive interference of light with guanine nanocrystals. More specifically, we show that 1) the hue of the vivid dorsolateral skin is modulated both by variation in geometry of structural, highly ordered narrowband reflectors, and by the presence of yellow pigments, and 2) that the reflectivity of the white belly and of dorsolateral pigmentary red marks, is increased by underlying structural disorganized broadband reflectors. Most importantly, these interactions require precise colocalization of yellow and red chromatophores with different types of iridophores, characterized by ordered and disordered nanocrystals, respectively. We validated these results through numerical simulations combining pigmentary components with a multilayer interferential optical model. Finally, we show that melanophores form dark lateral patterns but do not significantly contribute to variation in blue/green or red coloration, and that changes in the pH or redox state of pigments provide yet another source of color variation in squamates. Conclusions Precisely colocalized interacting pigmentary and structural elements generate extensive variation in lizard color patterns. Our results indicate the need to identify the developmental mechanisms responsible for the control of the size, shape, and orientation of nanocrystals, and the superposition of specific chromatophore types. This study opens up new perspectives on Phelsuma lizards as models in evolutionary developmental biology. PMID:24099066

Visualizing the molecular sociology at the HeLa cell nuclear periphery.

PubMed

Mahamid, Julia; Pfeffer, Stefan; Schaffer, Miroslava; Villa, Elizabeth; Danev, Radostin; Cuellar, Luis Kuhn; Förster, Friedrich; Hyman, Anthony A; Plitzko, Jürgen M; Baumeister, Wolfgang

2016-02-26

The molecular organization of eukaryotic nuclear volumes remains largely unexplored. Here we combined recent developments in cryo-electron tomography (cryo-ET) to produce three-dimensional snapshots of the HeLa cell nuclear periphery. Subtomogram averaging and classification of ribosomes revealed the native structure and organization of the cytoplasmic translation machinery. Analysis of a large dynamic structure-the nuclear pore complex-revealed variations detectable at the level of individual complexes. Cryo-ET was used to visualize previously elusive structures, such as nucleosome chains and the filaments of the nuclear lamina, in situ. Elucidation of the lamina structure provides insight into its contribution to metazoan nuclear stiffness. Copyright © 2016, American Association for the Advancement of Science.

Relative importance of local- and large-scale drivers of alpine soil microarthropod communities.

PubMed

Mitchell, Ruth J; Urpeth, Hannah M; Britton, Andrea J; Black, Helaina; Taylor, Astrid R

2016-11-01

Nitrogen (N) deposition and climate are acknowledged drivers of change in biodiversity and ecosystem function at large scales. However, at a local scale, their impact on functions and community structure of organisms is filtered by drivers like habitat quality and food quality/availability. This study assesses the relative impact of large-scale factors, N deposition and climate (rainfall and temperature), versus local-scale factors of habitat quality and food quality/availability on soil fauna communities at 15 alpine moss-sedge heaths along an N deposition gradient in the UK. Habitat quality and food quality/availability were the primary drivers of microarthropod communities. No direct impacts of N deposition on the microarthropod community were observed, but induced changes in habitat quality (decline in moss cover and depth) and food quality (decreased vegetation C:N) associated with increased N deposition strongly suggest an indirect impact of N. Habitat quality and climate explained variation in the composition of the Oribatida, Mesostigmata, and Collembola communities, while only habitat quality significantly impacted the Prostigmata. Food quality and prey availability were important in explaining the composition of the oribatid and mesostigmatid mite communities, respectively. This study shows that, in alpine habitats, soil microarthropod community structure responds most strongly to local-scale variation in habitat quality and food availability rather than large-scale variation in climate and pollution. However, given the strong links between N deposition and the key habitat quality parameters, we conclude that N deposition indirectly drives changes in the soil microarthropod community, suggesting a mechanism by which large-scale drivers indirectly impacts these functionally important groups.

Anomalously strong observations of PKiKP/PcP amplitude ratios on a global scale

NASA Astrophysics Data System (ADS)

Waszek, Lauren; Deuss, Arwen

2015-07-01

The inner core boundary marks the phase transition between the solid inner core and the fluid outer core. As the site of inner core solidification, the boundary provides insight into the processes generating the seismic structures of the inner core. In particular, it may hold the key to understanding the previously observed hemispherical asymmetry in inner core seismic velocity, anisotropy, and attenuation. Here we use a large PKiKP-PcP amplitude ratio and travel time residual data set to investigate velocity and density contrast properties near the inner core boundary. Although hemispherical structure at the boundary has been proposed by previous inner core studies, we find no evidence for hemispheres in the amplitude ratios or travel time residuals. In addition, we find that the amplitude ratios are much larger than can be explained by variations in density contrast at the inner core boundary or core-mantle boundary. This indicates that PKiKP is primarily observed when it is anomalously large, due to focusing along its raypath. Using data in which PKiKP is not detected above the noise level, we calculate an upper estimate for the inner core boundary (ICB) density contrast of 1.2 kg m-3. The travel time residuals display large regional variations, which differ on long and short length scales. These regions may be explained by large-scale velocity variations in the F layer just above the inner core boundary, and/or small-scale topography of varying magnitude on the ICB, which also causes the large amplitudes. Such differences could arise from localized freezing and melting of the inner core.

Are We "Experienced Listeners"? A Review of the Musical Capacities that Do Not Depend on Formal Musical Training

ERIC Educational Resources Information Center

Bigand, E.; Poulin-Charronnat, B.

2006-01-01

The present paper reviews a set of studies designed to investigate different aspects of the capacity for processing Western music. This includes perceiving the relationships between a theme and its variations, perceiving musical tensions and relaxations, generating musical expectancies, integrating local structures in large-scale structures,…

Variation in Soil Microbial Community Structure Associated with Different Legume Species Is Greater than that Associated with Different Grass Species

PubMed Central

Zhou, Yang; Zhu, Honghui; Fu, Shenglei; Yao, Qing

2017-01-01

Plants are the essential factors shaping soil microbial community (SMC) structure. When most studies focus on the difference in the SMC structure associated different plant species, the variation in the SMC structure associated with phylogenetically close species is less investigated. Legume (Fabaceae) and grass (Poaceae) are functionally important plant groups; however, their influences on the SMC structure are seldom compared, and the variation in the SMC structure among legume or grass species is largely unknown. In this study, we grew three legume species vs. three grass species in mesocosms, and monitored the soil chemical property, quantified the abundance of bacteria and fungi. The SMC structure was also characterized using PCR-DGGE and Miseq sequencing. Results showed that legume and grass differentially affected soil pH, dissolved organic C, total N content, and available P content, and that legume enriched fungi more greatly than grass. Both DGGE profiling and Miseq-sequencing indicated that the bacterial diversity associated with legume was higher than that associated with grass. When legume increased the abundance of Verrucomicrobia, grass decreased it, and furthermore, linear discriminant analysis identified some group-specific microbial taxa as potential biomarkers of legume or grass. These data suggest that legume and grass differentially select for the SMC. More importantly, clustering analysis based on both DGGE profiling and Miseq-sequencing demonstrated that the variation in the SMC structure associated with three legume species was greater than that associated with three grass species. PMID:28620371

Spatial Structure of Large-Scale Plasma Density Perturbations HF-Induced in the Ionospheric F 2 Region

NASA Astrophysics Data System (ADS)

Frolov, V. L.; Komrakov, G. P.; Glukhov, Ya. V.; Andreeva, E. S.; Kunitsyn, V. E.; Kurbatov, G. A.

2016-07-01

We consider the experimental results obtained by studying the large-scale structure of the HF-disturbed ionospheric region. The experiments were performed using the SURA heating facility. The disturbed ionospheric region was sounded by signals radiated by GPS navigation satellite beacons as well as by signals of low-orbit satellites (radio tomography). The results of the experiments show that large-scale plasma density perturbations induced at altitudes higher than the F2 layer maximum can contribute significantly to the measured variations of the total electron density and can, with a certain arrangement of the reception points, be measured by the GPS sounding method.

Precision Composite Space Structures

DTIC Science & Technology

2007-10-15

large structures. 15. SUBJECT TERMS Composite materials, dimensional stability, microcracking, thermal expansion , space structures, degradation...Figure 32. Variation of normalized coefficients of thermal expansion α11(n), α22(n), and α33(n) with normalized crack density of an AS4/3501-6...coefficients of thermal expansion α11(n), α22(n), and α33(n) with normalized crack density of an AS4/3501-6 composite lamina with a fiber volume

Some issues related to the novel spectral acceleration method for the fast computation of radiation/scattering from one-dimensional extremely large scale quasi-planar structures

NASA Astrophysics Data System (ADS)

Torrungrueng, Danai; Johnson, Joel T.; Chou, Hsi-Tseng

2002-03-01

The novel spectral acceleration (NSA) algorithm has been shown to produce an $[\\mathcal{O}]$(Ntot) efficient iterative method of moments for the computation of radiation/scattering from both one-dimensional (1-D) and two-dimensional large-scale quasi-planar structures, where Ntot is the total number of unknowns to be solved. This method accelerates the matrix-vector multiplication in an iterative method of moments solution and divides contributions between points into ``strong'' (exact matrix elements) and ``weak'' (NSA algorithm) regions. The NSA method is based on a spectral representation of the electromagnetic Green's function and appropriate contour deformation, resulting in a fast multipole-like formulation in which contributions from large numbers of points to a single point are evaluated simultaneously. In the standard NSA algorithm the NSA parameters are derived on the basis of the assumption that the outermost possible saddle point, φs,max, along the real axis in the complex angular domain is small. For given height variations of quasi-planar structures, this assumption can be satisfied by adjusting the size of the strong region Ls. However, for quasi-planar structures with large height variations, the adjusted size of the strong region is typically large, resulting in significant increases in computational time for the computation of the strong-region contribution and degrading overall efficiency of the NSA algorithm. In addition, for the case of extremely large scale structures, studies based on the physical optics approximation and a flat surface assumption show that the given NSA parameters in the standard NSA algorithm may yield inaccurate results. In this paper, analytical formulas associated with the NSA parameters for an arbitrary value of φs,max are presented, resulting in more flexibility in selecting Ls to compromise between the computation of the contributions of the strong and weak regions. In addition, a ``multilevel'' algorithm, decomposing 1-D extremely large scale quasi-planar structures into more than one weak region and appropriately choosing the NSA parameters for each weak region, is incorporated into the original NSA method to improve its accuracy.

Large-Deformation Displacement Transfer Functions for Shape Predictions of Highly Flexible Slender Aerospace Structures

NASA Technical Reports Server (NTRS)

Ko, William L.; Fleischer, Van Tran

2013-01-01

Large deformation displacement transfer functions were formulated for deformed shape predictions of highly flexible slender structures like aircraft wings. In the formulation, the embedded beam (depth wise cross section of structure along the surface strain sensing line) was first evenly discretized into multiple small domains, with surface strain sensing stations located at the domain junctures. Thus, the surface strain (bending strains) variation within each domain could be expressed with linear of nonlinear function. Such piecewise approach enabled piecewise integrations of the embedded beam curvature equations [classical (Eulerian), physical (Lagrangian), and shifted curvature equations] to yield closed form slope and deflection equations in recursive forms.

Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale.

PubMed

Liu, Siyang; Huang, Shujia; Rao, Junhua; Ye, Weijian; Krogh, Anders; Wang, Jun

2015-01-01

Comprehensive recognition of genomic variation in one individual is important for understanding disease and developing personalized medication and treatment. Many tools based on DNA re-sequencing exist for identification of single nucleotide polymorphisms, small insertions and deletions (indels) as well as large deletions. However, these approaches consistently display a substantial bias against the recovery of complex structural variants and novel sequence in individual genomes and do not provide interpretation information such as the annotation of ancestral state and formation mechanism. We present a novel approach implemented in a single software package, AsmVar, to discover, genotype and characterize different forms of structural variation and novel sequence from population-scale de novo genome assemblies up to nucleotide resolution. Application of AsmVar to several human de novo genome assemblies captures a wide spectrum of structural variants and novel sequences present in the human population in high sensitivity and specificity. Our method provides a direct solution for investigating structural variants and novel sequences from de novo genome assemblies, facilitating the construction of population-scale pan-genomes. Our study also highlights the usefulness of the de novo assembly strategy for definition of genome structure.

Regional-Scale Drivers of Forest Structure and Function in Northwestern Amazonia

PubMed Central

Higgins, Mark A.; Asner, Gregory P.; Anderson, Christopher B.; Martin, Roberta E.; Knapp, David E.; Tupayachi, Raul; Perez, Eneas; Elespuru, Nydia; Alonso, Alfonso

2015-01-01

Field studies in Amazonia have found a relationship at continental scales between soil fertility and broad trends in forest structure and function. Little is known at regional scales, however, about how discrete patterns in forest structure or functional attributes map onto underlying edaphic or geological patterns. We collected airborne LiDAR (Light Detection and Ranging) data and VSWIR (Visible to Shortwave Infrared) imaging spectroscopy measurements over 600 km2 of northwestern Amazonian lowland forests. We also established 83 inventories of plant species composition and soil properties, distributed between two widespread geological formations. Using these data, we mapped forest structure and canopy reflectance, and compared them to patterns in plant species composition, soils, and underlying geology. We found that variations in soils and species composition explained up to 70% of variation in canopy height, and corresponded to profound changes in forest vertical profiles. We further found that soils and plant species composition explained more than 90% of the variation in canopy reflectance as measured by imaging spectroscopy, indicating edaphic and compositional control of canopy chemical properties. We last found that soils explained between 30% and 70% of the variation in gap frequency in these forests, depending on the height threshold used to define gaps. Our findings indicate that a relatively small number of edaphic and compositional variables, corresponding to underlying geology, may be responsible for variations in canopy structure and chemistry over large expanses of Amazonian forest. PMID:25793602

Structural stigma and the health and wellbeing of Australian LGB populations: Exploiting geographic variation in the results of the 2017 same-sex marriage plebiscite.

PubMed

Perales, Francisco; Todd, Abram

2018-05-14

Lesbian, gay, or bisexual (LGB) people experience poorer life outcomes than heterosexual people, with ongoing debates about the aetiology of these differences. Minority stress theory draws attention to the importance of structural stigma, which concerns hostile social environments for sexual minorities that constrain their opportunity structures. Yet few studies have operationalised structural stigma and tested its influence, with most focusing on the US context; even fewer studies examine the underlying mechanisms. This study expands the available evidence to Australia, which constitutes an interesting case study due to the implementation in late 2017 of a national postal plebiscite on same-sex marriage legislation. It also adds to knowledge by theorising and testing the mediating role of perceived social support in explaining the association between structural stigma and the life outcomes of LGB people. The analyses leverage geographical variation at the electorate level (n = 150) in the share of 'No' voters in the plebiscite as a measure of structural stigma. This aggregate-level information is merged to individual-level data from the Household, Income and Labour Dynamics in Australia Survey, a large, national probability sample (n∽15,000). Multilevel regression models yield results which are consistent with minority stress theory and previous US scholarship: LGB people report comparatively worse life satisfaction, mental health and overall health in constituencies with higher shares of 'No' voters, controlling for a large set of individual- and aggregate-level confounds. Perceived social support mediates a large portion of the effects of structural stigma on LGB outcomes. These findings have significant implications for policy and practice, highlighting the need for interventions aimed at reducing community levels of structural stigma and increasing social support to LGB populations. Copyright © 2018 Elsevier Ltd. All rights reserved.

Dispersion Measure Variation of Repeating Fast Radio Burst Sources

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

Yang, Yuan-Pei; Zhang, Bing, E-mail: yypspore@gmail.com, E-mail: zhang@physics.unlv.edu

The repeating fast radio burst (FRB) 121102 was recently localized in a dwarf galaxy at a cosmological distance. The dispersion measure (DM) derived for each burst from FRB 121102 so far has not shown significant evolution, even though an apparent increase was recently seen with newly detected VLA bursts. It is expected that more repeating FRB sources may be detected in the future. In this work, we investigate a list of possible astrophysical processes that might cause DM variation of a particular FRB source. The processes include (1) cosmological scale effects such as Hubble expansion and large-scale structure fluctuations; (2)more » FRB local effects such as gas density fluctuation, expansion of a supernova remnant (SNR), a pulsar wind nebula, and an H ii region; and (3) the propagation effect due to plasma lensing. We find that the DM variations contributed by the large-scale structure are extremely small, and any observable DM variation is likely caused by the plasma local to the FRB source. In addition to mechanisms that decrease DM over time, we suggest that an FRB source in an expanding SNR around a nearly neutral ambient medium during the deceleration (Sedov–Taylor and snowplow) phases or in a growing H ii region can increase DM. Some effects (e.g., an FRB source moving in an H ii region or plasma lensing) can produce either positive or negative DM variations. Future observations of DM variations of FRB 121102 and other repeating FRB sources can provide important clues regarding the physical origin of these sources.« less

Population size, center-periphery, and seed dispersers' effects on the genetic diversity and population structure of the Mediterranean relict shrub Cneorum tricoccon.

PubMed

Lázaro-Nogal, Ana; Matesanz, Silvia; García-Fernández, Alfredo; Traveset, Anna; Valladares, Fernando

2017-09-01

The effect of population size on population genetic diversity and structure has rarely been studied jointly with other factors such as the position of a population within the species' distribution range or the presence of mutualistic partners influencing dispersal. Understanding these determining factors for genetic variation is critical for conservation of relict plants that are generally suffering from genetic deterioration. Working with 16 populations of the vulnerable relict shrub Cneorum tricoccon throughout the majority of its western Mediterranean distribution range, and using nine polymorphic microsatellite markers, we examined the effects of periphery (peripheral vs. central), population size (large vs. small), and seed disperser (introduced carnivores vs. endemic lizards) on the genetic diversity and population structure of the species. Contrasting genetic variation ( H E : 0.04-0.476) was found across populations. Peripheral populations showed lower genetic diversity, but this was dependent on population size. Large peripheral populations showed high levels of genetic diversity, whereas small central populations were less diverse. Significant isolation by distance was detected, indicating that the effect of long-distance gene flow is limited relative to that of genetic drift, probably due to high selfing rates ( F IS  = 0.155-0.887), restricted pollen flow, and ineffective seed dispersal. Bayesian clustering also supported the strong population differentiation and highly fragmented structure. Contrary to expectations, the type of disperser showed no significant effect on either population genetic diversity or structure. Our results challenge the idea of an effect of periphery per se that can be mainly explained by population size, drawing attention to the need of integrative approaches considering different determinants of genetic variation. Furthermore, the very low genetic diversity observed in several small populations and the strong among-population differentiation highlight the conservation value of large populations throughout the species' range, particularly in light of climate change and direct human threats.

Organic pi-stacking Semiconducting Material: Design, Synthesis and the Analysis of Structure and Properties

NASA Astrophysics Data System (ADS)

Wilkinson, Taylor Marie

Oil shales are naturally occurring heterogeneous composites with micro-scale, micro-structural variations. They may be found throughout the world, with large deposits located in the United States; shales are composed of organic matter known as kerogen, clays, calcite, quartz, and other minerals. Typically their microstructure consists of a composite network where the organic matter is housed in open and closed pores between different mineral phases that range in size from sub-micron to several microns. Currently, it is unknown how the micro-scale heterogeneity of the shale will impact hydraulic fracture, which is the key extraction technique used for these materials. In this thesis, high-resolution topographic and modulus maps were collected from oil shales with the use of new nanoindentation techniques in order to characterize the micro-scale, micro-structural variations that are typical for these materials. Dynamic modulus mapping allows for substantially higher spatial resolution of properties across grains and intragranular regions of kerogen than has previously been produced with standard quasistatic indentation methods. For accurate scanning, surface variations were minimized to maintain uniform contact of the tip and appropriate quasi-static and dynamic forces were used to maintain displacement amplitudes that avoid plastic deformation of the sample. Sample preparation to minimize surface roughness was completed with the use of focused ion beam milling, however, some variation was still noted. Due to the large changes in modulus values between the constituents of the shale, there were variations in the recorded displacement amplitude values as well. In order to distinguish biased data due to surface topography or a lack of displacement amplitude, filtering techniques were developed, optimization and implemented. Variations in surface topography, which resulted in the indenter tip not being able to accurately resolve surface features, and inadequate displacement amplitude values that prohibit differentiation between material changes and the noise floor of the machine, were removed. These filters resulted in a more valid interpretation of the micro-scale, micro-structural features and arrangement, as well as the mechanical properties, that are common to oil shales.

Role of Defects on Regioselectivity of Nano Pristine Graphene.

PubMed

Kudur Jayaprakash, Gururaj; Casillas, Norberto; Astudillo-Sánchez, Pablo D; Flores-Moreno, Roberto

2016-11-17

Here analytical Fukui functions based on density functional theory are applied to investigate the redox reactivity of pristine and defected graphene lattices. A carbon H-terminated graphene structure (with 96 carbon atoms) and a graphene defected surface with Stone-Wales rearrangement and double vacancy defects are used as models. Pristine sp 2 -hybridized, hexagonal arranged carbon atoms exhibit a symmetric reactivity. In contrast, common carbon atoms at reconstructed polygons in Stone-Wales and double vacancy graphene display large reactivity variations. The improved reactivity and the regioselectivity at defected graphene is correlated to structural changes that caused carbon-carbon bond length variations at defected zones.

Whole Genome Sequencing Identifies a 78 kb Insertion from Chromosome 8 as the Cause of Charcot-Marie-Tooth Neuropathy CMTX3

PubMed Central

Brewer, Megan H.; Chaudhry, Rabia; Qi, Jessica; Kidambi, Aditi; Drew, Alexander P.; Ryan, Monique M.; Subramanian, Gopinath M.; Young, Helen K.; Zuchner, Stephan; Reddel, Stephen W.; Nicholson, Garth A.; Kennerson, Marina L.

2016-01-01

With the advent of whole exome sequencing, cases where no pathogenic coding mutations can be found are increasingly being observed in many diseases. In two large, distantly-related families that mapped to the Charcot-Marie-Tooth neuropathy CMTX3 locus at chromosome Xq26.3-q27.3, all coding mutations were excluded. Using whole genome sequencing we found a large DNA interchromosomal insertion within the CMTX3 locus. The 78 kb insertion originates from chromosome 8q24.3, segregates fully with the disease in the two families, and is absent from the general population as well as 627 neurologically normal chromosomes from in-house controls. Large insertions into chromosome Xq27.1 are known to cause a range of diseases and this is the first neuropathy phenotype caused by an interchromosomal insertion at this locus. The CMTX3 insertion represents an understudied pathogenic structural variation mechanism for inherited peripheral neuropathies. Our finding highlights the importance of considering all structural variation types when studying unsolved inherited peripheral neuropathy cases with no pathogenic coding mutations. PMID:27438001

Species composition and morphologic variation of Porites in the Gulf of California

NASA Astrophysics Data System (ADS)

López-Pérez, R. A.

2013-09-01

Morphometric analysis of corallite calices confirmed that from the late Miocene to the Recent, four species of Porites have inhabited the Gulf of California: the extinct Porites carrizensis, the locally extirpated Porites lobata and the extant Porites sverdrupi and Porites panamensis. Furthermore, large-scale spatial and temporal phenotypic plasticity was observed in the dominant species P. panamensis. Canonical discriminant analysis and ANOVA demonstrated that the calice structures of P. panamensis experienced size reduction between the late Pleistocene and Recent. Similarly, PERMANOVA, regression and correlation analyses demonstrated that across the 800 km north to south in the gulf, P. panamensis populations displayed a similar reduction in calice structures. Based on correlation analysis with environmental data, these large spatial changes are likely related to changes in nutrient concentration and sea surface temperature. As such, the large-scale spatial and temporal phenotypic variation recorded in populations of P. panamensis in the Gulf of California is likely related to optimization of corallite performance (energy acquisition) within various environmental scenarios. These findings may have relevance to modern conservation efforts within this ecological dominant genus.

Numerical simulation of scouring-deposition variations caused by rainfall-induced landslides in the upstream of Zengwun River, Taiwan

NASA Astrophysics Data System (ADS)

Lee, Ming-Hsi; Liao, Yi-Wen; Tsai, Kuang-Jung

2017-04-01

In recent years, the increasing sediment disasters of severe rainfall-induced landslides on human lives and lifeline facilities worldwide have advanced the necessity to find out both economically acceptable and useful techniques to predict the occurrence and destructive power of the disasters. In August 2009, Typhoon Morakot brought a large amount of rainfall with both high intensity and long duration to a vast area of Taiwan. Unfortunately, this resulted in a catastrophic landslide in watershed of Zengwun-River reservoir, southern Taiwan. Meanwhile, large amounts of landslides were formed in the upstream of Zengwun River. The major scope of this study is to apply numerical model to simulate the scouring-deposition variations caused by rainfall-induced landslides that occurred in the upstream of Zengwun River during Typhoon Morakot. This study proposed the relation diagrams of the intermediate diameter (d50), recurrence interval (T) and scouring-deposition depth (D), and applied the diagrams to understand the impacts of the scouring-deposition variations on the structures for water and soil conservation and their measurements. Based on the simulation of scouring-deposition variation at the Da-Bu dam and Da-Bang dam, this study also discussed the scouring-deposition variations of different sections under different scenarios (including flow rate, intermediate diameters and structures). In summary, the result suggested that the diagrams of the intermediate diameter, recurrence interval and scouring-deposition depth could be used as the reference for designing the check dams, ground sills and lateral constructions.

New Synthesis Of Poly(1,3,4-Oxadiazoles)

NASA Technical Reports Server (NTRS)

Connell, John W.; Hergenrother, Paul M.; Wolf, Peter

1992-01-01

Synthesis via aromatic nucleophilic displacement yields new high-molecular-weight polymers. Polymers exhibited good mechanical and thermal properties. Synthetic route provided high-molecular-weight POX of new chemical structure, potentially more economical. Availability of large variety of activated aromatic dihalides, facilitates variation of chemical structures. Exhibit properties making them useful as films. Also useful in coatings, adhesives, moldings, and composites.

Population structure of resident, immigrant, and swimming Corophium volutator (Amphipoda) on an intertidal mudflat in the Bay of Fundy, Canada

NASA Astrophysics Data System (ADS)

Drolet, David; Barbeau, Myriam A.

2012-05-01

Spatial variation in biotic and abiotic conditions, and differences in dispersive behavior of different life history stages can result in the formation of zones with different demography for infaunal and epifaunal species within vast intertidal flats. In this study, we evaluated within-mudflat homogeneity of the infaunal amphipod Corophium volutator found in the mud (residents), colonizing artificially disturbed areas (immigrants), and caught in the water column (swimmers) on a large mudflat in the upper Bay of Fundy, Canada. Densities of residents, immigrants, and swimmers were well structured in space (both along and across shore). Occasionally, significant differences in size structure, sex ratio, and proportion of ovigerous females were found at different intertidal levels, but these were short-lived. Comparisons of size and sex structure of residents, immigrants, and swimmers revealed occasional marked differences, with small juveniles and large adult males moving most. However, this size-bias in movement did not translate into zones with different population dynamics, suggesting that ample dispersal, through swimming and drifting in the water column, homogenized the population and masked potential effects of variation in environmental conditions. We therefore conclude that the mudflat represents one homogeneous population.

Magnetic properties of dendrimer structures with different coordination numbers: A Monte Carlo study

NASA Astrophysics Data System (ADS)

Masrour, R.; Jabar, A.

2016-11-01

We investigate the magnetic properties of Cayley trees of large molecules with dendrimer structure using Monte Carlo simulations. The thermal magnetization and magnetic susceptibility of a dendrimer structure are given with different coordination numbers, Z=3, 4, 5 and different generations g=3 and 2. The variation of magnetizations with the exchange interactions and crystal fields have been given of this system. The magnetic hysteresis cycles have been established.

Variation of employee benefit costs by age.

PubMed

Rappaport, A

2000-01-01

Health care, pension, and disability plans account for the bulk of employers' benefit costs, as defined in this article. Because those costs tend to rise as employees get older, the age structure of the workforce affects not only employers' costs but ultimately their competitiveness in global markets. How much costs vary depends in large part on the structure of the benefits package provided. The method a company chooses to finance benefits generally varies with its size. This article focuses primarily on the benefit practices of large, private employers. In the long run, such employers pay the costs associated with the demographics of their workers, whereas small employers can often pool costs with other companies in the community. In addition, small employers often offer fewer benefits, and the costs and financing of those benefits are subject to the insurance markets and state regulations. The discussion of benefit packages is illustrated by case studies based on benefits that are typical for three types of organizations--a large traditional company such as steel, automobile, and manufacturing; a large financial services company such as a bank or health care organization; and a medium-sized retail organization. The case studies demonstrate the extent to which the costs of typical packages vary and reveal that employers differ radically in the incentives they offer employees to retire at a specific time. An employer can shift the variation in cost by age by changing the structure of the benefit program. The major forces that drive age differences in benefit costs are the time value of money (the period of time available to earn investment income and the operation of compound interest) and rates of health care use, disability, and death. Those forces apply universally, in the United States and elsewhere, and they have not changed in recent years. However, the marketplace and the prevalence of various types of benefit programs have changed, and those changes have generally resulted in less cost variation by age and more frequent employer selection of benefit packages that exhibit less variation by age.

Wall of fundamental constants

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

Olive, Keith A.; School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota, 55455; Peloso, Marco

2011-02-15

We consider the signatures of a domain wall produced in the spontaneous symmetry breaking involving a dilatonlike scalar field coupled to electromagnetism. Domains on either side of the wall exhibit slight differences in their respective values of the fine-structure constant, {alpha}. If such a wall is present within our Hubble volume, absorption spectra at large redshifts may or may not provide a variation in {alpha} relative to the terrestrial value, depending on our relative position with respect to the wall. This wall could resolve the contradiction between claims of a variation of {alpha} based on Keck/Hires data and of themore » constancy of {alpha} based on Very Large Telescope data. We derive the properties of the wall and the parameters of the underlying microscopic model required to reproduce the possible spatial variation of {alpha}. We discuss the constraints on the existence of the low-energy domain wall and describe its observational implications concerning the variation of the fundamental constants.« less

Striking Phenotypic Variation yet Low Genetic Differentiation in Sympatric Lake Trout (Salvelinus namaycush)

PubMed Central

Coon, Andrew; Carson, Robert; Debes, Paul V.

2016-01-01

The study of population differentiation in the context of ecological speciation is commonly assessed using populations with obvious discreteness. Fewer studies have examined diversifying populations with occasional adaptive variation and minor reproductive isolation, so factors impeding or facilitating the progress of early stage differentiation are less understood. We detected non-random genetic structuring in lake trout (Salvelinus namaycush) inhabiting a large, pristine, postglacial lake (Mistassini Lake, Canada), with up to five discernible genetic clusters having distinctions in body shape, size, colouration and head shape. However, genetic differentiation was low (FST = 0.017) and genetic clustering was largely incongruent between several population- and individual-based clustering approaches. Genotype- and phenotype-environment associations with spatial habitat, depth and fish community structure (competitors and prey) were either inconsistent or weak. Striking morphological variation was often more continuous within than among defined genetic clusters. Low genetic differentiation was a consequence of relatively high contemporary gene flow despite large effective population sizes, not migration-drift disequilibrium. Our results suggest a highly plastic propensity for occupying multiple habitat niches in lake trout and a low cost of morphological plasticity, which may constrain the speed and extent of adaptive divergence. We discuss how factors relating to niche conservatism in this species may also influence how plasticity affects adaptive divergence, even where ample ecological opportunity apparently exists. PMID:27680019

Numerical modeling of an estuary: A comprehensive skill assessment

USGS Publications Warehouse

Warner, J.C.; Geyer, W.R.; Lerczak, J.A.

2005-01-01

Numerical simulations of the Hudson River estuary using a terrain-following, three-dimensional model (Regional Ocean Modeling System (ROMS)) are compared with an extensive set of time series and spatially resolved measurements over a 43 day period with large variations in tidal forcing and river discharge. The model is particularly effective at reproducing the observed temporal variations in both the salinity and current structure, including tidal, spring neap, and river discharge-induced variability. Large observed variations in stratification between neap and spring tides are captured qualitatively and quantitatively by the model. The observed structure and variations of the longitudinal salinity gradient are also well reproduced. The most notable discrepancy between the model and the data is in the vertical salinity structure. While the surface-to-bottom salinity difference is well reproduced, the stratification in the model tends to extend all the way to the water surface, whereas the observations indicate a distinct pycnocline and a surface mixed layer. Because the southern boundary coindition is located near the mouth the estuary, the salinity within the domain is particularly sensitive to the specification of salinity at the boundary. A boundary condition for the horizontal salinity gradient, based on the local value of salinity, is developed to incorporate physical processes beyond the open boundary not resolved by the model. Model results are sensitive to the specification of the bottom roughness length and vertical stability functions, insofar as they influence the intensity of vertical mixing. The results only varied slightly between different turbulence closure methods of k-??, k-??, and k-kl. Copyright 2005 by the American Geophysical Union.

Dissecting the relationship between protein structure and sequence variation

NASA Astrophysics Data System (ADS)

Shahmoradi, Amir; Wilke, Claus; Wilke Lab Team

2015-03-01

Over the past decade several independent works have shown that some structural properties of proteins are capable of predicting protein evolution. The strength and significance of these structure-sequence relations, however, appear to vary widely among different proteins, with absolute correlation strengths ranging from 0 . 1 to 0 . 8 . Here we present the results from a comprehensive search for the potential biophysical and structural determinants of protein evolution by studying more than 200 structural and evolutionary properties in a dataset of 209 monomeric enzymes. We discuss the main protein characteristics responsible for the general patterns of protein evolution, and identify sequence divergence as the main determinant of the strengths of virtually all structure-evolution relationships, explaining ~ 10 - 30 % of observed variation in sequence-structure relations. In addition to sequence divergence, we identify several protein structural properties that are moderately but significantly coupled with the strength of sequence-structure relations. In particular, proteins with more homogeneous back-bone hydrogen bond energies, large fractions of helical secondary structures and low fraction of beta sheets tend to have the strongest sequence-structure relation. BEACON-NSF center for the study of evolution in action.

Size and shape in Melipona quadrifasciata anthidioides Lepeletier, 1836 (Hymenoptera; Meliponini).

PubMed

Nunes, L A; Passos, G B; Carvalho, C A L; Araújo, E D

2013-11-01

This study aimed to identify differences in wing shape among populations of Melipona quadrifasciata anthidioides obtained in 23 locations in the semi-arid region of Bahia state (Brazil). Analysis of the Procrustes distances among mean wing shapes indicated that population structure did not determine shape variation. Instead, populations were structured geographically according to wing size. The Partial Mantel Test between morphometric (shape and size) distance matrices and altitude, taking geographic distances into account, was used for a more detailed understanding of size and shape determinants. A partial Mantel test between morphometris (shape and size) variation and altitude, taking geographic distances into account, revealed that size (but not shape) is largely influenced by altitude (r = 0.54 p < 0.01). These results indicate greater evolutionary constraints for the shape variation, which must be directly associated with aerodynamic issues in this structure. The size, however, indicates that the bees tend to have larger wings in populations located at higher altitudes.

Subducting seamounts control interplate coupling and seismic rupture in the 2014 Iquique earthquake area

PubMed Central

Geersen, Jacob; Ranero, César R.; Barckhausen, Udo; Reichert, Christian

2015-01-01

To date, the parameters that determine the rupture area of great subduction zone earthquakes remain contentious. On 1 April 2014, the Mw 8.1 Iquique earthquake ruptured a portion of the well-recognized northern Chile seismic gap but left large highly coupled areas un-ruptured. Marine seismic reflection and swath bathymetric data indicate that structural variations in the subducting Nazca Plate control regional-scale plate-coupling variations, and the limited extent of the 2014 earthquake. Several under-thrusting seamounts correlate to the southward and up-dip arrest of seismic rupture during the 2014 Iquique earthquake, thus supporting a causal link. By fracturing of the overriding plate, the subducting seamounts are likely further responsible for reduced plate-coupling in the shallow subduction zone and in a lowly coupled region around 20.5°S. Our data support that structural variations in the lower plate influence coupling and seismic rupture offshore Northern Chile, whereas the structure of the upper plate plays a minor role. PMID:26419949

Mapping and phasing of structural variation in patient genomes using nanopore sequencing.

PubMed

Cretu Stancu, Mircea; van Roosmalen, Markus J; Renkens, Ivo; Nieboer, Marleen M; Middelkamp, Sjors; de Ligt, Joep; Pregno, Giulia; Giachino, Daniela; Mandrile, Giorgia; Espejo Valle-Inclan, Jose; Korzelius, Jerome; de Bruijn, Ewart; Cuppen, Edwin; Talkowski, Michael E; Marschall, Tobias; de Ridder, Jeroen; Kloosterman, Wigard P

2017-11-06

Despite improvements in genomics technology, the detection of structural variants (SVs) from short-read sequencing still poses challenges, particularly for complex variation. Here we analyse the genomes of two patients with congenital abnormalities using the MinION nanopore sequencer and a novel computational pipeline-NanoSV. We demonstrate that nanopore long reads are superior to short reads with regard to detection of de novo chromothripsis rearrangements. The long reads also enable efficient phasing of genetic variations, which we leveraged to determine the parental origin of all de novo chromothripsis breakpoints and to resolve the structure of these complex rearrangements. Additionally, genome-wide surveillance of inherited SVs reveals novel variants, missed in short-read data sets, a large proportion of which are retrotransposon insertions. We provide a first exploration of patient genome sequencing with a nanopore sequencer and demonstrate the value of long-read sequencing in mapping and phasing of SVs for both clinical and research applications.

Altools: a user friendly NGS data analyser.

PubMed

Camiolo, Salvatore; Sablok, Gaurav; Porceddu, Andrea

2016-02-17

Genotyping by re-sequencing has become a standard approach to estimate single nucleotide polymorphism (SNP) diversity, haplotype structure and the biodiversity and has been defined as an efficient approach to address geographical population genomics of several model species. To access core SNPs and insertion/deletion polymorphisms (indels), and to infer the phyletic patterns of speciation, most such approaches map short reads to the reference genome. Variant calling is important to establish patterns of genome-wide association studies (GWAS) for quantitative trait loci (QTLs), and to determine the population and haplotype structure based on SNPs, thus allowing content-dependent trait and evolutionary analysis. Several tools have been developed to investigate such polymorphisms as well as more complex genomic rearrangements such as copy number variations, presence/absence variations and large deletions. The programs available for this purpose have different strengths (e.g. accuracy, sensitivity and specificity) and weaknesses (e.g. low computation speed, complex installation procedure and absence of a user-friendly interface). Here we introduce Altools, a software package that is easy to install and use, which allows the precise detection of polymorphisms and structural variations. Altools uses the BWA/SAMtools/VarScan pipeline to call SNPs and indels, and the dnaCopy algorithm to achieve genome segmentation according to local coverage differences in order to identify copy number variations. It also uses insert size information from the alignment of paired-end reads and detects potential large deletions. A double mapping approach (BWA/BLASTn) identifies precise breakpoints while ensuring rapid elaboration. Finally, Altools implements several processes that yield deeper insight into the genes affected by the detected polymorphisms. Altools was used to analyse both simulated and real next-generation sequencing (NGS) data and performed satisfactorily in terms of positive predictive values, sensitivity, the identification of large deletion breakpoints and copy number detection. Altools is fast, reliable and easy to use for the mining of NGS data. The software package also attempts to link identified polymorphisms and structural variants to their biological functions thus providing more valuable information than similar tools.

Quantifying side-chain conformational variations in protein structure

PubMed Central

Miao, Zhichao; Cao, Yang

2016-01-01

Protein side-chain conformation is closely related to their biological functions. The side-chain prediction is a key step in protein design, protein docking and structure optimization. However, side-chain polymorphism comprehensively exists in protein as various types and has been long overlooked by side-chain prediction. But such conformational variations have not been quantitatively studied and the correlations between these variations and residue features are vague. Here, we performed statistical analyses on large scale data sets and found that the side-chain conformational flexibility is closely related to the exposure to solvent, degree of freedom and hydrophilicity. These analyses allowed us to quantify different types of side-chain variabilities in PDB. The results underscore that protein side-chain conformation prediction is not a single-answer problem, leading us to reconsider the assessment approaches of side-chain prediction programs. PMID:27845406

Quantifying side-chain conformational variations in protein structure

NASA Astrophysics Data System (ADS)

Miao, Zhichao; Cao, Yang

2016-11-01

Protein side-chain conformation is closely related to their biological functions. The side-chain prediction is a key step in protein design, protein docking and structure optimization. However, side-chain polymorphism comprehensively exists in protein as various types and has been long overlooked by side-chain prediction. But such conformational variations have not been quantitatively studied and the correlations between these variations and residue features are vague. Here, we performed statistical analyses on large scale data sets and found that the side-chain conformational flexibility is closely related to the exposure to solvent, degree of freedom and hydrophilicity. These analyses allowed us to quantify different types of side-chain variabilities in PDB. The results underscore that protein side-chain conformation prediction is not a single-answer problem, leading us to reconsider the assessment approaches of side-chain prediction programs.

Quantifying side-chain conformational variations in protein structure.

PubMed

Miao, Zhichao; Cao, Yang

2016-11-15

Protein side-chain conformation is closely related to their biological functions. The side-chain prediction is a key step in protein design, protein docking and structure optimization. However, side-chain polymorphism comprehensively exists in protein as various types and has been long overlooked by side-chain prediction. But such conformational variations have not been quantitatively studied and the correlations between these variations and residue features are vague. Here, we performed statistical analyses on large scale data sets and found that the side-chain conformational flexibility is closely related to the exposure to solvent, degree of freedom and hydrophilicity. These analyses allowed us to quantify different types of side-chain variabilities in PDB. The results underscore that protein side-chain conformation prediction is not a single-answer problem, leading us to reconsider the assessment approaches of side-chain prediction programs.

Atmospheric pressure, density, temperature and wind variations between 50 and 200 km

NASA Technical Reports Server (NTRS)

Justus, C. G.; Woodrum, A.

1972-01-01

Data on atmospheric pressure, density, temperature and winds between 50 and 200 km were collected from sources including Meteorological Rocket Network data, ROBIN falling sphere data, grenade release and pitot tube data, meteor winds, chemical release winds, satellite data, and others. These data were analyzed by a daily difference method and results on the distribution statistics, magnitude, and spatial structure of the irregular atmospheric variations are presented. Time structures of the irregular variations were determined by the analysis of residuals from harmonic analysis of time series data. The observed height variations of irregular winds and densities are found to be in accord with a theoretical relation between these two quantities. The latitude variations (at 50 - 60 km height) show an increasing trend with latitude. A possible explanation of the unusually large irregular wind magnitudes of the White Sands MRN data is given in terms of mountain wave generation by the Sierra Nevada range about 1000 km west of White Sands. An analytical method is developed which, based on an analogy of the irregular motion field with axisymmetric turbulence, allows measured or model correlation or structure functions to be used to evaluate the effective frequency spectra of scalar and vector quantities of a spacecraft moving at any speed and at any trajectory elevation angle.

Proposed square spiral microfabrication architecture for large three-dimensional photonic band gap crystals.

PubMed

Toader, O; John, S

2001-05-11

We present a blueprint for a three-dimensional photonic band gap (PBG) material that is amenable to large-scale microfabrication on the optical scale using glancing angle deposition methods. The proposed chiral crystal consists of square spiral posts on a tetragonal lattice. In the case of silicon posts in air (direct structure), the full PBG can be as large as 15% of the gap center frequency, whereas for air posts in a silicon background (inverted structure) the maximum PBG is 24% of the center frequency. This PBG occurs between the fourth and fifth bands of the photon dispersion relation and is very robust to variations (disorder) in the geometrical parameters of the crystal.

System for inspecting large size structural components

DOEpatents

Birks, Albert S.; Skorpik, James R.

1990-01-01

The present invention relates to a system for inspecting large scale structural components such as concrete walls or the like. The system includes a mobile gamma radiation source and a mobile gamma radiation detector. The source and detector are constructed and arranged for simultaneous movement along parallel paths in alignment with one another on opposite sides of a structural component being inspected. A control system provides signals which coordinate the movements of the source and detector and receives and records the radiation level data developed by the detector as a function of source and detector positions. The radiation level data is then analyzed to identify areas containing defects corresponding to unexpected variations in the radiation levels detected.

Association mapping of starch chain length distribution and amylose content in pea (Pisum sativum L.) using carbohydrate metabolism candidate genes.

PubMed

Carpenter, Margaret A; Shaw, Martin; Cooper, Rebecca D; Frew, Tonya J; Butler, Ruth C; Murray, Sarah R; Moya, Leire; Coyne, Clarice J; Timmerman-Vaughan, Gail M

2017-08-01

Although starch consists of large macromolecules composed of glucose units linked by α-1,4-glycosidic linkages with α-1,6-glycosidic branchpoints, variation in starch structural and functional properties is found both within and between species. Interest in starch genetics is based on the importance of starch in food and industrial processes, with the potential of genetics to provide novel starches. The starch metabolic pathway is complex but has been characterized in diverse plant species, including pea. To understand how allelic variation in the pea starch metabolic pathway affects starch structure and percent amylose, partial sequences of 25 candidate genes were characterized for polymorphisms using a panel of 92 diverse pea lines. Variation in the percent amylose composition of extracted seed starch and (amylopectin) chain length distribution, one measure of starch structure, were characterized for these lines. Association mapping was undertaken to identify polymorphisms associated with the variation in starch chain length distribution and percent amylose, using a mixed linear model that incorporated population structure and kinship. Associations were found for polymorphisms in seven candidate genes plus Mendel's r locus (which conditions the round versus wrinkled seed phenotype). The genes with associated polymorphisms are involved in the substrate supply, chain elongation and branching stages of the pea carbohydrate and starch metabolic pathways. The association of polymorphisms in carbohydrate and starch metabolic genes with variation in amylopectin chain length distribution and percent amylose may help to guide manipulation of pea seed starch structural and functional properties through plant breeding.

Seismic Constraints on the Mantle Viscosity Structure beneath Antarctica

NASA Astrophysics Data System (ADS)

Wiens, Douglas; Heeszel, David; Aster, Richard; Nyblade, Andrew; Wilson, Terry

2015-04-01

Lateral variations in upper mantle viscosity structure can have first order effects on glacial isostatic adjustment. These variations are expected to be particularly large for the Antarctic continent because of the stark geological contrast between ancient cratonic and recent tectonically active terrains in East and West Antarctica, respectively. A large misfit between observed and predicted GPS rates for West Antarctica probably results in part from the use of a laterally uniform viscosity structure. Although not linked by a simple relationship, mantle seismic velocities can provide important constraints on mantle viscosity structure, as they are both largely controlled by temperature and water content. Recent higher resolution seismic models for the Antarctic mantle, derived from data acquired by new seismic stations deployed in the AGAP/GAMSEIS and ANET/POLENET projects, offer the opportunity to use the seismic velocity structure to place new constraints on the viscosity of the Antarctic upper mantle. We use an Antarctic shear wave velocity model derived from array analysis of Rayleigh wave phase velocities [Heeszel et al, in prep] and examine a variety of methodologies for relating seismic, thermal and rheological parameters to compute a suite of viscosity models for the Antarctic mantle. A wide variety of viscosity structures can be derived using various assumptions, but they share several robust common elements. There is a viscosity contrast of at least two orders of magnitude between East and West Antarctica at depths of 80-250 km, reflecting the boundary between cold cratonic lithosphere in East Antarctica and warm upper mantle in West Antarctica. The region beneath the Ellsworth-Whitmore Mtns and extending to the Pensacola Mtns. shows intermediate viscosity between the extremes of East and West Antarctica. There are also significant variations between different parts of West Antarctica, with the lowest viscosity occurring beneath the Marie Byrd Land (MBL). The MBL Dome and adjacent coastal areas show extremely low viscosity (~1018Pa-s) for most parameterizations, suggesting that low mantle viscosity may produce a very rapid response to ice mass loss in this region.

Gray and white matter correlates of the Big Five personality traits.

PubMed

Privado, Jesús; Román, Francisco J; Saénz-Urturi, Carlota; Burgaleta, Miguel; Colom, Roberto

2017-05-04

Personality neuroscience defines the scientific study of the neurobiological basis of personality. This field assumes that individual differences in personality traits are related with structural and functional variations of the human brain. Gray and white matters are structural properties considered separately in previous research. Available findings in this regard are largely disparate. Here we analyze the relationships between gray matter (cortical thickness (CT), cortical surface area (CSA), and cortical volume) and integrity scores obtained after several white matter tracts connecting different brain regions, with individual differences in the personality traits comprised by the Five-Factor Model (extraversion, agreeableness, conscientiousness, neuroticism, and openness to experience). These psychological and biological data were obtained from young healthy women. The main findings showed statistically significant associations between occipital CSA variations and extraversion, as well as between parietal CT variations and neuroticism. Regarding white matter integrity, openness showed positive correlations with tracts connecting posterior and anterior brain regions. Therefore, variations in discrete gray matter clusters were associated with temperamental traits (extraversion and neuroticism), whereas long-distance structural connections were related with the dimension of personality that has been associated with high-level cognitive processes (openness). Copyright © 2017 IBRO. Published by Elsevier Ltd. All rights reserved.

Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences.

PubMed

Boussaha, Mekki; Michot, Pauline; Letaief, Rabia; Hozé, Chris; Fritz, Sébastien; Grohs, Cécile; Esquerré, Diane; Duchesne, Amandine; Philippe, Romain; Blanquet, Véronique; Phocas, Florence; Floriot, Sandrine; Rocha, Dominique; Klopp, Christophe; Capitan, Aurélien; Boichard, Didier

2016-11-15

In recent years, several bovine genome sequencing projects were carried out with the aim of developing genomic tools to improve dairy and beef production efficiency and sustainability. In this study, we describe the first French cattle genome variation dataset obtained by sequencing 274 whole genomes representing several major dairy and beef breeds. This dataset contains over 28 million single nucleotide polymorphisms (SNPs) and small insertions and deletions. Comparisons between sequencing results and SNP array genotypes revealed a very high genotype concordance rate, which indicates the good quality of our data. To our knowledge, this is the first large-scale catalog of small genomic variations in French dairy and beef cattle. This resource will contribute to the study of gene functions and population structure and also help to improve traits through genotype-guided selection.

Extreme-scale motions in turbulent plane Couette flows

NASA Astrophysics Data System (ADS)

Lee, Myoungkyu; Moser, Robert D.

2018-05-01

We study the size of large-scale motions in turbulent plane Couette flows at moderate Reynolds number up to $Re_\\tau$ = 500. Direct numerical simulation domains were as large as $100\\pi\\delta\\times2\\delta\\times5\\pi\\delta$, where $\\delta$ is half the distance between the walls. The results indicate that there are structures with streamwise extent, as measured by the wavelength, as long as 78$\\delta$ and at least 310$\\delta$ at $Re_\\tau$ = 220 and 500, respectively. The presence of these very long structures is apparent in the spectra of all three velocity components and the Reynolds stress. In DNS using a smaller domain, the large structures are constrained, eliminating the streamwise variations present in the larger domain. Effects of a smaller domain are also present in the mean velocity and the streamwise velocity variance in the outer flow.

Homeotic transformations and number changes in the vertebral column of Triturus newts

PubMed Central

Slijepčević, Maja; Galis, Frietson; Arntzen, Jan W.

2015-01-01

We explored intraspecific variation in vertebral formulae, more specifically the variation in the number of thoracic vertebrae and frequencies of transitional sacral vertebrae in Triturus newts (Caudata: Salamandridae). Within salamandrid salamanders this monophyletic group shows the highest disparity in the number of thoracic vertebrae and considerable intraspecific variation in the number of thoracic vertebrae. Triturus species also differ in their ecological preferences, from predominantly terrestrial to largely aquatic. Following Geoffroy St. Hilaire’s and Darwin’s rule which states that structures with a large number of serially homologous repetitive elements are more variable than structures with smaller numbers, we hypothesized that the variation in vertebral formulae increases in more elongated species with a larger number of thoracic vertebrae. We furthermore hypothesized that the frequency of transitional vertebrae will be correlated with the variation in the number of thoracic vertebrae within the species. We also investigated potential effects of species hybridization on the vertebral formula. The proportion of individuals with a number of thoracic vertebrae different from the modal number and the range of variation in number of vertebrae significantly increased in species with a larger number of thoracic vertebrae. Contrary to our expectation, the frequencies of transitional vertebrae were not correlated with frequencies of change in the complete vertebrae number. The frequency of transitional sacral vertebra in hybrids did not significantly differ from that of the parental species. Such a pattern could be a result of selection pressure against transitional vertebrae and/or a bias towards the development of full vertebrae numbers. Although our data indicate relaxed selection for vertebral count changes in more elongated, aquatic species, more data on different selective pressures in species with different numbers of vertebrae in the two contrasting, terrestrial and aquatic environments are needed to test for causality. PMID:26587355

Homeotic transformations and number changes in the vertebral column of Triturus newts.

PubMed

Slijepčević, Maja; Galis, Frietson; Arntzen, Jan W; Ivanović, Ana

2015-01-01

We explored intraspecific variation in vertebral formulae, more specifically the variation in the number of thoracic vertebrae and frequencies of transitional sacral vertebrae in Triturus newts (Caudata: Salamandridae). Within salamandrid salamanders this monophyletic group shows the highest disparity in the number of thoracic vertebrae and considerable intraspecific variation in the number of thoracic vertebrae. Triturus species also differ in their ecological preferences, from predominantly terrestrial to largely aquatic. Following Geoffroy St. Hilaire's and Darwin's rule which states that structures with a large number of serially homologous repetitive elements are more variable than structures with smaller numbers, we hypothesized that the variation in vertebral formulae increases in more elongated species with a larger number of thoracic vertebrae. We furthermore hypothesized that the frequency of transitional vertebrae will be correlated with the variation in the number of thoracic vertebrae within the species. We also investigated potential effects of species hybridization on the vertebral formula. The proportion of individuals with a number of thoracic vertebrae different from the modal number and the range of variation in number of vertebrae significantly increased in species with a larger number of thoracic vertebrae. Contrary to our expectation, the frequencies of transitional vertebrae were not correlated with frequencies of change in the complete vertebrae number. The frequency of transitional sacral vertebra in hybrids did not significantly differ from that of the parental species. Such a pattern could be a result of selection pressure against transitional vertebrae and/or a bias towards the development of full vertebrae numbers. Although our data indicate relaxed selection for vertebral count changes in more elongated, aquatic species, more data on different selective pressures in species with different numbers of vertebrae in the two contrasting, terrestrial and aquatic environments are needed to test for causality.

Preliminary Structural Sensitivity Study of Hypersonic Inflatable Aerodynamic Decelerator Using Probabilistic Methods

NASA Technical Reports Server (NTRS)

Lyle, Karen H.

2014-01-01

Acceptance of new spacecraft structural architectures and concepts requires validated design methods to minimize the expense involved with technology validation via flighttesting. This paper explores the implementation of probabilistic methods in the sensitivity analysis of the structural response of a Hypersonic Inflatable Aerodynamic Decelerator (HIAD). HIAD architectures are attractive for spacecraft deceleration because they are lightweight, store compactly, and utilize the atmosphere to decelerate a spacecraft during re-entry. However, designers are hesitant to include these inflatable approaches for large payloads or spacecraft because of the lack of flight validation. In the example presented here, the structural parameters of an existing HIAD model have been varied to illustrate the design approach utilizing uncertainty-based methods. Surrogate models have been used to reduce computational expense several orders of magnitude. The suitability of the design is based on assessing variation in the resulting cone angle. The acceptable cone angle variation would rely on the aerodynamic requirements.

Modeling the blockage of Lg waves from 3-D variations in crustal structure

NASA Astrophysics Data System (ADS)

Sanborn, Christopher J.; Cormier, Vernon F.

2018-05-01

Comprised of S waves trapped in Earth's crust, the high frequency (2-10 Hz) Lg wave is important to discriminating earthquakes from explosions by comparing its amplitude and waveform to those of Pg and Pn waves. Lateral variations in crustal structure, including variations in crustal thickness, intrinsic attenuation, and scattering, affect the efficiency of Lg propagation and its consistency as a source discriminant at regional (200-1500 km) distances. To investigate the effects of laterally varying Earth structure on the efficiency of propagation of Lg and Pg, we apply a radiative transport algorithm to model complete, high-frequency (2-4 Hz), regional coda envelopes. The algorithm propagates packets of energy with ray theory through large-scale 3-D structure, and includes stochastic effects of multiple-scattering by small-scale heterogeneities within the large-scale structure. Source-radiation patterns are described by moment tensors. Seismograms of explosion and earthquake sources are synthesized in canonical models to predict effects on waveforms of paths crossing regions of crustal thinning (pull-apart basins and ocean/continent transitions) and thickening (collisional mountain belts), For paths crossing crustal thinning regions, Lg is amplified at receivers within the thinned region but strongly disrupted and attenuated at receivers beyond the thinned region. For paths crossing regions of crustal thickening, Lg amplitude is attenuated at receivers within the thickened region, but experiences little or no reduction in amplitude at receivers beyond the thickened region. The length of the Lg propagation within a thickened region and the complexity of over- and under-thrust crustal layers, can produce localized zones of Lg amplification or attenuation. Regions of intense scattering within laterally homogeneous models of the crust increase Lg attenuation but do not disrupt its coda shape.

Microfocus diffraction from different regions of a protein crystal: structural variations and unit-cell polymorphism

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

Thompson, Michael C.; Cascio, Duilio; Yeates, Todd O.

Real macromolecular crystals can be non-ideal in a myriad of ways. This often creates challenges for structure determination, while also offering opportunities for greater insight into the crystalline state and the dynamic behavior of macromolecules. To evaluate whether different parts of a single crystal of a dynamic protein, EutL, might be informative about crystal and protein polymorphism, a microfocus X-ray synchrotron beam was used to collect a series of 18 separate data sets from non-overlapping regions of the same crystal specimen. A principal component analysis (PCA) approach was employed to compare the structure factors and unit cells across the datamore » sets, and it was found that the 18 data sets separated into two distinct groups, with largeRvalues (in the 40% range) and significant unit-cell variations between the members of the two groups. This categorization mapped the different data-set types to distinct regions of the crystal specimen. Atomic models of EutL were then refined against two different data sets obtained by separately merging data from the two distinct groups. A comparison of the two resulting models revealed minor but discernable differences in certain segments of the protein structure, and regions of higher deviation were found to correlate with regions where larger dynamic motions were predicted to occur by normal-mode molecular-dynamics simulations. The findings emphasize that large spatially dependent variations may be present across individual macromolecular crystals. This information can be uncovered by simultaneous analysis of multiple partial data sets and can be exploited to reveal new insights about protein dynamics, while also improving the accuracy of the structure-factor data ultimately obtained in X-ray diffraction experiments.« less

Probing structural changes in Ca(1-x)Nd2x/3TiO3 ceramics by Raman spectroscopy

NASA Astrophysics Data System (ADS)

Lowndes, Robert; Deluca, Marco; Azough, Feridoon; Freer, Robert

2013-01-01

Ceramics in the system Ca(1-x)Nd2x/3TiO3, intended for mobile communication applications, exhibit grossly non-linear variations in microwave dielectric properties with composition. There is evidence of a structural transition and the formation of vacancies on the A-site of the perovskite structure. High density, single phase perovskite Ca(1-x)Nd2x/3TiO3 ceramics have been prepared by the mixed oxide route. Raman spectroscopy was used to investigate the structural variations, which impact on dielectric properties. The Raman spectra show that with increasing Nd content, there is a transition from an ordered structure, to a disordered arrangement of cations and vacancies, and back to an ordered arrangement in Ca0.1Nd0.6TiO3. A structural phase transition from orthorhombic Pbnm to monoclinic C2/m coincides with the order-disorder transition at Ca0.1Nd0.6TiO3. Polarized Raman spectroscopy facilitated the assignment of the Raman modes and investigation of the role of importance of domain structures. Large variation in the plane angles was attributed to differences in domain structures. Differences in the angular dependence of the Raman modes with Nd content reflect changes in the preferred orientation of the domains from lamellar twins, to wedge shaped and back to lamellar twins.

Method for identifying subsurface fluid migration and drainage pathways in and among oil and gas reservoirs using 3-D and 4-D seismic imaging

DOEpatents

Anderson, R.N.; Boulanger, A.; Bagdonas, E.P.; Xu, L.; He, W.

1996-12-17

The invention utilizes 3-D and 4-D seismic surveys as a means of deriving information useful in petroleum exploration and reservoir management. The methods use both single seismic surveys (3-D) and multiple seismic surveys separated in time (4-D) of a region of interest to determine large scale migration pathways within sedimentary basins, and fine scale drainage structure and oil-water-gas regions within individual petroleum producing reservoirs. Such structure is identified using pattern recognition tools which define the regions of interest. The 4-D seismic data sets may be used for data completion for large scale structure where time intervals between surveys do not allow for dynamic evolution. The 4-D seismic data sets also may be used to find variations over time of small scale structure within individual reservoirs which may be used to identify petroleum drainage pathways, oil-water-gas regions and, hence, attractive drilling targets. After spatial orientation, and amplitude and frequency matching of the multiple seismic data sets, High Amplitude Event (HAE) regions consistent with the presence of petroleum are identified using seismic attribute analysis. High Amplitude Regions are grown and interconnected to establish plumbing networks on the large scale and reservoir structure on the small scale. Small scale variations over time between seismic surveys within individual reservoirs are identified and used to identify drainage patterns and bypassed petroleum to be recovered. The location of such drainage patterns and bypassed petroleum may be used to site wells. 22 figs.

Method for identifying subsurface fluid migration and drainage pathways in and among oil and gas reservoirs using 3-D and 4-D seismic imaging

DOEpatents

Anderson, Roger N.; Boulanger, Albert; Bagdonas, Edward P.; Xu, Liqing; He, Wei

1996-01-01

The invention utilizes 3-D and 4-D seismic surveys as a means of deriving information useful in petroleum exploration and reservoir management. The methods use both single seismic surveys (3-D) and multiple seismic surveys separated in time (4-D) of a region of interest to determine large scale migration pathways within sedimentary basins, and fine scale drainage structure and oil-water-gas regions within individual petroleum producing reservoirs. Such structure is identified using pattern recognition tools which define the regions of interest. The 4-D seismic data sets may be used for data completion for large scale structure where time intervals between surveys do not allow for dynamic evolution. The 4-D seismic data sets also may be used to find variations over time of small scale structure within individual reservoirs which may be used to identify petroleum drainage pathways, oil-water-gas regions and, hence, attractive drilling targets. After spatial orientation, and amplitude and frequency matching of the multiple seismic data sets, High Amplitude Event (HAE) regions consistent with the presence of petroleum are identified using seismic attribute analysis. High Amplitude Regions are grown and interconnected to establish plumbing networks on the large scale and reservoir structure on the small scale. Small scale variations over time between seismic surveys within individual reservoirs are identified and used to identify drainage patterns and bypassed petroleum to be recovered. The location of such drainage patterns and bypassed petroleum may be used to site wells.

Object Classification With Joint Projection and Low-Rank Dictionary Learning.

PubMed

Foroughi, Homa; Ray, Nilanjan; Hong Zhang

2018-02-01

For an object classification system, the most critical obstacles toward real-world applications are often caused by large intra-class variability, arising from different lightings, occlusion, and corruption, in limited sample sets. Most methods in the literature would fail when the training samples are heavily occluded, corrupted or have significant illumination or viewpoint variations. Besides, most of the existing methods and especially deep learning-based methods, need large training sets to achieve a satisfactory recognition performance. Although using the pre-trained network on a generic large-scale data set and fine-tune it to the small-sized target data set is a widely used technique, this would not help when the content of base and target data sets are very different. To address these issues simultaneously, we propose a joint projection and low-rank dictionary learning method using dual graph constraints. Specifically, a structured class-specific dictionary is learned in the low-dimensional space, and the discrimination is further improved by imposing a graph constraint on the coding coefficients, that maximizes the intra-class compactness and inter-class separability. We enforce structural incoherence and low-rank constraints on sub-dictionaries to reduce the redundancy among them, and also make them robust to variations and outliers. To preserve the intrinsic structure of data, we introduce a supervised neighborhood graph into the framework to make the proposed method robust to small-sized and high-dimensional data sets. Experimental results on several benchmark data sets verify the superior performance of our method for object classification of small-sized data sets, which include a considerable amount of different kinds of variation, and may have high-dimensional feature vectors.

Ecogeography, genetics, and the evolution of human body form.

PubMed

Roseman, Charles C; Auerbach, Benjamin M

2015-01-01

Genetic resemblances among groups are non-randomly distributed in humans. This population structure may influence the correlations between traits and environmental drivers of natural selection thus complicating the interpretation of the fossil record when modern human variation is used as a referential model. In this paper, we examine the effects of population structure and natural selection on postcranial traits that reflect body size and shape with application to the more general issue of how climate - using latitude as a proxy - has influenced hominin morphological variation. We compare models that include terms reflecting population structure, ascertained from globally distributed microsatellite data, and latitude on postcranial phenotypes derived from skeletal dimensions taken from a large global sample of modern humans. We find that models with a population structure term fit better than a model of natural selection along a latitudinal cline in all cases. A model including both latitude and population structure terms is a good fit to distal limb element lengths and bi-iliac breadth, indicating that multiple evolutionary forces shaped these morphologies. In contrast, a model that included only a population structure term best explained femoral head diameter and the crural index. The results demonstrate that population structure is an important part of human postcranial variation, and that clinally distributed natural selection is not sufficient to explain among-group differentiation. The distribution of human body form is strongly influenced by the contingencies of modern human origins, which calls for new ways to approach problems in the evolution of human variation, past and present. Copyright © 2014 Elsevier Ltd. All rights reserved.

Influence of magnetic pressure on stellar structure: A Mechanism for solar variability

NASA Technical Reports Server (NTRS)

Schatten, K. H.; Endal, A. S.

1980-01-01

A physical mechanism is proposed that couples the Sun's dynamo magnetic field to its gravitational potential energy. The mechanism involves the isotropic field pressure resulting in a lifting force on the convective envelope, thereby raising its potential energy. Decay of the field due to solar activity allows the envelop to subside and releases this energy, which can augment the otherwise steady solar luminosity. Equations are developed and applied to the Sun for several field configurations. The best estimate model suggests that uniform luminosity variations as large as 0.02% for half a sunspot cycle may occur. Brief temporal variations or the rotation of spatial structures could allow larger excursions in the energy released.

Improving Grasp Skills Using Schema Structured Learning

NASA Technical Reports Server (NTRS)

Platt, Robert; Grupen, ROderic A.; Fagg, Andrew H.

2006-01-01

Abstract In the control-based approach to robotics, complex behavior is created by sequencing and combining control primitives. While it is desirable for the robot to autonomously learn the correct control sequence, searching through the large number of potential solutions can be time consuming. This paper constrains this search to variations of a generalized solution encoded in a framework known as an action schema. A new algorithm, SCHEMA STRUCTURED LEARNING, is proposed that repeatedly executes variations of the generalized solution in search of instantiations that satisfy action schema objectives. This approach is tested in a grasping task where Dexter, the UMass humanoid robot, learns which reaching and grasping controllers maximize the probability of grasp success.

Study of Magnetic Field Spatial Variations in the Southern Hemisphere's Low Latitudes due to Different Interplanetary Structures Using the 3-D MHD SWMF/BATSRUS Model

NASA Astrophysics Data System (ADS)

Souza, V. M. C. E. S.; Jauer, P. R.; Alves, L. R.; Padilha, A. L.; Padua, M. B.; Vitorello, I.; Alves, M. V.; Da Silva, L. A.

2017-12-01

Interplanetary structures such as Coronal Mass Ejections (CME), Shocks, Corotating Interaction Regions (CIR) and Magnetic Clouds (MC) interfere directly on Space Weather conditions and can cause severe and intense disturbances in the Earth's magnetic field as measured in space and on the ground. During magnetically disturbed periods characterized by world-wide, abrupt variations of the geomagnetic field, large and intense current systems can be induced and amplified within the Earth even at low latitudes. Such current systems are known as geomagnetically induced currents (GIC) and can cause damage to power transmission lines, transformers and the degradation of pipelines. As part of an effort to estimate GIC intensities throughout the low to equatorial latitudes of the Brazilian territory, we used the 3-D MHD SWMF/BATSRUS code to estimate spatial variations of the geomagnetic field during periods when the magnetosphere is under the influence of CME and MC structures. Specifically, we used the CalcDeltaB tool (Rastatter et al., Space Weather, 2014) to provide a proxy for the spatial variations of the geomagnetic field, with a 1 minute cadence, at 31 virtual magnetometer stations located in the proposed study region. The stations are spatially arranged in a two-dimensional network with each station being 5 degrees apart in latitude and longitude. In a preliminary analysis, we found that prior to the arrival of each interplanetary structure, there is no appreciable variation in the components of the geomagnetic field between the virtual stations. However, when the interplanetary structures reach the magnetosphere, each station perceives the magnetic field variation differently, so that it is not possible to use a single station to represent the magnetic field perturbation throughout the Brazilian region. We discuss the minimum number and spacing between stations to adequately detail the geomagnetic field variations in this region.

Mixed severity fire effects within the Rim fire: Relative importance of local climate, fire weather, topography, and forest structure

Treesearch

Van R. Kane; C. Alina Cansler; Nicholas A. Povak; Jonathan T. Kane; Robert J. McGaughey; James A. Lutz; Derek J. Churchill; Malcolm P. North

2015-01-01

Recent and projected increases in the frequency and severity of large wildfires in the western U.S. makes understanding the factors that strongly affect landscape fire patterns a management priority for optimizing treatment location. We compared the influence of variations in the local environment on burn severity patterns on the large 2013 Rim fire that burned under...

A new method of presentation the large-scale magnetic field structure on the Sun and solar corona

NASA Technical Reports Server (NTRS)

Ponyavin, D. I.

1995-01-01

The large-scale photospheric magnetic field, measured at Stanford, has been analyzed in terms of surface harmonics. Changes of the photospheric field which occur within whole solar rotation period can be resolved by this analysis. For this reason we used daily magnetograms of the line-of-sight magnetic field component observed from Earth over solar disc. We have estimated the period during which day-to-day full disc magnetograms must be collected. An original algorithm was applied to resolve time variations of spherical harmonics that reflect time evolution of large-scale magnetic field within solar rotation period. This method of magnetic field presentation can be useful enough in lack of direct magnetograph observations due to sometimes bad weather conditions. We have used the calculated surface harmonics to reconstruct the large-scale magnetic field structure on the source surface near the sun - the origin of heliospheric current sheet and solar wind streams. The obtained results have been compared with spacecraft in situ observations and geomagnetic activity. We tried to show that proposed technique can trace shon-time variations of heliospheric current sheet and short-lived solar wind streams. We have compared also our results with those obtained traditionally from potential field approximation and extrapolation using synoptic charts as initial boundary conditions.

Tree structure and cavity microclimate: implications for bats and birds.

PubMed

Clement, Matthew J; Castleberry, Steven B

2013-05-01

It is widely assumed that tree cavity structure and microclimate affect cavity selection and use in cavity-dwelling bats and birds. Despite the interest in tree structure and microclimate, the relationship between the two has rarely been quantified. Currently available data often comes from artificial structures that may not accurately represent conditions in natural cavities. We collected data on tree cavity structure and microclimate from 45 trees in five cypress-gum swamps in the Coastal Plain of Georgia in the United States in 2008. We used hierarchical linear models to predict cavity microclimate from tree structure and ambient temperature and humidity, and used Aikaike's information criterion to select the most parsimonious models. We found large differences in microclimate among trees, but tree structure variables explained <28% of the variation, while ambient conditions explained >80% of variation common to all trees. We argue that the determinants of microclimate are complex and multidimensional, and therefore cavity microclimate cannot be deduced easily from simple tree structures. Furthermore, we found that daily fluctuations in ambient conditions strongly affect microclimate, indicating that greater weather fluctuations will cause greater differences among tree cavities.

2D Variations in Coda Amplitudes in the Middle East

DOE PAGES

Pasyanos, Michael E.; Gok, Rengin; Walter, William R.

2016-08-16

Here, coda amplitudes have proven to be a stable feature of seismograms, allowing one to reliably measure magnitudes for moderate to large-sized (M≥3) earthquakes over broad regions. Since smaller (M<3) earthquakes are only recorded at higher frequencies where we find larger interstation scatter, amplitude and magnitude estimates for these events are more variable, regional, and path dependent. In this study, we investigate coda amplitude measurements in the Middle East for 2-D variations in attenuation structure.

2D Variations in Coda Amplitudes in the Middle East

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

Pasyanos, Michael E.; Gok, Rengin; Walter, William R.

Here, coda amplitudes have proven to be a stable feature of seismograms, allowing one to reliably measure magnitudes for moderate to large-sized (M≥3) earthquakes over broad regions. Since smaller (M<3) earthquakes are only recorded at higher frequencies where we find larger interstation scatter, amplitude and magnitude estimates for these events are more variable, regional, and path dependent. In this study, we investigate coda amplitude measurements in the Middle East for 2-D variations in attenuation structure.

Final Report: DOE award: ER64516-1031199-0013966 2007-2011 Genomic Structure, Metagenomics, Horizontal Gene Transfer, and Natural Diversity of Prochlorococcus and Vibrio

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

Chisholm, Sally; Polz, Martin F.; Alm, Eric J

Our overarching goal with this proposal was to develop a deep understanding of the design of Prochlorococcus and Vibrio cells, the variations in their designs, and the constraints that have shaped this variation at the cell-environment interface. That is, we wanted to develop our understanding of the biology of these microbes at all scales of biological organization, from individual cell design to the dynamics of large populations.

Identification of both copy number variation-type and constant-type core elements in a large segmental duplication region of the mouse genome

PubMed Central

2013-01-01

Background Copy number variation (CNV), an important source of diversity in genomic structure, is frequently found in clusters called CNV regions (CNVRs). CNVRs are strongly associated with segmental duplications (SDs), but the composition of these complex repetitive structures remains unclear. Results We conducted self-comparative-plot analysis of all mouse chromosomes using the high-speed and large-scale-homology search algorithm SHEAP. For eight chromosomes, we identified various types of large SD as tartan-checked patterns within the self-comparative plots. A complex arrangement of diagonal split lines in the self-comparative-plots indicated the presence of large homologous repetitive sequences. We focused on one SD on chromosome 13 (SD13M), and developed SHEPHERD, a stepwise ab initio method, to extract longer repetitive elements and to characterize repetitive structures in this region. Analysis using SHEPHERD showed the existence of 60 core elements, which were expected to be the basic units that form SDs within the repetitive structure of SD13M. The demonstration that sequences homologous to the core elements (>70% homology) covered approximately 90% of the SD13M region indicated that our method can characterize the repetitive structure of SD13M effectively. Core elements were composed largely of fragmented repeats of a previously identified type, such as long interspersed nuclear elements (LINEs), together with partial genic regions. Comparative genome hybridization array analysis showed that whereas 42 core elements were components of CNVR that varied among mouse strains, 8 did not vary among strains (constant type), and the status of the others could not be determined. The CNV-type core elements contained significantly larger proportions of long terminal repeat (LTR) types of retrotransposon than the constant-type core elements, which had no CNV. The higher divergence rates observed in the CNV-type core elements than in the constant type indicate that the CNV-type core elements have a longer evolutionary history than constant-type core elements in SD13M. Conclusions Our methodology for the identification of repetitive core sequences simplifies characterization of the structures of large SDs and detailed analysis of CNV. The results of detailed structural and quantitative analyses in this study might help to elucidate the biological role of one of the SDs on chromosome 13. PMID:23834397

Settlement-Size Scaling among Prehistoric Hunter-Gatherer Settlement Systems in the New World

PubMed Central

Haas, W. Randall; Klink, Cynthia J.; Maggard, Greg J.; Aldenderfer, Mark S.

2015-01-01

Settlement size predicts extreme variation in the rates and magnitudes of many social and ecological processes in human societies. Yet, the factors that drive human settlement-size variation remain poorly understood. Size variation among economically integrated settlements tends to be heavy tailed such that the smallest settlements are extremely common and the largest settlements extremely large and rare. The upper tail of this size distribution is often formalized mathematically as a power-law function. Explanations for this scaling structure in human settlement systems tend to emphasize complex socioeconomic processes including agriculture, manufacturing, and warfare—behaviors that tend to differentially nucleate and disperse populations hierarchically among settlements. But, the degree to which heavy-tailed settlement-size variation requires such complex behaviors remains unclear. By examining the settlement patterns of eight prehistoric New World hunter-gatherer settlement systems spanning three distinct environmental contexts, this analysis explores the degree to which heavy-tailed settlement-size scaling depends on the aforementioned socioeconomic complexities. Surprisingly, the analysis finds that power-law models offer plausible and parsimonious statistical descriptions of prehistoric hunter-gatherer settlement-size variation. This finding reveals that incipient forms of hierarchical settlement structure may have preceded socioeconomic complexity in human societies and points to a need for additional research to explicate how mobile foragers came to exhibit settlement patterns that are more commonly associated with hierarchical organization. We propose that hunter-gatherer mobility with preferential attachment to previously occupied locations may account for the observed structure in site-size variation. PMID:26536241

Canopy area of large trees explains aboveground biomass variations across neotropical forest landscapes

NASA Astrophysics Data System (ADS)

Meyer, Victoria; Saatchi, Sassan; Clark, David B.; Keller, Michael; Vincent, Grégoire; Ferraz, António; Espírito-Santo, Fernando; d'Oliveira, Marcus V. N.; Kaki, Dahlia; Chave, Jérôme

2018-06-01

Large tropical trees store significant amounts of carbon in woody components and their distribution plays an important role in forest carbon stocks and dynamics. Here, we explore the properties of a new lidar-derived index, the large tree canopy area (LCA) defined as the area occupied by canopy above a reference height. We hypothesize that this simple measure of forest structure representing the crown area of large canopy trees could consistently explain the landscape variations in forest volume and aboveground biomass (AGB) across a range of climate and edaphic conditions. To test this hypothesis, we assembled a unique dataset of high-resolution airborne light detection and ranging (lidar) and ground inventory data in nine undisturbed old-growth Neotropical forests, of which four had plots large enough (1 ha) to calibrate our model. We found that the LCA for trees greater than 27 m (˜ 25-30 m) in height and at least 100 m2 crown size in a unit area (1 ha), explains more than 75 % of total forest volume variations, irrespective of the forest biogeographic conditions. When weighted by average wood density of the stand, LCA can be used as an unbiased estimator of AGB across sites (R2 = 0.78, RMSE = 46.02 Mg ha-1, bias = -0.63 Mg ha-1). Unlike other lidar-derived metrics with complex nonlinear relations to biomass, the relationship between LCA and AGB is linear and remains unique across forest types. A comparison with tree inventories across the study sites indicates that LCA correlates best with the crown area (or basal area) of trees with diameter greater than 50 cm. The spatial invariance of the LCA-AGB relationship across the Neotropics suggests a remarkable regularity of forest structure across the landscape and a new technique for systematic monitoring of large trees for their contribution to AGB and changes associated with selective logging, tree mortality and other types of tropical forest disturbance and dynamics.

Lessons from making the Structural Classification of Proteins (SCOP) and their implications for protein structure modelling.

PubMed

Andreeva, Antonina

2016-06-15

The Structural Classification of Proteins (SCOP) database has facilitated the development of many tools and algorithms and it has been successfully used in protein structure prediction and large-scale genome annotations. During the development of SCOP, numerous exceptions were found to topological rules, along with complex evolutionary scenarios and peculiarities in proteins including the ability to fold into alternative structures. This article reviews cases of structural variations observed for individual proteins and among groups of homologues, knowledge of which is essential for protein structure modelling. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

Quasi-steady solar wind dynamics

NASA Technical Reports Server (NTRS)

Pizzo, V. J.

1983-01-01

Progress in understanding the large scale dynamics of quasisteady, corotating solar wind structure was reviewed. The nature of the solar wind at large heliocentric distances preliminary calculations from a 2-D MHD model are used to demonstrate theoretical expectations of corotating structure out to 30 AU. It is found that the forward and reverse shocks from adjacent CIR's begin to interact at about 10 AU, producing new shock pairs flanking secondary CIR's. These sawtooth secondary CIR's interact again at about 20 AU and survive as visible entities to 30 AU. The model predicts the velocity jumps at the leading edge of the secondary CIR's at 30 AU should be very small but there should still be sizable variations in the thermodynamic and magnetic parameters. The driving dynamic mechanism in the distant solar wind is the relaxation of pressure gradients. The second topic is the influence of weak, nonimpulsive time dependence in quasisteady dynamics. It is suggested that modest large scale variations in the coronal flow speed on periods of several hours to a day may be responsible for many of the remaining discrepancies between theory and observation. Effects offer a ready explanation for the apparent rounding of stream fronts between 0.3 and 1.0 AU discovered by Helios.

Turbulence decay downstream of an active grid

NASA Astrophysics Data System (ADS)

Bewley, Gregory; Bodenschatz, Eberhard

2015-11-01

A grid in a wind tunnel stirs up turbulence that has a certain large-scale structure. The moving parts in a so-called ``active grid'' can be programmed to produce different structures. We use a special active grid in which each of 129 paddles on the grid has its own position-controlled servomotor that can move independently of the others. We observe among other things that the anisotropy in the amplitude of the velocity fluctuations and in the correlation lengths can be set and varied with an algorithm that oscillates the paddles in a specified way. The variation in the anisotropies that we observe can be explained by our earlier analysis of anisotropic ``soccer ball'' turbulence (Bewley, Chang and Bodenschatz 2012, Phys. Fluids). We define the influence of this variation in structure on the downstream evolution of the turbulence. with Eberhard Bodenschatz and others.

Assessing the effects of common variation in the FOXP2 gene on human brain structure.

PubMed

Hoogman, Martine; Guadalupe, Tulio; Zwiers, Marcel P; Klarenbeek, Patricia; Francks, Clyde; Fisher, Simon E

2014-01-01

The FOXP2 transcription factor is one of the most well-known genes to have been implicated in developmental speech and language disorders. Rare mutations disrupting the function of this gene have been described in different families and cases. In a large three-generation family carrying a missense mutation, neuroimaging studies revealed significant effects on brain structure and function, most notably in the inferior frontal gyrus, caudate nucleus, and cerebellum. After the identification of rare disruptive FOXP2 variants impacting on brain structure, several reports proposed that common variants at this locus may also have detectable effects on the brain, extending beyond disorder into normal phenotypic variation. These neuroimaging genetics studies used groups of between 14 and 96 participants. The current study assessed effects of common FOXP2 variants on neuroanatomy using voxel-based morphometry (VBM) and volumetric techniques in a sample of >1300 people from the general population. In a first targeted stage we analyzed single nucleotide polymorphisms (SNPs) claimed to have effects in prior smaller studies (rs2253478, rs12533005, rs2396753, rs6980093, rs7784315, rs17137124, rs10230558, rs7782412, rs1456031), beginning with regions proposed in the relevant papers, then assessing impact across the entire brain. In the second gene-wide stage, we tested all common FOXP2 variation, focusing on volumetry of those regions most strongly implicated from analyses of rare disruptive mutations. Despite using a sample that is more than 10 times that used for prior studies of common FOXP2 variation, we found no evidence for effects of SNPs on variability in neuroanatomy in the general population. Thus, the impact of this gene on brain structure may be largely limited to extreme cases of rare disruptive alleles. Alternatively, effects of common variants at this gene exist but are too subtle to be detected with standard volumetric techniques.

Spiral phyllotaxis underlies constrained variation in Anemone (Ranunculaceae) tepal arrangement.

PubMed

Kitazawa, Miho S; Fujimoto, Koichi

2018-05-01

Stabilization and variation of floral structures are indispensable for plant reproduction and evolution; however, the developmental mechanism regulating their structural robustness is largely unknown. To investigate this mechanism, we examined positional arrangement (aestivation) of excessively produced perianth organs (tepals) of six- and seven-tepaled (lobed) flowers in six Anemone species (Ranunculaceae). We found that the tepal arrangement that occurred in nature varied intraspecifically between spiral and whorled arrangements. Moreover, among the studied species, variation was commonly limited to three types, including whorls, despite five geometrically possible arrangements in six-tepaled flowers and two types among six possibilities in seven-tepaled flowers. A spiral arrangement, on the other hand, was unique to five-tepaled flowers. A spiral phyllotaxis model with stochasticity on initiating excessive primordia accounted for these limited variations in arrangement in cases when the divergence angle between preexisting primordia was less than 144°. Moreover, interspecific differences in the frequency of the observed arrangements were explained by the change of model parameters that represent meristematic growth and differential organ growth. These findings suggest that the phyllotaxis parameters are responsible for not only intraspecific stability but interspecific difference of floral structure. Decreasing arrangements from six-tepaled to seven-tepaled Anemone flowers demonstrate that the stabilization occurs as development proceeds to increase the component (organ) number, in contrast from the intuition that the variation will be larger due to increasing number of possible states (arrangements).

Factors affecting the remotely sensed response of coniferous forest plantations

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

Danson, F.M.; Curran, P.J.

1993-01-01

Remote sensing of forest biophysical properties has concentrated upon forest sites with a wide range of green vegetation amount and thereby leaf area index and canopy cover. However, coniferous forest plantations, an important forest type in Europe, are managed to maintain a large amount of green vegetation with little spatial variation. Therefore, the strength of the remotely sensed signal will, it is hypothesized, be determined more by the structure of this forest than by its cover. Airborne Thematic Mapper (ATM) and SPOT-1 HRV data were used to determine the effects of this structural variation on the remotely sensed response ofmore » a coniferous forest plantation in the United Kingdom. Red and near infrared radiance were strongly and negatively correlated with a range of structural properties and with the age of the stands but weakly correlated with canopy cover. A composite variable, related to the volume of the canopy, accounted for over 75% of the variation in near infrared radiance. A simple model that related forest structural variables to the remotely sensed response was used to understand and explain this response from a coniferous forest plantation.« less

Joint genetic analysis of hippocampal size in mouse and human identifies a novel gene linked to neurodegenerative disease.

PubMed

Ashbrook, David G; Williams, Robert W; Lu, Lu; Stein, Jason L; Hibar, Derrek P; Nichols, Thomas E; Medland, Sarah E; Thompson, Paul M; Hager, Reinmar

2014-10-03

Variation in hippocampal volume has been linked to significant differences in memory, behavior, and cognition among individuals. To identify genetic variants underlying such differences and associated disease phenotypes, multinational consortia such as ENIGMA have used large magnetic resonance imaging (MRI) data sets in human GWAS studies. In addition, mapping studies in mouse model systems have identified genetic variants for brain structure variation with great power. A key challenge is to understand how genetically based differences in brain structure lead to the propensity to develop specific neurological disorders. We combine the largest human GWAS of brain structure with the largest mammalian model system, the BXD recombinant inbred mouse population, to identify novel genetic targets influencing brain structure variation that are linked to increased risk for neurological disorders. We first use a novel cross-species, comparative analysis using mouse and human genetic data to identify a candidate gene, MGST3, associated with adult hippocampus size in both systems. We then establish the coregulation and function of this gene in a comprehensive systems-analysis. We find that MGST3 is associated with hippocampus size and is linked to a group of neurodegenerative disorders, such as Alzheimer's.

In silico quantitative structure-toxicity relationship study of aromatic nitro compounds.

PubMed

Pasha, Farhan Ahmad; Neaz, Mohammad Morshed; Cho, Seung Joo; Ansari, Mohiuddin; Mishra, Sunil Kumar; Tiwari, Sharvan

2009-05-01

Small molecules often have toxicities that are a function of molecular structural features. Minor variations in structural features can make large difference in such toxicity. Consequently, in silico techniques may be used to correlate such molecular toxicities with their structural features. Relative to nine different sets of aromatic nitro compounds having known observed toxicities against different targets, we developed ligand-based 2D quantitative structure-toxicity relationship models using 20 selected topological descriptors. The topological descriptors have several advantages such as conformational independency, facile and less time-consuming computation to yield good results. Multiple linear regression analysis was used to correlate variations of toxicity with molecular properties. The information index on molecular size, lopping centric index and Kier flexibility index were identified as fundamental descriptors for different kinds of toxicity, and further showed that molecular size, branching and molecular flexibility might be particularly important factors in quantitative structure-toxicity relationship analysis. This study revealed that topological descriptor-guided quantitative structure-toxicity relationship provided a very useful, cost and time-efficient, in silico tool for describing small-molecule toxicities.

Listening through Voices: Infant Statistical Word Segmentation across Multiple Speakers

ERIC Educational Resources Information Center

Graf Estes, Katharine; Lew-Williams, Casey

2015-01-01

To learn from their environments, infants must detect structure behind pervasive variation. This presents substantial and largely untested learning challenges in early language acquisition. The current experiments address whether infants can use statistical learning mechanisms to segment words when the speech signal contains acoustic variation…

Finite element analysis of large transient elastic-plastic deformations of simple structures, with application to the engine rotor fragment containment/deflection problem

NASA Technical Reports Server (NTRS)

Wu, R. W.; Witmer, E. A.

1972-01-01

Assumed-displacement versions of the finite-element method are developed to predict large-deformation elastic-plastic transient deformations of structures. Both the conventional and a new improved finite-element variational formulation are derived. These formulations are then developed in detail for straight-beam and curved-beam elements undergoing (1) Bernoulli-Euler-Kirchhoff or (2) Timoshenko deformation behavior, in one plane. For each of these categories, several types of assumed-displacement finite elements are developed, and transient response predictions are compared with available exact solutions for small-deflection, linear-elastic transient responses. The present finite-element predictions for large-deflection elastic-plastic transient responses are evaluated via several beam and ring examples for which experimental measurements of transient strains and large transient deformations and independent finite-difference predictions are available.

Increased heat transfer to a cylindrical leading edge due to spanwise variations in the freestream velocity

NASA Technical Reports Server (NTRS)

Rigby, D. L.; Vanfossen, G. J.

1991-01-01

The present study numerically demonstrates how small spanwise variations in velocity upstream of a body can cause relatively large increases in the spanwise-averaged heat transfer to the leading edge. Vorticity introduced by spanwise variations, first decays as it drifts downstream, then amplifies in the stagnation region as a result of vortex stretching. This amplification can cause a periodic array of 3 D structures, similar to horseshoe vortices, to form. The numerical results indicate that, for the given wavelength, there is an amplitude threshold below which a structure does not form. A one-dimensional analysis, to predict the decay of vorticity in the absence of the body, in conjunction with the full numerical results indicated that the threshold is more accurately stated as minimum level of vorticity required in the leading edge region for a structure to form. It is possible, using the one-dimensional analysis, to compute an optimum wavelength in terms of the maximum vorticity reaching the leading edge region for given amplitude. A discussion is presented which relates experimentally observed trends to the trends of the present phenomena.

Multiscale spatial and small-scale temporal variation in the composition of Riverine fish communities.

PubMed

Growns, Ivor; Astles, Karen; Gehrke, Peter

2006-03-01

We studied the multiscale (sites, river reaches and rivers) and short-term temporal (monthly) variability in a freshwater fish assemblage. We found that small-scale spatial variation and short-term temporal variability significantly influenced fish community structure in the Macquarie and Namoi Rivers. However, larger scale spatial differences between rivers were the largest source of variation in the data. The interaction between temporal change and spatial variation in fish community structure, whilst statistically significant, was smaller than the variation between rivers. This suggests that although the fish communities within each river changed between sampling occasions, the underlying differences between rivers were maintained. In contrast, the strongest interaction between temporal and spatial effects occurred at the smallest spatial scale, at the level of individual sites. This means whilst the composition of the fish assemblage at a given site may fluctuate, the magnitude of these changes is unlikely to affect larger scale differences between reaches within rivers or between rivers. These results suggest that sampling at any time within a single season will be sufficient to show spatial differences that occur over large spatial scales, such as comparisons between rivers or between biogeographical regions.

Ligand structure and mechanical properties of single-nanoparticle-thick membranes.

PubMed

Salerno, K Michael; Bolintineanu, Dan S; Lane, J Matthew D; Grest, Gary S

2015-06-01

The high mechanical stiffness of single-nanoparticle-thick membranes is believed to result from the local structure of ligand coatings that mediate interactions between nanoparticles. These ligand structures are not directly observable experimentally. We use molecular dynamics simulations to observe variations in ligand structure and simultaneously measure variations in membrane mechanical properties. We have shown previously that ligand end group has a large impact on ligand structure and membrane mechanical properties. Here we introduce and apply quantitative molecular structure measures to these membranes and extend analysis to multiple nanoparticle core sizes and ligand lengths. Simulations of nanoparticle membranes with a nanoparticle core diameter of 4 or 6 nm, a ligand length of 11 or 17 methylenes, and either carboxyl (COOH) or methyl (CH(3)) ligand end groups are presented. In carboxyl-terminated ligand systems, structure and interactions are dominated by an end-to-end orientation of ligands. In methyl-terminated ligand systems large ordered ligand structures form, but nanoparticle interactions are dominated by disordered, partially interdigitated ligands. Core size and ligand length also affect both ligand arrangement within the membrane and the membrane's macroscopic mechanical response, but are secondary to the role of the ligand end group. Moreover, the particular end group (COOH or CH(3)) alters the nature of how ligand length, in turn, affects the membrane properties. The effect of core size does not depend on the ligand end group, with larger cores always leading to stiffer membranes. Asymmetry in the stress and ligand density is observed in membranes during preparation at a water-vapor interface, with the stress asymmetry persisting in all membranes after drying.

Structural covariance of brain region volumes is associated with both structural connectivity and transcriptomic similarity.

PubMed

Yee, Yohan; Fernandes, Darren J; French, Leon; Ellegood, Jacob; Cahill, Lindsay S; Vousden, Dulcie A; Spencer Noakes, Leigh; Scholz, Jan; van Eede, Matthijs C; Nieman, Brian J; Sled, John G; Lerch, Jason P

2018-05-18

An organizational pattern seen in the brain, termed structural covariance, is the statistical association of pairs of brain regions in their anatomical properties. These associations, measured across a population as covariances or correlations usually in cortical thickness or volume, are thought to reflect genetic and environmental underpinnings. Here, we examine the biological basis of structural volume covariance in the mouse brain. We first examined large scale associations between brain region volumes using an atlas-based approach that parcellated the entire mouse brain into 318 regions over which correlations in volume were assessed, for volumes obtained from 153 mouse brain images via high-resolution MRI. We then used a seed-based approach and determined, for 108 different seed regions across the brain and using mouse gene expression and connectivity data from the Allen Institute for Brain Science, the variation in structural covariance data that could be explained by distance to seed, transcriptomic similarity to seed, and connectivity to seed. We found that overall, correlations in structure volumes hierarchically clustered into distinct anatomical systems, similar to findings from other studies and similar to other types of networks in the brain, including structural connectivity and transcriptomic similarity networks. Across seeds, this structural covariance was significantly explained by distance (17% of the variation, up to a maximum of 49% for structural covariance to the visceral area of the cortex), transcriptomic similarity (13% of the variation, up to maximum of 28% for structural covariance to the primary visual area) and connectivity (15% of the variation, up to a maximum of 36% for structural covariance to the intermediate reticular nucleus in the medulla) of covarying structures. Together, distance, connectivity, and transcriptomic similarity explained 37% of structural covariance, up to a maximum of 63% for structural covariance to the visceral area. Additionally, this pattern of explained variation differed spatially across the brain, with transcriptomic similarity playing a larger role in the cortex than subcortex, while connectivity explains structural covariance best in parts of the cortex, midbrain, and hindbrain. These results suggest that both gene expression and connectivity underlie structural volume covariance, albeit to different extents depending on brain region, and this relationship is modulated by distance. Copyright © 2018. Published by Elsevier Inc.

Spatio-temporal population structuring and genetic diversity retention in depleted Atlantic Bluefin tuna of the Mediterranean Sea

PubMed Central

Riccioni, Giulia; Landi, Monica; Ferrara, Giorgia; Milano, Ilaria; Cariani, Alessia; Zane, Lorenzo; Sella, Massimo; Barbujani, Guido; Tinti, Fausto

2010-01-01

Fishery genetics have greatly changed our understanding of population dynamics and structuring in marine fish. In this study, we show that the Atlantic Bluefin tuna (ABFT, Thunnus thynnus), an oceanic predatory species exhibiting highly migratory behavior, large population size, and high potential for dispersal during early life stages, displays significant genetic differences over space and time, both at the fine and large scales of variation. We compared microsatellite variation of contemporary (n = 256) and historical (n = 99) biological samples of ABFTs of the central-western Mediterranean Sea, the latter dating back to the early 20th century. Measures of genetic differentiation and a general heterozygote deficit suggest that differences exist among population samples, both now and 96–80 years ago. Thus, ABFTs do not represent a single panmictic population in the Mediterranean Sea. Statistics designed to infer changes in population size, both from current and past genetic variation, suggest that some Mediterranean ABFT populations, although still not severely reduced in their genetic potential, might have suffered from demographic declines. The short-term estimates of effective population size are straddled on the minimum threshold (effective population size = 500) indicated to maintain genetic diversity and evolutionary potential across several generations in natural populations. PMID:20080643

Downstream movement of fall Chinook salmon juveniles in the lower Snake River reservoirs during winter and early spring

USGS Publications Warehouse

Tiffan, Kenneth F.; Kock, Tobias J.; Connor, William P.; Mullins, Frank; Steinhorst, R. Kirk

2012-01-01

We conducted a 3-year radiotelemetry study in the lower Snake River to (1) determine whether juvenile fall Chinook salmon Oncorhynchus tshawytscha pass dams during winter, when bypass systems and structures designed to prevent mortality are not operated; (2) determine whether downstream movement rate varies annually, seasonally, and from reservoir to reservoir; and (3) identify some of the factors that contribute to annual, seasonal, and spatial variation in downstream movement rate. Fall Chinook salmon juveniles moved downstream up to 169 km and at a sufficiently fast rate (7.5 km/d) such that large percentages (up to 93%) of the fish passed one or more dams during the winter. Mean downstream movement rate varied annually (9.2–11.3 km/d), increased from winter (7.5 km/d) to spring (16.4 km/d), and increased (from 6.9 to 16.8 km/d) as fish moved downstream from reservoir to reservoir. Fish condition factor at tagging explained some of the annual variation in downstream movement rate, whereas water particle velocity and temperature explained portions of the seasonal variation. An increase in migrational disposition as fish moved downstream helped to explain the spatial variation. The potential cost of winter movement might be reduced survival due to turbine passage at a time when the bypass systems and spillway passage structures are not operated. Efforts to understand and increase passage survival of winter migrants in large impoundments might help to rehabilitate some imperiled anadromous salmonid populations.

The statistics of primordial density fluctuations

NASA Astrophysics Data System (ADS)

Barrow, John D.; Coles, Peter

1990-05-01

The statistical properties of the density fluctuations produced by power-law inflation are investigated. It is found that, even the fluctuations present in the scalar field driving the inflation are Gaussian, the resulting density perturbations need not be, due to stochastic variations in the Hubble parameter. All the moments of the density fluctuations are calculated, and is is argued that, for realistic parameter choices, the departures from Gaussian statistics are small and would have a negligible effect on the large-scale structure produced in the model. On the other hand, the model predicts a power spectrum with n not equal to 1, and this could be good news for large-scale structure.

Modelling Variable Fire Severity in Boreal Forests: Effects of Fire Intensity and Stand Structure

PubMed Central

Miquelajauregui, Yosune; Cumming, Steven G.; Gauthier, Sylvie

2016-01-01

It is becoming clear that fires in boreal forests are not uniformly stand-replacing. On the contrary, marked variation in fire severity, measured as tree mortality, has been found both within and among individual fires. It is important to understand the conditions under which this variation can arise. We integrated forest sample plot data, tree allometries and historical forest fire records within a diameter class-structured model of 1.0 ha patches of mono-specific black spruce and jack pine stands in northern Québec, Canada. The model accounts for crown fire initiation and vertical spread into the canopy. It uses empirical relations between fire intensity, scorch height, the percent of crown scorched and tree mortality to simulate fire severity, specifically the percent reduction in patch basal area due to fire-caused mortality. A random forest and a regression tree analysis of a large random sample of simulated fires were used to test for an effect of fireline intensity, stand structure, species composition and pyrogeographic regions on resultant severity. Severity increased with intensity and was lower for jack pine stands. The proportion of simulated fires that burned at high severity (e.g. >75% reduction in patch basal area) was 0.80 for black spruce and 0.11 for jack pine. We identified thresholds in intensity below which there was a marked sensitivity of simulated fire severity to stand structure, and to interactions between intensity and structure. We found no evidence for a residual effect of pyrogeographic region on simulated severity, after the effects of stand structure and species composition were accounted for. The model presented here was able to produce variation in fire severity under a range of fire intensity conditions. This suggests that variation in stand structure is one of the factors causing the observed variation in boreal fire severity. PMID:26919456

WS-SNPs&GO: a web server for predicting the deleterious effect of human protein variants using functional annotation

PubMed Central

2013-01-01

Background SNPs&GO is a method for the prediction of deleterious Single Amino acid Polymorphisms (SAPs) using protein functional annotation. In this work, we present the web server implementation of SNPs&GO (WS-SNPs&GO). The server is based on Support Vector Machines (SVM) and for a given protein, its input comprises: the sequence and/or its three-dimensional structure (when available), a set of target variations and its functional Gene Ontology (GO) terms. The output of the server provides, for each protein variation, the probabilities to be associated to human diseases. Results The server consists of two main components, including updated versions of the sequence-based SNPs&GO (recently scored as one of the best algorithms for predicting deleterious SAPs) and of the structure-based SNPs&GO3d programs. Sequence and structure based algorithms are extensively tested on a large set of annotated variations extracted from the SwissVar database. Selecting a balanced dataset with more than 38,000 SAPs, the sequence-based approach achieves 81% overall accuracy, 0.61 correlation coefficient and an Area Under the Curve (AUC) of the Receiver Operating Characteristic (ROC) curve of 0.88. For the subset of ~6,600 variations mapped on protein structures available at the Protein Data Bank (PDB), the structure-based method scores with 84% overall accuracy, 0.68 correlation coefficient, and 0.91 AUC. When tested on a new blind set of variations, the results of the server are 79% and 83% overall accuracy for the sequence-based and structure-based inputs, respectively. Conclusions WS-SNPs&GO is a valuable tool that includes in a unique framework information derived from protein sequence, structure, evolutionary profile, and protein function. WS-SNPs&GO is freely available at http://snps.biofold.org/snps-and-go. PMID:23819482

Modelling Variable Fire Severity in Boreal Forests: Effects of Fire Intensity and Stand Structure.

PubMed

Miquelajauregui, Yosune; Cumming, Steven G; Gauthier, Sylvie

2016-01-01

It is becoming clear that fires in boreal forests are not uniformly stand-replacing. On the contrary, marked variation in fire severity, measured as tree mortality, has been found both within and among individual fires. It is important to understand the conditions under which this variation can arise. We integrated forest sample plot data, tree allometries and historical forest fire records within a diameter class-structured model of 1.0 ha patches of mono-specific black spruce and jack pine stands in northern Québec, Canada. The model accounts for crown fire initiation and vertical spread into the canopy. It uses empirical relations between fire intensity, scorch height, the percent of crown scorched and tree mortality to simulate fire severity, specifically the percent reduction in patch basal area due to fire-caused mortality. A random forest and a regression tree analysis of a large random sample of simulated fires were used to test for an effect of fireline intensity, stand structure, species composition and pyrogeographic regions on resultant severity. Severity increased with intensity and was lower for jack pine stands. The proportion of simulated fires that burned at high severity (e.g. >75% reduction in patch basal area) was 0.80 for black spruce and 0.11 for jack pine. We identified thresholds in intensity below which there was a marked sensitivity of simulated fire severity to stand structure, and to interactions between intensity and structure. We found no evidence for a residual effect of pyrogeographic region on simulated severity, after the effects of stand structure and species composition were accounted for. The model presented here was able to produce variation in fire severity under a range of fire intensity conditions. This suggests that variation in stand structure is one of the factors causing the observed variation in boreal fire severity.

Isotopic structure of Lake Whitefish in Lake Huron: Evidence for regional and local populations based on resource use

USGS Publications Warehouse

Eberts, Rebecca L.; Wissel, Bjorn; Simpson, Gavin L.; Crawford, Stephen S.; Stott, Wendylee; Hanner, Robert H.; Manzon, Richard G.; Wilson, Joanna Y.; Boreham, Douglas R.; Somers, Christopher M.

2017-01-01

Lake Whitefish Coregonus clupeaformis is the most commercially valuable species in Lake Huron. The fishery for this species has historically been managed based on 25 management units (17 in Canada, 8 in the USA). However, congruence between the contemporary population structure of Lake Whitefish and management units is poorly understood. We used stable isotopes of carbon (δ13C) and nitrogen (δ15N), food web markers that reflect patterns in resource use (i.e., prey, location, habitat), to assess the population structure of spawning-phase Lake Whitefish collected from 32 sites (1,474 fish) across Lake Huron. We found large isotopic variation among fish from different sites (ranges: δ13C = 10.2‰, δ15N = 5.5‰) and variable niche size and levels of overlap (standard ellipse area = 1.0–4.3‰2). Lake Huron contained spawning-phase fish from four major isotopic clusters largely defined by extensive variation in δ13C, and the isotopic composition of fish sampled was spatially structured both within and between lake basins. Based on cluster compositions, we identified six putative regional groups, some of which represented sites of high diversity (three to four clusters) and others with less (one to two clusters). Analysis of isotopic values from Lake Whitefish collected from summer feeding locations and baseline prey items showed similar isotopic variation and established spatial linkage between spawning-phase and summer fish. Our results show that summer feeding location contributes strongly to the isotopic structure we observed in spawning-phase fish. One of the regional groups we identified in northern Georgian Bay is highly distinct based on isotopic composition and possibly ecologically unique within Lake Huron. Our findings are congruent with several previous studies using different markers (genetics, mark–recapture), and we conclude that current management units are generally too small and numerous to reflect the population structure of Lake Whitefish in Lake Huron.

Fabrication of large tungsten structures by chemical vapor deposition

NASA Technical Reports Server (NTRS)

Kahle, V. E.; Lewis, W. J.; Stubbs, V. R.

1971-01-01

Process is accomplished by reducing tungsten hexafluoride with hydrogen. Metallic tungsten of essentially 100 percent purity and density is produced and built up as dense deposit on heated mandrel assembly. Process variations are building up, sealing or bonding refractory metals at temperatures below transition temperatures of base metal substrates.

Patterns and processes of Mycobacterium bovis evolution revealed by phylogenomic analyses

USDA-ARS?s Scientific Manuscript database

Mycobacterium bovis is an important animal pathogen worldwide that parasitizes wild and domesticated vertebrate livestock as well as humans. A comparison of the five M. bovis complete genomes from UK, South Korea, Brazil and USA revealed four novel large-scale structural variations of at least 2,000...

Evolution of the fruit endocarp: molecular mechanisms underlying adaptations in seed protection and dispersal strategies

USDA-ARS?s Scientific Manuscript database

Plant evolution is largely driven by adaptations in seed protection and dispersal strategies that allow diversification into new niches. This is evident by the tremendous variation in flowering and fruiting structures present both across and within different plant lineages. Within a single plant f...

Spatial perspectives in state-and-transition models: A missing link to land management?

USDA-ARS?s Scientific Manuscript database

Conceptual models of alternative states and thresholds are based largely on observations of ecosystem processes at a few points in space. Because the distribution of alternative states in spatially-structured ecosystems is the result of variations in pattern-process interactions at different scales,...

Simulation of Surface Pressure Induced by Vortex/Body Interaction

NASA Astrophysics Data System (ADS)

He, M.; Islam, M.; Veitch, B.; Bose, N.; Colbourne, M. B.; Liu, P.

When a strong vortical wake impacts a structure, the pressure on the impacted surface sees large variations in its amplitude. This pressure fluctuation is one of the main sources causing severe structural vibration and hydrodynamic noise. Economical and effective prediction methods of the fluctuating pressure are required by engineers in many fields. This paper presents a wake impingement model (WIM) that has been incorporated into a panel method code, Propella, and its applications in simulations of a podded propeller wake impacting on a strut. Simulated strut surface pressure distributions and variations are compared with experimental data in terms of time-averaged components and phase-averaged components. The pressure comparisons show that the calculated results are in a good agreement with experimental data.

Quark mass variations of nuclear forces, BBN, and all that

NASA Astrophysics Data System (ADS)

Meissner, Ulf-G.

2014-03-01

In this talk, I discuss the modifications of the nuclear forces due to variations of the light quark masses and of the fine structure constant. This is based on the chiral nuclear effective field theory, that successfully describes a large body of data. The generation of the light elements in the Big Bang Nucleosynthesis provides important constraints on these modifications. In addition, I discuss the role of the anthropic principle in the triple-alpha process that underlies carbon and oxygen generation in hot stars. It appears that a fine-tuning of the quark masses and the fine structure constant within 2 to 3 per cent is required to make life on Earth viable. Supported in part by DFG, HGF and the BMBF.

Global Distribution of Density Irregularities in the Equatorial Ionosphere

NASA Technical Reports Server (NTRS)

Kil, Hyosub; Heelis, R. A.

1998-01-01

We analyzed measurements of ion number density made by the retarding potential analyzer aboard the Atmosphere Explorer-E (AE-E) satellite, which was in an approximately circular orbit at an altitude near 300 km in 1977 and later at an altitude near 400 km. Large-scale (greater than 60 km) density measurements in the high-altitude regions show large depletions of bubble-like structures which are confined to narrow local time longitude, and magnetic latitude ranges, while those in the low-altitude regions show relatively small depletions which are broadly distributed,in space. For this reason we considered the altitude regions below 300 km and above 350 km and investigated the global distribution of irregularities using the rms deviation delta N/N over a path length of 18 km as an indicator of overall irregularity intensity. Seasonal variations of irregularity occurrence probability are significant in the Pacific regions, while the occurrence probability is always high in die Atlantic-African regions and is always low in die Indian regions. We find that the high occurrence probability in the Pacific regions is associated with isolated bubble structures, while that near 0 deg longitude is produced by large depictions with bubble structures which are superimposed on a large-scale wave-like background. Considerations of longitude variations due to seeding mechanisms and due to F region winds and drifts are necessary to adequately explain the observations at low and high altitudes. Seeding effects are most obvious near 0 deg longitude, while the most easily observed effect of the F region is the suppression of irregularity growth by interhemispheric neutral winds.

Evolution of Precipitation Structure During the November DYNAMO MJO Event: Cloud-Resolving Model Intercomparison and Cross Validation Using Radar Observations

NASA Astrophysics Data System (ADS)

Li, Xiaowen; Janiga, Matthew A.; Wang, Shuguang; Tao, Wei-Kuo; Rowe, Angela; Xu, Weixin; Liu, Chuntao; Matsui, Toshihisa; Zhang, Chidong

2018-04-01

Evolution of precipitation structures are simulated and compared with radar observations for the November Madden-Julian Oscillation (MJO) event during the DYNAmics of the MJO (DYNAMO) field campaign. Three ground-based, ship-borne, and spaceborne precipitation radars and three cloud-resolving models (CRMs) driven by observed large-scale forcing are used to study precipitation structures at different locations over the central equatorial Indian Ocean. Convective strength is represented by 0-dBZ echo-top heights, and convective organization by contiguous 17-dBZ areas. The multi-radar and multi-model framework allows for more stringent model validations. The emphasis is on testing models' ability to simulate subtle differences observed at different radar sites when the MJO event passed through. The results show that CRMs forced by site-specific large-scale forcing can reproduce not only common features in cloud populations but also subtle variations observed by different radars. The comparisons also revealed common deficiencies in CRM simulations where they underestimate radar echo-top heights for the strongest convection within large, organized precipitation features. Cross validations with multiple radars and models also enable quantitative comparisons in CRM sensitivity studies using different large-scale forcing, microphysical schemes and parameters, resolutions, and domain sizes. In terms of radar echo-top height temporal variations, many model sensitivity tests have better correlations than radar/model comparisons, indicating robustness in model performance on this aspect. It is further shown that well-validated model simulations could be used to constrain uncertainties in observed echo-top heights when the low-resolution surveillance scanning strategy is used.

Total variation regularization of the 3-D gravity inverse problem using a randomized generalized singular value decomposition

NASA Astrophysics Data System (ADS)

Vatankhah, Saeed; Renaut, Rosemary A.; Ardestani, Vahid E.

2018-04-01

We present a fast algorithm for the total variation regularization of the 3-D gravity inverse problem. Through imposition of the total variation regularization, subsurface structures presenting with sharp discontinuities are preserved better than when using a conventional minimum-structure inversion. The associated problem formulation for the regularization is nonlinear but can be solved using an iteratively reweighted least-squares algorithm. For small-scale problems the regularized least-squares problem at each iteration can be solved using the generalized singular value decomposition. This is not feasible for large-scale, or even moderate-scale, problems. Instead we introduce the use of a randomized generalized singular value decomposition in order to reduce the dimensions of the problem and provide an effective and efficient solution technique. For further efficiency an alternating direction algorithm is used to implement the total variation weighting operator within the iteratively reweighted least-squares algorithm. Presented results for synthetic examples demonstrate that the novel randomized decomposition provides good accuracy for reduced computational and memory demands as compared to use of classical approaches.

Effects of variables upon pyrotechnically induced shock response spectra, part 2

NASA Technical Reports Server (NTRS)

Smith, James Lee

1988-01-01

Throughout the aerospace industry, large variations of 50 percent (6 dB) or more in shock response spectra (SRS) derived from pyrotechnic separation events continue to be reported from actual spaceflight data and from laboratory tests. As a result of these variations, NASA funded a research program for 1984 through 1986. The purpose of the 1984 through 1986 project was to analyze variations in pyrotechnically induced SRS and to determine if and to what degree manufacturing and assembly variables and tolerances, distance from the shock source, data acquisition instrumentation, and shock energy propagation affect the SRS. Sixty-four free-free boundary plate tests were performed. NASA funded an additional study for 1987 through 1988. This paper is a summary of the additional study. The purpose was to evaluate shock dissipation through various spacecraft structural joint types, to evaluate shock variation for various manufacturing and assembly variables on clamped boundary test plates, and to verify data correction techniques. Five clamped boundary plate tests investigated manufacturing and assembly variables and mass loading effects. Six free-free boundary plate tests investigated shock dissipation across spacecraft joint structures.

High-Resolution Seismic Velocity and Attenuation Models of the Caucasus-Caspian Region

DTIC Science & Technology

2009-09-30

region is part of the Alpine-Himalayan collision belt and is an area of complex structure accompanied by large variations in seismic wave velocities...velocity structure is developed using teleseismic receiver functions and surface waves. Joint inversion of surface wave group dispersion curves...Caucasus and the thinnest is in the Arabian Plate. Thin crust is also observed near the Caspian. The lithospheric mantle in the Greater Caucasus and the

Small-angle neutron scattering reveals the assembly mode and oligomeric architecture of TET, a large, dodecameric aminopeptidase

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

Appolaire, Alexandre; Girard, Eric; Colombo, Matteo

2014-11-01

The present work illustrates that small-angle neutron scattering, deuteration and contrast variation, combined with in vitro particle reconstruction, constitutes a very efficient approach to determine subunit architectures in large, symmetric protein complexes. In the case of the 468 kDa heterododecameric TET peptidase machine, it was demonstrated that the assembly of the 12 subunits is a highly controlled process and represents a way to optimize the catalytic efficiency of the enzyme. The specific self-association of proteins into oligomeric complexes is a common phenomenon in biological systems to optimize and regulate their function. However, de novo structure determination of these important complexesmore » is often very challenging for atomic-resolution techniques. Furthermore, in the case of homo-oligomeric complexes, or complexes with very similar building blocks, the respective positions of subunits and their assembly pathways are difficult to determine using many structural biology techniques. Here, an elegant and powerful approach based on small-angle neutron scattering is applied, in combination with deuterium labelling and contrast variation, to elucidate the oligomeric organization of the quaternary structure and the assembly pathways of 468 kDa, hetero-oligomeric and symmetric Pyrococcus horikoshii TET2–TET3 aminopeptidase complexes. The results reveal that the topology of the PhTET2 and PhTET3 dimeric building blocks within the complexes is not casual but rather suggests that their quaternary arrangement optimizes the catalytic efficiency towards peptide substrates. This approach bears important potential for the determination of quaternary structures and assembly pathways of large oligomeric and symmetric complexes in biological systems.« less

Single-molecule optical genome mapping of a human HapMap and a colorectal cancer cell line.

PubMed

Teo, Audrey S M; Verzotto, Davide; Yao, Fei; Nagarajan, Niranjan; Hillmer, Axel M

2015-01-01

Next-generation sequencing (NGS) technologies have changed our understanding of the variability of the human genome. However, the identification of genome structural variations based on NGS approaches with read lengths of 35-300 bases remains a challenge. Single-molecule optical mapping technologies allow the analysis of DNA molecules of up to 2 Mb and as such are suitable for the identification of large-scale genome structural variations, and for de novo genome assemblies when combined with short-read NGS data. Here we present optical mapping data for two human genomes: the HapMap cell line GM12878 and the colorectal cancer cell line HCT116. High molecular weight DNA was obtained by embedding GM12878 and HCT116 cells, respectively, in agarose plugs, followed by DNA extraction under mild conditions. Genomic DNA was digested with KpnI and 310,000 and 296,000 DNA molecules (≥ 150 kb and 10 restriction fragments), respectively, were analyzed per cell line using the Argus optical mapping system. Maps were aligned to the human reference by OPTIMA, a new glocal alignment method. Genome coverage of 6.8× and 5.7× was obtained, respectively; 2.9× and 1.7× more than the coverage obtained with previously available software. Optical mapping allows the resolution of large-scale structural variations of the genome, and the scaffold extension of NGS-based de novo assemblies. OPTIMA is an efficient new alignment method; our optical mapping data provide a resource for genome structure analyses of the human HapMap reference cell line GM12878, and the colorectal cancer cell line HCT116.

Atmospheric Structure and Diurnal Variations at Low Altitudes in the Martian Tropics

NASA Astrophysics Data System (ADS)

Hinson, David P.; Spiga, A.; Lewis, S.; Tellmann, S.; Pätzold, M.; Asmar, S.; Häusler, B.

2013-10-01

We are using radio occultation measurements from Mars Express, Mars Reconnaissance Orbiter, and Mars Global Surveyor to characterize the diurnal cycle in the lowest scale height above the surface. We focus on northern spring and summer, using observations from 4 Martian years at local times of 4-5 and 15-17 h. We supplement the observations with results obtained from large-eddy simulations and through data assimilation by the UK spectral version of the LMD Mars Global Circulation Model. We previously investigated the depth of the daytime convective boundary layer (CBL) and its variations with surface elevation and surface properties. We are now examining unusual aspects of the temperature structure observed at night. Most important, predawn profiles in the Tharsis region contain an unexpected layer of neutral static stability at pressures of 200-300 Pa with a depth of 4-5 km. The mixed layer is bounded above by a midlevel temperature inversion and below by another strong inversion adjacent to the surface. The narrow temperature minimum at the base of the midlevel inversion suggests the presence of a water ice cloud layer, with the further implication that radiative cooling at cloud level can induce convective activity at lower altitudes. Conversely, nighttime profiles in Amazonis show no sign of a midlevel inversion or a detached mixed layer. These regional variations in the nighttime temperature structure appear to arise in part from large-scale variations in topography, which have several notable effects. First, the CBL is much deeper in the Tharsis region than in Amazonis, owing to a roughly 6-km difference in surface elevation. Second, large-eddy simulations show that daytime convection is not only deeper above Tharsis but also considerably more intense than it is in Amazonis. Finally, the daytime surface temperatures are comparable in the two regions, so that Tharsis acts as an elevated heat source throughout the CBL. These topographic effects are expected to enhance the vertical mixing of water vapor above elevated terrain, which might lead to the formation and regional confinement of nighttime clouds.

Habitat degradation and fishing effects on the size structure of coral reef fish communities.

PubMed

Wilson, S K; Fisher, R; Pratchett, M S; Graham, N A J; Dulvy, N K; Turner, R A; Cakacaka, A; Polunin, N V C

2010-03-01

Overfishing and habitat degradation through climate change pose the greatest threats to sustainability of marine resources on coral reefs. We examined how changes in fishing pressure and benthic habitat composition influenced the size spectra of island-scale reef fish communities in Lau, Fiji. Between 2000 and 2006 fishing pressure declined in the Lau Islands due to declining human populations and reduced demand for fresh fish. At the same time, coral cover declined and fine-scale architectural complexity eroded due to coral bleaching and outbreaks of crown-of-thorns starfish, Acanthaster planci. We examined the size distribution of reef fish communities using size spectra analysis, the linearized relationship between abundance and body size class. Spatial variation in fishing pressure accounted for 31% of the variation in the slope of the size spectra in 2000, higher fishing pressure being associated with a steeper slope, which is indicative of fewer large-bodied fish and/or more small-bodied fish. Conversely, in 2006 spatial variation in habitat explained 53% of the variation in the size spectra slopes, and the relationship with fishing pressure was much weaker (approximately 12% of variation) than in 2000. Reduced cover of corals and lower structural complexity was associated with less steep size spectra slopes, primarily due to reduced abundance of fish < 20 cm. Habitat degradation will compound effects of fishing on coral reefs as increased fishing reduces large-bodied target species, while habitat loss results in fewer small-bodied juveniles and prey that replenish stocks and provide dietary resources for predatory target species. Effective management of reef resources therefore depends on both reducing fishing pressure and maintaining processes that encourage rapid recovery of coral habitat.

[Effect of environmental factors on macroinvertebrate community structure in the Huntai River basin in the Huntai River basin].

PubMed

Li, Yan-li; Li, Yan-fen; Xu, Zong-xue

2015-01-01

In May-June 2012, macroinvertebrates were investigated at 66 sampling sites in the Huntai River basin in Northeast of China. A total of 72 macrobenthos species were collected, of which, 51 species (70.83%) were aquatic insects, 10 species (13.89%) were mollusks, 7 species (9.72%) were annelids, and 4 species (5.56%) were arthropods. First, 13 candidate metrics (EPT taxa, Dominant taxon%, Ephemeroptera%, Trichoptera%, mollusks%, Heptageniidae/Ephemeroptera; Hydropsychidae/ Trichoptera, Oligochaeta%, intolerant taxon% , tolerant taxon%, Collector%, Clingers%, Shannon-wiener index.) which belonged to six types were chosen to represent macroinvertebrate community structure by correlation analysis. Then, relationships between anthropogenic and physiography pressures and macroinvertebrate community structure variables were measured using redundancy analysis. Then, this study compared the relative influences of anthropogenic and physiographic pressures on macroinvertebrate community structure and the relative influences of anthropogenic pressures at reach, riparian and catchment scales by pRDA. The results showed all environmental factors explained 72.23% of the variation of macroinvertebrate community structure. In addition, a large proportion of the explained variability in macroinvertebrate community structure was related to anthropogenic pressures (48.9%) and to physiographic variables (11.8%), anthropogenic pressures at reach scale influenced most significantly macroinvertebrate community structure which explained 35.3% of the variation of macroinvertebrate community structure. pH, habitat, TN, CODMn, hardness, conductivity, total dissolved particle and ammonia influenced respectively explained 4%, 3.6%, 1.8%, 1.7%, 1.7%, 0.9%, 0.9% and 0.9% of the variation of macroinvertebrate community structure. The land use at riparian and catchment scale respectively explained 10% and 7% of the variation of macroinvertebrate community structure. Finally, the relationships of land use at catchment and riparian scales and water quality factors, hydrological indicators, habitat, substrate types were analyzed. This study supports the idea that human pressures effects on river macroinvertebrate communities are linked at spatial scales and must be considered jointly.

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

Salerno, Kenneth Michael; Bolintineanu, Dan S.; Lane, J. Matthew D.

We believe that the high mechanical stiffness of single-nanoparticle-thick membranes is the result of the local structure of ligand coatings that mediate interactions between nanoparticles. These ligand structures are not directly observable experimentally. We use molecular dynamics simulations to observe variations in ligand structure and simultaneously measure variations in membrane mechanical properties. We have shown previously that ligand end group has a large impact on ligand structure and membrane mechanical properties. Here we introduce and apply quantitative molecular structure measures to these membranes and extend analysis to multiple nanoparticle core sizes and ligand lengths. Simulations of nanoparticle membranes with amore » nanoparticle core diameter of 4 or 6 nm, a ligand length of 11 or 17 methylenes, and either carboxyl (COOH) or methyl (CH 3) ligand end groups are presented. In carboxyl-terminated ligand systems, structure and interactions are dominated by an end-to-end orientation of ligands. In methyl-terminated ligand systems large ordered ligand structures form, but nanoparticle interactions are dominated by disordered, partially interdigitated ligands. Core size and ligand length also affect both ligand arrangement within the membrane and the membrane's macroscopic mechanical response, but are secondary to the role of the ligand end group. Additionally, the particular end group (COOH or CH 3) alters the nature of how ligand length, in turn, affects the membrane properties. The effect of core size does not depend on the ligand end group, with larger cores always leading to stiffer membranes. Asymmetry in the stress and ligand density is observed in membranes during preparation at a water-vapor interface, with the stress asymmetry persisting in all membranes after drying.« less

Compositional variations at ultra-structure length scales in coral skeleton

NASA Astrophysics Data System (ADS)

Meibom, Anders; Cuif, Jean-Pierre; Houlbreque, Fanny; Mostefaoui, Smail; Dauphin, Yannicke; Meibom, Karin L.; Dunbar, Robert

2008-03-01

Distributions of Mg and Sr in the skeletons of a deep-sea coral ( Caryophyllia ambrosia) and a shallow-water, reef-building coral ( Pavona clavus) have been obtained with a spatial resolution of 150 nm, using the NanoSIMS ion microprobe at the Muséum National d'Histoire Naturelle in Paris. These trace element analyses focus on the two primary ultra-structural components in the skeleton: centers of calcification (COC) and fibrous aragonite. In fibrous aragonite, the trace element variations are typically on the order of 10% or more, on length scales on the order of 1-10 μm. Sr/Ca and Mg/Ca variations are not correlated. However, Mg/Ca variations in Pavona are strongly correlated with the layered organization of the skeleton. These data allow for a direct comparison of trace element variations in zooxanthellate and non-zooxanthellate corals. In both corals, all trace elements show variations far beyond what can be attributed to variations in the marine environment. Furthermore, the observed trace element variations in the fibrous (bulk) part of the skeletons are not related to the activity of zooxanthellae, but result from other biological activity in the coral organism. To a large degree, this biological forcing is independent of the ambient marine environment, which is essentially constant on the growth timescales considered here. Finally, we discuss the possible detection of a new high-Mg calcium carbonate phase, which appears to be present in both deep-sea and reef-building corals and is neither aragonite nor calcite.

Resistance to malaria through structural variation of red blood cell invasion receptors

PubMed Central

Leffler, Ellen M.; Band, Gavin; Busby, George B.J.; Kivinen, Katja; Le, Quang Si; Clarke, Geraldine M.; Bojang, Kalifa A.; Conway, David J.; Jallow, Muminatou; Sisay-Joof, Fatoumatta; Bougouma, Edith C.; Mangano, Valentina D.; Modiano, David; Sirima, Sodiomon B.; Achidi, Eric; Apinjoh, Tobias O.; Marsh, Kevin; Ndila, Carolyne M.; Peshu, Norbert; Williams, Thomas N.; Drakeley, Chris; Manjurano, Alphaxard; Reyburn, Hugh; Riley, Eleanor; Kachala, David; Molyneux, Malcolm; Nyirongo, Vysaul; Taylor, Terrie; Thornton, Nicole; Tilley, Louise; Grimsley, Shane; Drury, Eleanor; Stalker, Jim; Cornelius, Victoria; Hubbart, Christina; Jeffreys, Anna E.; Rowlands, Kate; Rockett, Kirk A.; Spencer, Chris C.A.; Kwiatkowski, Dominic P.

2017-01-01

The malaria parasite Plasmodium falciparum invades human red blood cells via interactions between host and parasite surface proteins. By analyzing genome sequence data from human populations, including 1269 individuals from sub-Saharan Africa, we identify a diverse array of large copy number variants affecting the host invasion receptor genes GYPA and GYPB. We find that a nearby association with severe malaria is explained by a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which encode a serologically distinct blood group antigen known as Dantu. This variant reduces the risk of severe malaria by 40% and has recently risen in frequency in parts of Kenya, yet it appears to be absent from west Africa. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria. PMID:28522690

Resistance to malaria through structural variation of red blood cell invasion receptors.

PubMed

Leffler, Ellen M; Band, Gavin; Busby, George B J; Kivinen, Katja; Le, Quang Si; Clarke, Geraldine M; Bojang, Kalifa A; Conway, David J; Jallow, Muminatou; Sisay-Joof, Fatoumatta; Bougouma, Edith C; Mangano, Valentina D; Modiano, David; Sirima, Sodiomon B; Achidi, Eric; Apinjoh, Tobias O; Marsh, Kevin; Ndila, Carolyne M; Peshu, Norbert; Williams, Thomas N; Drakeley, Chris; Manjurano, Alphaxard; Reyburn, Hugh; Riley, Eleanor; Kachala, David; Molyneux, Malcolm; Nyirongo, Vysaul; Taylor, Terrie; Thornton, Nicole; Tilley, Louise; Grimsley, Shane; Drury, Eleanor; Stalker, Jim; Cornelius, Victoria; Hubbart, Christina; Jeffreys, Anna E; Rowlands, Kate; Rockett, Kirk A; Spencer, Chris C A; Kwiatkowski, Dominic P

2017-06-16

The malaria parasite Plasmodium falciparum invades human red blood cells by a series of interactions between host and parasite surface proteins. By analyzing genome sequence data from human populations, including 1269 individuals from sub-Saharan Africa, we identify a diverse array of large copy-number variants affecting the host invasion receptor genes GYPA and GYPB We find that a nearby association with severe malaria is explained by a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which encode a serologically distinct blood group antigen known as Dantu. This variant reduces the risk of severe malaria by 40% and has recently increased in frequency in parts of Kenya, yet it appears to be absent from west Africa. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria. Copyright © 2017, American Association for the Advancement of Science.

Cancer Genomics: Integrative and Scalable Solutions in R / Bioconductor | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

This proposal develops scalable R / Bioconductor software infrastructure and data resources to integrate complex, heterogeneous, and large cancer genomic experiments. The falling cost of genomic assays facilitates collection of multiple data types (e.g., gene and transcript expression, structural variation, copy number, methylation, and microRNA data) from a set of clinical specimens. Furthermore, substantial resources are now available from large consortium activities like The Cancer Genome Atlas (TCGA).

Vesta Mineralogy after Dawn Global Observations

NASA Technical Reports Server (NTRS)

ChristinaDeSanctis, Maria; Ammannito, E.; Capaccioni, F.; Cparia, M. T.; Carraro, F.; Fonte, S.; Frigeri, A.; Longobardo, A.; Marchi, S.; Palomba, E.;

Use of Machine Learning Techniques for Identification of Robust Teleconnections to East African Rainfall Variability

NASA Technical Reports Server (NTRS)

Roberts, J. Brent; Robertson, F. R.; Funk, C.

2014-01-01

Hidden Markov models can be used to investigate structure of subseasonal variability. East African short rain variability has connections to large-scale tropical variability. MJO - Intraseasonal variations connected with appearance of "wet" and "dry" states. ENSO/IOZM SST and circulation anomalies are apparent during years of anomalous residence time in the subseasonal "wet" state. Similar results found in previous studies, but we can interpret this with respect to variations of subseasonal wet and dry modes. Reveal underlying connections between MJO/IOZM/ENSO with respect to East African rainfall.

Molecular responses in root-associative rhizospheric bacteria to variations in plant exudates

NASA Astrophysics Data System (ADS)

Abdoun, Hamid; McMillan, Mary; Pereg, Lily

2015-04-01

Plant exudates are a major factor in the interface of plant-soil-microbe interactions and it is well documented that the microbial community structure in the rhizosphere is largely influenced by the particular exudates excreted by various plants. Azospirillum brasilense is a plant growth promoting rhizobacterium that is known to interact with a large number of plants, including important food crops. The regulatory gene flcA has an important role in this interaction as it controls morphological differentiation of the bacterium that is essential for attachment to root surfaces. Being a response regulatory gene, flcA mediates the response of the bacterial cell to signals from the surrounding rhizosphere. This makes this regulatory gene a good candidate for analysis of the response of bacteria to rhizospheric alterations, in this case, variations in root exudates. We will report on our studies on the response of Azospirillum, an ecologically, scientifically and agriculturally important bacterial genus, to variations in the rhizosphere.

Large Magneto-ionic Variations toward the Galactic Center Magnetar, PSR J1745-2900

NASA Astrophysics Data System (ADS)

Desvignes, G.; Eatough, R. P.; Pen, U. L.; Lee, K. J.; Mao, S. A.; Karuppusamy, R.; Schnitzeler, D. H. F. M.; Falcke, H.; Kramer, M.; Wucknitz, O.; Spitler, L. G.; Torne, P.; Liu, K.; Bower, G. C.; Cognard, I.; Lyne, A. G.; Stappers, B. W.

2018-01-01

Polarized radio emission from PSR J1745‑2900 has already been used to investigate the strength of the magnetic field in the Galactic center (GC), close to Sagittarius A*. Here we report how persistent radio emission from this magnetar, for over four years since its discovery, has revealed large changes in the observed Faraday rotation measure (RM), by up to 3500 rad m‑2 (a 5% fractional change). From simultaneous analysis of the dispersion measure, we determine that these fluctuations are dominated by variations in either the projected magnetic field or the free electron content within the GC, along the changing line of sight to the rapidly moving magnetar. From a structure function analysis of RM variations, and a recent epoch of rapid change of RM, we determine a minimum scale of magneto-ionic fluctuations of size ∼2 au at the GC distance, inferring PSR J1745‑2900 is just ∼0.1 pc behind an additional scattering screen.

Genomic variation and DNA repair associated with soybean transgenesis: a comparison to cultivars and mutagenized plants.

PubMed

Anderson, Justin E; Michno, Jean-Michel; Kono, Thomas J Y; Stec, Adrian O; Campbell, Benjamin W; Curtin, Shaun J; Stupar, Robert M

2016-05-12

The safety of mutagenized and genetically transformed plants remains a subject of scrutiny. Data gathered and communicated on the phenotypic and molecular variation induced by gene transfer technologies will provide a scientific-based means to rationally address such concerns. In this study, genomic structural variation (e.g. large deletions and duplications) and single nucleotide polymorphism rates were assessed among a sample of soybean cultivars, fast neutron-derived mutants, and five genetically transformed plants developed through Agrobacterium based transformation methods. On average, the number of genes affected by structural variations in transgenic plants was one order of magnitude less than that of fast neutron mutants and two orders of magnitude less than the rates observed between cultivars. Structural variants in transgenic plants, while rare, occurred adjacent to the transgenes, and at unlinked loci on different chromosomes. DNA repair junctions at both transgenic and unlinked sites were consistent with sequence microhomology across breakpoints. The single nucleotide substitution rates were modest in both fast neutron and transformed plants, exhibiting fewer than 100 substitutions genome-wide, while inter-cultivar comparisons identified over one-million single nucleotide polymorphisms. Overall, these patterns provide a fresh perspective on the genomic variation associated with high-energy induced mutagenesis and genetically transformed plants. The genetic transformation process infrequently results in novel genetic variation and these rare events are analogous to genetic variants occurring spontaneously, already present in the existing germplasm, or induced through other types of mutagenesis. It remains unclear how broadly these results can be applied to other crops or transformation methods.

Comparison of Genetic Structure of Epixylic Liverwort Crossocalyx hellerianus between Central European and Fennoscandian Populations.

PubMed

Holá, Eva; Košnar, Jiří; Kučera, Jan

2015-01-01

Patterns of genetic variation and spatial genetic structure (SGS) were investigated in Crossocalyx hellerianus, a strictly epixylic dioicous liverwort (Scapaniaceae s.l., Marchantiophyta). Studied populations were located in Fennoscandia and Central Europe, with localities differing in availability of substrate and the population connectivity, and their populations consequently different in size, density, and prevailing reproductive mode. A set of nine polymorphic microsatellites was successfully developed and used. Identical individuals were only found within populations. Especially in large populations, the majority of the individuals were genetically unique. Resampled number of genotypes, mean number of observed alleles per locus after rarefaction, and Nei's gene diversity in large populations reached high values and ranged between 4.41-4.97, 3.13-4.45, and 0.94-0.99, respectively. On the contrary, the values in small populations were lower and ranged between 1.00-4.42, 1.00-2.73, and 0.00-0.95, respectively. As expected, large populations were found to be more genetically diverse than small populations but relatively big diversity of genotypes was also found in small populations. This indicated that even small populations are important sources of genetic variation in bryophytes and processes causing loss of genetic variation might be compensated by other sources of variability, of which somatic mutations might play an important role. The presence of SGS was discovered in all populations. Large populations possessed less SGS, with individuals showing a pronounced decrease in kinship over 50 cm of distance. Apparent SGS of small populations even at distances up to 16 meters suggests the aggregation of similar genotypes, caused predominantly by the deposition of asexually formed gemmae. Although no strong kinship was detectable at the distances over 16 meters in both small and large populations, identical genotypes were occasionally detected at longer distances (20-80 m), suggesting effective dispersal of asexual propagules.

Comparison of Genetic Structure of Epixylic Liverwort Crossocalyx hellerianus between Central European and Fennoscandian Populations

PubMed Central

Holá, Eva; Košnar, Jiří; Kučera, Jan

2015-01-01

Patterns of genetic variation and spatial genetic structure (SGS) were investigated in Crossocalyx hellerianus, a strictly epixylic dioicous liverwort (Scapaniaceae s.l., Marchantiophyta). Studied populations were located in Fennoscandia and Central Europe, with localities differing in availability of substrate and the population connectivity, and their populations consequently different in size, density, and prevailing reproductive mode. A set of nine polymorphic microsatellites was successfully developed and used. Identical individuals were only found within populations. Especially in large populations, the majority of the individuals were genetically unique. Resampled number of genotypes, mean number of observed alleles per locus after rarefaction, and Nei’s gene diversity in large populations reached high values and ranged between 4.41–4.97, 3.13–4.45, and 0.94–0.99, respectively. On the contrary, the values in small populations were lower and ranged between 1.00–4.42, 1.00–2.73, and 0.00–0.95, respectively. As expected, large populations were found to be more genetically diverse than small populations but relatively big diversity of genotypes was also found in small populations. This indicated that even small populations are important sources of genetic variation in bryophytes and processes causing loss of genetic variation might be compensated by other sources of variability, of which somatic mutations might play an important role. The presence of SGS was discovered in all populations. Large populations possessed less SGS, with individuals showing a pronounced decrease in kinship over 50 cm of distance. Apparent SGS of small populations even at distances up to 16 meters suggests the aggregation of similar genotypes, caused predominantly by the deposition of asexually formed gemmae. Although no strong kinship was detectable at the distances over 16 meters in both small and large populations, identical genotypes were occasionally detected at longer distances (20–80 m), suggesting effective dispersal of asexual propagules. PMID:26186214

Defining the diverse spectrum of inversions, complex structural variation, and chromothripsis in the morbid human genome.

PubMed

Collins, Ryan L; Brand, Harrison; Redin, Claire E; Hanscom, Carrie; Antolik, Caroline; Stone, Matthew R; Glessner, Joseph T; Mason, Tamara; Pregno, Giulia; Dorrani, Naghmeh; Mandrile, Giorgia; Giachino, Daniela; Perrin, Danielle; Walsh, Cole; Cipicchio, Michelle; Costello, Maura; Stortchevoi, Alexei; An, Joon-Yong; Currall, Benjamin B; Seabra, Catarina M; Ragavendran, Ashok; Margolin, Lauren; Martinez-Agosto, Julian A; Lucente, Diane; Levy, Brynn; Sanders, Stephan J; Wapner, Ronald J; Quintero-Rivera, Fabiola; Kloosterman, Wigard; Talkowski, Michael E

2017-03-06

Structural variation (SV) influences genome organization and contributes to human disease. However, the complete mutational spectrum of SV has not been routinely captured in disease association studies. We sequenced 689 participants with autism spectrum disorder (ASD) and other developmental abnormalities to construct a genome-wide map of large SV. Using long-insert jumping libraries at 105X mean physical coverage and linked-read whole-genome sequencing from 10X Genomics, we document seven major SV classes at ~5 kb SV resolution. Our results encompass 11,735 distinct large SV sites, 38.1% of which are novel and 16.8% of which are balanced or complex. We characterize 16 recurrent subclasses of complex SV (cxSV), revealing that: (1) cxSV are larger and rarer than canonical SV; (2) each genome harbors 14 large cxSV on average; (3) 84.4% of large cxSVs involve inversion; and (4) most large cxSV (93.8%) have not been delineated in previous studies. Rare SVs are more likely to disrupt coding and regulatory non-coding loci, particularly when truncating constrained and disease-associated genes. We also identify multiple cases of catastrophic chromosomal rearrangements known as chromoanagenesis, including somatic chromoanasynthesis, and extreme balanced germline chromothripsis events involving up to 65 breakpoints and 60.6 Mb across four chromosomes, further defining rare categories of extreme cxSV. These data provide a foundational map of large SV in the morbid human genome and demonstrate a previously underappreciated abundance and diversity of cxSV that should be considered in genomic studies of human disease.

Structural variations in prefrontal cortex mediate the relationship between early childhood stress and spatial working memory

PubMed Central

Hanson, Jamie L.; Chung, Moo K.; Avants, Brian B.; Rudolph, Karen D.; Shirtcliff, Elizabeth A.; Gee, James C.; Davidson, Richard J.; Pollak, Seth D.

2012-01-01

A large corpus of research indicates exposure to stress impairs cognitive abilities, specifically executive functioning dependent on the prefrontal cortex (PFC). We collected structural MRI scans (n=61), well-validated assessments of executive functioning, and detailed interviews assessing stress exposure in humans, to examine whether cumulative life stress affected brain morphometry and one type of executive functioning, spatial working memory, during adolescence—a critical time of brain development and reorganization. Analysis of variations in brain structure revealed that cumulative life stress and spatial working memory were related to smaller volumes in the PFC, specifically prefrontal gray and white matter between the anterior cingulate and the frontal poles. Mediation analyses revealed that individual differences in prefrontal volumes accounted for the association between cumulative life stress and spatial working memory. These results suggest that structural changes in the PFC may serve as a mediating mechanism through which greater cumulative life stress engenders decrements in cognitive functioning. PMID:22674267

Combined effects of fishing and oil spills on marine fish: Role of stock demographic structure for offspring overlap with oil.

PubMed

Stige, Leif Chr; Ottersen, Geir; Yaragina, Natalia A; Vikebø, Frode B; Stenseth, Nils Chr; Langangen, Øystein

2018-04-01

It has been proposed that the multiple pressures of fishing and petroleum activities impact fish stocks in synergy, as fishing-induced demographic changes in a stock may lead to increased sensitivity to detrimental effects of acute oil spills. High fishing pressure may erode the demographic structure of fish stocks, lead to less diverse spawning strategies, and more concentrated distributions of offspring in space and time. Hence an oil spill may potentially hit a larger fraction of a year-class of offspring. Such a link between demographic structure and egg distribution was recently demonstrated for the Northeast Arctic stock of Atlantic cod for years 1959-1993. We here estimate that this variation translates into a two-fold variation in the maximal proportion of cod eggs potentially exposed to a large oil spill. With this information it is possible to quantitatively account for demographic structure in prospective studies of population effects of possible oil spills. Copyright © 2018 Elsevier Ltd. All rights reserved.

Cosmological structure formation from soft topological defects

NASA Technical Reports Server (NTRS)

Hill, Christopher T.; Schramm, David N.; Fry, J. N.

1988-01-01

Some models have extremely low-mass pseudo-Goldstone bosons that can lead to vacuum phase transitions at late times, after the decoupling of the microwave background.. This can generate structure formation at redshifts z greater than or approx 10 on mass scales as large as M approx 10 to the 18th solar masses. Such low energy transitions can lead to large but phenomenologically acceptable density inhomogeneities in soft topological defects (e.g., domain walls) with minimal variations in the microwave anisotropy, as small as delta Y/T less than or approx 10 to the minus 6 power. This mechanism is independent of the existence of hot, cold, or baryonic dark matter. It is a novel alternative to both cosmic string and to inflationary quantum fluctuations as the origin of structure in the Universe.

A guide to large-scale RNA sample preparation.

PubMed

Baronti, Lorenzo; Karlsson, Hampus; Marušič, Maja; Petzold, Katja

2018-05-01

RNA is becoming more important as an increasing number of functions, both regulatory and enzymatic, are being discovered on a daily basis. As the RNA boom has just begun, most techniques are still in development and changes occur frequently. To understand RNA functions, revealing the structure of RNA is of utmost importance, which requires sample preparation. We review the latest methods to produce and purify a variation of RNA molecules for different purposes with the main focus on structural biology and biophysics. We present a guide aimed at identifying the most suitable method for your RNA and your biological question and highlighting the advantages of different methods. Graphical abstract In this review we present different methods for large-scale production and purification of RNAs for structural and biophysical studies.

Linking lowermost mantle structure, core-mantle boundary heat flux and mantle plume formation

NASA Astrophysics Data System (ADS)

Li, Mingming; Zhong, Shijie; Olson, Peter

2018-04-01

The dynamics of Earth's lowermost mantle exert significant control on the formation of mantle plumes and the core-mantle boundary (CMB) heat flux. However, it is not clear if and how the variation of CMB heat flux and mantle plume activity are related. Here, we perform geodynamic model experiments that show how temporal variations in CMB heat flux and pulses of mantle plumes are related to morphologic changes of the thermochemical piles of large-scale compositional heterogeneities in Earth's lowermost mantle, represented by the large low shear velocity provinces (LLSVPs). We find good correlation between the morphologic changes of the thermochemical piles and the time variation of CMB heat flux. The morphology of the thermochemical piles is significantly altered during the initiation and ascent of strong mantle plumes, and the changes in pile morphology cause variations in the local and the total CMB heat flux. Our modeling results indicate that plume-induced episodic variations of CMB heat flux link geomagnetic superchrons to pulses of surface volcanism, although the relative timing of these two phenomena remains problematic. We also find that the density distribution in thermochemical piles is heterogeneous, and that the piles are denser on average than the surrounding mantle when both thermal and chemical effects are included.

A data set from flash X-ray imaging of carboxysomes

NASA Astrophysics Data System (ADS)

Hantke, Max F.; Hasse, Dirk; Ekeberg, Tomas; John, Katja; Svenda, Martin; Loh, Duane; Martin, Andrew V.; Timneanu, Nicusor; Larsson, Daniel S. D.; van der Schot, Gijs; Carlsson, Gunilla H.; Ingelman, Margareta; Andreasson, Jakob; Westphal, Daniel; Iwan, Bianca; Uetrecht, Charlotte; Bielecki, Johan; Liang, Mengning; Stellato, Francesco; Deponte, Daniel P.; Bari, Sadia; Hartmann, Robert; Kimmel, Nils; Kirian, Richard A.; Seibert, M. Marvin; Mühlig, Kerstin; Schorb, Sebastian; Ferguson, Ken; Bostedt, Christoph; Carron, Sebastian; Bozek, John D.; Rolles, Daniel; Rudenko, Artem; Foucar, Lutz; Epp, Sascha W.; Chapman, Henry N.; Barty, Anton; Andersson, Inger; Hajdu, Janos; Maia, Filipe R. N. C.

2016-08-01

Ultra-intense femtosecond X-ray pulses from X-ray lasers permit structural studies on single particles and biomolecules without crystals. We present a large data set on inherently heterogeneous, polyhedral carboxysome particles. Carboxysomes are cell organelles that vary in size and facilitate up to 40% of Earth’s carbon fixation by cyanobacteria and certain proteobacteria. Variation in size hinders crystallization. Carboxysomes appear icosahedral in the electron microscope. A protein shell encapsulates a large number of Rubisco molecules in paracrystalline arrays inside the organelle. We used carboxysomes with a mean diameter of 115±26 nm from Halothiobacillus neapolitanus. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min. Every diffraction pattern is a unique structure measurement and high-throughput imaging allows sampling the space of structural variability. The different structures can be separated and phased directly from the diffraction data and open a way for accurate, high-throughput studies on structures and structural heterogeneity in biology and elsewhere.

Population genomics and the causes of local differentiation.

PubMed

Tonsor, Stephen J

2012-11-01

Exactly 50 years ago, a revolution in empirical population genetics began with the introduction of methods for detecting allelic variation using protein electrophoresis (Throckmorton 1962; Hubby 1963; Lewontin & Hubby 1966). These pioneering scientists showed that populations are chock-full of genetic variation. This variation was a surprise that required a re-thinking of evolutionary genetic heuristics. Understanding the causes for the maintenance of this variation became and remains a major area of research. In the process of addressing the causes, this same group of scientists documented geographical genetic structure (Prakash et al. 1969), spawning the continued accumulation of what is now a huge case study catalogue of geographical differentiation (e.g. Loveless & Hamrick 1984; Linhart & Grant 1996). Geographical differentiation is clearly quite common. Yet, a truly general understanding of the patterns in and causes of spatial genetic structure across the genome remains elusive. To what extent is spatial structure driven by drift and phylogeography vs. geographical differences in environmental sources of selection? What proportion of the genome participates? A general understanding requires range-wide data on spatial patterning of variation across the entire genome. In this issue of Molecular Ecology, Lasky et al. (2012) make important strides towards addressing these issues, taking advantage of three contemporary revolutions in evolutionary biology. Two are technological: high-throughput sequencing and burgeoning computational power. One is cultural: open access to data from the community of scientists and especially data sets that result from large collaborative efforts. Together, these developments may at last put answers within reach.

Packing microstructure and local density variations of experimental and computational pebble beds

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

Auwerda, G. J.; Kloosterman, J. L.; Lathouwers, D.

2012-07-01

In pebble bed type nuclear reactors the fuel is contained in graphite pebbles, which form a randomly stacked bed with a non-uniform packing density. These variations can influence local coolant flow and power density and are a possible cause of hotspots. To analyse local density variations computational methods are needed that can generate randomly stacked pebble beds with a realistic packing structure on a pebble-to-pebble level. We first compare various properties of the local packing structure of a computed bed with those of an image made using computer aided X-ray tomography, looking at properties in the bulk of the bedmore » and near the wall separately. Especially for the bulk of the bed, properties of the computed bed show good comparison with the scanned bed and with literature, giving confidence our method generates beds with realistic packing microstructure. Results also show the packing structure is different near the wall than in the bulk of the bed, with pebbles near the wall forming ordered layers similar to hexagonal close packing. Next, variations in the local packing density are investigated by comparing probability density functions of the packing fraction of small clusters of pebbles throughout the bed. Especially near the wall large variations in local packing fractions exists, with a higher probability for both clusters of pebbles with low (<0.6) and high (>0.65) packing fraction, which could significantly affect flow rates and, together with higher power densities, could result in hotspots. (authors)« less

Anatomy of Mandibular Vital Structures. Part I: Mandibular Canal and Inferior Alveolar Neurovascular Bundle in Relation with Dental Implantology

PubMed Central

Wang, Hom-Lay; Sabalys, Gintautas

2010-01-01

ABSTRACT Objectives It is critical to determine the location and configuration of the mandibular canal and related vital structures during the implant treatment. The purpose of the present study was to review the literature concerning the mandibular canal and inferior alveolar neurovascular bundle anatomical variations related to the implant surgery. Material and Methods Literature was selected through the search of PubMed, Embase and Cochrane electronic databases. The keywords used for search were mandibular canal, inferior alveolar nerve, and inferior alveolar neurovascular bundle. The search was restricted to English language articles, published from 1973 to November 2009. Additionally, a manual search in the major anatomy, dental implant, prosthetic and periodontal journals and books were performed. Results In total, 46 literature sources were obtained and morphological aspects and variations of the anatomy related to implant treatment in posterior mandible were presented as two entities: intraosseous mandibular canal and associated inferior alveolar neurovascular bundle. Conclusions A review of morphological aspects and variations of the anatomy related to mandibular canal and mandibular vital structures are very important especially in implant therapy since inferior alveolar neurovascular bundle exists in different locations and possesses many variations. Individual, gender, age, race, assessing technique used and degree of edentulous alveolar bone atrophy largely influence these variations. It suggests that osteotomies in implant dentistry should not be developed in the posterior mandible until the position of the mandibular canal is established. PMID:24421958

Adaptive genetic variation mediates bottom-up and top-down control in an aquatic ecosystem

PubMed Central

Rudman, Seth M.; Rodriguez-Cabal, Mariano A.; Stier, Adrian; Sato, Takuya; Heavyside, Julian; El-Sabaawi, Rana W.; Crutsinger, Gregory M.

2015-01-01

Research in eco-evolutionary dynamics and community genetics has demonstrated that variation within a species can have strong impacts on associated communities and ecosystem processes. Yet, these studies have centred around individual focal species and at single trophic levels, ignoring the role of phenotypic variation in multiple taxa within an ecosystem. Given the ubiquitous nature of local adaptation, and thus intraspecific variation, we sought to understand how combinations of intraspecific variation in multiple species within an ecosystem impacts its ecology. Using two species that co-occur and demonstrate adaptation to their natal environments, black cottonwood (Populus trichocarpa) and three-spined stickleback (Gasterosteus aculeatus), we investigated the effects of intraspecific phenotypic variation on both top-down and bottom-up forces using a large-scale aquatic mesocosm experiment. Black cottonwood genotypes exhibit genetic variation in their productivity and consequently their leaf litter subsidies to the aquatic system, which mediates the strength of top-down effects from stickleback on prey abundances. Abundances of four common invertebrate prey species and available phosphorous, the most critically limiting nutrient in freshwater systems, are dictated by the interaction between genetic variation in cottonwood productivity and stickleback morphology. These interactive effects fit with ecological theory on the relationship between productivity and top-down control and are comparable in strength to the effects of predator addition. Our results illustrate that intraspecific variation, which can evolve rapidly, is an under-appreciated driver of community structure and ecosystem function, demonstrating that a multi-trophic perspective is essential to understanding the role of evolution in structuring ecological patterns. PMID:26203004

Adaptive genetic variation mediates bottom-up and top-down control in an aquatic ecosystem.

PubMed

Rudman, Seth M; Rodriguez-Cabal, Mariano A; Stier, Adrian; Sato, Takuya; Heavyside, Julian; El-Sabaawi, Rana W; Crutsinger, Gregory M

2015-08-07

Research in eco-evolutionary dynamics and community genetics has demonstrated that variation within a species can have strong impacts on associated communities and ecosystem processes. Yet, these studies have centred around individual focal species and at single trophic levels, ignoring the role of phenotypic variation in multiple taxa within an ecosystem. Given the ubiquitous nature of local adaptation, and thus intraspecific variation, we sought to understand how combinations of intraspecific variation in multiple species within an ecosystem impacts its ecology. Using two species that co-occur and demonstrate adaptation to their natal environments, black cottonwood (Populus trichocarpa) and three-spined stickleback (Gasterosteus aculeatus), we investigated the effects of intraspecific phenotypic variation on both top-down and bottom-up forces using a large-scale aquatic mesocosm experiment. Black cottonwood genotypes exhibit genetic variation in their productivity and consequently their leaf litter subsidies to the aquatic system, which mediates the strength of top-down effects from stickleback on prey abundances. Abundances of four common invertebrate prey species and available phosphorous, the most critically limiting nutrient in freshwater systems, are dictated by the interaction between genetic variation in cottonwood productivity and stickleback morphology. These interactive effects fit with ecological theory on the relationship between productivity and top-down control and are comparable in strength to the effects of predator addition. Our results illustrate that intraspecific variation, which can evolve rapidly, is an under-appreciated driver of community structure and ecosystem function, demonstrating that a multi-trophic perspective is essential to understanding the role of evolution in structuring ecological patterns. © 2015 The Author(s).

Summary of 2006 to 2010 FPMU Measurements of International Space Station Frame Potential Variations

NASA Technical Reports Server (NTRS)

Minow, Joseph I.; Wright, Kenneth H., Jr.; Chandler, Michael O.; Coffey, Victoria N.; Craven, Paul D.; Schneider, Todd A.; Parker, Linda N.; Ferguson, Dale C.; Koontz, Steve L.; Alred, John W.

2010-01-01

Electric potential variations on the International Space Station (ISS) structure in low Earth orbit are dominated by contributions from interactions of the United States (US) 160 volt solar arrays with the relatively high density, low temperature plasma environment and inductive potentials generated by motion of the large vehicle across the Earth?s magnetic field. The Floating Potential Measurement Unit (FPMU) instrument suite comprising two Langmuir probes, a plasma impedance probe, and a floating potential probe was deployed in August 2006 for use in characterizing variations in ISS potential, the state of the ionosphere along the ISS orbit and its effect on ISS charging, evaluating effects of payloads and visiting vehicles, and for supporting ISS plasma hazard assessments. This presentation summarizes observations of ISS frame potential variations obtained from the FPMU from deployment in 2006 through the current time. We first describe ISS potential variations due to current collection by solar arrays in the day time sector of the orbit including eclipse exit and entry charging events, potential variations due to plasma environment variations in the equatorial anomaly, and visiting vehicles docked to the ISS structure. Next, we discuss potential variations due to inductive electric fields generated by motion of the vehicle across the geomagnetic field and the effects of external electric fields in the ionosphere. Examples of night time potential variations at high latitudes and their possible relationship to auroral charging are described and, finally, we demonstrate effects on the ISS potential due to European Space Agency and US plasma contactor devices.

Bridging Enzymatic Structure Function via Mechanics: A Coarse-Grain Approach.

PubMed

Sacquin-Mora, S

2016-01-01

Flexibility is a central aspect of protein function, and ligand binding in enzymes involves a wide range of structural changes, ranging from large-scale domain movements to small loop or side-chain rearrangements. In order to understand how the mechanical properties of enzymes, and the mechanical variations that are induced by ligand binding, relate to enzymatic activity, we carried out coarse-grain Brownian dynamics simulations on a set of enzymes whose structures in the unbound and ligand-bound forms are available in the Protein Data Bank. Our results show that enzymes are remarkably heterogeneous objects from a mechanical point of view and that the local rigidity of individual residues is tightly connected to their part in the protein's overall structure and function. The systematic comparison of the rigidity of enzymes in their unbound and bound forms highlights the fact that small conformational changes can induce large mechanical effects, leading to either more or less flexibility depending on the enzyme's architecture and the location of its ligand-biding site. These mechanical variations target a limited number of specific residues that occupy key locations for enzymatic activity, and our approach thus offers a mean to detect perturbation-sensitive sites in enzymes, where the addition or removal of a few interactions will lead to important changes in the proteins internal dynamics. © 2016 Elsevier Inc. All rights reserved.

Three-dimensional velocity structure of crust and upper mantle in southwestern China and its tectonic implications

USGS Publications Warehouse

Wang, Chun-Yong; Chan, W.W.; Mooney, W.D.

2003-01-01

Using P and S arrival times from 4625 local and regional earthquakes recorded at 174 seismic stations and associated geophysical investigations, this paper presents a three-dimensional crustal and upper mantle velocity structure of southwestern China (21??-34??N, 97??-105??E). Southwestern China lies in the transition zone between the uplifted Tibetan plateau to the west and the Yangtze continental platform to the east. In the upper crust a positive velocity anomaly exists in the Sichuan Basin, whereas a large-scale negative velocity anomaly exists in the western Sichuan Plateau, consistent with the upper crustal structure under the southern Tibetan plateau. The boundary between these two anomaly zones is the Longmen Shan Fault. The negative velocity anomalies at 50-km depth in the Tengchong volcanic area and the Panxi tectonic zone appear to be associated with temperature and composition variations in the upper mantle. The Red River Fault is the boundary between the positive and negative velocity anomalies at 50-km depth. The overall features of the crustal and the upper mantle structures in southwestern China are a low average velocity, large crustal thickness variations, the existence of a high-conductivity layer in the crust or/and upper mantle, and a high heat flow value. All these features are closely related to the collision between the Indian and the Asian plates.

Computing 3-D wavefields in mantle circulations models to test hypotheses on the origin of lower mantle heterogeneity under Africa directly against seismic observations

NASA Astrophysics Data System (ADS)

Schuberth, Bernhard; Zaroli, Christophe; Nolet, Guust

2015-04-01

Of particular interest for the tectonic evolution of the Atlantic region is the influence of lower mantle structure under Africa on flow in the upper mantle beneath the ocean basin. Along with its Pacific counterpart, the large African anomaly in the lowermost mantle with strongly reduced seismic velocities has received considerable attention in seismological and geodynamic studies. Several seismological observations are typically taken as an indication that these two anomalies are being caused by large-scale compositional variations and that they are piles of material with higher density than normal mantle rock. This would imply negative buoyancy in the lowermost mantle under Africa, which has important implications for the flow at shallower depth and inferences on the processes that led to the formation of the Atlantic Ocean basin. However, a large number of recent studies argue for a strong thermal gradient across the core-mantle boundary that might provide an alternative explanation for the lower mantle anomaly through the resulting large lateral temperature variations. Recently, we developed a new joint forward modeling approach to test such geodynamic hypotheses directly against the seismic observations: Seismic heterogeneity is predicted by converting the temperature field of a high-resolution 3-D mantle circulation model into seismic velocities using thermodynamic models of mantle mineralogy. 3-D global wave propagation in the synthetic elastic structures is then simulated using a spectral element method. Being based on forward modelling only, this approach allows us to generate synthetic wavefields and seismograms independently of seismic observations. The statistics of observed long-period body wave traveltime variations show a markedly different behaviour for P- and S-waves: the standard deviation of P-wave delay times stays almost constant with ray turning depth, while that of the S-wave delay times increases strongly throughout the mantle. In an earlier study, we showed that synthetic traveltime variations computed for an isochemical mantle circulation model with strong core heating can reproduce these different trends. This was taken as a strong indication that seismic heterogeneity in the lower mantle is likely dominated by thermal variations on large length-scales (i.e., relevant for long-period body waves). We will discuss the robustness of this earlier conclusion by exploring the uncertainties in the mineralogical models used to convert temperatures to seismic velocities. In particular, we investigate the influence of anelasticity on the standard deviation of our synthetic traveltime variations. Owing to the differences in seismic frequency content between laboratory measurements (MHz to GHz) and the Earth (mHz to Hz), the seismic velocities given in the mineralogical model need to be adjusted; that is, corrected for dispersion due to anelastic effects.

Determination of field-effective soil properties in the tidewater region of North Carolina

Treesearch

J. McFero Grace; R.W. Skaggs

2013-01-01

Soils vary spatially in texture, structure, depth of horizons, and macropores, which can lead to a large variation in soil physical properties. In particular, saturated hydraulic conductivity (Ksat) and drainable porosity are critical properties required to model field hydrology in poorly drained lands. These soil-property values can be measured...

A large scale joint analysis of flowering time reveals independent temperate adaptations in maize

USDA-ARS?s Scientific Manuscript database

Modulating days to flowering is a key mechanism in plants for adapting to new environments, and variation in days to flowering drives population structure by limiting mating. To elucidate the genetic architecture of flowering across maize, a quantitative trait, we mapped flowering in five global pop...

Localized tidal deformations and dissipation in Enceladus

NASA Astrophysics Data System (ADS)

Beuthe, M.

2017-12-01

The geologic activity at Enceladus's south pole remains unexplained, though tidal deformations are probably the ultimate cause. Recent gravity and libration data indicate that Enceladus's icy crust floats on a global ocean, is rather thin, and has a strongly non-uniform thickness. Tidal effects are enhanced by crustal thinning at the south pole, so that realistic models of tidal tectonics and dissipation should include lateral variations of shell structure. I solve this problem with a new theory of non-uniform viscoelastic thin shells, allowing for large lateral variations of crustal thickness as well as large 3D variations of crustal rheology. The coupling to tidal forcing takes into account self-gravity, density stratification below the shell, core viscoelasticity, and crustal compressibility. The resulting tidal thin shell equations are two partial differential equations defined on the spherical surface, which can be solved numerically much faster than 3D Finite Element Methods. The error on tidal displacements is less than 5% if the thickness is less than 10% of the radius while the error on the deviatoric stress varies between 0 and 10%. If Enceladus's shell is conductive with isostatic thickness variations, crustal thinning increases surface stresses by 60% at the north pole and by a factor of more than 3 at the south pole. Similarly, the surface flux resulting from crustal dissipation increases by a factor of 3 at the south pole. If dissipation is an order of magnitude higher than predicted by the Maxwell model (as suggested by recent experimental data), the power dissipated in the crust could reach 50% of the total power required to maintain the crust in thermal equilibrium, and most of the surface flux variation could be explained by latitudinal variations of crustal dissipation. In all cases, a large part of the heat budget must be generated below the crust.

Analytic energy gradient of projected Hartree-Fock within projection after variation

NASA Astrophysics Data System (ADS)

Uejima, Motoyuki; Ten-no, Seiichiro

2017-03-01

We develop a geometrical optimization technique for the projection-after-variation (PAV) scheme of the recently refined projected Hartree-Fock (PHF) as a fast alternative to the variation-after-projection (VAP) approach for optimizing the structures of molecules/clusters in symmetry-adapted electronic states at the mean-field computational cost. PHF handles the nondynamic correlation effects by restoring the symmetry of a broken-symmetry single reference wavefunction and moreover enables a black-box treatment of orbital selections. Using HF orbitals instead of PHF orbitals, our approach saves the computational cost for the orbital optimization, avoiding the convergence problem that sometimes emerges in the VAP scheme. We show that PAV-PHF provides geometries comparable to those of the complete active space self-consistent field and VAP-PHF for the tested systems, namely, CH2, O3, and the [Cu2O2 ] 2 + core, where nondynamic correlation is abundant. The proposed approach is useful for large systems mainly dominated by nondynamic correlation to find stable structures in many symmetry-adapted states.

Contribution of above- and below-ground plant traits to the structure and function of grassland soil microbial communities

PubMed Central

Legay, N.; Baxendale, C.; Grigulis, K.; Krainer, U.; Kastl, E.; Schloter, M.; Bardgett, R. D.; Arnoldi, C.; Bahn, M.; Dumont, M.; Poly, F.; Pommier, T.; Clément, J. C.; Lavorel, S.

2014-01-01

Background and Aims Abiotic properties of soil are known to be major drivers of the microbial community within it. Our understanding of how soil microbial properties are related to the functional structure and diversity of plant communities, however, is limited and largely restricted to above-ground plant traits, with the role of below-ground traits being poorly understood. This study investigated the relative contributions of soil abiotic properties and plant traits, both above-ground and below-ground, to variations in microbial processes involved in grassland nitrogen turnover. Methods In mountain grasslands distributed across three European sites, a correlative approach was used to examine the role of a large range of plant functional traits and soil abiotic factors on microbial variables, including gene abundance of nitrifiers and denitrifiers and their potential activities. Key Results Direct effects of soil abiotic parameters were found to have the most significant influence on the microbial groups investigated. Indirect pathways via plant functional traits contributed substantially to explaining the relative abundance of fungi and bacteria and gene abundances of the investigated microbial communities, while they explained little of the variance in microbial activities. Gene abundances of nitrifiers and denitrifiers were most strongly related to below-ground plant traits, suggesting that they were the most relevant traits for explaining variation in community structure and abundances of soil microbes involved in nitrification and denitrification. Conclusions The results suggest that consideration of plant traits, and especially below-ground traits, increases our ability to describe variation in the abundances and the functional characteristics of microbial communities in grassland soils. PMID:25122656

Ligand structure and mechanical properties of single-nanoparticle thick membranes

DOE PAGES

Salerno, Kenneth Michael; Bolintineanu, Dan S.; Lane, J. Matthew D.; ...

2015-06-16

We believe that the high mechanical stiffness of single-nanoparticle-thick membranes is the result of the local structure of ligand coatings that mediate interactions between nanoparticles. These ligand structures are not directly observable experimentally. We use molecular dynamics simulations to observe variations in ligand structure and simultaneously measure variations in membrane mechanical properties. We have shown previously that ligand end group has a large impact on ligand structure and membrane mechanical properties. Here we introduce and apply quantitative molecular structure measures to these membranes and extend analysis to multiple nanoparticle core sizes and ligand lengths. Simulations of nanoparticle membranes with amore » nanoparticle core diameter of 4 or 6 nm, a ligand length of 11 or 17 methylenes, and either carboxyl (COOH) or methyl (CH 3) ligand end groups are presented. In carboxyl-terminated ligand systems, structure and interactions are dominated by an end-to-end orientation of ligands. In methyl-terminated ligand systems large ordered ligand structures form, but nanoparticle interactions are dominated by disordered, partially interdigitated ligands. Core size and ligand length also affect both ligand arrangement within the membrane and the membrane's macroscopic mechanical response, but are secondary to the role of the ligand end group. Additionally, the particular end group (COOH or CH 3) alters the nature of how ligand length, in turn, affects the membrane properties. The effect of core size does not depend on the ligand end group, with larger cores always leading to stiffer membranes. Asymmetry in the stress and ligand density is observed in membranes during preparation at a water-vapor interface, with the stress asymmetry persisting in all membranes after drying.« less

Analyzing structural variations along strike in a deep-water thrust belt

NASA Astrophysics Data System (ADS)

Totake, Yukitsugu; Butler, Robert W. H.; Bond, Clare E.; Aziz, Aznan

2018-03-01

We characterize a deep-water fold-thrust arrays imaged by a high-resolution 3D seismic dataset in the offshore NW Borneo, Malaysia, to understand the kinematics behind spatial arrangement of structural variations throughout the fold-thrust system. The seismic volume used covers two sub-parallel fold trains associated with a series of fore-thrusts and back-thrusts. We measured fault heave, shortening value, fold geometries (forelimb dip, interlimb angle and crest depth) along strike in individual fold trains. Heave plot on strike projection allows to identify individual thrust segments showing semi-elliptical to triangular to bimodal patterns, and linkages of these segments. The linkage sites are marked by local minima in cumulative heave. These local heave minima are compensated by additional structures, such as small imbricate thrusts and tight folds indicated by large forelimb dip and small interlimb angle. Complementary profiles of the shortening amount for the two fold trains result in smoother gradient of total shortening across the structures. We interpret this reflects kinematic interaction between two fold-thrust trains. This type of along-strike variation analysis provides comprehensive understanding of a fold-thrust system and may provide an interpretative strategy for inferring the presence of complex multiple faults in less well-imaged parts of seismic volumes.

Light-driven growth in Amazon evergreen forests explained by seasonal variations of vertical canopy structure.

PubMed

Tang, Hao; Dubayah, Ralph

2017-03-07

Light-regime variability is an important limiting factor constraining tree growth in tropical forests. However, there is considerable debate about whether radiation-induced green-up during the dry season is real, or an apparent artifact of the remote-sensing techniques used to infer seasonal changes in canopy leaf area. Direct and widespread observations of vertical canopy structures that drive radiation regimes have been largely absent. Here we analyze seasonal dynamic patterns between the canopy and understory layers in Amazon evergreen forests using observations of vertical canopy structure from a spaceborne lidar. We discovered that net leaf flushing of the canopy layer mainly occurs in early dry season, and is followed by net abscission in late dry season that coincides with increasing leaf area of the understory layer. Our observations of understory development from lidar either weakly respond to or are not correlated to seasonal variations in precipitation or insolation, but are strongly related to the seasonal structural dynamics of the canopy layer. We hypothesize that understory growth is driven by increased light gaps caused by seasonal variations of the canopy. This light-regime variability that exists in both spatial and temporal domains can better reveal the drought-induced green-up phenomenon, which appears less obvious when treating the Amazon forests as a whole.

On the implications of the classical ergodic theorems: analysis of developmental processes has to focus on intra-individual variation.

PubMed

Molenaar, Peter C M

2008-01-01

It is argued that general mathematical-statistical theorems imply that standard statistical analysis techniques of inter-individual variation are invalid to investigate developmental processes. Developmental processes have to be analyzed at the level of individual subjects, using time series data characterizing the patterns of intra-individual variation. It is shown that standard statistical techniques based on the analysis of inter-individual variation appear to be insensitive to the presence of arbitrary large degrees of inter-individual heterogeneity in the population. An important class of nonlinear epigenetic models of neural growth is described which can explain the occurrence of such heterogeneity in brain structures and behavior. Links with models of developmental instability are discussed. A simulation study based on a chaotic growth model illustrates the invalidity of standard analysis of inter-individual variation, whereas time series analysis of intra-individual variation is able to recover the true state of affairs. (c) 2007 Wiley Periodicals, Inc.

Evolutionary conservatism explains increasing relatedness of plant communities along a flooding gradient.

PubMed

Tanentzap, Andrew J; Lee, William G

2017-01-01

Abiotic filters have been found either to increase or reduce evolutionary relatedness in plant communities, making it difficult to generalize responses of this major feature of biodiversity to future environmental change. Here, we hypothesized that the responses of phylogenetic structure to environmental change ultimately depend on how species have evolved traits for tolerating the resulting abiotic changes. Working within ephemeral wetlands, we tested whether species were increasingly related as flooding duration intensified. We also identified the mechanisms underlying increased relatedness by measuring root aerenchyma volume (RAV), a trait which promotes waterlogging tolerance. We found that species-specific responses to flooding explained most of the variation in occurrence for 63 vascular plant species across 5170 plots. For a subset of 22 species, we attributed these responses to variation in RAV. Large RAV specifically increased occurrence when flooding lasted for longer time periods, because large RAV reduced above-ground biomass loss. As large RAV was evolutionarily conserved within obligate wetland species, communities were more phylogenetically related as flooding increased. Our study shows how reconstructing the evolutionary history of traits that influence the responses of species to environmental change can help to predict future patterns in phylogenetic structure. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Phylogenetic congruence of lichenised fungi and algae is affected by spatial scale and taxonomic diversity.

PubMed

Buckley, Hannah L; Rafat, Arash; Ridden, Johnathon D; Cruickshank, Robert H; Ridgway, Hayley J; Paterson, Adrian M

2014-01-01

The role of species' interactions in structuring biological communities remains unclear. Mutualistic symbioses, involving close positive interactions between two distinct organismal lineages, provide an excellent means to explore the roles of both evolutionary and ecological processes in determining how positive interactions affect community structure. In this study, we investigate patterns of co-diversification between fungi and algae for a range of New Zealand lichens at the community, genus, and species levels and explore explanations for possible patterns related to spatial scale and pattern, taxonomic diversity of the lichens considered, and the level sampling replication. We assembled six independent datasets to compare patterns in phylogenetic congruence with varied spatial extent of sampling, taxonomic diversity and level of specimen replication. For each dataset, we used the DNA sequences from the ITS regions of both the fungal and algal genomes from lichen specimens to produce genetic distance matrices. Phylogenetic congruence between fungi and algae was quantified using distance-based redundancy analysis and we used geographic distance matrices in Moran's eigenvector mapping and variance partitioning to evaluate the effects of spatial variation on the quantification of phylogenetic congruence. Phylogenetic congruence was highly significant for all datasets and a large proportion of variance in both algal and fungal genetic distances was explained by partner genetic variation. Spatial variables, primarily at large and intermediate scales, were also important for explaining genetic diversity patterns in all datasets. Interestingly, spatial structuring was stronger for fungal than algal genetic variation. As the spatial extent of the samples increased, so too did the proportion of explained variation that was shared between the spatial variables and the partners' genetic variation. Different lichen taxa showed some variation in their phylogenetic congruence and spatial genetic patterns and where greater sample replication was used, the amount of variation explained by partner genetic variation increased. Our results suggest that the phylogenetic congruence pattern, at least at small spatial scales, is likely due to reciprocal co-adaptation or co-dispersal. However, the detection of these patterns varies among different lichen taxa, across spatial scales and with different levels of sample replication. This work provides insight into the complexities faced in determining how evolutionary and ecological processes may interact to generate diversity in symbiotic association patterns at the population and community levels. Further, it highlights the critical importance of considering sample replication, taxonomic diversity and spatial scale in designing studies of co-diversification.

Geography of Genetic Structure in Barley Wild Relative Hordeum vulgare subsp. spontaneum in Jordan.

PubMed

Thormann, Imke; Reeves, Patrick; Reilley, Ann; Engels, Johannes M M; Lohwasser, Ulrike; Börner, Andreas; Pillen, Klaus; Richards, Christopher M

2016-01-01

Informed collecting, conservation, monitoring and utilization of genetic diversity requires knowledge of the distribution and structure of the variation occurring in a species. Hordeum vulgare subsp. spontaneum (K. Koch) Thell., a primary wild relative of barley, is an important source of genetic diversity for barley improvement and co-occurs with the domesticate within the center of origin. We studied the current distribution of genetic diversity and population structure in H. vulgare subsp. spontaneum in Jordan and investigated whether it is correlated with either spatial or climatic variation inferred from publically available climate layers commonly used in conservation and ecogeographical studies. The genetic structure of 32 populations collected in 2012 was analyzed with 37 SSRs. Three distinct genetic clusters were identified. Populations were characterized by admixture and high allelic richness, and genetic diversity was concentrated in the northern part of the study area. Genetic structure, spatial location and climate were not correlated. This may point out a limitation in using large scale climatic data layers to predict genetic diversity, especially as it is applied to regional genetic resources collections in H. vulgare subsp. spontaneum.

Defying stereotypes: the elusive search for a universal model of LysR-type regulation.

PubMed

Momany, Cory; Neidle, Ellen L

2012-02-01

LysR-type transcriptional regulators (LTTRs) compose the largest family of homologous regulators in bacteria. Considering their prevalence, it is not surprising that LTTRs control diverse metabolic functions. Arguably, the most unexpected aspect of LTTRs is the paucity of available structural information. Solubility issues are notoriously problematic, and structural studies have only recently begun to flourish. In this issue of Molecular Microbiology, Taylor et al. (2012) present the structure of AphB, a LysR-type regulator of virulence in Vibrio cholerae. This contribution adds significantly to the group of known full-length atomic LTTR structures, which remains small. Importantly, this report also describes an active-form variant. Small conformational changes in the effector-binding domain translate to global reorganization of the DNA-binding domain. Emerging from these results is a model of theme-and-variation among LTTRs rather than a unified regulatory scheme. Despite common structural folds, LTTRs exhibit differences in oligomerization, promoter recognition and communication with RNA polymerase. Such variation mirrors the diversity in sequence and function associated with members of this very large family. © 2012 Blackwell Publishing Ltd.

Geography of Genetic Structure in Barley Wild Relative Hordeum vulgare subsp. spontaneum in Jordan

PubMed Central

Reeves, Patrick; Reilley, Ann; Engels, Johannes M. M.; Lohwasser, Ulrike; Börner, Andreas; Pillen, Klaus; Richards, Christopher M.

2016-01-01

Informed collecting, conservation, monitoring and utilization of genetic diversity requires knowledge of the distribution and structure of the variation occurring in a species. Hordeum vulgare subsp. spontaneum (K. Koch) Thell., a primary wild relative of barley, is an important source of genetic diversity for barley improvement and co-occurs with the domesticate within the center of origin. We studied the current distribution of genetic diversity and population structure in H. vulgare subsp. spontaneum in Jordan and investigated whether it is correlated with either spatial or climatic variation inferred from publically available climate layers commonly used in conservation and ecogeographical studies. The genetic structure of 32 populations collected in 2012 was analyzed with 37 SSRs. Three distinct genetic clusters were identified. Populations were characterized by admixture and high allelic richness, and genetic diversity was concentrated in the northern part of the study area. Genetic structure, spatial location and climate were not correlated. This may point out a limitation in using large scale climatic data layers to predict genetic diversity, especially as it is applied to regional genetic resources collections in H. vulgare subsp. spontaneum. PMID:27513459

Genus age, provincial area and the taxonomic structure of marine faunas.

PubMed

Harnik, Paul G; Jablonski, David; Krug, Andrew Z; Valentine, James W

2010-11-22

Species are unevenly distributed among genera within clades and regions, with most genera species-poor and few species-rich. At regional scales, this structure to taxonomic diversity is generated via speciation, extinction and geographical range dynamics. Here, we use a global database of extant marine bivalves to characterize the taxonomic structure of climate zones and provinces. Our analyses reveal a general, Zipf-Mandelbrot form to the distribution of species among genera, with faunas from similar climate zones exhibiting similar taxonomic structure. Provinces that contain older taxa and/or encompass larger areas are expected to be more species-rich. Although both median genus age and provincial area correlate with measures of taxonomic structure, these relationships are interdependent, nonlinear and driven primarily by contrasts between tropical and extra-tropical faunas. Provincial area and taxonomic structure are largely decoupled within climate zones. Counter to the expectation that genus age and species richness should positively covary, diverse and highly structured provincial faunas are dominated by young genera. The marked differences between tropical and temperate faunas suggest strong spatial variation in evolutionary rates and invasion frequencies. Such variation contradicts biogeographic models that scale taxonomic diversity to geographical area.

Genus age, provincial area and the taxonomic structure of marine faunas

PubMed Central

Harnik, Paul G.; Jablonski, David; Krug, Andrew Z.; Valentine, James W.

2010-01-01

Species are unevenly distributed among genera within clades and regions, with most genera species-poor and few species-rich. At regional scales, this structure to taxonomic diversity is generated via speciation, extinction and geographical range dynamics. Here, we use a global database of extant marine bivalves to characterize the taxonomic structure of climate zones and provinces. Our analyses reveal a general, Zipf–Mandelbrot form to the distribution of species among genera, with faunas from similar climate zones exhibiting similar taxonomic structure. Provinces that contain older taxa and/or encompass larger areas are expected to be more species-rich. Although both median genus age and provincial area correlate with measures of taxonomic structure, these relationships are interdependent, nonlinear and driven primarily by contrasts between tropical and extra-tropical faunas. Provincial area and taxonomic structure are largely decoupled within climate zones. Counter to the expectation that genus age and species richness should positively covary, diverse and highly structured provincial faunas are dominated by young genera. The marked differences between tropical and temperate faunas suggest strong spatial variation in evolutionary rates and invasion frequencies. Such variation contradicts biogeographic models that scale taxonomic diversity to geographical area. PMID:20534619

Mapping human genetic diversity in Asia.

PubMed

Abdulla, Mahmood Ameen; Ahmed, Ikhlak; Assawamakin, Anunchai; Bhak, Jong; Brahmachari, Samir K; Calacal, Gayvelline C; Chaurasia, Amit; Chen, Chien-Hsiun; Chen, Jieming; Chen, Yuan-Tsong; Chu, Jiayou; Cutiongco-de la Paz, Eva Maria C; De Ungria, Maria Corazon A; Delfin, Frederick C; Edo, Juli; Fuchareon, Suthat; Ghang, Ho; Gojobori, Takashi; Han, Junsong; Ho, Sheng-Feng; Hoh, Boon Peng; Huang, Wei; Inoko, Hidetoshi; Jha, Pankaj; Jinam, Timothy A; Jin, Li; Jung, Jongsun; Kangwanpong, Daoroong; Kampuansai, Jatupol; Kennedy, Giulia C; Khurana, Preeti; Kim, Hyung-Lae; Kim, Kwangjoong; Kim, Sangsoo; Kim, Woo-Yeon; Kimm, Kuchan; Kimura, Ryosuke; Koike, Tomohiro; Kulawonganunchai, Supasak; Kumar, Vikrant; Lai, Poh San; Lee, Jong-Young; Lee, Sunghoon; Liu, Edison T; Majumder, Partha P; Mandapati, Kiran Kumar; Marzuki, Sangkot; Mitchell, Wayne; Mukerji, Mitali; Naritomi, Kenji; Ngamphiw, Chumpol; Niikawa, Norio; Nishida, Nao; Oh, Bermseok; Oh, Sangho; Ohashi, Jun; Oka, Akira; Ong, Rick; Padilla, Carmencita D; Palittapongarnpim, Prasit; Perdigon, Henry B; Phipps, Maude Elvira; Png, Eileen; Sakaki, Yoshiyuki; Salvador, Jazelyn M; Sandraling, Yuliana; Scaria, Vinod; Seielstad, Mark; Sidek, Mohd Ros; Sinha, Amit; Srikummool, Metawee; Sudoyo, Herawati; Sugano, Sumio; Suryadi, Helena; Suzuki, Yoshiyuki; Tabbada, Kristina A; Tan, Adrian; Tokunaga, Katsushi; Tongsima, Sissades; Villamor, Lilian P; Wang, Eric; Wang, Ying; Wang, Haifeng; Wu, Jer-Yuarn; Xiao, Huasheng; Xu, Shuhua; Yang, Jin Ok; Shugart, Yin Yao; Yoo, Hyang-Sook; Yuan, Wentao; Zhao, Guoping; Zilfalil, Bin Alwi

2009-12-11

Asia harbors substantial cultural and linguistic diversity, but the geographic structure of genetic variation across the continent remains enigmatic. Here we report a large-scale survey of autosomal variation from a broad geographic sample of Asian human populations. Our results show that genetic ancestry is strongly correlated with linguistic affiliations as well as geography. Most populations show relatedness within ethnic/linguistic groups, despite prevalent gene flow among populations. More than 90% of East Asian (EA) haplotypes could be found in either Southeast Asian (SEA) or Central-South Asian (CSA) populations and show clinal structure with haplotype diversity decreasing from south to north. Furthermore, 50% of EA haplotypes were found in SEA only and 5% were found in CSA only, indicating that SEA was a major geographic source of EA populations.

Enhanced sensitivity to the time variation of the fine-structure constant and m{p}/m{e} in diatomic molecules.

PubMed

Flambaum, V V; Kozlov, M G

2007-10-12

Sensitivity to temporal variation of the fundamental constants may be strongly enhanced in transitions between narrow close levels of different nature. This enhancement may be realized in a large number of molecules due to cancellation between the ground state fine-structure omega{f} and vibrational interval omega{v} [omega=omega{f}-nomega{v} approximately 0, delta omega/omega=K(2delta alpha/alpha+0.5 delta mu/mu), K>1, mu=m{p}/m{e}]. The intervals between the levels are conveniently located in microwave frequency range and the level widths are very small. Required accuracy of the shift measurements is about 0.01-1 Hz. As examples, we consider molecules Cl(+)(2), CuS, IrC, SiBr, and HfF(+).

Thermospheric O/N2 in the Sunlit Disk From More Than Five Years of GUVI/TIMED Observations

NASA Astrophysics Data System (ADS)

Craven, J. D.; Christensen, A. B.; Paxton, L. J.

2007-12-01

GUVI indirect observations of the thermospheric column density ratio, O/N2, in the sunlit hemisphere have been made on a nearly continuous basis from day 50 of 2002 to the present as part of the TIMED spacecraft mission. The basic large-scale spatial structure includes variations with local time (greater values in the morning), Universal Time (modulation at high latitudes due to the offset magnetic dipole), and season (greater values in the local winter hemisphere). These differences are seen to fade in the approach to solar minimum. Superposed on this reasonably well-behaved background structure are the complex, transient perturbations driven by auroral substorms and geomagnetic storms. The spatial and temporal variations are summarized in part by time-lapse movies

Local Energies and Energy Fluctuations — Applied to the High Entropy Alloy CrFeCoNi

NASA Astrophysics Data System (ADS)

Fukushima, Tetsuya; Katayama-Yoshida, Hiroshi; Sato, Kazunori; Ogura, Masako; Zeller, Rudolf; Dederichs, Peter H.

2017-11-01

High entropy alloys show a variety of fascinating properties like high hardness, wear resistance, corrosion resistance, etc. They are random solid solutions of many components with rather high concentrations. We perform ab-initio calculations for the high entropy alloy CrFeCoNi, which equal concentration of 25% for each element. By the KKRnano program package, which is based on an order-N screened Korringa-Kohn-Rostoker Green's function method, we consider a face-centered cubic (FCC) supercell with 1372 randomly distributed elements, and in addition also smaller supercells with 500 and 256 atoms. It is found from our calculations that the local moments of the Cr atoms show a large environmental variation, ranging from -1.70 μB to +1.01 μB with an average of about -0.51 μB. We present a new method to calculate "local energies" of all atoms. This is based on the partitioning of the whole space into Voronoi cells and allows to calculate the energetic contribution of each atomic cell to the total energy of the supercell. The supercell calculations show very large variations of the local energies, analogous to the variations of the local moments. This shows that the random solid solution is not stable and has a tendency to form an L12-structure with the Cr-atoms ordered at the corner of the cube and the elements Fe, Co, and Ni randomly distributed on the three other FCC sublattices. For this structure the variation of the local moments are much smaller.

Body Parts Dependent Joint Regressors for Human Pose Estimation in Still Images.

PubMed

Dantone, Matthias; Gall, Juergen; Leistner, Christian; Van Gool, Luc

2014-11-01

In this work, we address the problem of estimating 2d human pose from still images. Articulated body pose estimation is challenging due to the large variation in body poses and appearances of the different body parts. Recent methods that rely on the pictorial structure framework have shown to be very successful in solving this task. They model the body part appearances using discriminatively trained, independent part templates and the spatial relations of the body parts using a tree model. Within such a framework, we address the problem of obtaining better part templates which are able to handle a very high variation in appearance. To this end, we introduce parts dependent body joint regressors which are random forests that operate over two layers. While the first layer acts as an independent body part classifier, the second layer takes the estimated class distributions of the first one into account and is thereby able to predict joint locations by modeling the interdependence and co-occurrence of the parts. This helps to overcome typical ambiguities of tree structures, such as self-similarities of legs and arms. In addition, we introduce a novel data set termed FashionPose that contains over 7,000 images with a challenging variation of body part appearances due to a large variation of dressing styles. In the experiments, we demonstrate that the proposed parts dependent joint regressors outperform independent classifiers or regressors. The method also performs better or similar to the state-of-the-art in terms of accuracy, while running with a couple of frames per second.

Genet-specific DNA methylation probabilities detected in a spatial epigenetic analysis of a clonal plant population.

PubMed

Araki, Kiwako S; Kubo, Takuya; Kudoh, Hiroshi

2017-01-01

In sessile organisms such as plants, spatial genetic structures of populations show long-lasting patterns. These structures have been analyzed across diverse taxa to understand the processes that determine the genetic makeup of organismal populations. For many sessile organisms that mainly propagate via clonal spread, epigenetic status can vary between clonal individuals in the absence of genetic changes. However, fewer previous studies have explored the epigenetic properties in comparison to the genetic properties of natural plant populations. Here, we report the simultaneous evaluation of the spatial structure of genetic and epigenetic variation in a natural population of the clonal plant Cardamine leucantha. We applied a hierarchical Bayesian model to evaluate the effects of membership of a genet (a group of individuals clonally derived from a single seed) and vegetation cover on the epigenetic variation between ramets (clonal plants that are physiologically independent individuals). We sampled 332 ramets in a 20 m × 20 m study plot that contained 137 genets (identified using eight SSR markers). We detected epigenetic variation in DNA methylation at 24 methylation-sensitive amplified fragment length polymorphism (MS-AFLP) loci. There were significant genet effects at all 24 MS-AFLP loci in the distribution of subepiloci. Vegetation cover had no statistically significant effect on variation in the majority of MS-AFLP loci. The spatial aggregation of epigenetic variation is therefore largely explained by the aggregation of ramets that belong to the same genets. By applying hierarchical Bayesian analyses, we successfully identified a number of genet-specific changes in epigenetic status within a natural plant population in a complex context, where genotypes and environmental factors are unevenly distributed. This finding suggests that it requires further studies on the spatial epigenetic structure of natural populations of diverse organisms, particularly for sessile clonal species.

The Sun as a variable star: Solar and stellar irradiance variations; Colloquium of the International Astronomical Union, 143rd, Boulder, CO, Jun. 20-25, 1993

NASA Technical Reports Server (NTRS)

Pap, Judit M. (Editor); Froehlich, Claus (Editor); Hudson, Hugh S. (Editor); Tobiska, W. Kent (Editor)

1994-01-01

Variations in solar and stellar irradiances have long been of interest. An International Astronomical Union (IAU) colloquium reviewed such relevant subjects as observations, theoretical interpretations, and empirical and physical models, with a special emphasis on climatic impact of solar irradiance variability. Specific topics discussed included: (1) General Reviews on Observations of Solar and Stellar Irradiance Variability; (2) Observational Programs for Solar and Stellar Irradiance Variability; (3) Variability of Solar and Stellar Irradiance Related to the Network, Active Regions (Sunspots and Plages), and Large-Scale Magnetic Structures; (4) Empirical Models of Solar Total and Spectral Irradiance Variability; (5) Solar and Stellar Oscillations, Irradiance Variations and their Interpretations; and (6) The Response of the Earth's Atmosphere to Solar Irradiance Variations and Sun-Climate Connections.

Greater temporal changes of sediment microbial community than its waterborne counterpart in Tengchong hot springs, Yunnan Province, China

PubMed Central

Wang, Shang; Dong, Hailiang; Hou, Weiguo; Jiang, Hongchen; Huang, Qiuyuan; Briggs, Brandon R.; Huang, Liuqin

2014-01-01

Temporal variation in geochemistry can cause changes in microbial community structure and diversity. Here we studied temporal changes of microbial communities in Tengchong hot springs of Yunnan Province, China in response to geochemical variations by using microbial and geochemical data collected in January, June and August of 2011. Greater temporal variations were observed in individual taxa than at the whole community structure level. Water and sediment communities exhibited different temporal variation patterns. Water communities were largely stable across three sampling times and dominated by similar microbial lineages: Hydrogenobaculum in moderate-temperature acidic springs, Sulfolobus in high-temperature acidic springs, and Hydrogenobacter in high-temperature circumneutral to alkaline springs. Sediment communities were more diverse and responsive to changing physicochemical conditions. Most of the sediment communities in January and June were similar to those in waters. However, the August sediment community was more diverse and contained more anaerobic heterotrophs than the January and June: Desulfurella and Acidicaldus in moderate-temperature acidic springs, Ignisphaera and Desulfurococcus in high-temperature acidic springs, the candidate division OP1 and Fervidobacterium in alkaline springs, and Thermus and GAL35 in neutral springs. Temporal variations in physicochemical parameters including temperature, pH, and dissolved organic carbon may have triggered the observed microbial community shifts. PMID:25524763

The microgeographical patterns of morphological and molecular variation of a mixed ploidy population in the species complex Actinidia chinensis.

PubMed

Liu, Yifei; Li, Dawei; Yan, Ling; Huang, Hongwen

2015-01-01

Polyploidy and hybridization are thought to have significant impacts on both the evolution and diversification of the genus Actinidia, but the structure and patterns of morphology and molecular diversity relating to ploidy variation of wild Actinidia plants remain much less understood. Here, we examine the distribution of morphological variation and ploidy levels along geographic and environmental variables of a large mixed-ploidy population of the A. chinensis species complex. We then characterize the extent of both genetic and epigenetic diversity and differentiation exhibited between individuals of different ploidy levels. Our results showed that while there are three ploidy levels in this population, hexaploids were constituted the majority (70.3%). Individuals with different ploidy levels were microgeographically structured in relation to elevation and extent of niche disturbance. The morphological characters examined revealed clear difference between diploids and hexaploids, however tetraploids exhibited intermediate forms. Both genetic and epigenetic diversity were high but the differentiation among cytotypes was weak, suggesting extensive gene flow and/or shared ancestral variation occurred in this population even across ploidy levels. Epigenetic variation was clearly correlated with changes in altitudes, a trend of continuous genetic variation and gradual increase of epigenomic heterogeneities of individuals was also observed. Our results show that complex interactions between the locally microgeographical environment, ploidy and gene flow impact A. chinensis genetic and epigenetic variation. We posit that an increase in ploidy does not broaden the species habitat range, but rather permits A. chinensis adaptation to specific niches.

Geographic origin is not supported by the genetic variability found in a large living collection of Jatropha curcas with accessions from three continents

PubMed Central

Maghuly, Fatemeh; Jankowicz-Cieslak, Joanna; Pabinger, Stephan; Till, Bradley J; Laimer, Margit

2015-01-01

Increasing economic interest in Jatropha curcas requires a major research focus on the genetic background and geographic origin of this non-edible biofuel crop. To determine the worldwide genetic structure of this species, amplified fragment length polymorphisms, inter simple sequence repeats, and novel single nucleotide polymorphisms (SNPs) were employed for a large collection of 907 J. curcas accessions and related species (RS) from three continents, 15 countries and 53 regions. PCoA, phenogram, and cophenetic analyses separated RS from two J. curcas groups. Accessions from Mexico, Bolivia, Paraguay, Kenya, and Ethiopia with unknown origins were found in both groups. In general, there was a considerable overlap between individuals from different regions and countries. The Bayesian approach using structure demonstrated two groups with a low genetic variation. Analysis of molecular varience revealed significant variation among individuals within populations. SNPs found by in silico analyses of Δ12 fatty acid desaturase indicated possible changes in gene expression and thus in fatty acid profiles. SNP variation was higher in the curcin gene compared to genes involved in oil production. Novel SNPs allowed separating toxic, non-toxic, and Mexican accessions. The present study confirms that human activities had a major influence on the genetic diversity of J. curcas, not only because of domestication, but also because of biased selection. PMID:25511658

Genomic structural variation contributes to phenotypic change of industrial bioethanol yeast Saccharomyces cerevisiae.

PubMed

Zhang, Ke; Zhang, Li-Jie; Fang, Ya-Hong; Jin, Xin-Na; Qi, Lei; Wu, Xue-Chang; Zheng, Dao-Qiong

2016-03-01

Genomic structural variation (GSV) is a ubiquitous phenomenon observed in the genomes of Saccharomyces cerevisiae strains with different genetic backgrounds; however, the physiological and phenotypic effects of GSV are not well understood. Here, we first revealed the genetic characteristics of a widely used industrial S. cerevisiae strain, ZTW1, by whole genome sequencing. ZTW1 was identified as an aneuploidy strain and a large-scale GSV was observed in the ZTW1 genome compared with the genome of a diploid strain YJS329. These GSV events led to copy number variations (CNVs) in many chromosomal segments as well as one whole chromosome in the ZTW1 genome. Changes in the DNA dosage of certain functional genes directly affected their expression levels and the resultant ZTW1 phenotypes. Moreover, CNVs of large chromosomal regions triggered an aneuploidy stress in ZTW1. This stress decreased the proliferation ability and tolerance of ZTW1 to various stresses, while aneuploidy response stress may also provide some benefits to the fermentation performance of the yeast, including increased fermentation rates and decreased byproduct generation. This work reveals genomic characters of the bioethanol S. cerevisiae strain ZTW1 and suggests that GSV is an important kind of mutation that changes the traits of industrial S. cerevisiae strains. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Variations in the Quality of Care at Large Public Hospitals in Beijing, China: A Condition-Based Outcome Approach.

PubMed

Xu, Ye; Liu, Yuanli; Shu, Ting; Yang, Wei; Liang, Minghui

2015-01-01

Public hospitals deliver over ninety percent of all outpatient and inpatient services in China. Their quality is graded into three levels (A, B, and C) largely based on structural resources, but empirical evidence on the quality of process and outcome of care is extremely scarce. As expectations for quality care rise with higher living standards and cost of care, such evidence is urgently needed and vital to improve care and to inform future health reforms. We compiled and analyzed a multicenter database of over 4 million inpatient discharge summary records to provide a comprehensive assessment of the level and variations in clinical outcomes of hospitalization at 39 tertiary hospitals in Beijing. We assessed six outcome measures of clinical quality: in-hospital mortality rates (RSMR) for AMI, stroke, pneumonia and CABG, post-procedural complication rate (RS-CR), and failure-to-rescue rate (RS-FTR). The measures were adjusted for pre-admission patient case-mix using indirect standardization method with hierarchical linear mixed models. We found good overall quality with large variations by hospital and condition (mean/range, in %): RSMR-AMI: 6.23 (2.37-14.48), RSMR-stroke: 4.18 (3.58-4.44), RSMR-pneumonia: 7.78 (7.20-8.59), RSMR-CABG: 1.93 (1.55-2.23), RS-CR: 11.38 (9.9-12.88), and RS-FTR: 6.41 (5.17-7.58). Hospital grade was not significantly associated with any risk-adjusted outcome measures. Going to a higher grade public hospital does not always lead to better patient outcome because hospital grade only contains information about hospital structural resources. A hospital report card with some outcome measures of quality would provide valuable information to patients in choosing providers, and for regulators to identify gaps in health care quality. Reducing the variations in clinical practice and patient outcome should be a focus for policy makers in the next round of health sector reforms in China.

Characterizing directional variations in long-period ground motion amplifications in the Kanto Basin, Japan

NASA Astrophysics Data System (ADS)

Mukai, Y.; Furumura, T.; Maeda, T.

2017-12-01

In the Kanto Basin (including Tokyo in Japan), the long-period (T=3-10 s) ground motions are strongly developed when large earthquakes occur nearby. The amplitude of the long-period ground motion in the basin varies strongly among earthquakes; it is tremendous from the earthquakes in Niigata (northwest of Kanto), but is several times weaker from the earthquakes in Tohoku (north of Kanto). In this study, we examined the cause of such azimuthal-dependent amplitude variation for the 2004 Niigata Chuetsu (M6.8) and the 2011 Fukushima Hamadori (M7.0) earthquake based on numerical simulations of seismic wave propagation by the finite-difference method. We first examined the non-isotropic source-radiation effect of these events. By performing numerical simulations for different strike angles of these source faults, significant variation in amplitude of the long-period ground motions were observed in Tokyo for both the events. Among tested strike angles, the source of the 2004 event (strike = 212 deg.) produced the largest long-period ground motion due to strong radiation of surface wave towards the Kanto Basin, while the 2011 event (strike = 132 deg.) produced the least. The minimum-to-maximum ratio of their amplitudes with respect to strike angle is about 2 and 1.3, respectively. These investigations suggest the source radiation effect considerably contributes to the variations of the long-period ground motions. We then examined the effect of the 3D structure of the Kanto Basin on the generation of the long-period ground motion. For the 2004 event, we found that the long-period signal first arrives at the central Tokyo from the western edge of the Kanto Basin. Then, later signals containing both the Rayleigh and Love waves were amplified dramatically due to the localized low-velocity structure to the northwestern part of the basin. On the other hand, in the case of the 2011 event, the seismic waves propagating towards the basin were dissipated significantly as it travels over the ridge structure of the basement in the northern part of the basin, where the seismic wave speed is faster than the surroundings. Therefore, the large variation of the long-period ground motion among earthquakes occurs due to the combined effects of source radiation and propagation properties in the 3D heterogeneous structure of the Kanto Basin.

Electronic effects on melting: Comparison of aluminum cluster anions and cations

NASA Astrophysics Data System (ADS)

Starace, Anne K.; Neal, Colleen M.; Cao, Baopeng; Jarrold, Martin F.; Aguado, Andrés; López, José M.

2009-07-01

Heat capacities have been measured as a function of temperature for aluminum cluster anions with 35-70 atoms. Melting temperatures and latent heats are determined from peaks in the heat capacities; cohesive energies are obtained for solid clusters from the latent heats and dissociation energies determined for liquid clusters. The melting temperatures, latent heats, and cohesive energies for the aluminum cluster anions are compared to previous measurements for the corresponding cations. Density functional theory calculations have been performed to identify the global minimum energy geometries for the cluster anions. The lowest energy geometries fall into four main families: distorted decahedral fragments, fcc fragments, fcc fragments with stacking faults, and "disordered" roughly spherical structures. The comparison of the cohesive energies for the lowest energy geometries with the measured values allows us to interpret the size variation in the latent heats. Both geometric and electronic shell closings contribute to the variations in the cohesive energies (and latent heats), but structural changes appear to be mainly responsible for the large variations in the melting temperatures with cluster size. The significant charge dependence of the latent heats found for some cluster sizes indicates that the electronic structure can change substantially when the cluster melts.

Temperature Distribution and Influence Mechanism on Large Reflector Antennas under Solar Radiation

NASA Astrophysics Data System (ADS)

Wang, C. S.; Yuan, S.; Liu, X.; Xu, Q.; Wang, M.; Zhu, M. B.; Chen, G. D.; Duan, Y. H.

2017-10-01

The solar impact on antenna must be lessened for the large reflector antenna operating at high frequencies to have great electromagnetic performances. Therefore, researching the temperature distribution and its influence on large reflector antenna is necessary. The variation of solar incidence angle is first calculated. Then the model is simulated by the I-DEAS software, with the temperature, thermal stress, and thermal distortion distribution through the day obtained. In view of the important influence of shadow on antenna structure, a newly proposed method makes a comprehensive description of the temperature distribution on the reflector and its influence through the day by dividing a day into three different periods. The sound discussions and beneficial summary serve as the scientific foundation for the engineers to compensate the thermal distortion and optimize the antenna structure.

Anomalously large isotope effect in the glass transition of water

DOE PAGES

Gainaru, Catalin; Agapov, Alexander L.; Fuentes-Landete, Violeta; ...

2014-11-24

Here we present the discovery of an unusually large isotope effect in the structural relaxation and the glass transition temperature T g of water. Dielectric relaxation spectroscopy of low-density as well as of vapor deposited amorphous water reveal T g differences of 10±2K between H 2O and D 2O, sharply contrasting with other hydrogen bonded liquids for which H/D exchange increases T g by typically less than 1K. We show that the large isotope effect and the unusual variation of relaxation times in water at low temperatures can be explained in terms of quantum effects. Thus, our findings shed newmore » light on water's peculiar low-temperature dynamics and the possible role of quantum effects in its structural relaxation, and possibly in dynamics of other low molecular weight liquids.« less

Identification of structural variation in mouse genomes.

PubMed

Keane, Thomas M; Wong, Kim; Adams, David J; Flint, Jonathan; Reymond, Alexandre; Yalcin, Binnaz

2014-01-01

Structural variation is variation in structure of DNA regions affecting DNA sequence length and/or orientation. It generally includes deletions, insertions, copy-number gains, inversions, and transposable elements. Traditionally, the identification of structural variation in genomes has been challenging. However, with the recent advances in high-throughput DNA sequencing and paired-end mapping (PEM) methods, the ability to identify structural variation and their respective association to human diseases has improved considerably. In this review, we describe our current knowledge of structural variation in the mouse, one of the prime model systems for studying human diseases and mammalian biology. We further present the evolutionary implications of structural variation on transposable elements. We conclude with future directions on the study of structural variation in mouse genomes that will increase our understanding of molecular architecture and functional consequences of structural variation.

Analysis and design of lattice materials for large cord and curvature variations in skin panels of morphing wings

NASA Astrophysics Data System (ADS)

Vigliotti, Andrea; Pasini, Damiano

2015-03-01

In the past few decades, several concepts for morphing wings have been proposed with the aim of improving the structural and aerodynamic performance of conventional aircraft wings. One of the most interesting challenges in the design of a morphing wing is represented by the skin, which needs to meet specific deformation requirements. In particular when morphing involves changes of cord or curvature, the skin is required to undergo large recoverable deformation in the actuation direction, while maintaining the desired shape and strength in the others. One promising material concept that can meet these specifications is represented by lattice materials. This paper examines the use of alternative planar lattices in the embodiment of a skin panel for cord and camber morphing of an aircraft wing. We use a structural homogenization scheme capable of capturing large geometric nonlinearity, to examine the structural performance of lattice skin concepts, as well as to tune their mechanical properties in desired directions.

Crustal-Scale Fault Interaction at Rifted Margins and the Formation of Domain-Bounding Breakaway Complexes: Insights From Offshore Norway

NASA Astrophysics Data System (ADS)

Osmundsen, P. T.; Péron-Pinvidic, G.

2018-03-01

The large-magnitude faults that control crustal thinning and excision at rifted margins combine into laterally persistent structural boundaries that separate margin domains of contrasting morphology and structure. We term them breakaway complexes. At the Mid-Norwegian margin, we identify five principal breakaway complexes that separate the proximal, necking, distal, and outer margin domains. Downdip and lateral interactions between the faults that constitute breakaway complexes became fundamental to the evolution of the 3-D margin architecture. Different types of fault interaction are observed along and between these faults, but simple models for fault growth will not fully describe their evolution. These structures operate on the crustal scale, cut large thicknesses of heterogeneously layered lithosphere, and facilitate fundamental margin processes such as deformation coupling and exhumation. Variations in large-magnitude fault geometry, erosional footwall incision, and subsequent differential subsidence along the main breakaway complexes likely record the variable efficiency of these processes.

Solar Cycle Fine Structure and Surface Rotation from Ca II K-Line Time Series Data

NASA Astrophysics Data System (ADS)

Scargle, Jeff; Keil, Steve; Worden, Pete

2011-10-01

Analysis of three and a half decades of data from the NSO/AFRL/Sac Peak K-line monitoring program yields evidence for four components to the variation: (a) the solar cycle, with considerable fine structure and a quasi-periodicity of 122.4 days; (b) a stochastic process, faster than (a) and largely independent of it, (c) a quasi-periodic signal due to rotational modulation, and of course (d) observational errors (shown to be quite small). Correlation and power spectrum analyses elucidate periodic and aperiodic variation of these chromospheric parameters. Time-frequency analysis is especially useful for extracting information about differential rotation, and in particular elucidates the connection between its behavior and fine structure of the solar cycle on approximately one-year time scales. These results further suggest that similar analyses will be useful at detecting and characterizing differential rotation in stars from stellar light-curves such as those being produced by NASA's Kepler observatory. Component (b) consists of variations over a range of timescales, in the manner of a "1/f" random process. A time-dependent Wilson-Bappu effect appears to be present in the solar cycle variations (a), but not in the stochastic process (b). The data can be found at the National Solar Observatory web site http://nsosp.nso.edu/data/cak_mon.html, or by file transfer protocol at ftp://ftp.nso.edu/idl/cak.parameters.

Developing eThread pipeline using SAGA-pilot abstraction for large-scale structural bioinformatics.

PubMed

Ragothaman, Anjani; Boddu, Sairam Chowdary; Kim, Nayong; Feinstein, Wei; Brylinski, Michal; Jha, Shantenu; Kim, Joohyun

2014-01-01

While most of computational annotation approaches are sequence-based, threading methods are becoming increasingly attractive because of predicted structural information that could uncover the underlying function. However, threading tools are generally compute-intensive and the number of protein sequences from even small genomes such as prokaryotes is large typically containing many thousands, prohibiting their application as a genome-wide structural systems biology tool. To leverage its utility, we have developed a pipeline for eThread--a meta-threading protein structure modeling tool, that can use computational resources efficiently and effectively. We employ a pilot-based approach that supports seamless data and task-level parallelism and manages large variation in workload and computational requirements. Our scalable pipeline is deployed on Amazon EC2 and can efficiently select resources based upon task requirements. We present runtime analysis to characterize computational complexity of eThread and EC2 infrastructure. Based on results, we suggest a pathway to an optimized solution with respect to metrics such as time-to-solution or cost-to-solution. Our eThread pipeline can scale to support a large number of sequences and is expected to be a viable solution for genome-scale structural bioinformatics and structure-based annotation, particularly, amenable for small genomes such as prokaryotes. The developed pipeline is easily extensible to other types of distributed cyberinfrastructure.

Developing eThread Pipeline Using SAGA-Pilot Abstraction for Large-Scale Structural Bioinformatics

PubMed Central

Ragothaman, Anjani; Feinstein, Wei; Jha, Shantenu; Kim, Joohyun

2014-01-01

While most of computational annotation approaches are sequence-based, threading methods are becoming increasingly attractive because of predicted structural information that could uncover the underlying function. However, threading tools are generally compute-intensive and the number of protein sequences from even small genomes such as prokaryotes is large typically containing many thousands, prohibiting their application as a genome-wide structural systems biology tool. To leverage its utility, we have developed a pipeline for eThread—a meta-threading protein structure modeling tool, that can use computational resources efficiently and effectively. We employ a pilot-based approach that supports seamless data and task-level parallelism and manages large variation in workload and computational requirements. Our scalable pipeline is deployed on Amazon EC2 and can efficiently select resources based upon task requirements. We present runtime analysis to characterize computational complexity of eThread and EC2 infrastructure. Based on results, we suggest a pathway to an optimized solution with respect to metrics such as time-to-solution or cost-to-solution. Our eThread pipeline can scale to support a large number of sequences and is expected to be a viable solution for genome-scale structural bioinformatics and structure-based annotation, particularly, amenable for small genomes such as prokaryotes. The developed pipeline is easily extensible to other types of distributed cyberinfrastructure. PMID:24995285

Variation in Pockels constants of silicate glass-ceramics prepared by perfect surface crystallization

NASA Astrophysics Data System (ADS)

Takano, Kazuya; Takahashi, Yoshihiro; Miyazaki, Takamichi; Terakado, Nobuaki; Fujiwara, Takumi

2018-01-01

We investigated the Pockels effect in polycrystalline materials consisting of highly oriented polar fresnoite-type Sr2TiSi2O8 fabricated using perfectly surface-crystallized glass-ceramics (PSC-GCs). The chemical composition of the precursor glass was shown to significantly affect the crystallized texture, e.g., the crystal orientation and appearance of amorphous nanoparasites in the domains, resulting in variations in the Pockels constants. Single crystals exhibiting spontaneous polarization possessed large structural anisotropy, leading to a strong dependence of the nonlinear-optical properties on the direction of polarized light. This study suggests that variations in the Pockels constants (r13 and r33) and tuning of the r13/r33 ratio can be realized in PSC-GC materials.

Selecting Magnet Laminations Recipes Using the Meth-od of Sim-u-la-ted Annealing

NASA Astrophysics Data System (ADS)

Russell, A. D.; Baiod, R.; Brown, B. C.; Harding, D. J.; Martin, P. S.

1997-05-01

The Fermilab Main Injector project is building 344 dipoles using more than 7000 tons of steel. Budget and logistical constraints required that steel production, lamination stamping and magnet fabrication proceed in parallel. There were significant run-to-run variations in the magnetic properties of the steel (Martin, P.S., et al., Variations in the Steel Properties and the Excitation Characteristics of FMI Dipoles, this conference). The large lamination size (>0.5 m coil opening) resulted in variations of gap height due to differences in stress relief in the steel after stamping. To minimize magnet-to-magnet strength and field shape variations the laminations were shuffled based on the available magnetic and mechanical data and assigned to magnets using a computer program based on the method of simulated annealing. The lamination sets selected by the program have produced magnets which easily satisfy the design requirements. Variations of the average magnet gap are an order of magnitude smaller than the variations in lamination gaps. This paper discusses observed gap variations, the program structure and the strength uniformity results.

Implications of High Molecular Divergence of Nuclear rRNA and Phylogenetic Structure for the Dinoflagellate Prorocentrum (Dinophyceae, Prorocentrales).

PubMed

Boopathi, Thangavelu; Faria, Daphne Georgina; Cheon, Ju-Yong; Youn, Seok Hyun; Ki, Jang-Seu

2015-01-01

The small and large nuclear subunit molecular phylogeny of the genus Prorocentrum demonstrated that the species are dichotomized into two clades. These two clades were significantly different (one-factor ANOVA, p < 0.01) with patterns compatible for both small and large subunit Bayesian phylogenetic trees, and for a larger taxon sampled dinoflagellate phylogeny. Evaluation of the molecular divergence levels showed that intraspecies genetic variations were significantly low (t-test, p < 0.05), than those for interspecies variations (> 2.9% and > 26.8% dissimilarity in the small and large subunit [D1/D2], respectively). Based on the calculated molecular divergence, the genus comprises two genetically distinct groups that should be considered as two separate genera, thereby setting the pace for major systematic changes for the genus Prorocentrum sensu Dodge. Moreover, the information presented in this study would be useful for improving species identification, detection of novel clades from environmental samples. © 2015 The Author(s) Journal of Eukaryotic Microbiology © 2015 International Society of Protistologists.

The impact of galactic disc environment on star-forming clouds

NASA Astrophysics Data System (ADS)

Nguyen, Ngan K.; Pettitt, Alex R.; Tasker, Elizabeth J.; Okamoto, Takashi

2018-03-01

We explore the effect of different galactic disc environments on the properties of star-forming clouds through variations in the background potential in a set of isolated galaxy simulations. Rising, falling, and flat rotation curves expected in halo-dominated, disc-dominated, and Milky Way-like galaxies were considered, with and without an additional two-arm spiral potential. The evolution of each disc displayed notable variations that are attributed to different regimes of stability, determined by shear and gravitational collapse. The properties of a typical cloud were largely unaffected by the changes in rotation curve, but the production of small and large cloud associations was strongly dependent on this environment. This suggests that while differing rotation curves can influence where clouds are initially formed, the average bulk properties are effectively independent of the global environment. The addition of a spiral perturbation made the greatest difference to cloud properties, successfully sweeping the gas into larger, seemingly unbound, extended structures and creating large arm-interarm contrasts.

Modification of multi-ring basins - The Imbrium model

NASA Technical Reports Server (NTRS)

Whitford-Stark, J. L.

1981-01-01

It is shown that the gross variations in wall height around Imbrium result largely from intersection of the Imbrium basin with pre-existing basins and faulting: angle of impact and slumping played a lesser modifying role. The gross irregularities in plan of the northern part of Imbrium is hypothesized to result from the collapse of large crustal blocks into the Imbrium and Serenitatis cavities. Lithosphere thickness is believed to play an important role in the mechanisms of formation and modification of large craters and basins. The deduction of slow sub-lithospheric flow of material toward the cavity centers does not lend support to the tsunami model, requires a minor modification of the nested-crater model and provides a mechanism for the production of megaterraces. Spatial and temporal lithosphere variations satisfy constraints requiring the overlap of morphology/diameter characteristics, variable onset diameters between planets, variable ring spacings from planet to planet and provide a mechanism for producing local irregularities in ring structures.

Intrinsic uncertainty on the nature of dark energy

NASA Astrophysics Data System (ADS)

Valkenburg, Wessel; Kunz, Martin; Marra, Valerio

2013-12-01

We argue that there is an intrinsic noise on measurements of the equation of state parameter w = p/ρ from large-scale structure around us. The presence of the large-scale structure leads to an ambiguity in the definition of the background universe and thus there is a maximal precision with which we can determine the equation of state of dark energy. To study the uncertainty due to local structure, we model density perturbations stemming from a standard inflationary power spectrum by means of the exact Lemaître-Tolman-Bondi solution of Einstein’s equation, and show that the usual distribution of matter inhomogeneities in a ΛCDM cosmology causes a variation of w - as inferred from distance measures - of several percent. As we observe only one universe, or equivalently because of the cosmic variance, this uncertainty is systematic in nature.

New limits on variation of the fine-structure constant using atomic dysprosium.

PubMed

Leefer, N; Weber, C T M; Cingöz, A; Torgerson, J R; Budker, D

2013-08-09

We report on the spectroscopy of radio-frequency transitions between nearly degenerate, opposite-parity excited states in atomic dysprosium (Dy). Theoretical calculations predict that these states are very sensitive to variation of the fine-structure constant α owing to large relativistic corrections of opposite sign for the opposite-parity levels. The near degeneracy reduces the relative precision necessary to place constraints on variation of α, competitive with results obtained from the best atomic clocks in the world. Additionally, the existence of several abundant isotopes of Dy allows isotopic comparisons that suppress common-mode systematic errors. The frequencies of the 754-MHz transition in 164Dy and 235-MHz transition in 162Dy are measured over the span of two years. The linear variation of α is α·/α=(-5.8±6.9([1σ]))×10(-17)  yr(-1), consistent with zero. The same data are used to constrain the dimensionless parameter kα characterizing a possible coupling of α to a changing gravitational potential. We find that kα=(-5.5±5.2([1σ]))×10(-7), essentially consistent with zero and the best constraint to date.

Population structure and cultural geography of a folktale in Europe

PubMed Central

Ross, Robert M.; Greenhill, Simon J.; Atkinson, Quentin D.

2013-01-01

Despite a burgeoning science of cultural evolution, relatively little work has focused on the population structure of human cultural variation. By contrast, studies in human population genetics use a suite of tools to quantify and analyse spatial and temporal patterns of genetic variation within and between populations. Human genetic diversity can be explained largely as a result of migration and drift giving rise to gradual genetic clines, together with some discontinuities arising from geographical and cultural barriers to gene flow. Here, we adapt theory and methods from population genetics to quantify the influence of geography and ethnolinguistic boundaries on the distribution of 700 variants of a folktale in 31 European ethnolinguistic populations. We find that geographical distance and ethnolinguistic affiliation exert significant independent effects on folktale diversity and that variation between populations supports a clustering concordant with European geography. This pattern of geographical clines and clusters parallels the pattern of human genetic diversity in Europe, although the effects of geographical distance and ethnolinguistic boundaries are stronger for folktales than genes. Our findings highlight the importance of geography and population boundaries in models of human cultural variation and point to key similarities and differences between evolutionary processes operating on human genes and culture. PMID:23390109

Mapping population-based structural connectomes.

PubMed

Zhang, Zhengwu; Descoteaux, Maxime; Zhang, Jingwen; Girard, Gabriel; Chamberland, Maxime; Dunson, David; Srivastava, Anuj; Zhu, Hongtu

2018-05-15

Advances in understanding the structural connectomes of human brain require improved approaches for the construction, comparison and integration of high-dimensional whole-brain tractography data from a large number of individuals. This article develops a population-based structural connectome (PSC) mapping framework to address these challenges. PSC simultaneously characterizes a large number of white matter bundles within and across different subjects by registering different subjects' brains based on coarse cortical parcellations, compressing the bundles of each connection, and extracting novel connection weights. A robust tractography algorithm and streamline post-processing techniques, including dilation of gray matter regions, streamline cutting, and outlier streamline removal are applied to improve the robustness of the extracted structural connectomes. The developed PSC framework can be used to reproducibly extract binary networks, weighted networks and streamline-based brain connectomes. We apply the PSC to Human Connectome Project data to illustrate its application in characterizing normal variations and heritability of structural connectomes in healthy subjects. Copyright © 2018 Elsevier Inc. All rights reserved.

Variability of the Structural Coloration in Two Butterfly Species with Different Prezygotic Mating Strategies

PubMed Central

Kertész, Krisztián; Bálint, Zsolt; Biró, László Péter

2016-01-01

Structural coloration variability was investigated in two Blue butterfly species that are common in Hungary. The males of Polyommatus icarus (Common Blue) and Plebejus argus (Silver-studded Blue) use their blue wing coloration for conspecific recognition. Despite living in the same type of habitat, these two species display differences in prezygotic mating strategy: the males of P. icarus are patrolling, while P. argus males have sedentary behavior. Therefore, the species-specific photonic nanoarchitecture, which is the source of the structural coloration, may have been subjected to different evolutionary effects. Despite the increasing interest in photonic nanoarchitectures of biological origin, there is a lack of studies focused on the biological variability of structural coloration that examine a statistically relevant number of individuals from the same species. To investigate possible structural color variation within the same species in populations separated by large geographical distances, climatic differences, or applied experimental conditions, one has to be able to compare these variations to the normal biological variability within a single population. The structural coloration of the four wings of 25 male individuals (100 samples for each species) was measured and compared using different light-collecting setups: perpendicular and with an integrating sphere. Significant differences were found in the near UV wavelength region that are perceptible by these polyommatine butterflies but are invisible to human observers. The differences are attributed to the differences in the photonic nanoarchitecture in the scales of these butterflies. Differences in the intensity of structural coloration were also observed and were tentatively attributed to the different prezygotic mating strategies of these insects. Despite the optical complexity of the scale covered butterfly wings, for sufficiently large sample batches, the averaged normal incidence measurements and the averaged measurements using an integrating sphere are in agreement. PMID:27832120

Variability of the Structural Coloration in Two Butterfly Species with Different Prezygotic Mating Strategies.

PubMed

Piszter, Gábor; Kertész, Krisztián; Bálint, Zsolt; Biró, László Péter

2016-01-01

Structural coloration variability was investigated in two Blue butterfly species that are common in Hungary. The males of Polyommatus icarus (Common Blue) and Plebejus argus (Silver-studded Blue) use their blue wing coloration for conspecific recognition. Despite living in the same type of habitat, these two species display differences in prezygotic mating strategy: the males of P. icarus are patrolling, while P. argus males have sedentary behavior. Therefore, the species-specific photonic nanoarchitecture, which is the source of the structural coloration, may have been subjected to different evolutionary effects. Despite the increasing interest in photonic nanoarchitectures of biological origin, there is a lack of studies focused on the biological variability of structural coloration that examine a statistically relevant number of individuals from the same species. To investigate possible structural color variation within the same species in populations separated by large geographical distances, climatic differences, or applied experimental conditions, one has to be able to compare these variations to the normal biological variability within a single population. The structural coloration of the four wings of 25 male individuals (100 samples for each species) was measured and compared using different light-collecting setups: perpendicular and with an integrating sphere. Significant differences were found in the near UV wavelength region that are perceptible by these polyommatine butterflies but are invisible to human observers. The differences are attributed to the differences in the photonic nanoarchitecture in the scales of these butterflies. Differences in the intensity of structural coloration were also observed and were tentatively attributed to the different prezygotic mating strategies of these insects. Despite the optical complexity of the scale covered butterfly wings, for sufficiently large sample batches, the averaged normal incidence measurements and the averaged measurements using an integrating sphere are in agreement.

Dynamic Relaxation: A Technique for Detailed Thermo-Elastic Structural Analysis of Transportation Structures

NASA Astrophysics Data System (ADS)

Shoukry, Samir N.; William, Gergis W.; Riad, Mourad Y.; McBride, Kevyn C.

2006-08-01

Dynamic relaxation is a technique developed to solve static problems through an explicit integration in finite element. The main advantage of such a technique is the ability to solve a large problem in a relatively short time compared with the traditional implicit techniques, especially when using nonlinear material models. This paper describes the use of such a technique in analyzing large transportation structures as dowel jointed concrete pavements and 306-m-long, reinforced concrete bridge superstructure under the effect of temperature variations. The main feature of the pavement model is the detailed modeling of dowel bars and their interfaces with the surrounding concrete using extremely fine mesh of solid elements, while in the bridge structure it is the detailed modeling of the girder-deck interface as well as the bracing members between the girders. The 3DFE results were found to be in a good agreement with experimentally measured data obtained from an instrumented pavements sections and a highway bridge constructed in West Virginia. Thus, such a technique provides a good tool for analyzing the response of large structures to static loads in a fraction of the time required by traditional, implicit finite element methods.

The role of protein structural analysis in the next generation sequencing era.

PubMed

Yue, Wyatt W; Froese, D Sean; Brennan, Paul E

2014-01-01

Proteins are macromolecules that serve a cell's myriad processes and functions in all living organisms via dynamic interactions with other proteins, small molecules and cellular components. Genetic variations in the protein-encoding regions of the human genome account for >85% of all known Mendelian diseases, and play an influential role in shaping complex polygenic diseases. Proteins also serve as the predominant target class for the design of small molecule drugs to modulate their activity. Knowledge of the shape and form of proteins, by means of their three-dimensional structures, is therefore instrumental to understanding their roles in disease and their potentials for drug development. In this chapter we outline, with the wide readership of non-structural biologists in mind, the various experimental and computational methods available for protein structure determination. We summarize how the wealth of structure information, contributed to a large extent by the technological advances in structure determination to date, serves as a useful tool to decipher the molecular basis of genetic variations for disease characterization and diagnosis, particularly in the emerging era of genomic medicine, and becomes an integral component in the modern day approach towards rational drug development.

Acquiring a Variable Structure: An Interlanguage Analysis of Second Language Mood Use in Spanish

ERIC Educational Resources Information Center

Gudmestad, Aarnes

2012-01-01

This investigation connects issues in second language (L2) acquisition to topics in quantitative sociolinguistics by exploring the relationship between native-speaker (NS) and L2 variation. It is the first large-scale analysis of L2 mood use (the subjunctive-indicative contrast) in Spanish. It applies variationist findings on the range of…

Regional gradient analysis and spatial pattern of woody plant communities in Oregon forests.

Treesearch

J.L. Ohmann; T.A. Spies

1998-01-01

Knowledge of regional-scale patterns of ecological community structure, and of factors that control them, is largely conceptual. Regional- and local-scale factors associated with regional variation in community composition have not been quantified. We analyzed data on woody plant species abundance from 2443 field plots across natural and seminatural forests and...

Monozygotic Twins with Asperger Syndrome: Differences in Behaviour Reflect Variations in Brain Structure and Function

ERIC Educational Resources Information Center

Belmonte, Matthew K.; Carper, Ruth A.

2006-01-01

A pair of monozygotic twins discordant for symptoms of Asperger syndrome was evaluated at the age of 13.45 years using psychometric, morphometric, behavioural, and functional imaging methods. The lower-functioning twin had a smaller brain overall, a smaller right cerebellum, and a disproportionately large left frontal lobe, and manifested almost…

Water diffusion in silicate glasses: the effect of glass structure

NASA Astrophysics Data System (ADS)

Kuroda, M.; Tachibana, S.

2016-12-01

Water diffusion in silicate melts (glasses) is one of the main controlling factors of magmatism in a volcanic system. Water diffusivity in silicate glasses depends on its own concentration. However, the mechanism causing those dependences has not been fully understood yet. In order to construct a general model for water diffusion in various silicate glasses, we performed water diffusion experiments in silica glass and proposed a new water diffusion model [Kuroda et al., 2015]. In the model, water diffusivity is controlled by the concentration of both main diffusion species (i.e. molecular water) and diffusion pathways, which are determined by the concentrations of hydroxyl groups and network modifier cations. The model well explains the water diffusivity in various silicate glasses from silica glass to basalt glass. However, pre-exponential factors of water diffusivity in various glasses show five orders of magnitude variations although the pre-exponential factor should ideally represent the jump frequency and the jump distance of molecular water and show a much smaller variation. Here, we attribute the large variation of pre-exponential factors to a glass structure dependence of activation energy for molecular water diffusion. It has been known that the activation energy depends on the water concentration [Nowak and Behrens, 1997]. The concentration of hydroxyls, which cut Si-O-Si network in the glass structure, increases with water concentration, resulting in lowering the activation energy for water diffusion probably due to more fragmented structure. Network modifier cations are likely to play the same role as water. With taking the effect of glass structure into account, we found that the variation of pre-exponential factors of water diffusivity in silicate glasses can be much smaller than the five orders of magnitude, implying that the diffusion of molecular water in silicate glasses is controlled by the same atomic process.

Genomic variation among populations of threatened coral: Acropora cervicornis.

PubMed

Drury, C; Dale, K E; Panlilio, J M; Miller, S V; Lirman, D; Larson, E A; Bartels, E; Crawford, D L; Oleksiak, M F

2016-04-13

Acropora cervicornis, a threatened, keystone reef-building coral has undergone severe declines (>90 %) throughout the Caribbean. These declines could reduce genetic variation and thus hamper the species' ability to adapt. Active restoration strategies are a common conservation approach to mitigate species' declines and require genetic data on surviving populations to efficiently respond to declines while maintaining the genetic diversity needed to adapt to changing conditions. To evaluate active restoration strategies for the staghorn coral, the genetic diversity of A. cervicornis within and among populations was assessed in 77 individuals collected from 68 locations along the Florida Reef Tract (FRT) and in the Dominican Republic. Genotyping by Sequencing (GBS) identified 4,764 single nucleotide polymorphisms (SNPs). Pairwise nucleotide differences (π) within a population are large (~37 %) and similar to π across all individuals. This high level of genetic diversity along the FRT is similar to the diversity within a small, isolated reef. Much of the genetic diversity (>90 %) exists within a population, yet GBS analysis shows significant variation along the FRT, including 300 SNPs with significant FST values and significant divergence relative to distance. There are also significant differences in SNP allele frequencies over small spatial scales, exemplified by the large FST values among corals collected within Miami-Dade county. Large standing diversity was found within each population even after recent declines in abundance, including significant, potentially adaptive divergence over short distances. The data here inform conservation and management actions by uncovering population structure and high levels of diversity maintained within coral collections among sites previously shown to have little genetic divergence. More broadly, this approach demonstrates the power of GBS to resolve differences among individuals and identify subtle genetic structure, informing conservation goals with evolutionary implications.

Interactions of multi-scale heterogeneity in the lithosphere: Australia

NASA Astrophysics Data System (ADS)

Kennett, B. L. N.; Yoshizawa, K.; Furumura, T.

2017-10-01

Understanding the complex heterogeneity of the continental lithosphere involves a wide variety of spatial scales and the synthesis of multiple classes of information. Seismic surface waves and multiply reflected body waves provide the main constraints on broad-scale structure, and bounds on the extent of the lithosphere-asthenosphere transition (LAT) can be found from the vertical gradients of S wavespeed. Information on finer-scale structures comes through body wave studies, including detailed seismic tomography and P-wave reflectivity extracted from stacked autocorrelograms of continuous component records. With the inclusion of deterministic large-scale structure and realistic medium-scale stochastic features fine-scale variations are subdued. The resulting multi-scale heterogeneity model for the Australian region gives a good representation of the character of observed seismograms and their geographic variations and matches the observations of P-wave reflectivity. P reflections in the 0.5-3.0 Hz band in the uppermost mantle suggest variations on vertical scales of a few hundred metres with amplitudes of the order of 1%. Interference of waves reflected or converted at sequences of such modest variations in physical properties produce relatively simple behaviour for lower frequencies, which can suggest simpler structures than are actually present. Vertical changes in the character of fine-scale heterogeneity can produce apparent discontinuities. In Central Australia a 'mid-lithospheric discontinuity' can be tracked via changes in frequency content of station reflectivity, with links to the broad-scale pattern of wavespeed gradients and, in particular, the gradients of radial anisotropy. Comparisons with xenolith results from southeastern Australia indicate a strong tie between geochemical stratification and P-wave reflectivity.

The plasma environment, charge state, and currents of Saturn's C and D rings

NASA Technical Reports Server (NTRS)

Wilson, G. R.

1991-01-01

The charge state and associated currents of Saturn's C an D rings are studied by modeling the flow of ionospheric plasma from the mid- to low-latitude ionosphere to the vicinity of the rings. It is found that the plasma density near the C and D rings, at a given radial location, will experience a one to two order of magnitude diurnal variation. The surface charge density (SCD) of these rings can show significant radial and azimuthal variations due mainly to variation in the plasma density. The SCD also depends on structural features of the rings such as thickness and the nature of the particle size distribution. The associated azimuthal currents carried by these rings also show large diurnal variations resulting in field-aligned currents which close in the ionosphere. The resulting ionospheric electric field will probably not produce a significant amount of plasma convection in the topside ionosphere and inner plasmasphere.

Quadratic partial eigenvalue assignment in large-scale stochastic dynamic systems for resilient and economic design

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

Das, Sonjoy; Goswami, Kundan; Datta, Biswa N.

2014-12-10

Failure of structural systems under dynamic loading can be prevented via active vibration control which shifts the damped natural frequencies of the systems away from the dominant range of loading spectrum. The damped natural frequencies and the dynamic load typically show significant variations in practice. A computationally efficient methodology based on quadratic partial eigenvalue assignment technique and optimization under uncertainty has been formulated in the present work that will rigorously account for these variations and result in an economic and resilient design of structures. A novel scheme based on hierarchical clustering and importance sampling is also developed in this workmore » for accurate and efficient estimation of probability of failure to guarantee the desired resilience level of the designed system. Numerical examples are presented to illustrate the proposed methodology.« less

Natural Allelic Variations in Highly Polyploidy Saccharum Complex

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

Song, Jian; Yang, Xiping; Resende, Jr., Marcio F. R.

Sugarcane ( Saccharum spp.) is an important sugar and biofuel crop with high polyploid and complex genomes. The Saccharum complex, comprised of Saccharum genus and a few related genera, are important genetic resources for sugarcane breeding. A large amount of natural variation exists within the Saccharum complex. Though understanding their allelic variation has been challenging, it is critical to dissect allelic structure and to identify the alleles controlling important traits in sugarcane. To characterize natural variations in Saccharum complex, a target enrichment sequencing approach was used to assay 12 representative germplasm accessions. In total, 55,946 highly efficient probes were designedmore » based on the sorghum genome and sugarcane unigene set targeting a total of 6 Mb of the sugarcane genome. A pipeline specifically tailored for polyploid sequence variants and genotype calling was established. BWAmem and sorghum genome approved to be an acceptable aligner and reference for sugarcane target enrichment sequence analysis, respectively. Genetic variations including 1,166,066 non-redundant SNPs, 150,421 InDels, 919 gene copy number variations, and 1,257 gene presence/absence variations were detected. SNPs from three different callers (Samtools, Freebayes, and GATK) were compared and the validation rates were nearly 90%. Based on the SNP loci of each accession and their ploidy levels, 999,258 single dosage SNPs were identified and most loci were estimated as largely homozygotes. An average of 34,397 haplotype blocks for each accession was inferred. The highest divergence time among the Saccharum spp. was estimated as 1.2 million years ago (MYA). Saccharum spp. diverged from Erianthus and Sorghum approximately 5 and 6 MYA, respectively. Furthermore, the target enrichment sequencing approach provided an effective way to discover and catalog natural allelic variation in highly polyploid or heterozygous genomes.« less

Natural Allelic Variations in Highly Polyploidy Saccharum Complex

DOE PAGES

Song, Jian; Yang, Xiping; Resende, Jr., Marcio F. R.; ...

2016-06-08

Sugarcane ( Saccharum spp.) is an important sugar and biofuel crop with high polyploid and complex genomes. The Saccharum complex, comprised of Saccharum genus and a few related genera, are important genetic resources for sugarcane breeding. A large amount of natural variation exists within the Saccharum complex. Though understanding their allelic variation has been challenging, it is critical to dissect allelic structure and to identify the alleles controlling important traits in sugarcane. To characterize natural variations in Saccharum complex, a target enrichment sequencing approach was used to assay 12 representative germplasm accessions. In total, 55,946 highly efficient probes were designedmore » based on the sorghum genome and sugarcane unigene set targeting a total of 6 Mb of the sugarcane genome. A pipeline specifically tailored for polyploid sequence variants and genotype calling was established. BWAmem and sorghum genome approved to be an acceptable aligner and reference for sugarcane target enrichment sequence analysis, respectively. Genetic variations including 1,166,066 non-redundant SNPs, 150,421 InDels, 919 gene copy number variations, and 1,257 gene presence/absence variations were detected. SNPs from three different callers (Samtools, Freebayes, and GATK) were compared and the validation rates were nearly 90%. Based on the SNP loci of each accession and their ploidy levels, 999,258 single dosage SNPs were identified and most loci were estimated as largely homozygotes. An average of 34,397 haplotype blocks for each accession was inferred. The highest divergence time among the Saccharum spp. was estimated as 1.2 million years ago (MYA). Saccharum spp. diverged from Erianthus and Sorghum approximately 5 and 6 MYA, respectively. Furthermore, the target enrichment sequencing approach provided an effective way to discover and catalog natural allelic variation in highly polyploid or heterozygous genomes.« less

The Diversity Present in 5140 Human Mitochondrial Genomes

PubMed Central

Pereira, Luísa; Freitas, Fernando; Fernandes, Verónica; Pereira, Joana B.; Costa, Marta D.; Costa, Stephanie; Máximo, Valdemar; Macaulay, Vincent; Rocha, Ricardo; Samuels, David C.

2009-01-01

We analyzed the current status (as of the end of August 2008) of human mitochondrial genomes deposited in GenBank, amounting to 5140 complete or coding-region sequences, in order to present an overall picture of the diversity present in the mitochondrial DNA of the global human population. To perform this task, we developed mtDNA-GeneSyn, a computer tool that identifies and exhaustedly classifies the diversity present in large genetic data sets. The diversity observed in the 5140 human mitochondrial genomes was compared with all possible transitions and transversions from the standard human mitochondrial reference genome. This comparison showed that tRNA and rRNA secondary structures have a large effect in limiting the diversity of the human mitochondrial sequences, whereas for the protein-coding genes there is a bias toward less variation at the second codon positions. The analysis of the observed amino acid variations showed a tolerance of variations that convert between the amino acids V, I, A, M, and T. This defines a group of amino acids with similar chemical properties that can interconvert by a single transition. PMID:19426953

Deep ocean nutrients imply large latitudinal variation in particle transfer efficiency.

PubMed

Weber, Thomas; Cram, Jacob A; Leung, Shirley W; DeVries, Timothy; Deutsch, Curtis

2016-08-02

The "transfer efficiency" of sinking organic particles through the mesopelagic zone and into the deep ocean is a critical determinant of the atmosphere-ocean partition of carbon dioxide (CO2). Our ability to detect large-scale spatial variations in transfer efficiency is limited by the scarcity and uncertainties of particle flux data. Here we reconstruct deep ocean particle fluxes by diagnosing the rate of nutrient accumulation along transport pathways in a data-constrained ocean circulation model. Combined with estimates of organic matter export from the surface, these diagnosed fluxes reveal a global pattern of transfer efficiency to 1,000 m that is high (∼25%) at high latitudes and low (∼5%) in subtropical gyres, with intermediate values in the tropics. This pattern is well correlated with spatial variations in phytoplankton community structure and the export of ballast minerals, which control the size and density of sinking particles. These findings accentuate the importance of high-latitude oceans in sequestering carbon over long timescales, and highlight potential impacts on remineralization depth as phytoplankton communities respond to a warming climate.

Characterizing relative humidity with respect to ice in midlatitude cirrus clouds as a function of atmospheric state

NASA Astrophysics Data System (ADS)

Dzambo, Andrew M.; Turner, David D.

2016-10-01

Midlatitude cirrus cloud macrophysical and microphysical properties have been shown in previous studies to vary seasonally and in various large-scale dynamical regimes, but relative humidity with respect to ice (RHI) within cirrus clouds has not been studied extensively in this context. Using a combination of radiosonde and millimeter-wavelength cloud radar data, we identify 1076 cirrus clouds spanning a 7 year period from 2004 to 2011. These data are separated into five classes using a previously published algorithm that is based largely on synoptic conditions. Using these data and classification scheme, we find that RHI in cirrus clouds varies seasonally. Variations in cirrus cloud RHI exist within the prescribed classifications; however, most of the variations are within the measurement uncertainty. Additionally, with the exception of nonsummer class cirrus, these variations are not statistically significant. We also find that cirrus cloud occurrence is not necessarily correlated with higher observed values of RHI. The structure of RHI in cirrus clouds varies more in thicker clouds, which follows previous studies showing that macrophysical and microphysical variability increases in thicker cirrus clouds.

Deep ocean nutrients imply large latitudinal variation in particle transfer efficiency

PubMed Central

Weber, Thomas; Cram, Jacob A.; Leung, Shirley W.; DeVries, Timothy; Deutsch, Curtis

2016-01-01

The “transfer efficiency” of sinking organic particles through the mesopelagic zone and into the deep ocean is a critical determinant of the atmosphere−ocean partition of carbon dioxide (CO2). Our ability to detect large-scale spatial variations in transfer efficiency is limited by the scarcity and uncertainties of particle flux data. Here we reconstruct deep ocean particle fluxes by diagnosing the rate of nutrient accumulation along transport pathways in a data-constrained ocean circulation model. Combined with estimates of organic matter export from the surface, these diagnosed fluxes reveal a global pattern of transfer efficiency to 1,000 m that is high (∼25%) at high latitudes and low (∼5%) in subtropical gyres, with intermediate values in the tropics. This pattern is well correlated with spatial variations in phytoplankton community structure and the export of ballast minerals, which control the size and density of sinking particles. These findings accentuate the importance of high-latitude oceans in sequestering carbon over long timescales, and highlight potential impacts on remineralization depth as phytoplankton communities respond to a warming climate. PMID:27457946

Measuring the benefit of orthophosphate treatment on lead in drinking water.

PubMed

Cardew, P T

2009-03-01

Many water companies are adding low concentrations of orthophosphate to the water supply in order to reduce lead concentrations in drinking water produced from corrosion of lead service pipes. Despite the erratic nature of lead concentrations measured at customer properties it has been possible to quantify the impact of treatment on lead concentrations and thereby quantify the effectiveness of treatment at both a regional and zonal level. This showed that the treatment policy has delivered more than 90 per cent reduction in lead concentrations, and was largely in accordance with theory. Across the region, lead performance and the reduction in lead performance show significant variation. A large part of this variation can be accounted for by variations in the proportion of leaded properties supplied through lead service pipes. Analysis showed that the proportion of particulate lead has also reduced significantly over the last decade. This is attributed to improved mechanical robustness of the corrosion layer caused by changes in its physical structure. This appears to be a very slow process with a natural time-scale of years.

Deep ocean nutrients imply large latitudinal variation in particle transfer efficiency

NASA Astrophysics Data System (ADS)

Weber, Thomas; Cram, Jacob A.; Leung, Shirley W.; DeVries, Timothy; Deutsch, Curtis

2016-08-01

The “transfer efficiency” of sinking organic particles through the mesopelagic zone and into the deep ocean is a critical determinant of the atmosphere-ocean partition of carbon dioxide (CO2). Our ability to detect large-scale spatial variations in transfer efficiency is limited by the scarcity and uncertainties of particle flux data. Here we reconstruct deep ocean particle fluxes by diagnosing the rate of nutrient accumulation along transport pathways in a data-constrained ocean circulation model. Combined with estimates of organic matter export from the surface, these diagnosed fluxes reveal a global pattern of transfer efficiency to 1,000 m that is high (˜25%) at high latitudes and low (˜5%) in subtropical gyres, with intermediate values in the tropics. This pattern is well correlated with spatial variations in phytoplankton community structure and the export of ballast minerals, which control the size and density of sinking particles. These findings accentuate the importance of high-latitude oceans in sequestering carbon over long timescales, and highlight potential impacts on remineralization depth as phytoplankton communities respond to a warming climate.

Buccal Swabbing as a Noninvasive Method To Determine Bacterial, Archaeal, and Eukaryotic Microbial Community Structures in the Rumen

PubMed Central

Kirk, Michelle R.; Jonker, Arjan; McCulloch, Alan

2015-01-01

Analysis of rumen microbial community structure based on small-subunit rRNA marker genes in metagenomic DNA samples provides important insights into the dominant taxa present in the rumen and allows assessment of community differences between individuals or in response to treatments applied to ruminants. However, natural animal-to-animal variation in rumen microbial community composition can limit the power of a study considerably, especially when only subtle differences are expected between treatment groups. Thus, trials with large numbers of animals may be necessary to overcome this variation. Because ruminants pass large amounts of rumen material to their oral cavities when they chew their cud, oral samples may contain good representations of the rumen microbiota and be useful in lieu of rumen samples to study rumen microbial communities. We compared bacterial, archaeal, and eukaryotic community structures in DNAs extracted from buccal swabs to those in DNAs from samples collected directly from the rumen by use of a stomach tube for sheep on four different diets. After bioinformatic depletion of potential oral taxa from libraries of samples collected via buccal swabs, bacterial communities showed significant clustering by diet (R = 0.37; analysis of similarity [ANOSIM]) rather than by sampling method (R = 0.07). Archaeal, ciliate protozoal, and anaerobic fungal communities also showed significant clustering by diet rather than by sampling method, even without adjustment for potentially orally associated microorganisms. These findings indicate that buccal swabs may in future allow quick and noninvasive sampling for analysis of rumen microbial communities in large numbers of ruminants. PMID:26276109

Phenomenological and statistical analyses of turbulence in forced convection with temperature-dependent viscosity under non-Boussinesq condition.

PubMed

Yahya, S M; Anwer, S F; Sanghi, S

2013-10-01

In this work, Thermal Large Eddy Simulation (TLES) is performed to study the behavior of weakly compressible Newtonian fluids with anisotropic temperature-dependent viscosity in forced convection turbulent flow. A systematic analysis of variable-viscosity effects, isolated from gravity, with relevance to industrial cooling/heating applications is being carried out. A LES of a planar channel flow with significant heat transfer at a low Mach number was performed to study effects of fluid property variation on the near-wall turbulence structure. In this flow configuration the top wall is maintained at a higher temperature (T hot ) than the bottom wall (T cold ). The temperature ratio (R θ = T hot /T cold ) is fixed at 1.01, 2 and 3 to study the effects of property variations at low Mach number. Results indicate that average and turbulent fields undergo significant changes. Compared with isothermal flow with constant viscosity, we observe that turbulence is enhanced in the cold side of the channel, characterized by locally lower viscosity whereas a decrease of turbulent kinetic energy is found at the hot wall. The turbulent structures near the cold wall are very short and densely populated vortices but near the hot wall there seems to be a long streaky structure or large elongated vortices. Spectral study reveals that turbulence is completely suppressed at the hot side of the channel at a large temperature ratio because no inertial zone is obtained (i.e. index of Kolmogorov scaling law is zero) from the spectra in these region.

Physiology modulates social flexibility and collective behaviour in equids and other large ungulates.

PubMed

Gersick, Andrew S; Rubenstein, Daniel I

2017-08-19

Though morphologically very similar, equids across the extant species occupy ecological niches that are surprisingly non-overlapping. Occupancy of these distinct niches appears related to subtle physiological and behavioural adaptations which, in turn, correspond to significant differences in the social behaviours and emergent social systems characterizing the different species. Although instances of intraspecific behavioural variation in equids demonstrate that the same body plan can support a range of social structures, each of these morphologically similar species generally shows robust fidelity to its evolved social system. The pattern suggests a subtle relationship between physiological phenotypes and behavioural flexibility. While environmental conditions can vary widely within relatively short temporal or spatial scales, physiological changes and changes to the behaviours that regulate physiological processes, are constrained to longer cycles of adaptation. Physiology is then the limiting variable in the interaction between ecological variation and behavioural and socio-structural flexibility. Behavioural and socio-structural flexibility, in turn, will generate important feedbacks that will govern physiological function, thus creating a coupled web of interactions that can lead to changes in individual and collective behaviour. Longitudinal studies of equid and other large-bodied ungulate populations under environmental stress, such as those discussed here, may offer the best opportunities for researchers to examine, in real time, the interplay between individual behavioural plasticity, socio-structural flexibility, and the physiological and genetic changes that together produce adaptive change.This article is part of the themed issue 'Physiological determinants of social behaviour in animals'. © 2017 The Author(s).

Environmental characteristics drive variation in Amazonian understorey bird assemblages

PubMed Central

Magnusson, William E.; Anderson, Marti J.; Schlegel, Martin; Pe’er, Guy; Henle, Klaus

2017-01-01

Tropical bird assemblages display patterns of high alpha and beta diversity and, as tropical birds exhibit strong habitat specificity, their spatial distributions are generally assumed to be driven primarily by environmental heterogeneity and interspecific interactions. However, spatial distributions of some Amazonian forest birds are also often restricted by large rivers and other large-scale topographic features, suggesting that dispersal limitation may also play a role in driving species’ turnover. In this study, we evaluated the effects of environmental characteristics, topographic and spatial variables on variation in local assemblage structure and diversity of birds in an old-growth forest in central Amazonia. Birds were mist-netted in 72 plots distributed systematically across a 10,000 ha reserve in each of three years. Alpha diversity remained stable through time, but species composition changed. Spatial variation in bird-assemblage structure was significantly related to environmental and topographic variables but not strongly related to spatial variables. At a broad scale, we found bird assemblages to be significantly distinct between two watersheds that are divided by a central ridgeline. We did not detect an effect of the ridgeline per se in driving these patterns, indicating that most birds are able to fly across it, and that differences in assemblage structure between watersheds may be due to unmeasured environmental variables or unique combinations of measured variables. Our study indicates that complex geography and landscape features can act together with environmental variables to drive changes in the diversity and composition of tropical bird assemblages at local scales, but highlights that we still know very little about what makes different parts of tropical forest suitable for different species. PMID:28225774

A Finite Element Framework for Studying the Mechanical Response of Macromolecules: Application to the Gating of the Mechanosensitive Channel MscL

PubMed Central

Tang, Yuye; Cao, Guoxin; Chen, Xi; Yoo, Jejoong; Yethiraj, Arun; Cui, Qiang

2006-01-01

The gating pathways of mechanosensitive channels of large conductance (MscL) in two bacteria (Mycobacterium tuberculosis and Escherichia coli) are studied using the finite element method. The phenomenological model treats transmembrane helices as elastic rods and the lipid membrane as an elastic sheet of finite thickness; the model is inspired by the crystal structure of MscL. The interactions between various continuum components are derived from molecular-mechanics energy calculations using the CHARMM all-atom force field. Both bacterial MscLs open fully upon in-plane tension in the membrane and the variation of pore diameter with membrane tension is found to be essentially linear. The estimated gating tension is close to the experimental value. The structural variations along the gating pathway are consistent with previous analyses based on structural models with experimental constraints and biased atomistic molecular-dynamics simulations. Upon membrane bending, neither MscL opens substantially, although there is notable and nonmonotonic variation in the pore radius. This emphasizes that the gating behavior of MscL depends critically on the form of the mechanical perturbation and reinforces the idea that the crucial gating parameter is lateral tension in the membrane rather than the curvature of the membrane. Compared to popular all-atom-based techniques such as targeted or steered molecular-dynamics simulations, the finite element method-based continuum-mechanics framework offers a unique alternative to bridge detailed intermolecular interactions and biological processes occurring at large spatial scales and long timescales. It is envisioned that such a hierarchical multiscale framework will find great value in the study of a variety of biological processes involving complex mechanical deformations such as muscle contraction and mechanotransduction. PMID:16731564

Variability of interleaving structure of Atlantic Water during its propagation along the Eurasian basin (Arctic Ocean) continental margin

NASA Astrophysics Data System (ADS)

Zhurbas, Nataliya; Kuzmina, Natalia; Lyzhkov, Dmitry; Ostapchuk, Alexey

2017-04-01

In order to give detailed description of the interleaving structure in the Eurasian basin results of observations carried out during NABOS 2008 and Polarstern cruise in 1996 were analyzed. The study was focused on interleaving parameters (structure and vertical scale of intrusions) variability in the upper (150-300 meters) and intermediate (300-700 meters) layers of the ocean. Based on θ,S/θ,σ-diagrams (θ, S and σ are the potential temperature, salinity and potential density, correspondingly) analysis two main results were obtained. First of all it was shown that intrusive layers carried by the mean current along the Eurasian Basin continental margin become deeper relatively isopycnals and thus stimulate ventilation of pycnocline. Second, the area in Eurasian Basin thermocline was found where intrusive layers of large and small scale were absent. This distinctive feature can be explained by intensive mixing between two branches of Atlantic Water, one of which propagates along Eurasian basin continental margin and the other spreads across the basin due to large scale interleaving processes. Among others, one of the possible methods of integral estimation of Atlantic water masses heat and salt contents variations during their expansion along basin continental margin was proposed. Thus it is reasonable to assess variation of square under the θ(S)-diagrams, which illustrate the data obtained from two CTD-stations located on diametrically opposite sides of Eurasian Basin, taking 0.5°C isotherm as a reference value. For verification of the introduced approach the estimates of heat and salt contents variations were made by different methods. Detailed discussion of the results is presented. Work was supported by the Russian Foundation for Basic Research (Grant No 15-05-01479-a).

Methane related authigenic carbonates, chimneys and crusts from the Gulf of Cadiz

NASA Astrophysics Data System (ADS)

Magalhães, V.; Vasconcelos, C.; Gaspar, L.; Monteiro, H.; Pinheiro, L.; Ivanov, M.; Díaz-del-Río, V.; Somoza, L.

2003-04-01

During the TTR 11 and TTR 12 cruises (2001 and 2002), the area south and southwest of the Guadalquivir Diapiric Ridge was intensely surveyed with seismics, side scan sonar (MAK), underwater TV and sampling. This area is characterized by a very strong backscatter on the available side scan sonar images and a very irregular seafloor, with morphological and sedimentological features evidencing fluid escape structures (mud diapirs and mud volcanoes); and sedimentary structures associated with the outflow of the Mediterranean water (MOW). Based on the data and samples collected during the TTR11 and TTR12 cruises, complemented with data from the ANASTYA 2000 and 2001 cruises, it seems that this area corresponds to a large field of carbonate chimneys and crusts. Dredge profiles on the Iberico dome and west of this structure, on the main channel of the MOW, yielded a large amount of carbonate slabs and chimneys. These consist essentially of intrapelbiomicrite. Petrographic and XRD shows that their mineralogical composition consists mainly of dolomite, high magnesium calcite, quartz, feldspar and clays. Bioclasts of plantonic foraminifera (globigerinoids), ostracods and peletts are observed. Iron and manganese oxides are present and the cement is essentially biomicrite. In different samples from the same chimney a variation on the dolomite/calcite ratio is observed from the interior to the external part of the chimney. Values of dolomite show a variation from 47% in the interior to 17 % in the exterior. As regards Si02 (19-16%), Al2O3 (4-3%) and Fe2O3 (5-7%), the variations observed are not significant. Stable isotopic analysis of Carbon shown low d13C values (down to -46.88 per mil vs. PDB) and d18O up to + 4.90 per mil vs.

Comparative Anatomy of the Bony Labyrinth (Inner Ear) of Placental Mammals

PubMed Central

Ekdale, Eric G.

2013-01-01

Background Variation is a naturally occurring phenomenon that is observable at all levels of morphology, from anatomical variations of DNA molecules to gross variations between whole organisms. The structure of the otic region is no exception. The present paper documents the broad morphological diversity exhibited by the inner ear region of placental mammals using digital endocasts constructed from high-resolution X-ray computed tomography (CT). Descriptions cover the major placental clades, and linear, angular, and volumetric dimensions are reported. Principal Findings The size of the labyrinth is correlated to the overall body mass of individuals, such that large bodied mammals have absolutely larger labyrinths. The ratio between the average arc radius of curvature of the three semicircular canals and body mass of aquatic species is substantially lower than the ratios of related terrestrial taxa, and the volume percentage of the vestibular apparatus of aquatic mammals tends to be less than that calculated for terrestrial species. Aspects of the bony labyrinth are phylogenetically informative, including vestibular reduction in Cetacea, a tall cochlear spiral in caviomorph rodents, a low position of the plane of the lateral semicircular canal compared to the posterior canal in Cetacea and Carnivora, and a low cochlear aspect ratio in Primatomorpha. Significance The morphological descriptions that are presented add a broad baseline of anatomy of the inner ear across many placental mammal clades, for many of which the structure of the bony labyrinth is largely unknown. The data included here complement the growing body of literature on the physiological and phylogenetic significance of bony labyrinth structures in mammals, and they serve as a source of data for future studies on the evolution and function of the vertebrate ear. PMID:23805251

Large-scale properties of the interplanetary magnetic field

NASA Technical Reports Server (NTRS)

Schatten, K. H.

1972-01-01

Early theoretical work of Parker is presented along with the observational evidence supporting his Archimedes spiral model. Variations present in the interplanetary magnetic field from the spiral angle are related to structures in the solar wind. The causes of these structures are found to be either nonuniform radial solar wind flow or the time evolution of the photospheric field. Coronal magnetic models are related to the connection between the solar magnetic field and the interplanetary magnetic field. Direct extension of the solar field-magnetic nozzle controversy is discussed along with the coronal magnetic models. Effects of active regions on the interplanetary magnetic field is discussed with particular reference to the evolution of interplanetary sectors. Interplanetary magnetic field magnitude variations are shown throughout the solar cycle. The percentage of time the field magnitude is greater than 10 gamma is shown to closely parallel sunspot number. The sun's polar field influence on the interplanetary field and alternative views of the magnetic field structure out of the ecliptic plane are presented. In addition, a variety of significantly different interplanetary field structures are discussed.

Depressive Symptoms among Latino Farmworkers across the Agricultural Season: Structural and Situational Influences

PubMed Central

Grzywacz, Joseph G.; Quandt, Sara A.; Chen, Haiying; Isom, Scott; Kiang, Lisa; Vallejos, Quirina; Arcury, Thomas A.

2010-01-01

Immigrant Latino farmworkers confront multiple challenges that threaten their mental health. Previous farmworker mental health research has relied primarily on cross-sectional study designs, leaving little opportunity to describe how farmworker mental health changes or to identify factors that may contribute to these changes. This study used prospective data obtained at monthly intervals across one four-month agricultural season from a large sample of Latino farmworkers in NC (N=288) to document variation in depressive symptoms across the agricultural season and delineate structural and situational factors associated with mental health trajectories across time. Depressive symptoms generally followed a U-shaped distribution across the season, but there was substantial variation in this pattern. Structural stressors like marital status and situational stressors like the pace of work, crowded living conditions, and concerns about documentation predicted depressive symptoms. The pattern of results suggests that strategies to address mental health problems in this vulnerable population will require coordinated action at the individual and social level. PMID:20658876

Depressive symptoms among Latino farmworkers across the agricultural season: Structural and situational influences.

PubMed

Grzywacz, Joseph G; Quandt, Sara A; Chen, Haiying; Isom, Scott; Kiang, Lisa; Vallejos, Quirina; Arcury, Thomas A

2010-07-01

Immigrant Latino farmworkers confront multiple challenges that threaten their mental health. Previous farmworker mental health research has relied primarily on cross-sectional study designs, leaving little opportunity to describe how farmworker mental health changes or to identify factors that may contribute to these changes. This study used prospective data obtained at monthly intervals across one 4-month agricultural season from a large sample of Latino farmworkers in North Carolina (N = 288) to document variation in depressive symptoms across the agricultural season and delineate structural and situational factors associated with mental health trajectories across time. Depressive symptoms generally followed a U-shaped distribution across the season, but there was substantial variation in this pattern. Structural stressors like marital status and situational stressors like the pace of work, crowded living conditions, and concerns about documentation predicted depressive symptoms. The pattern of results suggests that strategies to address mental health problems in this vulnerable population will require coordinated action at the individual and social level.

Solar Cycle Fine Structure and Surface Rotation from Ca II K-Line Time Series Data

NASA Technical Reports Server (NTRS)

Scargle, Jeff; Keil, Steve; Worden, Pete

2011-01-01

Analysis of three and a half decades of data from the NSO/AFRL/Sac Peak K-line monitoring program yields evidence for four components to the variation: (a) the solar cycle, with considerable fine structure and a quasi-periodicity of 122.4 days; (b) a stochastic process, faster than (a) and largely independent of it, (c) a quasi-periodic signal due to rotational modulation, and of course (d) observational errors (shown to be quite small). Correlation and power spectrum analyses elucidate periodic and aperiodic variation of these chromospheric parameters. Time-frequency analysis is especially useful for extracting information about differential rotation, and in particular elucidates the connection between its behavior and fine structure of the solar cycle on approximately one-year time scales. These results further suggest that similar analyses will be useful at detecting and characterizing differential rotation in stars from stellar light-curves such as those being produced at NASA's Kepler observatory.

Large-scale impacts of herbivores on the structural diversity of African savannas

PubMed Central

Asner, Gregory P.; Levick, Shaun R.; Kennedy-Bowdoin, Ty; Knapp, David E.; Emerson, Ruth; Jacobson, James; Colgan, Matthew S.; Martin, Roberta E.

2009-01-01

African savannas are undergoing management intensification, and decision makers are increasingly challenged to balance the needs of large herbivore populations with the maintenance of vegetation and ecosystem diversity. Ensuring the sustainability of Africa's natural protected areas requires information on the efficacy of management decisions at large spatial scales, but often neither experimental treatments nor large-scale responses are available for analysis. Using a new airborne remote sensing system, we mapped the three-dimensional (3-D) structure of vegetation at a spatial resolution of 56 cm throughout 1640 ha of savanna after 6-, 22-, 35-, and 41-year exclusions of herbivores, as well as in unprotected areas, across Kruger National Park in South Africa. Areas in which herbivores were excluded over the short term (6 years) contained 38%–80% less bare ground compared with those that were exposed to mammalian herbivory. In the longer-term (> 22 years), the 3-D structure of woody vegetation differed significantly between protected and accessible landscapes, with up to 11-fold greater woody canopy cover in the areas without herbivores. Our maps revealed 2 scales of ecosystem response to herbivore consumption, one broadly mediated by geologic substrate and the other mediated by hillslope-scale variation in soil nutrient availability and moisture conditions. Our results are the first to quantitatively illustrate the extent to which herbivores can affect the 3-D structural diversity of vegetation across large savanna landscapes. PMID:19258457

Knowledge and Theme Discovery across Very Large Biological Data Sets Using Distributed Queries: A Prototype Combining Unstructured and Structured Data

PubMed Central

Repetski, Stephen; Venkataraman, Girish; Che, Anney; Luke, Brian T.; Girard, F. Pascal; Stephens, Robert M.

2013-01-01

As the discipline of biomedical science continues to apply new technologies capable of producing unprecedented volumes of noisy and complex biological data, it has become evident that available methods for deriving meaningful information from such data are simply not keeping pace. In order to achieve useful results, researchers require methods that consolidate, store and query combinations of structured and unstructured data sets efficiently and effectively. As we move towards personalized medicine, the need to combine unstructured data, such as medical literature, with large amounts of highly structured and high-throughput data such as human variation or expression data from very large cohorts, is especially urgent. For our study, we investigated a likely biomedical query using the Hadoop framework. We ran queries using native MapReduce tools we developed as well as other open source and proprietary tools. Our results suggest that the available technologies within the Big Data domain can reduce the time and effort needed to utilize and apply distributed queries over large datasets in practical clinical applications in the life sciences domain. The methodologies and technologies discussed in this paper set the stage for a more detailed evaluation that investigates how various data structures and data models are best mapped to the proper computational framework. PMID:24312478

Knowledge and theme discovery across very large biological data sets using distributed queries: a prototype combining unstructured and structured data.

PubMed

Mudunuri, Uma S; Khouja, Mohamad; Repetski, Stephen; Venkataraman, Girish; Che, Anney; Luke, Brian T; Girard, F Pascal; Stephens, Robert M

2013-01-01

As the discipline of biomedical science continues to apply new technologies capable of producing unprecedented volumes of noisy and complex biological data, it has become evident that available methods for deriving meaningful information from such data are simply not keeping pace. In order to achieve useful results, researchers require methods that consolidate, store and query combinations of structured and unstructured data sets efficiently and effectively. As we move towards personalized medicine, the need to combine unstructured data, such as medical literature, with large amounts of highly structured and high-throughput data such as human variation or expression data from very large cohorts, is especially urgent. For our study, we investigated a likely biomedical query using the Hadoop framework. We ran queries using native MapReduce tools we developed as well as other open source and proprietary tools. Our results suggest that the available technologies within the Big Data domain can reduce the time and effort needed to utilize and apply distributed queries over large datasets in practical clinical applications in the life sciences domain. The methodologies and technologies discussed in this paper set the stage for a more detailed evaluation that investigates how various data structures and data models are best mapped to the proper computational framework.

TomoMiner and TomoMinerCloud: A software platform for large-scale subtomogram structural analysis

PubMed Central

Frazier, Zachary; Xu, Min; Alber, Frank

2017-01-01

SUMMARY Cryo-electron tomography (cryoET) captures the 3D electron density distribution of macromolecular complexes in close to native state. With the rapid advance of cryoET acquisition technologies, it is possible to generate large numbers (>100,000) of subtomograms, each containing a macromolecular complex. Often, these subtomograms represent a heterogeneous sample due to variations in structure and composition of a complex in situ form or because particles are a mixture of different complexes. In this case subtomograms must be classified. However, classification of large numbers of subtomograms is a time-intensive task and often a limiting bottleneck. This paper introduces an open source software platform, TomoMiner, for large-scale subtomogram classification, template matching, subtomogram averaging, and alignment. Its scalable and robust parallel processing allows efficient classification of tens to hundreds of thousands of subtomograms. Additionally, TomoMiner provides a pre-configured TomoMinerCloud computing service permitting users without sufficient computing resources instant access to TomoMiners high-performance features. PMID:28552576

Population genetic structure in migratory sandhill cranes and the role of Pleistocene glaciations.

PubMed

Jones, Kenneth L; Krapu, Gary L; Brandt, David A; Ashley, Mary V

2005-08-01

Previous studies of migratory sandhill cranes (Grus canadensis) have made significant progress explaining evolution of this group at the species scale, but have been unsuccessful in explaining the geographically partitioned variation in morphology seen on the population scale. The objectives of this study were to assess the population structure and gene flow patterns among migratory sandhill cranes using microsatellite DNA genotypes and mitochondrial DNA haplotypes of a large sample of individuals across three populations. In particular, we were interested in evaluating the roles of Pleistocene glaciation events and postglaciation gene flow in shaping the present-day population structure. Our results indicate substantial gene flow across regions of the Midcontinental population that are geographically adjacent, suggesting that gene flow for most of the region follows an isolation-by-distance model. Male-mediated gene flow and strong female philopatry may explain the differing patterns of nuclear and mitochondrial variation. Taken in context with precise geographical information on breeding locations, the morphologic and microsatellite DNA variation shows a gradation from the Arctic-nesting subspecies G. c. canadensis to the nonArctic subspecies G. c. tabida. Analogous to other Arctic-nesting birds, it is probable that the population structure seen in Midcontinental sandhill cranes reflects the result of postglacial secondary contact. Our data suggest that subspecies of migratory sandhills experience significant gene flow and therefore do not represent distinct and independent genetic entities.

Temporal variation in plankton assemblages and physicochemistry of Devils Lake, North Dakota

USGS Publications Warehouse

Leland, H.V.; Berkas, W.R.

1998-01-01

Seasonal and annual variation in biomass and structure of algal assemblages of hyposaline Devils Lake were examined in relation to turbidity, ambient concentrations of major ions, trace elements and nutrients, and the standing crop of herbivores. Lake level declined during the early years of study, but rose markedly in subsequent years as historically large volumes of water flowed into this hydrologically-closed basin. Winter algal assemblages were dominated (in biomass) most years by small, non-motile chlorophytes ( Choricystis minor, Kirchneriella lunaris or Dunaliella sp.), or Euglena sp. in the most saline sub-basin. Spring assemblages were dominated by diatoms (Stephanodiscus cf. minutulus, Surirella peisonis, Cyclotella meneghiniana and Entomoneis paludosa were especially prominent) or chlorophytes ( C. minor) until the lake level rose. C. minor abundances then declined in spring assemblages and diatoms ( Stephanodiscus cf. agassizensis and S. niagarae; E. paludosa in the more saline sub-basins) dominated. The potential for nitrogen-deficient conditions for phytoplankton growth was evidenced most summers and early autumns by consistently high concentrations of reactive-P relative to inorganic-N and blooms of the N-fixing cyanophyte Aphanizomenon flos-aquae; Microcystis aeruginosa typically was a co-dominant (>30% of biomass) in these assemblages. Pulses of diatoms ( S. cf. agassizensis and C. meneghiniana) occurred in summers following unusually prolonged periods of calm weather or large water inflows. Physical (irradiance, turbulence) and chemical (major nutrients) variables were the primary factors associated with phytoplankton growth. Transparency and major nutrient concentrations accounted for more of the annual variation in phytoplankton structure than did salinity. Seasonal abundance patterns of the dominant zooplankton (the copepod Diaptomus sicilis; the cladocerans Ceriodaphnia quadrangula, Chydorus sphaericus, Daphnia pulex and Diaphanosoma birgei; and the rotifers Brachionus spp., Filinia longiseta, Keratella cochlearis and K. quadrata) also indicated variation in algal populations related to grazing.

Limited Phylogeographic Signal in Sex-Linked and Autosomal Loci Despite Geographically, Ecologically, and Phenotypically Concordant Structure of mtDNA Variation in the Holarctic Avian Genus Eremophila

PubMed Central

Drovetski, Sergei V.; Raković, Marko; Semenov, Georgy; Fadeev, Igor V.; Red’kin, Yaroslav A.

2014-01-01

Phylogeographic studies of Holarctic birds are challenging because they involve vast geographic scale, complex glacial history, extensive phenotypic variation, and heterogeneous taxonomic treatment across countries, all of which require large sample sizes. Knowledge about the quality of phylogeographic information provided by different loci is crucial for study design. We use sequences of one mtDNA gene, one sex-linked intron, and one autosomal intron to elucidate large scale phylogeographic patterns in the Holarctic lark genus Eremophila. The mtDNA ND2 gene identified six geographically, ecologically, and phenotypically concordant clades in the Palearctic that diverged in the Early - Middle Pleistocene and suggested paraphyly of the horned lark (E. alpestris) with respect to the Temminck's lark (E. bilopha). In the Nearctic, ND2 identified five subclades which diverged in the Late Pleistocene. They overlapped geographically and were not concordant phenotypically or ecologically. Nuclear alleles provided little information on geographic structuring of genetic variation in horned larks beyond supporting the monophyly of Eremophila and paraphyly of the horned lark. Multilocus species trees based on two nuclear or all three loci provided poor support for haplogroups identified by mtDNA. The node ages calculated using mtDNA were consistent with the available paleontological data, whereas individual nuclear loci and multilocus species trees appeared to underestimate node ages. We argue that mtDNA is capable of discovering independent evolutionary units within avian taxa and can provide a reasonable phylogeographic hypothesis when geographic scale, geologic history, and phenotypic variation in the study system are too complex for proposing reasonable a priori hypotheses required for multilocus methods. Finally, we suggest splitting the currently recognized horned lark into five Palearctic and one Nearctic species. PMID:24498139

Variability in vegetation effects on density and nesting success of grassland birds

USGS Publications Warehouse

Winter, Maiken; Johnson, Douglas H.; Shaffer, Jill A.

2005-01-01

The structure of vegetation in grassland systems, unlike that in forest systems, varies dramatically among years on the same sites, and among regions with similar vegetation. The role of this variation in vegetation structure on bird density and nesting success of grassland birds is poorly understood, primarily because few studies have included sufficiently large temporal and spatial scales to capture the variation in vegetation structure, bird density, or nesting success. To date, no large-scale study on grassland birds has been conducted to investigate whether grassland bird density and nesting success respond similarly to changes in vegetation structure. However, reliable management recommendations require investigations into the distribution and nesting success of grassland birds over larger temporal and spatial scales. In addition, studies need to examine whether bird density and nesting success respond similarly to changing environmental conditions. We investigated the effect of vegetation structure on the density and nesting success of 3 grassland-nesting birds: clay-colored sparrow (Spizella pallida), Savannah sparrow (Passerculus sandwichensis), and bobolink (Dolichonyx oryzivorus) in 3 regions of the northern tallgrass prairie in 1998-2001. Few vegetation features influenced the densities of our study species, and each species responded differently to those vegetation variables. We could identify only 1 variable that clearly influenced nesting success of 1 species: clay-colored sparrow nesting success increased with increasing percentage of nest cover from the surrounding vegetation. Because responses of avian density and nesting success to vegetation measures varied among regions, years, and species, land managers at all times need to provide grasslands with different types of vegetation structure. Management guidelines developed from small-scale, short-term studies may lead to misrepresentations of the needs of grassland-nesting birds.

SYSTEMATIC AND STOCHASTIC VARIATIONS IN PULSAR DISPERSION MEASURES

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

Lam, M. T.; Cordes, J. M.; Chatterjee, S.

2016-04-10

We analyze deterministic and random temporal variations in the dispersion measure (DM) from the full three-dimensional velocities of pulsars with respect to the solar system, combined with electron-density variations over a wide range of length scales. Previous treatments have largely ignored pulsars’ changing distances while favoring interpretations involving changes in sky position from transverse motion. Linear trends in pulsar DMs observed over 5–10 year timescales may signify sizable DM gradients in the interstellar medium (ISM) sampled by the changing direction of the line of sight to the pulsar. We show that motions parallel to the line of sight can alsomore » account for linear trends, for the apparent excess of DM variance over that extrapolated from scintillation measurements, and for the apparent non-Kolmogorov scalings of DM structure functions inferred in some cases. Pulsar motions through atomic gas may produce bow-shock ionized gas that also contributes to DM variations. We discuss the possible causes of periodic or quasi-periodic changes in DM, including seasonal changes in the ionosphere, annual variations of the solar elongation angle, structure in the heliosphere and ISM boundary, and substructure in the ISM. We assess the solar cycle’s role on the amplitude of ionospheric and solar wind variations. Interstellar refraction can produce cyclic timing variations from the error in transforming arrival times to the solar system barycenter. We apply our methods to DM time series and DM gradient measurements in the literature and assess their consistency with a Kolmogorov medium. Finally, we discuss the implications of DM modeling in precision pulsar timing experiments.« less

Neural control and transient analysis of the LCL-type resonant converter

NASA Astrophysics Data System (ADS)

Zouggar, S.; Nait Charif, H.; Azizi, M.

2000-07-01

This paper proposes a generalised inverse learning structure to control the LCL converter. A feedforward neural network is trained to act as an inverse model of the LCL converter then both are cascaded such that the composed system results in an identity mapping between desired response and the LCL output voltage. Using the large signal model, we analyse the transient output response of the controlled LCL converter in the case of large variation of the load. The simulation results show the efficiency of using neural networks to regulate the LCL converter.

Evaluating Agronomic Performance and Investigating Molecular Structure of Drought and Heat Tolerant Wild Alfalfa (Medicago sativa L.) Collection from the Southeastern Turkey.

PubMed

Basbag, Mehmet; Aydin, Ali; Sakiroglu, Muhammet

2017-02-01

Drought is a major stress factor for agricultural production including alfalfa production. One way to counterbalance the yield losses is the introgression of drought tolerant germplasm into breeding programs. As an effort to exploit such germplasm, 16 individual plants were selected from the Southeastern Turkey from their natural habitat and clonally propagated in field trials with an ultimate goal to use the germplasm as parents for releasing a synthetic cultivar. Forage yield and forage quality traits were evaluated and molecular genetic diversity among genotypes were determined using inter simple sequence repeat markers. Genotypes showed a variation from growth habit to yield and quality traits indicating sufficient phenotypic variation for diverse breeding efforts (for grazing or harvesting) and long term selection schemes. A large amount of genetic variation was observed even with a limited number of marker and genotypes. However, no pattern of spatial genetic structure was observed for the scale of the study when genetic variation is linked to the geographic origin. We conclude that ex situ natural variation provides a wealth of germplasm that could be incorporated into breeding programs aiming to improve drought tolerance. We also suggest an extensive collection of seeds/plant tissue from unique plants with desirable traits rather than putting more efforts to create a spatial germplasm sampling efforts in narrow regions.

Relative contributions of neutral and non-neutral genetic differentiation to inform conservation of steelhead trout across highly variable landscapes

PubMed Central

Matala, Andrew P; Ackerman, Michael W; Campbell, Matthew R; Narum, Shawn R

2014-01-01

Mounting evidence of climatic effects on riverine environments and adaptive responses of fishes have elicited growing conservation concerns. Measures to rectify population declines include assessment of local extinction risk, population ecology, viability, and genetic differentiation. While conservation planning has been largely informed by neutral genetic structure, there has been a dearth of critical information regarding the role of non-neutral or functional genetic variation. We evaluated genetic variation among steelhead trout of the Columbia River Basin, which supports diverse populations distributed among dynamic landscapes. We categorized 188 SNP loci as either putatively neutral or candidates for divergent selection (non-neutral) using a multitest association approach. Neutral variation distinguished lineages and defined broad-scale population structure consistent with previous studies, but fine-scale resolution was also detected at levels not previously observed. Within distinct coastal and inland lineages, we identified nine and 22 candidate loci commonly associated with precipitation or temperature variables and putatively under divergent selection. Observed patterns of non-neutral variation suggest overall climate is likely to shape local adaptation (e.g., potential rapid evolution) of steelhead trout in the Columbia River region. Broad geographic patterns of neutral and non-neutral variation demonstrated here can be used to accommodate priorities for regional management and inform long-term conservation of this species. PMID:25067950

Achievable flatness in a large microwave power transmitting antenna

NASA Technical Reports Server (NTRS)

Ried, R. C.

1980-01-01

A dual reference SPS system with pseudoisotropic graphite composite as a representative dimensionally stable composite was studied. The loads, accelerations, thermal environments, temperatures and distortions were calculated for a variety of operational SPS conditions along with statistical considerations of material properties, manufacturing tolerances, measurement accuracy and the resulting loss of sight (LOS) and local slope distributions. A LOS error and a subarray rms slope error of two arc minutes can be achieved with a passive system. Results show that existing materials measurement, manufacturing, assembly and alignment techniques can be used to build the microwave power transmission system antenna structure. Manufacturing tolerance can be critical to rms slope error. The slope error budget can be met with a passive system. Structural joints without free play are essential in the assembly of the large truss structure. Variations in material properties, particularly for coefficient of thermal expansion from part to part, is more significant than actual value.

Anisotropy of the Cosmic Microwave Background Radiation on Large and Medium Angular Scales

NASA Technical Reports Server (NTRS)

Houghton, Anthony; Timbie, Peter

1998-01-01

This grant has supported work at Brown University on measurements of the 2.7 K Cosmic Microwave Background Radiation (CMB). The goal has been to characterize the spatial variations in the temperature of the CMB in order to understand the formation of large-scale structure in the universe. We have concurrently pursued two measurements using millimeter-wave telescopes carried aloft by scientific balloons. Both systems operate over a range of wavelengths, chosen to allow spectral removal of foreground sources such as the atmosphere, Galaxy, etc. The angular resolution of approx. 25 arcminutes is near the angular scale at which the most structure is predicted by current models to be visible in the CMB angular power spectrum. The main goal is to determine the angular scale of this structure; in turn we can infer the density parameter, Omega, for the universe as well as other cosmological parameters, such as the Hubble constant.

Visualizing Structure and Dynamics of Disaccharide Simulations

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

Matthews, J. F.; Beckham, G. T.; Himmel, M. E.

2012-01-01

We examine the effect of several solvent models on the conformational properties and dynamics of disaccharides such as cellobiose and lactose. Significant variation in timescale for large scale conformational transformations are observed. Molecular dynamics simulation provides enough detail to enable insight through visualization of multidimensional data sets. We present a new way to visualize conformational space for disaccharides with Ramachandran plots.

Pretreatment variation in overstory and understory vegetation [Chapter 2

Treesearch

Richy J. Harrod; Erich Kyle Dodson; Nicholas A. Povak; David W. Peterson

2009-01-01

Changes in forest vegetation as a result of fire exclusion, sheep and cattle grazing, and large-tree logging have been well documented for western forests (Agee 1998; Arno et al. 1997; Covington and Moore 1994; Everett et al. 2000; Harrod et al. 1999; Hessburg and Agee 2003; Hessburg et al. 2000, 2005). These changes in forest structure and composition have...

The rotation of the sun - Observations at Stanford

NASA Technical Reports Server (NTRS)

Scherrer, P. H.; Wilcox, J. M.; Svalgaard, L.

1980-01-01

Daily observations of the photospheric rotation rate using the Doppler effect have been made at the Stanford Solar Observatory since May 1976. These observations show no daily or long-period variations in the rotation rate that exceed the observational error of about 1%. The average rotation rate is the same as that of the sunspots and the large-scale magnetic field structures.

Intraspecific variation in body size does not alter the effects of mesopredators on prey.

PubMed

Gallagher, Austin J; Brandl, Simon J; Stier, Adrian C

2016-12-01

As humans continue to alter the species composition and size structure of marine food webs, it is critical to understand size-dependent effects of predators on prey. Yet, how shifts in predator body size mediate the effect of predators is understudied in tropical marine ecosystems, where anthropogenic harvest has indirectly increased the density and size of small-bodied predators. Here, we combine field surveys and a laboratory feeding experiment in coral reef fish communities to show that small and large predators of the same species can have similar effects. Specifically, surveys show that the presence of a small predator ( Paracirrhites arcatus ) was correlated with lower chances of prey fish presence, but these correlations were independent of predator size. Experimental trials corroborated the size-independent effect of the predator; attack rates were indistinguishable between small and large predators, suggesting relatively even effects of hawkfish in various size classes on the same type of prey. Our results indicate that the effects of small predators on coral reefs can be size-independent, suggesting that variation in predator size-structure alone may not always affect the functional role of these predators.

Variations in abundance, diversity and community composition of airborne fungi in swine houses across seasons

NASA Astrophysics Data System (ADS)

Kumari, Priyanka; Woo, Cheolwoon; Yamamoto, Naomichi; Choi, Hong-Lim

2016-11-01

We examined the abundance, diversity and community composition of airborne fungi in swine houses during winter and summer seasons by using quantitative PCR and Illumina HiSeq sequencing of ITS1 region. The abundance of airborne fungi varied significantly only between seasons, while fungal diversity varied significantly both within and between seasons, with both abundance and diversity peaked in winter. The fungal OTU composition was largely structured by the swine house unit and season as well as by their interactions. Of the measured microclimate variables, relative humidity, particulate matters (PMs), ammonia, and stocking density were significantly correlated with fungal OTU composition. The variation in beta diversity was higher within swine houses during summer, which indicates that the airborne fungal community composition was more heterogeneous in summer compared to winter. We also identified several potential allergen/pathogen related fungal genera in swine houses. The total relative abundance of potential allergen/pathogen related fungal genera varied between swine houses in both seasons, and showed positive correlation with PM2.5. Overall, our findings show that the abundance, diversity and composition of airborne fungi are highly variable in swine houses and to a large extent structured by indoor microclimate variables of swine houses.

Shape coexistence, shape evolution and Gamow-Teller {beta}-decay of neutron-rich A Asymptotically-Equal-To 100 nuclei

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

Petrovici, A.; Schmid, K. W.; Faessler, A.

The structure of neutron-rich nuclei in the A Asymptotically-Equal-To 100 mass region relevant for the astrophysical r process manifests drastic changes in some isotopic chains and often sudden variations of particular nuclear properties have been identified. For a realistic description of the evolution in structure with increasing energy, spin, and isospin determined by shape coexistence and mixing beyond-mean-field approaches are required. Our recent studies represent an attempt to the self-consistent description of the shape coexistence phenomena in neutron-rich A Asymptotically-Equal-To 100 nuclei within the complex Excited Vampir variational model with symmetry projection before variation using a realistic effective interaction basedmore » on the Bonn A potential in a large model space. Results concerning the triple shape coexistence and the shape evolution in the N=58 Sr and Zr isotopes, the shape evolution in a chain of Zr nuclei, as well as the Gamow-Teller {beta}-decay properties of neutron-rich Zr and Tc nuclei are presented.« less

Temporal variation in leaf nitrogen partitioning of a broad-leaved evergreen tree, Quercus myrsinaefolia.

PubMed

Yasumura, Yuko; Ishida, Atsushi

2011-01-01

We examined temporal changes in the amount of nitrogenous compounds in leaves from the outer and inner parts of the crown of Quercus myrsinaefolia growing in a seasonal climate. Throughout the leaf life span, metabolic protein and Rubisco content closely correlated with total nitrogen content, while structural protein content was relatively stable after full leaf expansion. Chlorophyll content was affected by shading as well as total nitrogen content in outer leaves that were overtopped by new shoots in the second year. Outer leaves showed a large seasonal variation in photosynthetic nitrogen-use efficiency (PNUE; the light-saturated photosynthetic rate per unit leaf nitrogen content) during the first year of their life, with PNUE decreasing from the peak in summer towards winter. Outer and inner leaves both showed age-related decline in PNUE in the second year. There were no such drastic changes in leaf nitrogen partitioning that could explain seasonal and yearly variations in PNUE. Nitrogen resorption occurred in overwintering leaves in spring. Metabolic protein explained the majority of nitrogen being resorbed, whereas structural protein, which was low in degradability, contributed little to nitrogen resorption.

Diversity of bile salts in fish and amphibians: evolution of a complex biochemical pathway.

PubMed

Hagey, Lee R; Møller, Peter R; Hofmann, Alan F; Krasowski, Matthew D

2010-01-01

Bile salts are the major end metabolites of cholesterol and are also important in lipid and protein digestion, as well as shaping of the gut microflora. Previous studies had demonstrated variation of bile salt structures across vertebrate species. We greatly extend prior surveys of bile salt variation in fish and amphibians, particularly in analysis of the biliary bile salts of Agnatha and Chondrichthyes. While there is significant structural variation of bile salts across all fish orders, bile salt profiles are generally stable within orders of fish and do not correlate with differences in diet. This large data set allowed us to infer evolutionary changes in the bile salt synthetic pathway. The hypothesized ancestral bile salt synthetic pathway, likely exemplified in extant hagfish, is simpler and much shorter than the pathway of most teleost fish and terrestrial vertebrates. Thus, the bile salt synthetic pathway has become longer and more complex throughout vertebrate evolution. Analysis of the evolution of bile salt synthetic pathways provides a rich model system for the molecular evolution of a complex biochemical pathway in vertebrates.

Sequence variation and structural conservation allows development of novel function and immune evasion in parasite surface protein families

PubMed Central

Higgins, Matthew K; Carrington, Mark

2014-01-01

Trypanosoma and Plasmodium species are unicellular, eukaryotic pathogens that have evolved the capacity to survive and proliferate within a human host, causing sleeping sickness and malaria, respectively. They have very different survival strategies. African trypanosomes divide in blood and extracellular spaces, whereas Plasmodium species invade and proliferate within host cells. Interaction with host macromolecules is central to establishment and maintenance of an infection by both parasites. Proteins that mediate these interactions are under selection pressure to bind host ligands without compromising immune avoidance strategies. In both parasites, the expansion of genes encoding a small number of protein folds has established large protein families. This has permitted both diversification to form novel ligand binding sites and variation in sequence that contributes to avoidance of immune recognition. In this review we consider two such parasite surface protein families, one from each species. In each case, known structures demonstrate how extensive sequence variation around a conserved molecular architecture provides an adaptable protein scaffold that the parasites can mobilise to mediate interactions with their hosts. PMID:24442723

Decoupling Contributions from Canopy Structure and Leaf Optics is Critical for Remote Sensing Leaf Biochemistry (Reply to Townsend, et al.)

NASA Technical Reports Server (NTRS)

Knyazikhin, Yuri; Lewis, Philip; Disney, Mathias I.; Stenberg, Pauline; Mottus, Matti; Rautianinen, Miina; Kaufmann, Robert K.; Marshak, Alexander; Schull, Mitchell A.; Carmona, Pedro Latorre;

Extensive lava flow fields on Venus: Preliminary investigation of source elevation and regional slope variations

NASA Technical Reports Server (NTRS)

Magee-Roberts, K.; Head, James W., III; Lancaster, M. G.

1992-01-01

Large-volume lava flow fields have been identified on Venus, the most areally extensive of which are known as fluctus and have been subdivided into six morphologic types. Sheetlike flow fields (Type 1) lack the numerous, closely spaced, discrete lava flow lobes that characterize digitate flow fields. Transitional flow fields (Type 2) are similar to sheetlike flow fields but contain one or more broad flow lobes. Digitate flow fields are divided further into divergent (Types 3-5) and subparallel (Type 6) classes on the basis of variations in the amount of downstream flow divergence. As a result of our previous analysis of the detailed morphology, stratigraphy, and tectonic associations of Mylitta Fluctus, we have formulated a number of questions to apply to all large flow fields on Venus. In particular, we would like to address the following: (1) eruption conditions and style of flow emplacement (effusion rate, eruption duration), (2) the nature of magma storage zones (presence of neutral buoyancy zones, deep or shallow crustal magma chambers), (3) the origin of melt and possible link to mantle plumes, and (4) the importance of large flow fields in plains evolution. To answer these questions we have begun to examine variations in flow field dimension and morphology; the distribution of large flow fields in terms of elevation above the mean planetary radius; links to regional tectonic or volcanic structures (e.g., associations with large shield edifices, coronae, or rift zones); statigraphic relationships between large flow fields, volcanic plains, shields, and coronae; and various models of flow emplacement in order to estimate eruption parameters. In this particular study, we have examined the proximal elevations and topographic slopes of 16 of the most distinctive flow fields that represent each of the 6 morphologic types.

2.5D global-disk oscillation models of the Be shell star ζ Tauri. I. Spectroscopic and polarimetric analysis

NASA Astrophysics Data System (ADS)

Escolano, C.; Carciofi, A. C.; Okazaki, A. T.; Rivinius, T.; Baade, D.; Štefl, S.

2015-04-01

Context. A large number of Be stars exhibit intensity variations of their violet and red emission peaks in their H i lines observed in emission. This is the so-called V/R phenomenon, usually explained by the precession of a one-armed spiral density perturbation in the circumstellar disk. That global-disk oscillation scenario was confirmed, both observationally and theoretically, in the previous series of two papers analyzing the Be shell star ζ Tauri. The vertically averaged (2D) global-disk oscillation model used at the time was able to reproduce the V/R variations observed in Hα, as well as the spatially resolved interferometric data from AMBER/VLTI. Unfortunately, that model failed to reproduce the V/R phase of Br15 and the amplitude of the polarization variation, suggesting that the inner disk structure predicted by the model was incorrect. Aims: The first aim of the present paper is to quantify the temporal variations of the shell-line characteristics of ζ Tauri. The second aim is to better understand the physics underlying the V/R phenomenon by modeling the shell-line variations together with the V/R and polarimetric variations. The third aim is to test a new 2.5D disk oscillation model, which solves the set of equations that describe the 3D perturbed disk structure but keeps only the equatorial (i.e., 2D) component of the solution. This approximation was adopted to allow comparisons with the previous 2D model, and as a first step toward a future 3D model. Methods: We carried out an extensive analysis of ζ Tauri's spectroscopic variations by measuring various quantities characterizing its Balmer line profiles: red and violet emission peak intensities (for Hα, Hβ, and Br15), depth and asymmetry of the shell absorption (for Hβ, Hγ, and Hδ), and the respective position (i.e., radial velocity) of each component. We attempted to model the observed variations by implementing in the radiative transfer code HDUST the perturbed disk structure computed with a recently developed 2.5D global-disk oscillation model. Results: The observational analysis indicates that the peak separation and the position of the shell absorption both exhibit variations following the V/R variations and, thus, may provide good diagnostic tools of the global-disk oscillation phenomenon. The shell absorption seems to become slightly shallower close to the V/R maximum, but the scarcity of the data does not allow the exact pattern to be identified. The asymmetry of the shell absorption does not seem to correlate with the V/R cycle; no significant variations of this parameter are observed, except during certain periods where Hα and Hβ exhibit perturbed emission profiles. The origin of these so-called triple-peak phases remains unknown. On the theoretical side, the new 2.5D formalism appears to improve the agreement with the observed V/R variations of Hα and Br15, under the proviso that a large value of the viscosity parameter, α = 0.8, be adopted. It remains challenging for the models to reproduce consistently the amplitude and the average level of the polarization data. The 2D formalism provides a better match to the peak separation, although the variation amplitude predicted by both the 2D and 2.5D models is smaller than the observed value. Shell-line variations are difficult for the models to reproduce, whatever formalism is adopted. Appendices are available in electronic form at http://www.aanda.org

Geographical Genomics of Human Leukocyte Gene Expression Variation in Southern Morocco

PubMed Central

Idaghdour, Youssef; Czika, Wendy; Shianna, Kevin V.; Lee, S. Hong; Visscher, Peter M.; Martin, Hilary C.; Miclaus, Kelci; Jadallah, Sami J.; Goldstein, David B.; Wolfinger, Russell D.; Gibson, Greg

2009-01-01

Studies of the genetics of gene expression reveal expression SNPs that explain variation in transcript abundance. Here we address the robustness of eSNP associations to environmental geography and population structure in a comparison of 194 Arab and Amazigh individuals from a city and two villages in southern Morocco. Gene expression differed between pairs of locations for up to a third of all transcripts, with notable enrichment for ribosomal biosynthesis and oxidative phosphorylation. Robust associations were observed in the leukocyte samples with cis-eSNPs (P < 10−08) for 346 genes, and trans-eSNPs (P < 10−11) with 10 genes. All of these were consistent across the three sample locations and after controlling for ethnicity and relatedness. No evidence for large-effect trans-acting mediators of the pervasive environmental influence was found and instead genetic and environmental factors acted in a largely additive manner. PMID:19966804

Search for the 700,000-year-old source crater of the Australasian tektite strewn field

NASA Technical Reports Server (NTRS)

Schnetzler, C. C.; Garvin, J. B.

1992-01-01

Many tektite investigations have hypothesized that the impact crater that was the source of the extensive Australasian strewn field lies somewhere in or near Indochina. This is due to variations in abundance and size of tektites across the strewn field, variation of thickness of microtektite layers in ocean cores, nature and ablation characteristics across the field, and, above all, the occurrence of the large, blocky, layered Muong Nong-type tektites in Indochina. A recent study of the location and chemistry of Muong Nong-type and splash-form tektites suggests that the source region can be further narrowed to a limited area in eastern Thailand and southern Loas. Satellite multispectral imagery, a digital elevation dataset, and maps showing drainage patterns were used to search within this area for possible anomalous features that may be large degraded impact craters. Four interesting structures were identified from these datasets, and they are presented.

Overview of Sea-Ice Properties, Distribution and Temporal Variations, for Application to Ice-Atmosphere Chemical Processes.

NASA Astrophysics Data System (ADS)

Moritz, R. E.

2005-12-01

The properties, distribution and temporal variation of sea-ice are reviewed for application to problems of ice-atmosphere chemical processes. Typical vertical structure of sea-ice is presented for different ice types, including young ice, first-year ice and multi-year ice, emphasizing factors relevant to surface chemistry and gas exchange. Time average annual cycles of large scale variables are presented, including ice concentration, ice extent, ice thickness and ice age. Spatial and temporal variability of these large scale quantities is considered on time scales of 1-50 years, emphasizing recent and projected changes in the Arctic pack ice. The amount and time evolution of open water and thin ice are important factors that influence ocean-ice-atmosphere chemical processes. Observations and modeling of the sea-ice thickness distribution function are presented to characterize the range of variability in open water and thin ice.

The effects of season and sand mining activities on thermal regime and water quality in a large shallow tropical lake.

PubMed

Sharip, Zati; Zaki, Ahmad Taqiyuddin Ahmad

2014-08-01

Thermal structure and water quality in a large and shallow lake in Malaysia were studied between January 2012 and June 2013 in order to understand variations in relation to water level fluctuations and in-stream mining activities. Environmental variables, namely temperature, turbidity, dissolved oxygen, pH, electrical conductivity, chlorophyll-A and transparency, were measured using a multi-parameter probe and a Secchi disk. Measurements of environmental variables were performed at 0.1 m intervals from the surface to the bottom of the lake during the dry and wet seasons. High water level and strong solar radiation increased temperature stratification. River discharges during the wet season, and unsustainable sand mining activities led to an increased turbidity exceeding 100 NTU, and reduced transparency, which changed the temperature variation and subsequently altered the water quality pattern.

Banana production systems: identification of alternative systems for more sustainable production.

PubMed

Bellamy, Angelina Sanderson

2013-04-01

Large-scale, monoculture production systems dependent on synthetic fertilizers and pesticides, increase yields, but are costly and have deleterious impacts on human health and the environment. This research investigates variations in banana production practices in Costa Rica, to identify alternative systems that combine high productivity and profitability, with reduced reliance on agrochemicals. Farm workers were observed during daily production activities; 39 banana producers and 8 extension workers/researchers were interviewed; and a review of field experiments conducted by the National Banana Corporation between 1997 and 2002 was made. Correspondence analysis showed that there is no structured variation in large-scale banana producers' practices, but two other banana production systems were identified: a small-scale organic system and a small-scale conventional coffee-banana intercropped system. Field-scale research may reveal ways that these practices can be scaled up to achieve a productive and profitable system producing high-quality export bananas with fewer or no pesticides.

Biodiversity of Costa Rican salamanders: Implications of high levels of genetic differentiation and phylogeographic structure for species formation

PubMed Central

García-París, Mario; Good, David A.; Parra-Olea, Gabriela; Wake, David B.

2000-01-01

Although salamanders are characteristic amphibians in Holarctic temperate habitats, in tropical regions they have diversified evolutionarily only in tropical America. An adaptive radiation centered in Middle America occurred late in the history of a single clade, the supergenus Bolitoglossa (Plethodontidae), and large numbers of species now occur in diverse habitats. Sublineages within this clade decrease in number from the northern to southern parts of Middle America, and in Costa Rica, there are but three. Despite this phylogenetic constraint, Costa Rica has many species; the number of salamander species on one local elevational transect in the Cordillera de Talamanca may be the largest for any such transect in the world. Extraordinary variation in sequences of the mitochondrial gene cytochrome b within a clade of the genus Bolitoglossa in Costa Rica reveals strong phylogeographic structure within a single species, Bolitoglossa pesrubra. Allozymic variation in 19 proteins reveals a pattern largely concordant with the mitochondrial DNA phylogeography. More species exist than are currently recognized. Diversification occurs in restricted geographic areas and involves sharp geographic and elevational differentiation and zonation. In their degree of genetic differentiation at a local scale, these species of the deep tropics exceed the known variation of extratropical salamanders, which also differ in being less restricted in elevational range. Salamanders display “tropicality” in that although speciose, they are usually local in distribution and rare. They display strong ecological and physiological differentiation that may contribute importantly to morphological divergence and species formation. PMID:10677512

Conditional Random Fields for Fast, Large-Scale Genome-Wide Association Studies

PubMed Central

Huang, Jim C.; Meek, Christopher; Kadie, Carl; Heckerman, David

2011-01-01

Understanding the role of genetic variation in human diseases remains an important problem to be solved in genomics. An important component of such variation consist of variations at single sites in DNA, or single nucleotide polymorphisms (SNPs). Typically, the problem of associating particular SNPs to phenotypes has been confounded by hidden factors such as the presence of population structure, family structure or cryptic relatedness in the sample of individuals being analyzed. Such confounding factors lead to a large number of spurious associations and missed associations. Various statistical methods have been proposed to account for such confounding factors such as linear mixed-effect models (LMMs) or methods that adjust data based on a principal components analysis (PCA), but these methods either suffer from low power or cease to be tractable for larger numbers of individuals in the sample. Here we present a statistical model for conducting genome-wide association studies (GWAS) that accounts for such confounding factors. Our method scales in runtime quadratic in the number of individuals being studied with only a modest loss in statistical power as compared to LMM-based and PCA-based methods when testing on synthetic data that was generated from a generalized LMM. Applying our method to both real and synthetic human genotype/phenotype data, we demonstrate the ability of our model to correct for confounding factors while requiring significantly less runtime relative to LMMs. We have implemented methods for fitting these models, which are available at http://www.microsoft.com/science. PMID:21765897

Neuronal correlates of the five factor model (FFM) of human personality: Multimodal imaging in a large healthy sample.

PubMed

Bjørnebekk, Astrid; Fjell, Anders M; Walhovd, Kristine B; Grydeland, Håkon; Torgersen, Svenn; Westlye, Lars T

2013-01-15

Advances in neuroimaging techniques have recently provided glimpse into the neurobiology of complex traits of human personality. Whereas some intriguing findings have connected aspects of personality to variations in brain morphology, the relations are complex and our current understanding is incomplete. Therefore, we aimed to provide a comprehensive investigation of brain-personality relations using a multimodal neuroimaging approach in a large sample comprising 265 healthy individuals. The NEO Personality Inventory was used to provide measures of core aspects of human personality, and imaging phenotypes included measures of total and regional brain volumes, regional cortical thickness and arealization, and diffusion tensor imaging indices of white matter (WM) microstructure. Neuroticism was the trait most clearly linked to brain structure. Higher neuroticism including facets reflecting anxiety, depression and vulnerability to stress was associated with smaller total brain volume, widespread decrease in WM microstructure, and smaller frontotemporal surface area. Higher scores on extraversion were associated with thinner inferior frontal gyrus, and conscientiousness was negatively associated with arealization of the temporoparietal junction. No reliable associations between brain structure and agreeableness and openness, respectively, were found. The results provide novel evidence of the associations between brain structure and variations in human personality, and corroborate previous findings of a consistent neuroanatomical basis of negative emotionality. Copyright © 2012 Elsevier Inc. All rights reserved.

Crystal Structure Variations of Sn Nanoparticles upon Heating

NASA Astrophysics Data System (ADS)

Mittal, Jagjiwan; Lin, Kwang-Lung

2018-04-01

Structural changes in Sn nanoparticles during heating below the melting point have been investigated using differential scanning calorimetry (DSC), x-ray diffraction (XRD) analysis, electron diffraction (ED), and high-resolution transmission electron microscopy (HRTEM). DSC revealed that the heat required to melt the nanoparticles (28.43 J/g) was about half compared with Sn metal (52.80 J/g), which was attributed to the large surface energy contribution for the nanoparticles. ED and XRD analyses of the Sn nanoparticles revealed increased intensity for crystal planes having large interplaner distances compared with regular crystal planes with increasing heat treatment temperature (HTT). HRTEM revealed an increase in interlayer spacing at the surface and near joints between nanoparticles with the HTT, leading to an amorphous structure of nanoparticles at the surface at 220°C. These results highlight the changes that occur in the morphology and crystal structure of Sn nanoparticles at the surface and in the interior with increase of the heat treatment temperature.

Molecularly "engineered" anode adsorbates for probing OLED interfacial structure-charge injection/luminance relationships: large, structure-dependent effects.

PubMed

Huang, Qinglan; Evmenenko, Guennadi; Dutta, Pulak; Marks, Tobin J

2003-12-03

Molecule-scale structure effects at organic light-emitting diodes (OLED) anode-organic transport layer interfaces are probed via a self-assembly approach. A series of ITO anode-linked silyltriarylamine molecules differing in aryl group and linker density are synthesized for this purpose and used to probe the relationship between nanoscale interfacial chemical structure, charge injection and electroluminescence properties. Dramatic variations in hole injection magnitude and OLED performance can be correlated with the molecular structures and electrochemically derived heterogeneous electron-transfer rates of such triarylamine fragments, placed precisely at the anode-hole transport layer interface. Very bright and efficient ( approximately 70 000 cd/m2 and approximately 2.5% forward external quantum efficiency) OLEDs have thereby been fabricated.

Structure of the Epiphyte Community in a Tropical Montane Forest in SW China

PubMed Central

Zhao, Mingxu; Geekiyanage, Nalaka; Xu, Jianchu; Khin, Myo Myo; Nurdiana, Dian Ridwan; Paudel, Ekananda; Harrison, Rhett Daniel

2015-01-01

Vascular epiphytes are an understudied and particularly important component of tropical forest ecosystems. However, owing to the difficulties of access, little is known about the properties of epiphyte-host tree communities and the factors structuring them, especially in Asia. We investigated factors structuring the vascular epiphyte-host community and its network properties in a tropical montane forest in Xishuangbanna, SW China. Vascular epiphytes were surveyed in six plots located in mature forests. Six host and four micro-site environmental factors were investigated. Epiphyte diversity was strongly correlated with host size (DBH, diameter at breast height), while within hosts the highest epiphyte diversity was in the middle canopy and epiphyte diversity was significantly higher in sites with canopy soil or a moss mat than on bare bark. DBH, elevation and stem height explained 22% of the total variation in the epiphyte species assemblage among hosts, and DBH was the most important factor which alone explained 6% of the variation. Within hosts, 51% of the variation in epiphyte assemblage composition was explained by canopy position and substrate, and the most important single factor was substrate which accounted for 16% of the variation. Analysis of network properties indicated that the epiphyte host community was highly nested, with a low level of epiphyte specialization, and an almost even interaction strength between epiphytes and host trees. Together, these results indicate that large trees harbor a substantial proportion of the epiphyte community in this forest. PMID:25856457

Absence of geographical structure of chloroplast DNA variation in sallow, Salix caprea L.

PubMed

Palmé, A E; Semerikov, V; Lascoux, M

2003-11-01

In the present study, we have used PCR-RFLP markers to investigate the chloroplast DNA variation in 24 European populations of Salix caprea L. A subset of these populations has also been analysed with chloroplast microsatellites. The main feature of both markers is the absence of a clear geographic structure (G(ST(PCR-RFLP))=0.090, G(ST(microsatellites))=-0.017) and high levels of variation within populations. This lack of phylogeographic structure in S. caprea is suggested to be the consequence of the joint action of several factors: (i) presence of intermediate latitude refugia with large population sizes during the last glacial maximum, (ii) a high speed of recolonisation and dispersal ability, (iii) a high mutation rate and (iv) extensive hybridisation with other willow species. In addition to the S. caprea samples, a limited number of individuals from several other Salix species were also analysed with PCR-RFLP: S. cinerea, S. aurita, S. purpurea, S. atrocinerea, S. appendiculata, S. elaeagnos, S. fragilis and S. alba. Many of the haplotypes found in Salix caprea were also detected in S. cinerea, S. aurita, S. purpurea, S. atrocinerea and/ or S. appendiculata but not in S. alba, S. elaeagnos or S. fragilis. Our data suggest that hybridisation and gene flow have occurred within these two groups but not between them.

What Drives National Differences in Intensive Grandparental Childcare in Europe?

PubMed Central

Glaser, Karen; Price, Debora; Ribe, Eloi; Tinker, Anthea

2016-01-01

Objectives. Grandparents play an important role in looking after grandchildren, although intensive grandparental childcare varies considerably across Europe. Few studies have explicitly investigated the extent to which such cross-national variations are associated with national level differences in individual demographic and socio-economic distributions along with contextual-structural and cultural factors (e.g., variations in female labor force participation, childcare provision, and cultural attitudes). Methods. We used multilevel models to examine associations between intensive grandparental childcare and contextual-structural and cultural factors, after controlling for grandparent, parent, and child characteristics using nationally representative data from the Survey of Health, Ageing and Retirement in Europe. Results. Even controlling for cross-national differences in demographic and socio-economic distributions, contextual-structural factors play an important role in explaining grandparental childcare variations in Europe. In particular, higher levels of intensive grandparental childcare are found in countries with low labor force participation among younger and older women, and low formal childcare provision, where mothers in paid work largely rely on grandparental support on an almost daily basis. Discussion. Encouraging older women to remain in paid work is likely to have an impact on grandchild care which in turn may affect mothers’ employment, particularly in Southern European countries where there is little formal childcare. PMID:25783973

Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21.

PubMed

Patil, N; Berno, A J; Hinds, D A; Barrett, W A; Doshi, J M; Hacker, C R; Kautzer, C R; Lee, D H; Marjoribanks, C; McDonough, D P; Nguyen, B T; Norris, M C; Sheehan, J B; Shen, N; Stern, D; Stokowski, R P; Thomas, D J; Trulson, M O; Vyas, K R; Frazer, K A; Fodor, S P; Cox, D R

2001-11-23

Global patterns of human DNA sequence variation (haplotypes) defined by common single nucleotide polymorphisms (SNPs) have important implications for identifying disease associations and human traits. We have used high-density oligonucleotide arrays, in combination with somatic cell genetics, to identify a large fraction of all common human chromosome 21 SNPs and to directly observe the haplotype structure defined by these SNPs. This structure reveals blocks of limited haplotype diversity in which more than 80% of a global human sample can typically be characterized by only three common haplotypes.

Optimal placement of excitations and sensors for verification of large dynamical systems

NASA Technical Reports Server (NTRS)

Salama, M.; Rose, T.; Garba, J.

1987-01-01

The computationally difficult problem of the optimal placement of excitations and sensors to maximize the observed measurements is studied within the framework of combinatorial optimization, and is solved numerically using a variation of the simulated annealing heuristic algorithm. Results of numerical experiments including a square plate and a 960 degrees-of-freedom Control of Flexible Structure (COFS) truss structure, are presented. Though the algorithm produces suboptimal solutions, its generality and simplicity allow the treatment of complex dynamical systems which would otherwise be difficult to handle.

Genome Reduction Uncovers a Large Dispensable Genome and Adaptive Role for Copy Number Variation in Asexually Propagated Solanum tuberosum[OPEN

PubMed Central

Hardigan, Michael A.; Crisovan, Emily; Hamilton, John P.; Laimbeer, Parker; Leisner, Courtney P.; Manrique-Carpintero, Norma C.; Newton, Linsey; Pham, Gina M.; Vaillancourt, Brieanne; Zeng, Zixian; Jiang, Jiming

2016-01-01

Clonally reproducing plants have the potential to bear a significantly greater mutational load than sexually reproducing species. To investigate this possibility, we examined the breadth of genome-wide structural variation in a panel of monoploid/doubled monoploid clones generated from native populations of diploid potato (Solanum tuberosum), a highly heterozygous asexually propagated plant. As rare instances of purely homozygous clones, they provided an ideal set for determining the degree of structural variation tolerated by this species and deriving its minimal gene complement. Extensive copy number variation (CNV) was uncovered, impacting 219.8 Mb (30.2%) of the potato genome with nearly 30% of genes subject to at least partial duplication or deletion, revealing the highly heterogeneous nature of the potato genome. Dispensable genes (>7000) were associated with limited transcription and/or a recent evolutionary history, with lower deletion frequency observed in genes conserved across angiosperms. Association of CNV with plant adaptation was highlighted by enrichment in gene clusters encoding functions for environmental stress response, with gene duplication playing a part in species-specific expansions of stress-related gene families. This study revealed unique impacts of CNV in a species with asexual reproductive habits and how CNV may drive adaption through evolution of key stress pathways. PMID:26772996

Numerical Study of the Response of an Atmospheric Surface Layer to a Spatially Nonuniform Plant Canopy

NASA Astrophysics Data System (ADS)

Qiu, J.; Gu, Z. L.; Wang, Z. S.

2008-05-01

High-accuracy large-eddy simulations of neutral atmospheric surface-layer flow over a gapped plant canopy strip have been performed. Subgrid-scale (SGS) motions are parameterized by the Sagaut mixed length SGS model, with a modification to compute the SGS characteristic length self-adaptively. Shaw’s plant canopy model, taking the vertical variation of leaf area density into account, is applied to study the response of the atmospheric surface layer to the gapped dense forest strip. Differences in the region far away from the gap and in the middle of the gap are investigated, according to the instantaneous velocity magnitude, the zero-plane displacement, the potential temperature and the streamlines. The large-scale vortex structure, in the form of a roll vortex, is revealed in the region far away from the gap. The nonuniform spatial distribution of plants appears to cause the formation of the coherent structure. The roll vortex starts in the wake of the canopy, and results in strong fluctuations throughout the entire canopy region. Wind sweeps and ejections in the plant canopy are also attributed to the large vortex structure.

Preservation of large-scale chromatin structure in FISH experiments

PubMed Central

Hepperger, Claudia; Otten, Simone; von Hase, Johann

2006-01-01

The nuclear organization of specific endogenous chromatin regions can be investigated only by fluorescence in situ hybridization (FISH). One of the two fixation procedures is typically applied: (1) buffered formaldehyde or (2) hypotonic shock with methanol acetic acid fixation followed by dropping of nuclei on glass slides and air drying. In this study, we compared the effects of these two procedures and some variations on nuclear morphology and on FISH signals. We analyzed mouse erythroleukemia and mouse embryonic stem cells because their clusters of subcentromeric heterochromatin provide an easy means to assess preservation of chromatin. Qualitative and quantitative analyses revealed that formaldehyde fixation provided good preservation of large-scale chromatin structures, while classical methanol acetic acid fixation after hypotonic treatment severely impaired nuclear shape and led to disruption of chromosome territories, heterochromatin structures, and large transgene arrays. Our data show that such preparations do not faithfully reflect in vivo nuclear architecture. Electronic supplementary material Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00412-006-0084-2 and is accessible for authorized users. PMID:17119992

[Correlation of intraocular pressure variation after visual field examination with 24-hour intraocular pressure variations in primary open-angle glaucoma].

PubMed

Noro, Takahiko; Nakamoto, Kenji; Sato, Makoto; Yasuda, Noriko; Ito, Yoshinori; Ogawa, Shumpei; Nakano, Tadashi; Tsuneoka, Hiroshi

2014-10-01

We retrospectively examined intraocular pressure variations after visual field examination in primary open angle glaucoma (POAG), together with its influencing factors and its association with 24-hour intraocular pressure variations. Subjects were 94 eyes (52 POAG patients) subjected to measurements of 24-hour intraocular pressure and of changes in intraocular pressure after visual field examination using a Humphrey Visual Field Analyzer. Subjects were classified into three groups according to the magnitude of variation (large, intermediate and small), and 24-hour intraocular pressure variations were compared among the three groups. Factors influencing intraocular pressure variations after visual field examination and those associated with the large variation group were investigated. Average intraocular pressure variation after visual field examination was -0.28 ± 1.90 (range - 6.0(-) + 5.0) mmHg. No significant influencing factors were identified. The intraocular pressure at 3 a.m. was significantly higher in the large variation group than other two groups (p < 0.001). Central corneal thickness was correlated with the large variation group (odds ratio = 1.04; 95% confidence interval, 1.01-1.07 ; p = 0.02). No particular tendencies in intraocular pressure variations were found after visual field examination. Increases in intraocular pressure during the night might be associated with large intraocular pressure variations after visual field examination.

Macrophytes shape trophic niche variation among generalist fishes.

PubMed

Vejříková, Ivana; Eloranta, Antti P; Vejřík, Lukáš; Šmejkal, Marek; Čech, Martin; Sajdlová, Zuzana; Frouzová, Jaroslava; Kiljunen, Mikko; Peterka, Jiří

2017-01-01

Generalist species commonly have a fundamental role in ecosystems as they can integrate spatially distinct habitats and food-web compartments, as well as control the composition, abundance and behavior of organisms at different trophic levels. Generalist populations typically consist of specialized individuals, but the potential for and hence degree of individual niche variation can be largely determined by habitat complexity. We compared individual niche variation within three generalist fishes between two comparable lakes in the Czech Republic differing in macrophyte cover, i.e. macrophyte-rich Milada and macrophyte-poor Most. We tested the hypothesis that large individual niche variation among generalist fishes is facilitated by the presence of macrophytes, which provides niches and predation shelter for fish and their prey items. Based on results from stable nitrogen (δ15N) and carbon (δ13C) isotopic mixing models, perch (Perca fluviatilis L.) and rudd (Scardinius erythrophthalmus (L.)) showed larger individual variation (i.e., variance) in trophic position in Milada as compared to Most, whereas no significant between-lake differences were observed for roach (Rutilus rutilus (L.)). Contrary to our hypothesis, all the three species showed significantly lower individual variation in the relative reliance on littoral food resources in Milada than in Most. Rudd relied significantly more whereas perch and roach relied less on littoral food resources in Milada than in Most, likely due to prevalent herbivory by rudd and prevalent zooplanktivory by perch and roach in the macrophyte-rich Milada as compared to macrophyte-poor Most. Our study demonstrates how the succession of macrophyte vegetation, via its effects on the physical and biological complexity of the littoral zone and on the availability of small prey fish and zooplankton, can strongly influence individual niche variation among generalist fishes with different ontogenetic trajectories, and hence the overall food-web structures in lake ecosystems.

Strainmeters and tiltmeters in geophysics

NASA Technical Reports Server (NTRS)

Goulty, N. R.

1976-01-01

Several types of sensitive strainmeters and tiltmeters have been developed, and it is now becoming clear which geophysical applications are most suitable for these instruments. In general, strainmeters and tiltmeters are used for observing ground deformation at periods of minutes to days. Small-scale lateral inhomogeneities at the instrument sites distort signals by a few percent, although the effects of large structures can be calculated. In earth tide work these lateral inhomogeneities and unknown ocean loading signals prevent accurate values of the regional tide from being obtained. This limits tidal investigations to looking for temporal variations, possibly associated with pre-earthquake dilatancy, and spatial variations caused by gross elasticity contrasts in the local geological structure. Strainmeters and tiltmeters are well suited for observing long-period seismic waves, seismic slip events on faults and volcano tumescence, where small site-induced distortions in the measured signals are seldom important.

The structure of cross-cultural musical diversity.

PubMed

Rzeszutek, Tom; Savage, Patrick E; Brown, Steven

2012-04-22

Human cultural traits, such as languages, musics, rituals and material objects, vary widely across cultures. However, the majority of comparative analyses of human cultural diversity focus on between-culture variation without consideration for within-culture variation. In contrast, biological approaches to genetic diversity, such as the analysis of molecular variance (AMOVA) framework, partition genetic diversity into both within- and between-population components. We attempt here for the first time to quantify both components of cultural diversity by applying the AMOVA model to music. By employing this approach with 421 traditional songs from 16 Austronesian-speaking populations, we show that the vast majority of musical variability is due to differences within populations rather than differences between. This demonstrates a striking parallel to the structure of genetic diversity in humans. A neighbour-net analysis of pairwise population musical divergence shows a large amount of reticulation, indicating the pervasive occurrence of borrowing and/or convergent evolution of musical features across populations.

Isospin-symmetry-breaking effects in A˜70 nuclei within beyond-mean-field approach

NASA Astrophysics Data System (ADS)

Petrovici, A.; Andrei, O.

2015-02-01

Particular isospin-symmetry-breaking probes including Coulomb energy differences (CED), mirror energy differences (MED), and triplet energy differences (TED) manifest anomalies in the A˜70 isovector triplets of nuclei. The structure of proton-rich nuclei in the A˜70 mass region suggests shape coexistence and competition between pairing correlations in different channels. Recent results concerning the interplay between isospin-mixing and shape-coexistence effects on exotic phenomena in A˜70 nuclei obtained within the beyond-mean-field complex Excited Vampir variational model with symmetry projection before variation using a realistic effective interaction in a relatively large model space are presented. Excited Vampir predictions concerning the Gamow-Teller β decay to the odd-odd N=Z 66As and 70Br nuclei correlated with the pair structure analysis in the T=1 and T=0 channel of the involved wave functions are discussed.

Petrology of Impact-Melt Rocks at the Chicxulub Multiring Basin, Yucatan, Mexico

NASA Technical Reports Server (NTRS)

Schuraytz, Benjamin C.; Sharpton, Virgil L.; Marin, Luis E.

1994-01-01

Compositions and textures of melt rocks from the upper part of the Chicxulub structure are typical of melt rocks at other large terrestrial impact structures. Apart from variably elevated iridium concentrations (less than 1.5 to 13.5 +/- 0.9 ppb) indicating nonuniform dissemination of a meteoritic component, bulk rock and phenocryst compositions imply that these melt rocks were derived exclusively from continental crust and platform-sediment target lithologies. Modest differences in bulk chemistry among samples from wells located approximately 40 km apart suggest minor variations in relative contributions of these target lithologies to the melts. Subtle variations in the compositions of early-formed pyroxene and plagioclase also support minor primary differences in chemistry between the melts. Evidence for pervasive hydrothermal alteration of the porous mesostasis includes albite, K-feldspar, quartz, epidote, chlorite, and other phyllosilicates, as well as siderophile element-enriched sulfides, suggesting the possibility that Chicxulub, like Sudbury, may host important ore deposits.

Early stages of transition in viscosity-stratified channel flow

NASA Astrophysics Data System (ADS)

Govindarajan, Rama; Jose, Sharath; Brandt, Luca

2013-11-01

In parallel shear flows, it is well known that transition to turbulence usually occurs through a subcritical process. In this work we consider a flow through a channel across which there is a linear temperature variation. The temperature gradient leads to a viscosity variation across the channel. A large body of work has been done in the linear regime for this problem, and it has been seen that viscosity stratification can lead to considerable changes in stability and transient growth characteristics. Moreover contradictory effects of introducing a non uniform viscosity in the system have been reported. We conduct a linear stability analysis and direct numerical simulations (DNS) for this system. We show that the optimal initial structures in the viscosity-stratified case, unlike in unstratified flow, do not span the width of the channel, but are focussed near one wall. The nonlinear consequences of the localisation of the structures will be discussed.

The structure of cross-cultural musical diversity

PubMed Central

Rzeszutek, Tom; Savage, Patrick E.; Brown, Steven

2012-01-01

Human cultural traits, such as languages, musics, rituals and material objects, vary widely across cultures. However, the majority of comparative analyses of human cultural diversity focus on between-culture variation without consideration for within-culture variation. In contrast, biological approaches to genetic diversity, such as the analysis of molecular variance (AMOVA) framework, partition genetic diversity into both within- and between-population components. We attempt here for the first time to quantify both components of cultural diversity by applying the AMOVA model to music. By employing this approach with 421 traditional songs from 16 Austronesian-speaking populations, we show that the vast majority of musical variability is due to differences within populations rather than differences between. This demonstrates a striking parallel to the structure of genetic diversity in humans. A neighbour-net analysis of pairwise population musical divergence shows a large amount of reticulation, indicating the pervasive occurrence of borrowing and/or convergent evolution of musical features across populations. PMID:22072606

Prediction of solar energetic particle event histories using real-time particle and solar wind measurements

NASA Technical Reports Server (NTRS)

Roelof, E. C.; Gold, R. E.

1978-01-01

The comparatively well-ordered magnetic structure in the solar corona during the decline of Solar Cycle 20 revealed a characteristic dependence of solar energetic particle injection upon heliographic longitude. When analyzed using solar wind mapping of the large scale interplanetary magnetic field line connection from the corona to the Earth, particle fluxes display an approximately exponential dependence on heliographic longitude. Since variations in the solar wind velocity (and hence the coronal connection longitude) can severely distort the simple coronal injection profile, the use of real-time solar wind velocity measurements can be of great aid in predicting the decay of solar particle events. Although such exponential injection profiles are commonplace during 1973-1975, they have also been identified earlier in Solar Cycle 20, and hence this structure may be present during the rise and maximum of the cycle, but somewhat obscured by greater temporal variations in particle injection.

Isospin-symmetry-breaking effects in A∼70 nuclei within beyond-mean-field approach

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

Petrovici, A.; Andrei, O.

2015-02-24

Particular isospin-symmetry-breaking probes including Coulomb energy differences (CED), mirror energy differences (MED), and triplet energy differences (TED) manifest anomalies in the A∼70 isovector triplets of nuclei. The structure of proton-rich nuclei in the A∼70 mass region suggests shape coexistence and competition between pairing correlations in different channels. Recent results concerning the interplay between isospin-mixing and shape-coexistence effects on exotic phenomena in A∼70 nuclei obtained within the beyond-mean-field complex Excited Vampir variational model with symmetry projection before variation using a realistic effective interaction in a relatively large model space are presented. Excited Vampir predictions concerning the Gamow-Teller β decay to themore » odd-odd N=Z {sup 66}As and {sup 70}Br nuclei correlated with the pair structure analysis in the T=1 and T=0 channel of the involved wave functions are discussed.« less

A high-quality human reference panel reveals the complexity and distribution of genomic structural variants.

PubMed

Hehir-Kwa, Jayne Y; Marschall, Tobias; Kloosterman, Wigard P; Francioli, Laurent C; Baaijens, Jasmijn A; Dijkstra, Louis J; Abdellaoui, Abdel; Koval, Vyacheslav; Thung, Djie Tjwan; Wardenaar, René; Renkens, Ivo; Coe, Bradley P; Deelen, Patrick; de Ligt, Joep; Lameijer, Eric-Wubbo; van Dijk, Freerk; Hormozdiari, Fereydoun; Uitterlinden, André G; van Duijn, Cornelia M; Eichler, Evan E; de Bakker, Paul I W; Swertz, Morris A; Wijmenga, Cisca; van Ommen, Gert-Jan B; Slagboom, P Eline; Boomsma, Dorret I; Schönhuth, Alexander; Ye, Kai; Guryev, Victor

2016-10-06

Structural variation (SV) represents a major source of differences between individual human genomes and has been linked to disease phenotypes. However, the majority of studies provide neither a global view of the full spectrum of these variants nor integrate them into reference panels of genetic variation. Here, we analyse whole genome sequencing data of 769 individuals from 250 Dutch families, and provide a haplotype-resolved map of 1.9 million genome variants across 9 different variant classes, including novel forms of complex indels, and retrotransposition-mediated insertions of mobile elements and processed RNAs. A large proportion are previously under reported variants sized between 21 and 100 bp. We detect 4 megabases of novel sequence, encoding 11 new transcripts. Finally, we show 191 known, trait-associated SNPs to be in strong linkage disequilibrium with SVs and demonstrate that our panel facilitates accurate imputation of SVs in unrelated individuals.

Multi-agent electricity market modeling with EMCAS.

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

North, M.; Macal, C.; Conzelmann, G.

2002-09-05

Electricity systems are a central component of modern economies. Many electricity markets are transitioning from centrally regulated systems to decentralized markets. Furthermore, several electricity markets that have recently undergone this transition have exhibited extremely unsatisfactory results, most notably in California. These high stakes transformations require the introduction of largely untested regulatory structures. Suitable tools that can be used to test these regulatory structures before they are applied to real systems are required. Multi-agent models can provide such tools. To better understand the requirements such as tool, a live electricity market simulation was created. This experience helped to shape the developmentmore » of the multi-agent Electricity Market Complex Adaptive Systems (EMCAS) model. To explore EMCAS' potential, several variations of the live simulation were created. These variations probed the possible effects of changing power plant outages and price setting rules on electricity market prices.« less

A climate-associated multispecies cryptic cline in the northwest Atlantic

PubMed Central

DiBacco, Claudio; Lowen, Ben; Beiko, Robert G.; Bentzen, Paul; Brickman, David; Johnson, Catherine; Wang, Zeliang; Wringe, Brendan F.; Bradbury, Ian R.

2018-01-01

The spatial genetic structure of most species in the open marine environment remains largely unresolved. This information gap creates uncertainty in the sustainable management, recovery, and associated resilience of marine communities and our capacity to extrapolate beyond the few species for which such information exists. We document a previously unidentified multispecies biogeographic break aligned with a steep climatic gradient and driven by seasonal temperature minima in the northwest Atlantic. The coherence of this genetic break across our five study species with contrasting life histories suggests a pervasive macroecological phenomenon. The integration of this genetic structure with habitat suitability models and climate forecasts predicts significant variation in northward distributional shifts among populations and availability of suitable habitat in future oceans. The results of our integrated approach provide new perspective on how cryptic intraspecific diversity associated with climatic variation influences species and community response to climate change beyond simple poleward shifts. PMID:29600272

Genotype-Specific Variation in the Structure of Root Fungal Communities Is Related to Chickpea Plant Productivity

PubMed Central

Hamel, Chantal; Gan, Yantai; Tar'an, Bunyamin; Knight, Joan Diane

2015-01-01

Increasing evidence supports the existence of variations in the association of plant roots with symbiotic fungi that can improve plant growth and inhibit pathogens. However, it is unclear whether intraspecific variations in the symbiosis exist among plant cultivars and if they can be used to improve crop productivity. In this study, we determined genotype-specific variations in the association of chickpea roots with soil fungal communities and evaluated the effect of root mycota on crop productivity. A 2-year field experiment was conducted in southwestern Saskatchewan, the central zone of the chickpea growing region of the Canadian prairie. The effects of 13 cultivars of chickpea, comprising a wide range of phenotypes and genotypes, were tested on the structure of root-associated fungal communities based on internal transcribed spacer (ITS) and 18S rRNA gene markers using 454 amplicon pyrosequencing. Chickpea cultivar significantly influenced the structure of the root fungal community. The magnitude of the effect varied with the genotypes evaluated, and effects were consistent across years. For example, the roots of CDC Corrine, CDC Cory, and CDC Anna hosted the highest fungal diversity and CDC Alma and CDC Xena the lowest. Fusarium sp. was dominant in chickpea roots but was less abundant in CDC Corrine than the other cultivars. A bioassay showed that certain of these fungal taxa, including Fusarium species, can reduce the productivity of chickpea, whereas Trichoderma harzianum can increase chickpea productivity. The large variation in the profile of chickpea root mycota, which included growth-promoting and -inhibiting species, supports the possibility of improving the productivity of chickpea by improving its root mycota in chickpea genetic improvement programs using traditional breeding techniques. PMID:25616789

Large-scale deformational systems in the South Polar Layered Deposits (Promethei Lingula, Mars): "Soft-sediment" and Deep-Seated Gravitational Slope Deformations Mechanisms

NASA Astrophysics Data System (ADS)

Guallini, Luca; Brozzetti, Francesco; Marinangeli, Lucia

2012-08-01

The present study is the first attempt at a detailed structural and kinematic analysis of large-scale deformational systems observed in the South Polar Layered Deposits (SPLDs) in the Promethei Lingula (PL) margins (Mars). By systematically collecting attitude data referable to previously unknown deformational structures and defining the cross-cut relationships of the structures, we reconstructed a deformational history consisting of two superimposed, well-defined stages. The first stage is dominated by large-scale strike-slip and transtensional faults arranged into conjugate systems and delimiting shear zones that show a wide range of subsidiary structures, including normal and reverse faults, drag folds, boudins, S-C tectonites and sub-horizontal interstratal shear planes marked by sygmoidal boudins. Other typical structures referable to this event are ductile folds (locally true convolute folds) and lobes (ball-and-pillow structures) affecting certain marker beds of the succession. We suggest that the structural assemblage might be the expression of a shallow soft-sediment tectonics that possibly occurred during warm periods of the South Pole climate. The second stage seems to affect the weaker and in certain cases pre-deformed stratigraphic levels of the SPLD succession. This stage is mainly characterized by extensional deformations caused by gravity. The consequence of the deformations is the nucleation of Deep-Seated Gravitational Slope Deformations (DSGSDs) marked by typical morphostructures, such as scarps, trenches and bulging basal contractant zones. These phenomena were never observed within an ice cap. According to terrestrial modeling, these slow collapses were caused by (1) the presence of detachment levels (i.e., subhorizontal bedding planes) along which the ice-sheet margins can slide and (2) the development of listric faults within the glacial mass, which merge with sub-horizontal shear planes in the subsurface. The presence of complex deformational systems in the SPLD necessarily implies that a large-scale dynamics of the ice-sheet occurred in the past. The relatively fast internal creep and basal/internal sliding, inferable from the structure assemblage, can be due to partial melting of the ice possibly caused by climatic changes in the Promethei Lingula region. In this manner, we believe that climate heating (which, according to the literature, is likely caused by orbital variations) softened some of the SPLD layers, triggering or accelerating the ice sheet's outward movement. The evidence of a marked disharmonic deformational style through the SPLD succession suggests the possibility of local periodic compositional variations in the sequence.

Sound production due to large-scale coherent structures

NASA Technical Reports Server (NTRS)

Gatski, T. B.

1979-01-01

The acoustic pressure fluctuations due to large-scale finite amplitude disturbances in a free turbulent shear flow are calculated. The flow is decomposed into three component scales; the mean motion, the large-scale wave-like disturbance, and the small-scale random turbulence. The effect of the large-scale structure on the flow is isolated by applying both a spatial and phase average on the governing differential equations and by initially taking the small-scale turbulence to be in energetic equilibrium with the mean flow. The subsequent temporal evolution of the flow is computed from global energetic rate equations for the different component scales. Lighthill's theory is then applied to the region with the flowfield as the source and an observer located outside the flowfield in a region of uniform velocity. Since the time history of all flow variables is known, a minimum of simplifying assumptions for the Lighthill stress tensor is required, including no far-field approximations. A phase average is used to isolate the pressure fluctuations due to the large-scale structure, and also to isolate the dynamic process responsible. Variation of mean square pressure with distance from the source is computed to determine the acoustic far-field location and decay rate, and, in addition, spectra at various acoustic field locations are computed and analyzed. Also included are the effects of varying the growth and decay of the large-scale disturbance on the sound produced.

Five features of value-based insurance design plans were associated with higher rates of medication adherence.

PubMed

Choudhry, Niteesh K; Fischer, Michael A; Smith, Benjamin F; Brill, Gregory; Girdish, Charmaine; Matlin, Olga S; Brennan, Troyen A; Avorn, Jerry; Shrank, William H

2014-03-01

Value-based insurance design (VBID) plans selectively lower cost sharing to increase medication adherence. Existing plans have been structured in a variety of ways, and these variations could influence the effectiveness of VBID plans. We evaluated seventy-six plans introduced by a large pharmacy benefit manager during 2007-10. We found that after we adjusted for the other features and baseline trends, VBID plans that were more generous, targeted high-risk patients, offered wellness programs, did not offer disease management programs, and made the benefit available only for medication ordered by mail had a significantly greater impact on adherence than plans without these features. The effects were as large as 4-5 percentage points. These findings can provide guidance for the structure of future VBID plans.

PHOTOMETRIC TRENDS IN THE VISIBLE SOLAR CONTINUUM AND THEIR SENSITIVITY TO THE CENTER-TO-LIMB PROFILE

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

Peck, C. L.; Rast, M. P.

2015-08-01

Solar irradiance variations over solar rotational timescales are largely determined by the passage of magnetic structures across the visible solar disk. Variations on solar cycle timescales are thought to be similarly due to changes in surface magnetism with activity. Understanding the contribution of magnetic structures to total solar irradiance and solar spectral irradiance requires assessing their contributions as a function of disk position. Since only relative photometry is possible from the ground, the contrasts of image pixels are measured with respect to a center-to-limb intensity profile. Using nine years of full-disk red and blue continuum images from the Precision Solarmore » Photometric Telescope at the Mauna Loa Solar Observatory, we examine the sensitivity of continuum contrast measurements to the center-to-limb profile definition. Profiles which differ only by the amount of magnetic activity allowed in the pixels used to determine them yield oppositely signed solar cycle length continuum contrast trends, either agreeing with previous results and showing negative correlation with solar cycle or disagreeing and showing positive correlation with solar cycle. Changes in the center-to-limb profile shape over the solar cycle are responsible for the contradictory contrast results, and we demonstrate that the lowest contrast structures, internetwork and network, are most sensitive to these. Thus the strengths of the full-disk, internetwork, and network photometric trends depend critically on the magnetic flux density used in the quiet-Sun definition. We conclude that the contributions of low contrast magnetic structures to variations in the solar continuum output, particularly to long-term variations, are difficult, if not impossible, to determine without the use of radiometric imaging.« less

Hierarchical drivers of reef-fish metacommunity structure.

PubMed

MacNeil, M Aaron; Graham, Nicholas A J; Polunin, Nicholas V C; Kulbicki, Michel; Galzin, René; Harmelin-Vivien, Mireille; Rushton, Steven P

2009-01-01

Coral reefs are highly complex ecological systems, where multiple processes interact across scales in space and time to create assemblages of exceptionally high biodiversity. Despite the increasing frequency of hierarchically structured sampling programs used in coral-reef science, little progress has been made in quantifying the relative importance of processes operating across multiple scales. The vast majority of reef studies are conducted, or at least analyzed, at a single spatial scale, ignoring the implicitly hierarchical structure of the overall system in favor of small-scale experiments or large-scale observations. Here we demonstrate how alpha (mean local number of species), beta diversity (degree of species dissimilarity among local sites), and gamma diversity (overall species richness) vary with spatial scale, and using a hierarchical, information-theoretic approach, we evaluate the relative importance of site-, reef-, and atoll-level processes driving the fish metacommunity structure among 10 atolls in French Polynesia. Process-based models, representing well-established hypotheses about drivers of reef-fish community structure, were assembled into a candidate set of 12 hierarchical linear models. Variation in fish abundance, biomass, and species richness were unevenly distributed among transect, reef, and atoll levels, establishing the relative contribution of variation at these spatial scales to the structure of the metacommunity. Reef-fish biomass, species richness, and the abundance of most functional-groups corresponded primarily with transect-level habitat diversity and atoll-lagoon size, whereas detritivore and grazer abundances were largely correlated with potential covariates of larval dispersal. Our findings show that (1) within-transect and among-atoll factors primarily drive the relationship between alpha and gamma diversity in this reef-fish metacommunity; (2) habitat is the primary correlate with reef-fish metacommunity structure at multiple spatial scales; and (3) inter-atoll connectedness was poorly correlated with the nonrandom clustering of reef-fish species. These results demonstrate the importance of modeling hierarchical data and processes in understanding reef-fish metacommunity structure.

Influence of Tree Species Composition and Community Structure on Carbon Density in a Subtropical Forest

PubMed Central

Hu, Yanqiu; Su, Zhiyao; Li, Wenbin; Li, Jingpeng; Ke, Xiandong

2015-01-01

We assessed the impact of species composition and stand structure on the spatial variation of forest carbon density using data collected from a 4-ha plot in a subtropical forest in southern China. We found that 1) forest biomass carbon density significantly differed among communities, reflecting a significant effect of community structure and species composition on carbon accumulation; 2) soil organic carbon density increased whereas stand biomass carbon density decreased across communities, indicating that different mechanisms might account for the accumulation of stand biomass carbon and soil organic carbon in the subtropical forest; and 3) a small number of tree individuals of the medium- and large-diameter class contributed predominantly to biomass carbon accumulation in the community, whereas a large number of seedlings and saplings were responsible for a small proportion of the total forest carbon stock. These findings demonstrate that both biomass carbon and soil carbon density in the subtropical forest are sensitive to species composition and community structure, and that heterogeneity in species composition and stand structure should be taken into account to ensure accurate forest carbon accounting. PMID:26317523

Large-area, freestanding, single-layer graphene-gold: a hybrid plasmonic nanostructure.

PubMed

Iyer, Ganjigunte R Swathi; Wang, Jian; Wells, Garth; Guruvenket, Srinivasan; Payne, Scott; Bradley, Michael; Borondics, Ferenc

2014-06-24

Graphene-based plasmonic devices have recently drawn great attention. However, practical limitations in fabrication and device architectures prevent studies from being carried out on the intrinsic properties of graphene and their change by plasmonic structures. The influence of a quasi-infinite object (i.e., the substrate) on graphene, being a single sheet of carbon atoms, and the plasmonic device is overwhelming. To address this and put the intrinsic properties of the graphene-plasmonic nanostructures in focus, we fabricate large-area, freestanding, single-layer graphene-gold (LFG-Au) sandwich structures and Au nanoparticle decorated graphene (formed via thermal treatment) hybrid plasmonic nanostructures. We observed two distinct plasmonic enhancement routes of graphene unique to each structure via surface-enhanced Raman spectroscopy. The localized electronic structure variation in the LFG due to graphene-Au interaction at the nanoscale is mapped using scanning transmission X-ray microscopy. The measurements show an optical density of ∼0.007, which is the smallest experimentally determined for single-layer graphene thus far. Our results on freestanding graphene-Au plasmonic structures provide great insight for the rational design and future fabrication of graphene plasmonic hybrid nanostructures.

Influence of Tree Species Composition and Community Structure on Carbon Density in a Subtropical Forest.

PubMed

Hu, Yanqiu; Su, Zhiyao; Li, Wenbin; Li, Jingpeng; Ke, Xiandong

2015-01-01

We assessed the impact of species composition and stand structure on the spatial variation of forest carbon density using data collected from a 4-ha plot in a subtropical forest in southern China. We found that 1) forest biomass carbon density significantly differed among communities, reflecting a significant effect of community structure and species composition on carbon accumulation; 2) soil organic carbon density increased whereas stand biomass carbon density decreased across communities, indicating that different mechanisms might account for the accumulation of stand biomass carbon and soil organic carbon in the subtropical forest; and 3) a small number of tree individuals of the medium- and large-diameter class contributed predominantly to biomass carbon accumulation in the community, whereas a large number of seedlings and saplings were responsible for a small proportion of the total forest carbon stock. These findings demonstrate that both biomass carbon and soil carbon density in the subtropical forest are sensitive to species composition and community structure, and that heterogeneity in species composition and stand structure should be taken into account to ensure accurate forest carbon accounting.

Ultralight anisotropic foams from layered aligned carbon nanotube sheets

NASA Astrophysics Data System (ADS)

Faraji, Shaghayegh; L. Stano, Kelly; Yildiz, Ozkan; Li, Ang; Zhu, Yuntian; Bradford, Philip D.

2015-10-01

In this work, we present large scale, ultralight aligned carbon nanotube (CNT) structures which have densities an order of magnitude lower than CNT arrays, have tunable properties and exhibit resiliency after compression. By stacking aligned sheets of carbon nanotubes and then infiltrating with a pyrolytic carbon (PyC), resilient foam-like materials were produced that exhibited complete recovery from 90% compressive strain. With density as low as 3.8 mg cm-3, the foam structure is over 500 times less dense than bulk graphite. Microscopy revealed that PyC coated the junctions among CNTs, and also increased CNT surface roughness. These changes in the morphology explain the transition from inelastic behavior to foam-like recovery of the layered CNT sheet structure. Mechanical and thermal properties of the foams were tuned for different applications through variation of PyC deposition duration while dynamic mechanical analysis showed no change in mechanical properties over a large temperature range. Observation of a large and linear electrical resistance change during compression of the aligned CNT/carbon (ACNT/C) foams makes strain/pressure sensors a relevant application. The foams have high oil absorption capacities, up to 275 times their own weight, which suggests they may be useful in water treatment and oil spill cleanup. Finally, the ACNT/C foam's high porosity, surface area and stability allow for demonstration of the foams as catalyst support structures.In this work, we present large scale, ultralight aligned carbon nanotube (CNT) structures which have densities an order of magnitude lower than CNT arrays, have tunable properties and exhibit resiliency after compression. By stacking aligned sheets of carbon nanotubes and then infiltrating with a pyrolytic carbon (PyC), resilient foam-like materials were produced that exhibited complete recovery from 90% compressive strain. With density as low as 3.8 mg cm-3, the foam structure is over 500 times less dense than bulk graphite. Microscopy revealed that PyC coated the junctions among CNTs, and also increased CNT surface roughness. These changes in the morphology explain the transition from inelastic behavior to foam-like recovery of the layered CNT sheet structure. Mechanical and thermal properties of the foams were tuned for different applications through variation of PyC deposition duration while dynamic mechanical analysis showed no change in mechanical properties over a large temperature range. Observation of a large and linear electrical resistance change during compression of the aligned CNT/carbon (ACNT/C) foams makes strain/pressure sensors a relevant application. The foams have high oil absorption capacities, up to 275 times their own weight, which suggests they may be useful in water treatment and oil spill cleanup. Finally, the ACNT/C foam's high porosity, surface area and stability allow for demonstration of the foams as catalyst support structures. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr03899e

Evaluating the utility of vegetation indices to monitoring forests in South America, Western & Central Africa, and Southeast Asia

NASA Astrophysics Data System (ADS)

Cherrington, E. A.; Vincent, G.; Barbier, N.; Pélissier, R.; Sabatier, D.; Berger, U.

2017-12-01

In recent years, there has been controversy regarding applying vegetation indices (VIs) for monitoring tropical forests because of data artefacts related to sun-sensor geometry issues. One means of addressing the issue is comparing the VI variation of tropical forests in similar latitudes. That is, if intra-annual variation in VIs is not driven by real structural and biological changes in the vegetation, then one would expect that forests on the same latitudes should display similar patterns of VI variation. Data from multiple vegetation indices (from MODIS and SPOT VEGETATION) were analyzed over three ten degree by ten degree tiles covering the Guianas, western-central Africa, and northern Borneo in Southeast Asia. In addition to comparing the intra-annual trends across the three regions, the trends were also compared with intra-annual patterns of temporal variation, to see if these explained the VI variation. Those analyses showed that not only did the VI variation across the three regions differ significantly, but the patterns in VI variation for at least two of the three regions were largely correlated with intra-annual variation in environmental factors such as rainfall or light availability. For the Guianas, the pattern of VI variation was largely correlated with the variation in solar radiation, while for western-central Africa, the pattern of variation was more correlated to the variation in rainfall. In contrast, for northern Borneo, the pattern of VI variation did not correlate well with either variation in solar elevation or with intra-annual variation in environmental factors. Firstly, the data would seem to suggest that the patterns of variation in VI data for tropical forests are not strongly biased by artefacts related to sun-sensor geometry effects. More importantly, however, the results also suggest that the phenological of forests in both the Guianas and in western-central Africa are governed by different environmental regimes. That is to say, the forests in the Guianas appear to be light-limited, whereas in contrast, the forests in western-central Africa appear to be moisture-limited. This research suggests that vegetation index data - when corrected for artefacts related to bi-directional effects - can indeed be used to study patterns of temporal variation of forests in the tropics.

Gigwa-Genotype investigator for genome-wide analyses.

PubMed

Sempéré, Guilhem; Philippe, Florian; Dereeper, Alexis; Ruiz, Manuel; Sarah, Gautier; Larmande, Pierre

2016-06-06

Exploring the structure of genomes and analyzing their evolution is essential to understanding the ecological adaptation of organisms. However, with the large amounts of data being produced by next-generation sequencing, computational challenges arise in terms of storage, search, sharing, analysis and visualization. This is particularly true with regards to studies of genomic variation, which are currently lacking scalable and user-friendly data exploration solutions. Here we present Gigwa, a web-based tool that provides an easy and intuitive way to explore large amounts of genotyping data by filtering it not only on the basis of variant features, including functional annotations, but also on genotype patterns. The data storage relies on MongoDB, which offers good scalability properties. Gigwa can handle multiple databases and may be deployed in either single- or multi-user mode. In addition, it provides a wide range of popular export formats. The Gigwa application is suitable for managing large amounts of genomic variation data. Its user-friendly web interface makes such processing widely accessible. It can either be simply deployed on a workstation or be used to provide a shared data portal for a given community of researchers.

Human Y chromosome copy number variation in the next generation sequencing era and beyond.

PubMed

Massaia, Andrea; Xue, Yali

2017-05-01

The human Y chromosome provides a fertile ground for structural rearrangements owing to its haploidy and high content of repeated sequences. The methodologies used for copy number variation (CNV) studies have developed over the years. Low-throughput techniques based on direct observation of rearrangements were developed early on, and are still used, often to complement array-based or sequencing approaches which have limited power in regions with high repeat content and specifically in the presence of long, identical repeats, such as those found in human sex chromosomes. Some specific rearrangements have been investigated for decades; because of their effects on fertility, or their outstanding evolutionary features, the interest in these has not diminished. However, following the flourishing of large-scale genomics, several studies have investigated CNVs across the whole chromosome. These studies sometimes employ data generated within large genomic projects such as the DDD study or the 1000 Genomes Project, and often survey large samples of healthy individuals without any prior selection. Novel technologies based on sequencing long molecules and combinations of technologies, promise to stimulate the study of Y-CNVs in the immediate future.

Atmospheric Response to Zonal Variations in Midlatitude SST: Transient and Stationary Eddies and Their Feedback(.

NASA Astrophysics Data System (ADS)

Inatsu, Masaru; Mukougawa, Hitoshi; Xie, Shang-Ping

2003-10-01

Midwinter storm track response to zonal variations in midlatitude sea surface temperatures (SSTs) has been investigated using an atmospheric general circulation model under aquaplanet and perpetual-January conditions. Zonal wavenumber-1 SST variations with a meridionally confined structure are placed at various latitudes. Having these SST variations centered at 30°N leads to a zonally localized storm track, while the storm track becomes nearly zonally uniform when the same SST forcing is moved farther north at 40° and 50°N. Large (small) baroclinic energy conversion north of the warm (cold) SST anomaly near the axis of the storm track (near 40°N) is responsible for the large (small) storm growth. The equatorward transfer of eddy kinetic energy by the ageostrophic motion and the mechanical damping are important to diminish the storm track activity in the zonal direction.Significant stationary eddies form in the upper troposphere, with a ridge (trough) northeast of the warm (cold) SST anomaly at 30°N. Heat and vorticity budget analyses indicate that zonally localized condensational heating in the storm track is the major cause for these stationary eddies, which in turn exert a positive feedback to maintain the localized storm track by strengthening the vertical shear near the surface. These results indicate an active role of synoptic eddies in inducing deep, tropospheric-scale response to midlatitude SST variations. Finally, the application of the model results to the real atmosphere is discussed.

Modeling stimulus variation in three common implicit attitude tasks.

PubMed

Wolsiefer, Katie; Westfall, Jacob; Judd, Charles M

2017-08-01

We explored the consequences of ignoring the sampling variation due to stimuli in the domain of implicit attitudes. A large literature in psycholinguistics has examined the statistical treatment of random stimulus materials, but the recommendations from this literature have not been applied to the social psychological literature on implicit attitudes. This is partly because of inherent complications in applying crossed random-effect models to some of the most common implicit attitude tasks, and partly because no work to date has demonstrated that random stimulus variation is in fact consequential in implicit attitude measurement. We addressed this problem by laying out statistically appropriate and practically feasible crossed random-effect models for three of the most commonly used implicit attitude measures-the Implicit Association Test, affect misattribution procedure, and evaluative priming task-and then applying these models to large datasets (average N = 3,206) that assess participants' implicit attitudes toward race, politics, and self-esteem. We showed that the test statistics from the traditional analyses are substantially (about 60 %) inflated relative to the more-appropriate analyses that incorporate stimulus variation. Because all three tasks used the same stimulus words and faces, we could also meaningfully compare the relative contributions of stimulus variation across the tasks. In an appendix, we give syntax in R, SAS, and SPSS for fitting the recommended crossed random-effects models to data from all three tasks, as well as instructions on how to structure the data file.

Geomorphic variation in riparian tree mortality and stream coarse woody debris recruitment from record flooding in a coastal plain stream

Treesearch

Brian J. Palik; Stephen W. Golladay; P. Charles Goebel; Brad W. Taylor

1998-01-01

Large floods are an important process controlling the structure and function of stream ecosystems. One of the ways floods affect streams is through the recruitment of coarse woody debris from stream-side forests. Stream valley geomorphology may mediate this interaction by altering flood velocity, depth, and duration. Little research has examined how floods and...

Decomposing risk: landscape structure and wolf behavior generate different predation patterns in two sympatric ungulates.

PubMed

Gervasi, Vincenzo; Sand, Hakan; Zimmermann, Barbara; Mattisson, Jenny; Wabakken, Petter; Linnell, John D C

2013-10-01

Recolonizing carnivores can have a large impact on the status of wild ungulates, which have often modified their behavior in the absence of predation. Therefore, understanding the dynamics of reestablished predator-prey systems is crucial to predict their potential ecosystem effects. We decomposed the spatial structure of predation by recolonizing wolves (Canis lupus) on two sympatric ungulates, moose (Alces alces) and roe deer (Capreolus capreolus), in Scandinavia during a 10-year study. We monitored 18 wolves with GPS collars, distributed over 12 territories, and collected records from predation events. By using conditional logistic regression, we assessed the contributions of three main factors, the utilization patterns of each wolf territory, the spatial distribution of both prey species, and fine-scale landscape structure, in determining the spatial structure of moose and roe deer predation risk. The reestablished predator-prey system showed a remarkable spatial variation in kill occurrence at the intra-territorial level, with kill probabilities varying by several orders of magnitude inside the same territory. Variation in predation risk was evident also when a spatially homogeneous probability for a wolf to encounter a prey was simulated. Even inside the same territory, with the same landscape structure, and when exposed to predation by the same wolves, the two prey species experienced an opposite spatial distribution of predation risk. In particular, increased predation risk for moose was associated with open areas, especially clearcuts and young forest stands, whereas risk was lowered for roe deer in the same habitat types. Thus, fine-scale landscape structure can generate contrasting predation risk patterns in sympatric ungulates, so that they can experience large differences in the spatial distribution of risk and refuge areas when exposed to predation by a recolonizing predator. Territories with an earlier recolonization were not associated with a lower hunting success for wolves. Such constant efficiency in wolf predation during the recolonization process is in line with previous findings about the naive nature of Scandinavian moose to wolf predation. This, together with the human-dominated nature of the Scandinavian ecosystem, seems to limit the possibility for wolves to have large ecosystem effects and to establish a behaviorally mediated trophic cascade in Scandinavia.

Structure and variation of the mitochondrial genome of fishes.

PubMed

Satoh, Takashi P; Miya, Masaki; Mabuchi, Kohji; Nishida, Mutsumi

2016-09-07

The mitochondrial (mt) genome has been used as an effective tool for phylogenetic and population genetic analyses in vertebrates. However, the structure and variability of the vertebrate mt genome are not well understood. A potential strategy for improving our understanding is to conduct a comprehensive comparative study of large mt genome data. The aim of this study was to characterize the structure and variability of the fish mt genome through comparative analysis of large datasets. An analysis of the secondary structure of proteins for 250 fish species (248 ray-finned and 2 cartilaginous fishes) illustrated that cytochrome c oxidase subunits (COI, COII, and COIII) and a cytochrome bc1 complex subunit (Cyt b) had substantial amino acid conservation. Among the four proteins, COI was the most conserved, as more than half of all amino acid sites were invariable among the 250 species. Our models identified 43 and 58 stems within 12S rRNA and 16S rRNA, respectively, with larger numbers than proposed previously for vertebrates. The models also identified 149 and 319 invariable sites in 12S rRNA and 16S rRNA, respectively, in all fishes. In particular, the present result verified that a region corresponding to the peptidyl transferase center in prokaryotic 23S rRNA, which is homologous to mt 16S rRNA, is also conserved in fish mt 16S rRNA. Concerning the gene order, we found 35 variations (in 32 families) that deviated from the common gene order in vertebrates. These gene rearrangements were mostly observed in the area spanning the ND5 gene to the control region as well as two tRNA gene cluster regions (IQM and WANCY regions). Although many of such gene rearrangements were unique to a specific taxon, some were shared polyphyletically between distantly related species. Through a large-scale comparative analysis of 250 fish species mt genomes, we elucidated various structural aspects of the fish mt genome and the encoded genes. The present results will be important for understanding functions of the mt genome and developing programs for nucleotide sequence analysis. This study demonstrated the significance of extensive comparisons for understanding the structure of the mt genome.

Buccal swabbing as a noninvasive method to determine bacterial, archaeal, and eukaryotic microbial community structures in the rumen.

PubMed

Kittelmann, Sandra; Kirk, Michelle R; Jonker, Arjan; McCulloch, Alan; Janssen, Peter H

2015-11-01

Analysis of rumen microbial community structure based on small-subunit rRNA marker genes in metagenomic DNA samples provides important insights into the dominant taxa present in the rumen and allows assessment of community differences between individuals or in response to treatments applied to ruminants. However, natural animal-to-animal variation in rumen microbial community composition can limit the power of a study considerably, especially when only subtle differences are expected between treatment groups. Thus, trials with large numbers of animals may be necessary to overcome this variation. Because ruminants pass large amounts of rumen material to their oral cavities when they chew their cud, oral samples may contain good representations of the rumen microbiota and be useful in lieu of rumen samples to study rumen microbial communities. We compared bacterial, archaeal, and eukaryotic community structures in DNAs extracted from buccal swabs to those in DNAs from samples collected directly from the rumen by use of a stomach tube for sheep on four different diets. After bioinformatic depletion of potential oral taxa from libraries of samples collected via buccal swabs, bacterial communities showed significant clustering by diet (R = 0.37; analysis of similarity [ANOSIM]) rather than by sampling method (R = 0.07). Archaeal, ciliate protozoal, and anaerobic fungal communities also showed significant clustering by diet rather than by sampling method, even without adjustment for potentially orally associated microorganisms. These findings indicate that buccal swabs may in future allow quick and noninvasive sampling for analysis of rumen microbial communities in large numbers of ruminants. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Structure of small-scale magnetic fields in the kinematic dynamo theory.

PubMed

Schekochihin, Alexander; Cowley, Steven; Maron, Jason; Malyshkin, Leonid

2002-01-01

A weak fluctuating magnetic field embedded into a a turbulent conducting medium grows exponentially while its characteristic scale decays. In the interstellar medium and protogalactic plasmas, the magnetic Prandtl number is very large, so a broad spectrum of growing magnetic fluctuations is excited at small (subviscous) scales. The condition for the onset of nonlinear back reaction depends on the structure of the field lines. We study the statistical correlations that are set up in the field pattern and show that the magnetic-field lines possess a folding structure, where most of the scale decrease is due to the field variation across itself (rapid transverse direction reversals), while the scale of the field variation along itself stays approximately constant. Specifically, we find that, though both the magnetic energy and the mean-square curvature of the field lines grow exponentially, the field strength and the field-line curvature are anticorrelated, i.e., the curved field is relatively weak, while the growing field is relatively flat. The detailed analysis of the statistics of the curvature shows that it possesses a stationary limiting distribution with the bulk located at the values of curvature comparable to the characteristic wave number of the velocity field and a power tail extending to large values of curvature where it is eventually cut off by the resistive regularization. The regions of large curvature, therefore, occupy only a small fraction of the total volume of the system. Our theoretical results are corroborated by direct numerical simulations. The implication of the folding effect is that the advent of the Lorentz back reaction occurs when the magnetic energy approaches that of the smallest turbulent eddies. Our results also directly apply to the problem of statistical geometry of the material lines in a random flow.

Variations in the Quality of Care at Large Public Hospitals in Beijing, China: A Condition-Based Outcome Approach

PubMed Central

Xu, Ye; Liu, Yuanli; Shu, Ting; Yang, Wei; Liang, Minghui

2015-01-01

Background Public hospitals deliver over ninety percent of all outpatient and inpatient services in China. Their quality is graded into three levels (A, B, and C) largely based on structural resources, but empirical evidence on the quality of process and outcome of care is extremely scarce. As expectations for quality care rise with higher living standards and cost of care, such evidence is urgently needed and vital to improve care and to inform future health reforms. Methods We compiled and analyzed a multicenter database of over 4 million inpatient discharge summary records to provide a comprehensive assessment of the level and variations in clinical outcomes of hospitalization at 39 tertiary hospitals in Beijing. We assessed six outcome measures of clinical quality: in-hospital mortality rates (RSMR) for AMI, stroke, pneumonia and CABG, post-procedural complication rate (RS-CR), and failure-to-rescue rate (RS-FTR). The measures were adjusted for pre-admission patient case-mix using indirect standardization method with hierarchical linear mixed models. Results We found good overall quality with large variations by hospital and condition (mean/range, in %): RSMR-AMI: 6.23 (2.37–14.48), RSMR-stroke: 4.18 (3.58–4.44), RSMR-pneumonia: 7.78 (7.20–8.59), RSMR-CABG: 1.93 (1.55–2.23), RS-CR: 11.38 (9.9–12.88), and RS-FTR: 6.41 (5.17–7.58). Hospital grade was not significantly associated with any risk-adjusted outcome measures. Conclusions Going to a higher grade public hospital does not always lead to better patient outcome because hospital grade only contains information about hospital structural resources. A hospital report card with some outcome measures of quality would provide valuable information to patients in choosing providers, and for regulators to identify gaps in health care quality. Reducing the variations in clinical practice and patient outcome should be a focus for policy makers in the next round of health sector reforms in China. PMID:26430748

Compton imaging tomography for nondestructive evaluation of large multilayer aircraft components and structures

NASA Astrophysics Data System (ADS)

Romanov, Volodymyr; Grubsky, Victor; Zahiri, Feraidoon

2017-02-01

We present a novel NDT/NDE tool for non-contact, single-sided 3D inspection of aerospace components, based on Compton Imaging Tomography (CIT) technique, which is applicable to large, non-uniform, and/or multilayer structures made of composites or lightweight metals. CIT is based on the registration of Compton-scattered X-rays, and permits the reconstruction of the full 3D (tomographic) image of the inspected objects. Unlike conventional computerized tomography (CT), CIT requires only single-sided access to objects, and therefore can be applied to large structures without their disassembly. The developed tool provides accurate detection, identification, and precise 3D localizations and measurements of any possible internal and surface defects (corrosions, cracks, voids, delaminations, porosity, and inclusions), and also disbonds, core and skin defects, and intrusion of foreign fluids (e.g., fresh and salt water, oil) inside of honeycomb sandwich structures. The NDE capabilities of the system were successfully demonstrated on various aerospace structure samples provided by several major aerospace companies. Such a CIT-based tool can detect and localize individual internal defects with dimensions about 1-2 mm3, and honeycomb disbond defects less than 6 mm by 6 mm area with the variations in the thickness of the adhesive by 100 m. Current maximum scanning speed of aircraft/spacecraft structures is about 5-8 min/ft2 (50-80 min/m2).

Thermo-mechanical behavior of power electronic packaging assemblies: From characterization to predictive simulation of lifetimes

NASA Astrophysics Data System (ADS)

Dalverny, O.; Alexis, J.

2018-02-01

This article deals with thermo-mechanical behavior of power electronic modules used in several transportation applications as railway, aeronautic or automotive systems. Due to a multi-layered structures, involving different materials with a large variation of coefficient of thermal expansion, temperature variations originated from active or passive cycling (respectively from die dissipation or environmental constraint) induces strain and stresses field variations, giving fatigue phenomenon of the system. The analysis of the behavior of these systems and their dimensioning require the implementation of complex modeling strategies by both the multi-physical and the multi-scale character of the power modules. In this paper we present some solutions for studying the thermomechanical behavior of brazed assemblies as well as taking into account the interfaces represented by the numerous metallizations involved in the process assembly.

Microsatellite and mtDNA analysis of lake trout, Salvelinus namaycush, from Great Bear Lake, Northwest Territories: impacts of historical and contemporary evolutionary forces on Arctic ecosystems

PubMed Central

Harris, Les N; Howland, Kimberly L; Kowalchuk, Matthew W; Bajno, Robert; Lindsay, Melissa M; Taylor, Eric B

2013-01-01

Resolving the genetic population structure of species inhabiting pristine, high latitude ecosystems can provide novel insights into the post-glacial, evolutionary processes shaping the distribution of contemporary genetic variation. In this study, we assayed genetic variation in lake trout (Salvelinus namaycush) from Great Bear Lake (GBL), NT and one population outside of this lake (Sandy Lake, NT) at 11 microsatellite loci and the mtDNA control region (d-loop). Overall, population subdivision was low, but significant (global FST θ = 0.025), and pairwise comparisons indicated that significance was heavily influenced by comparisons between GBL localities and Sandy Lake. Our data indicate that there is no obvious genetic structure among the various basins within GBL (global FST = 0.002) despite the large geographic distances between sampling areas. We found evidence of low levels of contemporary gene flow among arms within GBL, but not between Sandy Lake and GBL. Coalescent analyses suggested that some historical gene flow occurred among arms within GBL and between GBL and Sandy Lake. It appears, therefore, that contemporary (ongoing dispersal and gene flow) and historical (historical gene flow and large founding and present-day effective population sizes) factors contribute to the lack of neutral genetic structure in GBL. Overall, our results illustrate the importance of history (e.g., post-glacial colonization) and contemporary dispersal ecology in shaping genetic population structure of Arctic faunas and provide a better understanding of the evolutionary ecology of long-lived salmonids in pristine, interconnected habitats. PMID:23404390

Invertebrate muscles: thin and thick filament structure; molecular basis of contraction and its regulation, catch and asynchronous muscle

PubMed Central

Hooper, Scott L.; Hobbs, Kevin H.; Thuma, Jeffrey B.

2008-01-01

This is the second in a series of canonical reviews on invertebrate muscle. We cover here thin and thick filament structure, the molecular basis of force generation and its regulation, and two special properties of some invertebrate muscle, catch and asynchronous muscle. Invertebrate thin filaments resemble vertebrate thin filaments, although helix structure and tropomyosin arrangement show small differences. Invertebrate thick filaments, alternatively, are very different from vertebrate striated thick filaments and show great variation within invertebrates. Part of this diversity stems from variation in paramyosin content, which is greatly increased in very large diameter invertebrate thick filaments. Other of it arises from relatively small changes in filament backbone structure, which results in filaments with grossly similar myosin head placements (rotating crowns of heads every 14.5 nm) but large changes in detail (distances between heads in azimuthal registration varying from three to thousands of crowns). The lever arm basis of force generation is common to both vetebrates and invertebrates, and in some invertebrates this process is understood on the near atomic level. Invertebrate actomyosin is both thin (tropomyosin:troponin) and thick (primarily via direct Ca++ binding to myosin) filament regulated, and most invertebrate muscles are dually regulated. These mechanisms are well understood on the molecular level, but the behavioral utility of dual regulation is less so. The phosphorylation state of the thick filament associated giant protein, twitchin, has been recently shown to be the molecular basis of catch. The molecular basis of the stretch activation underlying asynchronous muscle activity, however, remains unresolved. PMID:18616971

Microsatellite and mtDNA analysis of lake trout, Salvelinus namaycush, from Great Bear Lake, Northwest Territories: impacts of historical and contemporary evolutionary forces on Arctic ecosystems.

PubMed

Harris, Les N; Howland, Kimberly L; Kowalchuk, Matthew W; Bajno, Robert; Lindsay, Melissa M; Taylor, Eric B

2012-01-01

Resolving the genetic population structure of species inhabiting pristine, high latitude ecosystems can provide novel insights into the post-glacial, evolutionary processes shaping the distribution of contemporary genetic variation. In this study, we assayed genetic variation in lake trout (Salvelinus namaycush) from Great Bear Lake (GBL), NT and one population outside of this lake (Sandy Lake, NT) at 11 microsatellite loci and the mtDNA control region (d-loop). Overall, population subdivision was low, but significant (global F(ST) θ = 0.025), and pairwise comparisons indicated that significance was heavily influenced by comparisons between GBL localities and Sandy Lake. Our data indicate that there is no obvious genetic structure among the various basins within GBL (global F(ST) = 0.002) despite the large geographic distances between sampling areas. We found evidence of low levels of contemporary gene flow among arms within GBL, but not between Sandy Lake and GBL. Coalescent analyses suggested that some historical gene flow occurred among arms within GBL and between GBL and Sandy Lake. It appears, therefore, that contemporary (ongoing dispersal and gene flow) and historical (historical gene flow and large founding and present-day effective population sizes) factors contribute to the lack of neutral genetic structure in GBL. Overall, our results illustrate the importance of history (e.g., post-glacial colonization) and contemporary dispersal ecology in shaping genetic population structure of Arctic faunas and provide a better understanding of the evolutionary ecology of long-lived salmonids in pristine, interconnected habitats.

Longitudinal Variations in the Variability of Spread F Occurrence

NASA Astrophysics Data System (ADS)

Groves, K. M.; Bridgwood, C.; Carrano, C. S.

2017-12-01

The complex dynamics of the equatorial ionosphere have attracted the interest and attention of researchers for many decades. The relatively local processes that give rise to large meridional gradients have been well documented and the associated terminology has entered the common lexicon of ionospheric research (e.g., fountain effect, equatorial anomaly, bubbles, Spread F). Zonal variations have also been noted, principally at the level of determining longitudinal differences in seasonal activity patterns. Due to a historical lack of high resolution ground-based observations at low latitudes, the primary source of data for such analyses has been space-based observations from satellites such as ROCSAT, DMSP, C/NOFS that measure in situ electron density variations. An important longitudinal variation in electron density structure associated with non-migrating diurnal tides was discovered by Immel et al. in 2006 using data from the FUV sensor aboard the NASA IMAGE satellite. These satellite observations have been very helpful in identifying the structural characteristics of the equatorial ionosphere and the occurrence of Spread F, but they provide little insight into variations in scintillation features and potential differences in bubble development characteristics. Moreover space-based studies tend towards the statistics of occurrence frequency over periods of weeks to months. A recent analysis of daily spread F occurrence as determined by low latitude VHF scintillation activity shows that statistical results that are consistent with previous space-based observations, but the level of variability in the occurrence data show marked variations with longitude. For example, the American sector shows very low in-season variability while the African and Asian sectors exhibit true day-to-day variability regardless of seasonal variations. The results have significant implications for space weather as they suggest that long-term forecasts of equatorial scintillation may be meaningful within specific longitude boundaries.

Oceanographic variation influences spatial genomic structure in the sea scallop, Placopecten magellanicus.

PubMed

Van Wyngaarden, Mallory; Snelgrove, Paul V R; DiBacco, Claudio; Hamilton, Lorraine C; Rodríguez-Ezpeleta, Naiara; Zhan, Luyao; Beiko, Robert G; Bradbury, Ian R

2018-03-01

Environmental factors can influence diversity and population structure in marine species and accurate understanding of this influence can both improve fisheries management and help predict responses to environmental change. We used 7163 SNPs derived from restriction site-associated DNA sequencing genotyped in 245 individuals of the economically important sea scallop, Placopecten magellanicus , to evaluate the correlations between oceanographic variation and a previously identified latitudinal genomic cline. Sea scallops span a broad latitudinal area (>10 degrees), and we hypothesized that climatic variation significantly drives clinal trends in allele frequency. Using a large environmental dataset, including temperature, salinity, chlorophyll a, and nutrient concentrations, we identified a suite of SNPs (285-621, depending on analysis and environmental dataset) potentially under selection through correlations with environmental variation. Principal components analysis of different outlier SNPs and environmental datasets revealed similar northern and southern clusters, with significant associations between the first axes of each ( R 2 adj  = .66-.79). Multivariate redundancy analysis of outlier SNPs and the environmental principal components indicated that environmental factors explained more than 32% of the variance. Similarly, multiple linear regressions and random-forest analysis identified winter average and minimum ocean temperatures as significant parameters in the link between genetic and environmental variation. This work indicates that oceanographic variation is associated with the observed genomic cline in this species and that seasonal periods of extreme cold may restrict gene flow along a latitudinal gradient in this marine benthic bivalve. Incorporating this finding into management may improve accuracy of management strategies and future predictions.

Magnetic resonance imaging of the calcaneus: preliminary assessment of trabecular bone-dependent regional variations in marrow relaxation time compared with dual X-ray absorptiometry

NASA Technical Reports Server (NTRS)

Guglielmi, G.; Selby, K.; Blunt, B. A.; Jergas, M.; Newitt, D. C.; Genant, H. K.; Majumdar, S.

1996-01-01

RATIONALE AND OBJECTIVES: Marrow transverse relaxation time (T2*) in magnetic resonance (MR) imaging may be related to the density and structure of the surrounding trabecular network. We investigated regional variations of T2* in the human calcaneus and compared the findings with bone mineral density (BMD), as measured by dual X-ray absorpiometry (DXA). Short- and long-term precisions were evaluated first to determine whether MR imaging would be useful for the clinical assessment of disease status and progression in osteoporosis. METHODS: Gradient-recalled echo MR images of the calcaneus were acquired at 1.5 T from six volunteers. Measurements of T2* were compared with BMD and (for one volunteer) conventional radiography. RESULTS: T2* values showed significant regional variation; they typically were shortest in the superior region of the calcaneus. There was a linear correlation between MR and DXA measurements (r = .66 for 1/T2* versus BMD). Differences in T2* attributable to variations in analysis region-of-interest placement were not significant for five of the six volunteers. Sagittal MR images had short- and long-term precision errors of 4.2% and 3.3%, respectively. For DXA, the precision was 1.3% (coefficient of variation). CONCLUSION: MR imaging may be useful for trabecular bone assessment in the calcaneus. However, given the large regional variations in bone density and structure, the choice of an ROI is likely to play a major role in the accuracy, precision, and overall clinical efficacy of T2* measurements.

Complex pattern of variation in neurocranial ontogeny revealed by CT-scanning.

PubMed

Anzelmo, Marisol; Ventrice, Fernando; Kelmansky, Diana; Sardi, Marina

2018-05-01

The neurocranium of hominid species has been largely studied with reference to the midsagittal plane, with variations being attributed to brain evolution. By contrast, there is limited information on variation in non-midsagittal regions, which are the points of insertion of muscles and bony structures related to mastication. This work aims to analyze ontogenetic changes and sexual dimorphism (SD) in midsagittal and non-midsagittal neurocranial structures from a contemporary human sample comprising 138 computed tomography (CT) cranial images of individuals ranging from infants to adults. Morphology of the vault and the base was assessed by registering landmarks and semilandmarks, which were analyzed by geometric morphometrics, and the endocranial volume (EV). The results of regressions and Kruskal-Wallis test indicate that the major size and shape changes in both midsagittal and non-midsagittal regions occur during infancy and juvenility; shape changes are also associated with an increase in EV. The size of the midsagittal vault, the shape of the non-midsagittal vault and the size of the base show an extension of ontogenetic trajectories. Sexes show similar changes in shape but different changes in size. We conclude that brain growth appears to be an important factor influencing the morphology of the neurocranium, at least during infancy and childhood. Subsequent changes may be attributed to osteogenic activity and the differential growth of the brain lobes. Masticatory-related bony structures and muscles may not be strong enough factors to induce independent modifications in non-midsagittal structures. The small influence of the cranial muscles would explain why the human neurocranium is a quite integrated structure.

The Heterogeneity and Spatial Patterning of Structure and Physiology across the Leaf Surface in Giant Leaves of Alocasia macrorrhiza

PubMed Central

Li, Shuai; Zhang, Yong-Jiang; Sack, Lawren; Scoffoni, Christine; Ishida, Atsushi; Chen, Ya-Jun; Cao, Kun-Fang

2013-01-01

Leaf physiology determines the carbon acquisition of the whole plant, but there can be considerable variation in physiology and carbon acquisition within individual leaves. Alocasia macrorrhiza (L.) Schott is an herbaceous species that can develop very large leaves of up to 1 m in length. However, little is known about the hydraulic and photosynthetic design of such giant leaves. Based on previous studies of smaller leaves, and on the greater surface area for trait variation in large leaves, we hypothesized that A. macrorrhiza leaves would exhibit significant heterogeneity in structure and function. We found evidence of reduced hydraulic supply and demand in the outer leaf regions; leaf mass per area, chlorophyll concentration, and guard cell length decreased, as did stomatal conductance, net photosynthetic rate and quantum efficiency of photosystem II. This heterogeneity in physiology was opposite to that expected from a thinner boundary layer at the leaf edge, which would have led to greater rates of gas exchange. Leaf temperature was 8.8°C higher in the outer than in the central region in the afternoon, consistent with reduced stomatal conductance and transpiration caused by a hydraulic limitation to the outer lamina. The reduced stomatal conductance in the outer regions would explain the observed homogeneous distribution of leaf water potential across the leaf surface. These findings indicate substantial heterogeneity in gas exchange across the leaf surface in large leaves, greater than that reported for smaller-leafed species, though the observed structural differences across the lamina were within the range reported for smaller-leafed species. Future work will determine whether the challenge of transporting water to the outer regions can limit leaf size for plants experiencing drought, and whether the heterogeneity of function across the leaf surface represents a particular disadvantage for large simple leaves that might explain their global rarity, even in resource-rich environments. PMID:23776594

The heterogeneity and spatial patterning of structure and physiology across the leaf surface in giant leaves of Alocasia macrorrhiza.

PubMed

Li, Shuai; Zhang, Yong-Jiang; Sack, Lawren; Scoffoni, Christine; Ishida, Atsushi; Chen, Ya-Jun; Cao, Kun-Fang

2013-01-01

Leaf physiology determines the carbon acquisition of the whole plant, but there can be considerable variation in physiology and carbon acquisition within individual leaves. Alocasia macrorrhiza (L.) Schott is an herbaceous species that can develop very large leaves of up to 1 m in length. However, little is known about the hydraulic and photosynthetic design of such giant leaves. Based on previous studies of smaller leaves, and on the greater surface area for trait variation in large leaves, we hypothesized that A. macrorrhiza leaves would exhibit significant heterogeneity in structure and function. We found evidence of reduced hydraulic supply and demand in the outer leaf regions; leaf mass per area, chlorophyll concentration, and guard cell length decreased, as did stomatal conductance, net photosynthetic rate and quantum efficiency of photosystem II. This heterogeneity in physiology was opposite to that expected from a thinner boundary layer at the leaf edge, which would have led to greater rates of gas exchange. Leaf temperature was 8.8°C higher in the outer than in the central region in the afternoon, consistent with reduced stomatal conductance and transpiration caused by a hydraulic limitation to the outer lamina. The reduced stomatal conductance in the outer regions would explain the observed homogeneous distribution of leaf water potential across the leaf surface. These findings indicate substantial heterogeneity in gas exchange across the leaf surface in large leaves, greater than that reported for smaller-leafed species, though the observed structural differences across the lamina were within the range reported for smaller-leafed species. Future work will determine whether the challenge of transporting water to the outer regions can limit leaf size for plants experiencing drought, and whether the heterogeneity of function across the leaf surface represents a particular disadvantage for large simple leaves that might explain their global rarity, even in resource-rich environments.

Population genetic structure of traditional populations in the Peruvian Central Andes and implications for South American population history.

PubMed

Cabana, Graciela S; Lewis, Cecil M; Tito, Raúl Y; Covey, R Alan; Cáceres, Angela M; Cruz, Augusto F De La; Durand, Diana; Housman, Genevieve; Hulsey, Brannon I; Iannacone, Gian Carlo; López, Paul W; Martínez, Rolando; Medina, Ángel; Dávila, Olimpio Ortega; Pinto, Karla Paloma Osorio; Santillán, Susan I Polo; Domínguez, Percy Rojas; Rubel, Meagan; Smith, Heather F; Smith, Silvia E; Massa, Verónica Rubín de Celis; Lizárraga, Beatriz; Stone, Anne C

2014-01-01

Molecular-based characterizations of Andean peoples are traditionally conducted in the service of elucidating continent-level evolutionary processes in South America. Consequently, genetic variation among "western" Andean populations is often represented in relation to variation among "eastern" Amazon and Orinoco River Basin populations. This west-east contrast in patterns of population genetic variation is typically attributed to large-scale phenomena, such as dual founder colonization events or differing long-term microevolutionary histories. However, alternative explanations that consider the nature and causes of population genetic diversity within the Andean region remain underexplored. Here we examine population genetic diversity in the Peruvian Central Andes using data from the mtDNA first hypervariable region and Y-chromosome short tandem repeats among 17 newly sampled populations and 15 published samples. Using this geographically comprehensive data set, we first reassessed the currently accepted pattern of western versus eastern population genetic structure, which our results ultimately reject: mtDNA population diversities were lower, rather than higher, within Andean versus eastern populations, and only highland Y-chromosomes exhibited significantly higher within-population diversities compared with eastern groups. Multiple populations, including several highland samples, exhibited low genetic diversities for both genetic systems. Second, we explored whether the implementation of Inca state and Spanish colonial policies starting at about ad 1400 could have substantially restructured population genetic variation and consequently constitute a primary explanation for the extant pattern of population diversity in the Peruvian Central Andes. Our results suggest that Peruvian Central Andean population structure cannot be parsimoniously explained as the sole outcome of combined Inca and Spanish policies on the region's population demography: highland populations differed from coastal and lowland populations in mtDNA genetic structure only; highland groups also showed strong evidence of female-biased gene flow and/or effective sizes relative to other Peruvian ecozones. Taken together, these findings indicate that population genetic structure in the Peruvian Central Andes is considerably more complex than previously reported and that characterizations of and explanations for genetic variation may be best pursued within more localized regions and defined time periods.

Regulating the chromatin landscape: structural and mechanistic perspectives.

PubMed

Bartholomew, Blaine

2014-01-01

A large family of chromatin remodelers that noncovalently modify chromatin is crucial in cell development and differentiation. They are often the targets of cancer, neurological disorders, and other human diseases. These complexes alter nucleosome positioning, higher-order chromatin structure, and nuclear organization. They also assemble chromatin, exchange out histone variants, and disassemble chromatin at defined locations. We review aspects of the structural organization of these complexes, the functional properties of their protein domains, and variation between complexes. We also address the mechanistic details of these complexes in mobilizing nucleosomes and altering chromatin structure. A better understanding of these issues will be vital for further analyses of subunits of these chromatin remodelers, which are being identified as targets in human diseases by NGS (next-generation sequencing).

Social structure affects mating competition in a damselfish

NASA Astrophysics Data System (ADS)

Wacker, Sebastian; Ness, Miriam Horstad; Östlund-Nilsson, Sara; Amundsen, Trond

2017-12-01

The strength of mating competition and sexual selection varies over space and time in many animals. Such variation is typically driven by ecological and demographic factors, including adult sex ratio and consequent availability of mates. The spatial scale at which demographic factors affect mating competition and sexual selection may vary but is not often investigated. Here, we analyse variation in size and sex ratio of social groups, and how group structure affects mating competition, in the site-attached damselfish Chrysiptera cyanea. Site-attached reef fishes are known to show extensive intraspecific variation in social structure. Previous work has focused on species for which the size and dynamics of social groups are constrained by habitat, whereas species with group structure unconstrained by habitat have received little attention. Chrysiptera cyanea is such a species, with individuals occurring in spatial clusters that varied widely in size and sex ratio. Typically, only one male defended a nest in multi-male groups. Nest-holding males were frequently visited by mate-searching females, with more visits in groups with more females, suggesting that courtship and mating mostly occur within groups and that male mating success depends on the number of females in the group. Male-male aggression was frequent in multi-male groups but absent in single-male groups. These findings demonstrate that groups are distinct social units. In consequence, the dynamics of mating and reproduction are mainly a result of group structure, largely unaffected short term by overall population demography which would be important in open social systems. Future studies of the C. cyanea model system should analyse longer-term dynamics, including how groups are formed, how they vary in relation to density and time of season and how social structure affects sexual selection.

Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server.

PubMed

Abriata, Luciano A; Bovigny, Christophe; Dal Peraro, Matteo

2016-06-17

Protein variability can now be studied by measuring high-resolution tolerance-to-substitution maps and fitness landscapes in saturated mutational libraries. But these rich and expensive datasets are typically interpreted coarsely, restricting detailed analyses to positions of extremely high or low variability or dubbed important beforehand based on existing knowledge about active sites, interaction surfaces, (de)stabilizing mutations, etc. Our new webserver PsychoProt (freely available without registration at http://psychoprot.epfl.ch or at http://lucianoabriata.altervista.org/psychoprot/index.html ) helps to detect, quantify, and sequence/structure map the biophysical and biochemical traits that shape amino acid preferences throughout a protein as determined by deep-sequencing of saturated mutational libraries or from large alignments of naturally occurring variants. We exemplify how PsychoProt helps to (i) unveil protein structure-function relationships from experiments and from alignments that are consistent with structures according to coevolution analysis, (ii) recall global information about structural and functional features and identify hitherto unknown constraints to variation in alignments, and (iii) point at different sources of variation among related experimental datasets or between experimental and alignment-based data. Remarkably, metabolic costs of the amino acids pose strong constraints to variability at protein surfaces in nature but not in the laboratory. This and other differences call for caution when extrapolating results from in vitro experiments to natural scenarios in, for example, studies of protein evolution. We show through examples how PsychoProt can be a useful tool for the broad communities of structural biology and molecular evolution, particularly for studies about protein modeling, evolution and design.

Seismic Structure of the Oceanic Plate Entering the Central Part of the Japan Trench Obtained from Ocean-Bottom Seismic Data

NASA Astrophysics Data System (ADS)

Ohira, A.; Kodaira, S.; Fujie, G.; No, T.; Nakamura, Y.; Miura, S.

2017-12-01

In trench-outer rise regions, the normal faults develop due to the bending of the incoming plate, which cause numerous normal-faulting earthquakes and systematic structural variations toward trenches. In addition to the effects on the bend-related normal fault, structural variations which are interpreted to be attributed to pseudofaults, a fracture zone, and petit-spot volcanic activities are observed in the oceanic plate entering the central part of the Japan Trench, off Miyagi. In May-June 2017, to understand detail structural variations and systematic structural changes of the oceanic plate toward the trench, we conducted an active-source seismic survey off Miyagi using R/V Kaimei, a new research vessel of JAMSTEC. Along a 100 km-long seismic profile which is approximately perpendicular to the trench axis, we deployed 40 ocean-bottom seismometers at intervals of 2 km and fired a large airgun array (total volume 10,600 cubic inches) with 100 m shooting intervals. Multi-channel seismic reflection data were also collected along the profile. On OBS records we observed refractions from the sedimentary layer and the oceanic crust (Pg), wide-angle reflections from the crust-mantle boundary (PmP), and refractions from the uppermost mantle (Pn). Pg is typically observed clearly at near offsets (approximately 20 km) but it highly attenuates at far offsets (> 20 km). A triplication of Pg-PmP-Pn with strong amplitudes is observed at ranges from 30 km to 60 km offsets. Pn is typically weak and its apparent velocity is approximately 8 km/sec. High attenuation of Pg and weak Pn may indicate the complex crustal structure related to petit-spot volcanic activities and/or a fracture zone, which are recognized in bathymetry data around the profile.

Large deviation approach to the generalized random energy model

NASA Astrophysics Data System (ADS)

Dorlas, T. C.; Dukes, W. M. B.

2002-05-01

The generalized random energy model is a generalization of the random energy model introduced by Derrida to mimic the ultrametric structure of the Parisi solution of the Sherrington-Kirkpatrick model of a spin glass. It was solved exactly in two special cases by Derrida and Gardner. A complete solution for the thermodynamics in the general case was given by Capocaccia et al. Here we use large deviation theory to analyse the model in a very straightforward way. We also show that the variational expression for the free energy can be evaluated easily using the Cauchy-Schwarz inequality.

Landslides in Valles Marineris, Mars.

USGS Publications Warehouse

Lucchitta, B.K.

1979-01-01

Large landslides in the Martian equatorial troughs have been investigated with respect to morphology, geologic structure of the troughs, time of emplacement, similarity to terrestrial landslides, and origin and mechanism of transport. The morphologic variations of the landslides can be attributed mainly to their degree of confinement on trough floors. The huge size of many landslides is due to their occurrence on fault scarps that may have attained several kilometers in height in the absence of vigorous fluvial erosion on Mars. The mechanical efficiency of the Martian landslides is high but in accord with predictions from large landslides on earth. -from Author

Linking plant and ecosystem functional biogeography.

PubMed

Reichstein, Markus; Bahn, Michael; Mahecha, Miguel D; Kattge, Jens; Baldocchi, Dennis D

2014-09-23

Classical biogeographical observations suggest that ecosystems are strongly shaped by climatic constraints in terms of their structure and function. On the other hand, vegetation function feeds back on the climate system via biosphere-atmosphere exchange of matter and energy. Ecosystem-level observations of this exchange reveal very large functional biogeographical variation of climate-relevant ecosystem functional properties related to carbon and water cycles. This variation is explained insufficiently by climate control and a classical plant functional type classification approach. For example, correlations between seasonal carbon-use efficiency and climate or environmental variables remain below 0.6, leaving almost 70% of variance unexplained. We suggest that a substantial part of this unexplained variation of ecosystem functional properties is related to variations in plant and microbial traits. Therefore, to progress with global functional biogeography, we should seek to understand the link between organismic traits and flux-derived ecosystem properties at ecosystem observation sites and the spatial variation of vegetation traits given geoecological covariates. This understanding can be fostered by synergistic use of both data-driven and theory-driven ecological as well as biophysical approaches.

Linking plant and ecosystem functional biogeography

PubMed Central

Reichstein, Markus; Bahn, Michael; Mahecha, Miguel D.; Kattge, Jens; Baldocchi, Dennis D.

2014-01-01

Classical biogeographical observations suggest that ecosystems are strongly shaped by climatic constraints in terms of their structure and function. On the other hand, vegetation function feeds back on the climate system via biosphere–atmosphere exchange of matter and energy. Ecosystem-level observations of this exchange reveal very large functional biogeographical variation of climate-relevant ecosystem functional properties related to carbon and water cycles. This variation is explained insufficiently by climate control and a classical plant functional type classification approach. For example, correlations between seasonal carbon-use efficiency and climate or environmental variables remain below 0.6, leaving almost 70% of variance unexplained. We suggest that a substantial part of this unexplained variation of ecosystem functional properties is related to variations in plant and microbial traits. Therefore, to progress with global functional biogeography, we should seek to understand the link between organismic traits and flux-derived ecosystem properties at ecosystem observation sites and the spatial variation of vegetation traits given geoecological covariates. This understanding can be fostered by synergistic use of both data-driven and theory-driven ecological as well as biophysical approaches. PMID:25225392

Space Technology 5 Multipoint Observations of Temporal and Spatial Variability of Field-Aligned Currents

NASA Technical Reports Server (NTRS)

Le, G.; Wang, Y.; Slavin, J. A.; Strangeway, R. L.

2009-01-01

Space Technology 5 (ST5) is a constellation mission consisting of three microsatellites. It provides the first multipoint magnetic field measurements in low Earth orbit, which enables us to separate spatial and temporal variations. In this paper, we present a study of the temporal variability of field-aligned currents using the ST5 data. We examine the field-aligned current observations during and after a geomagnetic storm and compare the magnetic field profiles at the three spacecraft. The multipoint data demonstrate that mesoscale current structures, commonly embedded within large-scale current sheets, are very dynamic with highly variable current density and/or polarity in approx.10 min time scales. On the other hand, the data also show that the time scales for the currents to be relatively stable are approx.1 min for mesoscale currents and approx.10 min for large-scale currents. These temporal features are very likely associated with dynamic variations of their charge carriers (mainly electrons) as they respond to the variations of the parallel electric field in auroral acceleration region. The characteristic time scales for the temporal variability of mesoscale field-aligned currents are found to be consistent with those of auroral parallel electric field.

Population Structure and Domestication Revealed by High-Depth Resequencing of Korean Cultivated and Wild Soybean Genomes†

PubMed Central

Chung, Won-Hyong; Jeong, Namhee; Kim, Jiwoong; Lee, Woo Kyu; Lee, Yun-Gyeong; Lee, Sang-Heon; Yoon, Woongchang; Kim, Jin-Hyun; Choi, Ik-Young; Choi, Hong-Kyu; Moon, Jung-Kyung; Kim, Namshin; Jeong, Soon-Chun

2014-01-01

Despite the importance of soybean as a major crop, genome-wide variation and evolution of cultivated soybeans are largely unknown. Here, we catalogued genome variation in an annual soybean population by high-depth resequencing of 10 cultivated and 6 wild accessions and obtained 3.87 million high-quality single-nucleotide polymorphisms (SNPs) after excluding the sites with missing data in any accession. Nuclear genome phylogeny supported a single origin for the cultivated soybeans. We identified 10-fold longer linkage disequilibrium (LD) in the wild soybean relative to wild maize and rice. Despite the small population size, the long LD and large SNP data allowed us to identify 206 candidate domestication regions with significantly lower diversity in the cultivated, but not in the wild, soybeans. Some of the genes in these candidate regions were associated with soybean homologues of canonical domestication genes. However, several examples, which are likely specific to soybean or eudicot crop plants, were also observed. Consequently, the variation data identified in this study should be valuable for breeding and for identifying agronomically important genes in soybeans. However, the long LD of wild soybeans may hinder pinpointing causal gene(s) in the candidate regions. PMID:24271940

Structural variation in transition-metal bispidine compounds.

PubMed

Comba, Peter; Kerscher, Marion; Merz, Michael; Müller, Vera; Pritzkow, Hans; Remenyi, Rainer; Schiek, Wolfgang; Xiong, Yun

2002-12-16

The experimentally determined molecular structures of 40 transition metal complexes with the tetradentate bispyridine-substituted bispidone ligand, 2,4-bis(2-pyridine)-3,7-diazabicyclo[3.3.1]nonane-9-one [M(bisp)XYZ]n+; M = CrIII, MnII, FeII, CoII, CuII, CuI, ZnII; X, Y, Z = mono- or bidentate co-ligands; penta-, hexa- or heptacoordinate complexes) are characterized in detail, supported by force-field and DFT calculations. While the bispidine ligand is very rigid (N3...N7 distance = 2.933 +/- 0.025 A), it tolerates a large range of metal-donor bond lengths (2.07 A < sigma(M-N)/4 < 2.35 A). Of particular interest is the ratio of the bond lengths between the metal center and the two tertiary amine donors (0.84 A < M-N3/M-N7 < 1.05 A) and the fact that, in terms of this ratio there seem to be two clusters with M-N3 < M-N7 and M-N3 > or = M-N7. Calculations indicate that the two structural types are close to degenerate, and the structural form therefore depends on the metal ion, the number and type of co-ligands, as well as structural variations of the bispidine ligand backbone. Tuning of the structures is of importance since the structurally differing complexes have very different stabilities and reactivities.

Optimizing weak lensing mass estimates for cluster profile uncertainty

DOE PAGES

Gruen, D.; Bernstein, G. M.; Lam, T. Y.; ...

2011-09-11

Weak lensing measurements of cluster masses are necessary for calibrating mass-observable relations (MORs) to investigate the growth of structure and the properties of dark energy. However, the measured cluster shear signal varies at fixed mass M 200m due to inherent ellipticity of background galaxies, intervening structures along the line of sight, and variations in the cluster structure due to scatter in concentrations, asphericity and substructure. We use N-body simulated halos to derive and evaluate a weak lensing circular aperture mass measurement M ap that minimizes the mass estimate variance <(M ap - M 200m) 2> in the presence of allmore » these forms of variability. Depending on halo mass and observational conditions, the resulting mass estimator improves on M ap filters optimized for circular NFW-profile clusters in the presence of uncorrelated large scale structure (LSS) about as much as the latter improve on an estimator that only minimizes the influence of shape noise. Optimizing for uncorrelated LSS while ignoring the variation of internal cluster structure puts too much weight on the profile near the cores of halos, and under some circumstances can even be worse than not accounting for LSS at all. As a result, we discuss the impact of variability in cluster structure and correlated structures on the design and performance of weak lensing surveys intended to calibrate cluster MORs.« less

A crustal seismic velocity model for the UK, Ireland and surrounding seas

USGS Publications Warehouse

Kelly, A.; England, R.W.; Maguire, Peter K.H.

2007-01-01

A regional model of the 3-D variation in seismic P-wave velocity structure in the crust of NW Europe has been compiled from wide-angle reflection/refraction profiles. Along each 2-D profile a velocity-depth function has been digitised at 5 km intervals. These 1-D velocity functions were mapped into three dimensions using ordinary kriging with weights determined to minimise the difference between digitised and interpolated values. An analysis of variograms of the digitised data suggested a radial isotropic weighting scheme was most appropriate. Horizontal dimensions of the model cells are optimised at 40 ?? 40 km and the vertical dimension at 1 km. The resulting model provides a higher resolution image of the 3-D variation in seismic velocity structure of the UK, Ireland and surrounding areas than existing models. The construction of the model through kriging allows the uncertainty in the velocity structure to be assessed. This uncertainty indicates the high density of data required to confidently interpolate the crustal velocity structure, and shows that for this region the velocity is poorly constrained for large areas away from the input data. ?? 2007 The Authors Journal compilation ?? 2007 RAS.

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

Yang, Hao; Lee, H. S.; Sarahan, M. C.

Grain boundaries (GBs) in complex oxides such as perovskites have been shown to readily accommodate nonstoichiometry changing the electrostatic potential at the boundary plane and effectively controlling material properties such as capacitance, magnetoresistance and superconductivity. Understanding and quantifying exactly how variations in atomic scale nonstoichiometry at the boundary plane extend to the practical mesoscale operating length of the system is therefore critical for improving the overall properties. Bicrystals of SrTiO 3 were fabricated to provide the model GB model structures that are analysed in this paper. We show that statistical analysis of aberration-corrected scanning transmission electron microscope images acquired frommore » a large area of GB is an effective routine to understanding the variation in boundary structure that occurs to accommodate nonstoichiometry. In the case of the SrTiO 3 22.6° Σ13 (510)/[100] GB analysed here, the symmetric atomic structures observed from a micron-long GB can be categorized as two different competing structural arrangements, with and without a rigid-body translation along the boundary plane. How this quantified experimental approach can provide direct insights into the GB energetics is further confirmed from the first principles density functional theory, and the effect of nonstoichiometry in determining the GB energies is quantified.« less

A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome

PubMed Central

Mathias, Rasika Ann; Taub, Margaret A.; Gignoux, Christopher R.; Fu, Wenqing; Musharoff, Shaila; O'Connor, Timothy D.; Vergara, Candelaria; Torgerson, Dara G.; Pino-Yanes, Maria; Shringarpure, Suyash S.; Huang, Lili; Rafaels, Nicholas; Boorgula, Meher Preethi; Johnston, Henry Richard; Ortega, Victor E.; Levin, Albert M.; Song, Wei; Torres, Raul; Padhukasahasram, Badri; Eng, Celeste; Mejia-Mejia, Delmy-Aracely; Ferguson, Trevor; Qin, Zhaohui S.; Scott, Alan F.; Yazdanbakhsh, Maria; Wilson, James G.; Marrugo, Javier; Lange, Leslie A.; Kumar, Rajesh; Avila, Pedro C.; Williams, L. Keoki; Watson, Harold; Ware, Lorraine B.; Olopade, Christopher; Olopade, Olufunmilayo; Oliveira, Ricardo; Ober, Carole; Nicolae, Dan L.; Meyers, Deborah; Mayorga, Alvaro; Knight-Madden, Jennifer; Hartert, Tina; Hansel, Nadia N.; Foreman, Marilyn G.; Ford, Jean G.; Faruque, Mezbah U.; Dunston, Georgia M.; Caraballo, Luis; Burchard, Esteban G.; Bleecker, Eugene; Araujo, Maria Ilma; Herrera-Paz, Edwin Francisco; Gietzen, Kimberly; Grus, Wendy E.; Bamshad, Michael; Bustamante, Carlos D.; Kenny, Eimear E.; Hernandez, Ryan D.; Beaty, Terri H.; Ruczinski, Ingo; Akey, Joshua; Campbell, Monica; Chavan, Sameer; Foster, Cassandra; Gao, Li; Horowitz, Edward; Ortiz, Romina; Potee, Joseph; Gao, Jingjing; Hu, Yijuan; Hansen, Mark; Deshpande, Aniket; Locke, Devin P.; Grammer, Leslie; Kim, Kwang-YounA; Schleimer, Robert; De La Vega, Francisco M.; Szpiech, Zachary A.; Oluwole, Oluwafemi; Arinola, Ganiyu; Correa, Adolfo; Musani, Solomon; Chong, Jessica; Nickerson, Deborah; Reiner, Alexander; Maul, Pissamai; Maul, Trevor; Martinez, Beatriz; Meza, Catherine; Ayestas, Gerardo; Landaverde-Torres, Pamela; Erazo, Said Omar Leiva; Martinez, Rosella; Mayorga, Luis F.; Ramos, Hector; Saenz, Allan; Varela, Gloria; Vasquez, Olga Marina; Samms-Vaughan, Maureen; Wilks, Rainford J.; Adegnika, Akim; Ateba-Ngoa, Ulysse; Barnes, Kathleen C.

2016-01-01

The African Diaspora in the Western Hemisphere represents one of the largest forced migrations in history and had a profound impact on genetic diversity in modern populations. To date, the fine-scale population structure of descendants of the African Diaspora remains largely uncharacterized. Here we present genetic variation from deeply sequenced genomes of 642 individuals from North and South American, Caribbean and West African populations, substantially increasing the lexicon of human genomic variation and suggesting much variation remains to be discovered in African-admixed populations in the Americas. We summarize genetic variation in these populations, quantifying the postcolonial sex-biased European gene flow across multiple regions. Moreover, we refine estimates on the burden of deleterious variants carried across populations and how this varies with African ancestry. Our data are an important resource for empowering disease mapping studies in African-admixed individuals and will facilitate gene discovery for diseases disproportionately affecting individuals of African ancestry. PMID:27725671

Escher in color space: individual-differences multidimensional scaling of color dissimilarities collected with a gestalt formation task.

PubMed

Bimler, David; Kirkland, John; Pichler, Shaun

2004-02-01

The structure of color perception can be examined by collecting judgments about color dissimilarities. In the procedure used here, stimuli are presented three at a time on a computer monitor and the spontaneous grouping of most-similar stimuli into gestalts provides the dissimilarity comparisons. Analysis with multidimensional scaling allows such judgments to be pooled from a number of observers without obscuring the variations among them. The anomalous perceptions of color-deficient observers produce comparisons that are represented well by a geometric model of compressed individual color spaces, with different forms of deficiency distinguished by different directions of compression. The geometrical model is also capable of accommodating the normal spectrum of variation, so that there is greater variation in compression parameters between tests on normal subjects than in those between repeated tests on individual subjects. The method is sufficiently sensitive and the variations sufficiently large that they are not obscured by the use of a range of monitors, even under somewhat loosely controlled conditions.

Helioseismology Observations of Solar Cycles and Dynamo Modeling

NASA Astrophysics Data System (ADS)

Kosovichev, A. G.; Guerrero, G.; Pipin, V.

2017-12-01

Helioseismology observations from the SOHO and SDO, obtained in 1996-2017, provide unique insight into the dynamics of the Sun's deep interior for two solar cycles. The data allow us to investigate variations of the solar interior structure and dynamics, and compare these variations with dynamo models and simulations. We use results of the local and global helioseismology data processing pipelines at the SDO Joint Science Operations Center (Stanford University) to study solar-cycle variations of the differential rotation, meridional circulation, large-scale flows and global asphericity. By comparing the helioseismology results with the evolution of surface magnetic fields we identify characteristic changes associated the initiation and development of Solar Cycles 23 and 24. For the physical interpretation of observed variations, the results are compared with the current mean-field dynamo models and 3D MHD dynamo simulations. It is shown that the helioseismology inferences provide important constraints on the solar dynamo mechanism, may explain the fundamental difference between the two solar cycles, and also give information about the next solar cycle.

Structural inheritance and selective reactivation in the central Andes: Cenozoic deformation guided by pre-Andean structures in southern Peru

NASA Astrophysics Data System (ADS)

Perez, Nicholas D.; Horton, Brian K.; Carlotto, Victor

2016-03-01

Structural, stratigraphic, and geochronologic constraints from the Eastern Cordillera in the central Andean plateau of southern Peru (14-15°S) demonstrate the existence and position of major pre-Andean structures that controlled the accumulation of Triassic synrift fill and guided subsequent Cenozoic deformation. The timing of initial clastic deposition of the Triassic Mitu Group is here constrained to ~ 242-233 Ma on the basis of detrital and volcanic zircon U-Pb geochronology. Regionally distinct provenance variations, as provided by U-Pb age populations from localized synrift accumulations, demonstrate Triassic erosion of multiple diagnostic sources from diverse rift-flank uplifts. Stratigraphic correlations suggest synchronous initiation of extensional basins containing the Mitu Group, in contrast with previous interpretations of southward rift propagation. Triassic motion along the NE-dipping San Anton normal fault accommodated up to 7 km of throw and hanging-wall deposition of a synrift Mitu succession > 2.5 km thick. The contrasting orientation of a non-reactivated Triassic normal fault suggests selective inversion of individual structures in the Eastern Cordillera was dependent on fault dip and strike. Selective preservation of a ~ 4 km thick succession of Carboniferous-Permian strata in the down-dropped San Anton hanging wall, beneath the synrift Mitu Group, suggests large-scale erosional removal in the uplifted footwall. Field and map observations identify additional pre-Andean thrust faults and folds attributed to poorly understood Paleozoic orogenic events preserved in the San Anton hanging wall. Selective thrust reactivation of normal and reverse faults during later compression largely guided Cenozoic deformation in the Eastern Cordillera. The resulting structural compartmentalization and across-strike variations in kinematics and deformation style highlight the influence of inherited Paleozoic structures and Triassic normal faults on the long-term history of convergent margin deformation in the Andes.

Investigation of magnetization dynamics in 2D Ni80Fe20 diatomic nanodot arrays

NASA Astrophysics Data System (ADS)

De, Anulekha; Mondal, Sucheta; Banerjee, Chandrima; Chaurasiya, Avinash K.; Mandal, Ruma; Otani, Yoshichika; Mitra, Rajib K.; Barman, Anjan

2017-09-01

Magnetization dynamics in Ni80Fe20 (Py) diatomic nanodots (nanodots of the same thickness but with large and small diameters that are closely placed to each other so as to act as a diatomic basis structure) embedded in 2D arrays have been investigated by the Brillouin light scattering technique. A distinct variation of resonant mode characteristics for different in-plane bias magnetic field applied along two different orientations of the lattice has been observed. Micromagnetic simulations reproduced the observed dynamical behaviour and revealed the variation of spatial distribution of collective modes of constituent single nanodots with different diameter and a diatomic unit forming the large array to understand the evolution of the magnetization dynamics from a single dot to the large array via a diatomic unit. The changes in mode frequency, spatial profiles of the modes, and appearance of new modes in a diatomic unit and its array from that of the constituent single dots indicate the strong magnetostatic interaction among the dots within the diatomic unit. Also, the occurrence of the new interacting mode at different frequencies for different orientations of the bias field indicates the change in the nature of interaction among the dots within the diatomic unit with bias magnetic field. The mode profiles also show distinct behaviour for smooth and rough-edged dots. This work motivates the study of magnonic band structure formation of such a dipolarly coupled nanodot array containing a complex double-dot unit cell.

Estimating Eulerian spectra from pairs of drifters

NASA Astrophysics Data System (ADS)

LaCasce, Joe

2017-04-01

GPS-tracked surface drifters offer the possibility of sampling energetic variations at the ocean surface on scales of only 10s of meters, much less than that resolved by satellite. Here we investigate whether velocity differences between pairs of drifters can be used to estimate kinetic energy spectra. Theoretical relations between the spectrum and the second-order longitudinal structure function for 2D non-divergent flow are derived. The structure function is a natural statistic for particle pairs and is easily calculated. However it integrates contributions across wavenumber, and this tends to obscure the spectral dependencies when turbulent inertial ranges are of finite extent. Nevertheless, the transform from spectrum to structure function is robust, as illustrated with Eulerian data collected from aircraft. The inverse transform, from structure function to spectrum, is much less robust, yielding poor results in particular at large wavenumbers. This occurs because the transform involves a filter function which magnifies contributions from large pair separations, which tend to be noisy. Fitting the structure function to a polynomial improves the spectral estimate, but not sufficiently to distinguish correct inertial range dependencies. Thus with Lagrangian data, it is appears preferable to focus on structure functions, despite their shortcomings.

Seismic velocity variation along the Izu-Bonin arc estaimated from traveltime tomography using OBS data

NASA Astrophysics Data System (ADS)

Obana, K.; Tamura, Y.; Takahashi, T.; Kodaira, S.

2014-12-01

The Izu-Bonin (Ogasawara) arc is an intra-oceanic island arc along the convergent plate boundary between the subducting Pacific and overriding Philippine Sea plates. Recent active seismic studies in the Izu-Bonin arc reveal significant along-arc variations in crustal structure [Kodaira et al., 2007]. The thickness of the arc crust shows a remarkable change between thicker Izu (~30 km) and thinner Bonin (~10 km) arcs. In addition to this, several geological and geophysical contrasts, such as seafloor topography and chemical composition of volcanic rocks, between Izu and Bonin arc have been reported [e.g., Yuasa 1992]. We have conducted earthquake observations using ocean bottom seismographs (OBSs) to reveal seismic velocity structure of the crust and mantle wedge in the Izu-Bonin arc and to investigate origin of the along-arc structure variations. We deployed 40 short-period OBSs in Izu and Bonin area in 2006 and 2009, respectively. The OBS data were processed with seismic data recorded at routine seismic stations on Hachijo-jima, Aoga-shima, and Chichi-jima operated by National Research Institute for Earth Science and Disaster Prevention (NIED). More than 5000 earthquakes were observed during about three-months observation period in each experiment. We conducted three-dimensional seismic tomography using manually picked P- and S-wave arrival time data. The obtained image shows a different seismic velocity structures in the mantle beneath the volcanic front between Izu and Bonin arcs. Low P-wave velocity anomalies in the mantle beneath the volcanic front in the Izu arc are limited at depths deeper than those in the Bonin arc. On the other hand, P-wave velocity in the low velocity anomalies beneath volcanic front in the Bonin arc is slower than that in the Izu arc. These large-scale along-arc structure variations in the mantle could relate to the geological and geophysical contrasts between Izu and Bonin arcs.

Among-Population Variation in Microbial Community Structure in the Floral Nectar of the Bee-Pollinated Forest Herb Pulmonaria officinalis L

PubMed Central

Jacquemyn, Hans; Lenaerts, Marijke; Brys, Rein; Willems, Kris; Honnay, Olivier; Lievens, Bart

2013-01-01

Background Microbial communities in floral nectar have been shown to be characterized by low levels of species diversity, yet little is known about among-plant population variation in microbial community composition. Methodology/Principal Findings We investigated the microbial community structure (yeasts and bacteria) in floral nectar of ten fragmented populations of the bee-pollinated forest herb Pulmonaria officinalis. We also explored possible relationships between plant population size and microbial diversity in nectar, and related microbial community composition to the distance separating plant populations. Culturable bacteria and yeasts occurring in the floral nectar of a total of 100 plant individuals were isolated and identified by partially sequencing the 16S rRNA gene and D1/D2 domains of the 26S rRNA gene, respectively. A total of 9 and 11 yeast and 28 and 39 bacterial OTUs was found, taking into account a 3% (OTU0.03) and 1% sequence dissimilarity cut-off (OTU0.01). OTU richness at the plant population level (i.e. the number of OTUs per population) was low for yeasts (mean: 1.7, range: 0–4 OTUs0.01/0.03 per population), whereas on average 6.9 (range: 2–13) OTUs0.03 and 7.9 (range 2–16) OTUs0.01 per population were found for bacteria. Both for yeasts and bacteria, OTU richness was not significantly related to plant population size. Similarity in community composition among populations was low (average Jaccard index: 0.14), and did not decline with increasing distance between populations. Conclusions/Significance We found low similarity in microbial community structure among populations, suggesting that the assembly of nectar microbiota is to a large extent context-dependent. Although the precise factors that affect variation in microbial community structure in floral nectar require further study, our results indicate that both local and regional processes may contribute to among-population variation in microbial community structure in nectar. PMID:23536759

Among-population variation in microbial community structure in the floral nectar of the bee-pollinated forest herb Pulmonaria officinalis L.

PubMed

Jacquemyn, Hans; Lenaerts, Marijke; Brys, Rein; Willems, Kris; Honnay, Olivier; Lievens, Bart

2013-01-01

Microbial communities in floral nectar have been shown to be characterized by low levels of species diversity, yet little is known about among-plant population variation in microbial community composition. We investigated the microbial community structure (yeasts and bacteria) in floral nectar of ten fragmented populations of the bee-pollinated forest herb Pulmonaria officinalis. We also explored possible relationships between plant population size and microbial diversity in nectar, and related microbial community composition to the distance separating plant populations. Culturable bacteria and yeasts occurring in the floral nectar of a total of 100 plant individuals were isolated and identified by partially sequencing the 16S rRNA gene and D1/D2 domains of the 26S rRNA gene, respectively. A total of 9 and 11 yeast and 28 and 39 bacterial OTUs was found, taking into account a 3% (OTU0.03) and 1% sequence dissimilarity cut-off (OTU0.01). OTU richness at the plant population level (i.e. the number of OTUs per population) was low for yeasts (mean: 1.7, range: 0-4 OTUs0.01/0.03 per population), whereas on average 6.9 (range: 2-13) OTUs0.03 and 7.9 (range 2-16) OTUs0.01 per population were found for bacteria. Both for yeasts and bacteria, OTU richness was not significantly related to plant population size. Similarity in community composition among populations was low (average Jaccard index: 0.14), and did not decline with increasing distance between populations. We found low similarity in microbial community structure among populations, suggesting that the assembly of nectar microbiota is to a large extent context-dependent. Although the precise factors that affect variation in microbial community structure in floral nectar require further study, our results indicate that both local and regional processes may contribute to among-population variation in microbial community structure in nectar.

Dissecting the multi-scale spatial relationship of earthworm assemblages with soil environmental variability.

PubMed

Jiménez, Juan J; Decaëns, Thibaud; Lavelle, Patrick; Rossi, Jean-Pierre

2014-12-05

Studying the drivers and determinants of species, population and community spatial patterns is central to ecology. The observed structure of community assemblages is the result of deterministic abiotic (environmental constraints) and biotic factors (positive and negative species interactions), as well as stochastic colonization events (historical contingency). We analyzed the role of multi-scale spatial component of soil environmental variability in structuring earthworm assemblages in a gallery forest from the Colombian "Llanos". We aimed to disentangle the spatial scales at which species assemblages are structured and determine whether these scales matched those expressed by soil environmental variables. We also tested the hypothesis of the "single tree effect" by exploring the spatial relationships between root-related variables and soil nutrient and physical variables in structuring earthworm assemblages. Multivariate ordination techniques and spatially explicit tools were used, namely cross-correlograms, Principal Coordinates of Neighbor Matrices (PCNM) and variation partitioning analyses. The relationship between the spatial organization of earthworm assemblages and soil environmental parameters revealed explicitly multi-scale responses. The soil environmental variables that explained nested population structures across the multi-spatial scale gradient differed for earthworms and assemblages at the very-fine- (<10 m) to medium-scale (10-20 m). The root traits were correlated with areas of high soil nutrient contents at a depth of 0-5 cm. Information on the scales of PCNM variables was obtained using variogram modeling. Based on the size of the plot, the PCNM variables were arbitrarily allocated to medium (>30 m), fine (10-20 m) and very fine scales (<10 m). Variation partitioning analysis revealed that the soil environmental variability explained from less than 1% to as much as 48% of the observed earthworm spatial variation. A large proportion of the spatial variation did not depend on the soil environmental variability for certain species. This finding could indicate the influence of contagious biotic interactions, stochastic factors, or unmeasured relevant soil environmental variables.

Intra-isolate genome variation in arbuscular mycorrhizal fungi persists in the transcriptome.

PubMed

Boon, E; Zimmerman, E; Lang, B F; Hijri, M

2010-07-01

Arbuscular mycorrhizal fungi (AMF) are heterokaryotes with an unusual genetic makeup. Substantial genetic variation occurs among nuclei within a single mycelium or isolate. AMF reproduce through spores that contain varying fractions of this heterogeneous population of nuclei. It is not clear whether this genetic variation on the genome level actually contributes to the AMF phenotype. To investigate the extent to which polymorphisms in nuclear genes are transcribed, we analysed the intra-isolate genomic and cDNA sequence variation of two genes, the large subunit ribosomal RNA (LSU rDNA) of Glomus sp. DAOM-197198 (previously known as G. intraradices) and the POL1-like sequence (PLS) of Glomus etunicatum. For both genes, we find high sequence variation at the genome and transcriptome level. Reconstruction of LSU rDNA secondary structure shows that all variants are functional. Patterns of PLS sequence polymorphism indicate that there is one functional gene copy, PLS2, which is preferentially transcribed, and one gene copy, PLS1, which is a pseudogene. This is the first study that investigates AMF intra-isolate variation at the transcriptome level. In conclusion, it is possible that, in AMF, multiple nuclear genomes contribute to a single phenotype.

STELLAR STRUCTURE AND TESTS OF MODIFIED GRAVITY

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

Chang, Philip; Hui, Lam, E-mail: pchang@cita.utoronto.ca, E-mail: lhui@astro.columbia.edu

2011-05-01

Theories that attempt to explain cosmic acceleration by modifying gravity typically introduces a long-range scalar force that needs to be screened on small scales. One common screening mechanism is the chameleon, where the scalar force is screened in environments with a sufficiently deep gravitational potential, but acts unimpeded in regions with a shallow gravitational potential. This leads to a variation in the overall gravitational G with environment. We show that such a variation can occur within a star itself, significantly affecting its evolution and structure, provided that the host galaxy is unscreened. The effect is most pronounced for red giants,more » which would be smaller by a factor of tens of percent and thus hotter by hundreds of Kelvin, depending on the parameters of the underlying scalar-tensor theory. Careful measurements of these stars in suitable environments (nearby dwarf galaxies not associated with groups or clusters) would provide constraints on the chameleon mechanism that are four orders of magnitude better than current large-scale structure limits and two orders of magnitude better than present solar system tests.« less

Review of probabilistic analysis of dynamic response of systems with random parameters

NASA Technical Reports Server (NTRS)

Kozin, F.; Klosner, J. M.

1989-01-01

The various methods that have been studied in the past to allow probabilistic analysis of dynamic response for systems with random parameters are reviewed. Dynamic response may have been obtained deterministically if the variations about the nominal values were small; however, for space structures which require precise pointing, the variations about the nominal values of the structural details and of the environmental conditions are too large to be considered as negligible. These uncertainties are accounted for in terms of probability distributions about their nominal values. The quantities of concern for describing the response of the structure includes displacements, velocities, and the distributions of natural frequencies. The exact statistical characterization of the response would yield joint probability distributions for the response variables. Since the random quantities will appear as coefficients, determining the exact distributions will be difficult at best. Thus, certain approximations will have to be made. A number of techniques that are available are discussed, even in the nonlinear case. The methods that are described were: (1) Liouville's equation; (2) perturbation methods; (3) mean square approximate systems; and (4) nonlinear systems with approximation by linear systems.

Numerical modeling of the load effect on PZT-induced guided wave for load compensation of damage detection

NASA Astrophysics Data System (ADS)

Sun, Hu; Zhang, Aijia; Wang, Yishou; Qing, Xinlin P.

2017-04-01

Guided wave-based structural health monitoring (SHM) has been given considerable attention and widely studied for large-scale aircraft structures. Nevertheless, it is difficult to apply SHM systems on board or online, for which one of the most serious reasons is the environmental influence. Load is one fact that affects not only the host structure, in which guided wave propagates, but also the PZT, by which guided wave is transmitted and received. In this paper, numerical analysis using finite element method is used to study the load effect on guided wave acquired by PZT. The static loads with different grades are considered to analyze its effect on guided wave signals that PZT transmits and receives. Based on the variation trend of guided waves versus load, a load compensation method is developed to eliminate effects of load in the process of damage detection. The probabilistic reconstruction algorithm based on the signal variation of transmitter-receiver path is employed to identify the damage. Numerical tests is conducted to verify the feasibility and effectiveness of the given method.

Local richness along gradients in the Siskiyou herb flora: R.H. Whittaker revisited

USGS Publications Warehouse

Grace, James B.; Harrison, Susan; Damschen, Ellen Ingman

2011-01-01

In his classic study in the Siskiyou Mountains (Oregon, USA), one of the most botanically rich forested regions in North America, R. H. Whittaker (1960) foreshadowed many modern ideas on the multivariate control of local species richness along environmental gradients related to productivity. Using a structural equation model to analyze his data, which were never previously statistically analyzed, we demonstrate that Whittaker was remarkably accurate in concluding that local herb richness in these late-seral forests is explained to a large extent by three major abiotic gradients (soils, topography, and elevation), and in turn, by the effects of these gradients on tree densities and the numbers of individual herbs. However, while Whittaker also clearly appreciated the significance of large-scale evolutionary and biogeographic influences on community composition, he did not fully articulate the more recent concept that variation in the species richness of local communities could be explained in part by variation in the sizes of regional species pools. Our model of his data is among the first to use estimates of regional species pool size to explain variation in local community richness along productivity-related gradients. We find that regional pool size, combined with a modest number of other interacting abiotic and biotic factors, explains most of the variation in local herb richness in the Siskiyou biodiversity hotspot.

Copy number variation signature to predict human ancestry

PubMed Central

2012-01-01

Background Copy number variations (CNVs) are genomic structural variants that are found in healthy populations and have been observed to be associated with disease susceptibility. Existing methods for CNV detection are often performed on a sample-by-sample basis, which is not ideal for large datasets where common CNVs must be estimated by comparing the frequency of CNVs in the individual samples. Here we describe a simple and novel approach to locate genome-wide CNVs common to a specific population, using human ancestry as the phenotype. Results We utilized our previously published Genome Alteration Detection Analysis (GADA) algorithm to identify common ancestry CNVs (caCNVs) and built a caCNV model to predict population structure. We identified a 73 caCNV signature using a training set of 225 healthy individuals from European, Asian, and African ancestry. The signature was validated on an independent test set of 300 individuals with similar ancestral background. The error rate in predicting ancestry in this test set was 2% using the 73 caCNV signature. Among the caCNVs identified, several were previously confirmed experimentally to vary by ancestry. Our signature also contains a caCNV region with a single microRNA (MIR270), which represents the first reported variation of microRNA by ancestry. Conclusions We developed a new methodology to identify common CNVs and demonstrated its performance by building a caCNV signature to predict human ancestry with high accuracy. The utility of our approach could be extended to large case–control studies to identify CNV signatures for other phenotypes such as disease susceptibility and drug response. PMID:23270563

Attenuation Model Using the Large-N Array from the Source Physics Experiment

NASA Astrophysics Data System (ADS)

Atterholt, J.; Chen, T.; Snelson, C. M.; Mellors, R. J.

2017-12-01

The Source Physics Experiment (SPE) consists of a series of chemical explosions at the Nevada National Security Site. SPE seeks to better characterize the influence of subsurface heterogeneities on seismic wave propagation and energy dissipation from explosions. As a part of this experiment, SPE-5, a 5000 kg TNT equivalent chemical explosion, was detonated in 2016. During the SPE-5 experiment, a Large-N array of 996 geophones (half 3-component and half z-component) was deployed. This array covered an area that includes loosely consolidated alluvium (weak rock) and weathered granite (hard rock), and recorded the SPE-5 explosion as well as 53 weight drops. We use these Large-N recordings to develop an attenuation model of the area to better characterize how geologic structures influence source energy partitioning. We found a clear variation in seismic attenuation for different rock types: high attenuation (low Q) for alluvium and low attenuation (high Q) for granite. The attenuation structure correlates well with local geology, and will be incorporated into the large simulation effort of the SPE program to validate predictive models. (LA-UR-17-26382)

Patterns in Benthic Biodiversity Link Lake Trophic Status to Structure and Potential Function of Three Large, Deep Lakes

PubMed Central

Hayford, Barbara L.; Caires, Andrea M.; Chandra, Sudeep; Girdner, Scott F.

2015-01-01

Relative to their scarcity, large, deep lakes support a large proportion of the world’s freshwater species. This biodiversity is threatened by human development and is in need of conservation. Direct comparison of biodiversity is the basis of biological monitoring for conservation but is difficult to conduct between large, insular ecosystems. The objective of our study was to conduct such a comparison of benthic biodiversity between three of the world’s largest lakes: Lake Tahoe, USA; Lake Hövsgöl, Mongolia; and Crater Lake, USA. We examined biodiversity of common benthic organism, the non-biting midges (Chironomidae) and determined lake trophic status using chironomid-based lake typology, tested whether community structure was similar between the three lakes despite geographic distance; and tested whether chironomid diversity would show significant variation within and between lakes. Typology analysis indicated that Lake Hövsgöl was ultra-oligotrophic, Crater Lake was oligotrophic, and Lake Tahoe was borderline oligotrophic/mesotrophic. These results were similar to traditional pelagic measures of lake trophic status for Lake Hövsgöl and Crater Lake but differed for Lake Tahoe, which has been designated as ultra-oligotrophic by traditional pelagic measures such as transparency found in the literature. Analysis of similarity showed that Lake Tahoe and Lake Hövsgöl chironomid communities were more similar to each other than either was to Crater Lake communities. Diversity varied between the three lakes and spatially within each lake. This research shows that chironomid communities from these large lakes were sensitive to trophic conditions. Chironomid communities were similar between the deep environments of Lake Hövsgöl and Lake Tahoe, indicating that chironomid communities from these lakes may be useful in comparing trophic state changes in large lakes. Spatial variation in Lake Tahoe’s diversity is indicative of differential response of chironomid communities to nutrient enrichment which may be an indication of changes in trophic state within and across habitats. PMID:25594516

[Soil and forest structure in the Colombian Amazon].

PubMed

Calle-Rendón, Bayron R; Moreno, Flavio; Cárdenas López, Dairon

2011-09-01

Forests structural differences could result of environmental variations at different scales. Because soils are an important component of plant's environment, it is possible that edaphic and structural variables are associated and that, in consequence, spatial autocorrelation occurs. This paper aims to answer two questions: (1) are structural and edaphic variables associated at local scale in a terra firme forest of Colombian Amazonia? and (2) are these variables regionalized at the scale of work? To answer these questions we analyzed the data of a 6ha plot established in a terra firme forest of the Amacayacu National Park. Structural variables included basal area and density of large trees (diameter > or = 10cm) (Gdos and Ndos), basal area and density of understory individuals (diameter < 10cm) (Gsot and Nsot) and number of species of large trees (sp). Edaphic variables included were pH, organic matter, P, Mg, Ca, K, Al, sand, silt and clay. Structural and edaphic variables were reduced through a principal component analysis (PCA); then, the association between edaphic and structural components from PCA was evaluated by multiple regressions. The existence of regionalization of these variables was studied through isotropic variograms, and autocorrelated variables were spatially mapped. PCA found two significant components for structure, corresponding to the structure of large trees (G, Gdos, Ndos and sp) and of small trees (N, Nsot and Gsot), which explained 43.9% and 36.2% of total variance, respectively. Four components were identified for edaphic variables, which globally explained 81.9% of total variance and basically represent drainage and soil fertility. Regression analyses were significant (p < 0.05) and showed that the structure of both large and small trees is associated with greater sand contents and low soil fertility, though they explained a low proportion of total variability (R2 was 4.9% and 16.5% for the structure of large trees and small tress, respectively). Variables with spatial autocorrelation were the structure of small trees, Al, silt, and sand. Among them, Nsot and sand content showed similar patterns of spatial distribution inside the plot.

Large-scale variability in marine stratocumulus clouds defined from simultaneous aircraft and satellite measurements

NASA Technical Reports Server (NTRS)

Albrecht, Bruce A.; Barlow, Roy W.

1990-01-01

Satellite images often show significant variations in the structure of marine stratocumulus clouds on scales ranging from 10 to 1000 km. This is illustrated where a GOES West satellite image shows a well-defined variation in cloud structure near 32 N, 122 W on 30 June 1987. Aircraft measurements were made with the UK C-130 and the NCAR Electra on this day as part of the FIRE Marine Stratocumulus Intensive Field Observations (IFO). The mean, turbulent, and the microphysical structure of the clouds sampled in these two areas are compared an an attempt is made to explain the differences in cloud structure. In an attempt to identify any systematic differences between the measurements made with the two aircraft, data were analyzed that were collected on 14 July 1987 with the C-130 and the Electra flying in close formation at an altitude of 250 m. The microphysical and turbulence data are being compared in an attempt to explain the differences in the cloud liquid water content obtained with the two aircraft and the differences in cloud structure shown by the GOES image. In addition, data are being analyzed for three other days during the experiment when coordinated downstream flights were made with the Electra and the C-130.

Excitonic fine-structure splitting in telecom-wavelength InAs/GaAs quantum dots: Statistical distribution and height-dependence

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

Goldmann, Elias, E-mail: goldmann@itp.uni-bremen.de; Barthel, Stefan; Florian, Matthias

The variation of the excitonic fine-structure splitting is studied for semiconductor quantum dots under the influence of a strain-reducing layer, utilized to shift the emission wavelength of the excitonic transition into the telecom-wavelength regime of 1.3–1.5 μm. By means of a sp{sup 3}s{sup *}-tight-binding model and configuration interaction, we calculate wavelength shifts and fine-structure splittings for various quantum dot geometries. We find the splittings remaining small and even decreasing with strain-reducing layer composition for quantum dots with large height. Combined with an observed increased emission efficiency, the applicability for generation of entanglement photons is persistent.

Gas hydrate and spatial venting variations in the continental margin offshore Southwestern Taiwan

NASA Astrophysics Data System (ADS)

Lin, S.; Lim, Y.; Hsieh, W.; Yang, T.; Wang, Y.

2006-12-01

Strong BSR, high methane contents and rapid sulfate reduction were found in the continental margin sediments offshore southwestern Taiwan. In order to identify the venting phenomena and its relationship with gas hydrate, this research investigate sea floor vent features using WHOI?|s Towcam system as well as piston core in the study region. A total of 10 dives were conducted on board the r/v OR-1. Pore water sulfate, dissolved sulfide, methane, chloride, del O18 ratio, sediment organic carbon, carbonate content and carbonate del C13 ratio, pyrite-S were measured Large spatial variations were found based on pictures obtained from Towcam system and piston cores. Active venting features include bacteria mat, live dense bivalve patches, gas plume, temperature and salinity fluctuations, rapid sulfate reduction and high concentrations of methane in sediments. In addition, vent chimney, pockmark and large authigenic carbonate buildup were also observed in the active venting area. In contrast, in some areas without active venting features, scatter dead chimney, semi- buried carbonate structures, and dead bivalves were found. Total sulfate depletion was found at depth as shallow as 1 meter below sediment water interface in area near active vent whereas almost no sulfate depletion was observed in areas without any vent feature. Stages of carbonate build up existed, with initial phase dominated by small tube, chimney, and later with massive carbonate structures protruding the sea floor. The appearances of massive carbonate buildup structures seemed to indicate the end stage of gas hydrate venting phenomena.

Anthropogenic disturbance and environmental associations with fish assemblage structure in two nonwadeable rivers

USGS Publications Warehouse

Parks, T. P.; Quist, Michael C.; Pierce, C.L.

2016-01-01

Nonwadeable rivers are unique ecosystems that support high levels of aquatic biodiversity, yet they have been greatly altered by human activities. Although riverine fish assemblages have been studied in the past, we still have an incomplete understanding of how fish assemblages respond to both natural and anthropogenic influences in large rivers. The purpose of this study was to evaluate associations between fish assemblage structure and reach-scale habitat, dam, and watershed land use characteristics. In the summers of 2011 and 2012, comprehensive fish and environmental data were collected from 33 reaches in the Iowa and Cedar rivers of eastern-central Iowa. Canonical correspondence analysis (CCA) was used to evaluate environmental relationships with species relative abundance, functional trait abundance (e.g. catch rate of tolerant species), and functional trait composition (e.g. percentage of tolerant species). On the basis of partial CCAs, reach-scale habitat, dam characteristics, and watershed land use features explained 25.0–81.1%, 6.2–25.1%, and 5.8–47.2% of fish assemblage variation, respectively. Although reach-scale, dam, and land use factors contributed to overall assemblage structure, the majority of fish assemblage variation was constrained by reach-scale habitat factors. Specifically, mean annual discharge was consistently selected in nine of the 11 CCA models and accounted for the majority of explained fish assemblage variance by reach-scale habitat. This study provides important insight on the influence of anthropogenic disturbances across multiple spatial scales on fish assemblages in large river systems.

Diurnal stratospheric tide in meridional wind, 30 to 60 KM, by season and monthly mean temperatures, 20 to 60 KM, at 80 deg N and to 0 deg N

NASA Technical Reports Server (NTRS)

Nastrom, G. D.; Belmont, A. D.

1975-01-01

The diurnal component in meridional wind was observed for each season at twelve rocket stations. Amplitudes and phases are presented as a function of height-latitude or as vertical profiles. Many of the gross features of the tide persist throughout the year, but as they migrate in height and latitude the amplitude or phase at a given location may undergo large changes with season. Longitudinal variations in the diurnal tide are found in the mid-stratosphere, and it is suggested they are coupled with longitudinal variations in the tropospheric temperature structure.

X-ray wind tomography of IGR J17252-3616

NASA Astrophysics Data System (ADS)

Manousakis, Antonios; Walter, Roland

IGR J17252-3616 is an heavily absorbed and eclipsing High Mass X-ray Binary with an ab-sorbing hydrogen column density >1023 cm-2 . We have observed it with XMM-Newton to understand the geometry of the absorbing material. Observations were scheduled in order to cover as many orbital phases as possible. Timing analysis is constraining the orbital solution and the physical parameters of the system. Spectral analysis reveals remarkable variations of the absorbing column density and of the Iron Kα fluorescence line around the eclipse. These variations allow to map the geometry of the absorbing and reflection material. Very large accretion structures could be imaged for the first time.

First principle calculation in FeCo overlayer on GaAs substrate

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

Jain, Vishal, E-mail: vjain045@gmail.com; Lakshmi, N.; Jain, Vivek Kumar

In this work the first principle electronic structure calculation is reported for FeCo/GaAs thin film system to investigate the effect of orientation on the electronic structural properties. A unit cell describing FeCo layers and GaAs layers is constructed for (100), (110), (111) orientation with vacuum of 30Å to reduce dimensions. It is found that although the (110) orientation is energetically more favorable than others, the magnetic moment is quite large in (100) and (111) system compared to the (110) and is due to the total DOS variation with orientation.

Image processing for optical mapping.

PubMed

Ravindran, Prabu; Gupta, Aditya

2015-01-01

Optical Mapping is an established single-molecule, whole-genome analysis system, which has been used to gain a comprehensive understanding of genomic structure and to study structural variation of complex genomes. A critical component of Optical Mapping system is the image processing module, which extracts single molecule restriction maps from image datasets of immobilized, restriction digested and fluorescently stained large DNA molecules. In this review, we describe robust and efficient image processing techniques to process these massive datasets and extract accurate restriction maps in the presence of noise, ambiguity and confounding artifacts. We also highlight a few applications of the Optical Mapping system.

The rotation of the Sun: Observations at Stanford. [using the Doppler effect

NASA Technical Reports Server (NTRS)

Scherrer, J. M.; Wilcox, J. M.; Svalgaard, L.

1980-01-01

Daily observations of the photospheric rotation rate using the Doppler effect made at the Stanford Solar Observatory since May 1976 are analyzed. Results show that these observations show no daily or long period variations in the rotation rate that exceed the observational error of about one percent. The average rotation rate is the same as that of the sunspot and the large-scale magnetic field structures.

Using landscape ecology to test hypotheses about large-scale abundance patterns in migratory birds

USGS Publications Warehouse

Flather, C.H.; Sauer, J.R.

1996-01-01

The hypothesis that Neotropical migrant birds may be undergoing widespread declines due to land use activities on the breeding grounds has been examined primarily by synthesizing results from local studies. Growing concern for the cumulative influence of land use activities on ecological systems has heightened the need for large-scale studies to complement what has been observed at local scales. We investigated possible landscape effects on Neotropical migrant bird populations for the eastern United States by linking two large-scale inventories designed to monitor breeding-bird abundances and land use patterns. The null hypothesis of no relation between landscape structure and Neotropical migrant abundance was tested by correlating measures of landscape structure with bird abundance, while controlling for the geographic distance among samples. Neotropical migrants as a group were more 'sensitive' to landscape structure than either temperate migrants or permanent residents. Neotropical migrants tended to be more abundant in landscapes with a greater proportion of forest and wetland habitats, fewer edge habitats, large forest patches, and with forest habitats well dispersed throughout the scene. Permanent residents showed few correlations with landscape structure and temperate migrants were associated with habitat diversity and edge attributes rather than with the amount, size, and dispersion of forest habitats. The association between Neotropical migrant abundance and forest fragmentation differed among physiographic strata, suggesting that land-scape context affects observed relations between bird abundance and landscape structure. Finally, associations between landscape structure and temporal trends in Neotropical migrant abundance were negatively correlated with forest habitats. These results suggest that extrapolation of patterns observed in some landscapes is not likely to hold regionally, and that conservation policies must consider the variation in landscape structure associations observed among different types of bird species and in physiographic strata with varying land use histories.

Variations in abundance, diversity and community composition of airborne fungi in swine houses across seasons

PubMed Central

Kumari, Priyanka; Woo, Cheolwoon; Yamamoto, Naomichi; Choi, Hong-Lim

2016-01-01

We examined the abundance, diversity and community composition of airborne fungi in swine houses during winter and summer seasons by using quantitative PCR and Illumina HiSeq sequencing of ITS1 region. The abundance of airborne fungi varied significantly only between seasons, while fungal diversity varied significantly both within and between seasons, with both abundance and diversity peaked in winter. The fungal OTU composition was largely structured by the swine house unit and season as well as by their interactions. Of the measured microclimate variables, relative humidity, particulate matters (PMs), ammonia, and stocking density were significantly correlated with fungal OTU composition. The variation in beta diversity was higher within swine houses during summer, which indicates that the airborne fungal community composition was more heterogeneous in summer compared to winter. We also identified several potential allergen/pathogen related fungal genera in swine houses. The total relative abundance of potential allergen/pathogen related fungal genera varied between swine houses in both seasons, and showed positive correlation with PM2.5. Overall, our findings show that the abundance, diversity and composition of airborne fungi are highly variable in swine houses and to a large extent structured by indoor microclimate variables of swine houses. PMID:27892507

SDSS-III Baryon Oscillation Spectroscopic Survey data release 12: Galaxy target selection and large-scale structure catalogues

DOE PAGES

Reid, Beth; Ho, Shirley; Padmanabhan, Nikhil; ...

2015-11-17

The Baryon Oscillation Spectroscopic Survey (BOSS), part of the Sloan Digital Sky Survey (SDSS) III project, has provided the largest survey of galaxy redshifts available to date, in terms of both the number of galaxy redshifts measured by a single survey, and the effective cosmological volume covered. Key to analysing the clustering of these data to provide cosmological measurements is understanding the detailed properties of this sample. Potential issues include variations in the target catalogue caused by changes either in the targeting algorithm or properties of the data used, the pattern of spectroscopic observations, the spatial distribution of targets formore » which redshifts were not obtained, and variations in the target sky density due to observational systematics. We document here the target selection algorithms used to create the galaxy samples that comprise BOSS. We also present the algorithms used to create large-scale structure catalogues for the final Data Release (DR12) samples and the associated random catalogues that quantify the survey mask. The algorithms are an evolution of those used by the BOSS team to construct catalogues from earlier data, and have been designed to accurately quantify the galaxy sample. Furthermore, the code used, designated mksample, is released with this paper.« less

Modeling of central reactivity worth measurements in Lady Godiva

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

Wenz, T.R.; Busch, R.D.

The central reactivity worth measurements performed in Lady Godiva were duplicated using TWODANT, a deterministic neutron transport code, and the 16-group Hansen-Roach cross-section library. The purpose of this work was to determine how well the Hansen-Roach library predicts the reactivity worths for a fast neutron system. Lady Godiva is a spherical uranium metal (93.7 wt% [sup 235]U) critical assembly with a neutron flux distribution dominant in the first five groups of the Hansen-Roach energy structure (0.1 MeV and up). Provided that the cross sections of the replacement material do not undergo large variations (less than an order of magnitude) inmore » any of the aforementioned groups, the calculated reactivities were within 10% of the experimental values. For cases where the reactivities were outside this range, a large variation in the cross section was found to exist in one of the groups, which was not fully accounted for in the Hansen-Roach group structure. However, even in the cases where the agreement between calculation and experiment was not good, the calculated reactivity appeared to be an extremum in that the effect was found to be either more negative or more positive than the experimental value.« less

A Proposal of Monitoring and Forecasting Method for Crustal Activity in and around Japan with 3-dimensional Heterogeneous Medium Using a Large-scale High-fidelity Finite Element Simulation

NASA Astrophysics Data System (ADS)

Hori, T.; Agata, R.; Ichimura, T.; Fujita, K.; Yamaguchi, T.; Takahashi, N.

2017-12-01

Recently, we can obtain continuous dense surface deformation data on land and partly on the sea floor, the obtained data are not fully utilized for monitoring and forecasting of crustal activity, such as spatio-temporal variation in slip velocity on the plate interface including earthquakes, seismic wave propagation, and crustal deformation. For construct a system for monitoring and forecasting, it is necessary to develop a physics-based data analysis system including (1) a structural model with the 3D geometry of the plate inter-face and the material property such as elasticity and viscosity, (2) calculation code for crustal deformation and seismic wave propagation using (1), (3) inverse analysis or data assimilation code both for structure and fault slip using (1) & (2). To accomplish this, it is at least necessary to develop highly reliable large-scale simulation code to calculate crustal deformation and seismic wave propagation for 3D heterogeneous structure. Unstructured FE non-linear seismic wave simulation code has been developed. This achieved physics-based urban earthquake simulation enhanced by 1.08 T DOF x 6.6 K time-step. A high fidelity FEM simulation code with mesh generator has also been developed to calculate crustal deformation in and around Japan with complicated surface topography and subducting plate geometry for 1km mesh. This code has been improved the code for crustal deformation and achieved 2.05 T-DOF with 45m resolution on the plate interface. This high-resolution analysis enables computation of change of stress acting on the plate interface. Further, for inverse analyses, waveform inversion code for modeling 3D crustal structure has been developed, and the high-fidelity FEM code has been improved to apply an adjoint method for estimating fault slip and asthenosphere viscosity. Hence, we have large-scale simulation and analysis tools for monitoring. We are developing the methods for forecasting the slip velocity variation on the plate interface. Although the prototype is for elastic half space model, we are applying it for 3D heterogeneous structure with the high-fidelity FE model. Furthermore, large-scale simulation codes for monitoring are being implemented on the GPU clusters and analysis tools are developing to include other functions such as examination in model errors.

A very slow basal layer underlying large-scale low-velocity anomalies in the lower mantle beneath the Pacific: evidence from core phases

NASA Astrophysics Data System (ADS)

Garnero, Edward J.; Helmberger, Donald V.

A multi-phase analysis using long-period World Wide Standardized Seismograph Network and Canadian Network data has been conducted using core-phases for deep focus events from the southwest Pacific. These include SKS, S2KS, SV diff, and SP dKS. The last phase emerges from SKS near 106° and is associated with a P-wave diffracting along the bottom of the mantle. Patterns in S2KS - SKS differential travel times ( TS2KS - SKS) correlate with those in SP dKS - SKS ( TSP dKS - SKS ). TS2KS - SKS values strongly depend on variations in VS structure in the lower third of the mantle, whereas TSP dKS - SKS values mainly depend on VP structure and variations in a thin zone (100 km or less) at the very base of the mantle. Anomalously large TS2KS - SKS and TSP dKS - SKS values (relative to the Preliminary Reference Earth Model (PREM)) are present for Fiji-Tonga and Kermadec events (recorded in North and South America), along with anomalously large SV diff amplitudes well into the core's shadow. More northerly paths beneath the Pacific to North America for Indonesian and Solomon events display both PREM-like and anomalous times. A model compatible with the observations is presented, and contains a thin very-low-velocity layer at the base of the mantle that underlies the large volumetric lower-mantle low-velocity regions in the southwest Pacific. A low-velocity layer of 20-100 km thickness with reductions of up to 5-10% (relative to PREM) can reproduce TSP dKS - SKS as well as SV diff amplitudes. Large-scale (more than 1000 km) lower-mantle VS heterogeneity (2-4%) can explain long-wavelength trends in TS2KS - SKS. The exact thickness and velocity reduction in the basal layer is uncertain, owing to difficulties in resolving whether anomalous structure occurs on the source- and/or receiver-side of wavepaths (at the CMB).

The properties and causes of rippling in quasi-perpendicular collisionless shock fronts

NASA Astrophysics Data System (ADS)

Lowe, R. E.; Burgess, D.

2003-03-01

The overall structure of quasi-perpendicular, high Mach number collisionless shocks is controlled to a large extent by ion reflection at the shock ramp. Departure from a strictly one-dimensional structure is indicated by simulation results showing that the surface of such shocks is rippled, with variations in the density and all field components. We present a detailed analysis of these shock ripples, using results from a two-dimensional hybrid (particle ions, electron fluid) simulation. The process that generates the ripples is poorly understood, because the large gradients at the shock ramp make it difficult to identify instabilities. Our analysis reveals new features of the shock ripples, which suggest the presence of a surface wave mode dominating the shock normal magnetic field component of the ripples, as well as whistler waves excited by reflected ions.

Trophic disruption: a meta-analysis of how habitat fragmentation affects resource consumption in terrestrial arthropod systems.

PubMed

Martinson, Holly M; Fagan, William F

2014-09-01

Habitat fragmentation is a complex process that affects ecological systems in diverse ways, altering everything from population persistence to ecosystem function. Despite widespread recognition that habitat fragmentation can influence food web interactions, consensus on the factors underlying variation in the impacts of fragmentation across systems remains elusive. In this study, we conduct a systematic review and meta-analysis to quantify the effects of habitat fragmentation and spatial habitat structure on resource consumption in terrestrial arthropod food webs. Across 419 studies, we found a negative overall effect of fragmentation on resource consumption. Variation in effect size was extensive but predictable. Specifically, resource consumption was reduced on small, isolated habitat fragments, higher at patch edges, and neutral with respect to landscape-scale spatial variables. In general, resource consumption increased in fragmented settings for habitat generalist consumers but decreased for specialist consumers. Our study demonstrates widespread disruption of trophic interactions in fragmented habitats and describes variation among studies that is largely predictable based on the ecological traits of the interacting species. We highlight future prospects for understanding how changes in spatial habitat structure may influence trophic modules and food webs. © 2014 John Wiley & Sons Ltd/CNRS.

Population genetic structure and vocal dialects in an amazon parrot.

PubMed Central

Wright, T F; Wilkinson, G S

2001-01-01

The relationship between cultural and genetic evolution was examined in the yellow-naped amazon Amazona auropalliata. This species has previously been shown to have regional dialects defined by large shifts in the acoustic structure of its learned contact call. Mitochondrial DNA sequence variation from a 680 base pair segment of the first domain of the control region was assayed in 41 samples collected from two neighbouring dialects in Costa Rica. The relationship of genetic variation to vocal variation was examined using haplotype analysis, genetic distance analysis, a maximum-likelihood estimator of migration rates and phylogenetic reconstructions. All analyses indicated a high degree of gene flow and, thus, individual dispersal across dialect boundaries. Calls sampled from sound libraries suggested that temporally stable contact call dialects occur throughout the range of the yellow-naped amazon, while the presence of similar dialects in the sister species Amazona ochrocephala suggests that the propensity to form dialects is ancestral in this clade. These results indicate that genes and culture are not closely associated in the yellow-naped amazon. Rather, they suggest that regional diversity in vocalizations is maintained by selective pressures that promote social learning and allow individual repertoires to conform to local call types. PMID:11297178

Recent independent emergence of multiple multidrug-resistant Serratia marcescens clones within the United Kingdom and Ireland

PubMed Central

Moradigaravand, Danesh; Boinett, Christine J.; Martin, Veronique; Peacock, Sharon J.; Parkhill, Julian

2016-01-01

Serratia marcescens, a member of the Enterobacteriaceae family, is a Gram-negative bacterium responsible for a wide range of nosocomial infections. The emergence of multidrug-resistant strains is an increasing danger to public health. To design effective means to control the dissemination of S. marcescens, an in-depth analysis of the population structure and variation is required. Utilizing whole-genome sequencing, we characterized the population structure and variation, as well as the antimicrobial resistance determinants, of a systematic collection of antimicrobial-resistant S. marcescens associated with bloodstream infections in hospitals across the United Kingdom and Ireland between 2001 and 2011. Our results show that S. marcescens is a diverse species with a high level of genomic variation. However, the collection was largely composed of a limited number of clones that emerged from this diverse background within the past few decades. We identified potential recent transmissions of these clones, within and between hospitals, and showed that they have acquired antimicrobial resistance determinants for different beta-lactams, ciprofloxacin, and tetracyclines on multiple occasions. The expansion of these multidrug-resistant clones suggests that the treatment of S. marcescens infections will become increasingly difficult in the future. PMID:27432456

Mantle shear-wave tomography and the fate of subducted slabs.

PubMed

Grand, Steven P

2002-11-15

A new seismic model of the three-dimensional variation in shear velocity throughout the Earth's mantle is presented. The model is derived entirely from shear bodywave travel times. Multibounce shear waves, core-reflected waves and SKS and SKKS waves that travel through the core are used in the analysis. A unique aspect of the dataset used in this study is the use of bodywaves that turn at shallow depths in the mantle, some of which are triplicated. The new model is compared with other global shear models. Although competing models show significant variations, several large-scale structures are common to most of the models. The high-velocity anomalies are mostly associated with subduction zones. In some regions the anomalies only extend into the shallow lower mantle, whereas in other regions tabular high-velocity structures seem to extend to the deepest mantle. The base of the mantle shows long-wavelength high-velocity zones also associated with subduction zones. The heterogeneity seen in global tomography models is difficult to interpret in terms of mantle flow due to variations in structure from one subduction zone to another. The simplest interpretation of the seismic images is that slabs in general penetrate to the deepest mantle, although the flow is likely to be sporadic. The interruption in slab sinking is likely to be associated with the 660 km discontinuity.

What Drives National Differences in Intensive Grandparental Childcare in Europe?

PubMed

Di Gessa, Giorgio; Glaser, Karen; Price, Debora; Ribe, Eloi; Tinker, Anthea

2016-01-01

Grandparents play an important role in looking after grandchildren, although intensive grandparental childcare varies considerably across Europe. Few studies have explicitly investigated the extent to which such cross-national variations are associated with national level differences in individual demographic and socio-economic distributions along with contextual-structural and cultural factors (e.g., variations in female labor force participation, childcare provision, and cultural attitudes). We used multilevel models to examine associations between intensive grandparental childcare and contextual-structural and cultural factors, after controlling for grandparent, parent, and child characteristics using nationally representative data from the Survey of Health, Ageing and Retirement in Europe. Even controlling for cross-national differences in demographic and socio-economic distributions, contextual-structural factors play an important role in explaining grandparental childcare variations in Europe. In particular, higher levels of intensive grandparental childcare are found in countries with low labor force participation among younger and older women, and low formal childcare provision, where mothers in paid work largely rely on grandparental support on an almost daily basis. Encouraging older women to remain in paid work is likely to have an impact on grandchild care which in turn may affect mothers' employment, particularly in Southern European countries where there is little formal childcare. © The Author 2015. Published by Oxford University Press on behalf of The Gerontological Society of America.

Extensive Diversity of Prion Strains Is Defined by Differential Chaperone Interactions and Distinct Amyloidogenic Regions

PubMed Central

Stein, Kevin C.; True, Heather L.

2014-01-01

Amyloidogenic proteins associated with a variety of unrelated diseases are typically capable of forming several distinct self-templating conformers. In prion diseases, these different structures, called prion strains (or variants), confer dramatic variation in disease pathology and transmission. Aggregate stability has been found to be a key determinant of the diverse pathological consequences of different prion strains. Yet, it remains largely unclear what other factors might account for the widespread phenotypic variation seen with aggregation-prone proteins. Here, we examined a set of yeast prion variants of the [RNQ+] prion that differ in their ability to induce the formation of another yeast prion called [PSI+]. Remarkably, we found that the [RNQ+] variants require different, non-contiguous regions of the Rnq1 protein for both prion propagation and [PSI+] induction. This included regions outside of the canonical prion-forming domain of Rnq1. Remarkably, such differences did not result in variation in aggregate stability. Our analysis also revealed a striking difference in the ability of these [RNQ+] variants to interact with the chaperone Sis1. Thus, our work shows that the differential influence of various amyloidogenic regions and interactions with host cofactors are critical determinants of the phenotypic consequences of distinct aggregate structures. This helps reveal the complex interdependent factors that influence how a particular amyloid structure may dictate disease pathology and progression. PMID:24811344

Intraspecific variation in mitochondrial genome sequence, structure, and gene content in Silene vulgaris, an angiosperm with pervasive cytoplasmic male sterility.

PubMed

Sloan, Daniel B; Müller, Karel; McCauley, David E; Taylor, Douglas R; Storchová, Helena

2012-12-01

In angiosperms, mitochondrial-encoded genes can cause cytoplasmic male sterility (CMS), resulting in the coexistence of female and hermaphroditic individuals (gynodioecy). We compared four complete mitochondrial genomes from the gynodioecious species Silene vulgaris and found unprecedented amounts of intraspecific diversity for plant mitochondrial DNA (mtDNA). Remarkably, only about half of overall sequence content is shared between any pair of genomes. The four mtDNAs range in size from 361 to 429 kb and differ in gene complement, with rpl5 and rps13 being intact in some genomes but absent or pseudogenized in others. The genomes exhibit essentially no conservation of synteny and are highly repetitive, with evidence of reciprocal recombination occurring even across short repeats (< 250 bp). Some mitochondrial genes exhibit atypically high degrees of nucleotide polymorphism, while others are invariant. The genomes also contain a variable number of small autonomously mapping chromosomes, which have only recently been identified in angiosperm mtDNA. Southern blot analysis of one of these chromosomes indicated a complex in vivo structure consisting of both monomeric circles and multimeric forms. We conclude that S. vulgaris harbors an unusually large degree of variation in mtDNA sequence and structure and discuss the extent to which this variation might be related to CMS. © 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.

Phylogenetically structured traits in root systems influence arbuscular mycorrhizal colonization in woody angiosperms

DOE PAGES

Valverde-Barrantes, Oscar J.; Horning, Amber L.; Smemo, Kurt A.; ...

2016-02-10

In this study, there is little quantitative information about the relationship between root traits and the extent of arbuscular mycorrhizal fungi (AMF) colonization. We expected that ancestral species with thick roots will maximize AMF habitat by maintaining similar root traits across root orders (i.e., high root trait integration), whereas more derived species are expected to display a sharp transition from acquisition to structural roots. Moreover, we hypothesized that interspecific morphological differences rather than soil conditions will be the main driver of AMF colonization We analyzed 14 root morphological and chemical traits and AMF colonization rates for the first three rootmore » orders of 34 temperate tree species grown in two common gardens. We also collected associated soil to measure the effect of soil conditions on AMF colonization Results Thick-root magnoliids showed less variation in root traits along root orders than more-derived angiosperm groups. Variation in stele:root diameter ratio was the best indicator of AMF colonization within and across root orders. Root functional traits rather than soil conditions largely explained the variation in AMF colonization among species. In conclusion, not only the traits of first order but the entire structuring of the root system varied among plant lineages, suggesting alternative evolutionary strategies of resource acquisition. Understanding evolutionary pathways in below ground organs could open new avenues to understand tree species influence on soil carbon and nutrient cycling.« less

Anatomy of Mandibular Vital Structures. Part II: Mandibular Incisive Canal, Mental Foramen and Associated Neurovascular Bundles in Relation with Dental Implantology

PubMed Central

Wang, Hom-Lay; Sabalys, Gintautas

2010-01-01

ABSTRACT Objectives The purpose of the present study was to review the literature of how to identify the mental foramen, mandibular incisive canal and associated neurovascular bundles during implant surgery and how to detect and avoid the damage of these vital structures during implant therapy. Material and Methods Literature was selected through a search of PubMed, Embase and Cochrane electronic databases. The keywords used for search were mandibular incisive canal, mental foramen, mental nerve, anterior mental loop. The search was restricted to English language articles, published from 1979 to November 2009. Additionally, a manual search in the major anatomy, dental implant, and periodontal journals and books was performed. Results In total, 47 literature sources were obtained and reviewed. The morphology and variations of the mandibular incisive canal, mental foramen and associated neurovascular bundles were presented as two entities. It suggested that clinicians should carefully assess these vital structures to avoid nerve/artery damage. Conclusions The mandibular incisive canal, mental foramen and associated neurovascular bundles exist in different locations and possess many variations. Individual, gender, age, race, assessing technique used and degree of edentulous alveolar bone atrophy largely influence these variations. It suggests that the clinicians should carefully identify these anatomical landmarks, by analyzing all influencing factors, prior to their implant surgical operation. PMID:24421959

Phylogenetically structured traits in root systems influence arbuscular mycorrhizal colonization in woody angiosperms

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

Valverde-Barrantes, Oscar J.; Horning, Amber L.; Smemo, Kurt A.

In this study, there is little quantitative information about the relationship between root traits and the extent of arbuscular mycorrhizal fungi (AMF) colonization. We expected that ancestral species with thick roots will maximize AMF habitat by maintaining similar root traits across root orders (i.e., high root trait integration), whereas more derived species are expected to display a sharp transition from acquisition to structural roots. Moreover, we hypothesized that interspecific morphological differences rather than soil conditions will be the main driver of AMF colonization We analyzed 14 root morphological and chemical traits and AMF colonization rates for the first three rootmore » orders of 34 temperate tree species grown in two common gardens. We also collected associated soil to measure the effect of soil conditions on AMF colonization Results Thick-root magnoliids showed less variation in root traits along root orders than more-derived angiosperm groups. Variation in stele:root diameter ratio was the best indicator of AMF colonization within and across root orders. Root functional traits rather than soil conditions largely explained the variation in AMF colonization among species. In conclusion, not only the traits of first order but the entire structuring of the root system varied among plant lineages, suggesting alternative evolutionary strategies of resource acquisition. Understanding evolutionary pathways in below ground organs could open new avenues to understand tree species influence on soil carbon and nutrient cycling.« less

Is there a species spectrum within the world-wide leaf economics spectrum? Major variations in leaf functional traits in the Mediterranean sclerophyll Quercus ilex.

PubMed

Niinemets, Ulo

2015-01-01

The leaf economics spectrum is a general concept describing coordinated variation in foliage structural, chemical and physiological traits across resource gradients. Yet, within this concept,the role of within-species variation, including ecotypic and plastic variation components, has been largely neglected. This study hypothesized that there is a within-species economics spectrum within the general spectrum in the evergreen sclerophyll Quercus ilex which dominates low resource ecosystems over an exceptionally wide range. An extensive database of foliage traits covering the full species range was constructed, and improved filtering algorithms were developed. Standardized data filtering was deemed absolutely essential as additional variation sources can result in trait variation of 10–300%,blurring the broad relationships. Strong trait variation, c. two-fold for most traits to up to almost an order of magnitude, was uncovered.Although the Q. ilex spectrum is part of the general spectrum, within-species trait and climatic relationships in this species partly differed from the overall spectrum. Contrary to world-wide trends, Q. ilex does not necessarily have a low nitrogen content per mass and can increase photosynthetic capacity with increasing foliage robustness. This study argues that the within-species economics spectrum needs to be considered in regional- to biome-level analyses.

Life history and past demography maintain genetic structure, outcrossing rate, contemporary pollen gene flow of an understory herb in a highly fragmented rainforest

PubMed Central

Suárez-Montes, Pilar; Chávez-Pesqueira, Mariana

2016-01-01

Introduction Theory predicts that habitat fragmentation, by reducing population size and increasing isolation among remnant populations, can alter their genetic diversity and structure. A cascade of effects is expected: genetic drift and inbreeding after a population bottleneck, changes in biotic interactions that may affect, as in the case of plants, pollen dynamics, mating system, reproductive success. The detection of the effects of contemporary habitat fragmentation on the genetic structure of populations are conditioned by the magnitude of change, given the few number of generations since the onset of fragmentation, especially for long-lived organisms. However, the present-day genetic structure of populations may bear the signature of past demography events. Here, we examine the effects of rainforest fragmentation on the genetic diversity, population structure, mating system (outcrossing rate), indirect gene flow and contemporary pollen dynamics in the understory herb Aphelandra aurantiaca. Also, we assessed its present-day genetic structure under different past demographic scenarios. Methods Twelve populations of A. aurantiaca were sampled in large (4), medium (3), and small (5) forest fragments in the lowland tropical rainforest at Los Tuxtlas region. Variation at 11 microsatellite loci was assessed in 28–30 reproductive plants per population. In two medium- and two large-size fragments we estimated the density of reproductive plants, and the mating system by analyzing the progeny of different mother plants per population. Results Despite prevailing habitat fragmentation, populations of A. aurantiaca possess high genetic variation (He = 0.61), weak genetic structure (Rst = 0.037), and slight inbreeding in small fragments. Effective population sizes (Ne) were large, but slightly lower in small fragments. Migrants derive mostly from large and medium size fragments. Gene dispersal is highly restricted but long distance gene dispersal events were detected. Aphelandra aurantiaca shows a mixed mating system (tm = 0.81) and the outcrossing rate have not been affected by habitat fragmentation. A strong pollen pool structure was detected due to few effective pollen donors (Nep) and low distance pollen movement, pointing that most plants received pollen from close neighbors. Past demographic fluctuations may have affected the present population genetic structure as Bayesian coalescent analysis revealed the signature of past population expansion, possibly during warmer conditions after the last glacial maximum. Discussion Habitat fragmentation has not increased genetic differentiation or reduced genetic diversity of A. aurantiaca despite dozens of generations since the onset of fragmentation in the region of Los Tuxtlas. Instead, past population expansion is compatible with the lack of observed genetic structure. The predicted negative effects of rainforest fragmentation on genetic diversity and population structure of A. aurantiaca seem to have been buffered owing to its large effective populations and long-distance dispersal events. In particular, its mixed-mating system, mostly of outcrossing, suggests high efficiency of pollinators promoting connectivity and reducing inbreeding. However, some results point that the effects of fragmentation are underway, as two small fragments showed higher membership probabilities to their population of origin, suggesting genetic isolation. Our findings underscore the importance of fragment size to maintain genetic connectivity across the landscape. PMID:28028460

Geometry of a large-scale, low-angle, midcrustal thrust (Woodroffe Thrust, central Australia)

NASA Astrophysics Data System (ADS)

Wex, S.; Mancktelow, N. S.; Hawemann, F.; Camacho, A.; Pennacchioni, G.

2017-11-01

The Musgrave Block in central Australia exposes numerous large-scale mylonitic shear zones developed during the intracontinental Petermann Orogeny around 560-520 Ma. The most prominent structure is the crustal-scale, over 600 km long, E-W trending Woodroffe Thrust, which is broadly undulate but generally dips shallowly to moderately to the south and shows an approximately top-to-north sense of movement. The estimated metamorphic conditions of mylonitization indicate a regional variation from predominantly midcrustal (circa 520-620°C and 0.8-1.1 GPa) to lower crustal ( 650°C and 1.0-1.3 GPa) levels in the direction of thrusting, which is also reflected in the distribution of preserved deformation microstructures. This variation in metamorphic conditions is consistent with a south dipping thrust plane but is only small, implying that a ≥60 km long N-S segment of the Woodroffe Thrust was originally shallowly dipping at an average estimated angle of ≤6°. The reconstructed geometry suggests that basement-cored, thick-skinned, midcrustal thrusts can be very shallowly dipping on a scale of many tens of kilometers in the direction of movement. Such a geometry would require the rocks along the thrust to be weak, but field observations (e.g., large volumes of syntectonic pseudotachylyte) argue for a strong behavior, at least transiently. Localization on a low-angle, near-planar structure that crosscuts lithological layers requires a weak precursor, such as a seismic rupture in the middle to lower crust. If this was a single event, the intracontinental earthquake must have been large, with the rupture extending laterally over hundreds of kilometers.

InP Based Ternary And Quaternary Thin Film Structures On Large Areas Grown By LP-MOVPE

NASA Astrophysics Data System (ADS)

Schmitz, D.; Strauch, , G.; Jurgensen, H.; Heyen, M.; Harde, P.

1989-11-01

Using low pressure MOVPE and higher linear flow velocities high purity GalnAs/lnP and GalnAsP heterostructures can be prepared. Excellent homogeneity in thickness, composition, and doping on a 2" InP substrate can be realized by this approach for optimized conditions. The low growth rates required for the deposition of very narrow well structures are achieved by selecting reduced pressures of the group III and group V compounds used for deposition. The method yields structures with high electron mobilities of the two dimensional electron gas in the well and narrow PL (i.e. 2.2 meV for 20 nm wells) line widths, which is indicative of low impurity incorporation and abrupt heterojunctions. The observed energy shifts (up to 528 meV) demonstrate the large range of bandgap variation attainable by this method. A study of dopant incorporation shows, that Zn yields steep transitions in InGaAs.

Mitochondrial DNA sequence variation and phylogeography of the scarlet kingsnake (Lampropeltis elapsoides).

PubMed

Friedman, Michael; Schaffer, Les

2011-02-01

BACKGROUND AND AIMS. With the goal of assessing population structure and geographic distribution of haplotype lineages among Lampropeltis elapsoides, we sequenced the ND4 mitochondrial DNA locus from 96 specimens of this snake across its area of distribution. MATERIALS AND METHODS. We relied heavily on formalin-fixed museum specimens to accomplish this analysis. RESULTS. The sequence alignment consisted of 491 bp of the selected gene, with 28% missing data. A simulation used to assess the effect of missing data on population genetic and phylogenetic resolution indicated increased character conflict, but with minimal loss of phylogenetic structure. CONCLUSION. This limited dataset suggests that L. elapsoides constitutes a largely unstructured population, with both widespread haplotypes and large number of private haplotypes, a moderate level of nucleotide diversity, and a low, but significant, degree of north-south population differentiation. Haplotype structure and frequency, nucleotide frequency, and values for Tajima's D and Fu's F(S) indicate a recent range or population expansion following a historic bottleneck.

Statistical study of conductance properties in one-dimensional quantum wires focusing on the 0.7 anomaly

NASA Astrophysics Data System (ADS)

Smith, L. W.; Al-Taie, H.; Sfigakis, F.; See, P.; Lesage, A. A. J.; Xu, B.; Griffiths, J. P.; Beere, H. E.; Jones, G. A. C.; Ritchie, D. A.; Kelly, M. J.; Smith, C. G.

2014-07-01

The properties of conductance in one-dimensional (1D) quantum wires are statistically investigated using an array of 256 lithographically identical split gates, fabricated on a GaAs/AlGaAs heterostructure. All the split gates are measured during a single cooldown under the same conditions. Electron many-body effects give rise to an anomalous feature in the conductance of a one-dimensional quantum wire, known as the "0.7 structure" (or "0.7 anomaly"). To handle the large data set, a method of automatically estimating the conductance value of the 0.7 structure is developed. Large differences are observed in the strength and value of the 0.7 structure [from 0.63 to 0.84×(2e2/h)], despite the constant temperature and identical device design. Variations in the 1D potential profile are quantified by estimating the curvature of the barrier in the direction of electron transport, following a saddle-point model. The 0.7 structure appears to be highly sensitive to the specific confining potential within individual devices.

Seismicity and S-wave velocity structure of the crust and the upper mantle in the Baikal rift and adjacent regions

NASA Astrophysics Data System (ADS)

Seredkina, Alena; Kozhevnikov, Vladimir; Melnikova, Valentina; Solovey, Oksana

2016-12-01

Correlations between seismicity, seismotectonic deformation (STD) field and velocity structure of the crust and the upper mantle in the Baikal rift and the adjacent areas of the Siberian platform and the Mongol-Okhotsk fold belt have been investigated. The 3D S-wave velocity structure up to the depths of 500 km has been modeled using a representative sample of Rayleigh wave group velocity dispersion curves (about 3200 paths) at periods from 10 to 250 s. The STD pattern has been reconstructed from mechanisms of large earthquakes, and is in good agreement with GPS and structural data. Analysis of the results has shown that most of large shallow earthquakes fall in regions of low S-wave velocities in the uppermost mantle (western Mongolia and areas of recent mountain building in southern Siberia) and in zones of their relatively high lateral variations (northeastern flank of the Baikal rift). In the first case the dominant STD regime is compression manifested in a mixture of thrust and strike-slip deformations. In the second case we observe a general predominance of extension.

Improved Nazca slab structure from teleseismic P-wave tomography along the Andean margin

NASA Astrophysics Data System (ADS)

Portner, D. E.; Beck, S. L.; Scire, A. C.; Zandt, G.

2017-12-01

South America marks the longest continuous ocean-continent subduction zone. As such, there is significant along-strike variability in the subducting Nazca slab structure and the tectonics of the South American margin. Most notably two gaps in the otherwise continuous volcanic arc are correlated with regions of flat slab subduction, indicating that the structure of the Nazca slab plays a controlling role in South American tectonics. Traditionally in subduction zones, our knowledge of slab structure is defined by Wadati-Benioff zone earthquakes. While this method allows for the determination of large-scale variations in Nazca slab structure such as regions of flat slab subduction, a scarcity of intermediate-depth earthquakes hinders our ability to observe the smaller-scale structural variations in the slab that may be critical to our understanding of the geologic record. We use an updated, larger dataset for finite-frequency teleseismic P-wave tomography including relative arrival times from >700 seismic stations along the Andean margin to image the detailed Nazca slab structure throughout the upper mantle and uppermost lower mantle between latitudes 5°S and 45°S. Our results show prominent variations in slab character along the margin. Slab dip varies significantly, from sub-vertical inboard of the Peruvian flat slab segment to 30° dip south of the Pampean flat slab, while the slab's velocity anomaly amplitude changes dramatically near the Pampean flat slab region. High slab velocities north of the Pampean region relative to the south indicate variable slab thermal structures that correspond roughly with the locations of deep (>500 km depth) earthquakes that also occur exclusively north of the Pampean region. Additionally, a wider regional footprint increases our sampling of the upper-lower mantle boundary, improving constraints on the slab's interaction with the 660 km discontinuity along strike. We see that the Nazca slab appears to penetrate into the lower mantle along the majority of the margin.

Stable Isotopes Provide Insight into Population Structure and Segregation in Eastern North Atlantic Sperm Whales

PubMed Central

Borrell, Asunción; Velásquez Vacca, Adriana; Pinela, Ana M.; Kinze, Carl; Lockyer, Christina H.; Vighi, Morgana; Aguilar, Alex

2013-01-01

In pelagic species inhabiting large oceans, genetic differentiation tends to be mild and populations devoid of structure. However, large cetaceans have provided many examples of structuring. Here we investigate whether the sperm whale, a pelagic species with large population sizes and reputedly highly mobile, shows indication of structuring in the eastern North Atlantic, an ocean basin in which a single population is believed to occur. To do so, we examined stable isotope values in sequential growth layer groups of teeth from individuals sampled in Denmark and NW Spain. In each layer we measured oxygen- isotope ratios (δ18O) in the inorganic component (hydroxyapatite), and nitrogen and carbon isotope ratios (δ15N: δ13C) in the organic component (primarily collagenous). We found significant differences between Denmark and NW Spain in δ15N and δ18O values in the layer deposited at age 3, considered to be the one best representing the baseline of the breeding ground, in δ15N, δ13C and δ18O values in the period up to age 20, and in the ontogenetic variation of δ15N and δ18O values. These differences evidence that diet composition, use of habitat and/or migratory destinations are dissimilar between whales from the two regions and suggest that the North Atlantic population of sperm whales is more structured than traditionally accepted. PMID:24324782

PIV measurements of in-cylinder, large-scale structures in a water-analogue Diesel engine

NASA Astrophysics Data System (ADS)

Kalpakli Vester, A.; Nishio, Y.; Alfredsson, P. H.

2016-11-01

Swirl and tumble are large-scale structures that develop in an engine cylinder during the intake stroke. Their structure and strength depend on the design of the inlet ports and valves, but also on the valve lift history. Engine manufacturers make their design to obtain a specific flow structure that is assumed to give the best engine performance. Despite many efforts, there are still open questions, such as how swirl and tumble depend on the dynamics of the valves/piston as well as how cycle-to-cycle variations should be minimized. In collaboration with Swedish vehicle industry we perform PIV measurements of the flow dynamics during the intake stroke inside a cylinder of a water-analogue engine model having the same geometrical characteristics as a typical truck Diesel engine. Water can be used since during the intake stroke the flow is nearly incompressible. The flow from the valves moves radially outwards, hits the vertical walls of the cylinder, entrains surrounding fluid, moves along the cylinder walls and creates a central backflow, i.e. a tumble motion. Depending on the port and valve design and orientation none, low, or high swirl can be established. For the first time, the effect of the dynamic motion of the piston/valves on the large-scale structures is captured. Supported by the Swedish Energy Agency, Scania CV AB and Volvo GTT, through the FFI program.

Spatial and Temporal Dynamics of Pacific Oyster Hemolymph Microbiota across Multiple Scales

PubMed Central

Lokmer, Ana; Goedknegt, M. Anouk; Thieltges, David W.; Fiorentino, Dario; Kuenzel, Sven; Baines, John F.; Wegner, K. Mathias

2016-01-01

Unveiling the factors and processes that shape the dynamics of host associated microbial communities (microbiota) under natural conditions is an important part of understanding and predicting an organism's response to a changing environment. The microbiota is shaped by host (i.e., genetic) factors as well as by the biotic and abiotic environment. Studying natural variation of microbial community composition in multiple host genetic backgrounds across spatial as well as temporal scales represents a means to untangle this complex interplay. Here, we combined a spatially-stratified with a longitudinal sampling scheme within differentiated host genetic backgrounds by reciprocally transplanting Pacific oysters between two sites in the Wadden Sea (Sylt and Texel). To further differentiate contingent site from host genetic effects, we repeatedly sampled the same individuals over a summer season to examine structure, diversity and dynamics of individual hemolymph microbiota following experimental removal of resident microbiota by antibiotic treatment. While a large proportion of microbiome variation could be attributed to immediate environmental conditions, we observed persistent effects of antibiotic treatment and translocation suggesting that hemolymph microbial community dynamics is subject to within-microbiome interactions and host population specific factors. In addition, the analysis of spatial variation revealed that the within-site microenvironmental heterogeneity resulted in high small-scale variability, as opposed to large-scale (between-site) stability. Similarly, considerable within-individual temporal variability was in contrast with the overall temporal stability at the site level. Overall, our longitudinal, spatially-stratified sampling design revealed that variation in hemolymph microbiota is strongly influenced by site and immediate environmental conditions, whereas internal microbiome dynamics and oyster-related factors add to their long-term stability. The combination of small and large scale resolution of spatial and temporal observations therefore represents a crucial but underused tool to study host-associated microbiome dynamics. PMID:27630625

Velocity structure of the shallow lunar crust

NASA Technical Reports Server (NTRS)

Gangi, A. F.; Yen, T. E.

1979-01-01

Data from the thumper shots of the Apollo 14 and Apollo 16 active seismic experiments, testing whether the velocity variation in the shallow lunar crust (depths less than or equal to 10 m) can be represented by a self-compacting-power-layer or by a constant-velocity-layer model, are analyzed. Although filtering and stacking improved the S/N ratios, it was found that measuring the arrival times or amplitudes of arrivals beyond 32 m was not possible. The data quality precluded a definitive distinction between the power-law velocity variation and the layered-velocity model. Furthermore, it was found that the shallow lunar regolith is made up of fine particles, which supports the idea of a 1/6 power-velocity model. Analysis of the amplitudes of first arrivals revealed large errors in the data due to variations in the geophone sensitivities and shot strengths; a least-squares method, that uses data redundancy was employed to eliminate them.

Sensing sheet: the response of full-bridge strain sensors to thermal variations for detecting and characterizing cracks

NASA Astrophysics Data System (ADS)

Tung, S.-T.; Glisic, B.

2016-12-01

Sensing sheets based on large-area electronics consist of a dense array of unit strain sensors. This new technology has potential for becoming an effective and affordable monitoring tool that can identify, localize and quantify surface damage in structures. This research contributes to their development by investigating the response of full-bridge unit strain sensors to thermal variations. Overall, this investigation quantifies the effects of temperature on thin-film full-bridge strain sensors monitoring uncracked and cracked concrete. Additionally, an empirical formula is developed to estimate crack width given an observed strain change and a measured temperature change. This research led to the understanding of the behavior of full-bridge strain sensors installed on cracked concrete and exposed to temperature variations. It proves the concept of the sensing sheet and its suitability for application in environments with variable temperature.

Nationwide Analysis of U.S. Commercial Building Solar Photovoltaic (PV) Breakeven Conditions

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

Davidson, Carolyn; Gagnon, Pieter; Denholm, Paul

2015-10-01

The commercial sector offers strong potential for solar photovoltaics (PV) owing to abundant available roof space suitable for PV and the opportunity to offset the sector's substantial retail electricity purchases. This report evaluated the breakeven price of PV for 15 different building types and various financing options by calculating electricity savings based on detailed rate structures for most U.S. utility territories (representing approximately two thirds of U.S. commercial customers). We find that at current capital costs, an estimated 1/3 of U.S. commercial customers break even in the cash scenario and approximately 2/3 break even in the loan scenario. Variation inmore » retail rates is a stronger driver of breakeven prices than is variation in building load or solar generation profiles. At the building level, variation in the average breakeven price is largely driven by the ability for a PV system to reduce demand charges.« less

Limits on the time variation of the electromagnetic fine-structure constant in the low energy limit from absorption lines in the spectra of distant quasars.

PubMed

Srianand, R; Chand, H; Petitjean, P; Aracil, B

2004-03-26

We present the results of a detailed many-multiplet analysis performed on a new sample of Mg ii systems observed in high quality quasar spectra obtained using the Very Large Telescope. The weighted mean value of the variation in alpha derived from our analysis over the redshift range 0.4

Effects of the Variation in Brain Tissue Mechanical Properties on the Intracranial Response of a 6-Year-Old Child.

PubMed

Cui, Shihai; Li, Haiyan; Li, Xiangnan; Ruan, Jesse

2015-01-01

Brain tissue mechanical properties are of importance to investigate child head injury using finite element (FE) method. However, these properties used in child head FE model normally vary in a large range in published literatures because of the insufficient child cadaver experiments. In this work, a head FE model with detailed anatomical structures is developed from the computed tomography (CT) data of a 6-year-old healthy child head. The effects of brain tissue mechanical properties on traumatic brain response are also analyzed by reconstruction of a head impact on engine hood according to Euro-NCAP testing regulation using FE method. The result showed that the variations of brain tissue mechanical parameters in linear viscoelastic constitutive model had different influences on the intracranial response. Furthermore, the opposite trend was obtained in the predicted shear stress and shear strain of brain tissues caused by the variations of mentioned parameters.

Genomic analysis of local variation and recent evolution in Plasmodium vivax

PubMed Central

Pearson, Richard D; Miotto, Olivo; Almagro-Garcia, Jacob; Amaratunga, Chanaki; Suon, Seila; Mao, Sivanna; Noviyanti, Rintis; Trimarsanto, Hidayat; Marfurt, Jutta; Anstey, Nicholas M; William, Timothy; Boni, Maciej F; Dolecek, Christiane; Hien, Tinh Tran; White, Nicholas J; Michon, Pascal; Siba, Peter; Tavul, Livingstone; Harrison, Gabrielle; Barry, Alyssa; Mueller, Ivo; Ferreira, Marcelo U; Karunaweera, Nadira; Randrianarivelojosia, Milijaona; Gao, Qi; Hubbart, Christina; Hart, Lee; Jeffery, Ben; Drury, Eleanor; Mead, Daniel; Kekre, Mihir; Campino, Susana; Manske, Magnus; Cornelius, Victoria J; MacInnis, Bronwyn; Rockett, Kirk A; Miles, Alistair; Rayner, Julian C; Fairhurst, Rick M; Nosten, Francois; Price, Ric N; Kwiatkowski, Dominic P

2016-01-01

The widespread distribution and relapsing nature of Plasmodium vivax infection present major challenges for malaria elimination. To characterise the genetic diversity of this parasite within individual infections and across the population, we performed deep genome sequencing of >200 clinical samples collected across the Asia-Pacific region, and analysed data on >300,000 SNPs and 9 regions of the genome with large copy number variations. Individual infections showed complex patterns of genetic structure, with variation not only in the number of dominant clones but also in their level of relatedness and inbreeding. At the population level, we observed strong signals of recent evolutionary selection both in known drug resistance genes and at novel loci, and these varied markedly between geographical locations. These findings reveal a dynamic landscape of local evolutionary adaptation in P. vivax populations, and provide a foundation for genomic surveillance to guide effective strategies for control and elimination. PMID:27348299

Improving Disease Prediction by Incorporating Family Disease History in Risk Prediction Models with Large-Scale Genetic Data.

PubMed

Gim, Jungsoo; Kim, Wonji; Kwak, Soo Heon; Choi, Hosik; Park, Changyi; Park, Kyong Soo; Kwon, Sunghoon; Park, Taesung; Won, Sungho

2017-11-01

Despite the many successes of genome-wide association studies (GWAS), the known susceptibility variants identified by GWAS have modest effect sizes, leading to notable skepticism about the effectiveness of building a risk prediction model from large-scale genetic data. However, in contrast to genetic variants, the family history of diseases has been largely accepted as an important risk factor in clinical diagnosis and risk prediction. Nevertheless, the complicated structures of the family history of diseases have limited their application in clinical practice. Here, we developed a new method that enables incorporation of the general family history of diseases with a liability threshold model, and propose a new analysis strategy for risk prediction with penalized regression analysis that incorporates both large numbers of genetic variants and clinical risk factors. Application of our model to type 2 diabetes in the Korean population (1846 cases and 1846 controls) demonstrated that single-nucleotide polymorphisms accounted for 32.5% of the variation explained by the predicted risk scores in the test data set, and incorporation of family history led to an additional 6.3% improvement in prediction. Our results illustrate that family medical history provides valuable information on the variation of complex diseases and improves prediction performance. Copyright © 2017 by the Genetics Society of America.

Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits.

PubMed

Imprialou, Martha; Kahles, André; Steffen, Joshua G; Osborne, Edward J; Gan, Xiangchao; Lempe, Janne; Bhomra, Amarjit; Belfield, Eric; Visscher, Anne; Greenhalgh, Robert; Harberd, Nicholas P; Goram, Richard; Hein, Jotun; Robert-Seilaniantz, Alexandre; Jones, Jonathan; Stegle, Oliver; Kover, Paula; Tsiantis, Miltos; Nordborg, Magnus; Rätsch, Gunnar; Clark, Richard M; Mott, Richard

2017-04-01

To understand the population genetics of structural variants and their effects on phenotypes, we developed an approach to mapping structural variants that segregate in a population sequenced at low coverage. We avoid calling structural variants directly. Instead, the evidence for a potential structural variant at a locus is indicated by variation in the counts of short-reads that map anomalously to that locus. These structural variant traits are treated as quantitative traits and mapped genetically, analogously to a gene expression study. Association between a structural variant trait at one locus, and genotypes at a distant locus indicate the origin and target of a transposition. Using ultra-low-coverage (0.3×) population sequence data from 488 recombinant inbred Arabidopsis thaliana genomes, we identified 6502 segregating structural variants. Remarkably, 25% of these were transpositions. While many structural variants cannot be delineated precisely, we validated 83% of 44 predicted transposition breakpoints by polymerase chain reaction. We show that specific structural variants may be causative for quantitative trait loci for germination and resistance to infection by the fungus Albugo laibachii , isolate Nc14. Further we show that the phenotypic heritability attributable to read-mapping anomalies differs from, and, in the case of time to germination and bolting, exceeds that due to standard genetic variation. Genes within structural variants are also more likely to be silenced or dysregulated. This approach complements the prevalent strategy of structural variant discovery in fewer individuals sequenced at high coverage. It is generally applicable to large populations sequenced at low-coverage, and is particularly suited to mapping transpositions. Copyright © 2017 by the Genetics Society of America.

Structural and climatic determinants of demographic rates of Scots pine forests across the Iberian Peninsula.

PubMed

Vilà-Cabrera, Albert; Martínez-Vilalta, Jordi; Vayreda, Jordi; Retana, Javier

2011-06-01

The demographic rates of tree species typically show large spatial variation across their range. Understanding the environmental factors underlying this variation is a key topic in forest ecology, with far-reaching management implications. Scots pine (Pinus sylvestris L.) covers large areas of the Northern Hemisphere, the Iberian Peninsula being its southwestern distribution limit. In recent decades, an increase in severe droughts and a densification of forests as a result of changes in forest uses have occurred in this region. Our aim was to use climate and stand structure data to explain mortality and growth patterns of Scots pine forests across the Iberian Peninsula. We used data from 2392 plots dominated by Scots pine, sampled for the National Forest Inventory of Spain. Plots were sampled from 1986 to 1996 (IFN2) and were resampled from 1997 to 2007 (IFN3), allowing for the calculation of growth and mortality rates. We fitted linear models to assess the response of growth and mortality rates to the spatial variability of climate, climatic anomalies, and forest structure. Over the period of approximately 10 years between the IFN2 and IFN3, the amount of standing dead trees increased 11-fold. Higher mortality rates were related to dryness, and growth was reduced with increasing dryness and temperature, but results also suggested that effects of climatic stressors were not restricted to dry sites only. Forest structure was strongly related to demographic rates, suggesting that stand development and competition are the main factors associated with demography. In the case of mortality, forest structure interacted with climate, suggesting that competition for water resources induces tree mortality in dry sites. A slight negative relationship was found between mortality and growth, indicating that both rates are likely to be affected by the same stress factors. Additionally, regeneration tended to be lower in plots with higher mortality. Taken together, our results suggest a large-scale self-thinning related to the recent densification of Scots pine forests. This process appears to be enhanced by dry conditions and may lead to a mismatch in forest turnover. Forest management may be an essential adaptive tool under the drier conditions predicted by most climate models.

The majority of genetic variation in orangutan personality and subjective well-being is nonadditive.

PubMed

Adams, Mark James; King, James E; Weiss, Alexander

2012-07-01

The heritability of human personality is well-established. Recent research indicates that nonadditive genetic effects, such as dominance and epistasis, play a large role in personality variation. One possible explanation for the latter finding is that there has been recent selection on human personality. To test this possibility, we estimated additive and nonadditive genetic variance in personality and subjective well-being of zoo-housed orangutans. More than half of the genetic variance in these traits could be attributed to nonadditive genetic effects, modeled as dominance. Subjective well-being had genetic overlap with personality, though less so than has been found in humans or chimpanzees. Since a large portion of nonadditive genetic variance in personality is not unique to humans, the nonadditivity of human personality is not sufficient evidence for recent selection of personality in humans. Nonadditive genetic variance may be a general feature of the genetic structure of personality in primates and other animals.

A tripolar pattern as an internal mode of the East Asian summer monsoon

NASA Astrophysics Data System (ADS)

Hirota, Nagio; Takahashi, Masaaki

2012-11-01

A tripolar anomaly pattern with centers located around the Philippines, China/Japan, and East Siberia dominantly appears in climate variations of the East Asian summer monsoon. In this study, we extracted this pattern as the first mode of a singular value decomposition (SVD1) over East Asia. The squared covariance fraction of SVD1 was 59 %, indicating that this pattern can be considered a dominant pattern of climate variations. Moreover, the results of numerical experiments suggested that the structure is also a dominant pattern of linear responses, even if external forcing is distributed homogeneously over the Northern Hemisphere. Thus, the tripolar pattern can be considered an internal mode that is characterized by the internal atmospheric processes. In this pattern, the moist processes strengthen the circulation anomalies, the dynamical energy conversion supplies energy to the anomalies, and the Rossby waves propagate northward in the lower troposphere and southeastward in the upper troposphere. These processes are favorable for the pattern to have large amplitude and to influence a large area.

Mode characteristics of nonplanar double-heterojunction and large-optical-cavity laser structures

NASA Technical Reports Server (NTRS)

Butler, J. K.; Botez, D.

1982-01-01

Mode behavior of nonplanar double-heterojunction (DH) and large-optical-cavity (LOC) lasers is investigated using the effective index method to model the lateral field distribution. The thickness variations of various layers for the devices discussed are correlated with the growth characteristics of liquid-phase epitaxy over topographical features (channels, mesas) etched into the substrate. The effective dielectric profiles of constricted double-heterojunction (CDH)-LOC lasers show a strong influence on transverse mode operation: the fundamental transverse mode (i.e., in the plane perpendicular to the junction) may be laterally index-guided, while the first (high)-order mode is laterally index-antiguided. The analytical model developed uses a smoothly varying hyperbolic cosine distribution to characterize lateral index variations. The waveguide model is applied to several lasers to illustrate conditions necessary to convert leaky modes to trapped ones via the active-region gain distribution. Theoretical radiation patterns are calculated using model parameters, and matched to an experimental far-field pattern.

Early genetic consequences of defaunation in a large-seeded vertebrate-dispersed palm (Syagrus romanzoffiana)

PubMed Central

Giombini, M I; Bravo, S P; Sica, Y V; Tosto, D S

2017-01-01

Plant populations are seriously threatened by anthropogenic habitat disturbance. In particular, defaunation may disrupt plant-disperser mutualisms, thus reducing levels of seed-mediated gene flow and genetic variation in animal-dispersed plants. This may ultimately limit their adaptive potential and ability to cope with environmental change. Tropical forest remnants are typically deprived of medium to large vertebrates upon which many large-seeded plants rely for accomplishing effective seed dispersal. Our main goal was to examine the potential early genetic consequences of the loss of large vertebrates for large-seeded vertebrate-dispersed plants. We compared the genetic variation in early-stage individuals of the large-seeded palm Syagrus romanzoffiana between continuous protected forest and nearby partially defaunated fragments in the Atlantic Forest of South America. Using nine microsatellites, we found lower allelic richness and stronger fine-scale spatial genetic structure in the disturbed area. In addition, the percentage of dispersed recruits around conspecific adults was lower, although not significantly, in the disturbed area (median values: 0.0 vs 14.4%). On the other hand, no evidence of increased inbreeding or reduced pollen-mediated gene flow (selfing rate and diversity of pollen donors) was found in the disturbed area. Our findings are strongly suggestive of some early genetic consequences resulting from the limitation in contemporary gene flow via seeds, but not pollen, in defaunated areas. Plant-disperser mutualisms involving medium–large frugivores, which are seriously threatened in tropical systems, should therefore be protected to warrant the maintenance of seed-mediated gene flow and genetic diversity in large-seeded plants. PMID:28121308

An activity index for geomagnetic paleosecular variation, excursions, and reversals

NASA Astrophysics Data System (ADS)

Panovska, S.; Constable, C. G.

2017-04-01

Magnetic indices provide quantitative measures of space weather phenomena that are widely used by researchers in geomagnetism. We introduce an index focused on the internally generated field that can be used to evaluate long term variations or climatology of modern and paleomagnetic secular variation, including geomagnetic excursions, polarity reversals, and changes in reversal rate. The paleosecular variation index, Pi, represents instantaneous or average deviation from a geocentric axial dipole field using normalized ratios of virtual geomagnetic pole colatitude and virtual dipole moment. The activity level of the index, σPi, provides a measure of field stability through the temporal standard deviation of Pi. Pi can be calculated on a global grid from geomagnetic field models to reveal large scale geographic variations in field structure. It can be determined for individual time series, or averaged at local, regional, and global scales to detect long term changes in geomagnetic activity, identify excursions, and transitional field behavior. For recent field models, Pi ranges from less than 0.05 to 0.30. Conventional definitions for geomagnetic excursions are characterized by Pi exceeding 0.5. Strong field intensities are associated with low Pi unless they are accompanied by large deviations from axial dipole field directions. σPi provides a measure of geomagnetic stability that is modulated by the level of PSV or frequency of excursional activity and reversal rate. We demonstrate uses of Pi for paleomagnetic observations and field models and show how it could be used to assess whether numerical simulations of the geodynamo exhibit Earth-like properties.

Utilizing Gravity Methods for Regional Studies in Basin Delineation: Case Study at Jornada del Muerto basin, New Mexico

NASA Astrophysics Data System (ADS)

Villalobos, J. I.

2005-12-01

The modeling of basin structures is an important step in the development of plans and policies for ground water management. To facilitate in the analysis of large scale regional structures, gravity data is implemented to examine the overall structural trend of the region. The gravitational attraction of structures in the upper mantle and crust provide vital information about the possible structure and composition of a region. Improved availability of gravity data via internet has promoted extensive construction and interpretation of gravity maps in the analysis of sub-surface structural anomalies. The utilization of gravity data appears to be particularly worthwhile because it is a non-invasive and inexpensive means of addressing the subsurface tectonic framework of large scale regions. In this paper, the author intends to illustrate 1) acquisition of gravity data and its processing; 2) interpretation of gravity data; and 3) sources of uncertainty and errors by using a case study of the Jornada del Muerto basin in South-Central New Mexico where integrated gravity data inferred several faults, sub-basins and thickness variations within the basins structure. The author also explores the integration of gravity method with other geophysical methods to further refine the delineation of basins.

Structural Variation of Type I-F CRISPR RNA Guided DNA Surveillance.

PubMed

Pausch, Patrick; Müller-Esparza, Hanna; Gleditzsch, Daniel; Altegoer, Florian; Randau, Lennart; Bange, Gert

2017-08-17

CRISPR-Cas systems are prokaryotic immune systems against invading nucleic acids. Type I CRISPR-Cas systems employ highly diverse, multi-subunit surveillance Cascade complexes that facilitate duplex formation between crRNA and complementary target DNA for R-loop formation, retention, and DNA degradation by the subsequently recruited nuclease Cas3. Typically, the large subunit recognizes bona fide targets through the PAM (protospacer adjacent motif), and the small subunit guides the non-target DNA strand. Here, we present the Apo- and target-DNA-bound structures of the I-Fv (type I-F variant) Cascade lacking the small and large subunits. Large and small subunits are functionally replaced by the 5' terminal crRNA cap Cas5fv and the backbone protein Cas7fv, respectively. Cas5fv facilitates PAM recognition from the DNA major groove site, in contrast to all other described type I systems. Comparison of the type I-Fv Cascade with an anti-CRISPR protein-bound I-F Cascade reveals that the type I-Fv structure differs substantially at known anti-CRISPR protein target sites and might therefore be resistant to viral Cascade interception. Copyright © 2017 Elsevier Inc. All rights reserved.

A Multilevel Gamma-Clustering Layout Algorithm for Visualization of Biological Networks

PubMed Central

Hruz, Tomas; Lucas, Christoph; Laule, Oliver; Zimmermann, Philip

2013-01-01

Visualization of large complex networks has become an indispensable part of systems biology, where organisms need to be considered as one complex system. The visualization of the corresponding network is challenging due to the size and density of edges. In many cases, the use of standard visualization algorithms can lead to high running times and poorly readable visualizations due to many edge crossings. We suggest an approach that analyzes the structure of the graph first and then generates a new graph which contains specific semantic symbols for regular substructures like dense clusters. We propose a multilevel gamma-clustering layout visualization algorithm (MLGA) which proceeds in three subsequent steps: (i) a multilevel γ-clustering is used to identify the structure of the underlying network, (ii) the network is transformed to a tree, and (iii) finally, the resulting tree which shows the network structure is drawn using a variation of a force-directed algorithm. The algorithm has a potential to visualize very large networks because it uses modern clustering heuristics which are optimized for large graphs. Moreover, most of the edges are removed from the visual representation which allows keeping the overview over complex graphs with dense subgraphs. PMID:23864855

Three-dimensional morphological and textural complexity of Archean putative microfossils from the Northeastern Pilbara Craton: indications of biogenicity of large (>15 microm) spheroidal and spindle-like structures.

PubMed

Sugitani, Kenichiro; Grey, Kathleen; Nagaoka, Tsutomu; Mimura, Koichi

2009-09-01

We recently reported a diverse assemblage of carbonaceous structures (thread-like, film-like, spheroidal, and spindle-like) from chert in the ca. 3.0 Ga Farrel Quartzite of the Gorge Creek Group in the Pilbara Craton, Western Australia. Results from a rigorous examination of occurrence, composition, morphological complexity, size distributions, and taphonomy provided presumptive evidence for biogenicity. In this study, we present new data of morphological and textural complexity of large (>15 microm) spheroidal and spindle-like structures, using an in-focus, 3-D image reconstruction system, which further raises the scale of credibility that these structures are microfossils. While many of the large spheroids are single-walled, and the wall is irregularly folded, a few specimens are partially blistered, double walled, or have a dimpled wall. The wall-surface texture varies from smooth and homogeneous (hyaline) to patchy, granular or reticulate. Such variation is best explained as resulting from taphonomic processes. Additionally, an inner solitary body, present in some large spheroids, is hollow and partially broken, which indicates a primary origin for this substructure. Spindle-like structures have two types of flange-like appendage; one is attached at the equatorial plane of the body, whereas the other appears to be attached peripherally. In both cases, the appendage tends to have a flat geometry, a tapering thickness, and constancy in shape, proportions, and dimensions. Spindle-wall surfaces are variously textured and heterogeneous. These morphological and textural complexities and heterogeneity refute potential abiogenic formation models for these structures, such as crystals coated with organic matter, fenestrae, and the diagenetic redistribution of carbonaceous matter. When coupled with other data from Raman spectroscopy, NanoSIMS analysis, and palynology, the evidence that these large carbonaceous structures are biogenic appears compelling, though it is still equivocal as to whether they are cells or outer envelopes of colonies of smaller cells.

Comparison of manual and automatic segmentation methods for brain structures in the presence of space-occupying lesions: a multi-expert study

PubMed Central

Deeley, M A; Chen, A; Datteri, R; Noble, J; Cmelak, A; Donnelly, E; Malcolm, A; Moretti, L; Jaboin, J; Niermann, K; Yang, Eddy S; Yu, David S; Yei, F; Koyama, T; Ding, G X; Dawant, B M

2011-01-01

The purpose of this work was to characterize expert variation in segmentation of intracranial structures pertinent to radiation therapy, and to assess a registration-driven atlas-based segmentation algorithm in that context. Eight experts were recruited to segment the brainstem, optic chiasm, optic nerves, and eyes, of 20 patients who underwent therapy for large space-occupying tumors. Performance variability was assessed through three geometric measures: volume, Dice similarity coefficient, and Euclidean distance. In addition, two simulated ground truth segmentations were calculated via the simultaneous truth and performance level estimation (STAPLE) algorithm and a novel application of probability maps. The experts and automatic system were found to generate structures of similar volume, though the experts exhibited higher variation with respect to tubular structures. No difference was found between the mean Dice coefficient (DSC) of the automatic and expert delineations as a group at a 5% significance level over all cases and organs. The larger structures of the brainstem and eyes exhibited mean DSC of approximately 0.8–0.9, whereas the tubular chiasm and nerves were lower, approximately 0.4–0.5. Similarly low DSC have been reported previously without the context of several experts and patient volumes. This study, however, provides evidence that experts are similarly challenged. The average maximum distances (maximum inside, maximum outside) from a simulated ground truth ranged from (−4.3, +5.4) mm for the automatic system to (−3.9, +7.5) mm for the experts considered as a group. Over all the structures in a rank of true positive rates at a 2 mm threshold from the simulated ground truth, the automatic system ranked second of the nine raters. This work underscores the need for large scale studies utilizing statistically robust numbers of patients and experts in evaluating quality of automatic algorithms. PMID:21725140

Comparison of manual and automatic segmentation methods for brain structures in the presence of space-occupying lesions: a multi-expert study

NASA Astrophysics Data System (ADS)

Deeley, M. A.; Chen, A.; Datteri, R.; Noble, J. H.; Cmelak, A. J.; Donnelly, E. F.; Malcolm, A. W.; Moretti, L.; Jaboin, J.; Niermann, K.; Yang, Eddy S.; Yu, David S.; Yei, F.; Koyama, T.; Ding, G. X.; Dawant, B. M.

2011-07-01

The purpose of this work was to characterize expert variation in segmentation of intracranial structures pertinent to radiation therapy, and to assess a registration-driven atlas-based segmentation algorithm in that context. Eight experts were recruited to segment the brainstem, optic chiasm, optic nerves, and eyes, of 20 patients who underwent therapy for large space-occupying tumors. Performance variability was assessed through three geometric measures: volume, Dice similarity coefficient, and Euclidean distance. In addition, two simulated ground truth segmentations were calculated via the simultaneous truth and performance level estimation algorithm and a novel application of probability maps. The experts and automatic system were found to generate structures of similar volume, though the experts exhibited higher variation with respect to tubular structures. No difference was found between the mean Dice similarity coefficient (DSC) of the automatic and expert delineations as a group at a 5% significance level over all cases and organs. The larger structures of the brainstem and eyes exhibited mean DSC of approximately 0.8-0.9, whereas the tubular chiasm and nerves were lower, approximately 0.4-0.5. Similarly low DSCs have been reported previously without the context of several experts and patient volumes. This study, however, provides evidence that experts are similarly challenged. The average maximum distances (maximum inside, maximum outside) from a simulated ground truth ranged from (-4.3, +5.4) mm for the automatic system to (-3.9, +7.5) mm for the experts considered as a group. Over all the structures in a rank of true positive rates at a 2 mm threshold from the simulated ground truth, the automatic system ranked second of the nine raters. This work underscores the need for large scale studies utilizing statistically robust numbers of patients and experts in evaluating quality of automatic algorithms.

Variations in the Crust-Mantle Transition Beneath the Andean Cordillera and Implications for Orogenic Processes.

NASA Astrophysics Data System (ADS)

Koch, C.; Isaacs, D.; Delph, J. R.; Beck, S. L.

2017-12-01

The South American Andes, generated along an active oceanic-continental convergent margin between the Nazca and South American plates, make up the world's longest arc and encompass the second highest orogenic plateau on Earth. Along-strike variations in shortening, slab subduction angle, and volcanism, along with other tectonic processes, have created extraordinarily complex topography, crustal thickness, and compositional variations reflected in the seismic characteristics of the region. Ps receiver functions (PRFs) have been widely used to investigate the Andes, and these studies provide a wealth of information regarding the structure of the Andean crust and the continental Moho beneath the orogen. However, these studies have focused largely on individual networks or latitudinal segments of the Andes, and a regional-scale model that combines all available data has yet to be analyzed, hence it is hard to compare the amplitudes of conversions at the major discontinuities. This study compiles and analyzes all available data from permanent and temporary seismic networks from (1989-2017) to create a continuous, high spatial resolution common conversion point (CCP) volume for the Andes. In total, receiver functions were calculated for over 1500 seismic stations in the Andes, enabling us to obtain high-resolution, regional-scale CCP images of the continental Moho beneath the Andes from Colombia to southern Chile. The resulting CCP volume shows strong lateral variations in P-to-S conversion amplitudes at the base of the crust, indicating a complex and variable crust-mantle transition. In some places, the back-arc of the central Andes is characterized by relatively thick crust (60 - 75 km) and a broad, low amplitude Moho conversion indicative of a gradational Moho possibly due to the eclogitization of the lower crust. Combined with other geophysical data, this may suggest these are sites of ongoing delamination in the central Andes. Additionally, in the central Andes, beneath the interior plateau, parts of the active arc and backarc, we image a pervasive, relatively shallow (15-25 km depth), large-amplitude negative P-to-S converter that exhibits variations in amplitude and structure along strike, likely corresponding to the top of the Andean low velocity zone.

Firn thickness variations across the Northeast Greenland Ice Stream margins indicating nonlinear densification rates

NASA Astrophysics Data System (ADS)

Riverman, K. L.; Anandakrishnan, S.; Alley, R. B.; Peters, L. E.; Christianson, K. A.; Muto, A.

2013-12-01

Northeast Greenland Ice Stream (NEGIS) is the largest ice stream in Greenland, draining approximately 8.4% of the ice sheet's area. The flow pattern and stability mechanism of this ice stream are unique to others in Greenland and Antarctica, and merit further study to ascertain the sensitivity of this ice stream to future climate change. Geophysical methods are valuable tools for this application, but their results are sensitive to the structure of the firn and any spatial variations in firn properties across a given study region. Here we present firn data from a 40-km-long seismic profile across the upper reaches of NEGIS, collected in the summer of 2012 as part of an integrated ground-based geophysical survey. We find considerable variations in firn thickness that are coincident with the ice stream shear margins, where a thinner firn layer is present within the margins, and a thicker, more uniform firn layer is present elsewhere in our study region. Higher accumulation rates in the marginal surface troughs due to drift-snow trapping can account for some of this increased densification; however, our seismic results also highlight enhanced anisotropy within the firn and upper ice column that is confined to narrow bands within the shear margins. We thus interpret these large firn thickness variations and abrupt changes in anisotropy as indicators of firn densification dependent on the effective stress state as well as the overburden pressure, suggesting that the strain rate increases nonlinearly with stress across the shear margins. A GPS strain grid maintained for three weeks across both margins observed strong side shearing, with rapid stretching and then compression along particle paths, indicating large deviatoric stresses in the margins. This work demonstrates the importance of developing a high-resolution firn densification model when conducting geophysical field work in regions possessing a complex ice flow history; it also motivates the need for a more detailed firn densification study along NEGIS to better understand the evolution of these abrupt structural variations within the firn.

Seasonal and spatial variations in fish and macrocrustacean assemblage structure in Mad Island Marsh estuary, Texas

NASA Astrophysics Data System (ADS)

Akin, S.; Winemiller, K. O.; Gelwick, F. P.

2003-05-01

Fish and macrocrustacean assemblage structure was analyzed along an estuarine gradient at Mad Island Marsh (MIM), Matagorda Bay, TX, during March 1998-August 1999. Eight estuarine-dependent fish species accounted for 94% of the individual fishes collected, and three species accounted for 96% of macrocrustacean abundance. Consistent with evidence from other Gulf of Mexico estuarine studies, species richness and abundance were highest during late spring and summer, and lowest during winter and early spring. Sites near the bay supported the most individuals and species. Associations between fish abundance and environmental variables were examined with canonical correspondence analysis. The dominant gradient was associated with water depth and distance from the bay. The secondary gradient reflected seasonal variation and was associated with temperature, salinity, dissolved oxygen, and vegetation cover. At the scales examined, estuarine biota responded to seasonal variation more than spatial variation. Estuarine-dependent species dominated the fauna and were common throughout the open waters of the shallow lake during winter-early spring when water temperature and salinity were low and dissolved oxygen high. During summer-early fall, sub-optimal environmental conditions (high temperature, low DO) in upper reaches accounted for strong spatial variation in assemblage composition. Small estuarine-resident fishes and the blue crab ( Callinectes sapidus) were common in warm, shallow, vegetated inland sites during summer-fall. Estuarine-dependent species were common at deeper, more saline locations near the bay during this period. During summer, freshwater species, such as gizzard shad ( Dorosoma cepedianum) and gars ( Lepisosteus spp.), were positively associated with water depth and proximity to the bay. The distribution and abundance of fishes in MIM appear to result from the combined effects of endogenous, seasonal patterns of reproduction and migration operating on large spatial scales, and species-specific response to local environmental variation.

Hazard assessment of long-period ground motions for the Nankai Trough earthquakes

NASA Astrophysics Data System (ADS)

Maeda, T.; Morikawa, N.; Aoi, S.; Fujiwara, H.

2013-12-01

We evaluate a seismic hazard for long-period ground motions associated with the Nankai Trough earthquakes (M8~9) in southwest Japan. Large interplate earthquakes occurring around the Nankai Trough have caused serious damages due to strong ground motions and tsunami; most recent events were in 1944 and 1946. Such large interplate earthquake potentially causes damages to high-rise and large-scale structures due to long-period ground motions (e.g., 1985 Michoacan earthquake in Mexico, 2003 Tokachi-oki earthquake in Japan). The long-period ground motions are amplified particularly on basins. Because major cities along the Nankai Trough have developed on alluvial plains, it is therefore important to evaluate long-period ground motions as well as strong motions and tsunami for the anticipated Nankai Trough earthquakes. The long-period ground motions are evaluated by the finite difference method (FDM) using 'characterized source models' and the 3-D underground structure model. The 'characterized source model' refers to a source model including the source parameters necessary for reproducing the strong ground motions. The parameters are determined based on a 'recipe' for predicting strong ground motion (Earthquake Research Committee (ERC), 2009). We construct various source models (~100 scenarios) giving the various case of source parameters such as source region, asperity configuration, and hypocenter location. Each source region is determined by 'the long-term evaluation of earthquakes in the Nankai Trough' published by ERC. The asperity configuration and hypocenter location control the rupture directivity effects. These parameters are important because our preliminary simulations are strongly affected by the rupture directivity. We apply the system called GMS (Ground Motion Simulator) for simulating the seismic wave propagation based on 3-D FDM scheme using discontinuous grids (Aoi and Fujiwara, 1999) to our study. The grid spacing for the shallow region is 200 m and 100 m in horizontal and vertical, respectively. The grid spacing for the deep region is three times coarser. The total number of grid points is about three billion. The 3-D underground structure model used in the FD simulation is the Japan integrated velocity structure model (ERC, 2012). Our simulation is valid for period more than two seconds due to the lowest S-wave velocity and grid spacing. However, because the characterized source model may not sufficiently support short period components, we should be interpreted the reliable period of this simulation with caution. Therefore, we consider the period more than five seconds instead of two seconds for further analysis. We evaluate the long-period ground motions using the velocity response spectra for the period range between five and 20 second. The preliminary simulation shows a large variation of response spectra at a site. This large variation implies that the ground motion is very sensitive to different scenarios. And it requires studying the large variation to understand the seismic hazard. Our further study will obtain the hazard curves for the Nankai Trough earthquake (M 8~9) by applying the probabilistic seismic hazard analysis to the simulation results.

Large Temporal and Spatial Variations in the Eastern Himalayan Syntaxis Exhumation From Detrital Thermochronology

NASA Astrophysics Data System (ADS)

Enkelmann, Eva; Ehlers, Todd A.

2010-05-01

The exhumation rates at the Eastern Himalayan Syntaxis, and in particular at the Namche Barwa anticline, are some of the highest in the Himalaya. At the core of the anticline high-grade metamorphic rocks of Indian crust were exhumed from ca. 40 km depth within <10 Ma. Bedrock thermochronology shows rapid exhumation since <4 Ma that has since migrated north and west of the anticline. The structural history of the anticline and its northern and western surroundings are relatively well studied. However, the geology and exhumation history of the southeastern flank is largely unknown. We present 1500 new detrital zircon fission track cooling ages from 15 modern river samples of the Tsangpo-Siang River and its tributaries. These samples provide cooling ages from drainage basins in the Namche Barwa anticline and the region north, west, and south of it (China and India). Results are as follows: (1) we find eight age populations (0.9 ± 0.2 Ma , 3.5 ± 1 Ma, 7 Ma, 11 ± 2 Ma, 18 ± 2 Ma, 24 ± 2 Ma, 35 ± 5 Ma and 50 - 55 Ma) that quantify temporal variations in the exhumation history of the eastern syntaxis since the Paleocene/Eocene. (2) Cooling ages are consistent with the development of the anticline structure since the Late Miocene. (3) Previous studies have suggested that ~ 50% of the Siang River sediments exiting the Himalaya today originate from only a small area of the Namche Barwa massif. However, our data reveal that the zone of localized rapid exhumation extends significantly (ca. 40 km) further to the southwest of the anticline than previously assumed. Finally, (4) spatial variations in cooling age populations suggest structural differences between the northwestern and southeastern flanks of the anticline. Northwest of the anticline rapid exhumation has migrated beyond the anticline and into the hangingwall (Asia). In the Southeast, the zone of exhumation is strictly limited to the anticline and bounded by a sharp structural boundary along by the Siang River. This spatial pattern suggests a northwestward migration of the syntaxial zone of exhumation in the last ca. 10 Ma.

Systematic study of electron-phonon coupling to oxygen modes across the cuprates

NASA Astrophysics Data System (ADS)

Johnston, S.; Vernay, F.; Moritz, B.; Shen, Z.-X.; Nagaosa, N.; Zaanen, J.; Devereaux, T. P.

2010-08-01

The large variations in Tc across the cuprate families is one of the major unsolved puzzles in condensed matter physics and is poorly understood. Although there appears to be a great deal of universality in the cuprates, several orders of magnitude changes in Tc can be achieved through changes in the chemical composition and structure of the unit cell. In this paper we formulate a systematic examination of the variations in electron-phonon coupling to oxygen phonons in the cuprates, incorporating a number of effects arising from several aspects of chemical composition and doping across cuprate families. It is argued that the electron-phonon coupling is a very sensitive probe of the material-dependent variations in chemical structure, affecting the orbital character of the band crossing the Fermi level, the strength of local electric fields arising from structural-induced symmetry breaking, doping-dependent changes in the underlying band structure, and ionicity of the crystal governing the ability of the material to screen c -axis perturbations. Using electrostatic Ewald calculations and known experimental structural data, we establish a connection between the material’s maximal Tc at optimal doping and the strength of coupling to c -axis modes. We demonstrate that materials with the largest coupling to the out-of-phase bond-buckling (B1g) oxygen phonon branch also have the largest Tc ’s. In light of this observation we present model Tc calculations using a two-well model where phonons work in conjunction with a dominant pairing interaction, presumably due to spin fluctuations, indicating how phonons can generate sizeable enhancements to Tc despite the relatively small coupling strengths. Combined, these results can provide a natural framework for understanding the doping and material dependence of Tc across the cuprates.

A feature-based developmental model of the infant brain in structural MRI.

PubMed

Toews, Matthew; Wells, William M; Zöllei, Lilla

2012-01-01

In this paper, anatomical development is modeled as a collection of distinctive image patterns localized in space and time. A Bayesian posterior probability is defined over a random variable of subject age, conditioned on data in the form of scale-invariant image features. The model is automatically learned from a large set of images exhibiting significant variation, used to discover anatomical structure related to age and development, and fit to new images to predict age. The model is applied to a set of 230 infant structural MRIs of 92 subjects acquired at multiple sites over an age range of 8-590 days. Experiments demonstrate that the model can be used to identify age-related anatomical structure, and to predict the age of new subjects with an average error of 72 days.

Relation between Kitaev magnetism and structure in α -RuCl3

NASA Astrophysics Data System (ADS)

Glamazda, A.; Lemmens, P.; Do, S.-H.; Kwon, Y. S.; Choi, K.-Y.

2017-05-01

Raman scattering has been employed to investigate lattice and magnetic excitations of the honeycomb Kitaev material α -RuCl3 and its Heisenberg counterpart CrCl3. Our phonon Raman spectra give evidence for a first-order structural transition from a monoclinic to a rhombohedral structure for both compounds. Significantly, only α -RuCl3 features a large thermal hysteresis, consistent with the formation of a wide phase of coexistence. In the related temperature interval of 70 -170 K, we observe a hysteretic behavior of magnetic excitations as well. The stronger magnetic response in the rhombohedral compared to the monoclinic phase evidences a coupling between the crystallographic structure and low-energy magnetic response. Our results demonstrate that the Kitaev magnetism concomitant with fractionalized excitations is susceptible to small variations of bonding geometry.

The relationship between amplitude modulation, coherent structure and critical layers in wall turbulence

NASA Astrophysics Data System (ADS)

McKeon, Beverley

2015-11-01

The importance of critical layers in determining aspects of the structure of wall turbulence is discussed. We have shown (Jacobi & McKeon, 2013) that the amplitude modulation coefficient investigated most recently by Hutchins & Marusic (2007) and co-authors, which describes the correlation between large scales above a (spatial) wavelength filter with the envelope of small scales below the filter, is dominated by very large scale motion (VLSM) at a single wavelength. The resolvent analysis of McKeon & Sharma (2010) gives a suitable model for the three-dimensional, three-component form of the VLSM and energetic structure at other wavelengths. This model is used to identify the three-dimensional spatial variation of instantaneous critical layers in the presence of a mean velocity profile and to relate this to earlier observations of coherent structure in unperturbed flows (both experimental and via the resolvent model, Sharma & McKeon, 2013); to the phase relationships between scales identified by Chung & McKeon (2010, 2014); and to the structure of wall turbulence that has been modified by the addition of single synthetic scales, e.g. Jacobi & McKeon (2011), Duvvuri & McKeon (2015). The support of AFOSR under grant number FA 9550-12-1-0469 is gratefully acknowledged.

Life-history and habitat features influence the within-river genetic structure of Atlantic salmon.

PubMed

Vähä, Juha-Pekka; Erkinaro, Jaakko; Niemelä, Eero; Primmer, Craig R

2007-07-01

Defining populations and identifying ecological and life-history characteristics affecting genetic structure is important for understanding species biology and hence, for managing threatened or endangered species or populations. In this study, populations of the world's largest indigenous Atlantic salmon (Salmo salar) stock were first inferred using model-based clustering methods, following which life-history and habitat variables best predicting the genetic diversity of populations were identified. This study revealed that natal homing of Atlantic salmon within the Teno River system is accurate at least to the tributary level. Generally, defining populations by main tributaries was observed to be a reasonable approach in this large river system, whereas in the mainstem of the river, the number of inferred populations was fewer than the number of distinct sampling sites. Mainstem and headwater populations were genetically more diverse and less diverged, while each tributary fostered a distinct population with high genetic differentiation and lower genetic diversity. Population structure and variation in genetic diversity among populations were poorly explained by geographical distance. In contrast, age-structure, as estimated by the proportion of multisea-winter spawners, was the most predictive variable in explaining the variation in the genetic diversity of the populations. This observation, being in agreement with theoretical predictions, emphasizes the essence of large multisea-winter females in maintaining the genetic diversity of populations. In addition, the unique genetic diversity of populations, as estimated by private allele richness, was affected by the ease of accessibility of a site, with more difficult to access sites having lower unique genetic diversity. Our results show that despite this species' high capacity for migration, tributaries foster relatively closed populations with little gene flow which will be important to consider when developing management strategies for the system.

Fishing degrades size structure of coral reef fish communities.

PubMed

Robinson, James P W; Williams, Ivor D; Edwards, Andrew M; McPherson, Jana; Yeager, Lauren; Vigliola, Laurent; Brainard, Russell E; Baum, Julia K

2017-03-01

Fishing pressure on coral reef ecosystems has been frequently linked to reductions of large fishes and reef fish biomass. Associated impacts on overall community structure are, however, less clear. In size-structured aquatic ecosystems, fishing impacts are commonly quantified using size spectra, which describe the distribution of individual body sizes within a community. We examined the size spectra and biomass of coral reef fish communities at 38 US-affiliated Pacific islands that ranged in human presence from near pristine to human population centers. Size spectra 'steepened' steadily with increasing human population and proximity to market due to a reduction in the relative biomass of large fishes and an increase in the dominance of small fishes. Reef fish biomass was substantially lower on inhabited islands than uninhabited ones, even at inhabited islands with the lowest levels of human presence. We found that on populated islands size spectra exponents decreased (analogous to size spectra steepening) linearly with declining biomass, whereas on uninhabited islands there was no relationship. Size spectra were steeper in regions of low sea surface temperature but were insensitive to variation in other environmental and geomorphic covariates. In contrast, reef fish biomass was highly sensitive to oceanographic conditions, being influenced by both oceanic productivity and sea surface temperature. Our results suggest that community size structure may be a more robust indicator than fish biomass to increasing human presence and that size spectra are reliable indicators of exploitation impacts across regions of different fish community compositions, environmental drivers, and fisheries types. Size-based approaches that link directly to functional properties of fish communities, and are relatively insensitive to abiotic variation across biogeographic regions, offer great potential for developing our understanding of fishing impacts in coral reef ecosystems. © 2016 John Wiley & Sons Ltd.

Unified risk analysis of fatigue failure in ductile alloy components during all three stages of fatigue crack evolution process.

PubMed

Patankar, Ravindra

2003-10-01

Statistical fatigue life of a ductile alloy specimen is traditionally divided into three stages, namely, crack nucleation, small crack growth, and large crack growth. Crack nucleation and small crack growth show a wide variation and hence a big spread on cycles versus crack length graph. Relatively, large crack growth shows a lesser variation. Therefore, different models are fitted to the different stages of the fatigue evolution process, thus treating different stages as different phenomena. With these independent models, it is impossible to predict one phenomenon based on the information available about the other phenomenon. Experimentally, it is easier to carry out crack length measurements of large cracks compared to nucleating cracks and small cracks. Thus, it is easier to collect statistical data for large crack growth compared to the painstaking effort it would take to collect statistical data for crack nucleation and small crack growth. This article presents a fracture mechanics-based stochastic model of fatigue crack growth in ductile alloys that are commonly encountered in mechanical structures and machine components. The model has been validated by Ray (1998) for crack propagation by various statistical fatigue data. Based on the model, this article proposes a technique to predict statistical information of fatigue crack nucleation and small crack growth properties that uses the statistical properties of large crack growth under constant amplitude stress excitation. The statistical properties of large crack growth under constant amplitude stress excitation can be obtained via experiments.

Reliability of plasma polar metabolite concentrations in a large-scale cohort study using capillary electrophoresis-mass spectrometry.

PubMed

Harada, Sei; Hirayama, Akiyoshi; Chan, Queenie; Kurihara, Ayako; Fukai, Kota; Iida, Miho; Kato, Suzuka; Sugiyama, Daisuke; Kuwabara, Kazuyo; Takeuchi, Ayano; Akiyama, Miki; Okamura, Tomonori; Ebbels, Timothy M D; Elliott, Paul; Tomita, Masaru; Sato, Asako; Suzuki, Chizuru; Sugimoto, Masahiro; Soga, Tomoyoshi; Takebayashi, Toru

2018-01-01

Cohort studies with metabolomics data are becoming more widespread, however, large-scale studies involving 10,000s of participants are still limited, especially in Asian populations. Therefore, we started the Tsuruoka Metabolomics Cohort Study enrolling 11,002 community-dwelling adults in Japan, and using capillary electrophoresis-mass spectrometry (CE-MS) and liquid chromatography-mass spectrometry. The CE-MS method is highly amenable to absolute quantification of polar metabolites, however, its reliability for large-scale measurement is unclear. The aim of this study is to examine reproducibility and validity of large-scale CE-MS measurements. In addition, the study presents absolute concentrations of polar metabolites in human plasma, which can be used in future as reference ranges in a Japanese population. Metabolomic profiling of 8,413 fasting plasma samples were completed using CE-MS, and 94 polar metabolites were structurally identified and quantified. Quality control (QC) samples were injected every ten samples and assessed throughout the analysis. Inter- and intra-batch coefficients of variation of QC and participant samples, and technical intraclass correlation coefficients were estimated. Passing-Bablok regression of plasma concentrations by CE-MS on serum concentrations by standard clinical chemistry assays was conducted for creatinine and uric acid. In QC samples, coefficient of variation was less than 20% for 64 metabolites, and less than 30% for 80 metabolites out of the 94 metabolites. Inter-batch coefficient of variation was less than 20% for 81 metabolites. Estimated technical intraclass correlation coefficient was above 0.75 for 67 metabolites. The slope of Passing-Bablok regression was estimated as 0.97 (95% confidence interval: 0.95, 0.98) for creatinine and 0.95 (0.92, 0.96) for uric acid. Compared to published data from other large cohort measurement platforms, reproducibility of metabolites common to the platforms was similar to or better than in the other studies. These results show that our CE-MS platform is suitable for conducting large-scale epidemiological studies.

COMPUTER SIMULATION STUDY OF AMYLOID FIBRIL FORMATION BY PALINDROMIC SEQUENCES IN PRION PEPTIDES

PubMed Central

Wagoner, Victoria; Cheon, Mookyung; Chang, Iksoo; Hall, Carol

2011-01-01

We simulate the aggregation of large systems containing palindromic peptides from the Syrian hamster prion protein SHaPrP 113–120 (AGAAAAGA) and the mouse prion protein MoPrP 111–120 (VAGAAAAGAV) and eight sequence variations: GAAAAAAG, (AG)4, A8, GAAAGAAA, A10, V10, GAVAAAAVAG, and VAVAAAAVAV The first two peptides are thought to act as the Velcro that holds the parent prion proteins together in amyloid structures and can form fibrils themselves. Kinetic events along the fibrillization pathway influence the types of structures that occur and variations in the sequence affect aggregation kinetics and fibrillar structure. Discontinuous molecular dynamics simulations using the PRIME20 force field are performed on systems containing 48 peptides starting from a random coil configuration. Depending on the sequence, fibrillar structures form spontaneously over a range of temperatures, below which amorphous aggregates form and above which no aggregation occurs. AGAAAAGA forms well organized fibrillar structures whereas VAGAAAAGAV forms less well organized structures that are partially fibrillar and partially amorphous. The degree of order in the fibrillar structure stems in part from the types of kinetic events leading up to its formation, with AGAAAAGA forming less amorphous structures early in the simulation than VAGAAAAGAV. The ability to form fibrils increases as the chain length and the length of the stretch of hydrophobic residues increase. However as the hydrophobicity of the sequence increases, the ability to form well-ordered structures decreases. Thus, longer hydrophobic sequences form slightly disordered aggregates that are partially fibrillar and partially amorphous. Subtle changes in sequence result in slightly different fibril structures. PMID:21557317

Analysis of grain characters in temperate grasses reveals distinctive patterns of endosperm organization associated with grain shape

PubMed Central

Drea, Sinéad

2012-01-01

Members of the core pooids represent the most important crops in temperate zones including wheat, barley, and oats. Their importance as crops is largely due to the grain, particularly the storage capabilities of the endosperm. In this study, a comprehensive survey of grain morphology and endosperm organization in representatives of wild and cultivated species throughout the core pooids was performed. As sister to the core pooid tribes Poeae, Aveneae, Triticeae, and Bromeae within the Pooideae subfamily, Brachypodium provides a taxonomically relevant reference point. Using macroscopic, histological, and molecular analyses distinct patterns of grain tissue organization in these species, focusing on the peripheral and modified aleurone, are described. The results indicate that aleurone organization is correlated with conventional grain quality characters such as grain shape and starch content. In addition to morphological and organizational variation, expression patterns of candidate gene markers underpinning this variation were examined. Features commonly associated with grains are largely defined by analyses on lineages within the Triticeae and knowledge of grain structure may be skewed as a result of the focus on wheat and barley. Specifically, the data suggest that the modified aleurone is largely restricted to species in the Triticeae tribe. PMID:23081982

Spatio-temporal variability of airborne bacterial communities and their correlation with particulate matter chemical composition across two urban areas.

PubMed

Gandolfi, I; Bertolini, V; Bestetti, G; Ambrosini, R; Innocente, E; Rampazzo, G; Papacchini, M; Franzetti, A

2015-06-01

The study of spatio-temporal variability of airborne bacterial communities has recently gained importance due to the evidence that airborne bacteria are involved in atmospheric processes and can affect human health. In this work, we described the structure of airborne microbial communities in two urban areas (Milan and Venice, Northern Italy) through the sequencing, by the Illumina platform, of libraries containing the V5-V6 hypervariable regions of the 16S rRNA gene and estimated the abundance of airborne bacteria with quantitative PCR (qPCR). Airborne microbial communities were dominated by few taxa, particularly Burkholderiales and Actinomycetales, more abundant in colder seasons, and Chloroplasts, more abundant in warmer seasons. By partitioning the variation in bacterial community structure, we could assess that environmental and meteorological conditions, including variability between cities and seasons, were the major determinants of the observed variation in bacterial community structure, while chemical composition of atmospheric particulate matter (PM) had a minor contribution. Particularly, Ba, SO4 (2-) and Mg(2+) concentrations were significantly correlated with microbial community structure, but it was not possible to assess whether they simply co-varied with seasonal shifts of bacterial inputs to the atmosphere, or their variation favoured specific taxa. Both local sources of bacteria and atmospheric dispersal were involved in the assembling of airborne microbial communities, as suggested, to the one side by the large abundance of bacteria typical of lagoon environments (Rhodobacterales) observed in spring air samples from Venice and to the other by the significant effect of wind speed in shaping airborne bacterial communities at all sites.

Temperate Snake Community in South America: Is Diet Determined by Phylogeny or Ecology?

PubMed Central

Etchepare, Eduardo G.

2015-01-01

Communities are complex and dynamic systems that change with time. The first attempts to explain how they were structured involve contemporary phenomena like ecological interactions between species (e.g., competition and predation) and led to the competition-predation hypothesis. Recently, the deep history hypothesis has emerged, which suggests that profound differences in the evolutionary history of organisms resulted in a number of ecological features that remain largely on species that are part of existing communities. Nevertheless, both phylogenetic structure and ecological interactions can act together to determine the structure of a community. Because diet is one of the main niche axes, in this study we evaluated, for the first time, the impact of ecological and phylogenetic factors on the diet of Neotropical snakes from the subtropical-temperate region of South America. Additionally, we studied their relationship with morphological and environmental aspects to understand the natural history and ecology of this community. A canonical phylogenetical ordination analysis showed that phylogeny explained most of the variation in diet, whereas ecological characters explained very little of this variation. Furthermore, some snakes that shared the habitat showed some degree of diet convergence, in accordance with the competition-predation hypothesis, although phylogeny remained the major determinant in structuring this community. The clade with the greatest variability was the subfamily Dipsadinae, whose members had a very different type of diet, based on soft-bodied invertebrates. Our results are consistent with the deep history hypothesis, and we suggest that the community under study has a deep phylogenetic effect that explains most of the variation in the diet. PMID:25945501

Multidimensional structure-function relationships in human β-cardiac myosin from population-scale genetic variation

PubMed Central

Homburger, Julian R.; Green, Eric M.; Caleshu, Colleen; Sunitha, Margaret S.; Taylor, Rebecca E.; Ruppel, Kathleen M.; Metpally, Raghu Prasad Rao; Colan, Steven D.; Michels, Michelle; Day, Sharlene M.; Olivotto, Iacopo; Bustamante, Carlos D.; Dewey, Frederick E.; Ho, Carolyn Y.; Spudich, James A.; Ashley, Euan A.

2016-01-01

Myosin motors are the fundamental force-generating elements of muscle contraction. Variation in the human β-cardiac myosin heavy chain gene (MYH7) can lead to hypertrophic cardiomyopathy (HCM), a heritable disease characterized by cardiac hypertrophy, heart failure, and sudden cardiac death. How specific myosin variants alter motor function or clinical expression of disease remains incompletely understood. Here, we combine structural models of myosin from multiple stages of its chemomechanical cycle, exome sequencing data from two population cohorts of 60,706 and 42,930 individuals, and genetic and phenotypic data from 2,913 patients with HCM to identify regions of disease enrichment within β-cardiac myosin. We first developed computational models of the human β-cardiac myosin protein before and after the myosin power stroke. Then, using a spatial scan statistic modified to analyze genetic variation in protein 3D space, we found significant enrichment of disease-associated variants in the converter, a kinetic domain that transduces force from the catalytic domain to the lever arm to accomplish the power stroke. Focusing our analysis on surface-exposed residues, we identified a larger region significantly enriched for disease-associated variants that contains both the converter domain and residues on a single flat surface on the myosin head described as the myosin mesa. Notably, patients with HCM with variants in the enriched regions have earlier disease onset than patients who have HCM with variants elsewhere. Our study provides a model for integrating protein structure, large-scale genetic sequencing, and detailed phenotypic data to reveal insight into time-shifted protein structures and genetic disease. PMID:27247418

Mechanisms governing brittle fault mechanics - a multi-scale study from the Permian Khao-Kwang fold-and-thrust belt, Thailand

NASA Astrophysics Data System (ADS)

von Hagke, Christoph; Morley, Chris; Kanitpanyacharoen, Waruntorn

2017-04-01

Despite our qualitative understanding of factors contributing to thrust and detachment weakness such as mineralogy, pore fluid pressure, or efficiency of structure localization, it is difficult to assess the contribution of the individual factors. Here we present multi-scale analysis of a mixed clay / carbonate high displacement (kms of heave) thrust zone, where it is possible to study structures formed within a similar temperature and pressure regime, and thus only varying due to lithological contrasts. We mapped the well-exposed thrust zone in a large quarry at outcrop scale in five separate sections present along a strike-distance of 1 km. The thrust zone shows considerable variations in structural style, as well as localization within different clay and limestone horizons. Zones of low and high strain have been identified. We investigate these changes in macroscopic deformation style using Virtual Polarizing Microscopy, and the combined methods of Broad Ion Beam milling and Scanning Electron Microscopy in addition with XRD analysis. We characterize structural and mineralogical variations in the thrust zone at all scales, from outcrop down to nano-meters. Results show strain localization is heterogeneous, with strong variations along strike. Within the clay package, strain localizes along zones rich in organic matter. Microstructures are complex, and show multiple deformation events, including crack-seal processes and reworking of vein material. Pressure solution is dominant. XRD analysis shows mineralogical differences between zones of high and low strain within the shale-dominated package. However, highest strain does not only occur in the clay units, but partly is accommodated in the surrounding limestone.

PSOCT studies of intervertebral disk

NASA Astrophysics Data System (ADS)

Matcher, Stephen J.; Winlove, Peter C.; Gangnus, Sergey V.

2004-07-01

Polarization-sensitive optical coherence tomography (PSOCT) is an emerging optical imaging technique that is sensitive to the birefringence properties of tissues. It thus has applications in studying the large-scale ordering of collagen fibers within connective tissues. This ordering not only provides useful insights into the relationship between structure and function for various anatomical structures but also is an indicator of pathology. Intervertebral disk is an elastic tissue of the spine and possesses a 3-D collagen structure well suited to study using PSOCT. Since the outer layer of the disk has a lamellar structure with collagen fibers oriented in a trellis-like arrangement between lamellae, the birefringence fast-axis shows pronounced variations with depth, on a spatial scale of about 100 μm. The lamellar thickness varies with age and possibly with disease. We have used a polarisation-sensitive optical coherence tomography system to measure the birefringence properties of freshly excised, hydrated bovine caudal intervertebral disk and compared this with equine flexor tendon. Our results clearly demonstrate the ability of PSOCT to detect the outer three lamellae, down to a depth of at least 700 μm, via discontinuities in the depth-resolved retardance. We have applied a simple semi-empirical model based on Jones calculus to quantify the variation in the fast-axis orientation with depth. Our data and modeling is in broad agreement with previous studies using x-ray diffraction and polarization microscopy applied to histological sections of dehydrated disk. Our results imply that PSOCT may prove a useful tool to study collagen organisation within intervertebral disk in vitro and possibly in vivo and its variation with age and disease.

Role and Mechanism of Structural Variation in Progression of Breast Cancer

DTIC Science & Technology

2012-09-01

models  of  CGR  genesis,  and  strongly  argue...numbers  of  tandem   duplications,  and   GBM  samples  showing  numerous  large-­‐scale  rearrangements.  We  also...higher   incidence  in   GBM  (38.9%)  relative  to  the  other  tumor  types  (8.7%).   This  definitively  shows

Middle Atmosphere Program. Handbook for MAP. Volume 16: Atmospheric Structure and Its Variation in the Region 20 to 120 Km. Draft of a New Reference Middle Atmosphere

NASA Technical Reports Server (NTRS)

Labitzke, K. (Editor); Barnett, J. J. (Editor); Edwards, B. (Editor)

1985-01-01

A draft of a new reference atmosphere for the region between 20 and 80 km which depends largely on recent satellite experiments covering the globe from 80 deg S to 80 deg N is given. A separate international tropical reference atmosphere is given, as well as reference ozone models for the middle atmosphere.

Structure and Dynamics of Bimodal Colloidal Dispersions in a Low-Molecular-Weight Polymer Solution

DOE PAGES

Zhang, Fan; Allen, Andrew J.; Levine, Lyle E.; ...

2017-02-24

We present an experimental study of the structural and dynamical properties of bimodal, micrometersized colloidal dispersions (size ratio ≈ 2) in an aqueous solution of low-molecular weight polymer (polyethylene glycol 2000) using synchrotron ultra-small angle X-ray scattering (USAXS) and USAXSbased X-ray photon correlation spectroscopy. We fixed the volume fraction of the large particles at 5 % and systematically increased the volume fraction of the small particles from 0 % to 5 % to evaluate its effect on the structure and dynamics. The bimodal dispersions were homogenous through the investigated parameter space. We found that the partial structure factors can bemore » satisfactorily retrieved for the bimodal colloidal dispersions using a Percus-Yevick hard sphere potential when the particle size distributions of the particles were taken into account. We also found that the partial structure factor between the large particles does not exhibit significant variation with increasing volume fraction of small particles, whereas the isothermal compressibility of the binary mixture was found to decrease with increasing volume fraction of small particles. The dynamics of single-component large particle dispersion obey the principles of de Gennes narrowing, where the wave vector dependence of the interparticle diffusion coefficient is inversely proportional to the interparticle structure factor. The dynamics of the bimodal dispersions demonstrate strong dependence on the fraction of small particles. As a result, we also made a comparison between the experimental effective dynamic viscosity of the bimodal dispersion with theoretical predictions, which suggest that the complex mutual interactions between large and small particles have a strong effect on the dynamic behaviors of bimodal dispersions.« less

Structure and Dynamics of Bimodal Colloidal Dispersions in a Low-Molecular-Weight Polymer Solution.

PubMed

Zhang, Fan; Allen, Andrew J; Levine, Lyle E; Tsai, De-Hao; Ilavsky, Jan

2017-03-21

We present an experimental study of the structural and dynamical properties of bimodal, micrometer-sized colloidal dispersions (size ratio ≈ 2) in an aqueous solution of low-molecular-weight polymer (polyethylene glycol 2000) using synchrotron ultra-small angle X-ray scattering (USAXS) and USAXS-based X-ray photon correlation spectroscopy. We fixed the volume fraction of the large particles at 5% and systematically increased the volume fraction of the small particles from 0 to 5% to evaluate their effects on the structure and dynamics. The bimodal dispersions were homogenous through the investigated parameter space. We found that the partial structure factors can be satisfactorily retrieved for the bimodal colloidal dispersions using a Percus-Yevick hard-sphere potential when the size distributions of the particles were taken into account. We also found that the partial structure factor between the large particles did not exhibit a significant variation with increasing volume fraction of the small particles, whereas the isothermal compressibility of the binary mixture was found to decrease with increasing volume fraction of the small particles. The dynamics of single-component large-particle dispersion obey the principles of de Gennes narrowing, where the wave vector dependence of the interparticle diffusion coefficient is inversely proportional to the interparticle structure factor. The dynamics of the bimodal dispersions demonstrate a strong dependence on the fraction of small particles. We also made a comparison between the experimental effective dynamic viscosity of the bimodal dispersion with the theoretical predictions, which suggest that the complex mutual interactions between the large and small particles have a strong effect on the dynamic behaviors of bimodal dispersions.

Structure and Dynamics of Bimodal Colloidal Dispersions in a Low-Molecular-Weight Polymer Solution

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

Zhang, Fan; Allen, Andrew J.; Levine, Lyle E.

We present an experimental study of the structural and dynamical properties of bimodal, micrometersized colloidal dispersions (size ratio ≈ 2) in an aqueous solution of low-molecular weight polymer (polyethylene glycol 2000) using synchrotron ultra-small angle X-ray scattering (USAXS) and USAXSbased X-ray photon correlation spectroscopy. We fixed the volume fraction of the large particles at 5 % and systematically increased the volume fraction of the small particles from 0 % to 5 % to evaluate its effect on the structure and dynamics. The bimodal dispersions were homogenous through the investigated parameter space. We found that the partial structure factors can bemore » satisfactorily retrieved for the bimodal colloidal dispersions using a Percus-Yevick hard sphere potential when the particle size distributions of the particles were taken into account. We also found that the partial structure factor between the large particles does not exhibit significant variation with increasing volume fraction of small particles, whereas the isothermal compressibility of the binary mixture was found to decrease with increasing volume fraction of small particles. The dynamics of single-component large particle dispersion obey the principles of de Gennes narrowing, where the wave vector dependence of the interparticle diffusion coefficient is inversely proportional to the interparticle structure factor. The dynamics of the bimodal dispersions demonstrate strong dependence on the fraction of small particles. As a result, we also made a comparison between the experimental effective dynamic viscosity of the bimodal dispersion with theoretical predictions, which suggest that the complex mutual interactions between large and small particles have a strong effect on the dynamic behaviors of bimodal dispersions.« less