Direct and indirect influence of parental bedrock on streambed microbial community structure in forested streams.

PubMed

Mosher, Jennifer J; Findlay, Robert H

2011-11-01

A correlative study was performed to determine if variation in streambed microbial community structure in low-order forested streams can be directly or indirectly linked to the chemical nature of the parental bedrock of the environments through which the streams flow. Total microbial and photosynthetic biomass (phospholipid phosphate [PLP] and chlorophyll a), community structure (phospholipid fatty acid analysis), and physical and chemical parameters were measured in six streams, three located in sandstone and three in limestone regions of the Bankhead National Forest in northern Alabama. Although stream water flowing through the two different bedrock types differed significantly in chemical composition, there were no significant differences in total microbial and photosynthetic biomass in the sediments. In contrast, sedimentary microbial community structure differed between the bedrock types and was significantly correlated with stream water ion concentrations. A pattern of seasonal variation in microbial community structure was also observed. Further statistical analysis indicated dissolved organic matter (DOM) quality, which was previously shown to be influenced by geological variation, correlated with variation in bacterial community structure. These results indicate that the geology of underlying bedrock influences benthic microbial communities directly via changes in water chemistry and also indirectly via stream water DOM quality.

Using active shape modeling based on MRI to study morphologic and pitch-related functional changes affecting vocal structures and the airway.

PubMed

Miller, Nicola A; Gregory, Jennifer S; Aspden, Richard M; Stollery, Peter J; Gilbert, Fiona J

2014-09-01

The shape of the vocal tract and associated structures (eg, tongue and velum) is complicated and varies according to development and function. This variability challenges interpretation of voice experiments. Quantifying differences between shapes and understanding how vocal structures move in relation to each other is difficult using traditional linear and angle measurements. With statistical shape models, shape can be characterized in terms of independent modes of variation. Here, we build an active shape model (ASM) to assess morphologic and pitch-related functional changes affecting vocal structures and the airway. Using a cross-sectional study design, we obtained six midsagittal magnetic resonance images from 10 healthy adults (five men and five women) at rest, while breathing out, and while listening to, and humming low and high notes. Eighty landmark points were chosen to define the shape of interest and an ASM was built using these (60) images. Principal component analysis was used to identify independent modes of variation, and statistical analysis was performed using one-way repeated-measures analysis of variance. Twenty modes of variation were identified with modes 1 and 2 accounting for half the total variance. Modes 1 and 9 were significantly associated with humming low and high notes (P < 0.001) and showed coordinated changes affecting the cervical spine, vocal structures, and airway. Mode 2 highlighted wide structural variations between subjects. This study highlights the potential of active shape modeling to advance understanding of factors underlying morphologic and pitch-related functional variations affecting vocal structures and the airway in health and disease. Copyright © 2014 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

Short and long periodic atmospheric variations between 25 and 200 km

NASA Technical Reports Server (NTRS)

Justus, C. G.; Woodrum, A.

1973-01-01

Previously collected data on atmospheric pressure, density, temperature and winds between 25 and 200 km 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 were analyzed by a daily difference method and results on the distribution statistics, magnitude, and spatial structure of gravity wave and planetary wave atmospheric variations are presented. Time structure of the gravity wave variations were determined by the analysis of residuals from harmonic analysis of time series data. Planetary wave contributions in the 25-85 km range were discovered and found to have significant height and latitudinal variation. Long period planetary waves, and seasonal variations were also computed by harmonic analysis. Revised height variations of the gravity wave contributions in the 25 to 85 km height range were computed. An engineering method and design values for gravity wave magnitudes and wave lengths are given to be used for such tasks as evaluating the effects on the dynamical heating, stability and control of spacecraft such as the space shuttle vehicle in launch or reentry trajectories.

Genetic diversity and structure of elite cotton germplasm (Gossypium hirsutum L.) using genome-wide SNP data.

PubMed

Ai, XianTao; Liang, YaJun; Wang, JunDuo; Zheng, JuYun; Gong, ZhaoLong; Guo, JiangPing; Li, XueYuan; Qu, YanYing

2017-10-01

Cotton (Gossypium spp.) is the most important natural textile fiber crop, and Gossypium hirsutum L. is responsible for 90% of the annual cotton crop in the world. Information on cotton genetic diversity and population structure is essential for new breeding lines. In this study, we analyzed population structure and genetic diversity of 288 elite Gossypium hirsutum cultivar accessions collected from around the world, and especially from China, using genome-wide single nucleotide polymorphisms (SNP) markers. The average polymorphsim information content (PIC) was 0.25, indicating a relatively low degree of genetic diversity. Population structure analysis revealed extensive admixture and identified three subgroups. Phylogenetic analysis supported the subgroups identified by STRUCTURE. The results from both population structure and phylogenetic analysis were, for the most part, in agreement with pedigree information. Analysis of molecular variance revealed a larger amount of variation was due to diversity within the groups. Establishment of genetic diversity and population structure from this study could be useful for genetic and genomic analysis and systematic utilization of the standing genetic variation in upland cotton.

Genomic regions showing copy number variations associate with resistance or susceptibility to gastrointestinal nematodes in Angus cattle

USDA-ARS?s Scientific Manuscript database

Genomic structural variation is an important and abundant source of genetic and phenotypic variation. We previously reported an initial analysis of copy number variations (CNVs) in Angus cattle selected for resistance or susceptibility to gastrointestinal nematodes. In this study, we performed a lar...

Genomic regions showing copy number variations associate with resistance or susceptibility to gastrointestinal nematodes in Angus Cattle

USDA-ARS?s Scientific Manuscript database

Genomic structural variation is an important and abundant source of genetic and phenotypic variation. We previously reported an initial analysis of copy number variations (CNVs) in Angus cattle selected for resistance or susceptibility to intestinal nematodes. In this study, we performed a large sca...

The structural studies of vanadium substituted lithium-bismuth-boro-tellurite glass

NASA Astrophysics Data System (ADS)

Madhu, A.; Eraiah, B.

2018-05-01

The structural studies of vanadium substituted lithium-bismuth-boro-tellurite glass is successfully prepared and certain analysis like XRD,FTIR,DTA/TGA with density, molar volume are done. The amorphous phase has been identified based on X-ray diffraction analysis. The vanadium oxide plays the role as a glass-modifier and influences on BO3 ↔ BO4 conversion. The observed nonlinear variation in Tg with vanadium oxide increase, it reflects structural changes. The nonlinear variation of density and molar volume can be attributed to vanadium oxide incorporation have increased the number of Non-bridging oxygen (NBO'S).

Analyzing the Magnetopause Internal Structure: New Possibilities Offered by MMS Tested in a Case Study

NASA Astrophysics Data System (ADS)

Rezeau, L.; Belmont, G.; Manuzzo, R.; Aunai, N.; Dargent, J.

2018-01-01

We explore the structure of the magnetopause using a crossing observed by the Magnetospheric Multiscale (MMS) spacecraft on 16 October 2015. Several methods (minimum variance analysis, BV method, and constant velocity analysis) are first applied to compute the normal to the magnetopause considered as a whole. The different results obtained are not identical, and we show that the whole boundary is not stationary and not planar, so that basic assumptions of these methods are not well satisfied. We then analyze more finely the internal structure for investigating the departures from planarity. Using the basic mathematical definition of what is a one-dimensional physical problem, we introduce a new single spacecraft method, called LNA (local normal analysis) for determining the varying normal, and we compare the results so obtained with those coming from the multispacecraft minimum directional derivative (MDD) tool developed by Shi et al. (2005). This last method gives the dimensionality of the magnetic variations from multipoint measurements and also allows estimating the direction of the local normal when the variations are locally 1-D. This study shows that the magnetopause does include approximate one-dimensional substructures but also two- and three-dimensional structures. It also shows that the dimensionality of the magnetic variations can differ from the variations of other fields so that, at some places, the magnetic field can have a 1-D structure although all the plasma variations do not verify the properties of a global one-dimensional problem. A generalization of the MDD tool is proposed.

Identification and Modelling of the In-Plane Reinforcement Orientation Variations in a CFRP Laminate Produced by Manual Lay-Up

NASA Astrophysics Data System (ADS)

Davila, Yves; Crouzeix, Laurent; Douchin, Bernard; Collombet, Francis; Grunevald, Yves-Henri

2017-08-01

Reinforcement angle orientation has a significant effect on the mechanical properties of composite materials. This work presents a methodology to introduce variable reinforcement angles into finite element (FE) models of composite structures. The study of reinforcement orientation variations uses meta-models to identify and control a continuous variation across the composite ply. First, the reinforcement angle is measured through image analysis techniques of the composite plies during the lay-up phase. Image analysis results show that variations in the mean ply orientations are between -0.5 and 0.5° with standard deviations ranging between 0.34 and 0.41°. An automatic post-treatment of the images determines the global and local angle variations yielding good agreements visually and numerically between the analysed images and the identified parameters. A composite plate analysed at the end of the cooling phase is presented as a case of study. Here, the variation in residual strains induced by the variability in the reinforcement orientation are up to 28% of the strain field of the homogeneous FE model. The proposed methodology has shown its capabilities to introduce material and geometrical variability into FE analysis of layered composite structures.

Identification and Modelling of the In-Plane Reinforcement Orientation Variations in a CFRP Laminate Produced by Manual Lay-Up

NASA Astrophysics Data System (ADS)

Davila, Yves; Crouzeix, Laurent; Douchin, Bernard; Collombet, Francis; Grunevald, Yves-Henri

2018-06-01

Reinforcement angle orientation has a significant effect on the mechanical properties of composite materials. This work presents a methodology to introduce variable reinforcement angles into finite element (FE) models of composite structures. The study of reinforcement orientation variations uses meta-models to identify and control a continuous variation across the composite ply. First, the reinforcement angle is measured through image analysis techniques of the composite plies during the lay-up phase. Image analysis results show that variations in the mean ply orientations are between -0.5 and 0.5° with standard deviations ranging between 0.34 and 0.41°. An automatic post-treatment of the images determines the global and local angle variations yielding good agreements visually and numerically between the analysed images and the identified parameters. A composite plate analysed at the end of the cooling phase is presented as a case of study. Here, the variation in residual strains induced by the variability in the reinforcement orientation are up to 28% of the strain field of the homogeneous FE model. The proposed methodology has shown its capabilities to introduce material and geometrical variability into FE analysis of layered composite structures.

Genetic Variability and Population Structure of Disanthus cercidifolius subsp. longipes (Hamamelidaceae) Based on AFLP Analysis

PubMed Central

Yu, Yi; Fan, Qiang; Shen, Rujiang; Guo, Wei; Jin, Jianhua; Cui, Dafang; Liao, Wenbo

2014-01-01

Disanthus cercidifolius subsp. longipes is an endangered species in China. Genetic diversity and structure analysis of this species was investigated using amplified fragments length polymorphism (AFLP) fingerprinting. Nei's gene diversity ranged from 0.1290 to 0.1394. The AMOVA indicated that 75.06% of variation was distributed within populations, while the between-group component 5.04% was smaller than the between populations-within-group component 19.90%. Significant genetic differentiation was detected between populations. Genetic and geographical distances were not correlated. PCA and genetic structure analysis showed that populations from East China were together with those of the Nanling Range. These patterns of genetic diversity and levels of genetic variation may be the result of D. c. subsp. longipes restricted to several isolated habitats and “excess flowers production, but little fruit set”. It is necessary to protect all existing populations of D. c. subsp. longipes in order to preserve as much genetic variation as possible. PMID:25250583

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

Voylov, D. N.; Griffin, P. J.; Mercado, B.

In this detailed analysis of the static structure factor S(Q) in several glass-forming liquids we show that the temperature variations of the width of the main diffraction peak Q(T ) correlate with the fragility of these liquids. Our observation suggests a direct connection between rather subtle structural changes and sharp slowing down of structural relaxation in glass-forming liquids. We also show that this observation can be rationalized using the Adam-Gibbs approach, through a connection between temperature variations of structural correlation length, lc 2 /Q, and the size of cooperatively rearranging regions.

Localized variations in electronic structure of AlGaN/GaN heterostructures grown by molecular-beam epitaxy

NASA Astrophysics Data System (ADS)

Smith, K. V.; Yu, E. T.; Elsass, C. R.; Heying, B.; Speck, J. S.

2001-10-01

Local electronic properties in a molecular-beam-epitaxy-grown AlxGa1-xN/GaN heterostructure field-effect transistor epitaxial layer structure are probed using depth-resolved scanning capacitance microscopy. Theoretical analysis of contrast observed in scanning capacitance images acquired over a range of bias voltages is used to assess the possible structural origins of local inhomogeneities in electronic structure, which are shown to be concentrated in areas where Ga droplets had formed on the surface during growth. Within these regions, there are significant variations in the local electronic structure that are attributed to variations in both AlxGa1-xN layer thickness and Al composition. Increased charge trapping is also observed in these regions.

Conservation genetics of bull trout: Geographic distribution of variation at microsatellite loci.

Treesearch

P. Spruell; A.R. Hemmingsen; P.J. Howell; N. Kanda; F.W. Allendorf

2003-01-01

We describe the genetic population structure of 65 bull trout (Salvelinus confluentus) populations from the northwestern United States using four microsatellite loci. The distribution of genetic variation as measured by microsatellites is consistent with previous allozyme and mitochondrial DNA analysis. There is relatively little genetic variation...

A Macro Analysis of DoD Logistics Systems. Volume 3. A Framework for Policy-Level Logistics Management

DTIC Science & Technology

1978-12-01

prioritization. 5 (We have chosen to use a variation of Saaty’s method in our hierarchical analysis, discussed in chapter 5, but for a purpose different ...the word "framework" to refer to an abstract structure for think- ing through policy-tieel management problems. This structure raises method - ological...readiness and logistics system performance, and we relied heavily on "structural" and trend analysis. By structural analysis, we meant a formal method for

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

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.

Morphological and Genetic Analysis of Four Color Morphs of Bean Leaf Beetle.

PubMed

Tiroesele, Bamphitlhi; Skoda, Steven R; Hunt, Thomas E; Lee, Donald J; Ullah, Muhammad Irfan; Molina-Ochoa, Jaime; Foster, John E

2018-03-01

Bean leaf beetle (BLB), Cerotoma trifurcata (Forster; Coleoptera: Chrysomelidae), exhibits considerable color variation but little is known about the underlying genetic structure and gene flow among color phenotypes. Genetic and morphological variation among four color phenotypes-green with spots (G+S), green without spots (G-S), red with spots (R+S) and red without spots (R-S)-were analyzed using amplified fragment length polymorphisms (AFLP) and morphometrics, respectively. AFLP generated 175 markers that showed ≥80% polymorphism. Analysis of molecular variance (AMOVA) indicated that genetic variation was greatest within phenotypes (82.6-84.0%); gene flow among the four phenotypes was relatively high (Nm = 3.82). The dendrogram and STRUCTURE analysis indicated some population divergence of G-S from the other phenotypes. Morphological parameters were similar among phenotypes except that R+S showed significant differences in weight and body-length. Canonical variables 1 and 2, based on average morphometric characters, accounted for 98% of the total variation; some divergence was indicated between G+S and R+S from each other and from the G-S/R-S BLB color morphs. The pattern of genetic variation indicated potential divergence of G-S and G+S from each other and from R-S and R+S. Although these results indicate that the four different color morphs are not genetically or reproductively isolated, there is some genetic differentiation/structure and morphological dissimilarity suggesting weak/incomplete isolation.

A methodology for formulating a minimal uncertainty model for robust control system design and analysis

NASA Technical Reports Server (NTRS)

Belcastro, Christine M.; Chang, B.-C.; Fischl, Robert

1989-01-01

In the design and analysis of robust control systems for uncertain plants, the technique of formulating what is termed an M-delta model has become widely accepted and applied in the robust control literature. The M represents the transfer function matrix M(s) of the nominal system, and delta represents an uncertainty matrix acting on M(s). The uncertainty can arise from various sources, such as structured uncertainty from parameter variations or multiple unstructured uncertainties from unmodeled dynamics and other neglected phenomena. In general, delta is a block diagonal matrix, and for real parameter variations the diagonal elements are real. As stated in the literature, this structure can always be formed for any linear interconnection of inputs, outputs, transfer functions, parameter variations, and perturbations. However, very little of the literature addresses methods for obtaining this structure, and none of this literature addresses a general methodology for obtaining a minimal M-delta model for a wide class of uncertainty. Since have a delta matrix of minimum order would improve the efficiency of structured singular value (or multivariable stability margin) computations, a method of obtaining a minimal M-delta model would be useful. A generalized method of obtaining a minimal M-delta structure for systems with real parameter variations is given.

Teleseismic array analysis of upper mantle compressional velocity structure. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Walck, M. C.

1984-01-01

Relative array analysis of upper mantle lateral velocity variations in southern California, analysis techniques for dense data profiles, the P-wave upper mantle structure beneath an active spreading center: the Gulf of California, and the upper mantle under the Cascade ranges: a comparison with the Gulf of California are presented.

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.

Characterization and analysis of temporal and spatial variations in habitat and macroinvertebrate community structure, Fountain Creek basin, Colorado Springs and vicinity, Colorado, 1998-2001

USGS Publications Warehouse

Bruce, James F.

2002-01-01

The Fountain Creek Basin in and around Colorado Springs, Colorado, is affected by various land- and water-use activities. Biological, hydrological, water-quality, and land-use data were collected at 10 sites in the Fountain Creek Basin from April 1998 through April 2001 to provide a baseline characterization of macroinvertebrate communities and habitat conditions for comparison in subsequent studies; and to assess variation in macroinvertebrate community structure relative to habitat quality. Analysis of variance results indicated that instream and riparian variables were not affected by season, but significant differences were found among sites. Nine metrics were used to describe and evaluate macroinvertebrate community structure. Statistical analysis indicated that for six of the nine metrics, significant variability occurred between spring and fall seasons for 60 percent of the sites. Cluster analysis (unweighted pair group method average) using macroinvertebrate presence-absence data showed a well-defined separation between spring and fall samples. Six of the nine metrics had significant spatial variation. Cluster analysis using Sorenson?s Coefficient of Community values computed from macroinvertebrate density (number of organisms per square meter) data showed that macroinvertebrate community structure was more similar among tributary sites than main-stem sites. Canonical correspondence analysis identified a substrate particle-size gradient from site-specific species-abundance data and environmental correlates that decreased the 10 sites to 5 site clusters and their associated taxa.

A factor analysis of landscape pattern and structure metrics

Treesearch

Kurt H. Riitters; R.V. O' Neill; C.T. Hunsaker; James D. Wickham; D.H. Yankee; S.P. Timmins; K.B. Jones; B.L. Jackson

1995-01-01

Fifty-five metrics of landscape pattern and structure were calculated for 85 maps of land use and land cover. A multivariate factor analysis was used to identify the common axes (or dimensions) of pattern and structure which were measured by a reduced set of 26 metrics. The first six factors explained about 87% of the variation in the 26 landscape metrics. These...

Comments on the variational modified-hypernetted-chain theory for simple fluids

NASA Astrophysics Data System (ADS)

Rosenfeld, Yaakov

1986-02-01

The variational modified-hypernetted-chain (VMHNC) theory, based on the approximation of universality of the bridge functions, is reformulated. The new formulation includes recent calculations by Lado and by Lado, Foiles, and Ashcroft, as two stages in a systematic approach which is analyzed. A variational iterative procedure for solving the exact (diagrammatic) equations for the fluid structure which is formally identical to the VMHNC is described, featuring the theory of simple classical fluids as a one-iteration theory. An accurate method for calculating the pair structure for a given potential and for inverting structure factor data in order to obtain the potential and the thermodynamic functions, follows from our analysis.

Impact of inhomogeneity on SH-type wave propagation in an initially stressed composite structure

NASA Astrophysics Data System (ADS)

Saha, S.; Chattopadhyay, A.; Singh, A. K.

2018-02-01

The present analysis has been made on the influence of distinct form of inhomogeneity in a composite structure comprised of double superficial layers lying over a half-space, on the phase velocity of SH-type wave propagating through it. Propagation of SH-type wave in the said structure has been examined in four distinct cases of inhomogeneity viz. when inhomogeneity in double superficial layer is due to exponential variation in density only (Case I); when inhomogeneity in double superficial layers is due to exponential variation in rigidity only (Case II); when inhomogeneity in double superficial layer is due to exponential variation in rigidity, density and initial stress (Case III) and when inhomogeneity in double superficial layer is due to linear variation in rigidity, density and initial stress (Case IV). Closed-form expression of dispersion relation has been accomplished for all four aforementioned cases through extensive application of Debye asymptotic analysis. Deduced dispersion relations for all the cases are found in well-agreement to the classical Love-wave equation. Numerical computation has been carried out to graphically demonstrate the effect of inhomogeneity parameters, initial stress parameters as well as width ratio associated with double superficial layers in the composite structure for each of the four aforesaid cases on dispersion curve. Meticulous examination of distinct cases of inhomogeneity and initial stress in context of considered problem has been carried out with detailed analysis in a comparative approach.

Strength of single-pole utility structures

Treesearch

Ronald W. Wolfe

2006-01-01

This section presents three basic methods for deriving and documenting Rn as an LTL value along with the coefficient of variation (COVR) for single-pole structures. These include the following: 1. An empirical analysis based primarily on tests of full-sized poles. 2. A theoretical analysis of mechanics-based models used in...

Crustal and uppermost mantle structures of the South China from joint analysis of receiver functions and Rayleigh wave dispersions

NASA Astrophysics Data System (ADS)

Guo, Zhi; Gao, Xing; Li, Tong; Wang, Wei

2018-05-01

We use P-wave receiver function H-k stacking and joint inversion of receiver functions and Rayleigh wave dispersions to investigate crustal and uppermost mantle structure beneath the South China. The obtained results reveal prominent crustal structure variations in the study area, Moho depth increases from ∼30 km in the Cathaysia Block to more than ∼60 km in the eastern Tibetan Plateau. A Moho undulation and Vp/Vs ratio variations can be observed from the Cathaysia Block to Yangtze Craton. These observations consistent with the crustal structures predict by the flat slab subduction model. We interpret these lateral crustal structure variations reflect the tectonic evolution of the Yangtze Craton and Cathaysia Block prior the Mesozoic and the post-orogenic magmatism due to the breaking up of the subducted flat slab and subsequent slab rollback in the South China. The observed variations of the crustal structures not only reveal the lateral crustal inhomogeneity, but also provide constraints on the geodynamic evolution of the South China.

Spatial variations in zooplankton community structure along the Japanese coastline in the Japan Sea: influence of the coastal current

NASA Astrophysics Data System (ADS)

Kodama, Taketoshi; Wagawa, Taku; Iguchi, Naoki; Takada, Yoshitake; Takahashi, Takashi; Fukudome, Ken-Ichi; Morimoto, Haruyuki; Goto, Tsuneo

2018-06-01

This study evaluates spatial variations in zooplankton community structure and potential controlling factors along the Japanese coast under the influence of the coastal branch of the Tsushima Warm Current (CBTWC). Variations in the density of morphologically identified zooplankton in the surface layer in May were investigated for a 15-year period. The density of zooplankton (individuals per cubic meter) varied between sampling stations, but there was no consistent west-east trend. Instead, there were different zooplankton community structures in the west and east, with that in Toyama Bay particularly distinct: Corycaeus affinis and Calanus sinicus were dominant in the west and Oithona atlantica was dominant in Toyama Bay. Distance-based redundancy analysis (db-RDA) was used to characterize the variation in zooplankton community structure, and four axes (RD1-4) provided significant explanation. RD2-4 only explained < 4.8 % of variation in the zooplankton community and did not show significant spatial difference; however, RD1, which explained 89.9 % of variation, did vary spatially. Positive and negative species scores on RD1 represent warm- and cold-water species, respectively, and their variation was mainly explained by water column mean temperature, and it is considered to vary spatially with the CBTWC. The CBTWC intrusion to the cold Toyama Bay is weak and occasional due to the submarine canyon structure of the bay. Therefore, the varying bathymetric characteristics along the Japanese coast of the Japan Sea generate the spatial variation in zooplankton community structure, and dominance of warm-water species can be considered an indicator of the CBTWC.

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.

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.

Structural Patterns in Empirical Research Articles: A Cross-Disciplinary Study

ERIC Educational Resources Information Center

Lin, Ling; Evans, Stephen

2012-01-01

This paper presents an analysis of the major generic structures of empirical research articles (RAs), with a particular focus on disciplinary variation and the relationship between the adjacent sections in the introductory and concluding parts. The findings were derived from a close "manual" analysis of 433 recent empirical RAs from high-impact…

Population Genetic Structure of Apple Scab (Venturia inaequalis (Cooke) G. Winter) in Iran

PubMed Central

Ebrahimi, Leila; Fotuhifar, Khalil-Berdi; Javan Nikkhah, Mohammad; Naghavi, Mohammad-Reza; Baisakh, Niranjan

2016-01-01

The population genetic structure of 278 Venturia inaequalis isolates, collected from different apple cultivars of eighteen different provinces in Iran, was investigated using 22 polymorphic microsatellite markers. Analysis of molecular variation, Bayesian clustering and Nei's genetic distance analyses based on 88 microsatellite alleles indicated substantial levels of gene flow among the collection sites. Ninety three percent of the variation was observed among the individuals within the populations and only 7% variation was observed among the populations. Structure analysis grouped the isolates into two populations. Maximum number of pathogen genotypes (44) was observed in the North of Iran that grows various different apple cultivars. Investigation on the variation of the pathogen on different cultivars in the North of Iran suggested a significant differentiation of the pathogen populations between wild apple and commercial cultivars. During sampling, varying ranges of scab infection were observed on various apple cultivars in forests, monoculture and mix orchards. Wild type apple (Malus orientalis) along the Caspian Sea Coast had the most infection in comparison with the Iranian endemic and commercial cultivars. Based on the genetic analysis and host tracking scenario of the pathogen, it was presumed that Iran could potentially be the center of origin of V. inaequalis, which requires further detailed studies with isolates collected from different parts of central Asia and world for confirmation. PMID:27631622

Spatial Evolution of the Thickness Variations over a CFRP Laminated Structure

NASA Astrophysics Data System (ADS)

Davila, Yves; Crouzeix, Laurent; Douchin, Bernard; Collombet, Francis; Grunevald, Yves-Henri

2017-10-01

Ply thickness is one of the main drivers of the structural performance of a composite part. For stress analysis calculations (e.g., finite element analysis), composite plies are commonly considered to have a constant thickness compared to the reality (coefficients of variation up to 9% of the mean ply thickness). Unless this variability is taken into account reliable property predictions cannot be made. A modelling approach of such variations is proposed using parameters obtained from a 16-ply quasi-isotropic CFRP plate cured in an autoclave. A discrete Fourier transform algorithm is used to analyse the frequency response of the observed ply and plate thickness profiles. The model inputs, obtained by a mathematical representation of the ply thickness profiles, permit the generation of a representative stratification considering the spatial continuity of the thickness variations that are in good agreement with the real ply profiles spread over the composite part. A residual deformation FE model of the composite plate is used to illustrate the feasibility of the approach.

Shape design sensitivity analysis and optimal design of structural systems

NASA Technical Reports Server (NTRS)

Choi, Kyung K.

1987-01-01

The material derivative concept of continuum mechanics and an adjoint variable method of design sensitivity analysis are used to relate variations in structural shape to measures of structural performance. A domain method of shape design sensitivity analysis is used to best utilize the basic character of the finite element method that gives accurate information not on the boundary but in the domain. Implementation of shape design sensitivty analysis using finite element computer codes is discussed. Recent numerical results are used to demonstrate the accuracy obtainable using the method. Result of design sensitivity analysis is used to carry out design optimization of a built-up structure.

Dynamic analysis of elastic rubber tired car wheel breaking under variable normal load

NASA Astrophysics Data System (ADS)

Fedotov, A. I.; Zedgenizov, V. G.; Ovchinnikova, N. I.

2017-10-01

The purpose of the paper is to analyze the dynamics of the braking of the wheel under normal load variations. The paper uses a mathematical simulation method according to which the calculation model of an object as a mechanical system is associated with a dynamically equivalent schematic structure of the automatic control. Transfer function tool analyzing structural and technical characteristics of an object as well as force disturbances were used. It was proved that the analysis of dynamic characteristics of the wheel subjected to external force disturbances has to take into account amplitude and phase-frequency characteristics. Normal load variations impact car wheel braking subjected to disturbances. The closer slip to the critical point is, the higher the impact is. In the super-critical area, load variations cause fast wheel blocking.

Vertical structure of medium-scale traveling ionospheric disturbances

NASA Astrophysics Data System (ADS)

Ssessanga, Nicholas; Kim, Yong Ha; Kim, Eunsol

2015-11-01

We develop an algorithm of computerized ionospheric tomography (CIT) to infer information on the vertical and horizontal structuring of electron density during nighttime medium-scale traveling ionospheric disturbances (MSTIDs). To facilitate digital CIT we have adopted total electron contents (TEC) from a dense Global Positioning System (GPS) receiver network, GEONET, which contains more than 1000 receivers. A multiplicative algebraic reconstruction technique was utilized with a calibrated IRI-2012 model as an initial solution. The reconstructed F2 peak layer varied in altitude with average peak-to-peak amplitude of ~52 km. In addition, the F2 peak layer anticorrelated with TEC variations. This feature supports a theory in which nighttime MSTID is composed of oscillating electric fields due to conductivity variations. Moreover, reconstructed TEC variations over two stations were reasonably close to variations directly derived from the measured TEC data set. Our tomographic analysis may thus help understand three-dimensional structure of MSTIDs in a quantitative way.

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

In situ structural analysis of the Yersinia enterocolitica injectisome

PubMed Central

Kudryashev, Mikhail; Stenta, Marco; Schmelz, Stefan; Amstutz, Marlise; Wiesand, Ulrich; Castaño-Díez, Daniel; Degiacomi, Matteo T; Münnich, Stefan; Bleck, Christopher KE; Kowal, Julia; Diepold, Andreas; Heinz, Dirk W; Dal Peraro, Matteo; Cornelis, Guy R; Stahlberg, Henning

2013-01-01

Injectisomes are multi-protein transmembrane machines allowing pathogenic bacteria to inject effector proteins into eukaryotic host cells, a process called type III secretion. Here we present the first three-dimensional structure of Yersinia enterocolitica and Shigella flexneri injectisomes in situ and the first structural analysis of the Yersinia injectisome. Unexpectedly, basal bodies of injectisomes inside the bacterial cells showed length variations of 20%. The in situ structures of the Y. enterocolitica and S. flexneri injectisomes had similar dimensions and were significantly longer than the isolated structures of related injectisomes. The crystal structure of the inner membrane injectisome component YscD appeared elongated compared to a homologous protein, and molecular dynamics simulations documented its elongation elasticity. The ring-shaped secretin YscC at the outer membrane was stretched by 30–40% in situ, compared to its isolated liposome-embedded conformation. We suggest that elasticity is critical for some two-membrane spanning protein complexes to cope with variations in the intermembrane distance. DOI: http://dx.doi.org/10.7554/eLife.00792.001 PMID:23908767

Raman investigation with group theoretical method on structural polymorphism of the nonlinear optical hexamine: p-nitrophenol cocrystals

NASA Astrophysics Data System (ADS)

Vijayalakshmi, S.; Kalyanaraman, S.; Ravindran, T. R.

2014-09-01

We have synthesized organic non-centrosymmetric cocrystals of 1:1 and 1:2 mole ratios of non-proton-transferred hexamine and p-nitrophenol complexes by using a slow evaporation method. The cocrystal with different stoichiometric variation gets crystallized into different crystallographic structures. The non-proton-transfer process of the complexes and the charge transfer (CT) interaction are established through Fourier transform infrared (FTIR) spectroscopy. The contribution of the water molecule in the 1:2 adduct is explained through FTIR analysis. The result has an important bearing in our present study. Existence of two different crystallographic structures (polymorphism) is confirmed by the lower frequency modes that appeared in Raman spectra. The variation in the Raman active modes at lower frequencies that arise on account of polymorphism is addressed through factor group analysis. From the UV-vis analysis, the interesting result of hyperchromic and hypochromic shifts being observed in the 1:1 and 1:2 adducts, respectively, supports the polymorphic behavior. On seeing the variation in properties, particularly nonlinear optical properties, the higher second harmonic generation (SHG) efficiency compared with KDP is observed by using the Kurtz-Perry method for both complexes.

A Quantitative Comparison of the Similarity between Genes and Geography in Worldwide Human Populations

PubMed Central

Wang, Chaolong; Zöllner, Sebastian; Rosenberg, Noah A.

2012-01-01

Multivariate statistical techniques such as principal components analysis (PCA) and multidimensional scaling (MDS) have been widely used to summarize the structure of human genetic variation, often in easily visualized two-dimensional maps. Many recent studies have reported similarity between geographic maps of population locations and MDS or PCA maps of genetic variation inferred from single-nucleotide polymorphisms (SNPs). However, this similarity has been evident primarily in a qualitative sense; and, because different multivariate techniques and marker sets have been used in different studies, it has not been possible to formally compare genetic variation datasets in terms of their levels of similarity with geography. In this study, using genome-wide SNP data from 128 populations worldwide, we perform a systematic analysis to quantitatively evaluate the similarity of genes and geography in different geographic regions. For each of a series of regions, we apply a Procrustes analysis approach to find an optimal transformation that maximizes the similarity between PCA maps of genetic variation and geographic maps of population locations. We consider examples in Europe, Sub-Saharan Africa, Asia, East Asia, and Central/South Asia, as well as in a worldwide sample, finding that significant similarity between genes and geography exists in general at different geographic levels. The similarity is highest in our examples for Asia and, once highly distinctive populations have been removed, Sub-Saharan Africa. Our results provide a quantitative assessment of the geographic structure of human genetic variation worldwide, supporting the view that geography plays a strong role in giving rise to human population structure. PMID:22927824

A quantitative comparison of the similarity between genes and geography in worldwide human populations.

PubMed

Wang, Chaolong; Zöllner, Sebastian; Rosenberg, Noah A

2012-08-01

Multivariate statistical techniques such as principal components analysis (PCA) and multidimensional scaling (MDS) have been widely used to summarize the structure of human genetic variation, often in easily visualized two-dimensional maps. Many recent studies have reported similarity between geographic maps of population locations and MDS or PCA maps of genetic variation inferred from single-nucleotide polymorphisms (SNPs). However, this similarity has been evident primarily in a qualitative sense; and, because different multivariate techniques and marker sets have been used in different studies, it has not been possible to formally compare genetic variation datasets in terms of their levels of similarity with geography. In this study, using genome-wide SNP data from 128 populations worldwide, we perform a systematic analysis to quantitatively evaluate the similarity of genes and geography in different geographic regions. For each of a series of regions, we apply a Procrustes analysis approach to find an optimal transformation that maximizes the similarity between PCA maps of genetic variation and geographic maps of population locations. We consider examples in Europe, Sub-Saharan Africa, Asia, East Asia, and Central/South Asia, as well as in a worldwide sample, finding that significant similarity between genes and geography exists in general at different geographic levels. The similarity is highest in our examples for Asia and, once highly distinctive populations have been removed, Sub-Saharan Africa. Our results provide a quantitative assessment of the geographic structure of human genetic variation worldwide, supporting the view that geography plays a strong role in giving rise to human population structure.

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.

Influence of cross section variations on the structural behaviour of composite rotor blades

NASA Astrophysics Data System (ADS)

Rapp, Helmut; Woerndle, Rudolf

1991-09-01

A highly sophisticated structural analysis is required for helicopter rotor blades with nonhomogeneous cross sections made from nonisotropic material. Combinations of suitable analytical techniques with FEM-based techniques permit a cost effective and sufficiently accurate analysis of these complicated structures. It is determined that in general the 1D engineering theory of bending combined with 2D theories for determining the cross section properties is sufficient to describe the structural blade behavior.

Scale characters analysis for gully structure in the watersheds of loess landforms based on digital elevation models

NASA Astrophysics Data System (ADS)

Zhu, Hongchun; Zhao, Yipeng; Liu, Haiying

2018-04-01

Scale is the basic attribute for expressing and describing spatial entity and phenomena. It offers theoretical significance in the study of gully structure information, variable characteristics of watershed morphology, and development evolution at different scales. This research selected five different areas in China's Loess Plateau as the experimental region and used DEM data at different scales as the experimental data. First, the change rule of the characteristic parameters of the data at different scales was analyzed. The watershed structure information did not change along with a change in the data scale. This condition was proven by selecting indices of gully bifurcation ratio and fractal dimension as characteristic parameters of watershed structure information. Then, the change rule of the characteristic parameters of gully structure with different analysis scales was analyzed by setting the scale sequence of analysis at the extraction gully. The gully structure of the watershed changed with variations in the analysis scale, and the change rule was obvious when the gully level changed. Finally, the change rule of the characteristic parameters of the gully structure at different areas was analyzed. The gully fractal dimension showed a significant numerical difference in different areas, whereas the variation of the gully branch ratio was small. The change rule indicated that the development degree of the gully obviously varied in different regions, but the morphological structure was basically similar.

Scale characters analysis for gully structure in the watersheds of loess landforms based on digital elevation models

NASA Astrophysics Data System (ADS)

Zhu, Hongchun; Zhao, Yipeng; Liu, Haiying

2018-06-01

Scale is the basic attribute for expressing and describing spatial entity and phenomena. It offers theoretical significance in the study of gully structure information, variable characteristics of watershed morphology, and development evolution at different scales. This research selected five different areas in China's Loess Plateau as the experimental region and used DEM data at different scales as the experimental data. First, the change rule of the characteristic parameters of the data at different scales was analyzed. The watershed structure information did not change along with a change in the data scale. This condition was proven by selecting indices of gully bifurcation ratio and fractal dimension as characteristic parameters of watershed structure information. Then, the change rule of the characteristic parameters of gully structure with different analysis scales was analyzed by setting the scale sequence of analysis at the extraction gully. The gully structure of the watershed changed with variations in the analysis scale, and the change rule was obvious when the gully level changed. Finally, the change rule of the characteristic parameters of the gully structure at different areas was analyzed. The gully fractal dimension showed a significant numerical difference in different areas, whereas the variation of the gully branch ratio was small. The change rule indicated that the development degree of the gully obviously varied in different regions, but the morphological structure was basically similar.

A unified approach to the analysis and design of elasto-plastic structures with mechanical contact

NASA Technical Reports Server (NTRS)

Bendsoe, Martin P.; Olhoff, Niels; Taylor, John E.

1990-01-01

With structural design in mind, a new unified variational model has been developed which represents the mechanics of deformation elasto-plasticity with unilateral contact conditions. For a design problem formulated as maximization of the load carrying capacity of a structure under certain constraints, the unified model allows for a simultaneous analysis and design synthesis for a whole range of mechanical behavior.

Genetic variation and genetic structure of the endangered species Sinowilsonia henryi Hemsi. (Hamamelidaceae) revealed by amplified fragment length polymorphism (AFLP) markers.

PubMed

Zhang, H; Ji, W L; Li, M; Zhou, L Y

2015-10-14

Comprehensive research of genetic variation is crucial in designing conservation strategies for endangered and threatened species. Sinowilsonia henryi Hemsi. is a tertiary relic with a limited geographical distribution in the central and western areas of China. It is endangered because of climate change and habitat fragmentation over the last thousands of years. In this study, amplified fragment length polymorphism markers were utilized to estimate genetic diversity and genetic structure in and among S. henryi. In this study, Nei's genetic diversity and Shannon's information index were found to be 0.192 and 0.325 respectively, indicating a moderate-to-high genetic diversity in species. According to analysis of molecular variation results, 32% of the genetic variation was shown to be partitioned among populations, demonstrating a relatively high genetic divergence; this was supported by principal coordinate analysis and unweighted pair-group method with arithmetic average analysis. Moreover, the Mantel test showed that there was no significant correlation between genetic and geographical distances. The above results can be explained by the effects of habitat fragmentation, history traits, and gene drift. Based on the results, several implications were indicated and suggestions proposed for preservation strategies for this species.

Differences in glycosyltransferase family 61 accompany variation in seed coat mucilage composition in Plantago spp.

PubMed

Phan, Jana L; Tucker, Matthew R; Khor, Shi Fang; Shirley, Neil; Lahnstein, Jelle; Beahan, Cherie; Bacic, Antony; Burton, Rachel A

2016-12-01

Xylans are the most abundant non-cellulosic polysaccharide found in plant cell walls. A diverse range of xylan structures influence tissue function during growth and development. Despite the abundance of xylans in nature, details of the genes and biochemical pathways controlling their biosynthesis are lacking. In this study we have utilized natural variation within the Plantago genus to examine variation in heteroxylan composition and structure in seed coat mucilage. Compositional assays were combined with analysis of the glycosyltransferase family 61 (GT61) family during seed coat development, with the aim of identifying GT61 sequences participating in xylan backbone substitution. The results reveal natural variation in heteroxylan content and structure, particularly in P. ovata and P. cunninghamii, species which show a similar amount of heteroxylan but different backbone substitution profiles. Analysis of the GT61 family identified specific sequences co-expressed with IRREGULAR XYLEM 10 genes, which encode putative xylan synthases, revealing a close temporal association between xylan synthesis and substitution. Moreover, in P. ovata, several abundant GT61 sequences appear to lack orthologues in P. cunninghamii. Our results indicate that natural variation in Plantago species can be exploited to reveal novel details of seed coat development and polysaccharide biosynthetic pathways. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Structural diversity of domain superfamilies in the CATH database.

PubMed

Reeves, Gabrielle A; Dallman, Timothy J; Redfern, Oliver C; Akpor, Adrian; Orengo, Christine A

2006-07-14

The CATH database of domain structures has been used to explore the structural variation of homologous domains in 294 well populated domain structure superfamilies, each containing at least three sequence diverse relatives. Our analyses confirm some previously detected trends relating sequence divergence to structural variation but for a much larger dataset and in some superfamilies the new data reveal exceptional structural variation. Use of a new algorithm (2DSEC) to analyse variability in secondary structure compositions across a superfamily sheds new light on how structures evolve. 2DSEC detects inserted secondary structures that embellish the core of conserved secondary structures found throughout the superfamily. Analysis showed that for 56% of highly populated superfamilies (>9 sequence diverse relatives), there are twofold or more increases in the numbers of secondary structures in some relatives. In some families fivefold increases occur, sometimes modifying the fold of the domain. Manual inspection of secondary structure insertions or embellishments in 48 particularly variable superfamilies revealed that although these insertions were usually discontiguous in the sequence they were often co-located in 3D resulting in a larger structural motif that often modified the geometry of the active site or the surface conformation promoting diverse domain partnerships and protein interactions. These observations, supported by automatic analysis of all well populated CATH families, suggest that accretion of small secondary structure insertions may provide a simple mechanism for evolving new functions in diverse relatives. Some layered domain architectures (e.g. mainly-beta and alpha-beta sandwiches) that recur highly in the genomes more frequently exploit these types of embellishments to modify function. In these architectures, aggregation occurs most often at the edges, top or bottom of the beta-sheets. Information on structural variability across domain superfamilies has been made available through the CATH Dictionary of Homologous Structures (DHS).

Worldwide variation in within-canopy photosynthetic acclimation: differences in temporal and environmental controls among plant functional types

NASA Astrophysics Data System (ADS)

Niinemets, Ülo; Keenan, Trevor

2017-04-01

Major light gradients, characteristically 10- to 50-fold, constitute the most prominent feature of plant canopies. These gradients drive within-canopy variation in foliage structural, chemical and physiological traits. As a key acclimation response to variation in light availability, foliage photosynthetic capacity per area (Aarea) increases with increasing light availability within the canopy, maximizing whole canopy photosynthesis. Recently, a worldwide database including 831 within-canopy gradients with standardized light estimates for 304 species belonging to major vascular plant functional types was constructed and within-canopy variation in photosynthetic acclimation was characterized (Niinemets Ü, Keenan TF, Hallik L (2015) Tansley review. A worldwide analysis of within-canopy variations in leaf structural, chemical and physiological traits across plant functional types. The New Phytologist 205: 973-993). However, the understanding of how within-canopy photosynthetic gradients vary during the growing season and in response to site and stand characteristics is still limited. Here we analyzed temporal, environmental and site (nutrient availability, stand density, ambient CO2 concentration, water availability) sources of variation in within-canopy photosynthetic acclimation in different plant functional types. Variation in key structural (leaf dry mass per unit area, MA), chemical (nitrogen content per dry mass, NM, and area, NA) and physiological (photosynthetic nitrogen use efficiency, EN) photosynthetic capacity per dry mass, Amass and area, Aarea) was examined. The analysis demonstrates major, typically 1.5-2-fold, time-, environment and site-dependent modifications in within-canopy variation in foliage photosynthetic capacity. However, the magnitude and direction of temporal and environmental variations in plasticity significantly varied among functional types. Species with longer leaf life span and low rates of canopy expansion or flush-type canopy formation had lower within canopy plasticity during the growing season and in response to environmental and site modifications than species with high rates of canopy expansion and leaf turnover. The fast canopy-expanding species that grow in highly dynamic light environments, actively modified Aarea by nitrogen reallocation among and partitioning within leaves. In contrast, species with low rate of leaf turnover generally exhibited a passive acclimation response with variation in Aarea primarily determined by light-dependent modifications in leaf structure during leaf growth. Due to limited reacclimation capacity in species with low leaf turnover, within-canopy variation in Aarea decreased with increasing leaf age in these species. Furthermore, the plasticity responded less to modifications in environmental and site characteristics than in species with faster leaf turnover. This analysis concludes that the rate of leaf turnover is the key trait determining the temporal variation and environmental responses of canopy photosynthetic acclimation.

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

Variation Principles and Applications in the Study of Cell Structure and Aging

NASA Technical Reports Server (NTRS)

Economos, Angelos C.; Miquel, Jaime; Ballard, Ralph C.; Johnson, John E., Jr.

1981-01-01

In this report we have attempted to show that "some reality lies concealed in biological variation". This "reality" has its principles, laws, mechanisms, and rules, only a few of which we have sketched. A related idea we pursued was that important information may be lost in the process of ignoring frequency distributions of physiological variables (as is customary in experimental physiology and gerontology). We suggested that it may be advantageous to expand one's "statistical field of vision" beyond simple averages +/- standard deviations. Indeed, frequency distribution analysis may make visible some hidden information not evident from a simple qualitative analysis, particularly when the effect of some external factor or condition (e.g., aging, dietary chemicals) is being investigated. This was clearly illustrated by the application of distribution analysis in the study of variation in mouse liver cellular and fine structure, and may be true of fine structural studies in general. In living systems, structure and function interact in a dynamic way; they are "inseparable," unlike in technological systems or machines. Changes in fine structure therefore reflect changes in function. If such changes do not exceed a certain physiologic range, a quantitative analysis of structure will provide valuable information on quantitative changes in function that may not be possible or easy to measure directly. Because there is a large inherent variation in fine structure of cells in a given organ of an individual and among individuals, changes in fine structure can be analyzed only by studying frequency distribution curves of various structural characteristics (dimensions). Simple averages +/- S.D. do not in general reveal all information on the effect of a certain factor, because often this effect is not uniform; on the contrary, this will be apparent from distribution analysis because the form of the curves will be affected. We have also attempted to show in this chapter that similar general statistical principles and mechanisms may be operative in biological and technological systems. Despite the common belief that most biological and technological characteristics of interest have a symmetric bell-shaped (normal or Gaussian) distribution, we have shown that more often than not, distributions tend to be asymmetric and often resemble a so-called log-normal distribution. We saw that at least three general mechanisms may be operative, i.e., nonadditivity of influencing factors, competition among individuals for a common resource, and existence of an "optimum" value for a studied characteristic; more such mechanisms could exist.

Inbreeding Avoidance Drives Consistent Variation of Fine-Scale Genetic Structure Caused by Dispersal in the Seasonal Mating System of Brandt’s Voles

PubMed Central

Liu, Xiao Hui; Yue, Ling Fen; Wang, Da Wei; Li, Ning; Cong, Lin

2013-01-01

Inbreeding depression is a major evolutionary and ecological force influencing population dynamics and the evolution of inbreeding-avoidance traits such as mating systems and dispersal. Mating systems and dispersal are fundamental determinants of population genetic structure. Resolving the relationships among genetic structure, seasonal breeding-related mating systems and dispersal will facilitate our understanding of the evolution of inbreeding avoidance. The goals of this study were as follows: (i) to determine whether females actively avoided mating with relatives in a group-living rodent species, Brandt’s voles (Lasiopodomys brandtii), by combined analysis of their mating system, dispersal and genetic structure; and (ii) to analyze the relationships among the variation in fine-genetic structure, inbreeding avoidance, season-dependent mating strategies and individual dispersal. Using both individual- and population-level analyses, we found that the majority of Brandt’s vole groups consisted of close relatives. However, both group-specific FISs, an inbreeding coefficient that expresses the expected percentage rate of homozygosity arising from a given breeding system, and relatedness of mates showed no sign of inbreeding. Using group pedigrees and paternity analysis, we show that the mating system of Brandt’s voles consists of a type of polygyny for males and extra-group polyandry for females, which may decrease inbreeding by increasing the frequency of mating among distantly-related individuals. The consistent variation in within-group relatedness, among-group relatedness and fine-scale genetic structures was mostly due to dispersal, which primarily occurred during the breeding season. Biologically relevant variation in the fine-scale genetic structure suggests that dispersal during the mating season may be a strategy to avoid inbreeding and drive the polygynous and extra-group polyandrous mating system of this species. PMID:23516435

The initiation, propagation, and effect of matrix microcracks in cross-ply and related laminates

NASA Technical Reports Server (NTRS)

Nairn, John A.; Hu, Shoufeng; Liu, Siulie; Bark, Jong

1991-01-01

Recently, a variational mechanics approach was used to determine the thermoelastic stress state in cracked laminates. Described here is a generalization of the variational mechanics techniques to handle other cross-ply laminates, related laminates, and to account for delaminations emanating from microcrack tips. Microcracking experiments on Hercules 3501-6/AS4 carbon fiber/epoxy laminates show a staggered cracking pattern. These results can be explained by the variational mechanics analysis. The analysis of delaminations emanating from microcrack tips has resulted in predictions about the structural and material variables controlling competition between microcracking and delamination failure modes.

Investigation of skin structures based on infrared wave parameter indirect microscopic imaging

NASA Astrophysics Data System (ADS)

Zhao, Jun; Liu, Xuefeng; Xiong, Jichuan; Zhou, Lijuan

2017-02-01

Detailed imaging and analysis of skin structures are becoming increasingly important in modern healthcare and clinic diagnosis. Nanometer resolution imaging techniques such as SEM and AFM can cause harmful damage to the sample and cannot measure the whole skin structure from the very surface through epidermis, dermis to subcutaneous. Conventional optical microscopy has the highest imaging efficiency, flexibility in onsite applications and lowest cost in manufacturing and usage, but its image resolution is too low to be accepted for biomedical analysis. Infrared parameter indirect microscopic imaging (PIMI) uses an infrared laser as the light source due to its high transmission in skins. The polarization of optical wave through the skin sample was modulated while the variation of the optical field was observed at the imaging plane. The intensity variation curve of each pixel was fitted to extract the near field polarization parameters to form indirect images. During the through-skin light modulation and image retrieving process, the curve fitting removes the blurring scattering from neighboring pixels and keeps only the field variations related to local skin structures. By using the infrared PIMI, we can break the diffraction limit, bring the wide field optical image resolution to sub-200nm, in the meantime of taking advantage of high transmission of infrared waves in skin structures.

[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.

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.

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

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.

The Moho discontinuity beneath Taiwan orogenic zone inferred from receiver function analysis

NASA Astrophysics Data System (ADS)

Chang, H.; Chen, C.; Liang, W.

2013-12-01

We determine the depth variations of the Moho discontinuity beneath Taiwan from receiver function analysis. Taiwan is a young (~6.5 Ma) orogenic zone as a consequence of oblique collision between the Philippine Sea Plate and the Eurasian Plate. In northeastern Taiwan, the Philippine Sea Plate subducts northwestward under the Eurasian Plate along the Ryukyu Trench; in southern Taiwan, the Eurasian Plate subducts eastward beneath the Philippine Sea Plate along the Manila Trench. Recent tomographic models of Taiwan reveal P-wave velocity variations of the lithospheric structure that provide important constraints on the orogenic processes in this region. However, the depth variations of the Moho discontinuity, a key observation for better understanding crustal deformation, remain elusive. In this study, we aim to delineate the Moho depth variations by analyzing seismic converted phases indicative of the presence of discontinuity structure. We analyze waveform data from teleseismic events recorded at the Broadband Array in Taiwan for Seismology (BATS). Preliminary results of receiver functions beneath BATS stations in eastern Taiwan show that more than one converted phase (P-to-S) are likely present in crustal depths, suggesting possible multiple crustal layering, which may complicate the detection of the Moho. We further carry out synthetic experiments to explore possible crustal structures that reconcile our observations.

ANALYSIS OF GLYCANS DERIVED FROM GLYCOCONJUGATES BY CAPILLARY ELECTROPHORESIS-MASS SPECTROMETRY

PubMed Central

Mechref, Yehia

2012-01-01

The high structural variation of glycan derived from glycoconjugates, which substantially increases with the molecular size of a protein, contributes to the complexity of glycosylation patterns commonly associated with glycoconjugates. In the case of glycoproteins, such variation originates from the multiple glycosylation sites of proteins and the number of glycan structures associated with each site (microheterogeneity). The ability to comprehensively characterize highly complex mixture of glycans has been analytically stimulating and challenging. Although the most powerful mass spectrometric (MS) and tandem MS techniques are capable of providing a wealth of structural information, they are still not able to readily identify isomeric glycan structures without high order tandem MS (MSn). The analysis of isomeric glycan structures has been attained using several separation methods, including high-pH anion exchange chromatography (HPAEC), hydrophilic interaction chromatography (HILIC) and gas chromatography (GC). However, capillary electrophoresis (CE) and microfluidics capillary electrophoresis (MCE) offer high separation efficiency and resolutions, allowing the separation of closely related glycan structures. Therefore, interfacing CE and MCE to MS is a powerful analytical approach, allowing potentially comprehensive and sensitive analysis of complex glycan samples. This review describes and discusses the utility of different CE and MCE approaches in the structural characterization of glycoproteins and the feasibility of interfacing these approaches to mass spectrometry. PMID:22180203

Quantum structural fluctuation in para-hydrogen clusters revealed by the variational path integral method

NASA Astrophysics Data System (ADS)

Miura, Shinichi

2018-03-01

In this paper, the ground state of para-hydrogen clusters for size regime N ≤ 40 has been studied by our variational path integral molecular dynamics method. Long molecular dynamics calculations have been performed to accurately evaluate ground state properties. The chemical potential of the hydrogen molecule is found to have a zigzag size dependence, indicating the magic number stability for the clusters of the size N = 13, 26, 29, 34, and 39. One-body density of the hydrogen molecule is demonstrated to have a structured profile, not a melted one. The observed magic number stability is examined using the inherent structure analysis. We also have developed a novel method combining our variational path integral hybrid Monte Carlo method with the replica exchange technique. We introduce replicas of the original system bridging from the structured to the melted cluster, which is realized by scaling the potential energy of the system. Using the enhanced sampling method, the clusters are demonstrated to have the structured density profile in the ground state.

Quantum structural fluctuation in para-hydrogen clusters revealed by the variational path integral method.

PubMed

Miura, Shinichi

2018-03-14

In this paper, the ground state of para-hydrogen clusters for size regime N ≤ 40 has been studied by our variational path integral molecular dynamics method. Long molecular dynamics calculations have been performed to accurately evaluate ground state properties. The chemical potential of the hydrogen molecule is found to have a zigzag size dependence, indicating the magic number stability for the clusters of the size N = 13, 26, 29, 34, and 39. One-body density of the hydrogen molecule is demonstrated to have a structured profile, not a melted one. The observed magic number stability is examined using the inherent structure analysis. We also have developed a novel method combining our variational path integral hybrid Monte Carlo method with the replica exchange technique. We introduce replicas of the original system bridging from the structured to the melted cluster, which is realized by scaling the potential energy of the system. Using the enhanced sampling method, the clusters are demonstrated to have the structured density profile in the ground state.

A research about characteristics of longitudinal variations of ES layers irregularities based on CHAMP occultation measurements

NASA Astrophysics Data System (ADS)

Liao, Sunmin

2018-04-01

Based on the data of CHAMP occultation measurements, this paper makes a preliminary analysis of the longitudinal variations of ES irregular structure by using Fourier decomposition and reconstruction technique. It is found that the longitudinal variations of the ES irregular structure show the features of multiple wave-numbers, which is dominated by the wave number 1 to the wave number 5 components, and decrease from the amplitudes of the wave number 6 components. The features of wave number structures are very different in different DIP latitude and different seasons. The number of crests in summer and autumn is mostly 3 or 4 crest structures, while the number of crests in spring achieves 5 at DIP 15°N with small fluctuates, the crests number of winter is the least. In the multiple wave-numbers structure, the wave number 4 component shows a significant dependence on the season, mainly in the summer and autumn, particularly obvious from July to October.

Implementation of Speed Variation in the Structural Dynamic Assessment of Turbomachinery Flow-Path Components

NASA Technical Reports Server (NTRS)

Brown, Andrew M.; Davis, R. Benjamin; DeHaye, Michael

2013-01-01

During the design of turbomachinery flow path components, the assessment of possible structural resonant conditions is critical. Higher frequency modes of these structures are frequently found to be subject to resonance, and in these cases, design criteria require a forced response analysis of the structure with the assumption that the excitation speed exactly equals the resonant frequency. The design becomes problematic if the response analysis shows a violation of the HCF criteria. One possible solution is to perform "finite-life" analysis, where Miner's rule is used to calculate the actual life in seconds in comparison to the required life. In this situation, it is beneficial to incorporate the fact that, for a variety of turbomachinery control reasons, the speed of the rotor does not actually dwell at a single value but instead dithers about a nominal mean speed and during the time that the excitation frequency is not equal to the resonant frequency, the damage accumulated by the structure is diminished significantly. Building on previous investigations into this process, we show that a steady-state assumption of the response is extremely accurate for this typical case, resulting in the ability to quickly account for speed variation in the finite-life analysis of a component which has previously had its peak dynamic stress at resonance calculated. A technique using Monte Carlo simulation is also presented which can be used when specific speed time histories are not available. The implementation of these techniques can prove critical for successful turbopump design, as the improvement in life when speed variation is considered is shown to be greater than a factor of two

Spatial variations in food web structures with alternative stable states: evidence from stable isotope analysis in a large eutrophic lake

NASA Astrophysics Data System (ADS)

Li, Yunkai; Zhang, Yuying; Xu, Jun; Zhang, Shuo

2018-03-01

Food web structures are well known to vary widely among ecosystems. Moreover, many food web studies of lakes have generally attempted to characterize the overall food web structure and have largely ignored internal spatial and environmental variations. In this study, we hypothesize that there is a high degree of spatial heterogeneity within an ecosystem and such heterogeneity may lead to strong variations in environmental conditions and resource availability, in turn resulting in different trophic pathways. Stable carbon and nitrogen isotopes were employed for the whole food web to describe the structure of the food web in different sub-basins within Taihu Lake. This lake is a large eutrophic freshwater lake that has been intensively managed and highly influenced by human activities for more than 50 years. The results show significant isotopic differences between basins with different environmental characteristics. Such differences likely result from isotopic baseline differences combining with a shift in food web structure. Both are related to local spatial heterogeneity in nutrient loading in waters. Such variation should be explicitly considered in future food web studies and ecosystem-based management in this lake ecosystem.

Advanced stress analysis methods applicable to turbine engine structures

NASA Technical Reports Server (NTRS)

Pian, T. H. H.

1985-01-01

Advanced stress analysis methods applicable to turbine engine structures are investigated. Constructions of special elements which containing traction-free circular boundaries are investigated. New versions of mixed variational principle and version of hybrid stress elements are formulated. A method is established for suppression of kinematic deformation modes. semiLoof plate and shell elements are constructed by assumed stress hybrid method. An elastic-plastic analysis is conducted by viscoplasticity theory using the mechanical subelement model.

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) ...

From Higher Education to Work: Public and Professional Sector Employment in Germany and Britain

ERIC Educational Resources Information Center

Leuze, Kathrin

2010-01-01

Comparative analysis of the transition from higher education to work often focuses on cross-national variations of higher education systems to explain country-specific mobility patterns of higher education graduates. The structure of graduate labour markets, however, has received less attention, despite differences across countries. Variations in…

Population differentiation in the red-legged kittiwake (Rissa brevirostris) as revealed by mitochondrial DNA

USGS Publications Warehouse

Patirana, A.; Hatcher, S.A.; Friesen, Vicki L.

2002-01-01

Population decline in red-legged kittiwakes (Rissa brevirostris) over recent decades has necessitated the collection of information on the distribution of genetic variation within and among colonies for implementation of suitable management policies. Here we present a preliminary study of the extent of genetic structuring and gene flow among the three principal breeding locations of red-legged kittiwakes using the hypervariable Domain I of the mitochondrial control region. Genetic variation was high relative to other species of seabirds, and was similar among locations. Analysis of molecular variance indicated that population genetic structure was statistically significant, and nested clade analysis suggested that kittiwakes breeding on Bering Island maybe genetically isolated from those elsewhere. However, phylogeographic structure was weak. Although this analysis involved only a single locus and a small number of samples, it suggests that red-legged kittiwakes probably constitute a single evolutionary significant unit; the possibility that they constitute two management units requires further investigation.

AIR POLLUTION EPIDEMIOLOGY: CAN INFORMATION BE OBTAINED FROM THE VARIATIONS IN SIGNIFICANCE AND RISK AS A FUNCTION OF DAYS AFTER EXPOSURE (LAG STRUCTURE)?

EPA Science Inventory

Determine if analysis of lag structure from time series epidemiology, using gases, particles, and source factor time series, can contribute to understanding the relationships among various air pollution indicators. Methods: Analyze lag structure from an epidemiologic study of ca...

Genetic diversity, structure and differentiation in cultivate walnut (Juglans regia L.)

Treesearch

M. Aradhya; K. Woeste; D. Velasco

2012-01-01

An analysis of genetic structure and differentiation in cultivated walnut (Juglans regia) using 15 microsatellite loci revealed a considerable amount of genetic variation with a mild genetic structure indicating five genetic groups corresponding to the centers of diversity within the home range of walnut in Eurasia. Despite the narrow genetic...

Frequency analysis of uncertain structures using imprecise probability

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

Modares, Mehdi; Bergerson, Joshua

2015-01-01

Two new methods for finite element based frequency analysis of a structure with uncertainty are developed. An imprecise probability formulation based on enveloping p-boxes is used to quantify the uncertainty present in the mechanical characteristics of the structure. For each element, independent variations are considered. Using the two developed methods, P-box Frequency Analysis (PFA) and Interval Monte-Carlo Frequency Analysis (IMFA), sharp bounds on natural circular frequencies at different probability levels are obtained. These methods establish a framework for handling incomplete information in structural dynamics. Numerical example problems are presented that illustrate the capabilities of the new methods along with discussionsmore » on their computational efficiency.« less

A Multiscale, Nonlinear, Modeling Framework Enabling the Design and Analysis of Composite Materials and Structures

NASA Technical Reports Server (NTRS)

Bednarcyk, Brett A.; Arnold, Steven M.

2012-01-01

A framework for the multiscale design and analysis of composite materials and structures is presented. The ImMAC software suite, developed at NASA Glenn Research Center, embeds efficient, nonlinear micromechanics capabilities within higher scale structural analysis methods such as finite element analysis. The result is an integrated, multiscale tool that relates global loading to the constituent scale, captures nonlinearities at this scale, and homogenizes local nonlinearities to predict their effects at the structural scale. Example applications of the multiscale framework are presented for the stochastic progressive failure of a SiC/Ti composite tensile specimen and the effects of microstructural variations on the nonlinear response of woven polymer matrix composites.

A Multiscale, Nonlinear, Modeling Framework Enabling the Design and Analysis of Composite Materials and Structures

NASA Technical Reports Server (NTRS)

Bednarcyk, Brett A.; Arnold, Steven M.

2011-01-01

A framework for the multiscale design and analysis of composite materials and structures is presented. The ImMAC software suite, developed at NASA Glenn Research Center, embeds efficient, nonlinear micromechanics capabilities within higher scale structural analysis methods such as finite element analysis. The result is an integrated, multiscale tool that relates global loading to the constituent scale, captures nonlinearities at this scale, and homogenizes local nonlinearities to predict their effects at the structural scale. Example applications of the multiscale framework are presented for the stochastic progressive failure of a SiC/Ti composite tensile specimen and the effects of microstructural variations on the nonlinear response of woven polymer matrix composites.

A Variational Principle for Reconstruction of Elastic Deformations in Shear Deformable Plates and Shells

NASA Technical Reports Server (NTRS)

Tessler, Alexander; Spangler, Jan L.

2003-01-01

A variational principle is formulated for the inverse problem of full-field reconstruction of three-dimensional plate/shell deformations from experimentally measured surface strains. The formulation is based upon the minimization of a least squares functional that uses the complete set of strain measures consistent with linear, first-order shear-deformation theory. The formulation, which accommodates for transverse shear deformation, is applicable for the analysis of thin and moderately thick plate and shell structures. The main benefit of the variational principle is that it is well suited for C(sup 0)-continuous displacement finite element discretizations, thus enabling the development of robust algorithms for application to complex civil and aeronautical structures. The methodology is especially aimed at the next generation of aerospace vehicles for use in real-time structural health monitoring systems.

Variation in psychotropic drug use in nursing homes.

PubMed

Castle, N G

1998-01-01

Numerous studies of health service use reveal considerable variation in the degree of services provided. In this article the variation in psychotropic drug use in nursing homes is examined. First, a descriptive analysis of nursing homes with and without high levels of psychotropic drug use is provided. Second, an analysis of the determinants of high levels of psychotropic drug use in nursing homes is provided. Factors such as ownership, staffing levels, having special care units, case-mix intensity, competitiveness of the nursing home market, and the state Medicaid reimbursement rate structure are examined. The results of these analyses are discussed in terms of their policy issues.

[Toward exploration of morphological diversity of measurable traits of mammalian skull. 2. Scalar and vector parameters of the forms of group variation].

PubMed

Lisovskiĭ, A A; Pavlinov, I Ia

2008-01-01

Any morphospace is partitioned by the forms of group variation, its structure is described by a set of scalar (range, overlap) and vector (direction) characteristics. They are analyzed quantitatively for the sex and age variations in the sample of 200 skulls of the pine marten described by 14 measurable traits. Standard dispersion and variance components analyses are employed, accompanied with several resampling methods (randomization and bootstrep); effects of changes in the analysis design on results of the above methods are also considered. Maximum likelihood algorithm of variance components analysis is shown to give an adequate estimates of portions of particular forms of group variation within the overall disparity. It is quite stable in respect to changes of the analysis design and therefore could be used in the explorations of the real data with variously unbalanced designs. A new algorithm of estimation of co-directionality of particular forms of group variation within the overall disparity is elaborated, which includes angle measures between eigenvectors of covariation matrices of effects of group variations calculated by dispersion analysis. A null hypothesis of random portion of a given group variation could be tested by means of randomization of the respective grouping variable. A null hypothesis of equality of both portions and directionalities of different forms of group variation could be tested by means of the bootstrep procedure.

Landscape genetics of Schistocephalus solidus parasites in threespine stickleback (Gasterosteus aculeatus) from Alaska.

PubMed

Sprehn, C Grace; Blum, Michael J; Quinn, Thomas P; Heins, David C

2015-01-01

The nature of gene flow in parasites with complex life cycles is poorly understood, particularly when intermediate and definitive hosts have contrasting movement potential. We examined whether the fine-scale population genetic structure of the diphyllobothriidean cestode Schistocephalus solidus reflects the habits of intermediate threespine stickleback hosts or those of its definitive hosts, semi-aquatic piscivorous birds, to better understand complex host-parasite interactions. Seventeen lakes in the Cook Inlet region of south-central Alaska were sampled, including ten in the Matanuska-Susitna Valley, five on the Kenai Peninsula, and two in the Bristol Bay drainage. We analyzed sequence variation across a 759 bp region of the mitochondrial DNA (mtDNA) cytochrome oxidase I region for 1,026 S. solidus individuals sampled from 2009-2012. We also analyzed allelic variation at 8 microsatellite loci for 1,243 individuals. Analysis of mtDNA haplotype and microsatellite genotype variation recovered evidence of significant population genetic structure within S. solidus. Host, location, and year were factors in structuring observed genetic variation. Pairwise measures revealed significant differentiation among lakes, including a pattern of isolation-by-distance. Bayesian analysis identified three distinct genotypic clusters in the study region, little admixture within hosts and lakes, and a shift in genotype frequencies over time. Evidence of fine-scale population structure in S. solidus indicates that movement of its vagile, definitive avian hosts has less influence on gene flow than expected based solely on movement potential. Observed patterns of genetic variation may reflect genetic drift, behaviors of definitive hosts that constrain dispersal, life history of intermediate hosts, and adaptive specificity of S. solidus to intermediate host genotype.

Fine-scale genetic population structure in a mobile marine mammal: inshore bottlenose dolphins in Moreton Bay, Australia.

PubMed

Ansmann, Ina C; Parra, Guido J; Lanyon, Janet M; Seddon, Jennifer M

2012-09-01

Highly mobile marine species in areas with no obvious geographic barriers are expected to show low levels of genetic differentiation. However, small-scale variation in habitat may lead to resource polymorphisms and drive local differentiation by adaptive divergence. Using nuclear microsatellite genotyping at 20 loci, and mitochondrial control region sequencing, we investigated fine-scale population structuring of inshore bottlenose dolphins (Tursiops aduncus) inhabiting a range of habitats in and around Moreton Bay, Australia. Bayesian structure analysis identified two genetic clusters within Moreton Bay, with evidence of admixture between them (F(ST) = 0.05, P = 0.001). There was only weak isolation by distance but one cluster of dolphins was more likely to be found in shallow southern areas and the other in the deeper waters of the central northern bay. In further analysis removing admixed individuals, southern dolphins appeared genetically restricted with lower levels of variation (AR = 3.252, π = 0.003) and high mean relatedness (r = 0.239) between individuals. In contrast, northern dolphins were more diverse (AR = 4.850, π = 0.009) and were mixing with a group of dolphins outside the bay (microsatellite-based STRUCTURE analysis), which appears to have historically been distinct from the bay dolphins (mtDNA Φ(ST) = 0.272, P < 0.001). This study demonstrates the ability of genetic techniques to expose fine-scale patterns of population structure and explore their origins and mechanisms. A complex variety of inter-related factors including local habitat variation, differential resource use, social behaviour and learning, and anthropogenic disturbances are likely to have played a role in driving fine-scale population structure among bottlenose dolphins in Moreton Bay. © 2012 Blackwell Publishing Ltd.

Scale-dependent variation in forest structures in naturally dynamic boreal forest landscapes

NASA Astrophysics Data System (ADS)

Kulha, Niko; Pasanen, Leena; De Grandpré, Louis; Kuuluvainen, Timo; Aakala, Tuomas

2017-04-01

Natural forest structures vary at multiple spatial scales. This variation reflects the occurrence of driving factors, such as disturbances and variation in soil or topography. To explore and understand the linkages of forest structural characteristics and factors driving their variation, we need to recognize how the structural characteristics vary in relation to spatial scale. This can be achieved by identifying scale-dependent features in forest structure within unmanaged forest landscapes. By identifying these features and examining their relationship with potential driving factors, we can better understand the dynamics of forest structural development. Here, we examine the spatial variation in forest structures at multiple spatial scales, utilizing data from old-growth boreal forests in two regions with contrasting disturbance regimes: northern Finland and north-eastern Québec, Canada ( 67° 45'N, 29° 36'E, 49° 39'N, 67° 55'W, respectively). The three landscapes (4 km2 each) in Finland are dominated by Pinus sylvestris and Picea abies, whereas the two landscapes in Québec are dominated by Abies balsamea and Picea mariana. Québec's forests are a subject to cyclic outbreaks of the eastern spruce budworm, causing extensive mortality especially in A. balsamea-dominated stands. In the Finnish landscapes, gap- to patch-scale disturbances due to tree senescence, fungi and wind, as well as infrequent surface fires in areas dominated by P. sylvestris, prevail. Owing to the differences in the species compositions and the disturbance regimes, we expect differing scales of variation between the landscapes. To quantify patterns of variation, we visually interpret stereopairs of recent aerial photographs. From the photographs, we collect information on forest canopy coverage, species composition and dead wood. For the interpretation, each 4 km2 plot is divided into 0.1ha square cells (4096 per plot). Interpretations are validated against field observations and compiled to raster maps. We analyze the raster maps with Bayesian scale space approach (iBSiZer), which aims in capturing credible variations at different spatial scales. As a result, we can detect structural entities (e.g. patches with higher canopy cover), which deviate credibly from their surroundings. The detected entities can further be linked to specific drivers. Our results show that the role of a particular driving factor varies in relation to spatial scale. For example, in the Finnish landscapes, topoedaphic factors exerted a stronger control on broad-scale forest structural characteristics, whereas recent disturbances (quantified as the amount of dead wood) appeared to play an important role in explaining the smaller scale variation of forest structures. Here, we showcase the methodology used in the detection of scale-dependent forest structural entities and present the results of our analysis of the spatial scales of variation in the natural boreal forest structures.

Analyzing Mixed-Dyadic Data Using Structural Equation Models

ERIC Educational Resources Information Center

Peugh, James L.; DiLillo, David; Panuzio, Jillian

2013-01-01

Mixed-dyadic data, collected from distinguishable (nonexchangeable) or indistinguishable (exchangeable) dyads, require statistical analysis techniques that model the variation within dyads and between dyads appropriately. The purpose of this article is to provide a tutorial for performing structural equation modeling analyses of cross-sectional…

Using Confirmatory Factor Analysis to Understand Executive Control in Preschool Children: Sources of Variation in Emergent Mathematic Achievement

ERIC Educational Resources Information Center

Bull, Rebecca; Espy, Kimberly Andrews; Wiebe, Sandra A.; Sheffield, Tiffany D.; Nelson, Jennifer Mize

2011-01-01

Latent variable modeling methods have demonstrated utility for understanding the structure of executive control (EC) across development. These methods are utilized to better characterize the relation between EC and mathematics achievement in the preschool period, and to understand contributing sources of individual variation. Using the sample and…

Investigation of the Crustal Structure in the Middle East from Body-Wave Analysis (POSTPRINT). Annual Report 2

DTIC Science & Technology

2012-06-05

Variations in the Zagros Fold and Trust Zone While crustal anisotropy may be indicative of tectonic stresses and alignments of faults and fracture zones...AFRL-RV-PS- AFRL-RV-PS- TP-2012-0042 TP-2012-0042 INVESTIGATION OF THE CRUSTAL STRUCTURE IN THE MIDDLE EAST FROM BODY-WAVE ANALYSIS...DATES COVERED (From - To) 01 Sep 2010 to 19 Mar 2012 4. TITLE AND SUBTITLE INVESTIGATION OF THE CRUSTAL STRUCTURE IN THE MIDDLE EAST FROM

Mechanical Response Analysis of Long-life Asphalt Pavement Structure of Yunluo High-speed on the Semi-rigid Base

NASA Astrophysics Data System (ADS)

Liu, Feng; Wu, Chuanhai; Xu, Xinquan; Li, Hao; Wang, Zhixiang

2018-01-01

In order to grasp the rule of the strain change of the semi-rigid asphalt pavement structure under the FWD load and provide a reliable theoretical and practical basis for the design of the pavement structure, based on the test section of Guangdong Yunluo expressway, taking FWD as the loading tool, by using the finite element analysis software ANSYS, the internal variation rules of each pavement structural layer were obtained. Based on the results of the theoretical analysis, the measured strain sensor was set up in the corresponding layer of the pavement structure, and the strain test plan was determined. Based on the analysis of the strain data obtained from several structural layers and field monitoring, the rationality of the type pavement structure and the strain test scheme were verified, so as to provide useful help for the design and the maintenance of the pavement structure.

Revisiting Interpretation of Canonical Correlation Analysis: A Tutorial and Demonstration of Canonical Commonality Analysis

ERIC Educational Resources Information Center

Nimon, Kim; Henson, Robin K.; Gates, Michael S.

2010-01-01

In the face of multicollinearity, researchers face challenges interpreting canonical correlation analysis (CCA) results. Although standardized function and structure coefficients provide insight into the canonical variates produced, they fall short when researchers want to fully report canonical effects. This article revisits the interpretation of…

Genome-wide network analysis of Wnt signaling in three pediatric cancers

NASA Astrophysics Data System (ADS)

Bao, Ju; Lee, Ho-Jin; Zheng, Jie J.

2013-10-01

Genomic structural alteration is common in pediatric cancers, and analysis of data generated by the Pediatric Cancer Genome Project reveals such tumor-related alterations in many Wnt signaling-associated genes. Most pediatric cancers are thought to arise within developing tissues that undergo substantial expansion during early organ formation, growth and maturation, and Wnt signaling plays an important role in this development. We examined three pediatric tumors--medullobastoma, early T-cell precursor acute lymphoblastic leukemia, and retinoblastoma--that show multiple genomic structural variations within Wnt signaling pathways. We mathematically modeled this pathway to investigate the effects of cancer-related structural variations on Wnt signaling. Surprisingly, we found that an outcome measure of canonical Wnt signaling was consistently similar in matched cancer cells and normal cells, even in the context of different cancers, different mutations, and different Wnt-related genes. Our results suggest that the cancer cells maintain a normal level of Wnt signaling by developing multiple mutations.

Structural efficiency study of composite wing rib structures

NASA Technical Reports Server (NTRS)

Swanson, Gary D.; Gurdal, Zafer; Starnes, James H., Jr.

1988-01-01

A series of short stiffened panel designs which may be applied to a preliminary design assessment of an aircraft wing rib is presented. The computer program PASCO is used as the primary design and analysis tool to assess the structural efficiency and geometry of a tailored corrugated panel, a corrugated panel with a continuous laminate, a hat stiffened panel, a blade stiffened panel, and an unstiffened flat plate. To correct some of the shortcomings in the PASCO analysis when shear is present, a two step iterative process using the computer program VICON is used. The loadings considered include combinations of axial compression, shear, and lateral pressure. The loading ranges considered are broad enough such that the designs presented may be applied to other stiffened panel applications. An assessment is made of laminate variations, increased spacing, and nonoptimum geometric variations, including a beaded panel, on the design of the panels.

AgRISTARS. Supporting research: Algorithms for scene modelling

NASA Technical Reports Server (NTRS)

Rassbach, M. E. (Principal Investigator)

1982-01-01

The requirements for a comprehensive analysis of LANDSAT or other visual data scenes are defined. The development of a general model of a scene and a computer algorithm for finding the particular model for a given scene is discussed. The modelling system includes a boundary analysis subsystem, which detects all the boundaries and lines in the image and builds a boundary graph; a continuous variation analysis subsystem, which finds gradual variations not well approximated by a boundary structure; and a miscellaneous features analysis, which includes texture, line parallelism, etc. The noise reduction capabilities of this method and its use in image rectification and registration are discussed.

Genetic Differentiation among Maruca vitrata F. (Lepidoptera: Crambidae) Populations on Cultivated Cowpea and Wild Host Plants: Implications for Insect Resistance Management and Biological Control Strategies

PubMed Central

Agunbiade, Tolulope A.; Coates, Brad S.; Datinon, Benjamin; Djouaka, Rousseau; Sun, Weilin; Tamò, Manuele; Pittendrigh, Barry R.

2014-01-01

Maruca vitrata Fabricius (Lepidoptera: Crambidae) is a polyphagous insect pest that feeds on a variety of leguminous plants in the tropics and subtropics. The contribution of host-associated genetic variation on population structure was investigated using analysis of mitochondrial cytochrome oxidase 1 (cox1) sequence and microsatellite marker data from M. vitrata collected from cultivated cowpea (Vigna unguiculata L. Walp.), and alternative host plants Pueraria phaseoloides (Roxb.) Benth. var. javanica (Benth.) Baker, Loncocarpus sericeus (Poir), and Tephrosia candida (Roxb.). Analyses of microsatellite data revealed a significant global FST estimate of 0.05 (P≤0.001). The program STRUCTURE estimated 2 genotypic clusters (co-ancestries) on the four host plants across 3 geographic locations, but little geographic variation was predicted among genotypes from different geographic locations using analysis of molecular variance (AMOVA; among group variation −0.68%) or F-statistics (F ST Loc = −0.01; P = 0.62). These results were corroborated by mitochondrial haplotype data (φSTLoc = 0.05; P = 0.92). In contrast, genotypes obtained from different host plants showed low but significant levels of genetic variation (F ST Host = 0.04; P = 0.01), which accounted for 4.08% of the total genetic variation, but was not congruent with mitochondrial haplotype analyses (φSTHost = 0.06; P = 0.27). Variation among host plants at a location and host plants among locations showed no consistent evidence for M. vitrata population subdivision. These results suggest that host plants do not significantly influence the genetic structure of M. vitrata, and this has implications for biocontrol agent releases as well as insecticide resistance management (IRM) for M. vitrata in West Africa. PMID:24647356

Reliability analysis of composite structures

NASA Technical Reports Server (NTRS)

Kan, Han-Pin

1992-01-01

A probabilistic static stress analysis methodology has been developed to estimate the reliability of a composite structure. Closed form stress analysis methods are the primary analytical tools used in this methodology. These structural mechanics methods are used to identify independent variables whose variations significantly affect the performance of the structure. Once these variables are identified, scatter in their values is evaluated and statistically characterized. The scatter in applied loads and the structural parameters are then fitted to appropriate probabilistic distribution functions. Numerical integration techniques are applied to compute the structural reliability. The predicted reliability accounts for scatter due to variability in material strength, applied load, fabrication and assembly processes. The influence of structural geometry and mode of failure are also considerations in the evaluation. Example problems are given to illustrate various levels of analytical complexity.

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.

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.

How fields vary.

PubMed

Krause, Monika

2018-03-01

Field theorists have long insisted that research needs to pay attention to the particular properties of each field studied. But while much field-theoretical research is comparative, either explicitly or implicitly, scholars have only begun to develop the language for describing the dimensions along which fields can be similar to and different from each other. In this context, this paper articulates an agenda for the analysis of variable properties of fields. It discusses variation in the degree but also in the kind of field autonomy. It discusses different dimensions of variation in field structure: fields can be more or less contested, and more or less hierarchical. The structure of symbolic oppositions in a field may take different forms. Lastly, it analyses the dimensions of variation highlighted by research on fields on the sub- and transnational scale. Post-national analysis allows us to ask how fields relate to fields of the same kind on different scales, and how fields relate to fields on the same scale in other national contexts. It allows us to ask about the role resources from other scales play in structuring symbolic oppositions within fields. A more fine-tuned vocabulary for field variation can help us better describe particular fields and it is a precondition for generating hypotheses about the conditions under which we can expect to observe fields with specified characteristics. © London School of Economics and Political Science 2017.

Growth history of cultured pearl oysters based on stable oxygen isotope analysis

NASA Astrophysics Data System (ADS)

Nakashima, R.; Furuta, N.; Suzuki, A.; Kawahata, H.; Shikazono, N.

2007-12-01

We investigated the oxygen isotopic ratio in shells of the pearl oyster Pinctada martensii cultivated in embayments in Mie Prefecture, central Japan, to evaluate the biomineralization of shell structures of the species and its pearls in response to environmental change. Microsamples for oxygen isotope analysis were collected from the surfaces of shells (outer, middle, and inner shell layers) and pearls. Water temperature variations were estimated from the oxygen isotope values of the carbonate. Oxygen isotope profiles of the prismatic calcite of the outer shell layer reflected seasonal variations of water temperature, whereas those of nacreous aragonites of the middle and inner shell layers and pearls recorded temperatures from April to November, June to September, and July to September, respectively. Lower temperatures in autumn and winter might slow the growth of nacreous aragonites. The oxygen isotope values are controlled by both variations of water temperature and shell structures; the prismatic calcite of this species is useful for reconstructing seasonal changes of calcification temperature.

Some uses of wavelets for imaging dynamic processes in live cochlear structures

NASA Astrophysics Data System (ADS)

Boutet de Monvel, J.

2007-09-01

A variety of image and signal processing algorithms based on wavelet filtering tools have been developed during the last few decades, that are well adapted to the experimental variability typically encountered in live biological microscopy. A number of processing tools are reviewed, that use wavelets for adaptive image restoration and for motion or brightness variation analysis by optical flow computation. The usefulness of these tools for biological imaging is illustrated in the context of the restoration of images of the inner ear and the analysis of cochlear motion patterns in two and three dimensions. I also report on recent work that aims at capturing fluorescence intensity changes associated with vesicle dynamics at synaptic zones of sensory hair cells. This latest application requires one to separate the intensity variations associated with the physiological process under study from the variations caused by motion of the observed structures. A wavelet optical flow algorithm for doing this is presented, and its effectiveness is demonstrated on artificial and experimental image sequences.

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

GCR Modulation by Small-Scale Features in the Interplanetary Medium

NASA Astrophysics Data System (ADS)

Jordan, A. P.; Spence, H. E.; Blake, J. B.; Mulligan, T. L.; Shaul, D. N.; Galametz, M.

2007-12-01

In an effort to uncover the properties of structures in the interplanetary medium (IPM) that modulate galactic cosmic rays (GCR) on short time-scales (from hours to days), we study periods of differing conditions in the IPM. We analyze GCR variations from spacecraft both inside and outside the magnetosphere, using the High Sensitivity Telescope (HIST) on Polar and the Spectrometer for INTEGRAL (SPI). We seek causal correlations between the observed GCR modulations and structures in the solar wind plasma and interplanetary magnetic field, as measured concurrently with ACE and/or Wind. Our analysis spans time-/size-scale variations ranging from classic Forbush decreases (Fds), to substructure embedded within Fds, to much smaller amplitude and shorter duration variations observed during comparatively benign interplanetary conditions. We compare and contrast the conditions leading to the range of different GCR responses to modulating structures in the IPM.

Length Variation in Mitochondrial DNA of the Minnow Cyprinella Spiloptera

PubMed Central

Broughton, R. E.; Dowling, T. E.

1994-01-01

Length differences in animal mitochondrial DNA (mtDNA) are common, frequently due to variation in copy number of direct tandem duplications. While such duplications appear to form without great difficulty in some taxonomic groups, they appear to be relatively short-lived, as typical duplication products are geographically restricted within species and infrequently shared among species. To better understand such length variation, we have studied a tandem and direct duplication of approximately 260 bp in the control region of the cyprinid fish, Cyprinella spiloptera. Restriction site analysis of 38 individuals was used to characterize population structure and the distribution of variation in repeat copy number. This revealed two length variants, including individuals with two or three copies of the repeat, and little geographic structure among populations. No standard length (single copy) genomes were found and heteroplasmy, a common feature of length variation in other taxa, was absent. Nucleotide sequence of tandem duplications and flanking regions localized duplication junctions in the phenylalanine tRNA and near the origin of replication. The locations of these junctions and the stability of folded repeat copies support the hypothesized importance of secondary structures in models of duplication formation. PMID:8001785

PDBFlex: exploring flexibility in protein structures

PubMed Central

Hrabe, Thomas; Li, Zhanwen; Sedova, Mayya; Rotkiewicz, Piotr; Jaroszewski, Lukasz; Godzik, Adam

2016-01-01

The PDBFlex database, available freely and with no login requirements at http://pdbflex.org, provides information on flexibility of protein structures as revealed by the analysis of variations between depositions of different structural models of the same protein in the Protein Data Bank (PDB). PDBFlex collects information on all instances of such depositions, identifying them by a 95% sequence identity threshold, performs analysis of their structural differences and clusters them according to their structural similarities for easy analysis. The PDBFlex contains tools and viewers enabling in-depth examination of structural variability including: 2D-scaling visualization of RMSD distances between structures of the same protein, graphs of average local RMSD in the aligned structures of protein chains, graphical presentation of differences in secondary structure and observed structural disorder (unresolved residues), difference distance maps between all sets of coordinates and 3D views of individual structures and simulated transitions between different conformations, the latter displayed using JSMol visualization software. PMID:26615193

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.

Mantle viscosity structure constrained by joint inversions of seismic velocities and density

NASA Astrophysics Data System (ADS)

Rudolph, M. L.; Moulik, P.; Lekic, V.

2017-12-01

The viscosity structure of Earth's deep mantle affects the thermal evolution of Earth, the ascent of mantle upwellings, sinking of subducted oceanic lithosphere, and the mixing of compositional heterogeneities in the mantle. Modeling the long-wavelength dynamic geoid allows us to constrain the radial viscosity profile of the mantle. Typically, in inversions for the mantle viscosity structure, wavespeed variations are mapped into density variations using a constant- or depth-dependent scaling factor. Here, we use a newly developed joint model of anisotropic Vs, Vp, density and transition zone topographies to generate a suite of solutions for the mantle viscosity structure directly from the seismologically constrained density structure. The density structure used to drive our forward models includes contributions from both thermal and compositional variations, including important contributions from compositionally dense material in the Large Low Velocity Provinces at the base of the mantle. These compositional variations have been neglected in the forward models used in most previous inversions and have the potential to significantly affect large-scale flow and thus the inferred viscosity structure. We use a transdimensional, hierarchical, Bayesian approach to solve the inverse problem, and our solutions for viscosity structure include an increase in viscosity below the base of the transition zone, in the shallow lower mantle. Using geoid dynamic response functions and an analysis of the correlation between the observed geoid and mantle structure, we demonstrate the underlying reason for this inference. Finally, we present a new family of solutions in which the data uncertainty is accounted for using covariance matrices associated with the mantle structure models.

Advanced stress analysis methods applicable to turbine engine structures

NASA Technical Reports Server (NTRS)

Pian, Theodore H. H.

1991-01-01

The following tasks on the study of advanced stress analysis methods applicable to turbine engine structures are described: (1) constructions of special elements which contain traction-free circular boundaries; (2) formulation of new version of mixed variational principles and new version of hybrid stress elements; (3) establishment of methods for suppression of kinematic deformation modes; (4) construction of semiLoof plate and shell elements by assumed stress hybrid method; and (5) elastic-plastic analysis by viscoplasticity theory using the mechanical subelement model.

Constructional and Conceptual Composition

ERIC Educational Resources Information Center

Dodge, Ellen Kirsten

2010-01-01

Goldberg's (1995) recognition that, in addition to various word-level constructions, sentences also instantiate meaningful argument structure constructions enables a non-polysemy-based analysis of various verb 'alternations' (Levin 1993). In such an analysis, meaning variations associated with the use of the same verb in different argument…

Estimation of the genetic diversity in tetraploid alfalfa populations based on RAPD markers for breeding purposes.

PubMed

Nagl, Nevena; Taski-Ajdukovic, Ksenija; Barac, Goran; Baburski, Aleksandar; Seccareccia, Ivana; Milic, Dragan; Katic, Slobodan

2011-01-01

Alfalfa is an autotetraploid, allogamous and heterozygous forage legume, whose varieties are synthetic populations. Due to the complex nature of the species, information about genetic diversity of germplasm used in any alfalfa breeding program is most beneficial. The genetic diversity of five alfalfa varieties, involved in progeny tests at Institute of Field and Vegetable Crops, was characterized based on RAPD markers. A total of 60 primers were screened, out of which 17 were selected for the analysis of genetic diversity. A total of 156 polymorphic bands were generated, with 10.6 bands per primer. Number and percentage of polymorphic loci, effective number of alleles, expected heterozygosity and Shannon's information index were used to estimate genetic variation. Variety Zuzana had the highest values for all tested parameters, exhibiting the highest level of variation, whereas variety RSI 20 exhibited the lowest. Analysis of molecular variance (AMOVA) showed that 88.39% of the total genetic variation was attributed to intra-varietal variance. The cluster analysis for individual samples and varieties revealed differences in their population structures: variety Zuzana showed a very high level of genetic variation, Banat and Ghareh were divided in subpopulations, while Pecy and RSI 20 were relatively uniform. Ways of exploiting the investigated germplasm in the breeding programs are suggested in this paper, depending on their population structure and diversity. The RAPD analysis shows potential to be applied in analysis of parental populations in semi-hybrid alfalfa breeding program in both, development of new homogenous germplasm, and identification of promising, complementary germplasm.

Fractal And Multi-fractal Analysis Of The Hydraulic Property Variations Of Karst Aquifers

NASA Astrophysics Data System (ADS)

Majone, B.; Bellin, A.; Borsato, A.

Karst aquifers are very heterogeneous systems with hydraulic property variations acting at several continuous and discrete scales, as a result of the fact that macro- structural elements, such as faults and karst channels, and fractures are intertwined in a complex, and largely unknown, manner. Many experimental studies on karst springs showed that the recession limb of the typical storm hydrograph can be divided into several regions with different decreasing rate, suggesting that the discharge is com- posed of contributions experiencing different travel times. Despite the importance of karst aquifers as a source of fresh water for most Mediterranean countries fostered the attention of scientists and practitioners, the mechanisms controlling runoff production in such a complex subsurface environment need to be further explored. A detailed sur- vey, lasting for one year and conducted by the Museo Tridentino di Scienze Naturali of Trento, represents a unique opportunity to analyze the imprint of hydraulic prop- erty variations on the hydrological signal recorded at the spring of Prese Val, located in the Dolomiti group near Trento. Data include water discharge (Q), temperature (T) and electric conductivity of water (E). Analysis of the data revealed that the power spectrum of E scales as 1/f, with slightly, but significantly, smaller than 1. The scaling nature of the E-signal has been confirmed by rescaled range analysis of the time series. Since the electric conductivity is proportional to the concentration of ions in the spring water, which increases with the residence time, one may conclude that the fractal structure of the E signal is the consequence of a similar structure in the hydraulic property variations. This finding confirms previous results of Kirchner et al. (2000), who reported a similar behavior for chloride concentration in the streamflow of three small Welsh catchments. A more detailed analysis revealed that E and T are both multifractal signals suggesting that transport is controlled by hydraulic property variations interesting several scales of variability. However, the travel time distribution is also shaped by the spatial variability of the dissolution rate and of the rainfall, as well as by the occurrence of rate limited dissolution processes. These phenomena may conspire to hide the imprint of the hydraulic property variations on the observed signal, complicating the inference of the geostatistical model of hydraulic property variations from the E signal. The discharge at Prese Val shows a multiscale power spectrum with convexity directed upward, such that the low frequency, long range, contributions to discharge are characterized by a much smaller slope than the high frequency contri- butions, which are characterized by much shorter travel times. This interpretation is consistent with the overall structure of the karst aquifers which is composed of the intertwined arrangement of macro-structures, such as faults and karstic channels, and small-scale diffused fractures, the latter showing a fractal dimension much smaller than that of the former.

Temperature-Dependent Second Shell Interference in the First Shell Analysis of Crystalline InP X-ray Absorption Spectroscopy Data

NASA Astrophysics Data System (ADS)

Schnohr, Claudia S.; Araujo, Leandro L.; Ridgway, Mark C.

2014-09-01

Analysing only the first nearest neighbour (NN) scattering signal is a commonly used and often successful way to treat extended X-ray absorption fine structure data. However, using temperature-dependent measurements of InP as an example, we demonstrate how this approach can lead to erroneous first NN structural parameters in systems with a weak first but strong second NN scatterer. In such cases, particularly low temperature data may suffer from an overlap of first and second NN scattering signals caused by the Fourier transformation (FT) even if the dominant peaks appear to be well separated. The first NN structural parameters then vary as a function of the FT settings if only the first NN scattering contribution is considered in the analysis. Although this variation is small, it can also lead to significant differences in other calculated properties such as the Einstein temperature. We demonstrate that these variations can be avoided either by choosing an appropriate FT window or by including the scattering contributions of higher shells in the analysis. The latter is achieved by a path fitting approach and yields structural parameters independent of the FT settings used.

Deuterium Labeling Together with Contrast Variation Small-angle Neutron Scattering Suggests How Skp Captures and Releases Unfolded Outer Membrane Proteins

PubMed Central

Zaccai, Nathan R.; Sandlin, Clifford W.; Hoopes, James T.; Curtis, Joseph E.; Fleming, Patrick J.; Fleming, Karen G.; Krueger, Susan

2016-01-01

In gram-negative bacteria, the chaperone protein Skp forms specific and stable complexes with membrane proteins while they are transported across the periplasm to the outer membrane. The jellyfish-like architecture of Skp is similar to the eukaryotic and archeal prefoldins and the mitochondrial Tim chaperones, that is α-helical ‘tentacles’ extend from a β-strand ‘body’ to create an internal cavity. Contrast variation small-angle neutron scattering (SANS) experiments on Skp alone in solution and bound in two different complexes to unfolded outer membrane proteins (uOMPs), OmpA and OmpW, demonstrate that the helical tentacles of Skp bind their substrate in a clamp-like mechanism in a conformation similar to that previously observed in the apo crystal structure of Skp. Deuteration of the uOMP component combined with contrast variation analysis allowed the shapes of Skp and uOMP as well as the location of uOMP with respect to Skp to be determined in both complexes. This represents unique information that could not be obtained without deuterium labeling of the uOMPs. The data yield the first direct structural evidence that the α-helical Skp tentacles move closer together on binding its substrate and that the structure of Skp is different when binding different uOMPs. This work presents, by example, a tutorial on performing SANS experiments using both deuterium labeling and contrast variation, including SANS theory, sample preparation, data collection, sample quality validation, data analysis and structure modeling. PMID:26791979

Deuterium Labeling Together with Contrast Variation Small-Angle Neutron Scattering Suggests How Skp Captures and Releases Unfolded Outer Membrane Proteins.

PubMed

Zaccai, Nathan R; Sandlin, Clifford W; Hoopes, James T; Curtis, Joseph E; Fleming, Patrick J; Fleming, Karen G; Krueger, Susan

2016-01-01

In Gram-negative bacteria, the chaperone protein Skp forms specific and stable complexes with membrane proteins while they are transported across the periplasm to the outer membrane. The jellyfish-like architecture of Skp is similar to the eukaryotic and archaeal prefoldins and the mitochondrial Tim chaperones, that is the α-helical "tentacles" extend from a β-strand "body" to create an internal cavity. Contrast variation small-angle neutron scattering (SANS) experiments on Skp alone in solution and bound in two different complexes to unfolded outer membrane proteins (uOMPs), OmpA and OmpW, demonstrate that the helical tentacles of Skp bind their substrate in a clamp-like mechanism in a conformation similar to that previously observed in the apo crystal structure of Skp. Deuteration of the uOMP component combined with contrast variation analysis allowed the shapes of Skp and uOMP as well as the location of uOMP with respect to Skp to be determined in both complexes. This represents unique information that could not be obtained without deuterium labeling of the uOMPs. The data yield the first direct structural evidence that the α-helical Skp tentacles move closer together on binding its substrate and that the structure of Skp is different when binding different uOMPs. This work presents, by example, a tutorial on performing SANS experiments using both deuterium labeling and contrast variation, including SANS theory, sample preparation, data collection, sample quality validation, data analysis, and structure modeling. © 2016 Elsevier Inc. All rights reserved.

Population genetic analysis of Bromus tectorum (Poaceae) indicates recent range expansion may be facilitated by specialist genotypes

Treesearch

Keith R. Merrill; Susan E. Meyer; Craig E. Coleman

2012-01-01

The mechanisms for range expansion in invasive species depend on how genetic variation is structured in the introduced range. This study examined neutral genetic variation in the invasive annual grass Bromus tectorum in the Intermountain Western United States. Patterns of microsatellite (SSR) genotype distribution in this highly inbreeding species were used to make...

Monitoring temporal microstructural variations of skeletal muscle tissues by multispectral Mueller matrix polarimetry

NASA Astrophysics Data System (ADS)

Dong, Yang; He, Honghui; He, Chao; Ma, Hui

2017-02-01

Mueller matrix polarimetry is a powerful tool for detecting microscopic structures, therefore can be used to monitor physiological changes of tissue samples. Meanwhile, spectral features of scattered light can also provide abundant microstructural information of tissues. In this paper, we take the 2D multispectral backscattering Mueller matrix images of bovine skeletal muscle tissues, and analyze their temporal variation behavior using multispectral Mueller matrix parameters. The 2D images of the Mueller matrix elements are reduced to the multispectral frequency distribution histograms (mFDHs) to reveal the dominant structural features of the muscle samples more clearly. For quantitative analysis, the multispectral Mueller matrix transformation (MMT) parameters are calculated to characterize the microstructural variations during the rigor mortis and proteolysis processes of the skeletal muscle tissue samples. The experimental results indicate that the multispectral MMT parameters can be used to judge different physiological stages for bovine skeletal muscle tissues in 24 hours, and combining with the multispectral technique, the Mueller matrix polarimetry and FDH analysis can monitor the microstructural variation features of skeletal muscle samples. The techniques may be used for quick assessment and quantitative monitoring of meat qualities in food industry.

Marine stratocumulus structure

NASA Technical Reports Server (NTRS)

Cahalan, Robert F.; Snider, Jack B.

1989-01-01

Thirty-three Landsat TM scenes of California stratocumulus cloud fields were acquired as part of the FIRE Marine Stratocumulus Intensive Field Observations in July 1987. They exhibit a wide variety of stratocumulus structures. Analysis has so far focused upon the July 7 scene, in which aircraft from NASA, NCAR, and the British Meteorological Office repeatedly gathered data across a stratocumulus-fair weather cumulus transition. The aircraft soundings validate the cloud base temperature threshold determined by spatial coherence analysis of the TM thermal band. Brightness variations in the stratocumulus region exhibit a -5/3 power-law decrease of the wavenumber spectra for scales larger than the cloud thickness, about 200 m, changing to a -3 power at smaller scales. Observations by an upward-looking three-channel microwave radiometer on San Nicolas Island also show the -5/3 power-law in total integrated liquid water, suggesting that the largest-scale TM brightness variations are primarily due to variations in the liquid water. The Kolmogorov 5/3 power suggests that for some purposes liquid water in turbulent stratocumulus clouds may be treated as a passive scalar, simply reflecting variations in vertical velocity. This may be tested using the velocities measured by the aircraft.

Survival analysis of infected mice reveals pathogenic variations in the genome of avian H1N1 viruses.

PubMed

Koçer, Zeynep A; Fan, Yiping; Huether, Robert; Obenauer, John; Webby, Richard J; Zhang, Jinghui; Webster, Robert G; Wu, Gang

2014-12-12

Most influenza pandemics have been caused by H1N1 viruses of purely or partially avian origin. Here, using Cox proportional hazard model, we attempt to identify the genetic variations in the whole genome of wild-type North American avian H1N1 influenza A viruses that are associated with their virulence in mice by residue variations, host origins of virus (Anseriformes-ducks or Charadriiformes-shorebirds), and host-residue interactions. In addition, through structural modeling, we predicted that several polymorphic sites associated with pathogenicity were located in structurally important sites, especially in the polymerase complex and NS genes. Our study introduces a new approach to identify pathogenic variations in wild-type viruses circulating in the natural reservoirs and ultimately to understand their infectious risks to humans as part of risk assessment efforts towards the emergence of future pandemic strains.

Constraints on a possible variation of the fine structure constant from galaxy cluster data

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

Holanda, R.F.L.; Landau, S.J.; Sánchez G, I.E.

2016-05-01

We propose a new method to probe a possible time evolution of the fine structure constant α from X-ray and Sunyaev-Zel'dovich measurements of the gas mass fraction ( f {sub gas}) in galaxy clusters. Taking into account a direct relation between variations of α and violations of the distance-duality relation, we discuss constraints on α for a class of dilaton runaway models. Although not yet competitive with bounds from high- z quasar absorption systems, our constraints, considering a sample of 29 measurements of f {sub gas}, in the redshift interval 0.14 < z < 0.89, provide an independent estimate ofmore » α variation at low and intermediate redshifts. Furthermore, current and planned surveys will provide a larger amount of data and thus allow to improve the limits on α variation obtained in the present analysis.« less

Systems definition study for shuttle demonstration flights of large space structures. Volume 3: Thermal analyses

NASA Technical Reports Server (NTRS)

1979-01-01

the development of large space structure technology is discussed. A detailed thermal analysis of a model space fabricated 1 meter beam is presented. Alternative thermal coatings are evaluated, and deflections, stresses, and stiffness variations resulting from flight orientations and solar conditions are predicted.

Constraining possible variations of the fine structure constant in strong gravitational fields with the Kα iron line

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

Bambi, Cosimo, E-mail: bambi@fudan.edu.cn

2014-03-01

In extensions of general relativity and in theories aiming at unifying gravity with the forces of the Standard Model, the value of the ''fundamental constants'' is often determined by the vacuum expectation value of new fields, which may thus change in different backgrounds. Variations of fundamental constants with respect to the values measured today in laboratories on Earth are expected to be more evident on cosmological timescales and/or in strong gravitational fields. In this paper, I show that the analysis of the Kα iron line observed in the X-ray spectrum of black holes can potentially be used to probe themore » fine structure constant α in gravitational potentials relative to Earth of Δφ ≈ 0.1. At present, systematic effects not fully under control prevent to get robust and stringent bounds on possible variations of the value of α with this technique, but the fact that current data can be fitted with models based on standard physics already rules out variations of the fine structure constant larger than some percent.« 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.

A mechanistic insight into the amyloidogenic structure of hIAPP peptide revealed from sequence analysis and molecular dynamics simulation.

PubMed

Chakraborty, Sandipan; Chatterjee, Barnali; Basu, Soumalee

2012-07-01

A collective approach of sequence analysis, phylogenetic tree and in silico prediction of amyloidogenecity using bioinformatics tools have been used to correlate the observed species-specific variations in IAPP sequences with the amyloid forming propensity. Observed substitution patterns indicate that probable changes in local hydrophobicity are instrumental in altering the aggregation propensity of the peptide. In particular, residues at 17th, 22nd and 23rd positions of the IAPP peptide are found to be crucial for amyloid formation. Proline25 primarily dictates the observed non-amyloidogenecity in rodents. Furthermore, extensive molecular dynamics simulation of 0.24 μs have been carried out with human IAPP (hIAPP) fragment 19-27, the portion showing maximum sequence variation across different species, to understand the native folding characteristic of this region. Principal component analysis in combination with free energy landscape analysis illustrates a four residue turn spanning from residue 22 to 25. The results provide a structural insight into the intramolecular β-sheet structure of amylin which probably is the template for nucleation of fibril formation and growth, a pathogenic feature of type II diabetes. Copyright © 2012 Elsevier B.V. All rights reserved.

Temperature induced distortions in space telescope mirrors

NASA Technical Reports Server (NTRS)

Nied, H. F.; Rudmann, A. A.

1993-01-01

In this paper, it is illustrated how measured instantaneous coefficients of thermal expansion (CTE) can be accurately taken into account when modeling the structural behavior of space based optical systems. In particular, the importance of including CTE spatial variations in the analysis of optical elements is emphasized. A comparison is made between the CTE's of three optical materials commonly used in the construction of space mirrors (ULE, Zerodur, and beryllium). The overall impact that selection of any one of these materials has on thermal distortions is briefly discussed. As an example of how temperature dependent spatial variations in thermal strain can be accurately incorporated in the thermo-structural analysis of a precision optical system, a finite element model is developed, which is used to estimate the thermally induced distortions in the Hubble Space Telescope's (HST) primary mirror. In addition to the structural analysis, the optical aberrations due to thermally induced distortions are also examined. These calculations indicate that thermal distortions in HST's primary mirror contribute mainly to defocus error with a relatively small contribution to spherical aberration.

Probabilistic Structural Analysis Methods (PSAM) for Select Space Propulsion System Components

NASA Technical Reports Server (NTRS)

1999-01-01

Probabilistic Structural Analysis Methods (PSAM) are described for the probabilistic structural analysis of engine components for current and future space propulsion systems. Components for these systems are subjected to stochastic thermomechanical launch loads. Uncertainties or randomness also occurs in material properties, structural geometry, and boundary conditions. Material property stochasticity, such as in modulus of elasticity or yield strength, exists in every structure and is a consequence of variations in material composition and manufacturing processes. Procedures are outlined for computing the probabilistic structural response or reliability of the structural components. The response variables include static or dynamic deflections, strains, and stresses at one or several locations, natural frequencies, fatigue or creep life, etc. Sample cases illustrates how the PSAM methods and codes simulate input uncertainties and compute probabilistic response or reliability using a finite element model with probabilistic methods.

Intragenomic sequence variation at the ITS1 - ITS2 region and at the 18S and 28S nuclear ribosomal DNA genes of the New Zealand mud snail, Potamopyrgus antipodarum (Hydrobiidae: mollusca)

USGS Publications Warehouse

Hoy, Marshal S.; Rodriguez, Rusty J.

2013-01-01

Molecular genetic analysis was conducted on two populations of the invasive non-native New Zealand mud snail (Potamopyrgus antipodarum), one from a freshwater ecosystem in Devil's Lake (Oregon, USA) and the other from an ecosystem of higher salinity in the Columbia River estuary (Hammond Harbor, Oregon, USA). To elucidate potential genetic differences between the two populations, three segments of nuclear ribosomal DNA (rDNA), the ITS1-ITS2 regions and the 18S and 28S rDNA genes were cloned and sequenced. Variant sequences within each individual were found in all three rDNA segments. Folding models were utilized for secondary structure analysis and results indicated that there were many sequences which contained structure-altering polymorphisms, which suggests they could be nonfunctional pseudogenes. In addition, analysis of molecular variance (AMOVA) was used for hierarchical analysis of genetic variance to estimate variation within and among populations and within individuals. AMOVA revealed significant variation in the ITS region between the populations and among clones within individuals, while in the 5.8S rDNA significant variation was revealed among individuals within the two populations. High levels of intragenomic variation were found in the ITS regions, which are known to be highly variable in many organisms. More interestingly, intragenomic variation was also found in the 18S and 28S rDNA, which has rarely been observed in animals and is so far unreported in Mollusca. We postulate that in these P. antipodarum populations the effects of concerted evolution are diminished due to the fact that not all of the rDNA genes in their polyploid genome should be essential for sustaining cellular function. This could lead to a lessening of selection pressures, allowing mutations to accumulate in some copies, changing them into variant sequences.                   

A molecular analysis of African lion (Panthera leo) mating structure and extra-group paternity in Etosha National Park.

PubMed

Lyke, M M; Dubach, J; Briggs, M B

2013-05-01

The recent incorporation of molecular methods into analyses of social and mating systems has provided evidence that mating patterns often differ from those predicted by group social organization. Based on field studies and paternity analyses at a limited number of sites, African lions are predicted to exhibit a strict within-pride mating system. Extra-group paternity has not been previously reported in African lions; however, observations of extra-group associations among lions inhabiting Etosha National Park in Namibia suggest deviation from the predicted within-pride mating pattern. We analysed variation in 14 microsatellite loci in a population of 164 African lions in Etosha National Park. Genetic analysis was coupled with demographic and observational data to examine pride structure, relatedness and extra-group paternity (EGP). EGP was found to occur in 57% of prides where paternity was analysed (n = 7), and the overall rate of EGP in this population was 41% (n = 34). Group sex ratio had a significant effect on the occurrence of EGP (P < 0.05), indicating that variation in pride-level social structure may explain intergroup variation in EGP. Prides with a lower male-to-female ratio were significantly more likely to experience EGP in this population. The results of this study challenge the current models of African lion mating systems and provide evidence that social structure may not reflect breeding structure in some social mammals. © 2013 Blackwell Publishing Ltd.

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.

Re-examination of population structure and phylogeography of hawksbill turtles in the wider Caribbean using longer mtDNA sequences.

PubMed

Leroux, Robin A; Dutton, Peter H; Abreu-Grobois, F Alberto; Lagueux, Cynthia J; Campbell, Cathi L; Delcroix, Eric; Chevalier, Johan; Horrocks, Julia A; Hillis-Starr, Zandy; Troëng, Sebastian; Harrison, Emma; Stapleton, Seth

2012-01-01

Management of the critically endangered hawksbill turtle in the Wider Caribbean (WC) has been hampered by knowledge gaps regarding stock structure. We carried out a comprehensive stock structure re-assessment of 11 WC hawksbill rookeries using longer mtDNA sequences, larger sample sizes (N = 647), and additional rookeries compared to previous surveys. Additional variation detected by 740 bp sequences between populations allowed us to differentiate populations such as Barbados-Windward and Guadeloupe (F (st) = 0.683, P < 0.05) that appeared genetically indistinguishable based on shorter 380 bp sequences. POWSIM analysis showed that longer sequences improved power to detect population structure and that when N < 30, increasing the variation detected was as effective in increasing power as increasing sample size. Geographic patterns of genetic variation suggest a model of periodic long-distance colonization coupled with region-wide dispersal and subsequent secondary contact within the WC. Mismatch analysis results for individual clades suggest a general population expansion in the WC following a historic bottleneck about 100 000-300 000 years ago. We estimated an effective female population size (N (ef)) of 6000-9000 for the WC, similar to the current estimated numbers of breeding females, highlighting the importance of these regional rookeries to maintaining genetic diversity in hawksbills. Our results provide a basis for standardizing future work to 740 bp sequence reads and establish a more complete baseline for determining stock boundaries in this migratory marine species. Finally, our findings illustrate the value of maintaining an archive of specimens for re-analysis as new markers become available.

Reliability Coupled Sensitivity Based Design Approach for Gravity Retaining Walls

NASA Astrophysics Data System (ADS)

Guha Ray, A.; Baidya, D. K.

2012-09-01

Sensitivity analysis involving different random variables and different potential failure modes of a gravity retaining wall focuses on the fact that high sensitivity of a particular variable on a particular mode of failure does not necessarily imply a remarkable contribution to the overall failure probability. The present paper aims at identifying a probabilistic risk factor ( R f ) for each random variable based on the combined effects of failure probability ( P f ) of each mode of failure of a gravity retaining wall and sensitivity of each of the random variables on these failure modes. P f is calculated by Monte Carlo simulation and sensitivity analysis of each random variable is carried out by F-test analysis. The structure, redesigned by modifying the original random variables with the risk factors, is safe against all the variations of random variables. It is observed that R f for friction angle of backfill soil ( φ 1 ) increases and cohesion of foundation soil ( c 2 ) decreases with an increase of variation of φ 1 , while R f for unit weights ( γ 1 and γ 2 ) for both soil and friction angle of foundation soil ( φ 2 ) remains almost constant for variation of soil properties. The results compared well with some of the existing deterministic and probabilistic methods and found to be cost-effective. It is seen that if variation of φ 1 remains within 5 %, significant reduction in cross-sectional area can be achieved. But if the variation is more than 7-8 %, the structure needs to be modified. Finally design guidelines for different wall dimensions, based on the present approach, are proposed.

Reliability Analysis of Retaining Walls Subjected to Blast Loading by Finite Element Approach

NASA Astrophysics Data System (ADS)

GuhaRay, Anasua; Mondal, Stuti; Mohiuddin, Hisham Hasan

2018-02-01

Conventional design methods adopt factor of safety as per practice and experience, which are deterministic in nature. The limit state method, though not completely deterministic, does not take into account effect of design parameters, which are inherently variable such as cohesion, angle of internal friction, etc. for soil. Reliability analysis provides a measure to consider these variations into analysis and hence results in a more realistic design. Several studies have been carried out on reliability of reinforced concrete walls and masonry walls under explosions. Also, reliability analysis of retaining structures against various kinds of failure has been done. However, very few research works are available on reliability analysis of retaining walls subjected to blast loading. Thus, the present paper considers the effect of variation of geotechnical parameters when a retaining wall is subjected to blast loading. However, it is found that the variation of geotechnical random variables does not have a significant effect on the stability of retaining walls subjected to blast loading.

Stress analysis in curved composites due to thermal loading

NASA Astrophysics Data System (ADS)

Polk, Jared Cornelius

Many structures in aircraft, cars, trucks, ships, machines, tools, bridges, and buildings, consist of curved sections. These sections vary from straight line segments that have curvature at either one or both ends, segments with compound curvatures, segments with two mutually perpendicular curvatures or Gaussian curvatures, and segments with a simple curvature. With the advancements made in multi-purpose composites over the past 60 years, composites slowly but steadily have been appearing in these various vehicles, compound structures, and buildings. These composite sections provide added benefits over isotropic, polymeric, and ceramic materials by generally having a higher specific strength, higher specific stiffnesses, longer fatigue life, lower density, possibilities in reduction of life cycle and/or acquisition cost, and greater adaptability to intended function of structure via material composition and geometry. To be able to design and manufacture a safe composite laminate or structure, it is imperative that the stress distributions, their causes, and effects are thoroughly understood in order to successfully accomplish mission objectives and manufacture a safe and reliable composite. The objective of the thesis work is to expand upon the knowledge of simply curved composite structures by exploring and ascertaining all pertinent parameters, phenomenon, and trends in stress variations in curved laminates due to thermal loading. The simply curved composites consist of composites with one radius of curvature throughout the span of the specimen about only one axis. Analytical beam theory, classical lamination theory, and finite element analysis were used to ascertain stress variations in a flat, isotropic beam. An analytical method was developed to ascertain the stress variations in an isotropic, simply curved beam under thermal loading that is under both free-free and fixed-fixed constraint conditions. This is the first such solution to Author's best knowledge of such a problem. It was ascertained and proven that the general, non-modified (original) version of classical lamination theory cannot be used for an analytical solution for a simply curved beam or any other structure that would require rotations of laminates out their planes in space. Finite element analysis was used to ascertain stress variations in a simply curved beam. It was verified that these solutions reduce to the flat beam solutions as the radius of curvature of the beams tends to infinity. MATLAB was used to conduct the classical lamination theory numerical analysis. A MATLAB program was written to conduct the finite element analysis for the flat and curved beams, isotropic and composite. It does not require incompatibility techniques used in mechanics of isotropic materials for indeterminate structures that are equivalent to fixed-beam problems. Finally, it has the ability to enable the user to define and create unique elements not accessible in commercial software, and modify finite element procedures to take advantage of new paradigms.

The relationship between observational scale and explained variance in benthic communities

PubMed Central

Flood, Roger D.; Frisk, Michael G.; Garza, Corey D.; Lopez, Glenn R.; Maher, Nicole P.

2018-01-01

This study addresses the impact of spatial scale on explaining variance in benthic communities. In particular, the analysis estimated the fraction of community variation that occurred at a spatial scale smaller than the sampling interval (i.e., the geographic distance between samples). This estimate is important because it sets a limit on the amount of community variation that can be explained based on the spatial configuration of a study area and sampling design. Six benthic data sets were examined that consisted of faunal abundances, common environmental variables (water depth, grain size, and surficial percent cover), and sonar backscatter treated as a habitat proxy (categorical acoustic provinces). Redundancy analysis was coupled with spatial variograms generated by multiscale ordination to quantify the explained and residual variance at different spatial scales and within and between acoustic provinces. The amount of community variation below the sampling interval of the surveys (< 100 m) was estimated to be 36–59% of the total. Once adjusted for this small-scale variation, > 71% of the remaining variance was explained by the environmental and province variables. Furthermore, these variables effectively explained the spatial structure present in the infaunal community. Overall, no scale problems remained to compromise inferences, and unexplained infaunal community variation had no apparent spatial structure within the observational scale of the surveys (> 100 m), although small-scale gradients (< 100 m) below the observational scale may be present. PMID:29324746

Global analysis of saliva as a source of bacterial genes for insights into human population structure and migration studies.

PubMed

Henne, Karsten; Li, Jing; Stoneking, Mark; Kessler, Olga; Schilling, Hildegard; Sonanini, Anne; Conrads, Georg; Horz, Hans-Peter

2014-08-22

The genetic diversity of the human microbiome holds great potential for shedding light on the history of our ancestors. Helicobacter pylori is the most prominent example as its analysis allowed a fine-scale resolution of past migration patterns including some that could not be distinguished using human genetic markers. However studies of H. pylori require stomach biopsies, which severely limits the number of samples that can be analysed. By focussing on the house-keeping gene gdh (coding for the glucose-6-phosphate dehydrogenase), on the virulence gene gtf (coding for the glucosyltransferase) of mitis-streptococci and on the 16S-23S rRNA internal transcribed spacer (ITS) region of the Fusobacterium nucleatum/periodonticum-group we here tested the hypothesis that bacterial genes from human saliva have the potential for distinguishing human populations. Analysis of 10 individuals from each of seven geographic regions, encompassing Africa, Asia and Europe, revealed that the genes gdh and ITS exhibited the highest number of polymorphic sites (59% and 79%, respectively) and most OTUs (defined at 99% identity) were unique to a given country. In contrast, the gene gtf had the lowest number of polymorphic sites (21%), and most OTUs were shared among countries. Most of the variation in the gdh and ITS genes was explained by the high clonal diversity within individuals (around 80%) followed by inter-individual variation of around 20%, leaving the geographic region as providing virtually no source of sequence variation. Conversely, for gtf the variation within individuals accounted for 32%, between individuals for 57% and among geographic regions for 11%. This geographic signature persisted upon extension of the analysis to four additional locations from the American continent. Pearson correlation analysis, pairwise Fst-cluster analysis as well as UniFrac analyses consistently supported a tree structure in which the European countries clustered tightly together and branched with American countries and South Africa, to the exclusion of Asian countries and the Congo. This study shows that saliva harbours protein-coding bacterial genes that are geographically structured, and which could potentially be used for addressing previously unresolved human migration events.

The utility of protein structure as a predictor of site-wise dN/dS varies widely among HIV-1 proteins.

PubMed

Meyer, Austin G; Wilke, Claus O

2015-10-06

Protein structure acts as a general constraint on the evolution of viral proteins. One widely recognized structural constraint explaining evolutionary variation among sites is the relative solvent accessibility (RSA) of residues in the folded protein. In influenza virus, the distance from functional sites has been found to explain an additional portion of the evolutionary variation in the external antigenic proteins. However, to what extent RSA and distance from a reference site in the protein can be used more generally to explain protein adaptation in other viruses and in the different proteins of any given virus remains an open question. To address this question, we have carried out an analysis of the distribution and structural predictors of site-wise dN/dS in HIV-1. Our results indicate that the distribution of dN/dS in HIV follows a smooth gamma distribution, with no special enrichment or depletion of sites with dN/dS at or above one. The variation in dN/dS can be partially explained by RSA and distance from a reference site in the protein, but these structural constraints do not act uniformly among the different HIV-1 proteins. Structural constraints are highly predictive in just one of the three enzymes and one of three structural proteins in HIV-1. For these two proteins, the protease enzyme and the gp120 structural protein, structure explains between 30 and 40% of the variation in dN/dS. Finally, for the gp120 protein of the receptor-binding complex, we also find that glycosylation sites explain just 2% of the variation in dN/dS and do not explain gp120 evolution independently of either RSA or distance from the apical surface. © 2015 The Author(s).

Language and Its Structure: Some Fundamental Linguistic Concepts.

ERIC Educational Resources Information Center

Langacker, Ronald W.

Intended for people with little or no training in linguistics, this book initially deals with such basic concepts as the definition of linguistics, the nature of language, and the linguistic variations within a society. The discussion then moves to a more detailed, non-historical analysis of language structure, focusing on lexical items,…

[Study on discrimination of varieties of fire resistive coating for steel structure based on near-infrared spectroscopy].

PubMed

Xue, Gang; Song, Wen-qi; Li, Shu-chao

2015-01-01

In order to achieve the rapid identification of fire resistive coating for steel structure of different brands in circulating, a new method for the fast discrimination of varieties of fire resistive coating for steel structure by means of near infrared spectroscopy was proposed. The raster scanning near infrared spectroscopy instrument and near infrared diffuse reflectance spectroscopy were applied to collect the spectral curve of different brands of fire resistive coating for steel structure and the spectral data were preprocessed with standard normal variate transformation(standard normal variate transformation, SNV) and Norris second derivative. The principal component analysis (principal component analysis, PCA)was used to near infrared spectra for cluster analysis. The analysis results showed that the cumulate reliabilities of PC1 to PC5 were 99. 791%. The 3-dimentional plot was drawn with the scores of PC1, PC2 and PC3 X 10, which appeared to provide the best clustering of the varieties of fire resistive coating for steel structure. A total of 150 fire resistive coating samples were divided into calibration set and validation set randomly, the calibration set had 125 samples with 25 samples of each variety, and the validation set had 25 samples with 5 samples of each variety. According to the principal component scores of unknown samples, Mahalanobis distance values between each variety and unknown samples were calculated to realize the discrimination of different varieties. The qualitative analysis model for external verification of unknown samples is a 10% recognition ration. The results demonstrated that this identification method can be used as a rapid, accurate method to identify the classification of fire resistive coating for steel structure and provide technical reference for market regulation.

Sequencing of a Patient with Balanced Chromosome Abnormalities and Neurodevelopmental Disease Identifies Disruption of Multiple High Risk Loci by Structural Variation

PubMed Central

Blake, Jonathon; Riddell, Andrew; Theiss, Susanne; Gonzalez, Alexis Perez; Haase, Bettina; Jauch, Anna; Janssen, Johannes W. G.; Ibberson, David; Pavlinic, Dinko; Moog, Ute; Benes, Vladimir; Runz, Heiko

2014-01-01

Balanced chromosome abnormalities (BCAs) occur at a high frequency in healthy and diseased individuals, but cost-efficient strategies to identify BCAs and evaluate whether they contribute to a phenotype have not yet become widespread. Here we apply genome-wide mate-pair library sequencing to characterize structural variation in a patient with unclear neurodevelopmental disease (NDD) and complex de novo BCAs at the karyotype level. Nucleotide-level characterization of the clinically described BCA breakpoints revealed disruption of at least three NDD candidate genes (LINC00299, NUP205, PSMD14) that gave rise to abnormal mRNAs and could be assumed as disease-causing. However, unbiased genome-wide analysis of the sequencing data for cryptic structural variation was key to reveal an additional submicroscopic inversion that truncates the schizophrenia- and bipolar disorder-associated brain transcription factor ZNF804A as an equally likely NDD-driving gene. Deep sequencing of fluorescent-sorted wild-type and derivative chromosomes confirmed the clinically undetected BCA. Moreover, deep sequencing further validated a high accuracy of mate-pair library sequencing to detect structural variants larger than 10 kB, proposing that this approach is powerful for clinical-grade genome-wide structural variant detection. Our study supports previous evidence for a role of ZNF804A in NDD and highlights the need for a more comprehensive assessment of structural variation in karyotypically abnormal individuals and patients with neurocognitive disease to avoid diagnostic deception. PMID:24625750

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.

Evaluating structural connectomics in relation to different Q-space sampling techniques.

PubMed

Rodrigues, Paulo; Prats-Galino, Alberto; Gallardo-Pujol, David; Villoslada, Pablo; Falcon, Carles; Prckovska, Vesna

2013-01-01

Brain networks are becoming forefront research in neuroscience. Network-based analysis on the functional and structural connectomes can lead to powerful imaging markers for brain diseases. However, constructing the structural connectome can be based upon different acquisition and reconstruction techniques whose information content and mutual differences has not yet been properly studied in a unified framework. The variations of the structural connectome if not properly understood can lead to dangerous conclusions when performing these type of studies. In this work we present evaluation of the structural connectome by analysing and comparing graph-based measures on real data acquired by the three most important Diffusion Weighted Imaging techniques: DTI, HARDI and DSI. We thus come to several important conclusions demonstrating that even though the different techniques demonstrate differences in the anatomy of the reconstructed fibers the respective connectomes show variations of 20%.

The L530R variation associated with recurrent kidney stones impairs the structure and function of TRPV5.

PubMed

Wang, Lingyun; Holmes, Ross P; Peng, Ji-Bin

2017-10-21

TRPV5 is a Ca 2+ -selective channel that plays a key role in the reabsorption of Ca 2+ ions in the kidney. Recently, a rare L530R variation (rs757494578) of TRPV5 was found to be associated with recurrent kidney stones in a founder population. However, it was unclear to what extent this variation alters the structure and function of TRPV5. To evaluate the function and expression of the TRPV5 variant, Ca 2+ uptake in Xenopus oocytes and western blot analysis were performed. The L530R variation abolished the Ca 2+ uptake activity of TRPV5 in Xenopus oocytes. The variant protein was expressed with drastic reduction in complex glycosylation. To assess the structural effects of this L530R variation, TRPV5 was modeled based on the crystal structure of TRPV6 and molecular dynamics simulations were carried out. Simulation results showed that the L530R variation disrupts the hydrophobic interaction between L530 and L502, damaging the secondary structure of transmembrane domain 5. The variation also alters its interaction with membrane lipid molecules. Compared to the electroneutral L530, the positively charged R530 residue shifts the surface electrostatic potential towards positive. R530 is attracted to the negatively charged phosphate group rather than the hydrophobic carbon atoms of membrane lipids. This shifts the pore helix where R530 is located and the D542 residue in the Ca 2+ -selective filter towards the surface of the membrane. These alterations may lead to misfolding of TRPV5, reduction in translocation of the channel to the plasma membrane and/or impaired Ca 2+ transport function of the channel, and ultimately disrupt TRPV5-mediated Ca 2+ reabsorption. Copyright © 2017 Elsevier Inc. All rights reserved.

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.

Statistical Analysis of CMC Constituent and Processing Data

NASA Technical Reports Server (NTRS)

Fornuff, Jonathan

2004-01-01

Ceramic Matrix Composites (CMCs) are the next "big thing" in high-temperature structural materials. In the case of jet engines, it is widely believed that the metallic superalloys currently being utilized for hot structures (combustors, shrouds, turbine vanes and blades) are nearing their potential limits of improvement. In order to allow for increased turbine temperatures to increase engine efficiency, material scientists have begun looking toward advanced CMCs and SiC/SiC composites in particular. Ceramic composites provide greater strength-to-weight ratios at higher temperatures than metallic alloys, but at the same time require greater challenges in micro-structural optimization that in turn increases the cost of the material as well as increases the risk of variability in the material s thermo-structural behavior. to model various potential CMC engine materials and examines the current variability in these properties due to variability in component processing conditions and constituent materials; then, to see how processing and constituent variations effect key strength, stiffness, and thermal properties of the finished components. Basically, this means trying to model variations in the component s behavior by knowing what went into creating it. inter-phase and manufactured by chemical vapor infiltration (CVI) and melt infiltration (MI) were considered. Examinations of: (1) the percent constituents by volume, (2) the inter-phase thickness, (3) variations in the total porosity, and (4) variations in the chemical composition of the Sic fiber are carried out and modeled using various codes used here at NASA-Glenn (PCGina, NASALife, CEMCAN, etc...). The effects of these variations and the ranking of their respective influences on the various thermo-mechanical material properties are studied and compared to available test data. The properties of the materials as well as minor changes to geometry are then made to the computer model and the detrimental effects observed using statistical analysis software. The ultimate purpose of this study is to determine what variations in material processing can lead to the most critical changes in the materials property. The work I have taken part in this summer explores, in general, the key properties needed In this study SiC/SiC composites of varying architectures, utilizing a boron-nitride (BN)

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

Meisner, Ludmila, E-mail: llm@ispms.tsc.ru; Meisner, Stanislav, E-mail: msn@ispms.tsc.ru; Mironov, Yurii, E-mail: myp@ispms.tsc.ru

The paper considers the effects arising on X-ray diffraction patterns taken in different diffraction geometries and how these effects can be interpreted to judge structural states in NiTi near-surface regions after electron and ion beam treatment. It is shown that qualitative and quantitative analysis of phase composition, lattice parameters of main phases, elastic stress states, and their in-depth variation requires X-ray diffraction patterns in both symmetric Bragg–Brentano and asymmetric Lambot–Vassamilleta geometries with variation in X-ray wavelengths and imaging conditions (with and with no β-filter). These techniques of structural phase analysis are more efficient when the thickness of modified NiTi surfacemore » layers is 1–10 μm (after electron beam treatment) and requires special imaging conditions when the thickness of modified NiTi surface layers is no greater than 1 μm (after ion beam treatment)« less

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.

Network structure and travel time perception.

PubMed

Parthasarathi, Pavithra; Levinson, David; Hochmair, Hartwig

2013-01-01

The purpose of this research is to test the systematic variation in the perception of travel time among travelers and relate the variation to the underlying street network structure. Travel survey data from the Twin Cities metropolitan area (which includes the cities of Minneapolis and St. Paul) is used for the analysis. Travelers are classified into two groups based on the ratio of perceived and estimated commute travel time. The measures of network structure are estimated using the street network along the identified commute route. T-test comparisons are conducted to identify statistically significant differences in estimated network measures between the two traveler groups. The combined effect of these estimated network measures on travel time is then analyzed using regression models. The results from the t-test and regression analyses confirm the influence of the underlying network structure on the perception of travel time.

Social support and anomie: a multilevel analysis of anomie in Europe and North America.

PubMed

Liqun Cao; Ruohui Zhao; Ling Ren; Zhao, Jihong Solomon

2010-08-01

On the basis of the reasoning of social support theory, the authors examine the macro effect of social support on anomie at the individual level. Data from international surveys have documented wide variation in anomie across nations, but to what extent this variation among nations can be contributed to structural characteristics has not been explored before. Using hierarchical linear modeling techniques to sort out the effects of structural context and personal characteristics on anomie across 31 European and North American nations, the authors test the hypothesis that variation in social support at the national level is inversely related to individuals' sense of anomie. The study results support the hypothesis that structural characteristics of a nation, such as social support and population growth, influence individuals' sense of anomie. At the individual level, the results are consistent with Merton's predictions about anomie and the reasoning of social support theory. Policy implication is discussed within the limitations of data.

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.

Variation effect on the insecticide activity of DDT analogues. A chemometric approach

NASA Astrophysics Data System (ADS)

Itoh, S.; Nagashima, U.

2002-08-01

We investigated a variation effect on the insecticide activity of DDT analogues by using the first principles electronic structure calculations and the neural network analysis. It has been found that the charge distribution at the specific atomic sites in the DDT molecule is related to their toxicity. This approach can contribute to designing a new insecticide and a new harmlessness process of the DDT analogues.

Geochemical differentiation processes for arc magma of the Sengan volcanic cluster, Northeastern Japan, constrained from principal component analysis

NASA Astrophysics Data System (ADS)

Ueki, Kenta; Iwamori, Hikaru

2017-10-01

In this study, with a view of understanding the structure of high-dimensional geochemical data and discussing the chemical processes at work in the evolution of arc magmas, we employed principal component analysis (PCA) to evaluate the compositional variations of volcanic rocks from the Sengan volcanic cluster of the Northeastern Japan Arc. We analyzed the trace element compositions of various arc volcanic rocks, sampled from 17 different volcanoes in a volcanic cluster. The PCA results demonstrated that the first three principal components accounted for 86% of the geochemical variation in the magma of the Sengan region. Based on the relationships between the principal components and the major elements, the mass-balance relationships with respect to the contributions of minerals, the composition of plagioclase phenocrysts, geothermal gradient, and seismic velocity structure in the crust, the first, the second, and the third principal components appear to represent magma mixing, crystallizations of olivine/pyroxene, and crystallizations of plagioclase, respectively. These represented 59%, 20%, and 6%, respectively, of the variance in the entire compositional range, indicating that magma mixing accounted for the largest variance in the geochemical variation of the arc magma. Our result indicated that crustal processes dominate the geochemical variation of magma in the Sengan volcanic cluster.

Structural behavior of composites with progressive fracture

NASA Technical Reports Server (NTRS)

Minnetyan, L.; Murthy, P. L. N.; Chamis, C. C.

1989-01-01

The objective of the study is to unify several computational tools developed for the prediction of progressive damage and fracture with efforts for the prediction of the overall response of damaged composite structures. In particular, a computational finite element model for the damaged structure is developed using a computer program as a byproduct of the analysis of progressive damage and fracture. Thus, a single computational investigation can predict progressive fracture and the resulting variation in structural properties of angleplied composites.

The influence of the focus position on laser machining and laser micro-structuring monocrystalline diamond surface

NASA Astrophysics Data System (ADS)

Wu, Mingtao; Guo, Bing; Zhao, Qingliang; Fan, Rongwei; Dong, Zhiwei; Yu, Xin

2018-06-01

Micro-structured surface on diamond is widely used in microelectronics, optical elements, MEMS and NEMS components, ultra-precision machining tools, etc. The efficient micro-structuring of diamond material is still a challenging task. In this article, the influence of the focus position on laser machining and laser micro-structuring monocrystalline diamond surface were researched. At the beginning, the ablation threshold and its incubation effect of monocrystalline diamond were determined and discussed. As the accumulated laser pulses ranged from 40 to 5000, the laser ablation threshold decreased from 1.48 J/cm2 to 0.97 J/cm2. Subsequently, the variation of the ablation width and ablation depth in laser machining were studied. With enough pulse energy, the ablation width mainly depended on the laser propagation attributes while the ablation depth was a complex function of the focus position. Raman analysis was used to detect the variation of the laser machined diamond surface after the laser machining experiments. Graphite formation was discovered on the machined diamond surface and graphitization was enhanced after the defocusing quantity exceeded 45 μm. At last, several micro-structured surfaces were successfully fabricated on diamond surface with the defined micro-structure patterns and structuring ratios just by adjusting the defocusing quantity. The experimental structuring ratio was consistent with the theoretical analysis.

Redesigning of a Canard Control Surface of an Advanced Fighter Aircraft: Effect on Buckling and Aerodynamic Behavior

NASA Astrophysics Data System (ADS)

Shrivastava, Sachin; Mohite, P. M.

2015-01-01

A redesign of canard control-surface of an advanced all-metallic fighter aircraft was carried out by using carbon fibre composite (CFC) for ribs and panels. In this study ply-orientations of CFC structure are optimized using a Genetic-Algorithm (GA) with an objective function to have minimum failure index (FI) according to Tsai-Wu failure criterion. The redesigned CFC structure was sufficiently strong to withstand aerodynamic loads from stress and deflection points of view. Now, in the present work CFC canard structure has been studied for its buckling strength in comparison to existing metallic design. In this study, the existing metallic design was found to be weak in buckling. Upon a detailed investigation, it was revealed that there are reported failures in the vicinity of zones where initial buckling modes are excited as predicted by the finite element based buckling analysis. In view of buckling failures, the redesigned CFC structure is sufficiently reinforced with stringers at specific locations. After providing reinforcements against buckling, the twist and the camber variations of the airfoil are checked and compared with existing structure data. Finally, the modal analysis has been carried out to compare the variation in excitation frequency due to material change. The CFC structure thus redesigned is safe from buckling and aerodynamic aspects as well.

Genetic Structure of Bluefin Tuna in the Mediterranean Sea Correlates with Environmental Variables

PubMed Central

Riccioni, Giulia; Stagioni, Marco; Landi, Monica; Ferrara, Giorgia; Barbujani, Guido; Tinti, Fausto

2013-01-01

Background Atlantic Bluefin Tuna (ABFT) shows complex demography and ecological variation in the Mediterranean Sea. Genetic surveys have detected significant, although weak, signals of population structuring; catch series analyses and tagging programs identified complex ABFT spatial dynamics and migration patterns. Here, we tested the hypothesis that the genetic structure of the ABFT in the Mediterranean is correlated with mean surface temperature and salinity. Methodology We used six samples collected from Western and Central Mediterranean integrated with a new sample collected from the recently identified easternmost reproductive area of Levantine Sea. To assess population structure in the Mediterranean we used a multidisciplinary framework combining classical population genetics, spatial and Bayesian clustering methods and a multivariate approach based on factor analysis. Conclusions FST analysis and Bayesian clustering methods detected several subpopulations in the Mediterranean, a result also supported by multivariate analyses. In addition, we identified significant correlations of genetic diversity with mean salinity and surface temperature values revealing that ABFT is genetically structured along two environmental gradients. These results suggest that a preference for some spawning habitat conditions could contribute to shape ABFT genetic structuring in the Mediterranean. However, further studies should be performed to assess to what extent ABFT spawning behaviour in the Mediterranean Sea can be affected by environmental variation. PMID:24260341

A Variational Formulation for the Finite Element Analysis of Sound Wave Propagation in a Spherical Shell

NASA Technical Reports Server (NTRS)

Lebiedzik, Catherine

1995-01-01

Development of design tools to furnish optimal acoustic environments for lightweight aircraft demands the ability to simulate the acoustic system on a workstation. In order to form an effective mathematical model of the phenomena at hand, we have begun by studying the propagation of acoustic waves inside closed spherical shells. Using a fully-coupled fluid-structure interaction model based upon variational principles, we have written a finite element analysis program and are in the process of examining several test cases. Future investigations are planned to increase model accuracy by incorporating non-linear and viscous effects.

Beyond bilateral symmetry: geometric morphometric methods for any type of symmetry

PubMed Central

2011-01-01

Background Studies of symmetric structures have made important contributions to evolutionary biology, for example, by using fluctuating asymmetry as a measure of developmental instability or for investigating the mechanisms of morphological integration. Most analyses of symmetry and asymmetry have focused on organisms or parts with bilateral symmetry. This is not the only type of symmetry in biological shapes, however, because a multitude of other types of symmetry exists in plants and animals. For instance, some organisms have two axes of reflection symmetry (biradial symmetry; e.g. many algae, corals and flowers) or rotational symmetry (e.g. sea urchins and many flowers). So far, there is no general method for the shape analysis of these types of symmetry. Results We generalize the morphometric methods currently used for the shape analysis of bilaterally symmetric objects so that they can be used for analyzing any type of symmetry. Our framework uses a mathematical definition of symmetry based on the theory of symmetry groups. This approach can be used to divide shape variation into a component of symmetric variation among individuals and one or more components of asymmetry. We illustrate this approach with data from a colonial coral that has ambiguous symmetry and thus can be analyzed in multiple ways. Our results demonstrate that asymmetric variation predominates in this dataset and that its amount depends on the type of symmetry considered in the analysis. Conclusions The framework for analyzing symmetry and asymmetry is suitable for studying structures with any type of symmetry in two or three dimensions. Studies of complex symmetries are promising for many contexts in evolutionary biology, such as fluctuating asymmetry, because these structures can potentially provide more information than structures with bilateral symmetry. PMID:21958045

Acoustic, genetic and morphological variations within the katydid Gampsocleis sedakovii (Orthoptera, Tettigonioidea)

PubMed Central

Zhang, Xue; Wen, Ming; Li, Junjian; Zhu, Hui; Wang, Yinliang; Ren, Bingzhong

2015-01-01

Abstract In an attempt to explain the variation within this species and clarify the subspecies classification, an analysis of the genetic, calling songs, and morphological variations within the species Gampsocleis sedakovii is presented from Inner Mongolia, China. Recordings were compared of the male calling songs and analysis performed of selected acoustic variables. This analysis is combined with sequencing of mtDNA - COI and examination of morphological traits to perform cluster analyses. The trees constructed from different datasets were structurally similar, bisecting the six geographical populations studied. Based on two large branches in the analysis, the species Gampsocleis sedakovii was partitioned into two subspecies, Gampsocleis sedakovii sedakovii (Fischer von Waldheim, 1846) and Gampsocleis sedakovii obscura (Walker, 1869). Comparing all the traits, the individual of Elunchun (ELC) was the intermediate type in this species according to the acoustic, genetic, and morphological characteristics. This study provides evidence for insect acoustic signal divergence and the process of subspeciation. PMID:26692795

Facial Structure Predicts Sexual Orientation in Both Men and Women.

PubMed

Skorska, Malvina N; Geniole, Shawn N; Vrysen, Brandon M; McCormick, Cheryl M; Bogaert, Anthony F

2015-07-01

Biological models have typically framed sexual orientation in terms of effects of variation in fetal androgen signaling on sexual differentiation, although other biological models exist. Despite marked sex differences in facial structure, the relationship between sexual orientation and facial structure is understudied. A total of 52 lesbian women, 134 heterosexual women, 77 gay men, and 127 heterosexual men were recruited at a Canadian campus and various Canadian Pride and sexuality events. We found that facial structure differed depending on sexual orientation; substantial variation in sexual orientation was predicted using facial metrics computed by a facial modelling program from photographs of White faces. At the univariate level, lesbian and heterosexual women differed in 17 facial features (out of 63) and four were unique multivariate predictors in logistic regression. Gay and heterosexual men differed in 11 facial features at the univariate level, of which three were unique multivariate predictors. Some, but not all, of the facial metrics differed between the sexes. Lesbian women had noses that were more turned up (also more turned up in heterosexual men), mouths that were more puckered, smaller foreheads, and marginally more masculine face shapes (also in heterosexual men) than heterosexual women. Gay men had more convex cheeks, shorter noses (also in heterosexual women), and foreheads that were more tilted back relative to heterosexual men. Principal components analysis and discriminant functions analysis generally corroborated these results. The mechanisms underlying variation in craniofacial structure--both related and unrelated to sexual differentiation--may thus be important in understanding the development of sexual orientation.

Lateral variations in geologic structure and tectonic setting from remote sensing data

NASA Astrophysics Data System (ADS)

Alexander, S. S.

1983-05-01

The principal objective of this study was: (1) to assess the usefulness of remote sensing digital imagery, principally LANDSAT multispectral scanning (MSS) data, for inferring lateral variations in geologic structure and tectonic setting; and (2) to determine the extent to which these inferred variations correlate with observed variations in seismic excitation from underground nuclear explosion test sites in the Soviet Union. Soviet, French and U.S. test sites have been investigated to compare their geologic and tectonic responses as seen by LANDSAT. The characteristics of "granite' intrusive bodies exposed at Semipalatinsk (Degelen), North Africa (Hoggar), NTS (Climax stock), and an analog site in Maine (Mt. Katahdin), have been studied in detail. The tectonic stress field inferred from the tectonic release portion of seismic signatures of explosions in these three areas is compared with local and regional fracture patterns discernable from imagery. The usefulness of satellite synthetic aperture radar (SAR) to determine geologic conditions and delineate fault (fracture) patterns is demonstrated by the analysis of SEASAT data for an area in the eastern United States. Algorithms to enhance structural boundaries and to use textures to identify rock types were developed and applied to several test sites.

The Effects of Cognitive Style on Edmodo Users' Behaviour: A Structural Equation Modeling-Based Multi-Group Analysis

ERIC Educational Resources Information Center

Ursavas, Omer Faruk; Reisoglu, Ilknur

2017-01-01

Purpose: The purpose of this paper is to explore the validity of extended technology acceptance model (TAM) in explaining pre-service teachers' Edmodo acceptance and the variation of variables related to TAM among pre-service teachers having different cognitive styles. Design/methodology/approach: Structural equation modeling approach was used to…

Genetic Variation and Population Differentiation in a Medical Herb Houttuynia cordata in China Revealed by Inter-Simple Sequence Repeats (ISSRs)

PubMed Central

Wei, Lin; Wu, Xian-Jin

2012-01-01

Houttuynia cordata is an important traditional Chinese herb with unresolved genetics and taxonomy, which lead to potential problems in the conservation and utilization of the resource. Inter-simple sequence repeat (ISSR) markers were used to assess the level and distribution of genetic diversity in 226 individuals from 15 populations of H. cordata in China. ISSR analysis revealed low genetic variations within populations but high genetic differentiations among populations. This genetic structure probably mainly reflects the historical association among populations. Genetic cluster analysis showed that the basal clade is composed of populations from Southwest China, and the other populations have continuous and eastward distributions. The structure of genetic diversity in H. cordata demonstrated that this species might have survived in Southwest China during the glacial age, and subsequently experienced an eastern postglacial expansion. Based on the results of genetic analysis, it was proposed that as many as possible targeted populations for conservation be included. PMID:22942696

Genetic variation and population differentiation in a medical herb Houttuynia cordata in China revealed by inter-simple sequence repeats (ISSRs).

PubMed

Wei, Lin; Wu, Xian-Jin

2012-01-01

Houttuynia cordata is an important traditional Chinese herb with unresolved genetics and taxonomy, which lead to potential problems in the conservation and utilization of the resource. Inter-simple sequence repeat (ISSR) markers were used to assess the level and distribution of genetic diversity in 226 individuals from 15 populations of H. cordata in China. ISSR analysis revealed low genetic variations within populations but high genetic differentiations among populations. This genetic structure probably mainly reflects the historical association among populations. Genetic cluster analysis showed that the basal clade is composed of populations from Southwest China, and the other populations have continuous and eastward distributions. The structure of genetic diversity in H. cordata demonstrated that this species might have survived in Southwest China during the glacial age, and subsequently experienced an eastern postglacial expansion. Based on the results of genetic analysis, it was proposed that as many as possible targeted populations for conservation be included.

Genome Editing of Structural Variations: Modeling and Gene Correction.

PubMed

Park, Chul-Yong; Sung, Jin Jea; Kim, Dong-Wook

2016-07-01

The analysis of chromosomal structural variations (SVs), such as inversions and translocations, was made possible by the completion of the human genome project and the development of genome-wide sequencing technologies. SVs contribute to genetic diversity and evolution, although some SVs can cause diseases such as hemophilia A in humans. Genome engineering technology using programmable nucleases (e.g., ZFNs, TALENs, and CRISPR/Cas9) has been rapidly developed, enabling precise and efficient genome editing for SV research. Here, we review advances in modeling and gene correction of SVs, focusing on inversion, translocation, and nucleotide repeat expansion. Copyright © 2016 Elsevier Ltd. All rights reserved.

PREFACE: 36th Risø International Symposium on Materials Science

NASA Astrophysics Data System (ADS)

Fæster, S.; Hansen, N.; Hong, C.; Huang, X.; Jensen, D. Juul; Mishin, O. V.; Sun, J.; Yu, T.; Zhang, Y. B.

2015-08-01

The 36th Risø Symposium focuses on the effects of deformation-induced structural variations on annealing mechanisms. Although it is widely recognized that the processes occurring during annealing of deformed metals are determined by the local environment in which they occur, much of the current understanding, analysis and modelling is based on larger scale considerations. Recent detailed investigations of deformation microstructures have led to a paradigm shift in the way these structures are characterized and analyzed. It is now clear that deformation microstructures are hierarchical, with dislocations and deformation-induced boundaries subdividing the original grains. This subdivision means that there are variations in the crystallographic orientations and in the distribution of stored energy on the scale of the subdivision, which typically is on the micrometer, sub-micrometer or nanometer scale. Structural variations in this subdivision may also be present from grain to grain in polycrystalline materials, thereby introducing variations on the grain scale. Finally, processing may also introduce structural variations on even larger scales. There are thus structural variations at many length scales, all of which play an essential role in subsequent annealing processes and in property optimization. Recent advances in incorporating these structural variations into the understanding of annealing mechanisms and of how they affect the mechanical and physical properties of annealed metals and alloys are addressed in these Proceedings. The Proceedings contain 15 key-note and 46 contributed papers. The 36th Risø International Symposium on Materials Science is organized by the Section for Materials Science and Advanced Characterization, Department of Wind Energy, Technical University of Denmark (DTU). We would like to thank all those at DTU who assisted in the preparations for the Symposium. We appreciate additionally the help from the international advisory committee consisting of: R.D. Doherty, USA; F.J. Humphreys, UK; E Pereloma; T. Sakai, Japan; M. Sugiyama, Japan; Q. Liu, China; R.A. Vandermeer, USA; Y.T. Zhu, USA. We gratefully acknowledge financial support from the following foundations: Civilingeniør Frederik Leth Christiansens Almennyttige Fond, Fabrikant Mads Clausens Fond, Knud Højgaards Fond, Kraks Fond and Otto Mønsteds Fond.

Population genetic variation in the tree fern Alsophila spinulosa (Cyatheaceae): effects of reproductive strategy.

PubMed

Wang, Ting; Su, Yingjuan; Li, Yuan

2012-01-01

Essentially all ferns can perform both sexual and asexual reproduction. Their populations represent suitable study objects to test the population genetic effects of different reproductive systems. Using the diploid homosporous fern Alsophila spinulosa as an example species, the main purpose of this study was to assess the relative impact of sexual and asexual reproduction on the level and structure of population genetic variation. Inter-simple sequence repeats analysis was conducted on 140 individuals collected from seven populations (HSG, LCH, BPC, MPG, GX, LD, and ZHG) in China. Seventy-four polymorphic bands discriminated a total of 127 multilocus genotypes. Character compatibility analysis revealed that 50.0 to 70.0% of the genotypes had to be deleted in order to obtain a tree-like structure in the data set from populations HSG, LCH, MPG, BPC, GX, and LD; and there was a gradual decrease of conflict in the data set when genotypes with the highest incompatibility counts were successively deleted. In contrast, in population ZHG, only 33.3% of genotypes had to be removed to achieve complete compatibility in the data set, which showed a sharp decline in incompatibility upon the deletion of those genotypes. All populations examined possessed similar levels of genetic variation. Population ZHG was not found to be more differentiated than the other populations. Sexual recombination is the predominant source of genetic variation in most of the examined populations of A. spinulosa. However, somatic mutation contributes most to the genetic variation in population ZHG. This change of the primary mode of reproduction does not cause a significant difference in the population genetic composition. Character compatibility analysis represents an effective approach to separate the role of sexual and asexual components in shaping the genetic pattern of fern populations.

Long-term Variation of Ventilation System in the East Sea (Japan Sea) Revealed by Heat Content Change and Water Mass Analysis

NASA Astrophysics Data System (ADS)

Yoon, S.; Chang, K. I.; Kim, K. R.; Lobanov, V. B.

2016-02-01

The semi-enclosed East Sea (ES) is called a miniature ocean with its own thermohaline circulation characterized by the formation of deep and intermediate water masses in the Japan Basin, southward discharge of those subsurface water masses towards the Ulleung and Yamato basins, and northward heat transport by the Tsushima Warm Current in the upper layer. Reports have been given of rapid changes of physical and biogeochemical properties associated with its ventilation system. We present results on upper ocean heat content variations and changes in water mass structure and properties from the analysis of historical and most recent hydrographic data. The analysis of non-seasonal heat content (HCA) variations in the upper 500 m from 1976 to 2007 highlights the 2-year lagged in-phase decadal-scale HCA variations in the eastern and western ES until 1995 followed by uncorrelated variations between two regions thereafter with pronounced interannual variations. Long-term trend of HCA in the entire ES shows an increasing trend, but with a large increase in the eastern part and relatively weaker but statistically significant decrease in the western part. The thickness variation of water warmer than 10°C mainly contributes to the HCA variation. Analyses of upper circulation in conjunction with climate indices suggest the importance of the wind-stress curl pattern represented by the Western Pacific index in the western ES and the influence of the Siberian High in the eastern ES. The thickness and temperature variation of 1-5°C representing the East Sea Intermediate Water (ESIW) is relatively minor contributor to the HCA variation in the upper 500 m. However, the thickness (temperature) of the ESIW has been increased (decreased) in the entire ES since 1992, which implies that the formation of the ESIW has been activated in recent decades. To investigate water mass changes in deeper than 500 m, we use full-depth CTD data obtained from CREAMS expeditions from 1993 to 2015. Temperature deeper than 1000 m has been increased about 0.03°C during 20 years and the depth of deep salinity minimum depth which is the lower (upper) limit of the East Sea Central Water (Deep Water) has been deepened. Other characteristics of water mass structure and property changes will be presented.

Infrared thermography for examination of paper structure

NASA Astrophysics Data System (ADS)

Kiiskinen, Harri T.; Pakarinen, Pekka I.

1998-03-01

The paper industry has used IR cameras primarily for troubleshooting, where the most common examples include the examination of the condition of dryer fabrics and dryer cylinders and the analysis of moisture variations in a paper web. Another application extensively using IR thermography is non-destructive testing of composite materials. This paper presents some recently developed laboratory methods using an IR camera to examine paper structure. Specific areas include cockling, moisture content, thermal uniformity, mechanism of failure, and an analysis of the copying process.

Kinetic parameters and structural variations in Cu-Al-Mn and Cu-Al-Mn-Mg shape memory alloys

NASA Astrophysics Data System (ADS)

Canbay, Canan Aksu

2017-02-01

In this work polycrystalline Cu-Al-Mn and Cu-Al-Mn-Mg SMAs were fabricated by arc melting. The thermal analysis was made to determine the characteristic transformation temperatures of the samples and kinetic parameters. Also the effect of Mg on transformation temperatures and kinetic parameters detected. The structural analysis was made to designate the diffraction planes of martensite phase at room temperature and this was supported by optical measurement observations.

On the potential for the Partial Triadic Analysis to grasp the spatio-temporal variability of groundwater hydrochemistry

NASA Astrophysics Data System (ADS)

Gourdol, L.; Hissler, C.; Pfister, L.

2012-04-01

The Luxembourg sandstone aquifer is of major relevance for the national supply of drinking water in Luxembourg. The city of Luxembourg (20% of the country's population) gets almost 2/3 of its drinking water from this aquifer. As a consequence, the study of both the groundwater hydrochemistry, as well as its spatial and temporal variations, are considered as of highest priority. Since 2005, a monitoring network has been implemented by the Water Department of Luxembourg City, with a view to a more sustainable management of this strategic water resource. The data collected to date forms a large and complex dataset, describing spatial and temporal variations of many hydrochemical parameters. The data treatment issue is tightly connected to this kind of water monitoring programs and complex databases. Standard multivariate statistical techniques, such as principal components analysis and hierarchical cluster analysis, have been widely used as unbiased methods for extracting meaningful information from groundwater quality data and are now classically used in many hydrogeological studies, in particular to characterize temporal or spatial hydrochemical variations induced by natural and anthropogenic factors. But these classical multivariate methods deal with two-way matrices, usually parameters/sites or parameters/time, while often the dataset resulting from qualitative water monitoring programs should be seen as a datacube parameters/sites/time. Three-way matrices, such as the one we propose here, are difficult to handle and to analyse by classical multivariate statistical tools and thus should be treated with approaches dealing with three-way data structures. One possible analysis approach consists in the use of partial triadic analysis (PTA). The PTA was previously used with success in many ecological studies but never to date in the domain of hydrogeology. Applied to the dataset of the Luxembourg Sandstone aquifer, the PTA appears as a new promising statistical instrument for hydrogeologists, in particular to characterize temporal and spatial hydrochemical variations induced by natural and anthropogenic factors. This new approach for groundwater management offers potential for 1) identifying a common multivariate spatial structure, 2) untapping the different hydrochemical patterns and explaining their controlling factors and 3) analysing the temporal variability of this structure and grasping hydrochemical changes.

Multivariate statistical analysis of diffusion imaging parameters using partial least squares: Application to white matter variations in Alzheimer's disease.

PubMed

Konukoglu, Ender; Coutu, Jean-Philippe; Salat, David H; Fischl, Bruce

2016-07-01

Diffusion magnetic resonance imaging (dMRI) is a unique technology that allows the noninvasive quantification of microstructural tissue properties of the human brain in healthy subjects as well as the probing of disease-induced variations. Population studies of dMRI data have been essential in identifying pathological structural changes in various conditions, such as Alzheimer's and Huntington's diseases (Salat et al., 2010; Rosas et al., 2006). The most common form of dMRI involves fitting a tensor to the underlying imaging data (known as diffusion tensor imaging, or DTI), then deriving parametric maps, each quantifying a different aspect of the underlying microstructure, e.g. fractional anisotropy and mean diffusivity. To date, the statistical methods utilized in most DTI population studies either analyzed only one such map or analyzed several of them, each in isolation. However, it is most likely that variations in the microstructure due to pathology or normal variability would affect several parameters simultaneously, with differing variations modulating the various parameters to differing degrees. Therefore, joint analysis of the available diffusion maps can be more powerful in characterizing histopathology and distinguishing between conditions than the widely used univariate analysis. In this article, we propose a multivariate approach for statistical analysis of diffusion parameters that uses partial least squares correlation (PLSC) analysis and permutation testing as building blocks in a voxel-wise fashion. Stemming from the common formulation, we present three different multivariate procedures for group analysis, regressing-out nuisance parameters and comparing effects of different conditions. We used the proposed procedures to study the effects of non-demented aging, Alzheimer's disease and mild cognitive impairment on the white matter. Here, we present results demonstrating that the proposed PLSC-based approach can differentiate between effects of different conditions in the same region as well as uncover spatial variations of effects across the white matter. The proposed procedures were able to answer questions on structural variations such as: "are there regions in the white matter where Alzheimer's disease has a different effect than aging or similar effect as aging?" and "are there regions in the white matter that are affected by both mild cognitive impairment and Alzheimer's disease but with differing multivariate effects?" Copyright © 2016 Elsevier Inc. All rights reserved.

Multivariate Statistical Analysis of Diffusion Imaging Parameters using Partial Least Squares: Application to White Matter Variations in Alzheimer’s Disease

PubMed Central

Konukoglu, Ender; Coutu, Jean-Philippe; Salat, David H.; Fischl, Bruce

2016-01-01

Diffusion magnetic resonance imaging (dMRI) is a unique technology that allows the noninvasive quantification of microstructural tissue properties of the human brain in healthy subjects as well as the probing of disease-induced variations. Population studies of dMRI data have been essential in identifying pathological structural changes in various conditions, such as Alzheimer’s and Huntington’s diseases1,2. The most common form of dMRI involves fitting a tensor to the underlying imaging data (known as Diffusion Tensor Imaging, or DTI), then deriving parametric maps, each quantifying a different aspect of the underlying microstructure, e.g. fractional anisotropy and mean diffusivity. To date, the statistical methods utilized in most DTI population studies either analyzed only one such map or analyzed several of them, each in isolation. However, it is most likely that variations in the microstructure due to pathology or normal variability would affect several parameters simultaneously, with differing variations modulating the various parameters to differing degrees. Therefore, joint analysis of the available diffusion maps can be more powerful in characterizing histopathology and distinguishing between conditions than the widely used univariate analysis. In this article, we propose a multivariate approach for statistical analysis of diffusion parameters that uses partial least squares correlation (PLSC) analysis and permutation testing as building blocks in a voxel-wise fashion. Stemming from the common formulation, we present three different multivariate procedures for group analysis, regressing-out nuisance parameters and comparing effects of different conditions. We used the proposed procedures to study the effects of non-demented aging, Alzheimer’s disease and mild cognitive impairment on the white matter. Here, we present results demonstrating that the proposed PLSC-based approach can differentiate between effects of different conditions in the same region as well as uncover spatial variations of effects across the white matter. The proposed procedures were able to answer questions on structural variations such as: “are there regions in the white matter where Alzheimer’s disease has a different effect than aging or similar effect as aging?” and “are there regions in the white matter that are affected by both mild cognitive impairment and Alzheimer’s disease but with differing multivariate effects?” PMID:27103138

Exaggeration and suppression of iridescence: the evolution of two-dimensional butterfly structural colours

PubMed Central

Wickham, Shelley; Large, Maryanne C.J; Poladian, Leon; Jermiin, Lars S

2005-01-01

Many butterfly species possess ‘structural’ colour, where colour is due to optical microstructures found in the wing scales. A number of such structures have been identified in butterfly scales, including three variations on a simple multi-layer structure. In this study, we optically characterize examples of all three types of multi-layer structure, as found in 10 species. The optical mechanism of the suppression and exaggeration of the angle-dependent optical properties (iridescence) of these structures is described. In addition, we consider the phylogeny of the butterflies, and are thus able to relate the optical properties of the structures to their evolutionary development. By applying two different types of analysis, the mechanism of adaptation is addressed. A simple parsimony analysis, in which all evolutionary changes are given an equal weighting, suggests convergent evolution of one structure. A Dollo parsimony analysis, in which the evolutionary ‘cost’ of losing a structure is less than that of gaining it, implies that ‘latent’ structures can be reused. PMID:16849221

Variational asymptotic modeling of composite dimensionally reducible structures

NASA Astrophysics Data System (ADS)

Yu, Wenbin

A general framework to construct accurate reduced models for composite dimensionally reducible structures (beams, plates and shells) was formulated based on two theoretical foundations: decomposition of the rotation tensor and the variational asymptotic method. Two engineering software systems, Variational Asymptotic Beam Sectional Analysis (VABS, new version) and Variational Asymptotic Plate and Shell Analysis (VAPAS), were developed. Several restrictions found in previous work on beam modeling were removed in the present effort. A general formulation of Timoshenko-like cross-sectional analysis was developed, through which the shear center coordinates and a consistent Vlasov model can be obtained. Recovery relations are given to recover the asymptotic approximations for the three-dimensional field variables. A new version of VABS has been developed, which is a much improved program in comparison to the old one. Numerous examples are given for validation. A Reissner-like model being as asymptotically correct as possible was obtained for composite plates and shells. After formulating the three-dimensional elasticity problem in intrinsic form, the variational asymptotic method was used to systematically reduce the dimensionality of the problem by taking advantage of the smallness of the thickness. The through-the-thickness analysis is solved by a one-dimensional finite element method to provide the stiffnesses as input for the two-dimensional nonlinear plate or shell analysis as well as recovery relations to approximately express the three-dimensional results. The known fact that there exists more than one theory that is asymptotically correct to a given order is adopted to cast the refined energy into a Reissner-like form. A two-dimensional nonlinear shell theory consistent with the present modeling process was developed. The engineering computer code VAPAS was developed and inserted into DYMORE to provide an efficient and accurate analysis of composite plates and shells. Numerical results are compared with the exact solutions, and the excellent agreement proves that one can use VAPAS to analyze composite plates and shells efficiently and accurately. In conclusion, rigorous modeling approaches were developed for composite beams, plates and shells within a general framework. No such consistent and general treatment is found in the literature. The associated computer programs VABS and VAPAS are envisioned to have many applications in industry.

Decay assessment through thermographic analysis in architectural and archaeological heritage

NASA Astrophysics Data System (ADS)

Gomez-Heras, Miguel; Martinez-Perez, Laura; Fort, Rafael; Alvarez de Buergo, Monica

2010-05-01

Any exposed stone-built structure is subject to thermal variations due to daily, seasonal and secular environmental temperature changes. Surface temperature is a function of air temperature (due to convective heat transfer) and of infrared radiation received through insolation. While convective heat transfer homogenizes surface temperature, stone response to insolation is much more complex and the temporal and spatial temperature differences across structures are enhanced. Surface temperature in stone-built structures will be affected by orientation, sunlight inclination and the complex patterns of light and shadows generated by the often intricate morphology of historical artefacts and structures. Surface temperature will also be affected by different material properties, such as albedo, thermal conductivity, transparency and absorbance to infrared radiation of minerals and rocks. Moisture and the occurrence of salts will also be a factor affecting surface temperatures. Surface temperatures may as well be affected by physical disruptions of rocks due to differences in thermal inertia generated by cracks and other discontinuities. Thermography is a non-invasive, non-destructive technique that measures temperature variations on the surface of a material. With this technique, surface temperature rates of change and their spatial variations can be analysed. This analysis may be used not only to evaluate the incidence of thermal decay as a factor that generates or enhances stone decay, but also to detect and evaluate other factors that affect the state of conservation of architectural and archaeological heritage, as for example moisture, salts or mechanical disruptions.

High-frequency health data and spline functions.

PubMed

Martín-Rodríguez, Gloria; Murillo-Fort, Carlos

2005-03-30

Seasonal variations are highly relevant for health service organization. In general, short run movements of medical magnitudes are important features for managers in this field to make adequate decisions. Thus, the analysis of the seasonal pattern in high-frequency health data is an appealing task. The aim of this paper is to propose procedures that allow the analysis of the seasonal component in this kind of data by means of spline functions embedded into a structural model. In the proposed method, useful adaptions of the traditional spline formulation are developed, and the resulting procedures are capable of capturing periodic variations, whether deterministic or stochastic, in a parsimonious way. Finally, these methodological tools are applied to a series of daily emergency service demand in order to capture simultaneous seasonal variations in which periods are different.

Grey Matter Alterations Co-Localize with Functional Abnormalities in Developmental Dyslexia: An ALE Meta-Analysis

PubMed Central

Linkersdörfer, Janosch; Lonnemann, Jan; Lindberg, Sven; Hasselhorn, Marcus; Fiebach, Christian J.

2012-01-01

The neural correlates of developmental dyslexia have been investigated intensively over the last two decades and reliable evidence for a dysfunction of left-hemispheric reading systems in dyslexic readers has been found in functional neuroimaging studies. In addition, structural imaging studies using voxel-based morphometry (VBM) demonstrated grey matter reductions in dyslexics in several brain regions. To objectively assess the consistency of these findings, we performed activation likelihood estimation (ALE) meta-analysis on nine published VBM studies reporting 62 foci of grey matter reduction in dyslexic readers. We found six significant clusters of convergence in bilateral temporo-parietal and left occipito-temporal cortical regions and in the cerebellum bilaterally. To identify possible overlaps between structural and functional deviations in dyslexic readers, we conducted additional ALE meta-analyses of imaging studies reporting functional underactivations (125 foci from 24 studies) or overactivations (95 foci from 11 studies ) in dyslexics. Subsequent conjunction analyses revealed overlaps between the results of the VBM meta-analysis and the meta-analysis of functional underactivations in the fusiform and supramarginal gyri of the left hemisphere. An overlap between VBM results and the meta-analysis of functional overactivations was found in the left cerebellum. The results of our study provide evidence for consistent grey matter variations bilaterally in the dyslexic brain and substantial overlap of these structural variations with functional abnormalities in left hemispheric regions. PMID:22916214

A procedure for damage detection and localization of framed buildings based on curvature variation

NASA Astrophysics Data System (ADS)

Ditommaso, Rocco; Carlo Ponzo, Felice; Auletta, Gianluca; Iacovino, Chiara; Mossucca, Antonello; Nigro, Domenico; Nigro, Antonella

2014-05-01

Structural Health Monitoring and Damage Detection are topics of current interest in civil, mechanical and aerospace engineering. Damage Detection approach based on dynamic monitoring of structural properties over time has received a considerable attention in recent scientific literature of the last years. The basic idea arises from the observation that spectral properties, described in terms of the so-called modal parameters (eigenfrequencies, mode shapes, and modal damping), are functions of the physical properties of the structure (mass, energy dissipation mechanisms and stiffness). Structural damage exhibits its main effects in terms of stiffness and damping variation. As a consequence, a permanent dynamic monitoring system makes it possible to detect and, if suitably concentrated on the structure, to localize structural and non-structural damage occurred on the structure during a strong earthquake. In the last years many researchers are working to set-up new methodologies for Non-destructive Damage Evaluation (NDE) based on the variation of the dynamic behaviour of structures under seismic loads. Pandey et al. (1991) highlighted on the possibility to use the structural mode shapes to extract useful information for structural damage localization. In this paper a new procedure for damage detection on framed structures based on changes in modal curvature is proposed. The proposed approach is based on the use of Stockwell Transform, a special kind of integral transformation that become a powerful tool for nonlinear signal analysis and then to analyse the nonlinear behaviour of a general structure. Using this kind of approach, it is possible to use a band-variable filter (Ditommaso et al., 2012) to extract from a signal recorded on a structure (excited by an earthquake) the response related to a single mode of vibration for which the related frequency changes over time (if the structure is being damaged). İn general, by acting simultaneously in both frequency and time domain, it is possible to use the band-variable filter to extract the dynamic characteristics of a system that evolves over time. Aim of this paper is to show, through practical examples, how it is possible to identify and to localize damage on a structure comparing mode shapes and the related curvature variations over time. It is possible to demonstrate that mode curvature variation is strongly related with the damage occurred on a structure. This paper resumes the main outcomes retrieved from many numerical non linear dynamic models of reinforced concrete framed structures characterized by different geometric configurations and designed for gravity loads only. The numerical campaign was conducted using both natural and artificial accelerograms compatible with the Italian code. The main results of experimental shaking table tests carried out on a steel framed model are also showed to confirm the effectiveness of the proposed procedure. REFERENCES Ditommaso R., Mucciarelli M., Ponzo F. C. (2012). Analysis of non-stationary structural systems by using a band-variable filter. Bulletin of Earthquake Engineering. Volume 10, Number 3, pp. 895-911. DOI: 10.1007/s10518-012-9338-y. Pandey AK, Biswas M, Samman MM (1991) "Damage detection from changes in curvature mode shapes", Journal of Sound and Vibration, Vol. 145: Issue 2, pp. 321-332.

Impact of variational assimilation using multivariate background error covariances on the simulation of monsoon depressions over India

NASA Astrophysics Data System (ADS)

Dhanya, M.; Chandrasekar, A.

2016-02-01

The background error covariance structure influences a variational data assimilation system immensely. The simulation of a weather phenomenon like monsoon depression can hence be influenced by the background correlation information used in the analysis formulation. The Weather Research and Forecasting Model Data assimilation (WRFDA) system includes an option for formulating multivariate background correlations for its three-dimensional variational (3DVar) system (cv6 option). The impact of using such a formulation in the simulation of three monsoon depressions over India is investigated in this study. Analysis and forecast fields generated using this option are compared with those obtained using the default formulation for regional background error correlations (cv5) in WRFDA and with a base run without any assimilation. The model rainfall forecasts are compared with rainfall observations from the Tropical Rainfall Measurement Mission (TRMM) and the other model forecast fields are compared with a high-resolution analysis as well as with European Centre for Medium-Range Weather Forecasts (ECMWF) ERA-Interim reanalysis. The results of the study indicate that inclusion of additional correlation information in background error statistics has a moderate impact on the vertical profiles of relative humidity, moisture convergence, horizontal divergence and the temperature structure at the depression centre at the analysis time of the cv5/cv6 sensitivity experiments. Moderate improvements are seen in two of the three depressions investigated in this study. An improved thermodynamic and moisture structure at the initial time is expected to provide for improved rainfall simulation. The results of the study indicate that the skill scores of accumulated rainfall are somewhat better for the cv6 option as compared to the cv5 option for at least two of the three depression cases studied, especially at the higher threshold levels. Considering the importance of utilising improved flow-dependent correlation structures for efficient data assimilation, the need for more studies on the impact of background error covariances is obvious.

Effects of English admixture and geographic distance on anthropometric variation and genetic structure in 19th-century Ireland.

PubMed

Relethford, J H

1988-05-01

The analysis of anthropometric data often allows investigation of patterns of genetic structure in historical populations. This paper focuses on interpopulational anthropometric variation in seven populations in Ireland using data collected in the 1890s. The seven populations were located within a 120-km range along the west coast of Ireland and include islands and mainland isolates. Two of the populations (the Aran Islands and Inishbofin) have a known history of English admixture in earlier centuries. Ten anthropometric measures (head length, breadth, and height; nose length and breadth; bizygomatic and bigonial breadth; stature; hand length; and forearm length) on 259 adult Irish males were analyzed following age adjustment. Discriminant and canonical variates analysis were used to determine the degree and pattern of among-group variation. Mahalanobis' distance measure, D2, was computed between each pair of populations and compared to distance measures based on geographic distance and English admixture (a binary measure indicating whether either of a pair of populations had historical indications of admixture). In addition, surname frequencies were used to construct distance measures based on random isonymy. Correlations were computed between distance measures, and their probabilities were derived using the Mantel matrix permutation method. English admixture has the greatest effect on anthropometric variation among these populations, followed by geographic distance. The correlation between anthropometric distance and geographic distance is not significant (r = -0.081, P = .590), but the correlation of admixture and anthropometric distance is significant (r = 0.829, P = .047). When the two admixed populations are removed from the analysis the correlation between geographic and anthropometric distance becomes significant (r = 0.718, P = .025). Isonymy distance shows a significant correlation with geographic distance (r = 0.425, P = .046) but not with admixture distance (r = -0.052, P = .524). The fact that anthropometrics show past patterns of gene flow and surnames do not reflects the greater impact of stochastic processes on surnames, along with the continued extinction of surnames. This study shows that 1) anthropometrics can be extremely useful in assessing population structure and history, 2) differential gene flow into populations can have a major impact on local genetic structure, and 3) microevolutionary processes can have different effects on biological characters and surnames.

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

Regional-scale drivers of marine nematode distribution in Southern Ocean continental shelf sediments

NASA Astrophysics Data System (ADS)

Hauquier, Freija; Verleyen, Elie; Tytgat, Bjorn; Vanreusel, Ann

2018-07-01

Many marine meiofauna taxa seem to possess cosmopolitan species distributions, despite their endobenthic lifestyle and restricted long-distance dispersal capacities. In light of this paradox we used a metacommunity framework to study spatial turnover in free-living nematode distribution and assess the importance of local environmental conditions in explaining differences between communities in surface and subsurface sediments of the Southern Ocean continental shelf. We analysed nematode community structure in two sediment layers (0-3 cm and 3-5 cm) of locations maximum 2400 km apart. We first focused on a subset of locations to evaluate whether the genus level is sufficiently taxonomically fine-grained to study large-scale patterns in nematode community structure. We subsequently used redundancy and variation partitioning analyses to quantify the unique and combined effects of local environmental conditions and spatial descriptors on genus-level community composition. Macroecological patterns in community structure were highly congruent at the genus and species level. Nematode community composition was highly divergent between both depth strata, likely as a result of local abiotic conditions. Variation in community structure between the different regions largely stemmed from turnover (i.e. genus/species replacement) rather than nestedness (i.e. genus/species loss). The level of turnover among communities increased with geographic distance and was more pronounced in subsurface layers compared to surface sediments. Variation partitioning analysis revealed that both environmental and spatial predictors significantly explained variation in community structure. Moreover, the shared fraction of both sets of variables was high, which suggested a substantial amount of spatially structured environmental variation. Additionally, the effect of space independent of environment was much higher than the effect of environment independent of space, which shows the importance of including spatial descriptors in meiofauna and nematode community ecology. Large-scale assessment of free-living nematode diversity and abundance in the Southern Ocean shelf zone revealed strong horizontal and vertical spatial structuring in response to local environmental conditions, in combination with (most likely) dispersal limitation.

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.

Geographic variations of the bird-borne structural risk of West Nile virus circulation in Europe

PubMed Central

Durand, Benoit; Tran, Annelise; Balança, Gilles

2017-01-01

The structural risk of West Nile Disease results from the usual functioning of the socio-ecological system, which may favour the introduction of the pathogen, its circulation and the occurrence of disease cases. Its geographic variations result from the local interactions between three components: (i) reservoir hosts, (ii) vectors, both characterized by their diversity, abundance and competence, (iii) and the socio-economic context that impacts the exposure of human to infectious bites. We developed a model of bird-borne structural risk of West Nile Virus (WNV) circulation in Europe, and analysed the association between the geographic variations of this risk and the occurrence of WND human cases between 2002 and 2014. A meta-analysis of WNV serosurveys conducted in wild bird populations was performed to elaborate a model of WNV seropositivity in European bird species, considered a proxy for bird exposure to WNV. Several eco-ethological traits of bird species were linked to seropositivity and the statistical model adequately fitted species-specific seropositivity data (area under the ROC curve: 0.85). Combined with species distribution maps, this model allowed deriving geographic variations of the bird-borne structural risk of WNV circulation. The association between this risk, and the occurrence of WND human cases across the European Union was assessed. Geographic risk variations of bird-borne structural risk allowed predicting WND case occurrence in administrative districts of the EU with a sensitivity of 86% (95% CI: 0.79–0.92), and a specificity of 68% (95% CI: 0.66–0.71). Disentangling structural and conjectural health risks is important for public health managers as risk mitigation procedures differ according to risk type. The results obtained show promise for the prevention of WND in Europe. Combined with analyses of vector-borne structural risk, they should allow designing efficient and targeted prevention measures. PMID:29023472

Mutations in exons 10 and 11 of human glucokinase result in conformational variations in the active site of the structure contributing to poor substrate binding - explains hyperglycemia in type 2 diabetic patients.

PubMed

Yellapu, Nandakumar; Mahto, Manoj Kumar; Valasani, Koteswara Rao; Sarma, P V G K; Matcha, Bhaskar

2015-01-01

Mutations in the glucokinase (GK) gene play a critical role in the establishment of type 2 diabetes. In our earlier study, R308K mutation in GK in a clinically proven type 2 diabetic patient showed, structural and functional variations that contributed immensely to the hyperglycemic condition. In the extension of this work, a cohort of 30 patients with established type 2 diabetic condition were chosen and the exons 10 and 11 of GK were PCR-amplified and sequenced. The sequence alignment showed A379S, D400Y, E300A, E395A, E395G, H380N, I348N, L301M, M298I, M381G, M402R, R308K, R394P, R397S, and S398R mutations in 12 different patients. The structural analysis of these mutated GKs, showed a variable number of β-α-β units, hairpins, β-bulges, strands, helices, helix-helix interactions, β-turns, and γ-turns along with the RMSD variations when compared to wild-type GK. Molecular modeling studies revealed that the substrate showed variable binding orientations and could not fit into the active site of these mutated structures; moreover, it was expelled out of the conformations. Therefore, these structural variations in GK due to mutations could be one of the strongest reasons for the hyperglycemic levels in these type 2 diabetic patients.

Sequencing Insights into Microbial Communities in the Water and Sediments of Fenghe River, China.

PubMed

Lu, Sidan; Sun, Yujiao; Zhao, Xuan; Wang, Lei; Ding, Aizhong; Zhao, Xiaohui

2016-07-01

The connection between microbial community structure and spatial variation and pollution in river waters has been widely investigated. However, water and sediments together have rarely been explored. In this study, Illumina high-throughput sequencing was performed to analyze microbes in 24 water and sediment samples from natural to anthropogenic sources and from headstream to downstream areas. These data were used to assess variability in microbial community structure and diversity along in the Fenghe River, China. The relationship between bacterial diversity and environmental parameters was statistically analyzed. An average of 1682 operational taxonomic units was obtained. Microbial diversity increased from the headstream to downstream and tended to be greater in sediment compared with water. The water samples near the headstream endured relatively low Shannon and Chao1 indices. These diversity indices and the number of observed species in the water and sediment samples increase downstream. The parameters also differ in the two river tributaries. Community structures shift based on the extent of nitrogen pollution variation in the sediment and water samples. The four most dominant genera in the water community were Escherichia, Acinetobacter, Comamonadaceae, and Pseudomonas. In the sediments, the most dominant genera were Stramenopiles, Flavobacterium, Pseudomonas, and Comamonadaceae. The number of ammonia-oxidizing archaea in the headstream water slightly differed from that in the sediment but varied considerably in the downstream sediments. Statistical analysis showed that community variation is correlated with changes in ammonia nitrogen, total nitrogen, and nitrate nitrogen. This study identified different microbial community structures in river water and sediments. Overall this study emphasized the need to elucidate spatial variations in bacterial diversity in water and sediments associated with physicochemical gradients and to show the effects of such variation on waterborne microbial community structures.

Meter scale variation in shrub dominance and soil moisture structure Arctic arthropod communities

PubMed Central

Hansen, Oskar Liset Pryds; Bowden, Joseph J.; Treier, Urs A.; Normand, Signe; Høye, Toke

2016-01-01

The Arctic is warming at twice the rate of the rest of the world. This impacts Arctic species both directly, through increased temperatures, and indirectly, through structural changes in their habitats. Species are expected to exhibit idiosyncratic responses to structural change, which calls for detailed investigations at the species and community level. Here, we investigate how arthropod assemblages of spiders and beetles respond to variation in habitat structure at small spatial scales. We sampled transitions in shrub dominance and soil moisture between three different habitats (fen, dwarf shrub heath, and tall shrub tundra) at three different sites along a fjord gradient in southwest Greenland, using yellow pitfall cups. We identified 2,547 individuals belonging to 47 species. We used species richness estimation, indicator species analysis and latent variable modeling to examine differences in arthropod community structure in response to habitat variation at local (within site) and regional scales (between sites). We estimated species responses to the environment by fitting species-specific generalized linear models with environmental covariates. Species assemblages were segregated at the habitat and site level. Each habitat hosted significant indicator species, and species richness and diversity were significantly lower in fen habitats. Assemblage patterns were significantly linked to changes in soil moisture and vegetation height, as well as geographic location. We show that meter-scale variation among habitats affects arthropod community structure, supporting the notion that the Arctic tundra is a heterogeneous environment. To gain sufficient insight into temporal biodiversity change, we require studies of species distributions detailing species habitat preferences. PMID:27478709

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.

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

Network Structure and Travel Time Perception

PubMed Central

Parthasarathi, Pavithra; Levinson, David; Hochmair, Hartwig

2013-01-01

The purpose of this research is to test the systematic variation in the perception of travel time among travelers and relate the variation to the underlying street network structure. Travel survey data from the Twin Cities metropolitan area (which includes the cities of Minneapolis and St. Paul) is used for the analysis. Travelers are classified into two groups based on the ratio of perceived and estimated commute travel time. The measures of network structure are estimated using the street network along the identified commute route. T-test comparisons are conducted to identify statistically significant differences in estimated network measures between the two traveler groups. The combined effect of these estimated network measures on travel time is then analyzed using regression models. The results from the t-test and regression analyses confirm the influence of the underlying network structure on the perception of travel time. PMID:24204932

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.

Population Genetic Structure of Glycyrrhiza inflata B. (Fabaceae) Is Shaped by Habitat Fragmentation, Water Resources and Biological Characteristics.

PubMed

Yang, Lulu; Chen, Jianjun; Hu, Weiming; Yang, Tianshun; Zhang, Yanjun; Yukiyoshi, Tamura; Zhou, Yanyang; Wang, Ying

2016-01-01

Habitat fragmentation, water resources and biological characteristics are important factors that shape the genetic structure and geographical distribution of desert plants. Analysis of the relationships between these factors and population genetic variation should help to determine the evolutionary potential and conservation strategies for genetic resources for desert plant populations. As a traditional Chinese herb, Glycyrrhiza inflata B. (Fabaceae) is restricted to the fragmented desert habitat in China and has undergone a dramatic decline due to long-term over-excavation. Determining the genetic structure of the G. inflata population and identifying a core collection could help with the development of strategies to conserve this species. We investigated the genetic variation of 25 G. inflata populations based on microsatellite markers. A high level of population genetic divergence (FST = 0.257), population bottlenecks, reduced gene flow and moderate genetic variation (HE = 0.383) were detected. The genetic distances between the populations significantly correlated with the geographical distances, and this suggests that habitat fragmentation has driven a special genetic structure of G. inflata in China through isolation by distance. STRUCTURE analysis showed that G. inflata populations were structured into three clusters and that the populations belonged to multiple water systems, which suggests that water resources were related to the genetic structure of G. inflata. In addition, the biological characteristics of the perennial species G. inflata, such as its long-lived seeds, asexual reproduction, and oasis ecology, may be related to its resistance to habitat fragmentation. A core collection of G. inflata, that included 57 accessions was further identified, which captured the main allelic diversity of G. inflata. Recent habitat fragmentation has accelerated genetic divergence. The population genetic structure of G. inflata has been shaped by habitat fragmentation, water resources and biological characteristics. This genetic information and core collection will facilitate the conservation of wild germplasm and breeding of this Chinese medicinal plant.

Population Genetic Structure of Glycyrrhiza inflata B. (Fabaceae) Is Shaped by Habitat Fragmentation, Water Resources and Biological Characteristics

PubMed Central

Yang, Lulu; Chen, Jianjun; Hu, Weiming; Yang, Tianshun; Zhang, Yanjun; Yukiyoshi, Tamura; Zhou, Yanyang; Wang, Ying

2016-01-01

Background Habitat fragmentation, water resources and biological characteristics are important factors that shape the genetic structure and geographical distribution of desert plants. Analysis of the relationships between these factors and population genetic variation should help to determine the evolutionary potential and conservation strategies for genetic resources for desert plant populations. As a traditional Chinese herb, Glycyrrhiza inflata B. (Fabaceae) is restricted to the fragmented desert habitat in China and has undergone a dramatic decline due to long-term over-excavation. Determining the genetic structure of the G. inflata population and identifying a core collection could help with the development of strategies to conserve this species. Results We investigated the genetic variation of 25 G. inflata populations based on microsatellite markers. A high level of population genetic divergence (FST = 0.257), population bottlenecks, reduced gene flow and moderate genetic variation (HE = 0.383) were detected. The genetic distances between the populations significantly correlated with the geographical distances, and this suggests that habitat fragmentation has driven a special genetic structure of G. inflata in China through isolation by distance. STRUCTURE analysis showed that G. inflata populations were structured into three clusters and that the populations belonged to multiple water systems, which suggests that water resources were related to the genetic structure of G. inflata. In addition, the biological characteristics of the perennial species G. inflata, such as its long-lived seeds, asexual reproduction, and oasis ecology, may be related to its resistance to habitat fragmentation. A core collection of G. inflata, that included 57 accessions was further identified, which captured the main allelic diversity of G. inflata. Conclusions Recent habitat fragmentation has accelerated genetic divergence. The population genetic structure of G. inflata has been shaped by habitat fragmentation, water resources and biological characteristics. This genetic information and core collection will facilitate the conservation of wild germplasm and breeding of this Chinese medicinal plant. PMID:27711241

Contemporary and historical evolutionary processes interact to shape patterns of within-lake phenotypic divergences in polyphenic pumpkinseed sunfish, Lepomis gibbosus.

PubMed

Weese, Dylan J; Ferguson, Moira M; Robinson, Beren W

2012-03-01

Historical and contemporary evolutionary processes can both contribute to patterns of phenotypic variation among populations of a species. Recent studies are revealing how interactions between historical and contemporary processes better explain observed patterns of phenotypic divergence than either process alone. Here, we investigate the roles of evolutionary history and adaptation to current environmental conditions in structuring phenotypic variation among polyphenic populations of sunfish inhabiting 12 postglacial lakes in eastern North America. The pumpkinseed sunfish polyphenism includes sympatric ecomorphs specialized for littoral or pelagic lake habitats. First, we use population genetic methods to test the evolutionary independence of within-lake phenotypic divergences of ecomorphs and to describe patterns of genetic structure among lake populations that clustered into three geographical groupings. We then used multivariate analysis of covariance (MANCOVA) to partition body shape variation (quantified with geometric morphometrics) among the effects of evolutionary history (reflecting phenotypic variation among genetic clusters), the shared phenotypic response of all populations to alternate habitats within lakes (reflecting adaptation to contemporary conditions), and unique phenotypic responses to habitats within lakes nested within genetic clusters. All effects had a significant influence on body form, but the effects of history and the interaction between history and contemporary habitat were larger than contemporary processes in structuring phenotypic variation. This highlights how divergence can be better understood against a known backdrop of evolutionary history.

Joint source based analysis of multiple brain structures in studying major depressive disorder

NASA Astrophysics Data System (ADS)

Ramezani, Mahdi; Rasoulian, Abtin; Hollenstein, Tom; Harkness, Kate; Johnsrude, Ingrid; Abolmaesumi, Purang

2014-03-01

We propose a joint Source-Based Analysis (jSBA) framework to identify brain structural variations in patients with Major Depressive Disorder (MDD). In this framework, features representing position, orientation and size (i.e. pose), shape, and local tissue composition are extracted. Subsequently, simultaneous analysis of these features within a joint analysis method is performed to generate the basis sources that show signi cant di erences between subjects with MDD and those in healthy control. Moreover, in a cross-validation leave- one-out experiment, we use a Fisher Linear Discriminant (FLD) classi er to identify individuals within the MDD group. Results show that we can classify the MDD subjects with an accuracy of 76% solely based on the information gathered from the joint analysis of pose, shape, and tissue composition in multiple brain structures.

Analysis and Design of Variable Stiffness Composite Cylinders

NASA Technical Reports Server (NTRS)

Tatting, Brian F.; Guerdal, Zafer

1998-01-01

An investigation of the possible performance improvements of thin circular cylindrical shells through the use of the variable stiffness concept is presented. The variable stiffness concept implies that the stiffness parameters change spatially throughout the structure. This situation is achieved mainly through the use of curvilinear fibers within a fiber-reinforced composite laminate, though the possibility of thickness variations and discrete stiffening elements is also allowed. These three mechanisms are incorporated into the constitutive laws for thin shells through the use of Classical Lamination Theory. The existence of stiffness variation within the structure warrants a formulation of the static equilibrium equations from the most basic principles. The governing equations include sufficient detail to correctly model several types of nonlinearity, including the formation of a nonlinear shell boundary layer as well as the Brazier effect due to nonlinear bending of long cylinders. Stress analysis and initial buckling estimates are formulated for a general variable stiffness cylinder. Results and comparisons for several simplifications of these highly complex governing equations are presented so that the ensuing numerical solutions are considered reliable and efficient enough for in-depth optimization studies. Four distinct cases of loading and stiffness variation are chosen to investigate possible areas of improvement that the variable stiffness concept may offer over traditional constant stiffness and/or stiffened structures. The initial investigation deals with the simplest solution for cylindrical shells in which all quantities are constant around the circumference of the cylinder. This axisymmetric case includes a stiffness variation exclusively in the axial direction, and the only pertinent loading scenarios include constant loads of axial compression, pressure, and torsion. The results for these cases indicate that little improvement over traditional laminates exists through the use of curvilinear fibers, mainly due to the presence of a weak link area within the stiffness variation that limits the ultimate load that the structure can withstand. Rigorous optimization studies reveal that even though slight increases in the critical loads can be produced for designs with an arbitrary variation of the fiber orientation angle, the improvements are not significant when compared to traditional design techniques that utilize ring stiffeners and frames. The second problem that is studied involves arbitrary loading of a cylinder with a stiffness variation that changes only in the circumferential direction. The end effects of the cylinder are ignored, so that the problem takes the form of an analysis of a cross-section for a short cylinder segment. Various load cases including axial compression, pressure, torsion, bending, and transverse shear forces are investigated. It is found that the most significant improvements in load-carrying capability exist for cases which involve loads that also vary around the circumference of the shell, namely bending and shear forces. The stiffness variation of the optimal designs contribute to the increased performance in two ways: lowering the stresses in the critical areas through redistribution of the stresses; and providing a relatively stiff region that alters the buckling behavior of the structure. These results lead to an in-depth optimization study involving weight optimization of a fuselage structure subjected to typical design constraints. Comparisons of the curvilinear fiber format to traditional stiffened structures constructed of isotropic and composite materials are included. It is found that standard variable stiffness designs are quite comparable in terms of weight and load-carrying capability yet offer the added advantage of tailorability of distinct regions of the structure that experience drastically different loading conditions. The last two problems presented in this work involve the nonlinear phenomenon of long tubes under bending. Though this scenario is not as applicable to fuselage structures as the previous problems, the mechanisms that produce the nonlinear effect are ideally suited to be controlled by the variable stiffness concept. This is due to the fact that the dominating influence for long cylinders under bending is the ovalization of the cross-section, which is governed mainly by the stiffness parameters of the cylindrical shell. Possible improvement of the critical buckling moments for these structures is investigated using either a circumferential or axial stiffness variation. For the circumferential case involving infinite length cylinders, it is found that slight improvements can be observed by designing structures that resist the cross-sectional deformation yet do not detract from the buckling resistance at the critical location. The results also indicate that buckling behavior is extremely dependent on cylinder length. This effect is most easily seen in the solution of finite length cylinders under bending that contain an axial stiffness variation. For these structures, the only mechanism that exhibits improved response are those that effectively shorten the length of the cylinder, thus reducing the cross-sectional deformation due to the forced restraint at the ends. It was found that the use of curvilinear fibers was not able to achieve this effect in sufficient degree to resist the deformation, but that ring stiffeners produced the desired response admirably. Thus, it is shown that the variable stiffness concept is most effective at improving the bending response of long cylinders through the use of a circumferential stiffness variation.

Anatomical variations of hepatic arterial system, coeliac trunk and renal arteries: an analysis with multidetector CT angiography.

PubMed

Ugurel, M S; Battal, B; Bozlar, U; Nural, M S; Tasar, M; Ors, F; Saglam, M; Karademir, I

2010-08-01

The purpose of our investigation was to determine the anatomical variations in the coeliac trunk-hepatic arterial system and the renal arteries in patients who underwent multidetector CT (MDCT) angiography of the abdominal aorta for various reasons. A total of 100 patients were analysed retrospectively. The coeliac trunk, hepatic arterial system and renal arteries were analysed individually and anatomical variations were recorded. Statistical analysis of the relationship between hepatocoeliac variations and renal artery variations was performed using a chi(2) test. There was a coeliac trunk trifurcation in 89% and bifurcation in 8% of the cases. Coeliac trunk was absent in 1%, a hepatosplenomesenteric trunk was seen in 1% and a splenomesenteric trunk was present in 1%. Hepatic artery variation was present in 48% of patients. Coeliac trunk and/or hepatic arterial variation was present in 23 (39.7%) of the 58 patients with normal renal arteries, and in 27 (64.3%) of the 42 patients with accessory renal arteries. There was a statistically significant correlation between renal artery variations and coeliac trunk-hepatic arterial system variations (p = 0.015). MDCT angiography permits a correct and detailed evaluation of hepatic and renal vascular anatomy. The prevalence of variations in the coeliac trunk and/or hepatic arteries is increased in people with accessory renal arteries. For that reason, when undertaking angiographic examinations directed towards any single organ, the possibility of variations in the vascular structure of other organs should be kept in mind.

Next Steps in Bayesian Structural Equation Models: Comments on, Variations of, and Extensions to Muthen and Asparouhov (2012)

ERIC Educational Resources Information Center

Rindskopf, David

2012-01-01

Muthen and Asparouhov (2012) made a strong case for the advantages of Bayesian methodology in factor analysis and structural equation models. I show additional extensions and adaptations of their methods and show how non-Bayesians can take advantage of many (though not all) of these advantages by using interval restrictions on parameters. By…

Evolution of plant δ 1-pyrroline-5-carboxylate reductases from phylogenetic and structural perspectives

DOE PAGES

Forlani, Giuseppe; Makarova, Kira S.; Ruszkowski, Milosz; ...

2015-08-03

Proline plays a crucial role in cell growth and stress responses, and its accumulation is essential for the tolerance of adverse environmental conditions in plants. Two routes are used to biosynthesize proline in plants. The main route uses glutamate as a precursor, while in the other route proline is derived from ornithine. The terminal step of both pathways, the conversion of δ 1-pyrroline-5-carboxylate (P5C) to L-proline, is catalyzed by P5C reductase (P5CR) using NADH or NADPH as a cofactor. Since P5CRs are important housekeeping enzymes, they are conserved across all domains of life and appear to be relatively unaffected throughoutmore » evolution. However, global analysis of these enzymes unveiled significant functional diversity in the preference for cofactors (NADPH vs. NADH), variation in metal dependence and the differences in the oligomeric state. In our study we investigated evolutionary patterns through phylogenetic and structural analysis of P5CR representatives from all kingdoms of life, with emphasis on the plant species. We attempted to correlate local sequence/structure variation among the functionally and structurally characterized members of the family.« less

Genetic, epigenetic, and HPLC fingerprint differentiation between natural and ex situ populations of Rhodiola sachalinensis from Changbai Mountain, China.

PubMed

Zhao, Wei; Shi, Xiaozheng; Li, Jiangnan; Guo, Wei; Liu, Chengbai; Chen, Xia

2014-01-01

Rhodiola sachalinensis is an endangered species with important medicinal value. We used inter-simple sequence repeat (ISSR) and methylation-sensitive amplified polymorphism (MSAP) markers to analyze genetic and epigenetic differentiation in different populations of R. sachalinensis, including three natural populations and an ex situ population. Chromatographic fingerprint was used to reveal HPLC fingerprint differentiation. According to our results, the ex situ population of R. sachalinensis has higher level genetic diversity and greater HPLC fingerprint variation than natural populations, but shows lower epigenetic diversity. Most genetic variation (54.88%) was found to be distributed within populations, and epigenetic variation was primarily distributed among populations (63.87%). UPGMA cluster analysis of ISSR and MSAP data showed identical results, with individuals from each given population grouping together. The results of UPGMA cluster analysis of HPLC fingerprint patterns was significantly different from results obtained from ISSR and MSAP data. Correlation analysis revealed close relationships among altitude, genetic structure, epigenetic structure, and HPLC fingerprint patterns (R2 = 0.98 for genetic and epigenetic distance; R2 = 0.90 for DNA methylation level and altitude; R2 = -0.95 for HPLC fingerprint and altitude). Taken together, our results indicate that ex situ population of R. sachalinensis show significantly different genetic and epigenetic population structures and HPLC fingerprint patterns. Along with other potential explanations, these findings suggest that the ex situ environmental factors caused by different altitude play an important role in keeping hereditary characteristic of R. sachalinensis.

Genetic, Epigenetic, and HPLC Fingerprint Differentiation between Natural and Ex Situ Populations of Rhodiola sachalinensis from Changbai Mountain, China

PubMed Central

Zhao, Wei; Shi, Xiaozheng; Li, Jiangnan; Guo, Wei; Liu, Chengbai; Chen, Xia

2014-01-01

Rhodiola sachalinensis is an endangered species with important medicinal value. We used inter-simple sequence repeat (ISSR) and methylation-sensitive amplified polymorphism (MSAP) markers to analyze genetic and epigenetic differentiation in different populations of R. sachalinensis, including three natural populations and an ex situ population. Chromatographic fingerprint was used to reveal HPLC fingerprint differentiation. According to our results, the ex situ population of R. sachalinensis has higher level genetic diversity and greater HPLC fingerprint variation than natural populations, but shows lower epigenetic diversity. Most genetic variation (54.88%) was found to be distributed within populations, and epigenetic variation was primarily distributed among populations (63.87%). UPGMA cluster analysis of ISSR and MSAP data showed identical results, with individuals from each given population grouping together. The results of UPGMA cluster analysis of HPLC fingerprint patterns was significantly different from results obtained from ISSR and MSAP data. Correlation analysis revealed close relationships among altitude, genetic structure, epigenetic structure, and HPLC fingerprint patterns (R2 = 0.98 for genetic and epigenetic distance; R2 = 0.90 for DNA methylation level and altitude; R2 = –0.95 for HPLC fingerprint and altitude). Taken together, our results indicate that ex situ population of R. sachalinensis show significantly different genetic and epigenetic population structures and HPLC fingerprint patterns. Along with other potential explanations, these findings suggest that the ex situ environmental factors caused by different altitude play an important role in keeping hereditary characteristic of R. sachalinensis. PMID:25386983

Population and allelic variation of A-to-I RNA editing in human transcriptomes.

PubMed

Park, Eddie; Guo, Jiguang; Shen, Shihao; Demirdjian, Levon; Wu, Ying Nian; Lin, Lan; Xing, Yi

2017-07-28

A-to-I RNA editing is an important step in RNA processing in which specific adenosines in some RNA molecules are post-transcriptionally modified to inosines. RNA editing has emerged as a widespread mechanism for generating transcriptome diversity. However, there remain significant knowledge gaps about the variation and function of RNA editing. In order to determine the influence of genetic variation on A-to-I RNA editing, we integrate genomic and transcriptomic data from 445 human lymphoblastoid cell lines by combining an RNA editing QTL (edQTL) analysis with an allele-specific RNA editing (ASED) analysis. We identify 1054 RNA editing events associated with cis genetic polymorphisms. Additionally, we find that a subset of these polymorphisms is linked to genome-wide association study signals of complex traits or diseases. Finally, compared to random cis polymorphisms, polymorphisms associated with RNA editing variation are located closer spatially to their respective editing sites and have a more pronounced impact on RNA secondary structure. Our study reveals widespread cis variation in RNA editing among genetically distinct individuals and sheds light on possible phenotypic consequences of such variation on complex traits and diseases.

Enhancement of the spectral selectivity of complex samples by measuring them in a frozen state at low temperatures in order to improve accuracy for quantitative analysis. Part II. Determination of viscosity for lube base oils using Raman spectroscopy.

PubMed

Kim, Mooeung; Chung, Hoeil

2013-03-07

The use of selectivity-enhanced Raman spectra of lube base oil (LBO) samples achieved by the spectral collection under frozen conditions at low temperatures was effective for improving accuracy for the determination of the kinematic viscosity at 40 °C (KV@40). A collection of Raman spectra from samples cooled around -160 °C provided the most accurate measurement of KV@40. Components of the LBO samples were mainly long-chain hydrocarbons with molecular structures that were deformable when these were frozen, and the different structural deformabilities of the components enhanced spectral selectivity among the samples. To study the structural variation of components according to the change of sample temperature from cryogenic to ambient condition, n-heptadecane and pristane (2,6,10,14-tetramethylpentadecane) were selected as representative components of LBO samples, and their temperature-induced spectral features as well as the corresponding spectral loadings were investigated. A two-dimensional (2D) correlation analysis was also employed to explain the origin for the improved accuracy. The asynchronous 2D correlation pattern was simplest at the optimal temperature, indicating the occurrence of distinct and selective spectral variations, which enabled the variation of KV@40 of LBO samples to be more accurately assessed.

Diet compositions and trophic guild structure of the eastern Chukchi Sea demersal fish community

NASA Astrophysics Data System (ADS)

Whitehouse, George A.; Buckley, Troy W.; Danielson, Seth L.

2017-01-01

Fishes are an important link in Arctic marine food webs, connecting production of lower trophic levels to apex predators. We analyzed 1773 stomach samples from 39 fish species collected during a bottom trawl survey of the eastern Chukchi Sea in the summer of 2012. We used hierarchical cluster analysis of diet dissimilarities on 21 of the most well sampled species to identify four distinct trophic guilds: gammarid amphipod consumers, benthic invertebrate generalists, fish and shrimp consumers, and zooplankton consumers. The trophic guilds reflect dominant prey types in predator diets. We used constrained analysis of principal coordinates (CAP) to determine if variation within the composite guild diets could be explained by a suite of non-diet variables. All CAP models explained a significant proportion of the variance in the diet matrices, ranging from 7% to 25% of the total variation. Explanatory variables tested included latitude, longitude, predator length, depth, and water mass. These results indicate a trophic guild structure is present amongst the demersal fish community during summer in the eastern Chukchi Sea. Regular monitoring of the food habits of the demersal fish community will be required to improve our understanding of the spatial, temporal, and interannual variation in diet composition, and to improve our ability to identify and predict the impacts of climate change and commercial development on the structure and functioning of the Chukchi Sea ecosystem.

Genetic variation and structure in remnant population of critically endangered Melicope zahlbruckneri

USGS Publications Warehouse

Raji, J. A.; Atkinson, Carter T.

2016-01-01

The distribution and amount of genetic variation within and between populations of plant species are important for their adaptability to future habitat changes and also critical for their restoration and overall management. This study was initiated to assess the genetic status of the remnant population of Melicope zahlbruckneri–a critically endangered species in Hawaii, and determine the extent of genetic variation and diversity in order to propose valuable conservation approaches. Estimated genetic structure of individuals based on molecular marker allele frequencies identified genetic groups with low overall differentiation but identified the most genetically diverse individuals within the population. Analysis of Amplified Fragment Length Polymorphic (AFLP) marker loci in the population based on Bayesian model and multivariate statistics classified the population into four subgroups. We inferred a mixed species population structure based on Bayesian clustering and frequency of unique alleles. The percentage of Polymorphic Fragment (PPF) ranged from 18.8 to 64.6% for all marker loci with an average of 54.9% within the population. Inclusion of all surviving M. zahlbruckneri trees in future restorative planting at new sites are suggested, and approaches for longer term maintenance of genetic variability are discussed. To our knowledge, this study represents the first report of molecular genetic analysis of the remaining population of M. zahlbruckneri and also illustrates the importance of genetic variability for conservation of a small endangered population.

Mixed variational formulations of finite element analysis of elastoacoustic/slosh fluid-structure interaction

NASA Technical Reports Server (NTRS)

Felippa, Carlos A.; Ohayon, Roger

1991-01-01

A general three-field variational principle is obtained for the motion of an acoustic fluid enclosed in a rigid or flexible container by the method of canonical decomposition applied to a modified form of the wave equation in the displacement potential. The general principle is specialized to a mixed two-field principle that contains the fluid displacement potential and pressure as independent fields. This principle contains a free parameter alpha. Semidiscrete finite-element equations of motion based on this principle are displayed and applied to the transient response and free-vibrations of the coupled fluid-structure problem. It is shown that a particular setting of alpha yields a rich set of formulations that can be customized to fit physical and computational requirements. The variational principle is then extended to handle slosh motions in a uniform gravity field, and used to derive semidiscrete equations of motion that account for such effects.

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…

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.

Full Field Photoelastic Stress Analysis

NASA Technical Reports Server (NTRS)

Lesniak, Jon R. (Inventor)

2000-01-01

A structural specimen coated with or constructed of photoelastic material, when illuminated with circularly polarized light will, when stressed: reflect or transmit elliptically polarized light, the direction of the axes of the ellipse and variation of the elliptically light from illuminating circular light will correspond to and indicate the direction and magnitude of the shear stresses for each illuminated point on the specimen. The principles of this invention allow for several embodiments of stress analyzing apparatus, ranging from those involving multiple rotating optical elements, to those which require no moving parts at all. A simple polariscope may be constructed having two polarizing filters with a single one-quarter waveplate placed between the polarizing filters. Light is projected through the first polarizing filter and the one-quarter waveplate and is reflected from a sub-fringe birefringent coating on a structure under load. Reflected light from the structure is analyzed with a polarizing filter. The two polarizing filters and the one-quarter waveplate may be rotated together or the analyzer alone may be rotated. Computer analysis of the variation in light intensity yields shear stress magnitude and direction.

Magnetic and topographical modifications of amorphous Co-Fe thin films induced by high energy Ag7+ ion irradiation

NASA Astrophysics Data System (ADS)

Pookat, G.; Hysen, T.; Al-Harthi, S. H.; Al-Omari, I. A.; Lisha, R.; Avasthi, D. K.; Anantharaman, M. R.

2013-09-01

We have investigated the effects of swift heavy ion irradiation on thermally evaporated 44 nm thick, amorphous Co77Fe23 thin films on silicon substrates using 100 MeV Ag7+ ions fluences of 1 × 1011 ions/cm2, 1 × 1012 ions/cm2, 1 × 1013 ions/cm2, and 3 × 1013 ions/cm2. The structural modifications upon swift heavy irradiation were investigated using glancing angle X-ray diffraction. The surface morphological evolution of thin film with irradiation was studied using Atomic Force Microscopy. Power spectral density analysis was used to correlate the roughness variation with structural modifications investigated using X-ray diffraction. Magnetic measurements were carried out using vibrating sample magnetometry and the observed variation in coercivity of the irradiated films is explained on the basis of stress relaxation. Magnetic force microscopy images are subjected to analysis using the scanning probe image processor software. These results are in agreement with the results obtained using vibrating sample magnetometry. The magnetic and structural properties are correlated.

Theoretical analysis of the structural phase transformation from B3 to B1 in BeO under high pressure

NASA Astrophysics Data System (ADS)

Jain, Arvind; Verma, Saligram; Nagarch, R. K.; Shah, S.; Kaurav, Netram

2018-05-01

We have performed the phase transformation and elastic properties of BeO at high pressure by formulating effective interionic interaction potential. The elastic constants, including the long-range Coulomb and van der Waals (vdW) interactions and the short-range repulsive interaction of up to second-neighbor ions within the Hafemeister and Flygare approach, are derived. Assuming that both the ions are polarizable, we employed the Slater-Kirkwood variational method to estimate the vdW coefficients, a structural phase transition (Pt) from ZnS structure (B3) to NaCl structure (B1) at 108 GPa has been predicted for BeO. The estimated value of the phase transition pressure (Pt) and the magnitude of the discontinuity in volume at the transition pressure are consistent as compared to the theoretical data. The variations of elastic constants with pressure follow a systematic trend identical to that observed in others compounds of ZnS type structure family.

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

Geostatistics for spatial genetic structures: study of wild populations of perennial ryegrass.

PubMed

Monestiez, P; Goulard, M; Charmet, G

1994-04-01

Methods based on geostatistics were applied to quantitative traits of agricultural interest measured on a collection of 547 wild populations of perennial ryegrass in France. The mathematical background of these methods, which resembles spatial autocorrelation analysis, is briefly described. When a single variable is studied, the spatial structure analysis is similar to spatial autocorrelation analysis, and a spatial prediction method, called "kriging", gives a filtered map of the spatial pattern over all the sampled area. When complex interactions of agronomic traits with different evaluation sites define a multivariate structure for the spatial analysis, geostatistical methods allow the spatial variations to be broken down into two main spatial structures with ranges of 120 km and 300 km, respectively. The predicted maps that corresponded to each range were interpreted as a result of the isolation-by-distance model and as a consequence of selection by environmental factors. Practical collecting methodology for breeders may be derived from such spatial structures.

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

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

Dispersal Ability Determines the Role of Environmental, Spatial and Temporal Drivers of Metacommunity Structure

PubMed Central

Padial, André A.; Ceschin, Fernanda; Declerck, Steven A. J.; De Meester, Luc; Bonecker, Cláudia C.; Lansac-Tôha, Fabio A.; Rodrigues, Liliana; Rodrigues, Luzia C.; Train, Sueli; Velho, Luiz F. M.; Bini, Luis M.

2014-01-01

Recently, community ecologists are focusing on the relative importance of local environmental factors and proxies to dispersal limitation to explain spatial variation in community structure. Albeit less explored, temporal processes may also be important in explaining species composition variation in metacommunities occupying dynamic systems. We aimed to evaluate the relative role of environmental, spatial and temporal variables on the metacommunity structure of different organism groups in the Upper Paraná River floodplain (Brazil). We used data on macrophytes, fish, benthic macroinvertebrates, zooplankton, periphyton, and phytoplankton collected in up to 36 habitats during a total of eight sampling campaigns over two years. According to variation partitioning results, the importance of predictors varied among biological groups. Spatial predictors were particularly important for organisms with comparatively lower dispersal ability, such as aquatic macrophytes and fish. On the other hand, environmental predictors were particularly important for organisms with high dispersal ability, such as microalgae, indicating the importance of species sorting processes in shaping the community structure of these organisms. The importance of watercourse distances increased when spatial variables were the main predictors of metacommunity structure. The contribution of temporal predictors was low. Our results emphasize the strength of a trait-based analysis and of better defining spatial variables. More importantly, they supported the view that “all-or- nothing” interpretations on the mechanisms structuring metacommunities are rather the exception than the rule. PMID:25340577

[Community structure of soil meso- and micro-fauna in different habitats of urbanized region].

PubMed

Qin, Zhong; Zhang, Jia-en; Li, Qing-fang

2009-12-01

Investigations were made in May, June, and November 2007 and January 2008 to study the structural characteristics and their seasonal variations of soil meso- and micro-fauna communities in six habitats of three land use types (forest land, constructed grassland and farmland) in Tianhe District of Guangzhou City. The horizontal spatial distribution of soil fauna differed with habitat. During the investigation periods, the Botanical Garden of South China Agricultural University had the highest individual number (1286) of soil mesa- and micro-fauna, while the farmland, especially in the Fenghuang Street area, had the lowest number of individuals and groups. The seasonal variation of the individual number was in order of autumn (1815) > spring (1623) > winter (1365) > summer (1276). Hierarchical clustering and detrended correspondence analysis also showed that the community composition of soil meso- and micro-fauna in different habitats exhibited distinct seasonal variation. In the same seasons, the community structure and composition of soil meso- and micro-fauna in different habitats were correlated to the degrees of human interferences and the properties of soil environment.

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.

Sensitivity analysis of a wing aeroelastic response

NASA Technical Reports Server (NTRS)

Kapania, Rakesh K.; Eldred, Lloyd B.; Barthelemy, Jean-Francois M.

1991-01-01

A variation of Sobieski's Global Sensitivity Equations (GSE) approach is implemented to obtain the sensitivity of the static aeroelastic response of a three-dimensional wing model. The formulation is quite general and accepts any aerodynamics and structural analysis capability. An interface code is written to convert one analysis's output to the other's input, and visa versa. Local sensitivity derivatives are calculated by either analytic methods or finite difference techniques. A program to combine the local sensitivities, such as the sensitivity of the stiffness matrix or the aerodynamic kernel matrix, into global sensitivity derivatives is developed. The aerodynamic analysis package FAST, using a lifting surface theory, and a structural package, ELAPS, implementing Giles' equivalent plate model are used.

Individual Differences in Dynamic Functional Brain Connectivity across the Human Lifespan.

PubMed

Davison, Elizabeth N; Turner, Benjamin O; Schlesinger, Kimberly J; Miller, Michael B; Grafton, Scott T; Bassett, Danielle S; Carlson, Jean M

2016-11-01

Individual differences in brain functional networks may be related to complex personal identifiers, including health, age, and ability. Dynamic network theory has been used to identify properties of dynamic brain function from fMRI data, but the majority of analyses and findings remain at the level of the group. Here, we apply hypergraph analysis, a method from dynamic network theory, to quantify individual differences in brain functional dynamics. Using a summary metric derived from the hypergraph formalism-hypergraph cardinality-we investigate individual variations in two separate, complementary data sets. The first data set ("multi-task") consists of 77 individuals engaging in four consecutive cognitive tasks. We observe that hypergraph cardinality exhibits variation across individuals while remaining consistent within individuals between tasks; moreover, the analysis of one of the memory tasks revealed a marginally significant correspondence between hypergraph cardinality and age. This finding motivated a similar analysis of the second data set ("age-memory"), in which 95 individuals, aged 18-75, performed a memory task with a similar structure to the multi-task memory task. With the increased age range in the age-memory data set, the correlation between hypergraph cardinality and age correspondence becomes significant. We discuss these results in the context of the well-known finding linking age with network structure, and suggest that hypergraph analysis should serve as a useful tool in furthering our understanding of the dynamic network structure of the brain.

Relationships between adaptive and neutral genetic diversity and ecological structure and functioning: a meta-analysis

PubMed Central

Whitlock, Raj

2014-01-01

Understanding the effects of intraspecific genetic diversity on the structure and functioning of ecological communities is a fundamentally important part of evolutionary ecology and may also have conservation relevance in identifying the situations in which genetic diversity coincides with species-level diversity.Early studies within this field documented positive relationships between genetic diversity and ecological structure, but recent studies have challenged these findings. Conceptual synthesis has been hampered because studies have used different measures of intraspecific variation (phenotypically adaptive vs. neutral) and have considered different measures of ecological structure in different ecological and spatial contexts. The aim of this study is to strengthen conceptual understanding by providing an empirical synthesis quantifying the relationship between genetic diversity and ecological structure.Here, I present a meta-analysis of the relationship between genetic diversity within plant populations and the structure and functioning of associated ecological communities (including 423 effect sizes from 70 studies). I used Bayesian meta-analyses to examine (i) the strength and direction of this relationship, (ii) the extent to which phenotypically adaptive and neutral (molecular) measures of diversity differ in their association with ecological structure and (iii) variation in outcomes among different measures of ecological structure and in different ecological contexts.Effect sizes measuring the relationship between adaptive diversity (genotypic richness) and both community- and ecosystem-level ecological responses were small, but significantly positive. These associations were supported by genetic effects on species richness and productivity, respectively.There was no overall association between neutral genetic diversity and measures of ecological structure, but a positive correlation was observed under a limited set of demographic conditions. These results suggest that adaptive and neutral genetic diversity should not be treated as ecologically equivalent measures of intraspecific variation.Synthesis. This study advances the debate over whether relationships between genetic diversity and ecological structure are either simply positive or negative, by showing how the strength and direction of these relationships changes with different measures of diversity and in different ecological contexts. The results provide a solid foundation for assessing when and where an expanded synthesis between ecology and genetics will be most fruitful. PMID:25210204

Primary structure of the hemoglobin alpha-chain of rose-ringed parakeet (Psittacula krameri).

PubMed

Islam, A; Beg, O U; Persson, B; Zaidi, Z H; Jörnvall, H

1988-10-01

The structure of the hemoglobin alpha-chain of Rose-ringed Parakeet was determined by sequence degradations of the intact subunit, the CNBr fragments, and peptides obtained by digestion with staphylococcal Glu-specific protease and trypsin. Using this analysis, the complete alpha-chain structure of 21 avian species is known, permitting comparisons of the protein structure and of avian relationships. The structure exhibits differences from previously established avian alpha-chains at a total of 61 positions, five of which have residues unique to those of the parakeet (Ser-12, Gly-65, Ser-67, Ala-121, and Leu-134). The analysis defines hemoglobin variation within an additional avian order (Psittaciformes), demonstrates distant patterns for evaluation of relationships within other avian orders, and lends support to taxonomic conclusions from molecular data.

The vehicle design evaluation program - A computer-aided design procedure for transport aircraft

NASA Technical Reports Server (NTRS)

Oman, B. H.; Kruse, G. S.; Schrader, O. E.

1977-01-01

The vehicle design evaluation program is described. This program is a computer-aided design procedure that provides a vehicle synthesis capability for vehicle sizing, external load analysis, structural analysis, and cost evaluation. The vehicle sizing subprogram provides geometry, weight, and balance data for aircraft using JP, hydrogen, or methane fuels. The structural synthesis subprogram uses a multistation analysis for aerodynamic surfaces and fuselages to develop theoretical weights and geometric dimensions. The parts definition subprogram uses the geometric data from the structural analysis and develops the predicted fabrication dimensions, parts material raw stock buy requirements, and predicted actual weights. The cost analysis subprogram uses detail part data in conjunction with standard hours, realization factors, labor rates, and material data to develop the manufacturing costs. The program is used to evaluate overall design effects on subsonic commercial type aircraft due to parameter variations.

Unraveling Cell Processes: Interference Imaging Interwoven with Data Analysis

PubMed Central

Brazhe, A. R.; Pavlov, A. N.; Erokhova, L. A.; Yusipovich, A. I.; Maksimov, G. V.; Mosekilde, E.; Sosnovtseva, O. V.

2006-01-01

The paper presents results on the application of interference microscopy and wavelet-analysis for cell visualization and studies of cell dynamics. We demonstrate that interference imaging of erythrocytes can reveal reorganization of the cytoskeleton and inhomogenity in the distribution of hemoglobin, and that interference imaging of neurons can show intracellular compartmentalization and submembrane structures. We investigate temporal and spatial variations of the refractive index for different cell types: isolated neurons, mast cells and erythrocytes. We show that the refractive dynamical properties differ from cell type to cell type and depend on the cellular compartment. Our results suggest that low frequency variations (0.1–0.6 Hz) result from plasma membrane processes and that higher frequency variations (20–26 Hz) are related to the movement of vesicles. Using double-wavelet analysis, we study the modulation of the 1 Hz rhythm in neurons and reveal its changes under depolarization and hyperpolarization of the plasma membrane. We conclude that interference microscopy combined with wavelet analysis is a useful technique for non-invasive cell studies, cell visualization, and investigation of plasma membrane properties. PMID:19669463

Classifying and mapping wetlands and peat resources using digital cartography

USGS Publications Warehouse

Cameron, Cornelia C.; Emery, David A.

1992-01-01

Digital cartography allows the portrayal of spatial associations among diverse data types and is ideally suited for land use and resource analysis. We have developed methodology that uses digital cartography for the classification of wetlands and their associated peat resources and applied it to a 1:24 000 scale map area in New Hampshire. Classifying and mapping wetlands involves integrating the spatial distribution of wetlands types with depth variations in associated peat quality and character. A hierarchically structured classification that integrates the spatial distribution of variations in (1) vegetation, (2) soil type, (3) hydrology, (4) geologic aspects, and (5) peat characteristics has been developed and can be used to build digital cartographic files for resource and land use analysis. The first three parameters are the bases used by the National Wetlands Inventory to classify wetlands and deepwater habitats of the United States. The fourth parameter, geological aspects, includes slope, relief, depth of wetland (from surface to underlying rock or substrate), wetland stratigraphy, and the type and structure of solid and unconsolidated rock surrounding and underlying the wetland. The fifth parameter, peat characteristics, includes the subsurface variation in ash, acidity, moisture, heating value (Btu), sulfur content, and other chemical properties as shown in specimens obtained from core holes. These parameters can be shown as a series of map data overlays with tables that can be integrated for resource or land use analysis.

Indian Ocean analyses

NASA Technical Reports Server (NTRS)

Meyers, Gary

1992-01-01

The background and goals of Indian Ocean thermal sampling are discussed from the perspective of a national project which has research goals relevant to variation of climate in Australia. The critical areas of SST variation are identified. The first goal of thermal sampling at this stage is to develop a climatology of thermal structure in the areas and a description of the annual variation of major currents. The sampling strategy is reviewed. Dense XBT sampling is required to achieve accurate, monthly maps of isotherm-depth because of the high level of noise in the measurements caused by aliasing of small scale variation. In the Indian Ocean ship routes dictate where adequate sampling can be achieved. An efficient sampling rate on available routes is determined based on objective analysis. The statistical structure required for objective analysis is described and compared at 95 locations in the tropical Pacific and 107 in the tropical Indian Oceans. XBT data management and quality control methods at CSIRO are reviewed. Results on the mean and annual variation of temperature and baroclinic structure in the South Equatorial Current and Pacific/Indian Ocean Throughflow are presented for the region between northwest Australia and Java-Timor. The mean relative geostrophic transport (0/400 db) of Throughflow is approximately 5 x 106 m3/sec. A nearly equal volume transport is associated with the reference velocity at 400 db. The Throughflow feeds the South Equatorial Current, which has maximum westward flow in August/September, at the end of the southeasterly Monsoon season. A strong semiannual oscillation in the South Java Current is documented. The results are in good agreement with the Semtner and Chervin (1988) ocean general circulation model. The talk concludes with comments on data inadequacies (insufficient coverage, timeliness) particular to the Indian Ocean and suggestions on the future role that can be played by Data Centers, particularly with regard to quality control of data as research bodies are replaced by operational bodies in the Global Ocean Observing System.

Precision atomic spectroscopy for improved limits on variation of the fine structure constant and local position invariance.

PubMed

Fortier, T M; Ashby, N; Bergquist, J C; Delaney, M J; Diddams, S A; Heavner, T P; Hollberg, L; Itano, W M; Jefferts, S R; Kim, K; Levi, F; Lorini, L; Oskay, W H; Parker, T E; Shirley, J; Stalnaker, J E

2007-02-16

We report tests of local position invariance and the variation of fundamental constants from measurements of the frequency ratio of the 282-nm 199Hg+ optical clock transition to the ground state hyperfine splitting in 133Cs. Analysis of the frequency ratio of the two clocks, extending over 6 yr at NIST, is used to place a limit on its fractional variation of <5.8x10(-6) per change in normalized solar gravitational potential. The same frequency ratio is also used to obtain 20-fold improvement over previous limits on the fractional variation of the fine structure constant of |alpha/alpha|<1.3x10(-16) yr-1, assuming invariance of other fundamental constants. Comparisons of our results with those previously reported for the absolute optical frequency measurements in H and 171Yb+ vs other 133Cs standards yield a coupled constraint of -1.5x10(-15)

The Mouse Genomes Project: a repository of inbred laboratory mouse strain genomes.

PubMed

Adams, David J; Doran, Anthony G; Lilue, Jingtao; Keane, Thomas M

2015-10-01

The Mouse Genomes Project was initiated in 2009 with the goal of using next-generation sequencing technologies to catalogue molecular variation in the common laboratory mouse strains, and a selected set of wild-derived inbred strains. The initial sequencing and survey of sequence variation in 17 inbred strains was completed in 2011 and included comprehensive catalogue of single nucleotide polymorphisms, short insertion/deletions, larger structural variants including their fine scale architecture and landscape of transposable element variation, and genomic sites subject to post-transcriptional alteration of RNA. From this beginning, the resource has expanded significantly to include 36 fully sequenced inbred laboratory mouse strains, a refined and updated data processing pipeline, and new variation querying and data visualisation tools which are available on the project's website ( http://www.sanger.ac.uk/resources/mouse/genomes/ ). The focus of the project is now the completion of de novo assembled chromosome sequences and strain-specific gene structures for the core strains. We discuss how the assembled chromosomes will power comparative analysis, data access tools and future directions of mouse genetics.

Analysing the magnetopause internal structure: new possibilities offered by MMS

NASA Astrophysics Data System (ADS)

Belmont, G.; Rezeau, L.; Manuzzo, R.; Aunai, N.; Dargent, J.

2017-12-01

We explore the structure of the magnetopause using a crossing observed by the MMS spacecraft on October 16th, 2015. Several methods (MVA, BV, CVA) are first applied to compute the normal to the magnetopause considered as a whole. The different results obtained are not identical and we show that the whole boundary is not stationary and not planar, so that basic assumptions of these methods are not well satisfied. We then analyse more finely the internal structure for investigating the departures from planarity. Using the basic mathematical definition of what is a one-dimensional physical problem, we introduce a new method, called LNA (Local Normal Analysis) for determining the varying normal, and we compare the results so obtained with those coming from the MDD tool developed by [Shi et al., 2005]. This method gives the dimensionality of the magnetic variations from multi-point measurements and allows estimating the direction of the local normal using the magnetic field. On the other hand, LNA is a single-spacecraft method which gives the local normal from the magnetic field and particle data. This study shows that the magnetopause does include approximate one-dimensional sub-structures but also two and three dimensional intervals. It also shows that the dimensionality of the magnetic variations can differ from the variations of the other fields so that, at some places, the magnetic field can have a 1D structure although all the plasma variations do not verify the properties of a global one-dimensional problem. Finally a generalisation and a systematic application of the MDD method to the physical quantities of interest is shown.

Crush analysis of the foam-filled bitubal circular tube under oblique impact

NASA Astrophysics Data System (ADS)

Djamaluddin, F.; Abdullah, S.; Arrifin, A. K.; Nopiah, Z. M.

2018-02-01

This paper presents crashworthiness analysis of bitubal cylindrical tubes under different impact angular. The numerical solution of double cylindrical tubes are determined by finite element analysis (FEA). Moreover, the structure was impacted by mass block as impactor respect to longitudinal direction of the tubes. The model of structure was developed by non-linear ABAQUS sofware with variations of load angle and dimensions of tube. The outcome of this study is the respons parameters such as the peak crusing force (PCF), energy absorption (EA) and specific energy absorption (SEA), thus it can be expected this tube as the great energy absorber.

Consistent linearization of the element-independent corotational formulation for the structural analysis of general shells

NASA Technical Reports Server (NTRS)

Rankin, C. C.

1988-01-01

A consistent linearization is provided for the element-dependent corotational formulation, providing the proper first and second variation of the strain energy. As a result, the warping problem that has plagued flat elements has been overcome, with beneficial effects carried over to linear solutions. True Newton quadratic convergence has been restored to the Structural Analysis of General Shells (STAGS) code for conservative loading using the full corotational implementation. Some implications for general finite element analysis are discussed, including what effect the automatic frame invariance provided by this work might have on the development of new, improved elements.

How Universal Is the Big Five? Testing the Five-Factor Model of Personality Variation Among Forager–Farmers in the Bolivian Amazon

PubMed Central

Gurven, Michael; von Rueden, Christopher; Massenkoff, Maxim; Kaplan, Hillard; Vie, Marino Lero

2014-01-01

The five-factor model (FFM) of personality variation has been replicated across a range of human societies, suggesting the FFM is a human universal. However, most studies of the FFM have been restricted to literate, urban populations, which are uncharacteristic of the majority of human evolutionary history. We present the first test of the FFM in a largely illiterate, indigenous society. Tsimane forager–horticulturalist men and women of Bolivia (n = 632) completed a translation of the 44-item Big Five Inventory (Benet-Martínez & John, 1998), a widely used metric of the FFM. We failed to find robust support for the FFM, based on tests of (a) internal consistency of items expected to segregate into the Big Five factors, (b) response stability of the Big Five, (c) external validity of the Big Five with respect to observed behavior, (d) factor structure according to exploratory and confirmatory factor analysis, and (e) similarity with a U.S. target structure based on Procrustes rotation analysis. Replication of the FFM was not improved in a separate sample of Tsimane adults (n = 430), who evaluated their spouses on the Big Five Inventory. Removal of reverse-scored items that may have elicited response biases produced factors suggestive of Extraversion, Agreeableness, and Conscientiousness, but fit to the FFM remained poor. Response styles may covary with exposure to education, but we found no better fit to the FFM among Tsimane who speak Spanish or have attended school. We argue that Tsimane personality variation displays 2 principal factors that may reflect socioecological characteristics common to small-scale societies. We offer evolutionary perspectives on why the structure of personality variation may not be invariant across human societies. PMID:23245291

How universal is the Big Five? Testing the five-factor model of personality variation among forager-farmers in the Bolivian Amazon.

PubMed

Gurven, Michael; von Rueden, Christopher; Massenkoff, Maxim; Kaplan, Hillard; Lero Vie, Marino

2013-02-01

The five-factor model (FFM) of personality variation has been replicated across a range of human societies, suggesting the FFM is a human universal. However, most studies of the FFM have been restricted to literate, urban populations, which are uncharacteristic of the majority of human evolutionary history. We present the first test of the FFM in a largely illiterate, indigenous society. Tsimane forager-horticulturalist men and women of Bolivia (n = 632) completed a translation of the 44-item Big Five Inventory (Benet-Martínez & John, 1998), a widely used metric of the FFM. We failed to find robust support for the FFM, based on tests of (a) internal consistency of items expected to segregate into the Big Five factors, (b) response stability of the Big Five, (c) external validity of the Big Five with respect to observed behavior, (d) factor structure according to exploratory and confirmatory factor analysis, and (e) similarity with a U.S. target structure based on Procrustes rotation analysis. Replication of the FFM was not improved in a separate sample of Tsimane adults (n = 430), who evaluated their spouses on the Big Five Inventory. Removal of reverse-scored items that may have elicited response biases produced factors suggestive of Extraversion, Agreeableness, and Conscientiousness, but fit to the FFM remained poor. Response styles may covary with exposure to education, but we found no better fit to the FFM among Tsimane who speak Spanish or have attended school. We argue that Tsimane personality variation displays 2 principal factors that may reflect socioecological characteristics common to small-scale societies. We offer evolutionary perspectives on why the structure of personality variation may not be invariant across human societies. (c) 2013 APA, all rights reserved.

Analysis on Inpatient Health Expenditures of Renal Cell Carcinoma in a Grade-A Tertiary Hospital in Beijing.

PubMed

Liu, Xin; Mao, Yong-Hui; He, Xue-Mei; Zhang, Yan-Jing; Sun, Ying

2017-10-20

Renal cell carcinoma (RCC) is the most common type of malignant renal tumors with a growing incidence in the recent years. This study aimed to investigate the influencing factors and variation trend of hospitalization expenditures among RCC patients in a single-centered hospital in Beijing during 5 consecutive years and to find the major cost items and fluctuation tendency of inpatient medical expenditures. The information of medical expenditures among RCC patients in a Grade-A tertiary hospital during the years 2012-2016 was investigated to find the main cost items and changes affecting the medical cost structure. Gray correlation method was adopted in quantitative analysis to analyze the composition of medical expenditures, and the variation of hospitalization expense structure during the five years was studied by analyzing the degree of structural variation. The cost item constitution of the hospitalization expenditures among RCC patients was relatively stable in the sample hospital during the past five years. To be specific, drug costs accounted for the largest proportion of medical expenditures each year, with the highest of 37.81% in 2012, and showed a slowly declining tendency in the coming years. The cost item with the highest correlation degree was drug costs, with the value of 1.0000; followed by the costs of surgeries, 0.8423. Furthermore, drug costs shared the largest proportion (40.95%) of structural variation, followed by the costs of surgeries (18.35%). Drug costs are the major influencing factors of the hospitalization expenditures among RCC patients. Thus, reasonable control on excessive drugs as well as the standardization of the diagnosis and treatment behaviors is conducive in reducing medical expenditures as well as easing patients' economic burdens. Besides, the positive growth on surgery costs suggests that the labor value of medical staffs has been gradually recognized.

Refinement of Molecular Diagnostic Protocol of Auditory Neuropathy Spectrum Disorder

PubMed Central

Chang, Mun Young; Kim, Ah Reum; Kim, Nayoung K.D.; Lee, Chung; Park, Woong-Yang; Choi, Byung Yoon

2015-01-01

Abstract Auditory neuropathy spectrum disorder (ANSD) is a sensorineural hearing disorder caused by dysfunction of auditory neural conduction. ANSD has a heterogeneous etiology, including genetic factors; the response to cochlear implantation significantly varies depending on the etiology. The results of timely cochlear implantation for OTOF-related ANSD (DFNB9) have been reported to be good. Therefore, identifying the causative gene of ANSD, especially OTOF, is an important issue to rehabilitate these patients. Six sporadic ANSD subjects without anatomical abnormality of the cochlear nerve, including the 4 subjects that were previously reported to be without detectable OTOF mutation, were included. We performed targeted resequencing (TRS) of known deafness genes and multiphasic bioinformatics analyses of the data that ensured detection of capture failure and structural variations. Exclusion of SNP was also double checked. The TRS data previously obtained from 2 subjects were reanalyzed. Through this study, we detected 2 mutant alleles of OTOF from 5 (83.3%) of 6 ANSD subjects. All of the 5 subjects carried at least 1 mutant allele carrying p.R1939Q. This variant was categorized as a simple SNP (rs201326023) in the database and it resided in the exon with frequent capture failures, which previously led to exclusion of this variant from eligible candidacy mistakenly. In addition, we detected a structural variation within OTOF from a previously undiagnosed ANSD subject, which was the second structural variation reported in DFNB9 subjects to date. We identify a strong etiologic homogeneity of prelingual ANSD in case of the anatomically normal cochlear nerve in Koreans and now report DFNB9 as the single overwhelming cause. Multiphasic analysis of TRS data ensuring detection of capture failure and structural variations would be expected to reveal DFNB9 from a substantial portion of previously undiagnosed ANSD subjects in Koreans. Based on our results, we propose a novel strategy that incorporates imaging studies, prevalent mutation screening and multiphasic analysis of TRS data in a stepwise manner to correctly detect DFNB9 in Koreans. PMID:26632695

Analysis of cracked RC beams under vibration

NASA Astrophysics Data System (ADS)

Capozucca, R.; Magagnini, E.

2017-05-01

Among the methods of monitoring of integrity, vibration analysis is more convenient as non-destructive testing (NDT) method. Many aspects regarding the vibration monitoring of the structural integrity of damaged RC elements have not been completely analysed in literature. The correlation between the development of the crack pattern on concrete surface under bending loadings, as well as the width and depth of cracks, and the variation of dynamic parameters on a structural element is an important aspects that has to be more investigated. This paper deals with cracked RC beams controlled by NDT based on natural vibration, which may be correlated to damage degree due to cracking of concrete under severe state of loading. An experimental investigation on the assessment of RC beams in different scale under loading has been done through dynamic tests in different constraint conditions of edges measuring frequency values and frequency variation. Envelope of Frequency Response Functions (FRFs) are shown and the changes of natural frequency values are related to the damage degree of RC beams subjected to static tests. Finally, a comparison between data obtained by finite element analysis and experimental results is shown.

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.

Qualitative analysis of MTEM response using instantaneous attributes

NASA Astrophysics Data System (ADS)

Fayemi, Olalekan; Di, Qingyun

2017-11-01

This paper introduces new technique for qualitative analysis of multi-transient electromagnetic (MTEM) earth impulse response over complex geological structures. Instantaneous phase and frequency attributes were used in place of the conventional common offset section for improved qualitative interpretation of MTEM data by obtaining more detailed information from the earth impulse response. The instantaneous attributes were used to describe the lateral variation in subsurface resistivity and the visible geological structure with respect to given offsets. Instantaneous phase attribute was obtained by converting the impulse response into a complex form using the Hilbert transform. Conversely, the polynomial phase difference (PPD) estimator was favored over the center finite difference (CFD) approximation method in calculating the instantaneous frequency attribute because it is computationally efficient and has the ability to give a smooth variation of the instantaneous frequency over a common offset section. The observed results from the instantaneous attributes were in good agreement with both the subsurface model used and the apparent resistivity section obtained from the MTEM earth impulse response. Hence, this study confirms the capability of both instantaneous phase and frequency attributes as highly effective tools for MTEM qualitative analysis.

Hey Big Spender! An Analysis of Australian Universities and How Much They Pay Their General Staff

ERIC Educational Resources Information Center

Dobson, Ian R.

2009-01-01

Analysis of aggregated data files on staff sent by all Australian universities to DEST in 2007 and of salary schedules posted on university websites reveals a considerable variation between salaries paid to general staff at each salary level and the relative seniority of those staff. This paper outlines the differences in staffing structures and…

Different effects of variation in Xanthium strumarium L. (Compositae) on two insect seed predators.

PubMed

Hare, J Daniel; Futuyma, Douglas J

1978-01-01

To determine the relative importance of variation in several plant characters on susceptibility to herbivores, we examined patterns of seed predation by two monophagous insect species and patterns of variation in ten populations of the cocklebur, Xanthium strumarium. Multiple regression analysis disclosed that one seed predator was most influenced by plant chemical variation, the other was significantly influenced by both chemical and morphological variation, but variation in yet another character, general burr size, was most important in conferring resistance to both insects simultaneously. The plant populations differed most in this character. Although many of the plant characters were correlated with each other, those important in determining susceptibility to each insect species were uncorrelated and independent of those conferring resistance to both insects simultaneously.These results imply that ecological similar herbivores may be influenced by different aspects of plant variation, and that predictions of evolutionary responses of local plant populations to herbivory may require knowledge of the structure of local herbivore communities and the dynamics of their establishment.

Does geography or ecology best explain 'cultural' variation among chimpanzee communities?

PubMed

Kamilar, Jason M; Marshack, Joshua L

2012-02-01

Much attention has been paid to geographic variation in chimpanzee behavior, but few studies have applied quantitative techniques to explain this variation. Here, we apply methods typically utilized in macroecology to explain variation in the putative cultural traits of chimpanzees. We analyzed published data containing 39 behavioral traits from nine chimpanzee communities. We used a canonical correspondence analysis to examine the relative importance of environmental characteristics and geography, which may be a proxy for inter-community gene flow and/or social transmission, for explaining geographic variation in chimpanzee behavior. We found that geography, and longitude in particular, was the best predictor of behavioral variation. Chimpanzee communities in close longitudinal proximity to each other exhibit similar behavioral repertoires, independent of local ecological factors. No ecological variables were significantly related to behavioral variation. These results support the idea that inter-community dispersal patterns have played a major role in structuring behavioral variation. We cannot be certain whether behavioral variation has a genetic basis, is the result of innovation and diffusion, or a combination of the two. Copyright © 2011 Elsevier Ltd. All rights reserved.

Temporal variations in a phytoplankton community in a subtropical reservoir: An interplay of extrinsic and intrinsic community effects.

PubMed

Yang, Wen; Zheng, Zhongming; Zheng, Cheng; Lu, Kaihong; Ding, Dewen; Zhu, Jinyong

2018-01-15

The phytoplankton community structure is potentially influenced by both extrinsic effects originating from the surrounding environment and intrinsic effects relying on interspecific interactions between two species. However, few studies have simultaneously considered both types of effects and assessed the relative importance of these factors. In this study, we used data collected over nine months (August 2012-May 2013) from a typical subtropical reservoir in southeast China to analyze the temporal variation of its phytoplankton community structure and develop a quantitative understanding of the extrinsic and intrinsic effects on phytoplankton community dynamics. Significant temporal variations were observed in environmental variables as well as the phytoplankton and zooplankton communities, whereas their variational trajectories and directions were entirely different. Variance partitioning analysis showed that extrinsic factors significantly explained only 31% of the variation in the phytoplankton community, thus suggesting that these factors were incomplete predictors of the community structure. Random forest-based models showed that 48% of qualified responsible phytoplankton species were more accurately predicted by phytoplankton-only models, which revealed clear effects of interspecific species-to-species interactions. Furthermore, we used association networks to model the interactions among phytoplankton, zooplankton and the environment. Network comparisons indicated that interspecific interactions were widely present in the phytoplankton community and dominated the network rather than those between phytoplankton and extrinsic factors. These findings expand the current understanding of the underlying mechanisms that govern phytoplankton community dynamics. Copyright © 2017 Elsevier B.V. All rights reserved.

Temperature-dependent conformational variation of chromophoric dissolved organic matter and its consequent interaction with phenanthrene.

PubMed

Chen, Wei; Liu, Xiao-Yang; Yu, Han-Qing

2017-03-01

Temperature variation caused by climate change, seasonal variation and geographic locations affects the physicochemical compositions of chromophoric dissolved organic matter (CDOM), resulting in difference in the fates of CDOM-related environmental pollutants. Exploration into the thermal induced structural transition of CDOM can help to better understand their environmental impacts, but information on this aspect is still lacking. Through integrating fluorescence excitation-emission matrix coupled parallel factor analysis with synchronous fluorescence two-dimensional correlation spectroscopy, this study provides an in-depth insight into the temperature-dependent conformational transitions of CDOM and their impact on its hydrophobic interaction with persistent organic pollutants (with phenanthrene as an example) in water. The fluorescence components in CDOM change linearly to water temperature with different extents and different temperature regions. The thermal induced transition priority in CDOM is protein-like component → fulvic-like component → humic-like component. Furthermore, the impact of thermal-induced conformational transition of CDOM on its hydrophobic interaction with phenanthrene is observed and explored. The fluorescence-based analytic results reveal that the conjugation degree of the aromatic groups in the fulvic- and humic-like substances, and the unfolding of the secondary structure in the protein-like substances with aromatic structure, contribute to the conformation variation. This integrated approach jointly enhances the characterization of temperature-dependent conformational variation of CDOM, and provides a promising way to elucidate the environmental behaviours of CDOM. Copyright © 2017 Elsevier Ltd. All rights reserved.

Design of a nano-layered tunable optical filter

NASA Astrophysics Data System (ADS)

Banerjee, A.; Awasthi, S. K.; Malaviya, U.; Ojha, S. P.

2006-12-01

A novel theory to design tunable band pass filters using one-dimensional nano-photonic structures is proposed. Periodic structures consisting of different dielectrics and semiconductor materials are considered. A detailed mathematical analysis is presented to predict allowed and forbidden bands of wavelengths with variation of angle of incidence and lattice parameters. It is possible to get desired ranges of the electromagnetic spectrum filtered with this structure by changing the incidence angle of light and/or changing the value of the lattice parameters.

Body weight of hypersonic aircraft, part 1

NASA Technical Reports Server (NTRS)

Ardema, Mark D.

1988-01-01

The load bearing body weight of wing-body and all-body hypersonic aircraft is estimated for a wide variety of structural materials and geometries. Variations of weight with key design and configuration parameters are presented and discussed. Both hot and cool structure approaches are considered in isotropic, organic composite, and metal matrix composite materials; structural shells are sandwich or skin-stringer. Conformal and pillow-tank designs are investigated for the all-body shape. The results identify the most promising hypersonic aircraft body structure design approaches and their weight trends. Geometric definition of vehicle shapes and structural analysis methods are presented in appendices.

Quantifying floral shape variation in 3D using microcomputed tomography: a case study of a hybrid line between actinomorphic and zygomorphic flowers.

PubMed

Wang, Chun-Neng; Hsu, Hao-Chun; Wang, Cheng-Chun; Lee, Tzu-Kuei; Kuo, Yan-Fu

2015-01-01

The quantification of floral shape variations is difficult because flower structures are both diverse and complex. Traditionally, floral shape variations are quantified using the qualitative and linear measurements of two-dimensional (2D) images. The 2D images cannot adequately describe flower structures, and thus lead to unsatisfactory discrimination of the flower shape. This study aimed to acquire three-dimensional (3D) images by using microcomputed tomography (μCT) and to examine the floral shape variations by using geometric morphometrics (GM). To demonstrate the advantages of the 3D-μCT-GM approach, we applied the approach to a second-generation population of florist's gloxinia (Sinningia speciosa) crossed from parents of zygomorphic and actinomorphic flowers. The flowers in the population considerably vary in size and shape, thereby served as good materials to test the applicability of the proposed phenotyping approach. Procedures were developed to acquire 3D volumetric flower images using a μCT scanner, to segment the flower regions from the background, and to select homologous characteristic points (i.e., landmarks) from the flower images for the subsequent GM analysis. The procedures identified 95 landmarks for each flower and thus improved the capability of describing and illustrating the flower shapes, compared with typically lower number of landmarks in 2D analyses. The GM analysis demonstrated that flower opening and dorsoventral symmetry were the principal shape variations of the flowers. The degrees of flower opening and corolla asymmetry were then subsequently quantified directly from the 3D flower images. The 3D-μCT-GM approach revealed shape variations that could not be identified using typical 2D approaches and accurately quantified the flower traits that presented a challenge in 2D images. The approach opens new avenues to investigate floral shape variations.

Advances in Micromechanics Modeling of Composites Structures for Structural Health Monitoring

NASA Astrophysics Data System (ADS)

Moncada, Albert

Although high performance, light-weight composites are increasingly being used in applications ranging from aircraft, rotorcraft, weapon systems and ground vehicles, the assurance of structural reliability remains a critical issue. In composites, damage is absorbed through various fracture processes, including fiber failure, matrix cracking and delamination. An important element in achieving reliable composite systems is a strong capability of assessing and inspecting physical damage of critical structural components. Installation of a robust Structural Health Monitoring (SHM) system would be very valuable in detecting the onset of composite failure. A number of major issues still require serious attention in connection with the research and development aspects of sensor-integrated reliable SHM systems for composite structures. In particular, the sensitivity of currently available sensor systems does not allow detection of micro level damage; this limits the capability of data driven SHM systems. As a fundamental layer in SHM, modeling can provide in-depth information on material and structural behavior for sensing and detection, as well as data for learning algorithms. This dissertation focuses on the development of a multiscale analysis framework, which is used to detect various forms of damage in complex composite structures. A generalized method of cells based micromechanics analysis, as implemented in NASA's MAC/GMC code, is used for the micro-level analysis. First, a baseline study of MAC/GMC is performed to determine the governing failure theories that best capture the damage progression. The deficiencies associated with various layups and loading conditions are addressed. In most micromechanics analysis, a representative unit cell (RUC) with a common fiber packing arrangement is used. The effect of variation in this arrangement within the RUC has been studied and results indicate this variation influences the macro-scale effective material properties and failure stresses. The developed model has been used to simulate impact damage in a composite beam and an airfoil structure. The model data was verified through active interrogation using piezoelectric sensors. The multiscale model was further extended to develop a coupled damage and wave attenuation model, which was used to study different damage states such as fiber-matrix debonding in composite structures with surface bonded piezoelectric sensors.

The structure of the Hospital Anxiety and Depression Scale in four cohorts of community-based, healthy older people: the HALCyon program.

PubMed

Gale, Catharine R; Allerhand, Michael; Sayer, Avan Aihie; Cooper, Cyrus; Dennison, Elaine M; Starr, John M; Ben-Shlomo, Yoav; Gallacher, John E; Kuh, Diana; Deary, Ian J

2010-06-01

The Hospital Anxiety and Depression Scale (HADS) is widely used but evaluation of its psychometric properties has produced equivocal results. Little is known about its structure in non-clinical samples of older people. We used data from four cohorts in the HALCyon collaborative research program into healthy aging: the Caerphilly Prospective Study, the Hertfordshire Ageing Study, the Hertfordshire Cohort Study, and the Lothian Birth Cohort 1921. We used exploratory factor analysis and confirmatory factor analysis with multi-group comparisons to establish the structure of the HADS and test for factorial invariance between samples. Exploratory factor analysis showed a bi-dimensional structure (anxiety and depression) of the scale in men and women in each cohort. We tested a hypothesized three-factor model but high correlations between two of the factors made a two-factor model more psychologically plausible. Multi-group confirmatory factor analysis revealed that the sizes of the respective item loadings on the two factors were effectively identical in men and women from the same cohort. There was more variation between cohorts, particularly those from different parts of the U.K. and in whom the HADS was administered differently. Differences in social-class distribution accounted for part of this variation. Scoring the HADS as two subscales of anxiety and depression is appropriate in non-clinical populations of older men and women. However, there were differences between cohorts in the way that individual items were linked with the constructs of anxiety and depression, perhaps due to differences in sociocultural factors and/or in the administration of the scale.

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.

Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets.

PubMed

Ashford, Paul; Moss, David S; Alex, Alexander; Yeap, Siew K; Povia, Alice; Nobeli, Irene; Williams, Mark A

2012-03-14

Protein structures provide a valuable resource for rational drug design. For a protein with no known ligand, computational tools can predict surface pockets that are of suitable size and shape to accommodate a complementary small-molecule drug. However, pocket prediction against single static structures may miss features of pockets that arise from proteins' dynamic behaviour. In particular, ligand-binding conformations can be observed as transiently populated states of the apo protein, so it is possible to gain insight into ligand-bound forms by considering conformational variation in apo proteins. This variation can be explored by considering sets of related structures: computationally generated conformers, solution NMR ensembles, multiple crystal structures, homologues or homology models. It is non-trivial to compare pockets, either from different programs or across sets of structures. For a single structure, difficulties arise in defining particular pocket's boundaries. For a set of conformationally distinct structures the challenge is how to make reasonable comparisons between them given that a perfect structural alignment is not possible. We have developed a computational method, Provar, that provides a consistent representation of predicted binding pockets across sets of related protein structures. The outputs are probabilities that each atom or residue of the protein borders a predicted pocket. These probabilities can be readily visualised on a protein using existing molecular graphics software. We show how Provar simplifies comparison of the outputs of different pocket prediction algorithms, of pockets across multiple simulated conformations and between homologous structures. We demonstrate the benefits of use of multiple structures for protein-ligand and protein-protein interface analysis on a set of complexes and consider three case studies in detail: i) analysis of a kinase superfamily highlights the conserved occurrence of surface pockets at the active and regulatory sites; ii) a simulated ensemble of unliganded Bcl2 structures reveals extensions of a known ligand-binding pocket not apparent in the apo crystal structure; iii) visualisations of interleukin-2 and its homologues highlight conserved pockets at the known receptor interfaces and regions whose conformation is known to change on inhibitor binding. Through post-processing of the output of a variety of pocket prediction software, Provar provides a flexible approach to the analysis and visualization of the persistence or variability of pockets in sets of related protein structures.

The role of staff in health promotion in community residences for people with intellectual disabilities: variation in views among managers and caregivers.

PubMed

Bergström, Helena; Wihlman, Ulla

2011-09-01

Managers and caregivers in community residences for people with intellectual disabilities are expected both to promote residents' health and to support their autonomy. The aim of this article was to explore variation in views among managers and caregivers on the role of staff in health promotion. A qualitative study was conducted using semi-structured interviews with six managers and six caregivers. The analysis used a phenomenographic approach to categorize variation in views. We identified five qualitatively different main categories of roles staff play in health promotion: the parent, the manipulator, the coach, the educator and the libertarian. In addition lifestyle-related risk factors for ill-health and barriers to a healthy lifestyle were analysed and described using qualitative content analysis. The results highlight the ethical conflict that faces staff trying to support a healthy lifestyle as well as the autonomy of the residents.

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

Statistical techniques applied to aerial radiometric surveys (STAARS): principal components analysis user's manual. [NURE program

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

Koch, C.D.; Pirkle, F.L.; Schmidt, J.S.

1981-01-01

A Principal Components Analysis (PCA) has been written to aid in the interpretation of multivariate aerial radiometric data collected by the US Department of Energy (DOE) under the National Uranium Resource Evaluation (NURE) program. The variations exhibited by these data have been reduced and classified into a number of linear combinations by using the PCA program. The PCA program then generates histograms and outlier maps of the individual variates. Black and white plots can be made on a Calcomp plotter by the application of follow-up programs. All programs referred to in this guide were written for a DEC-10. From thismore » analysis a geologist may begin to interpret the data structure. Insight into geological processes underlying the data may be obtained.« less

Genetic diversity and population structure of an extremely endangered species: the world's largest Rhododendron.

PubMed

Wu, Fu Qin; Shen, Shi Kang; Zhang, Xin Jun; Wang, Yue Hua; Sun, Wei Bang

2014-12-04

Comprehensive studies on the genetic diversity and structure of endangered species are urgently needed to promote effective conservation and management activities. The big tree rhododendron, Rhododendron protistum var. giganteum, is a highly endangered species with only two known endemic populations in a small area in the southern part of Yunnan Province in China. Unfortunately, limited information is available regarding the population genetics of this species. Therefore, we conducted amplified fragment length polymorphism (AFLP) analysis to characterize the genetic diversity and variation of this species within and between remaining populations. Twelve primer combinations of AFLP produced 447 unambiguous and repetitious bands. Among these bands, 298 (66.67 %) were polymorphic. We found high genetic diversity at the species level (percentage of polymorphic loci = 66.67 %, h = 0.240, I = 0.358) and low genetic differentiation (Gst = 0.110) between the two populations. Gene flow between populations (Nm) was relatively high at 4.065. Analysis of molecular variance results revealed that 22 % of the genetic variation was partitioned between populations and 78 % of the genetic variation was within populations. The presence of moderate to high genetic diversity and low genetic differentiation in the two populations can be explained by life history traits, pollen dispersal and high gene flow (Nm = 4.065). Bayesian structure and principal coordinate analysis revealed that 56 sampled trees were clustered into two groups. Our results suggest that some rare and endangered species are able to maintain high levels of genetic diversity even at small population sizes. These results will assist with the design of conservation and management programmes, such as in situ and ex situ conservation, seed collection for germplasm conservation and reintroduction. Published by Oxford University Press on behalf of the Annals of Botany Company.

Contrasting effects of geographical separation on the genetic population structure of sympatric species of mites in avocado orchards.

PubMed

Guzman-Valencia, S; Santillán-Galicia, M T; Guzmán-Franco, A W; González-Hernández, H; Carrillo-Benítez, M G; Suárez-Espinoza, J

2014-10-01

Oligonychus punicae and Oligonychus perseae (Acari: Tetranychidae) are the most important mite species affecting avocado orchards in Mexico. Here we used nucleotide sequence data from segments of the nuclear ribosomal internal transcribed spacers (ITS1 and ITS2) and mitochondrial cytochrome oxidase subunit I (COI) genes to assess the phylogenetic relationships between both sympatric mite species and, using only ITS sequence data, examine genetic variation and population structure in both species, to test the hypothesis that, although both species co-occur, their genetic population structures are different in both Michoacan state (main producer) and Mexico state. Phylogenetic analysis showed a clear separation between both species using ITS and COI sequence information. Haplotype network analysis done on 24 samples of O. punicae revealed low genetic diversity with only three haplotypes found but a significant geographical population structure confirmed by analysis of molecular variance (AMOVA) and Kimura-2-parameter (K2P) analyses. In addition, a Mantel test revealed that geographical isolation was a factor responsible for the genetic differentiation. In contrast, analyses of 22 samples of O. perseae revealed high genetic diversity with 15 haplotypes found but no geographical structure confirmed by the AMOVA, K2P and Mantel test analyses. We have suggested that geographical separation is one of the most important factors driving genetic variation, but that it affected each species differently. The role of the ecology of these species on our results, and the importance of our findings in the development of monitoring and control strategies are discussed.

Spectral analysis of magnetic anomalies in and around the Philippine Sea

NASA Astrophysics Data System (ADS)

Tanaka, A.; Ishihara, T.

2009-12-01

Regional compilations of lithospheric structure from various methods and data and comparison among them are useful to understand lithospheric structure and the processes behind its formation and evolution. We present constraints on the regional variations of the magnetic thicknesses in and around the Philippine Sea. We used a new global magnetic anomaly data [Quesnel et al, 2009], which is CM4-corrected [Comprehensive Model 4; Sabaka et al., 2004], cleaned and leveled to clarify the three-dimensional crustal magnetic structure of the Philippine Sea. The Philippine Sea is one of the largest marginal seas of the world. The north-south-trending Kyushu-Palau Ridge divides it into two parts: the West Philippine Basin and the Daito Ridge province in the west and the Shikoku and Parece Vela Basins in the east. The age of the basins increases westward [Karig, 1971]. And, there are three ridges in the Daito Ridge province west of the Kyushu-Palau Ridge; the Oki-Daito, Daito Ridges and the Amami Plateau from south to north, and small basins among them. Two-dimensional spectral analysis of marine magnetic anomalies is used to estimate the centroid of magnetic sources (Zo) to constrain the lithospheric structure [Tanaka and Ishihara, 2008]. The method is based on that of Spector and Grant [1970]. Zo distribution of the Philippine Sea shows occurrence of shallow magnetic layer areas with approximately less than 10 km in the Shikoku Basin. It also shows variations in deep and shallow magnetic layer areas in the Amami-Daito Province. These patters correspond to spatial variations of the crustal thickness deduced from the three-dimensional gravity modeling [Ishihara and Koda, 2007] and acoustic basement structures [Higuchi et al., 2007]. These three spatial distributions are roughly consistent with each other, although they may contain some scatters and bias due to the different characteristics and errors. This two-dimensional spectral analysis method is based upon an assumption that source distribution is random; therefore when magnetic anomalies represent linear features, this analysis based on ensembles of thin prisms may produce unreliable results. In this case, one-dimensional spectrum analysis based on a thin plate model composed of long bars is preferable. Makino and Okubo [1988] developed one-dimensional spectral analysis for marine linear magnetic anomalies. A linear relationship between the natural log of (power-density spectrum of magnetic profile) and wavelength gives the centroid depth of magnetic sources. The same method is applied to this area. This analysis requires a long profile to see deeper structure. It may not be possible to find good enough data. However, both methods give consistent results, and the obtained Zo distribution provides a comprehensive view of regional-scale features. The correlation between crustal thickness and Zo and its correspondence with tectonic regime indicates that Zo is useful to delineate regional crustal thermal structure. It is expected that Zo combined with multidisciplinary data should help to infer geophysical and geological information in the less explored regions.

Scanning capacitance microscopy of ErAs nanoparticles embedded in GaAs pn junctions

NASA Astrophysics Data System (ADS)

Park, K. W.; Nair, H. P.; Crook, A. M.; Bank, S. R.; Yu, E. T.

2011-09-01

Scanning capacitance microscopy is used to characterize the electronic properties of ErAs nanoparticles embedded in GaAs pn junctions grown by molecular beam epitaxy. Voltage-dependent capacitance images reveal localized variations in subsurface electronic structure near buried ErAs nanoparticles at lateral length scales of 20-30 nm. Numerical modeling indicates that these variations arise from inhomogeneities in charge modulation due to Fermi level pinning behavior associated with the embedded ErAs nanoparticles. Statistical analysis of image data yields an average particle radius of 6-8 nm—well below the direct resolution limit in scanning capacitance microscopy but discernible via analysis of patterns in nanoscale capacitance images.

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.

Distinct Phylogeographic Structures of Wild Radish (Raphanus sativus L. var. raphanistroides Makino) in Japan

PubMed Central

Han, Qingxiang; Higashi, Hiroyuki; Mitsui, Yuki; Setoguchi, Hiroaki

2015-01-01

Coastal plants with simple linear distribution ranges along coastlines provide a suitable system for improving our understanding of patterns of intra-specific distributional history and genetic variation. Due to the combination of high seed longevity and high dispersibility of seeds via seawater, we hypothesized that wild radish would poorly represent phylogeographic structure at the local scale. On the other hand, we also hypothesized that wild radish populations might be geographically differentiated, as has been exhibited by their considerable phenotypic variations along the islands of Japan. We conducted nuclear DNA microsatellite loci and chloroplast DNA haplotype analyses for 486 samples and 144 samples, respectively, from 18 populations to investigate the phylogeographic structure of wild radish in Japan. Cluster analysis supported the existence of differential genetic structures between the Ryukyu Islands and mainland Japan populations. A significant strong pattern of isolation by distance and significant evidence of a recent bottleneck were detected. The chloroplast marker analysis resulted in the generation of eight haplotypes, of which two haplotypes (A and B) were broadly distributed in most wild radish populations. High levels of variation in microsatellite loci were identified, whereas cpDNA displayed low levels of genetic diversity within populations. Our results indicate that the Kuroshio Current would have contributed to the sculpting of the phylogeographic structure by shaping genetic gaps between isolated populations. In addition, the Tokara Strait would have created a geographic barrier between the Ryukyu Islands and mainland Japan. Finally, extant habitat disturbances (coastal erosion), migration patterns (linear expansion), and geographic characteristics (small islands and sea currents) have influenced the expansion and historical population dynamics of wild radish. Our study is the first to record the robust phylogeographic structure in wild radish between the Ryukyu Islands and mainland Japan, and might provide new insight into the genetic differentiation of coastal plants across islands. PMID:26247202

Western North Pacific Tropical Cyclone Formation and Structure Change in TCS-08

DTIC Science & Technology

2011-09-30

cyclones often transition to a fast-moving and rapidly- developing extratropical cyclone that may contain gale-, storm -, or hurricane-force winds... storm begins the process of extratropical transition have revealed the role of vertical wind shear in defining structural variations related to the...horizontal wind radii as the storm starts the process of extratropical transition. Elsberry et al. (2011) have extended the analysis of the

Extensive Copy Number Variations in Admixed Indian Population of African Ancestry: Potential Involvement in Adaptation

PubMed Central

Dash, Debasis; Mukerji, Mitali

2014-01-01

Admixture mapping has been enormously resourceful in identifying genetic variations linked to phenotypes, adaptation, and diseases. In this study through analysis of copy number variable regions (CNVRs), we report extensive restructuring in the genomes of the recently admixed African-Indian population (OG-W-IP) that inhabits a highly saline environment in Western India. The study included subjects from OG-W-IP (OG), five different Indian and three HapMap populations that were genotyped using Affymetrix version 6.0 arrays. Copy number variations (CNVs) detected using Birdsuite were used to define CNVRs. Population structure with respect to CNVRs was delineated using random forest approach. OG genomes have a surprising excess of CNVs in comparison to other studied populations. Individual ancestry proportions computed using STRUCTURE also reveals a unique genetic component in OGs. Population structure analysis with CNV genotypes indicates OG to be distant from both the African and Indian ancestral populations. Interestingly, it shows genetic proximity with respect to CNVs to only one Indian population IE-W-LP4, which also happens to reside in the same geographical region. We also observe a significant enrichment of molecular processes related to ion binding and receptor activity in genes encompassing OG-specific CNVRs. Our results suggest that retention of CNVRs from ancestral natives and de novo acquisition of CNVRs could accelerate the process of adaptation especially in an extreme environment. Additionally, this population would be enormously useful for dissecting genes and delineating the involvement of CNVs in salt adaptation. PMID:25398783

Assessment of variations in taxonomic diversity, forest structure, and aboveground biomass using remote sensing along an altitudinal gradient in tropical montane forest of Costa Rica

NASA Astrophysics Data System (ADS)

Robinson, C. M.; Saatchi, S. S.; Clark, D.; Fricker, G. A.; Wolf, J.; Gillespie, T. W.; Rovzar, C. M.; Andelman, S.

2012-12-01

This research sought to understand how alpha and beta diversity of plants vary and relate to the three-dimensional vegetation structure and aboveground biomass along environmental gradients in the tropical montane forests of Braulio Carrillo National Park in Costa Rica. There is growing evidence that ecosystem structure plays an important role in defining patterns of species diversity and along with abiotic factors (climate and edaphic) control the phenotypic and functional variations across landscapes. It is well documented that strong subdivisions at local and regional scales are found mainly on geologic or climate gradients. These general determinants of biodiversity are best demonstrated in regions with natural gradients such as tropical montane forests. Altitudinal gradients provide a landscape scale changes through variations in topography, climate, and edaphic conditions on which we tested several theoretical and biological hypotheses regarding drivers of biodiversity. The study was performed by using forest inventory and botanical data from nine 1-ha plots ranging from 100 m to 2800 m above sea level and remote sensing data from airborne lidar and radar sensors to quantify variations in forest structure. In this study we report on the effectiveness of relating patterns of tree taxonomic alpha diversity to three-dimensional structure of a tropical montane forest using lidar and radar observations of forest structure and biomass. We assessed alpha and beta diversity at the species, genus, and family levels utilizing datasets provided by the Terrestrial Ecology Assessment and Monitoring (TEAM) Network. Through the comparison to active remote sensing imagery, our results show that there is a strong relationship between forest 3D-structure, and alpha and beta diversity controlled by variations in abiotic factors along the altitudinal gradient. Using spatial analysis with the aid of remote sensing data, we find distinct patterns along the environmental gradients defining species turnover and changes in functional diversity. The study will provide novel approaches to use detailed spatial information from remote sensing data to study relations between functional and taxonomic dimensions of diversity.

Dynamic response analysis of structure under time-variant interval process model

NASA Astrophysics Data System (ADS)

Xia, Baizhan; Qin, Yuan; Yu, Dejie; Jiang, Chao

2016-10-01

Due to the aggressiveness of the environmental factor, the variation of the dynamic load, the degeneration of the material property and the wear of the machine surface, parameters related with the structure are distinctly time-variant. Typical model for time-variant uncertainties is the random process model which is constructed on the basis of a large number of samples. In this work, we propose a time-variant interval process model which can be effectively used to deal with time-variant uncertainties with limit information. And then two methods are presented for the dynamic response analysis of the structure under the time-variant interval process model. The first one is the direct Monte Carlo method (DMCM) whose computational burden is relative high. The second one is the Monte Carlo method based on the Chebyshev polynomial expansion (MCM-CPE) whose computational efficiency is high. In MCM-CPE, the dynamic response of the structure is approximated by the Chebyshev polynomials which can be efficiently calculated, and then the variational range of the dynamic response is estimated according to the samples yielded by the Monte Carlo method. To solve the dependency phenomenon of the interval operation, the affine arithmetic is integrated into the Chebyshev polynomial expansion. The computational effectiveness and efficiency of MCM-CPE is verified by two numerical examples, including a spring-mass-damper system and a shell structure.

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

Harnessing cell-to-cell variations to probe bacterial structure and biophysics

NASA Astrophysics Data System (ADS)

Cass, Julie A.

Advances in microscopy and biotechnology have given us novel insights into cellular biology and physics. While bacteria were long considered to be relatively unstructured, the development of fluorescence microscopy techniques, and spatially and temporally resolved high-throughput quantitative studies, have uncovered that the bacterial cell is highly organized, and its structure rigorously maintained. In this thesis I will describe our gateTool software, designed to harness cell-to-cell variations to probe bacterial structure, and discuss two exciting aspects of structure that we have employed gateTool to investigate: (i) chromosome organization and the cellular mechanisms for controlling DNA dynamics, and (ii) the study of cell wall synthesis, and how the genes in the synthesis pathway impact cellular shape. In the first project, we develop a spatial and temporal mapping of cell-cycle-dependent chromosomal organization, and use this quantitative map to discover that chromosomal loci segregate from midcell with universal dynamics. In the second project, I describe preliminary time- lapse and snapshot imaging analysis suggesting phentoypical coherence across peptidoglycan synthesis pathways.

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.

Genetic variation, population structure and linkage disequilibrium in Switchgrass with ISSR, SCoT and EST-SSR markers.

PubMed

Zhang, Yu; Yan, Haidong; Jiang, Xiaomei; Wang, Xiaoli; Huang, Linkai; Xu, Bin; Zhang, Xinquan; Zhang, Lexin

2016-01-01

To evaluate genetic variation, population structure, and the extent of linkage disequilibrium (LD), 134 switchgrass ( Panicum virgatum L.) samples were analyzed with 51 markers, including 16 ISSRs, 20 SCoTs, and 15 EST-SSRs. In this study, a high level of genetic variation was observed in the switchgrass samples and they had an average Nei's gene diversity index (H) of 0.311. A total of 793 bands were obtained, of which 708 (89.28 %) were polymorphic. Using a parameter marker index (MI), the efficiency of the three types of markers (ISSR, SCoT, and EST-SSR) in the study were compared and we found that SCoT had a higher marker efficiency than the other two markers. The 134 switchgrass samples could be divided into two sub-populations based on STRUCTURE, UPGMA clustering, and principal coordinate analyses (PCA), and upland and lowland ecotypes could be separated by UPGMA clustering and PCA analyses. Linkage disequilibrium analysis revealed an average r 2 of 0.035 across all 51 markers, indicating a trend of higher LD in sub-population 2 than that in sub-population 1 ( P  < 0.01). The population structure revealed in this study will guide the design of future association studies using these switchgrass samples.

Tuning and Freezing Disorder in Photonic Crystals using Percolation Lithography.

PubMed

Burgess, Ian B; Abedzadeh, Navid; Kay, Theresa M; Shneidman, Anna V; Cranshaw, Derek J; Lončar, Marko; Aizenberg, Joanna

2016-01-21

Although common in biological systems, synthetic self-assembly routes to complex 3D photonic structures with tailored degrees of disorder remain elusive. Here we show how liquids can be used to finely control disorder in porous 3D photonic crystals, leading to complex and hierarchical geometries. In these optofluidic crystals, dynamically tunable disorder is superimposed onto the periodic optical structure through partial wetting or evaporation. In both cases, macroscopic symmetry breaking is driven by subtle sub-wavelength variations in the pore geometry. These variations direct site-selective infiltration of liquids through capillary interactions. Incorporating cross-linkable resins into our liquids, we developed methods to freeze in place the filling patterns at arbitrary degrees of partial wetting and intermediate stages of drying. These percolation lithography techniques produced permanent photonic structures with adjustable disorder. By coupling strong changes in optical properties to subtle differences in fluid behavior, optofluidic crystals may also prove useful in rapid analysis of liquids.

Hippocampal dentation: Structural variation and its association with episodic memory in healthy adults.

PubMed

Fleming Beattie, Julia; Martin, Roy C; Kana, Rajesh K; Deshpande, Hrishikesh; Lee, Seongtaek; Curé, Joel; Ver Hoef, Lawrence

2017-07-01

While the hippocampus has long been identified as a structure integral to memory, the relationship between morphology and function has yet to be fully explained. We present an analysis of hippocampal dentation, a morphological feature previously unexplored in regard to its relationship with episodic memory. "Hippocampal dentation" in this case refers to surface convolutions, primarily present in the CA1/subiculum on the inferior aspect of the hippocampus. Hippocampal dentation was visualized using ultra-high resolution structural MRI and evaluated using a novel visual rating scale. The degree of hippocampal dentation was found to vary considerably across individuals, and was positively associated with verbal memory recall and visual memory recognition in a sample of 22 healthy adults. This study is the first to characterize the variation in hippocampal dentation in a healthy cohort and to demonstrate its association with aspects of episodic memory. Copyright © 2017 Elsevier Ltd. All rights reserved.

A search for stability gradients in North American breeding bird communities

USGS Publications Warehouse

Noon, B.R.; Dawson, D.K.; Kelly, J.P.

1985-01-01

To search for the existence of stability gradients in North American breeding land bird communities we operationally defined stability (after Jarvinen 1979) as year-to-year persistence in species composition and distribution of species abundances. From the census data for 174 study plots we derived nine indices that estimate the annual variability of species composition, the species abundance distribution, diversity, and breeding density. The resulting matrix of study plot by stability indices was used to estimate the correlation structure of the stability indices. The correlation matrix was, in turn, subjected to a principal components analysis to derive synthetic gradients of variation. We then searched for patterns of variation in these stability gradients associated with either geographic location or habitat type. Three independent principal component axes reproduced most of the variation in the initial data and were interpreted as gradients of variation in species turnover, diversity, and breeding abundance. Thus, the annual stability of community structure apparently responds independently to species and abundance variation. Despite the clarity of the derived gradients, few patterns emerged when the plots were ordinated by either habitat or geographic location. In general, grasslands showed greater annual variation in diversity than forested habitats, and, for some habitats, northern communities were less stable than more southern communities. However, few of these patterns were very strong, and we interpret them cautiously.

Climate variables explain neutral and adaptive variation within salmonid metapopulations: The importance of replication in landscape genetics

USGS Publications Warehouse

Hand, Brian K.; Muhlfeld, Clint C.; Wade, Alisa A.; Kovach, Ryan; Whited, Diane C.; Narum, Shawn R.; Matala, Andrew P.; Ackerman, Michael W.; Garner, B. A.; Kimball, John S; Stanford, Jack A.; Luikart, Gordon

2016-01-01

Understanding how environmental variation influences population genetic structure is important for conservation management because it can reveal how human stressors influence population connectivity, genetic diversity and persistence. We used riverscape genetics modelling to assess whether climatic and habitat variables were related to neutral and adaptive patterns of genetic differentiation (population-specific and pairwise FST) within five metapopulations (79 populations, 4583 individuals) of steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin, USA. Using 151 putatively neutral and 29 candidate adaptive SNP loci, we found that climate-related variables (winter precipitation, summer maximum temperature, winter highest 5% flow events and summer mean flow) best explained neutral and adaptive patterns of genetic differentiation within metapopulations, suggesting that climatic variation likely influences both demography (neutral variation) and local adaptation (adaptive variation). However, we did not observe consistent relationships between climate variables and FST across all metapopulations, underscoring the need for replication when extrapolating results from one scale to another (e.g. basin-wide to the metapopulation scale). Sensitivity analysis (leave-one-population-out) revealed consistent relationships between climate variables and FST within three metapopulations; however, these patterns were not consistent in two metapopulations likely due to small sample sizes (N = 10). These results provide correlative evidence that climatic variation has shaped the genetic structure of steelhead populations and highlight the need for replication and sensitivity analyses in land and riverscape genetics.

Additive genetic variation and evolvability of a multivariate trait can be increased by epistatic gene action.

PubMed

Griswold, Cortland K

2015-12-21

Epistatic gene action occurs when mutations or alleles interact to produce a phenotype. Theoretically and empirically it is of interest to know whether gene interactions can facilitate the evolution of diversity. In this paper, we explore how epistatic gene action affects the additive genetic component or heritable component of multivariate trait variation, as well as how epistatic gene action affects the evolvability of multivariate traits. The analysis involves a sexually reproducing and recombining population. Our results indicate that under stabilizing selection conditions a population with a mixed additive and epistatic genetic architecture can have greater multivariate additive genetic variation and evolvability than a population with a purely additive genetic architecture. That greater multivariate additive genetic variation can occur with epistasis is in contrast to previous theory that indicated univariate additive genetic variation is decreased with epistasis under stabilizing selection conditions. In a multivariate setting, epistasis leads to less relative covariance among individuals in their genotypic, as well as their breeding values, which facilitates the maintenance of additive genetic variation and increases a population׳s evolvability. Our analysis involves linking the combinatorial nature of epistatic genetic effects to the ancestral graph structure of a population to provide insight into the consequences of epistasis on multivariate trait variation and evolution. Copyright © 2015 Elsevier Ltd. All rights reserved.

Lithospheric Structure from Mars Global Surveyor Topography and Gravity and Implications for the Early Thermal Evolution of Mars

NASA Technical Reports Server (NTRS)

Solomon, Sean C.; Zuber, Maria T.; Phillips, Roger J.; Smith, David E.; Tyler, G. Leonard; Aharonson, Oded; Balmino, Georges; Banerdt, W. B.; Head, James W.; Johnson, Catherine L.

2000-01-01

Regional variations in the thickness of the elastic lithosphere on Mars derived from a combined analysis of topography and gravity anomalies determined by Mars Global Surveyor provide new insight into the planet's thermal history.

Genotype-phenotype association study via new multi-task learning model

PubMed Central

Huo, Zhouyuan; Shen, Dinggang

2018-01-01

Research on the associations between genetic variations and imaging phenotypes is developing with the advance in high-throughput genotype and brain image techniques. Regression analysis of single nucleotide polymorphisms (SNPs) and imaging measures as quantitative traits (QTs) has been proposed to identify the quantitative trait loci (QTL) via multi-task learning models. Recent studies consider the interlinked structures within SNPs and imaging QTs through group lasso, e.g. ℓ2,1-norm, leading to better predictive results and insights of SNPs. However, group sparsity is not enough for representing the correlation between multiple tasks and ℓ2,1-norm regularization is not robust either. In this paper, we propose a new multi-task learning model to analyze the associations between SNPs and QTs. We suppose that low-rank structure is also beneficial to uncover the correlation between genetic variations and imaging phenotypes. Finally, we conduct regression analysis of SNPs and QTs. Experimental results show that our model is more accurate in prediction than compared methods and presents new insights of SNPs. PMID:29218896

COSMOS: accurate detection of somatic structural variations through asymmetric comparison between tumor and normal samples

PubMed Central

Yamagata, Koichi; Yamanishi, Ayako; Kokubu, Chikara; Takeda, Junji; Sese, Jun

2016-01-01

An important challenge in cancer genomics is precise detection of structural variations (SVs) by high-throughput short-read sequencing, which is hampered by the high false discovery rates of existing analysis tools. Here, we propose an accurate SV detection method named COSMOS, which compares the statistics of the mapped read pairs in tumor samples with isogenic normal control samples in a distinct asymmetric manner. COSMOS also prioritizes the candidate SVs using strand-specific read-depth information. Performance tests on modeled tumor genomes revealed that COSMOS outperformed existing methods in terms of F-measure. We also applied COSMOS to an experimental mouse cell-based model, in which SVs were induced by genome engineering and gamma-ray irradiation, followed by polymerase chain reaction-based confirmation. The precision of COSMOS was 84.5%, while the next best existing method was 70.4%. Moreover, the sensitivity of COSMOS was the highest, indicating that COSMOS has great potential for cancer genome analysis. PMID:26833260

NPSS Multidisciplinary Integration and Analysis

NASA Technical Reports Server (NTRS)

Hall, Edward J.; Rasche, Joseph; Simons, Todd A.; Hoyniak, Daniel

2006-01-01

The objective of this task was to enhance the capability of the Numerical Propulsion System Simulation (NPSS) by expanding its reach into the high-fidelity multidisciplinary analysis area. This task investigated numerical techniques to convert between cold static to hot running geometry of compressor blades. Numerical calculations of blade deformations were iteratively done with high fidelity flow simulations together with high fidelity structural analysis of the compressor blade. The flow simulations were performed with the Advanced Ducted Propfan Analysis (ADPAC) code, while structural analyses were performed with the ANSYS code. High fidelity analyses were used to evaluate the effects on performance of: variations in tip clearance, uncertainty in manufacturing tolerance, variable inlet guide vane scheduling, and the effects of rotational speed on the hot running geometry of the compressor blades.

Structural damage detection based on stochastic subspace identification and statistical pattern recognition: I. Theory

NASA Astrophysics Data System (ADS)

Ren, W. X.; Lin, Y. Q.; Fang, S. E.

2011-11-01

One of the key issues in vibration-based structural health monitoring is to extract the damage-sensitive but environment-insensitive features from sampled dynamic response measurements and to carry out the statistical analysis of these features for structural damage detection. A new damage feature is proposed in this paper by using the system matrices of the forward innovation model based on the covariance-driven stochastic subspace identification of a vibrating system. To overcome the variations of the system matrices, a non-singularity transposition matrix is introduced so that the system matrices are normalized to their standard forms. For reducing the effects of modeling errors, noise and environmental variations on measured structural responses, a statistical pattern recognition paradigm is incorporated into the proposed method. The Mahalanobis and Euclidean distance decision functions of the damage feature vector are adopted by defining a statistics-based damage index. The proposed structural damage detection method is verified against one numerical signal and two numerical beams. It is demonstrated that the proposed statistics-based damage index is sensitive to damage and shows some robustness to the noise and false estimation of the system ranks. The method is capable of locating damage of the beam structures under different types of excitations. The robustness of the proposed damage detection method to the variations in environmental temperature is further validated in a companion paper by a reinforced concrete beam tested in the laboratory and a full-scale arch bridge tested in the field.

A comparative molecular analysis of water-filled limestone sinkholes in north-eastern Mexico.

PubMed

Sahl, Jason W; Gary, Marcus O; Harris, J Kirk; Spear, John R

2011-01-01

Sistema Zacatón in north-eastern Mexico is host to several deep, water-filled, anoxic, karstic sinkholes (cenotes). These cenotes were explored, mapped, and geochemically and microbiologically sampled by the autonomous underwater vehicle deep phreatic thermal explorer (DEPTHX). The community structure of the filterable fraction of the water column and extensive microbial mats that coat the cenote walls was investigated by comparative analysis of small-subunit (SSU) 16S rRNA gene sequences. Full-length Sanger gene sequence analysis revealed novel microbial diversity that included three putative bacterial candidate phyla and three additional groups that showed high intra-clade distance with poorly characterized bacterial candidate phyla. Limited functional gene sequence analysis in these anoxic environments identified genes associated with methanogenesis, sulfate reduction and anaerobic ammonium oxidation. A directed, barcoded amplicon, multiplex pyrosequencing approach was employed to compare ∼100,000 bacterial SSU gene sequences from water column and wall microbial mat samples from five cenotes in Sistema Zacatón. A new, high-resolution sequence distribution profile (SDP) method identified changes in specific phylogenetic types (phylotypes) in microbial mats at varied depths; Mantel tests showed a correlation of the genetic distances between mat communities in two cenotes and the geographic location of each cenote. Community structure profiles from the water column of three neighbouring cenotes showed distinct variation; statistically significant differences in the concentration of geochemical constituents suggest that the variation observed in microbial communities between neighbouring cenotes are due to geochemical variation. © 2010 Society for Applied Microbiology and Blackwell Publishing Ltd.

Contrasting patterns of fine-scale herb layer species composition in temperate forests

NASA Astrophysics Data System (ADS)

Chudomelová, Markéta; Zelený, David; Li, Ching-Feng

2017-04-01

Although being well described at the landscape level, patterns in species composition of forest herb layer are rarely studied at smaller scales. Here, we examined fine-scale environmental determinants and spatial structures of herb layer communities in thermophilous oak- and hornbeam dominated forests of the south-eastern part of the Czech Republic. Species composition of herb layer vegetation and environmental variables were recorded within a fixed grid of 2 × 2 m subplots regularly distributed within 1-ha quadrate plots in three forest stands. For each site, environmental models best explaining species composition were constructed using constrained ordination analysis. Spatial eigenvector mapping was used to model and account for spatial structures in community variation. Mean Ellenberg indicator values calculated for each subplot were used for ecological interpretation of spatially structured residual variation. The amount of variation explained by environmental and spatial models as well as the selection of variables with the best explanatory power differed among sites. As an important environmental factor, relative elevation was common to all three sites, while pH and canopy openness were shared by two sites. Both environmental and community variation was mostly coarse-scaled, as was the spatially structured portion of residual variation. When corrected for bias due to spatial autocorrelation, those environmental factors with already weak explanatory power lost their significance. Only a weak evidence of possibly omitted environmental predictor was found for autocorrelated residuals of site models using mean Ellenberg indicator values. Community structure was determined by different factors at different sites. The relative importance of environmental filtering vs. spatial processes was also site specific, implying that results of fine-scale studies tend to be shaped by local conditions. Contrary to expectations based on other studies, overall dominance of spatial processes at fine scale has not been detected. Ecologists should keep this in mind when making generalizations about community dynamics.

Linear and nonlinear dynamic analysis by boundary element method. Ph.D. Thesis, 1986 Final Report

NASA Technical Reports Server (NTRS)

Ahmad, Shahid

1991-01-01

An advanced implementation of the direct boundary element method (BEM) applicable to free-vibration, periodic (steady-state) vibration and linear and nonlinear transient dynamic problems involving two and three-dimensional isotropic solids of arbitrary shape is presented. Interior, exterior, and half-space problems can all be solved by the present formulation. For the free-vibration analysis, a new real variable BEM formulation is presented which solves the free-vibration problem in the form of algebraic equations (formed from the static kernels) and needs only surface discretization. In the area of time-domain transient analysis, the BEM is well suited because it gives an implicit formulation. Although the integral formulations are elegant, because of the complexity of the formulation it has never been implemented in exact form. In the present work, linear and nonlinear time domain transient analysis for three-dimensional solids has been implemented in a general and complete manner. The formulation and implementation of the nonlinear, transient, dynamic analysis presented here is the first ever in the field of boundary element analysis. Almost all the existing formulation of BEM in dynamics use the constant variation of the variables in space and time which is very unrealistic for engineering problems and, in some cases, it leads to unacceptably inaccurate results. In the present work, linear and quadratic isoparametric boundary elements are used for discretization of geometry and functional variations in space. In addition, higher order variations in time are used. These methods of analysis are applicable to piecewise-homogeneous materials, such that not only problems of the layered media and the soil-structure interaction can be analyzed but also a large problem can be solved by the usual sub-structuring technique. The analyses have been incorporated in a versatile, general-purpose computer program. Some numerical problems are solved and, through comparisons with available analytical and numerical results, the stability and high accuracy of these dynamic analysis techniques are established.

The role of the mitochondrial ribosome in human disease: searching for mutations in 12S mitochondrial rRNA with high disruptive potential

PubMed Central

Smith, Paul M.; Elson, Joanna L.; Greaves, Laura C.; Wortmann, Saskia B.; Rodenburg, Richard J.T.; Lightowlers, Robert N.; Chrzanowska-Lightowlers, Zofia M.A.; Taylor, Robert W.; Vila-Sanjurjo, Antón

2014-01-01

Mutations of mitochondrial DNA are linked to many human diseases. Despite the identification of a large number of variants in the mitochondrially encoded rRNA (mt-rRNA) genes, the evidence supporting their pathogenicity is, at best, circumstantial. Establishing the pathogenicity of these variations is of major diagnostic importance. Here, we aim to estimate the disruptive effect of mt-rRNA variations on the function of the mitochondrial ribosome. In the absence of direct biochemical methods to study the effect of mt-rRNA variations, we relied on the universal conservation of the rRNA fold to infer their disruptive potential. Our method, named heterologous inferential analysis or HIA, combines conservational information with functional and structural data obtained from heterologous ribosomal sources. Thus, HIA's predictive power is superior to the traditional reliance on simple conservation indexes. By using HIA, we have been able to evaluate the disruptive potential for a subset of uncharacterized 12S mt-rRNA variations. Our analysis revealed the existence of variations in the rRNA component of the human mitoribosome with different degrees of disruptive power. In cases where sufficient information regarding the genetic and pathological manifestation of the mitochondrial phenotype is available, HIA data can be used to predict the pathogenicity of mt-rRNA mutations. In other cases, HIA analysis will allow the prioritization of variants for additional investigation. Eventually, HIA-inspired analysis of potentially pathogenic mt-rRNA variations, in the context of a scoring system specifically designed for these variants, could lead to a powerful diagnostic tool. PMID:24092330

Phenotypic and Genetic Variations in Obligate Parthenogenetic Populations of Eriosoma lanigerum Hausmann (Hemiptera: Aphididae).

PubMed

Ruiz-Montoya, L; Zúñiga, G; Cisneros, R; Salinas-Moreno, Y; Peña-Martínez, R; Machkour-M'Rabet, S

2015-12-01

The study of phenotypic and genetic variation of obligate parthenogenetic organisms contributes to an understanding of evolution in the absence of genetic variation produced by sexual reproduction. Eriosoma lanigerum Hausmann undergoes obligate parthenogenesis in Mexico City, Mexico, due to the unavailability of the host plants required for sexual reproduction. We analysed the phenotypic and genetic variation of E. lanigerum in relation to the dry and wet season and plant phenology. Aphids were collected on two occasions per season on a secondary host plant, Pyracantha koidzumii, at five different sites in the southern area of Mexico City, Mexico. Thirteen morphological characteristics were measured from 147 to 276 individuals per site and per season. A multivariate analysis of variance was performed to test the effect of the season, site and their interaction on morphological traits. Morphological variation was summarised using a principal component analysis. Genetic variation was described using six enzymatic loci, four of which were polymorphic. Our study showed that the site and season has a significant effect on morphological trait variation. The largest aphids were recorded during cold temperatures with low relative humidity and when the plant was at the end of the fruiting period. The mean genetic diversity was low (mean H e =  .161), and populations were genetically structured by season and site. Morphological and genetic variations appear to be associated with environmental factors that directly affect aphid development and/or indirectly by host plant phenology.

Characteristics of ACS-verified Level I and Level II trauma centers: A study linking trauma center verification review data and the National Trauma Data Bank of the American College of Surgeons Committee on Trauma.

PubMed

Shafi, Shahid; Barnes, Sunni; Ahn, Chul; Hemilla, Mark R; Cryer, H Gill; Nathens, Avery; Neal, Melanie; Fildes, John

2016-10-01

The Trauma Quality Improvement Project of the American College of Surgeons (ACS) has demonstrated variations in trauma center outcomes despite similar verification status. The purpose of this study was to identify structural characteristics of trauma centers that affect patient outcomes. Trauma registry data on 361,187 patients treated at 222 ACS-verified Level I and Level II trauma centers were obtained from the National Trauma Data Bank of ACS. These data were used to estimate each center's observed-to-expected (O-E) mortality ratio with 95% confidence intervals using multivariate logistic regression analysis. De-identified data on structural characteristics of these trauma centers were obtained from the ACS Verification Review Committee. Centers in the lowest quartile of mortality based on O-E ratio (n = 56) were compared to the rest (n = 166) using Classification and Regression Tree (CART) analysis to identify institutional characteristics independently associated with high-performing centers. Of the 72 structural characteristics explored, only 3 were independently associated with high-performing centers: annual patient visits to the emergency department of fewer than 61,000; proportion of patients on Medicare greater than 20%; and continuing medical education for emergency department physician liaison to the trauma program ranging from 55 and 113 hours annually. Each 5% increase in O-E mortality ratio was associated with an increase in total length of stay of one day (r = 0.25; p < 0.001). Very few structural characteristics of ACS-verified trauma centers are associated with risk-adjusted mortality. Thus, variations in patient outcomes across trauma centers are likely related to variations in clinical practices. Therapeutic study, level III.

The effect of unions on the distribution of wages of hospital-employed registered nurses in the United States.

PubMed

Spetz, Joanne; Ash, Michael; Konstantinidis, Charalampos; Herrera, Carolina

2011-01-01

We estimate the impact of unionisation on the wage structure of hospital-employed registered nurses in the USA. We examine whether unions have an effect on wage differences associated with race, gender, immigration status, education and experience, as well as whether there is less unexplained wage variation among unionised nurses. In the past decade, there has been resurgence in union activity in the health care industry in the USA, particularly in hospitals. Numerous studies have found that unions are associated with higher wages. Unions may also affect the structure of wages paid to workers, by compressing the wage structure and reducing unexplained variation in wages. Cross-sectional analysis of pooled secondary data from the United States Current Population Survey, 2003-2006. Multivariate regression analysis of factors that predict wages, with models derived from labour economics. There are no wage differences associated with gender, race or immigration status among unionised nurses, but there are wage penalties for black and immigrant nurses in the non-union sector. For the most part, the pay structures of the union and non-union sectors do not significantly differ. The wage penalty associated with diploma education for non-union nurses disappears among unionised nurses. Unionised nurses receive a lower return to experience, although the difference is not statistically significant. There is no evidence that unexplained variation in wages is lower among unionised nurses. While in theory unions may rationalise wage-setting and reduce wage dispersion, we found no evidence to support this hypothesis. The primary effect of hospital unions is to raise wages. Unionisation does not appear to have other important wage effects among hospital-employed nurses. © 2010 Blackwell Publishing Ltd.

Machine Learning and Network Analysis of Molecular Dynamics Trajectories Reveal Two Chains of Red/Ox-specific Residue Interactions in Human Protein Disulfide Isomerase.

PubMed

Karamzadeh, Razieh; Karimi-Jafari, Mohammad Hossein; Sharifi-Zarchi, Ali; Chitsaz, Hamidreza; Salekdeh, Ghasem Hosseini; Moosavi-Movahedi, Ali Akbar

2017-06-16

The human protein disulfide isomerase (hPDI), is an essential four-domain multifunctional enzyme. As a result of disulfide shuffling in its terminal domains, hPDI exists in two oxidation states with different conformational preferences which are important for substrate binding and functional activities. Here, we address the redox-dependent conformational dynamics of hPDI through molecular dynamics (MD) simulations. Collective domain motions are identified by the principal component analysis of MD trajectories and redox-dependent opening-closing structure variations are highlighted on projected free energy landscapes. Then, important structural features that exhibit considerable differences in dynamics of redox states are extracted by statistical machine learning methods. Mapping the structural variations to time series of residue interaction networks also provides a holistic representation of the dynamical redox differences. With emphasizing on persistent long-lasting interactions, an approach is proposed that compiled these time series networks to a single dynamic residue interaction network (DRIN). Differential comparison of DRIN in oxidized and reduced states reveals chains of residue interactions that represent potential allosteric paths between catalytic and ligand binding sites of hPDI.

Mapping local anisotropy axis for scattering media using backscattering Mueller matrix imaging

NASA Astrophysics Data System (ADS)

He, Honghui; Sun, Minghao; Zeng, Nan; Du, E.; Guo, Yihong; He, Yonghong; Ma, Hui

2014-03-01

Mueller matrix imaging techniques can be used to detect the micro-structure variations of superficial biological tissues, including the sizes and shapes of cells, the structures in cells, and the densities of the organelles. Many tissues contain anisotropic fibrous micro-structures, such as collagen fibers, elastin fibers, and muscle fibers. Changes of these fibrous structures are potentially good indicators for some pathological variations. In this paper, we propose a quantitative analysis technique based on Mueller matrix for mapping local anisotropy axis of scattering media. By conducting both experiments on silk sample and Monte Carlo simulation based on the sphere-cylinder scattering model (SCSM), we extract anisotropy axis parameters from different backscattering Mueller matrix elements. Moreover, we testify the possible applications of these parameters for biological tissues. The preliminary experimental results of human cancerous samples show that, these parameters are capable to map the local axis of fibers. Since many pathological changes including early stage cancers affect the well aligned structures for tissues, the experimental results indicate that these parameters can be used as potential tools in clinical applications for biomedical diagnosis purposes.

Lack of congruence in species diversity indices and community structures of planktonic groups based on local environmental factors.

PubMed

Doi, Hideyuki; Chang, Kwang-Hyeon; Nishibe, Yuichiro; Imai, Hiroyuki; Nakano, Shin-ichi

2013-01-01

The importance of analyzing the determinants of biodiversity and community composition by using multiple trophic levels is well recognized; however, relevant data are lacking. In the present study, we investigated variations in species diversity indices and community structures of the plankton taxonomic groups-zooplankton, rotifers, ciliates, and phytoplankton-under a range of local environmental factors in pond ecosystems. For each planktonic group, we estimated the species diversity index by using linear models and analyzed the community structure by using canonical correspondence analysis. We showed that the species diversity indices and community structures varied among the planktonic groups and according to local environmental factors. The observed lack of congruence among the planktonic groups may have been caused by niche competition between groups with similar trophic guilds or by weak trophic interactions. Our findings highlight the difficulty of predicting total biodiversity within a system, based upon a single taxonomic group. Thus, to conserve the biodiversity of an ecosystem, it is crucial to consider variations in species diversity indices and community structures of different taxonomic groups, under a range of local conditions.

Relative Importance of Biotic and Abiotic Forces on the Composition and Dynamics of a Soft-Sediment Intertidal Community

PubMed Central

Barbeau, Myriam A.

2016-01-01

Top-down, bottom-up, middle-out and abiotic factors are usually viewed as main forces structuring biological communities, although assessment of their relative importance, in a single study, is rarely done. We quantified, using multivariate methods, associations between abiotic and biotic (top-down, bottom-up and middle-out) variables and infaunal population/community variation on intertidal mudflats in the Bay of Fundy, Canada, over two years. Our analysis indicated that spatial structural factors like site and plot accounted for most of the community and population variation. Although we observed a significant relationship between the community/populations and the biotic and abiotic variables, most were of minor importance relative to the structural factors. We suggest that community and population structure were relatively uncoupled from the structuring influences of biotic and abiotic factors in this system because of high concentrations of resources that sustain high densities of infauna and limit exploitative competition. Furthermore, we hypothesize that the infaunal community primarily reflects stochastic spatial events, namely a “first come, first served” process. PMID:26790098

Determinants of echolocation call frequency variation in the Formosan lesser horseshoe bat (Rhinolophus monoceros)

PubMed Central

Chen, Shiang-Fan; Jones, Gareth; Rossiter, Stephen J.

2009-01-01

The origin and maintenance of intraspecific variation in vocal signals is important for population divergence and speciation. Where vocalizations are transmitted by vertical cultural inheritance, similarity will reflect co-ancestry, and thus vocal divergence should reflect genetic structure. Horseshoe bats are characterized by echolocation calls dominated by a constant frequency component that is partly determined by maternal imprinting. Although previous studies showed that constant frequency calls are also influenced by some non-genetic factors, it is not known how frequency relates to genetic structure. To test this, we related constant frequency variation to genetic and non-genetic variables in the Formosan lesser horseshoe bat (Rhinolophus monoceros). Recordings of bats from across Taiwan revealed that females called at higher frequencies than males; however, we found no effect of environmental or morphological factors on call frequency. By comparison, variation showed clear population structure, with frequencies lower in the centre and east, and higher in the north and south. Within these regions, frequency divergence was directional and correlated with geographical distance, suggesting that call frequencies are subject to cultural drift. However, microsatellite clustering analysis showed that broad differences in constant frequency among populations corresponded to discontinuities in allele frequencies resulting from vicariant events. Our results provide evidence that the processes shaping genetic subdivision have concomitant consequences for divergence in echolocation call frequency. PMID:19692399

Piezoelectric Lead Zirconate Titanate (PZT) Ring Shaped Contour-Mode MEMS Resonators

NASA Astrophysics Data System (ADS)

Kasambe, P. V.; Asgaonkar, V. V.; Bangera, A. D.; Lokre, A. S.; Rathod, S. S.; Bhoir, D. V.

2018-02-01

Flexibility in setting fundamental frequency of resonator independent of its motional resistance is one of the desired criteria in micro-electromechanical (MEMS) resonator design. It is observed that ring-shaped piezoelectric contour-mode MEMS resonators satisfy this design criterion than in case of rectangular plate MEMS resonators. Also ring-shaped contour-mode piezoelectric MEMS resonator has an advantage that its fundamental frequency is defined by in-plane dimensions, but they show variation of fundamental frequency with different Platinum (Pt) thickness referred as change in ratio of fNEW /fO . This paper presents the effects of variation in geometrical parameters and change in piezoelectric material on the resonant frequencies of Platinum piezoelectric-Aluminium ring-shaped contour-mode MEMS resonators and its electrical parameters. The proposed structure with Lead Zirconate Titanate (PZT) as the piezoelectric material was observed to be a piezoelectric material with minimal change in fundamental resonant frequency due to Platinum thickness variation. This structure was also found to exhibit extremely low motional resistance of 0.03 Ω as compared to the 31-35 Ω range obtained when using AlN as the piezoelectric material. CoventorWare 10 is used for the design, simulation and corresponding analysis of resonators which is Finite Element Method (FEM) analysis and design tool for MEMS devices.

The STAGS computer code

NASA Technical Reports Server (NTRS)

Almroth, B. O.; Brogan, F. A.

1978-01-01

Basic information about the computer code STAGS (Structural Analysis of General Shells) is presented to describe to potential users the scope of the code and the solution procedures that are incorporated. Primarily, STAGS is intended for analysis of shell structures, although it has been extended to more complex shell configurations through the inclusion of springs and beam elements. The formulation is based on a variational approach in combination with local two dimensional power series representations of the displacement components. The computer code includes options for analysis of linear or nonlinear static stress, stability, vibrations, and transient response. Material as well as geometric nonlinearities are included. A few examples of applications of the code are presented for further illustration of its scope.

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.

A protocol for searching the most probable phase-retrieved maps in coherent X-ray diffraction imaging by exploiting the relationship between convergence of the retrieved phase and success of calculation.

PubMed

Sekiguchi, Yuki; Hashimoto, Saki; Kobayashi, Amane; Oroguchi, Tomotaka; Nakasako, Masayoshi

2017-09-01

Coherent X-ray diffraction imaging (CXDI) is a technique for visualizing the structures of non-crystalline particles with size in the submicrometer to micrometer range in material sciences and biology. In the structural analysis of CXDI, the electron density map of a specimen particle projected along the direction of the incident X-rays can be reconstructed only from the diffraction pattern by using phase-retrieval (PR) algorithms. However, in practice, the reconstruction, relying entirely on the computational procedure, sometimes fails because diffraction patterns miss the data in small-angle regions owing to the beam stop and saturation of the detector pixels, and are modified by Poisson noise in X-ray detection. To date, X-ray free-electron lasers have allowed us to collect a large number of diffraction patterns within a short period of time. Therefore, the reconstruction of correct electron density maps is the bottleneck for efficiently conducting structure analyses of non-crystalline particles. To automatically address the correctness of retrieved electron density maps, a data analysis protocol to extract the most probable electron density maps from a set of maps retrieved from 1000 different random seeds for a single diffraction pattern is proposed. Through monitoring the variations of the phase values during PR calculations, the tendency for the PR calculations to succeed when the retrieved phase sets converged on a certain value was found. On the other hand, if the phase set was in persistent variation, the PR calculation tended to fail to yield the correct electron density map. To quantify this tendency, here a figure of merit for the variation of the phase values during PR calculation is introduced. In addition, a PR protocol to evaluate the similarity between a map of the highest figure of merit and other independently reconstructed maps is proposed. The protocol is implemented and practically examined in the structure analyses for diffraction patterns from aggregates of gold colloidal particles. Furthermore, the feasibility of the protocol in the structure analysis of organelles from biological cells is examined.

Structural adaptation of the subunit interface of oligomeric thermophilic and hyperthermophilic enzymes.

PubMed

Maugini, Elisa; Tronelli, Daniele; Bossa, Francesco; Pascarella, Stefano

2009-04-01

Enzymes from thermophilic and, particularly, from hyperthermophilic organisms are surprisingly stable. Understanding of the molecular origin of protein thermostability and thermoactivity attracted the interest of many scientist both for the perspective comprehension of the principles of protein structure and for the possible biotechnological applications through application of protein engineering. Comparative studies at sequence and structure levels were aimed at detecting significant differences of structural parameters related to protein stability between thermophilic and hyperhermophilic structures and their mesophilic homologs. Comparative studies were useful in the identification of a few recurrent themes which the evolution utilized in different combinations in different protein families. These studies were mostly carried out at the monomer level. However, maintenance of a proper quaternary structure is an essential prerequisite for a functional macromolecule. At the environmental temperatures experienced typically by hyper- and thermophiles, the subunit interactions mediated by the interface must be sufficiently stable. Our analysis was therefore aimed at the identification of the molecular strategies adopted by evolution to enhance interface thermostability of oligomeric enzymes. The variation of several structural properties related to protein stability were tested at the subunit interfaces of thermophilic and hyperthermophilic oligomers. The differences of the interface structural features observed between the hyperthermophilic and thermophilic enzymes were compared with the differences of the same properties calculated from pairwise comparisons of oligomeric mesophilic proteins contained in a reference dataset. The significance of the observed differences of structural properties was measured by a t-test. Ion pairs and hydrogen bonds do not vary significantly while hydrophobic contact area increases specially in hyperthermophilic interfaces. Interface compactness also appears to increase in the hyperthermophilic proteins. Variations of amino acid composition at the interfaces reflects the variation of the interface properties.

A simulation of the OMEGA/Mars Express observations: Analysis of the atmospheric contribution

NASA Astrophysics Data System (ADS)

Melchiorri, R.; Drossart, P.; Fouchet, T.; Bézard, B.; Forget, F.; Gendrin, A.; Bibring, J. P.; Manaud, N.; OMEGA Team; Berthé, M.; Bibring, J.-P.; Langevin, Y.; Forni, O.; Gendrin, A.; Gondet, B.; Manaud, N.; Poulet, F.; Poulleau, G.; Soufflot, A.; Mangold, N.; Bonello, G.; Forget, F.; Bezard, B.; Combes, M.; Drossart, P.; Encrenaz, T.; Fouchet, T.; Melchiorri, R.; Erard, S.; Bellucci, G.; Altieri, F.; Formisano, V.; Fonti, S.; Capaccioni, F.; Cerroni, P.; Coradini, A.; Kottsov, V.; Ignatiev, N.; Moroz, V.; Titov, D.; Zasova, L.; Pinet, P.; Schmitt, B.; Sotin, C.; Hauber, E.; Hoffmann, H.; Jaumann, R.; Keller, U.; Arvidson, R.; Mustard, J.; Duxbary, T.

2006-08-01

Spectral images of Mars obtained by the Mars Express/OMEGA experiment in the near infrared are the result of a complex combination of atmospheric, aerosol and ground features. Retrieving the atmospheric information from the data is important, not only to decorrelate mineralogical against atmospheric features, but also to retrieve the atmospheric variability. Once the illumination conditions have been taken into account, the main source of variation on the CO2 absorption is due to the altitude of the surface, which governs atmospheric pressure variation by more than an order of magnitude between the summit of Olympus Mons down to the bottom of Valles Marineris. In this article we present a simplified atmospheric spectral model without scattering, specially developed for the OMEGA observations, which is used to retrieve the local topography through the analysis of the 2.0μmCO2 band. OMEGA atmospheric observations increase the horizontal resolution compared to MOLA altimetry measurements, and therefore complement the mineralogical studies from the same instrument. Finally, residual variations of the pressure can be related to atmospheric structure variation.

Spatial variations in annual cycles of body-size spectra of planktonic ciliates and their environmental drivers in marine ecosystems.

PubMed

Xu, Henglong; Jiang, Yong; Xu, Guangjian

2016-11-15

Body-size spectra has proved to be a useful taxon-free resolution to summarize a community structure for bioassessment. The spatial variations in annual cycles of body-size spectra of planktonic ciliates and their environmental drivers were studied based on an annual dataset. Samples were biweekly collected at five stations in a bay of the Yellow Sea, northern China during a 1-year cycle. Based on a multivariate approach, the second-stage analysis, it was shown that the annual cycles of the body-size spectra were significantly different among five sampling stations. Correlation analysis demonstrated that the spatial variations in the body-size spectra were significantly related to changes of environmental conditions, especially dissolved nitrogen, alone or in combination with salinity and dissolve oxygen. Based on results, it is suggested that the nutrients may be the environmental drivers to shape the spatial variations in annual cycles of planktonic ciliates in terms of body-size spectra in marine ecosystems. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effects of structured versus non-structured learning on achievement and attitudes of fifth graders in a public aquarium

NASA Astrophysics Data System (ADS)

Kafka, Merryl Audrey

The investigator analyzed the main effect of a structured-learning experience in an informal setting, as well as interactions between the students' learning-style variations toward the element of structure and the imposed instructional conditions. The subjects consisted of 170 students enrolled in two public schools located in Brooklyn, New York. The students were predominantly a White multi-ethnic population consisting of 118 Caucasians, 25 Hispanics, 24 Asians, and 3 African-Americans. Three randomly assigned classes (n = 81) were provided trip sheets, which directed students on how to learn new information with written questions and directives. Three randomly assigned non-structured classes (n = 89) experienced the same exhibit in a free-form manner. Science-based criterion-referenced pre- and posttests were administered, in addition to Learning Style Inventories (Dunn, Dunn, & Price, 1996) and a modified Semantic Differential Scale (Pizzo, 1981), which was used to measure attitudinal levels. The non-structured group had access to similar content information in the form of exhibit graphics, but apparently they chose not to read it as carefully or engage in the information-seeking process as intensely as the students equipped with trip sheets. Analysis of covariance (ANCOVA) indicated that a structured-learning experience produced significantly higher science-achievement test scores than in a non-structured-learning experience (p = .0001). In addition, there was no single learning-style variation (preference, aversion, or no preference) to structure that produced significantly higher gains than another. Furthermore, attitudinal scores were not significantly different between structured and non-structured groups, as well as among homogeneous subsets of students with learning-style variations that matched, mismatched, or indicated no-preferenced positions on the element of structure. Hence, a moderate amount of structure resulted in academic gains without diminishing attitudinal scores. The fact that students' learning-style variations for sociological, design, and perceptual preferences were simultaneously accommodated in this setting may have contributed to the overall positive effects of this structure-based intervention. The diversified teaching resources of the exhibit and the sense of self-empowerment in a student-directed environment may have elevated students' attitudes regardless of their learning-style need for structure. The students' acceptance of a trip sheet that promoted the understanding of science concepts may have contributed to academic success.

Detection and measurement of the intracellular calcium variation in follicular cells.

PubMed

Herrera-Navarro, Ana M; Terol-Villalobos, Iván R; Jiménez-Hernández, Hugo; Peregrina-Barreto, Hayde; Gonzalez-Barboza, José-Joel

2014-01-01

This work presents a new method for measuring the variation of intracellular calcium in follicular cells. The proposal consists in two stages: (i) the detection of the cell's nuclei and (ii) the analysis of the fluorescence variations. The first stage is performed via watershed modified transformation, where the process of labeling is controlled. The detection process uses the contours of the cells as descriptors, where they are enhanced with a morphological filter that homogenizes the luminance variation of the image. In the second stage, the fluorescence variations are modeled as an exponential decreasing function, where the fluorescence variations are highly correlated with the changes of intracellular free Ca(2+). Additionally, it is introduced a new morphological called medium reconstruction process, which helps to enhance the data for the modeling process. This filter exploits the undermodeling and overmodeling properties of reconstruction operators, such that it preserves the structure of the original signal. Finally, an experimental process shows evidence of the capabilities of the proposal.

Detection and Measurement of the Intracellular Calcium Variation in Follicular Cells

PubMed Central

Herrera-Navarro, Ana M.; Terol-Villalobos, Iván R.; Jiménez-Hernández, Hugo; Peregrina-Barreto, Hayde; Gonzalez-Barboza, José-Joel

2014-01-01

This work presents a new method for measuring the variation of intracellular calcium in follicular cells. The proposal consists in two stages: (i) the detection of the cell's nuclei and (ii) the analysis of the fluorescence variations. The first stage is performed via watershed modified transformation, where the process of labeling is controlled. The detection process uses the contours of the cells as descriptors, where they are enhanced with a morphological filter that homogenizes the luminance variation of the image. In the second stage, the fluorescence variations are modeled as an exponential decreasing function, where the fluorescence variations are highly correlated with the changes of intracellular free Ca2+. Additionally, it is introduced a new morphological called medium reconstruction process, which helps to enhance the data for the modeling process. This filter exploits the undermodeling and overmodeling properties of reconstruction operators, such that it preserves the structure of the original signal. Finally, an experimental process shows evidence of the capabilities of the proposal. PMID:25342958

On the formulation of a minimal uncertainty model for robust control with structured uncertainty

NASA Technical Reports Server (NTRS)

Belcastro, Christine M.; Chang, B.-C.; Fischl, Robert

1991-01-01

In the design and analysis of robust control systems for uncertain plants, representing the system transfer matrix in the form of what has come to be termed an M-delta model has become widely accepted and applied in the robust control literature. The M represents a transfer function matrix M(s) of the nominal closed loop system, and the delta represents an uncertainty matrix acting on M(s). The nominal closed loop system M(s) results from closing the feedback control system, K(s), around a nominal plant interconnection structure P(s). The uncertainty can arise from various sources, such as structured uncertainty from parameter variations or multiple unsaturated uncertainties from unmodeled dynamics and other neglected phenomena. In general, delta is a block diagonal matrix, but for real parameter variations delta is a diagonal matrix of real elements. Conceptually, the M-delta structure can always be formed for any linear interconnection of inputs, outputs, transfer functions, parameter variations, and perturbations. However, very little of the currently available literature addresses computational methods for obtaining this structure, and none of this literature addresses a general methodology for obtaining a minimal M-delta model for a wide class of uncertainty, where the term minimal refers to the dimension of the delta matrix. Since having a minimally dimensioned delta matrix would improve the efficiency of structured singular value (or multivariable stability margin) computations, a method of obtaining a minimal M-delta would be useful. Hence, a method of obtaining the interconnection system P(s) is required. A generalized procedure for obtaining a minimal P-delta structure for systems with real parameter variations is presented. Using this model, the minimal M-delta model can then be easily obtained by closing the feedback loop. The procedure involves representing the system in a cascade-form state-space realization, determining the minimal uncertainty matrix, delta, and constructing the state-space representation of P(s). Three examples are presented to illustrate the procedure.

Balancing selection and recombination as evolutionary forces caused population genetic variations in golden pheasant MHC class I genes.

PubMed

Zeng, Qian-Qian; He, Ke; Sun, Dan-Dan; Ma, Mei-Ying; Ge, Yun-Fa; Fang, Sheng-Guo; Wan, Qiu-Hong

2016-02-18

The major histocompatibility complex (MHC) genes are vital partners in the acquired immune processes of vertebrates. MHC diversity may be directly associated with population resistance to infectious pathogens. Here, we screened for polymorphisms in exons 2 and 3 of the IA1 and IA2 genes in 12 golden pheasant populations across the Chinese mainland to characterize their genetic variation levels, to understand the effects of historical positive selection and recombination in shaping class I diversity, and to investigate the genetic structure of wild golden pheasant populations. Among 339 individual pheasants, we identified 14 IA1 alleles in exon 2 (IA1-E2), 11 IA1-E3 alleles, 27 IA2-E2 alleles, and 28 IA2-E3 alleles. The non-synonymous substitution rate was significantly greater than the synonymous substitution rate at sequences in the IA2 gene encoding putative peptide-binding sites but not in the IA1 gene; we also found more positively selected sites in IA2 than in IA1. Frequent recombination events resulted in at least 9 recombinant IA2 alleles, in accordance with the intermingling pattern of the phylogenetic tree. Although some IA alleles are widely shared among studied populations, large variation occurs in the number of IA alleles across these populations. Allele frequency analysis across 2 IA loci showed low levels of genetic differentiation among populations on small geographic scales; however, significant genetic differentiation was observed between pheasants from the northern and southern regions of the Yangtze River. Both STRUCTURE analysis and F-statistic (F ST ) value comparison classified those populations into 2 major groups: the northern region of the Yangtze River (NYR) and the southern region of the Yangtze River (SYR). More extensive polymorphisms in IA2 than IA1 indicate that IA2 has undergone much stronger positive-selection pressure during evolution. Moreover, the recombination events detected between the genes and the intermingled phylogenetic pattern indicate that interlocus recombination accounts for much of the allelic variation in IA2. Analysis of the population differentiation implied that homogenous balancing selection plays an important part in maintaining an even distribution of MHC variations. The natural barrier of the Yangtze River and heterogeneous balancing selection might help shape the NYR-SYR genetic structure in golden pheasants.

Individual Differences in Dynamic Functional Brain Connectivity across the Human Lifespan

PubMed Central

Davison, Elizabeth N.; Turner, Benjamin O.; Miller, Michael B.; Carlson, Jean M.

2016-01-01

Individual differences in brain functional networks may be related to complex personal identifiers, including health, age, and ability. Dynamic network theory has been used to identify properties of dynamic brain function from fMRI data, but the majority of analyses and findings remain at the level of the group. Here, we apply hypergraph analysis, a method from dynamic network theory, to quantify individual differences in brain functional dynamics. Using a summary metric derived from the hypergraph formalism—hypergraph cardinality—we investigate individual variations in two separate, complementary data sets. The first data set (“multi-task”) consists of 77 individuals engaging in four consecutive cognitive tasks. We observe that hypergraph cardinality exhibits variation across individuals while remaining consistent within individuals between tasks; moreover, the analysis of one of the memory tasks revealed a marginally significant correspondence between hypergraph cardinality and age. This finding motivated a similar analysis of the second data set (“age-memory”), in which 95 individuals, aged 18–75, performed a memory task with a similar structure to the multi-task memory task. With the increased age range in the age-memory data set, the correlation between hypergraph cardinality and age correspondence becomes significant. We discuss these results in the context of the well-known finding linking age with network structure, and suggest that hypergraph analysis should serve as a useful tool in furthering our understanding of the dynamic network structure of the brain. PMID:27880785

Structural variation within the potato Ve gene locus and correlation with molecular marker analysis

USDA-ARS?s Scientific Manuscript database

The disconnect between single genotype model systems and plant breeding using wide crosses of diverse germplasm is often too great to affect progress in understanding complex phenotypes. Whole genome sequencing allows researchers and breeders to quickly and inexpensively resequence interesting indiv...

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.

The effect of glycosylation on the transferrin structure: A molecular dynamic simulation analysis.

PubMed

Ghanbari, Z; Housaindokht, M R; Bozorgmehr, M R; Izadyar, M

2016-09-07

Transferrins have been defined by the highly cooperative binding of iron and a carbonate anion to form a Fe-CO3-Tf ternary complex. As such, the layout of the binding site residues affects transferrin function significantly; In contrast to N-lobe, C-lobe binding site of the transferrin structure has been less characterized and little research which surveyed the interaction of carbonate with transferrin in the C-lobe binding site has been found. In the present work, molecular dynamic simulation was employed to gain access into the molecular level understanding of carbonate binding site and their interactions in each lobe. Residues responsible for carbonate binding of transferrin structure were pointed out. In addition, native human transferrin is a glycoprotein that two N-linked complex glycan chains located in the C-lobe. Usually, in the molecular dynamic simulation for simplifying, glycan is removed from the protein structure. Here, we explore the effect of glycosylation on the transferrin structure. Glycosylation appears to have an effect on the layout of the binding site residue and transferrin structure. On the other hand, sometimes the entire transferrin formed by separated lobes that it allows the results to be interpreted in a straightforward manner rather than more parameters required for full length protein. But, it should be noted that there are differences between the separated lobe and full length transferrin, hence, a comparative analysis by the molecular dynamic simulation was performed to investigate such structural variations. Results revealed that separation in C-lobe caused a significant structural variation in comparison to N-lobe. Consequently, the separated lobes and the full length one are different, showing the importance of the interlobe communication and the impact of the lobes on each other in the transferrin structure. Copyright © 2016 Elsevier Ltd. All rights reserved.

Disaster Analysis: Police and Fire Departments. Phase 2.

DTIC Science & Technology

1989-03-01

more important conclusions are the following. Fire depart- ments have changed more than police departments in the last decade, taking on new tasks (e.g...than ten officers ( News Journal, 1989:A2). * 13 I! While there is considerable structural variation, the functions or tasks of the various departments...1966), organized responses in major disasters can be differentiated according to whether a new or old structure and a new or old function is manifested

Soil resources and topography shape local tree community structure in tropical forests

PubMed Central

Baldeck, Claire A.; Harms, Kyle E.; Yavitt, Joseph B.; John, Robert; Turner, Benjamin L.; Valencia, Renato; Navarrete, Hugo; Davies, Stuart J.; Chuyong, George B.; Kenfack, David; Thomas, Duncan W.; Madawala, Sumedha; Gunatilleke, Nimal; Gunatilleke, Savitri; Bunyavejchewin, Sarayudh; Kiratiprayoon, Somboon; Yaacob, Adzmi; Supardi, Mohd N. Nur; Dalling, James W.

2013-01-01

Both habitat filtering and dispersal limitation influence the compositional structure of forest communities, but previous studies examining the relative contributions of these processes with variation partitioning have primarily used topography to represent the influence of the environment. Here, we bring together data on both topography and soil resource variation within eight large (24–50 ha) tropical forest plots, and use variation partitioning to decompose community compositional variation into fractions explained by spatial, soil resource and topographic variables. Both soil resources and topography account for significant and approximately equal variation in tree community composition (9–34% and 5–29%, respectively), and all environmental variables together explain 13–39% of compositional variation within a plot. A large fraction of variation (19–37%) was spatially structured, yet unexplained by the environment, suggesting an important role for dispersal processes and unmeasured environmental variables. For the majority of sites, adding soil resource variables to topography nearly doubled the inferred role of habitat filtering, accounting for variation in compositional structure that would previously have been attributable to dispersal. Our results, illustrated using a new graphical depiction of community structure within these plots, demonstrate the importance of small-scale environmental variation in shaping local community structure in diverse tropical forests around the globe. PMID:23256196

Genetic variation among interconnected populations of Catostomus occidentalis: Implications for distinguishing impacts of contaminants from biogeographical structuring

USGS Publications Warehouse

Whitehead, A.; Anderson, S.L.; Kuivila, K.M.; Roach, J.L.; May, B.

2003-01-01

Exposure to contaminants can affect survivorship, recruitment, reproductive success, mutation rates and migration, and may play a significant role in the partitioning of genetic variation among exposed and nonexposed populations. However, the application of molecular population genetic data to evaluate such influences has been uncommon and often flawed. We tested whether patterns of genetic variation among native fish populations (Sacramento sucker, Catostomus occidentalis) in the Central Valley of California were consistent with long-term pesticide exposure history, or primarily with expectations based on biogeography. Field sampling was designed to rigorously test for both geographical and contamination influences. Fine-scale structure of these interconnected populations was detected with both amplified fragment length polymorphisms (AFLP) and microsatellite markers, and patterns of variation elucidated by the two marker systems were highly concordant. Analyses indicated that biogeographical hypotheses described the data set better than hypotheses relating to common historical pesticide exposure. Downstream populations had higher genetic diversity than upstream populations, regardless of exposure history, and genetic distances showed that populations from the same river system tended to cluster together. Relatedness among populations reflected primarily directions of gene flow, rather than convergence among contaminant-exposed populations. Watershed geography accounted for significant partitioning of genetic variation among populations, whereas contaminant exposure history did not. Genetic patterns indicating contaminant-induced selection, increased mutation rates or recent bottlenecks were weak or absent. We stress the importance of testing contaminant-induced genetic change hypotheses within a biogeographical context. Strategic application of molecular markers for analysis of fine-scale structure, and for evaluating contaminant impacts on gene pools, is discussed.

Analysis of structural diversity in wolf-like canids reveals post-domestication variants.

PubMed

Ramirez, Oscar; Olalde, Iñigo; Berglund, Jonas; Lorente-Galdos, Belen; Hernandez-Rodriguez, Jessica; Quilez, Javier; Webster, Matthew T; Wayne, Robert K; Lalueza-Fox, Carles; Vilà, Carles; Marques-Bonet, Tomas

2014-06-12

Although a variety of genetic changes have been implicated in causing phenotypic differences among dogs, the role of copy number variants (CNVs) and their impact on phenotypic variation is still poorly understood. Further, very limited knowledge exists on structural variation in the gray wolf, the ancestor of the dog, or other closely related wild canids. Documenting CNVs variation in wild canids is essential to identify ancestral states and variation that may have appeared after domestication. In this work, we genotyped 1,611 dog CNVs in 23 wolf-like canids (4 purebred dogs, one dingo, 15 gray wolves, one red wolf, one coyote and one golden jackal) to identify CNVs that may have arisen after domestication. We have found an increase in GC-rich regions close to the breakpoints and around 1 kb away from them suggesting that some common motifs might be associated with the formation of CNVs. Among the CNV regions that showed the largest differentiation between dogs and wild canids we found 12 genes, nine of which are related to two known functions associated with dog domestication; growth (PDE4D, CRTC3 and NEB) and neurological function (PDE4D, EML5, ZNF500, SLC6A11, ELAVL2, RGS7 and CTSB). Our results provide insight into the evolution of structural variation in canines, where recombination is not regulated by PRDM9 due to the inactivation of this gene. We also identified genes within the most differentiated CNV regions between dogs and wolves, which could reflect selection during the domestication process.

Genetic diversity and variation of Chinese fir from Fujian province and Taiwan, China, based on ISSR markers

PubMed Central

Chen, Yu; Peng, Zhuqing; Wu, Chao; Ma, Zhihui; Ding, Guochang; Cao, Guangqiu; Ruan, Shaoning; Lin, Sizu

2017-01-01

Genetic diversity and variation among 11 populations of Chinese fir from Fujian province and Taiwan were assessed using inter-simple sequence repeat (ISSR) markers to reveal the evolutionary relationship in their distribution range in this report. Analysis of genetic parameters of the different populations showed that populations in Fujian province exhibited a greater level of genetic diversity than did the populations in Taiwan. Compared to Taiwan populations, significant limited gene flow were observed among Fujian populations. An UPGMA cluster analysis showed that the most individuals of Taiwan populations formed a single cluster, whereas 6 discrete clusters were formed by each population from Fujian. All populations were divided into 3 main groups and that all 5 populations from Taiwan were gathered into a subgroup combined with 2 populations, Dehua and Liancheng, formed one of the 3 main groups, which indicated relative stronger relatedness. It is supported by a genetic structure analysis. All those results are suggesting different levels of genetic diversity and variation of Chinese fir between Fujian and Taiwan, and indicating different patterns of evolutionary process and local environmental adaption. PMID:28406956

Genetic diversity and variation of Chinese fir from Fujian province and Taiwan, China, based on ISSR markers.

PubMed

Chen, Yu; Peng, Zhuqing; Wu, Chao; Ma, Zhihui; Ding, Guochang; Cao, Guangqiu; Ruan, Shaoning; Lin, Sizu

2017-01-01

Genetic diversity and variation among 11 populations of Chinese fir from Fujian province and Taiwan were assessed using inter-simple sequence repeat (ISSR) markers to reveal the evolutionary relationship in their distribution range in this report. Analysis of genetic parameters of the different populations showed that populations in Fujian province exhibited a greater level of genetic diversity than did the populations in Taiwan. Compared to Taiwan populations, significant limited gene flow were observed among Fujian populations. An UPGMA cluster analysis showed that the most individuals of Taiwan populations formed a single cluster, whereas 6 discrete clusters were formed by each population from Fujian. All populations were divided into 3 main groups and that all 5 populations from Taiwan were gathered into a subgroup combined with 2 populations, Dehua and Liancheng, formed one of the 3 main groups, which indicated relative stronger relatedness. It is supported by a genetic structure analysis. All those results are suggesting different levels of genetic diversity and variation of Chinese fir between Fujian and Taiwan, and indicating different patterns of evolutionary process and local environmental adaption.

Secondary structure prediction and structure-specific sequence analysis of single-stranded DNA.

PubMed

Dong, F; Allawi, H T; Anderson, T; Neri, B P; Lyamichev, V I

2001-08-01

DNA sequence analysis by oligonucleotide binding is often affected by interference with the secondary structure of the target DNA. Here we describe an approach that improves DNA secondary structure prediction by combining enzymatic probing of DNA by structure-specific 5'-nucleases with an energy minimization algorithm that utilizes the 5'-nuclease cleavage sites as constraints. The method can identify structural differences between two DNA molecules caused by minor sequence variations such as a single nucleotide mutation. It also demonstrates the existence of long-range interactions between DNA regions separated by >300 nt and the formation of multiple alternative structures by a 244 nt DNA molecule. The differences in the secondary structure of DNA molecules revealed by 5'-nuclease probing were used to design structure-specific probes for mutation discrimination that target the regions of structural, rather than sequence, differences. We also demonstrate the performance of structure-specific 'bridge' probes complementary to non-contiguous regions of the target molecule. The structure-specific probes do not require the high stringency binding conditions necessary for methods based on mismatch formation and permit mutation detection at temperatures from 4 to 37 degrees C. Structure-specific sequence analysis is applied for mutation detection in the Mycobacterium tuberculosis katG gene and for genotyping of the hepatitis C virus.

Morphological variation of siscowet lake trout in Lake Superior

USGS Publications Warehouse

Bronte, C.R.; Moore, S.A.

2007-01-01

Historically, Lake Superior has contained many morphologically distinct forms of the lake trout Salvelinus namaycush that have occupied specific depths and locations and spawned at specific times of the year. Today, as was probably the case historically, the siscowet morphotype is the most abundant. Recent interest in harvesting siscowets to extract oil containing omega-3 fatty acids will require additional knowledge of the biology and stock structure of these lightly exploited populations. The objective of this study was to determine whether shape differences exist among siscowet populations across Lake Superior and whether these shape differences can be used to infer stock structure. Morphometric analysis (truss protocol) was used to differentiate among siscowets sampled from 23 locations in Lake Superior. We analyzed 31 distance measurements among 14 anatomical landmarks taken from digital images of fish recorded in the field. Cluster analysis of size-corrected data separated fish into three geographic groups: The Isle Royale, eastern (Michigan), and western regions (Michigan). Finer scales of stock structure were also suggested. Discriminant function analysis demonstrated that head measurements contributed to most of the observed variation. Cross-validation classification rates indicated that 67–71% of individual fish were correctly classified to their region of capture. This is the first study to present shape differences associated with location within a lake trout morphotype in Lake Superior.

A study of voice production characteristics of astronuat speech during Apollo 11 for speaker modeling in space.

PubMed

Yu, Chengzhu; Hansen, John H L

2017-03-01

Human physiology has evolved to accommodate environmental conditions, including temperature, pressure, and air chemistry unique to Earth. However, the environment in space varies significantly compared to that on Earth and, therefore, variability is expected in astronauts' speech production mechanism. In this study, the variations of astronaut voice characteristics during the NASA Apollo 11 mission are analyzed. Specifically, acoustical features such as fundamental frequency and phoneme formant structure that are closely related to the speech production system are studied. For a further understanding of astronauts' vocal tract spectrum variation in space, a maximum likelihood frequency warping based analysis is proposed to detect the vocal tract spectrum displacement during space conditions. The results from fundamental frequency, formant structure, as well as vocal spectrum displacement indicate that astronauts change their speech production mechanism when in space. Moreover, the experimental results for astronaut voice identification tasks indicate that current speaker recognition solutions are highly vulnerable to astronaut voice production variations in space conditions. Future recommendations from this study suggest that successful applications of speaker recognition during extended space missions require robust speaker modeling techniques that could effectively adapt to voice production variation caused by diverse space conditions.

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.

Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences.

PubMed

Wagner Mackenzie, Brett; Waite, David W; Taylor, Michael W

2015-01-01

The human gut contains dense and diverse microbial communities which have profound influences on human health. Gaining meaningful insights into these communities requires provision of high quality microbial nucleic acids from human fecal samples, as well as an understanding of the sources of variation and their impacts on the experimental model. We present here a systematic analysis of commonly used microbial DNA extraction methods, and identify significant sources of variation. Five extraction methods (Human Microbiome Project protocol, MoBio PowerSoil DNA Isolation Kit, QIAamp DNA Stool Mini Kit, ZR Fecal DNA MiniPrep, phenol:chloroform-based DNA isolation) were evaluated based on the following criteria: DNA yield, quality and integrity, and microbial community structure based on Illumina amplicon sequencing of the V4 region of bacterial and archaeal 16S rRNA genes. Our results indicate that the largest portion of variation within the model was attributed to differences between subjects (biological variation), with a smaller proportion of variation associated with DNA extraction method (technical variation) and intra-subject variation. A comprehensive understanding of the potential impact of technical variation on the human gut microbiota will help limit preventable bias, enabling more accurate diversity estimates.

Facial patterns in a tropical social wasp correlate with colony membership

NASA Astrophysics Data System (ADS)

Baracchi, David; Turillazzi, Stefano; Chittka, Lars

2016-10-01

Social insects excel in discriminating nestmates from intruders, typically relying on colony odours. Remarkably, some wasp species achieve such discrimination using visual information. However, while it is universally accepted that odours mediate a group level recognition, the ability to recognise colony members visually has been considered possible only via individual recognition by which wasps discriminate `friends' and `foes'. Using geometric morphometric analysis, which is a technique based on a rigorous statistical theory of shape allowing quantitative multivariate analyses on structure shapes, we first quantified facial marking variation of Liostenogaster flavolineata wasps. We then compared this facial variation with that of chemical profiles (generated by cuticular hydrocarbons) within and between colonies. Principal component analysis and discriminant analysis applied to sets of variables containing pure shape information showed that despite appreciable intra-colony variation, the faces of females belonging to the same colony resemble one another more than those of outsiders. This colony-specific variation in facial patterns was on a par with that observed for odours. While the occurrence of face discrimination at the colony level remains to be tested by behavioural experiments, overall our results suggest that, in this species, wasp faces display adequate information that might be potentially perceived and used by wasps for colony level recognition.

Impact of Parental Bos taurus and Bos indicus Origins on Copy Number Variation in Traditional Chinese Cattle Breeds

PubMed Central

Zhang, Liangzhi; Jia, Shangang; Plath, Martin; Huang, Yongzhen; Li, Congjun; Lei, Chuzhao; Zhao, Xin; Chen, Hong

2015-01-01

Copy number variation (CNV) is an important component of genomic structural variation and plays a role not only in evolutionary diversification but also in domestication. Chinese cattle were derived from Bos taurus and Bos indicus, and several breeds presumably are of hybrid origin, but the evolution of CNV regions (CNVRs) has not yet been examined in this context. Here, we of CNVRs, mtDNA D-loop sequence variation, and Y-chromosomal single nucleotide polymorphisms to assess the impact of maternal and paternal B. taurus and B. indicus origins on the distribution of CNVRs in 24 Chinese domesticated bulls. We discovered 470 genome-wide CNVRs, only 72 of which were shared by all three Y-lineages (B. taurus: Y1, Y2; B. indicus: Y3), whereas 265 were shared by inferred taurine or indicine paternal lineages, and 228 when considering their maternal taurine or indicine origins. Phylogenetic analysis uncovered eight taurine/indicine hybrids, and principal component analysis on CNVs corroborated genomic exchange during hybridization. The distribution patterns of CNVRs tended to be lineage-specific, and correlation analysis revealed significant positive or negative co-occurrences of CNVRs across lineages. Our study suggests that CNVs in Chinese cattle partly result from selective breeding during domestication, but also from hybridization and introgression. PMID:26260653

Evidence for azimuthal variations of the oxygen-abundance gradient tracing the spiral structure of the galaxy HCG 91c

NASA Astrophysics Data System (ADS)

Vogt, F. P. A.; Pérez, E.; Dopita, M. A.; Verdes-Montenegro, L.; Borthakur, S.

2017-05-01

Context. The distribution of elements in galaxies forms an important diagnostic tool to characterize these systems' formation and evolution. This tool is, however, complex to use in practice, as galaxies are subject to a range of simultaneous physical processes active from pc to kpc scales. This renders observations of the full optical extent of galaxies down to sub-kpc scales essential. Aims: Using the WiFeS integral field spectrograph, we previously detected abrupt and localized variations in the gas-phase oxygen abundance of the spiral galaxy HCG 91c. Here, we follow-up on these observations to map HCG 91c's disk out to 2 Re at a resolution of 600 pc, and characterize the non-radial variations of the gas-phase oxygen abundance in the system. Methods: We obtained deep MUSE observations of the target under 0.6 arcsec seeing conditions. We perform both a spaxel-based and aperture-based analysis of the data to map the spatial variations of 12 +log (O/H) across the disk of the galaxy. Results: We confirm the presence of rapid variations of the oxygen abundance across the entire extent of the galaxy previously detected with WiFeS, for all azimuths and radii. The variations can be separated in two categories: a) localized and associated with individual H II regions; and b) extended over kpc scales, and occurring at the boundaries of the spiral structures in the galaxy. Conclusions: Our MUSE observations suggest that the enrichment of the interstellar medium in HGC 91c has proceeded preferentially along spiral structures, and less efficiently across them. Our dataset highlights the importance of distinguishing individual star-forming regions down to scales of a few 100 pc when using integral field spectrographs to spatially resolve the distribution of oxygen abundances in a given system, and accurately characterize azimuthal variations and intrinsic scatter. The movie associated to Fig. 8 is available at http://www.aanda.org

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.

The Student Experience of Learning Using Networked Technologies: An Emergent Progression of Expanding Awareness

ERIC Educational Resources Information Center

Cutajar, Maria

2017-01-01

This article reports on phenomenographic research which explored the qualitative differences in post-secondary students' accounts of their networked learning experiences. Data was generated using semi-structured interviews with a purposive sample of participants. Phenomenographic analysis led to a configuration of variation in students' accounts…

Categorizing Variations of Student-Implemented Sorting Algorithms

ERIC Educational Resources Information Center

Taherkhani, Ahmad; Korhonen, Ari; Malmi, Lauri

2012-01-01

In this study, we examined freshmen students' sorting algorithm implementations in data structures and algorithms' course in two phases: at the beginning of the course before the students received any instruction on sorting algorithms, and after taking a lecture on sorting algorithms. The analysis revealed that many students have insufficient…

Relationships between Remotely-Sensed Surface Properties and Subsurface Structure in the Ocean.

DTIC Science & Technology

1988-01-06

Investigacion Cientifica y de Educacion 0 Superior de Ensenada (CICESE) surveyed the Gulf of California from 25 October to 4 November 1985 aboard USNS De...north into the Gulf. However, there are many mesoscale variations around these trends, especially in chlorophyll. In the multiple regression analysis

Overstory mortality and canopy disturbances in longleaf pine ecosystems

Treesearch

Brian J. Palik; Neil Pederson

1996-01-01

We studied longleaf pine (Pinus palustris Mill.) ecosystems to determine causes and rates of overstory mortality, size of canopy disturbances, and the effects of disturbance on canopy structure. Further, we used redundancy analysis to relate variation in characteristics of mortality across a landscape to site and stand variables. We analyzed...

Evaluation of variability in high-resolution protein structures by global distance scoring.

PubMed

Anzai, Risa; Asami, Yoshiki; Inoue, Waka; Ueno, Hina; Yamada, Koya; Okada, Tetsuji

2018-01-01

Systematic analysis of the statistical and dynamical properties of proteins is critical to understanding cellular events. Extraction of biologically relevant information from a set of high-resolution structures is important because it can provide mechanistic details behind the functional properties of protein families, enabling rational comparison between families. Most of the current structural comparisons are pairwise-based, which hampers the global analysis of increasing contents in the Protein Data Bank. Additionally, pairing of protein structures introduces uncertainty with respect to reproducibility because it frequently accompanies other settings for superimposition. This study introduces intramolecular distance scoring for the global analysis of proteins, for each of which at least several high-resolution structures are available. As a pilot study, we have tested 300 human proteins and showed that the method is comprehensively used to overview advances in each protein and protein family at the atomic level. This method, together with the interpretation of the model calculations, provide new criteria for understanding specific structural variation in a protein, enabling global comparison of the variability in proteins from different species.

Simulation and analysis of Au-MgF2 structure in plasmonic sensor in near infrared spectral region

NASA Astrophysics Data System (ADS)

Sharma, Anuj K.

2018-05-01

Plasmonic sensor based on metal-dielectric combination of gold and MgF2 layers is studied in near infrared (NIR) spectral region. An emphasis is given on the effect of variable thickness of MgF2 layer in combination with operating wavelength and gold layer thickness on the sensor's performance in NIR. It is established that the variation in MgF2 thickness in connection with plasmon penetration depth leads to significant variation in sensor's performance. The analysis leads to a conclusion that taking smaller values of MgF2 layer thickness and operating at longer NIR wavelength leads to enhanced sensing performance. Also, fluoride glass can provide better sensing performance than chalcogenide glass and silicon substrate.

Improve SSME power balance model

NASA Technical Reports Server (NTRS)

Karr, Gerald R.

1992-01-01

Effort was dedicated to development and testing of a formal strategy for reconciling uncertain test data with physically limited computational prediction. Specific weaknesses in the logical structure of the current Power Balance Model (PBM) version are described with emphasis given to the main routing subroutines BAL and DATRED. Selected results from a variational analysis of PBM predictions are compared to Technology Test Bed (TTB) variational study results to assess PBM predictive capability. The motivation for systematic integration of uncertain test data with computational predictions based on limited physical models is provided. The theoretical foundation for the reconciliation strategy developed in this effort is presented, and results of a reconciliation analysis of the Space Shuttle Main Engine (SSME) high pressure fuel side turbopump subsystem are examined.

Computational Analysis Reveals the Association of Threonine 118 Methionine Mutation in PMP22 Resulting in CMT-1A

PubMed Central

Swetha, Rayapadi G.

2014-01-01

The T118M mutation in PMP22 gene is associated with Charcot Marie Tooth, type 1A (CMT1A). CMT1A is a form of Charcot-Marie-Tooth disease, the most common inherited disorder of the peripheral nervous system. Mutations in CMT related disorder are seen to increase the stability of the protein resulting in the diseased state. We performed SNP analysis for all the nsSNPs of PMP22 protein and carried out molecular dynamics simulation for T118M mutation to compare the stability difference between the wild type protein structure and the mutant protein structure. The mutation T118M resulted in the overall increase in the stability of the mutant protein. The superimposed structure shows marked structural variation between the wild type and the mutant protein structures. PMID:25400662

Sequential development of structural heterogeneity in the Granny Creek oil field of West Virginia

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

Wilson, T.H.; Zheng, L.; Shumaker, R.C.

1993-08-01

Analysis of Vibroseis and weight-drop seismic data over the Granny Creek oil field in the Appalachian foreland of West Virginia indicates that the field's development has been effected by episodic Paleozoic reactivation of fault blocks rooted in the Precambrian crystalline basement. The imprint of structures associated with the Rome trough penetrates the overlying Paleozoic sedimentary cover. Reactivation histories of individual fault blocks vary considerably throughout the Paleozoic. In general, the relative displacement of these basement fault blocks decrease exponentially during the Paleozoic; however, this pattern is interrupted by periods of increased tectonic activity and relative inversion of offsets along somemore » faults. The distribution of late-stage detached structures during the Alleghenian orogeny also appears, in part, to be controlled by mechanical anisotrophy within the detached section related to the reactivation of deeper structures in the crystalline basement. The net effect is a complex time-variable pattern of structures that partly controls the location of the reservoir and heterogeneity within the geometric framework of the reservoir. Structural heterogeneity in the Granny Creek area is subdivided on the basis of scale into structures associated with variations of oil production within the reservoir. Variations of production within the field are related, in part, to small detached structures and reactivated basement faults.« less

Structural Insight Into the Role of Mutual Polymorphism and Conservatism in the Contact Zone of the NFR5-K1 Heterodimer With the Nod Factor.

PubMed

Igolkina, A A; Porozov, Yu B; Chizhevskaya, E P; Andronov, E E

2018-01-01

Sandwich-like docking configurations of the heterodimeric complex of NFR5 and K1 Vicia sativa receptor-like kinases together with the putative ligand, Nod factor (NF) of Rhizobium leguminosarum bv. viciae , were modeled and two of the most probable configurations were assessed through the analysis of the mutual polymorphisms and conservatism. We carried out this analysis based on the hypothesis that in a contact zone of two docked components (proteins or ligands) the population polymorphism or conservatism is mutual, i.e., the variation in one component has a reflected variation in the other component. The population material of 30 wild-growing V. sativa (leaf pieces) was collected from a large field (uncultivated for the past 25-years) and pooled; form this pool, 100 randomly selected cloned fragments of NFR5 gene and 100 of K1 gene were sequenced by the Sanger method. Congruence between population trees of NFR5 and K1 haplotypes allowed us to select two respective haplotypes, build their 3D structures, and perform protein-protein docking. In a separate simulation, the protein-ligand docking between NFR5 and NF was carried out. We merged the results of the two docking experiments and extracted NFR5-NF-K1 complexes, in which NF was located within the cavity between two receptors. Molecular dynamics simulations indicated two out of six complexes as stable. Regions of mutual polymorphism in the contact zone of one complex overlapped with known NF structural variations produced by R. leguminosarum bv. viciae . A total of 74% of the contact zone of another complex contained mutually polymorphic and conservative areas. Common traits of the obtained two stable structures allowed us to hypothesize the functional role of three-domain structure of plant LysM-RLKs in their heteromers.

Short Time Impulse Response Function (STIRF) for automatic evaluation of the variation of the dynamic parameters of reinforced concrete framed structures during strong earthquakes.

NASA Astrophysics Data System (ADS)

Carlo Ponzo, Felice; Ditommaso, Rocco

2015-04-01

This study presents an innovative strategy for automatic evaluation of the variable fundamental frequency and related damping factor of nonlinear structures during strong motion phases. Most of methods for damage detection are based on the assessment of the variations of the dynamic parameters characterizing the monitored structure. A crucial aspect of these methods is the automatic and accurate estimation of both structural eigen-frequencies and related damping factors also during the nonlinear behaviour. A new method, named STIRF (Short-Time Impulse Response Function - STIRF), based on the nonlinear interferometric analysis combined with the Fourier Transform (FT) here is proposed in order to allow scientists and engineers to characterize frequencies and damping variations of a monitored structure. The STIRF approach helps to overcome some limitation derived from the use of techniques based on simple Fourier Transform. These latter techniques provide good results when the response of the monitored system is stationary, but fails when the system exhibits a non-stationary, time-varying behaviour: even non-stationary input, soil-foundation and/or adjacent structures interaction phenomena can show the inadequacy of classic techniques to analysing the nonlinear and/or non-stationary behaviour of structures. In fact, using this kind of approach it is possible to improve some of the existing methods for the automatic damage detection providing stable results also during the strong motion phase. Results are consistent with those expected if compared with other techniques. The main advantage derived from the use of the proposed approach (STIRF) for Structural Health Monitoring is based on the simplicity of the interpretation of the nonlinear variations of the fundamental frequency and the related equivalent viscous damping factor. The proposed methodology has been tested on both numerical and experimental models also using data retrieved from shaking table tests. Based on the results provided in this study, the methodology seems to be able to evaluate fast variations (over time) of dynamic parameters of a generic reinforced concrete framed structure. Further analyses are necessary to better calibrate the length of the moving time-window (in order to minimize the spurious frequency within each Interferometric Response Function evaluated on both weak and strong motion phases) and to verify the possibility to use the STIRF to analyse the nonlinear behaviour of general systems. Acknowledgements This study was partially funded by the Italian Civil Protection Department within the project DPC-RELUIS 2014 - RS4 ''Seismic observatory of structures and health monitoring''. References R. Ditommaso, F.C. Ponzo (2015). Automatic evaluation of the fundamental frequency variations and related damping factor of reinforced concrete framed structures using the Short Time Impulse Response Function (STIRF). Engineering Structures, 82 (2015), 104-112. http://dx.doi.org/10.1016/j.engstruct.2014.10.023.

Temporal patterns of phyto- and bacterioplankton and their relationships with environmental factors in Lake Taihu, China.

PubMed

Su, Xiaomei; Steinman, Alan D; Xue, Qingju; Zhao, Yanyan; Tang, Xiangming; Xie, Liqiang

2017-10-01

Phytoplankton and bacterioplankton are integral components of aquatic food webs and play essential roles in the structure and function of freshwater ecosystems. However, little is known about how phyto- and bacterioplankton may respond synchronously to changing environmental conditions. Thus, we analyzed simultaneously the composition and structure of phyto- and bacterioplankton on a monthly basis over 12 months in cyanobacteria-dominated areas of Lake Taihu and compared their responses to changes in environmental factors. Metric multi-dimensional scaling (mMDS) revealed that the temporal variations of phyto- and bacterioplankton were significant. Time lag analysis (TLA) indicated that the temporal pattern of phytoplankton tended to exhibit convergent dynamics while bacterioplankton showed highly stable or stochastic variation. A significant directional change was found for bacterioplankton at the genus level and the slopes (rate of change) and regression R 2 (low stochasticity or stability) were greater if Cyanobacteria were included, suggesting a higher level of instability in the bacterial community at lower taxonomy level. Consequently, phytoplankton responded more rapidly to the change in environmental conditions than bacterioplankton when analyzed at the phylum level, while bacterioplankton were more sensitive at the finer taxonomic resolution in Lake Taihu. Redundancy analysis (RDA) results showed that environmental variables collectively explained 51.0% variance of phytoplankton and 46.7% variance of bacterioplankton, suggesting that environmental conditions have a significant influence on the temporal variations of phyto- and bacterioplankton. Furthermore, variance partitioning indicated that the bacterial community structure was largely explained by water temperature and nitrogen, suggesting that these factors were the primary drivers shaping bacterioplankton. Copyright © 2017. Published by Elsevier Ltd.

Spatial and Temporal Variation in DeSoto Canyon Macrofaunal Community Structure

NASA Astrophysics Data System (ADS)

Baco-Taylor, A.; Shantharam, A. K.

2016-02-01

Sediment-dwelling macrofauna (polychaetes, bivalves, and assorted crustaceans ≥ 300 µm) have long served as biological indicators of ecosystem stress. As part of evaluating the 2010 impact from the Deepwater Horizon blowout, we sampled 12 sites along and transverse to the DeSoto Canyon axis, Gulf of Mexico, as well as 2 control sites outside the Canyon. Sites ranged in depth from 479-2310 m. Three of the sites (PCB06, S36, and XC4) were sampled annually from 2012-2014. We provide an overview of the macrofauna community structure of canyon and non-canyon sites, as well as trends in community structure and diversity at the time-series sites. Compositionally, polychaetes dominated the communities, followed by tanaid crustaceans and bivalves. The total number of individuals was not significantly correlated with depth while the total number of taxa and species richness were. Rarefaction shows the deepest station, XC4 (2310 m) had the lowest diversity while NT800 (a non-canyon control at 800m) had the highest. Multivariate analysis shows the canyon assemblages fall into eight clusters with the non-canyon stations forming a separate ninth cluster, indicating a detectable difference in canyon and non-canyon communities. Time series stations show an increase in diversity from 2012-2014 with a strong overlap in community structure in 2013 and 2014 samples. Environmental analysis, via BEST, using data from 10 canyon sites and the controls, indicated depth in combination with latitude explain the most variation in macrofaunal community structure.

TEC Longitude Difference Using GIMS and the IRI Model

NASA Astrophysics Data System (ADS)

Natali, Maria Paula; Meza, Amalia Margarita; Mendoza, Gastón

2016-07-01

The main geomagnetic field declination has a global distribution with positive and negative values showing maximum east-west differences over North America and Oceania and minimum differences over America and Asia. Several authors study one or more of these regions using TEC data derived from GNSS observations to describe variations in TEC. They reported a pronounced longitudinal variation respect to zero magnetic declination. One of the important factors that cause the longitude difference at mid-latitude is a combined effect of the longitude variations of magnetic declination and the variations of the zonal thermospheric winds with local time. We propose to study this effect using Global Ionospheric Maps (GIMs) and the respective TEC values generated from the International Reference Ionospheric (IRI) model, during a solar cycle, applying Principal Component Analysis (PCA). Our works is focused over different local times and regions at mid-latitude. PCA involves a mathematical procedure that transforms a number of correlated variables into a number of uncorrelated variables using the data itself. The spatial structure of the ionosphere variability and its temporal evolution, together are called modes, and there are ordered according to their percentage of the variability of data from highest to lowest. In this analysis the first mode has more than the 90 % of the variability, representing the nominal behavior of the ionosphere, and the second and third modes are the more important for our analysis, because they show the strong longitudinal variation in the different regions using either GIMs or the IRI model.

Evidence for magnetic energy storage in coronal active regions

NASA Technical Reports Server (NTRS)

Krieger, A. S.; De Feiter, L. D.; Vaiana, G. S.

1976-01-01

Examination of X-ray images obtained by the S-054 X-ray spectrographic telescope on Skylab shows the presence of some atypical X-ray-emitting coronal structures in active regions which are not consistent with potential extrapolations of photospheric magnetic fields. Analysis of the observed temporal changes in the X-ray-emitting active-region structures demonstrates that the majority of these consist of brightness changes representing temperature (and perhaps density) variations of the material in the loops.

Real-Time Wing-Vortex and Pressure Distribution Estimation on Wings Via Displacements and Strains in Unsteady and Transitional Flight Conditions

DTIC Science & Technology

2016-09-07

approach in co simulation with fluid-dynamics solvers is used. An original variational formulation is developed for the inverse problem of...by the inverse solution meshing. The same approach is used to map the structural and fluid interface kinematics and loads during the fluid structure...co-simulation. The inverse analysis is verified by reconstructing the deformed solution obtained with a corresponding direct formulation, based on

Probabilistic models of genetic variation in structured populations applied to global human studies.

PubMed

Hao, Wei; Song, Minsun; Storey, John D

2016-03-01

Modern population genetics studies typically involve genome-wide genotyping of individuals from a diverse network of ancestries. An important problem is how to formulate and estimate probabilistic models of observed genotypes that account for complex population structure. The most prominent work on this problem has focused on estimating a model of admixture proportions of ancestral populations for each individual. Here, we instead focus on modeling variation of the genotypes without requiring a higher-level admixture interpretation. We formulate two general probabilistic models, and we propose computationally efficient algorithms to estimate them. First, we show how principal component analysis can be utilized to estimate a general model that includes the well-known Pritchard-Stephens-Donnelly admixture model as a special case. Noting some drawbacks of this approach, we introduce a new 'logistic factor analysis' framework that seeks to directly model the logit transformation of probabilities underlying observed genotypes in terms of latent variables that capture population structure. We demonstrate these advances on data from the Human Genome Diversity Panel and 1000 Genomes Project, where we are able to identify SNPs that are highly differentiated with respect to structure while making minimal modeling assumptions. A Bioconductor R package called lfa is available at http://www.bioconductor.org/packages/release/bioc/html/lfa.html jstorey@princeton.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Image analysis of representative food structures: application of the bootstrap method.

PubMed

Ramírez, Cristian; Germain, Juan C; Aguilera, José M

2009-08-01

Images (for example, photomicrographs) are routinely used as qualitative evidence of the microstructure of foods. In quantitative image analysis it is important to estimate the area (or volume) to be sampled, the field of view, and the resolution. The bootstrap method is proposed to estimate the size of the sampling area as a function of the coefficient of variation (CV(Bn)) and standard error (SE(Bn)) of the bootstrap taking sub-areas of different sizes. The bootstrap method was applied to simulated and real structures (apple tissue). For simulated structures, 10 computer-generated images were constructed containing 225 black circles (elements) and different coefficient of variation (CV(image)). For apple tissue, 8 images of apple tissue containing cellular cavities with different CV(image) were analyzed. Results confirmed that for simulated and real structures, increasing the size of the sampling area decreased the CV(Bn) and SE(Bn). Furthermore, there was a linear relationship between the CV(image) and CV(Bn) (.) For example, to obtain a CV(Bn) = 0.10 in an image with CV(image) = 0.60, a sampling area of 400 x 400 pixels (11% of whole image) was required, whereas if CV(image) = 1.46, a sampling area of 1000 x 100 pixels (69% of whole image) became necessary. This suggests that a large-size dispersion of element sizes in an image requires increasingly larger sampling areas or a larger number of images.

Quantitative analysis of structural variations in corpus callosum in adults with multiple system atrophy (MSA)

NASA Astrophysics Data System (ADS)

Bhattacharya, Debanjali; Sinha, Neelam; Saini, Jitender

2017-03-01

Multiple system atrophy (MSA) is a rare, non-curable, progressive neurodegenerative disorder that affects nervous system and movement, poses a considerable diagnostic challenge to medical researchers. Corpus callosum (CC) being the largest white matter structure in brain, enabling inter-hemispheric communication, quantification of callosal atrophy may provide vital information at the earliest possible stages. The main objective is to identify the differences in CC structure for this disease, based on quantitative analysis on the pattern of callosal atrophy. We report results of quantification of structural changes in regional anatomical thickness, area and length of CC between patient-groups with MSA with respect to healthy controls. The method utilizes isolating and parcellating the mid-sagittal CC into 100 segments along the length - measuring the width of each segment. It also measures areas within geometrically defined five callosal compartments of the well-known Witelson, and Hofer-Frahma schemes. For quantification, statistical tests are performed on these different callosal measurements. From the statistical analysis, it is concluded that compared to healthy controls, width is reduced drastically throughout CC for MSA group and as well as changes in area and length are also significant for MSA. The study is further extended to check if any significant difference in thickness is found between the two variations of MSA, Parkinsonian MSA and Cerebellar MSA group, using the same methodology. However area and length of this two sub-MSA group, no substantial difference is obtained. The study is performed on twenty subjects for each control and MSA group, who had T1-weighted MRI.

A case of isolation by distance and short-term temporal stability of population structure in brown trout (Salmo trutta) within the River Dart, southwest England

PubMed Central

Griffiths, Andrew M; Koizumi, Itsuro; Bright, Dylan; Stevens, Jamie R

2009-01-01

Salmonid fishes exhibit high levels of population differentiation. In particular, the brown trout (Salmo trutta L.) demonstrates complex within river drainage genetic structure. Increasingly, these patterns can be related to the underlying evolutionary models, of which three scenarios (member-vagrant hypothesis, metapopulation model and panmixia) facilitate testable predictions for investigations into population structure. We analysed 1225 trout collected from the River Dart, a 75 km long river located in southwest England. Specimens were collected from 22 sample sites across three consecutive summers (2001–2003) and genetic variation was examined at nine microsatellite loci. A hierarchical analysis of molecular variance revealed that negligible genetic variation was attributed among temporal samples. The highest levels of differentiation occurred among samples isolated above barriers to fish movement, and once these samples were removed, a significant effect of isolation-by-distance was observed. These results suggest that, at least in the short-term, ecological events are more important in shaping the population structure of Dart trout than stochastic extinction events, and certainly do not contradict the expectations of a member-vagrant hypothesis. Furthermore, individual-level spatial autocorrelation analyses support previous recommendations for the preservation of a number of spawning sites spaced throughout the tributary system to conserve the high levels of genetic variation identified in salmonid species. PMID:25567897

Variation in Genomic Methylation in Natural Populations of Chinese White Poplar

PubMed Central

Ma, Kaifeng; Song, Yuepeng; Yang, Xiaohui; Zhang, Zhiyi; Zhang, Deqiang

2013-01-01

Background It is thought that methylcytosine can be inherited through meiosis and mitosis, and that epigenetic variation may be under genetic control or correlation may be caused by neutral drift. However, DNA methylation also varies with tissue, developmental stage, and environmental factors. Eliminating these factors, we analyzed the levels and patterns, diversity and structure of genomic methylcytosine in the xylem of nine natural populations of Chinese white poplar. Principal Findings On average, the relative total methylation and non-methylation levels were approximately 26.567% and 42.708% (P<0.001), respectively. Also, the relative CNG methylation level was higher than the relative CG methylation level. The relative methylation/non-methylation levels were significantly different among the nine natural populations. Epigenetic diversity ranged from 0.811 (Gansu) to 1.211 (Shaanxi), and the coefficients of epigenetic differentiation (GST = 0.159) were assessed by Shannon’s diversity index. Co-inertia analysis indicated that methylation-sensitive polymorphism (MSP) and genomic methylation pattern (CG-CNG) profiles gave similar distributions. Using a between-group eigen analysis, we found that the Hebei and Shanxi populations were independent of each other, but the Henan population intersected with the other populations, to some degree. Conclusions Genome methylation in Populus tomentosa presented tissue-specific characteristics and the relative 5′-CCGG methylation level was higher in xylem than in leaves. Meanwhile, the genome methylation in the xylem shows great epigenetic variation and could be fixed and inherited though mitosis. Compared to genetic structure, data suggest that epigenetic and genetic variation do not completely match. PMID:23704963

Detecting taxonomic signal in an under-utilised character system: geometric morphometrics of the forcipular coxae of Scutigeromorpha (Chilopoda)

PubMed Central

Gutierrez, Beatriz Lopez; MacLeod, Norman; Edgecombe, Gregory D.

2011-01-01

Abstract To date, the forcipules have played almost no role in determining the systematics of scutigeromorph centipedes though in his 1974 review of taxonomic characters Markus Würmli suggested some potentially informative variation might be found in these structures. Geometric morphometric analyses were used to evaluate Würmli’s suggestion, specifically to determine whether the shape of the forcipular coxa contains information useful for diagnosing species. The geometry of the coxae of eight species from the genera Sphendononema, Scutigera, Dendrothereua, Thereuonema, Thereuopoda, Thereuopodina, Allothereua and Parascutigera was characterised using a combination of landmark- and semi-landmark-based sampling methods to summarize group-specific morphological variation. Canonical variates analysis of shape data characterizing the forcipular coxae indicates that these structures differ significantly between taxa at various systematic levels. Models calculated for the canonical variates space facilitate identification of the main shape differences between genera, including overall length/width, curvature of the external coxal margin, and the extent to which the coxofemoral condyle projects laterally. Jackknifed discriminant function analysis demonstrates that forcipular coxal training-set specimens were assigned to correct species in 61% of cases on average, the most accurate assignments being those of Parascutigera (Parascutigera guttata) and Thereuonema (Thereuonema microstoma). The geographically widespread species Thereuopoda longicornis, Sphendononema guildingii, Scutigera coleoptrata, and Dendrothereua linceci exhibit the least diagnostic coxae in our dataset. Thereuopoda longicornis populations sampled from different parts of East and Southeast Asia were significantly discriminated from each other, suggesting that, in this case, extensive synonymy may be obscuring diagnosable inter-species coxal shape differences. PMID:22303095

Influences of space, soil, nematodes and plants on microbial community composition of chalk grassland soils.

PubMed

Yergeau, Etienne; Bezemer, T Martijn; Hedlund, Katarina; Mortimer, Simon R; Kowalchuk, George A; Van Der Putten, Wim H

2010-08-01

Microbial communities respond to a variety of environmental factors related to resources (e.g. plant and soil organic matter), habitat (e.g. soil characteristics) and predation (e.g. nematodes, protozoa and viruses). However, the relative contribution of these factors on microbial community composition is poorly understood. Here, we sampled soils from 30 chalk grassland fields located in three different chalk hill ridges of Southern England, using a spatially explicit sampling scheme. We assessed microbial communities via phospholipid fatty acid (PLFA) analyses and PCR-denaturing gradient gel electrophoresis (DGGE) and measured soil characteristics, as well as nematode and plant community composition. The relative influences of space, soil, vegetation and nematodes on soil microorganisms were contrasted using variation partitioning and path analysis. Results indicate that soil characteristics and plant community composition, representing habitat and resources, shape soil microbial community composition, whereas the influence of nematodes, a potential predation factor, appears to be relatively small. Spatial variation in microbial community structure was detected at broad (between fields) and fine (within fields) scales, suggesting that microbial communities exhibit biogeographic patterns at different scales. Although our analysis included several relevant explanatory data sets, a large part of the variation in microbial communities remained unexplained (up to 92% in some analyses). However, in several analyses, significant parts of the variation in microbial community structure could be explained. The results of this study contribute to our understanding of the relative importance of different environmental and spatial factors in driving the composition of soil-borne microbial communities. © 2009 Society for Applied Microbiology and Blackwell Publishing Ltd.

ExDom: an integrated database for comparative analysis of the exon–intron structures of protein domains in eukaryotes

PubMed Central

Bhasi, Ashwini; Philip, Philge; Manikandan, Vinu; Senapathy, Periannan

2009-01-01

We have developed ExDom, a unique database for the comparative analysis of the exon–intron structures of 96 680 protein domains from seven eukaryotic organisms (Homo sapiens, Mus musculus, Bos taurus, Rattus norvegicus, Danio rerio, Gallus gallus and Arabidopsis thaliana). ExDom provides integrated access to exon-domain data through a sophisticated web interface which has the following analytical capabilities: (i) intergenomic and intragenomic comparative analysis of exon–intron structure of domains; (ii) color-coded graphical display of the domain architecture of proteins correlated with their corresponding exon-intron structures; (iii) graphical analysis of multiple sequence alignments of amino acid and coding nucleotide sequences of homologous protein domains from seven organisms; (iv) comparative graphical display of exon distributions within the tertiary structures of protein domains; and (v) visualization of exon–intron structures of alternative transcripts of a gene correlated to variations in the domain architecture of corresponding protein isoforms. These novel analytical features are highly suited for detailed investigations on the exon–intron structure of domains and make ExDom a powerful tool for exploring several key questions concerning the function, origin and evolution of genes and proteins. ExDom database is freely accessible at: http://66.170.16.154/ExDom/. PMID:18984624

Organizational culture, creative behavior, and information and communication technology (ICT) usage: a facet analysis.

PubMed

Carmeli, Abraham; Sternberg, Akiva; Elizur, D

2008-04-01

Despite the prominence of organizational culture (OC), this concept is controversial and its structure has yet to be systematically analyzed. This study develops a three-pronged formal definitional framework on the basis of facet theory (FT) and explores behavior modality, referent, and object. This facet analysis (FA) of OC accounts successfully for variation in both creative behavior at work and the usage of information and communication technologies (ICTs). An analysis of data collected from 230 employees in the financial industry indicates that a radex structure was obtained for work and ICT. The behavior modality facet ordered the space from center to periphery, and referents facet relates to the direction angles away from the origin.

Report for 2012 from the Bordeaux IVS Analysis Center

NASA Technical Reports Server (NTRS)

Charlot, Patrick; Bellanger, Antoine; Bouffet, Romuald; Bourda, Geraldine; Collioud, Arnaud; Baudry, Alain

2013-01-01

This report summarizes the activities of the Bordeaux IVS Analysis Center during the year 2012. The work focused on (i) regular analysis of the IVS-R1 and IVS-R4 sessions with the GINS software package; (ii) systematic VLBI imaging of the RDV sessions and calculation of the corresponding source structure index and compactness values; (iii) investigation of the correlation between astrometric position instabilities and source structure variations; and (iv) continuation of our VLBI observational program to identify optically-bright radio sources suitable for the link with the future Gaia frame. Also of importance is the 11th European VLBI Network Symposium, which we organized last October in Bordeaux and which drew much attention from the European and International VLBI communities.

Flight-determined stability analysis of multiple-input-multiple-output control systems

NASA Technical Reports Server (NTRS)

Burken, John J.

1992-01-01

Singular value analysis can give conservative stability margin results. Applying structure to the uncertainty can reduce this conservatism. This paper presents flight-determined stability margins for the X-29A lateral-directional, multiloop control system. These margins are compared with the predicted unscaled singular values and scaled structured singular values. The algorithm was further evaluated with flight data by changing the roll-rate-to-aileron command-feedback gain by +/- 20 percent. Minimum eigenvalues of the return difference matrix which bound the singular values are also presented. Extracting multiloop singular values from flight data and analyzing the feedback gain variations validates this technique as a measure of robustness. This analysis can be used for near-real-time flight monitoring and safety testing.

Flight-determined stability analysis of multiple-input-multiple-output control systems

NASA Technical Reports Server (NTRS)

Burken, John J.

1992-01-01

Singular value analysis can give conservative stability margin results. Applying structure to the uncertainty can reduce this conservatism. This paper presents flight-determined stability margins for the X-29A lateral-directional, multiloop control system. These margins are compared with the predicted unscaled singular values and scaled structured singular values. The algorithm was further evaluated with flight data by changing the roll-rate-to-aileron-command-feedback gain by +/- 20 percent. Also presented are the minimum eigenvalues of the return difference matrix which bound the singular values. Extracting multiloop singular values from flight data and analyzing the feedback gain variations validates this technique as a measure of robustness. This analysis can be used for near-real-time flight monitoring and safety testing.

[Genetic variation of some varieties of common juniper Juniperus communis L. inferred from analysis of allozyme loci].

PubMed

Khantemirova, E V; Semerikov, V L

2010-05-01

Using the method of allozyme analysis, genetic variation, diversity, and population structure of Juniperus communis L. var. communis and J. communis L. var. saxatilis Pall. (= J. sibirica Burgsd. = J. nana Wild), growing on the territory of Russia, J. c. var. communis from Sweden, and J. c. var. depressa Pursh from Northern America (Alaska), was investigated. The total level of genetic variation of these varieties was found to be higher than the values obtained for the other conifers. The population samples of J. c. var. depressa from Alaska and J. c. var. saxatilis from Sakhalin were noticeably different from all other populations examined. Between the other samples, no substantial genetic differences were observed. These populations were characterized by weak interpopulation differentiation along with the absence of expressed geographical pattern of the allele frequency spatial distribution. The only exception was the procumbent form of common juniper from the high mountain populations of South and North Ural, which was somewhat different from the others.

Global variation of the para hydrogen fraction in Jupiter's atmosphere and implications for dynamics on the outer planets

NASA Technical Reports Server (NTRS)

Conrath, B. J.; Gierasch, P. J.

1984-01-01

A detailed analysis of the Voyager infrared spectrometer measurements on Jupiter's atmosphere is presented, and possible implications of para hydrogen disequilibrium for the energetics and dynamics of that atmosphere are examined. The method of data analysis is described, and results for the large scale latitude variation of the para hydrogen fraction are presented. The Jovian results show pronounced latitude variation, and are compared with other parameters including wind fields, thermal structure, and various indicators of atmospheric clouds. The problem of equilibration rate is reexamined, and it is concluded that on Jupiter the equilibration time is longer than the radiative time constant at the level of emission to space, but that this inequality reverses at greater depths. A model for the interaction of fluid motions with the ortho-para conversion process is presented, and a consistent mixing length theory for the reacting ortho-para mixture is developed. Several implications of the Jovian data for atmospheric energetics and stability on the outer planets are presented.

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.

Evidence of increment of efficiency of the Mexican Stock Market through the analysis of its variations

NASA Astrophysics Data System (ADS)

Coronel-Brizio, H. F.; Hernández-Montoya, A. R.; Huerta-Quintanilla, R.; Rodríguez-Achach, M.

2007-07-01

It is well known that there exist statistical and structural differences between the stock markets of developed and emerging countries. In this work, and in order to find out if the efficiency of the Mexican Stock Market has been changing over time, we have performed and compared several analyses of the variations of the Mexican Stock Market index (IPC) and Dow Jones industrial average index (DJIA) for different periods of their historical daily data. We have analyzed the returns autocorrelation function (ACF) and used detrended fluctuation analysis (DFA) to study returns variations. We also analyze the volatility, mean value and standard deviation of both markets and compare their evolution. We conclude from the overall result of these studies, that they show compelling evidence of the increment of efficiency of the Mexican Stock Market over time. The data samples analyzed here, correspond to daily values of the IPC and DJIA for the period 10/30/1978-02/28/2006.

Anomalous Structure of Oceanic Lithosphere in the North Atlantic and Arctic Oceans: A Preliminary Analysis Based on Bathymetry, Gravity and Crustal Structure

NASA Astrophysics Data System (ADS)

Barantsrva, O.

2014-12-01

We present a preliminary analysis of the crustal and upper mantle structure for off-shore regions in the North Atlantic and Arctic oceans. These regions have anomalous oceanic lithosphere: the upper mantle of the North Atlantic ocean is affected by the Iceland plume, while the Arctic ocean has some of the slowest spreading rates. Our specific goal is to constrain the density structure of the upper mantle in order to understand the links between the deep lithosphere dynamics, ocean spreading, ocean floor bathymetry, heat flow and structure of the oceanic lithosphere in the regions where classical models of evolution of the oceanic lithosphere may not be valid. The major focus is on the oceanic lithosphere, but the Arctic shelves with a sufficient data coverage are also included into the analysis. Out major interest is the density structure of the upper mantle, and the analysis is based on the interpretation of GOCE satellite gravity data. To separate gravity anomalies caused by subcrustal anomalous masses, the gravitational effect of water, crust and the deep mantle is removed from the observed gravity field. For bathymetry we use the global NOAA database ETOPO1. The crustal correction to gravity is based on two crustal models: (1) global model CRUST1.0 (Laske, 2013) and, for a comparison, (2) a regional seismic model EUNAseis (Artemieva and Thybo, 2013). The crustal density structure required for the crustal correction is constrained from Vp data. Previous studies have shown that a large range of density values corresponds to any Vp value. To overcome this problem and to reduce uncertainty associated with the velocity-density conversion, we account for regional tectonic variations in the Northern Atlantics as constrained by numerous published seismic profiles and potential-field models across the Norwegian off-shore crust (e.g. Breivik et al., 2005, 2007), and apply different Vp-density conversions for different parts of the region. We present preliminary results, which we use to examine factors that control variations in bathymetry, sedimentary and crustal thicknesses in these anomalous oceanic domains.

3D quantitative comparative analysis of long bone diaphysis variations in microanatomy and cross-sectional geometry.

PubMed

Houssaye, Alexandra; Taverne, Maxime; Cornette, Raphaël

2018-05-01

Long bone inner structure and cross-sectional geometry display a strong functional signal, leading to convergences, and are widely analyzed in comparative anatomy at small and large taxonomic scales. Long bone microanatomical studies have essentially been conducted on transverse sections but also on a few longitudinal ones. Recent studies highlighted the interest in analyzing variations of the inner structure along the diaphysis using a qualitative as well as a quantitative approach. With the development of microtomography, it has become possible to study three-dimensional (3D) bone microanatomy and, in more detail, the form-function relationships of these features. This study focused on the selection of quantitative parameters to describe in detail the cross-sectional shape changes and distribution of the osseous tissue along the diaphysis. Two-dimensional (2D) virtual transverse sections were also performed in the two usual reference planes and results were compared with those obtained based on the whole diaphysis analysis. The sample consisted in 14 humeri and 14 femora of various mammalian taxa that are essentially terrestrial. Comparative quantitative analyses between different datasets made it possible to highlight the parameters that are strongly impacted by size and phylogeny and the redundant ones, and thus to estimate their relevance for use in form-function analyses. The analysis illustrated that results based on 2D transverse sections are similar for both sectional planes; thus if a strong bias exists when mixing sections from the two reference planes in the same analysis, it would not problematic to use either one plane or the other in comparative studies. However, this may no longer hold for taxa showing a much stronger variation in bone microstructure along the diaphysis. Finally, the analysis demonstrated the significant contribution of the parameters describing variations along the diaphysis, and thus the interest in performing 3D analyses; this should be even more fruitful for heterogeneous diaphyses. In addition, covariation analyses showed that there is a strong interest in removing the size effect to access the differences in the microstructure of the humerus and femur. This methodological study provides a reference for future quantitative analyses on long bone inner structure and should make it possible, through a detailed knowledge of each descriptive parameter, to better interpret results from the multivariate analyses associated with these studies. This will have direct implications for studies in vertebrate anatomy, but also in paleontology and anthropology. © 2018 Anatomical Society.

Dissecting the space-time structure of tree-ring datasets using the partial triadic analysis.

PubMed

Rossi, Jean-Pierre; Nardin, Maxime; Godefroid, Martin; Ruiz-Diaz, Manuela; Sergent, Anne-Sophie; Martinez-Meier, Alejandro; Pâques, Luc; Rozenberg, Philippe

2014-01-01

Tree-ring datasets are used in a variety of circumstances, including archeology, climatology, forest ecology, and wood technology. These data are based on microdensity profiles and consist of a set of tree-ring descriptors, such as ring width or early/latewood density, measured for a set of individual trees. Because successive rings correspond to successive years, the resulting dataset is a ring variables × trees × time datacube. Multivariate statistical analyses, such as principal component analysis, have been widely used for extracting worthwhile information from ring datasets, but they typically address two-way matrices, such as ring variables × trees or ring variables × time. Here, we explore the potential of the partial triadic analysis (PTA), a multivariate method dedicated to the analysis of three-way datasets, to apprehend the space-time structure of tree-ring datasets. We analyzed a set of 11 tree-ring descriptors measured in 149 georeferenced individuals of European larch (Larix decidua Miller) during the period of 1967-2007. The processing of densitometry profiles led to a set of ring descriptors for each tree and for each year from 1967-2007. The resulting three-way data table was subjected to two distinct analyses in order to explore i) the temporal evolution of spatial structures and ii) the spatial structure of temporal dynamics. We report the presence of a spatial structure common to the different years, highlighting the inter-individual variability of the ring descriptors at the stand scale. We found a temporal trajectory common to the trees that could be separated into a high and low frequency signal, corresponding to inter-annual variations possibly related to defoliation events and a long-term trend possibly related to climate change. We conclude that PTA is a powerful tool to unravel and hierarchize the different sources of variation within tree-ring datasets.

A discussion of plausible solar irradiance variations, 1700-1992

NASA Technical Reports Server (NTRS)

Hoyt, Douglas V.; Schatten, Kenneth H.

1993-01-01

From satellite observations the solar total irradiance is known to vary. Sunspot blocking, facular emission, and network emission are three identified causes for the variations. In this paper we examine several different solar indices measured over the past century that are potential proxy measures for the Sun's irradiance. These indices are (1) the equatorial solar rotation rate, (2) the sunspot structure, the decay rate of individual sunspots, and the number of sunspots without umbrae, and (3) the length and decay rate of the sunspot cycle. Each index can be used to develop a model for the Sun's total irradiance as seen at the Earth. Three solar indices allow the irradiance to be modeled back to the mid-1700s. The indices are (1) the length of the solar cycle, (2) the normalized decay rate of the solar cycle, and (3) the mean level of solar activity. All the indices are well correlated, and one possible explanation for their nearly simultaneous variations is changes in the Sun's convective energy transport. Although changes in the Sun's convective energy transport are outside the realm of normal stellar structure theory (e.g., mixing length theory), one can imagine variations arising from even the simplest view of sunspots as vertical tubes of magnetic flux, which would serve as rigid pillas affecting the energy flow patterns by ensuring larger-scale eddies. A composite solar irradiance model, based upon these proxies, is compared to the northern hemisphere temperature depatures for 1700-1992. Approximately 71% of the decadal variance in the last century can be modeled with these solar indices, although this analysis does not include anthropogenic or other variations which would affect the results. Over the entire three centuries, approx. 50% of the variance is modeled. Both this analysis and previous similar analyses have correlations of model solar irradiances and measured Earth surface temperatures that are significant at better than the 95% confidence level. To understand our present climate variations, we must place the anthropogenic variations in the context of natural variability from solar, volcanic, oceanic, and other sources.

Molecular Population Genetics of the Alcohol Dehydrogenase Gene Region of DROSOPHILA MELANOGASTER

PubMed Central

Aquadro, Charles F.; Desse, Susan F.; Bland, Molly M.; Langley, Charles H.; Laurie-Ahlberg, Cathy C.

1986-01-01

Variation in the DNA restriction map of a 13-kb region of chromosome II including the alcohol dehydrogenase structural gene (Adh) was examined in Drosophila melanogaster from natural populations. Detailed analysis of 48 D. melanogaster lines representing four eastern United States populations revealed extensive DNA sequence variation due to base substitutions, insertions and deletions. Cloning of this region from several lines allowed characterization of length variation as due to unique sequence insertions or deletions [nine sizes; 21–200 base pairs (bp)] or transposable element insertions (several sizes, 340 bp to 10.2 kb, representing four different elements). Despite this extensive variation in sequences flanking the Adh gene, only one length polymorphism is clearly associated with altered Adh expression (a copia element approximately 250 bp 5' to the distal transcript start site). Nonetheless, the frequency spectra of transposable elements within and between Drosophila species suggests they are slightly deleterious. Strong nonrandom associations are observed among Adh region sequence variants, ADH allozyme (Fast vs. Slow), ADH enzyme activity and the chromosome inversion ln(2L) t. Phylogenetic analysis of restriction map haplotypes suggest that the major twofold component of ADH activity variation (high vs. low, typical of Fast and Slow allozymes, respectively) is due to sequence variation tightly linked to and possibly distinct from that underlying the allozyme difference. The patterns of nucleotide and haplotype variation for Fast and Slow allozyme lines are consistent with the recent increase in frequency and spread of the Fast haplotype associated with high ADH activity. These data emphasize the important role of evolutionary history and strong nonrandom associations among tightly linked sequence variation as determinants of the patterns of variation observed in natural populations. PMID:3026893

On the role of magnetic field intensity for better micro-structural characterization during Barkhausen Noise analysis

NASA Astrophysics Data System (ADS)

Yusufzai, Mohd Zaheer Khan; Vashista, M.

2018-04-01

Barkhausen Noise analysis is a popular and preferred technique for micro-structural characterization. The root mean square value and peak value of Barkhausen Noise burst are important parameters to assess the micro-hardness and residual stress. Barkhausen Noise burst can be enveloped using a curve known as Barkhausen Noise profile. Peak position of profile changes with change in micro-structure. In the present work, raw signal of Barkhausen Noise burst was obtained from Ni based sample at various magnetic field intensity to observe the effect of variation in field intensity on Barkhausen Noise burst. Raw signal was opened using MATLAB to further process for microstructure analysis. Barkhausen Noise analysis parameters such as magnetizing frequency, number of burst, high pass and low pass filter frequency were kept constant and magnetizing field was varied in wide range between 200 Oe to 1200 Oe. The processed profiles of Barkhausen Noise burst obtained at various magnetizing field intensity clearly reveals requirement of optimum magnetic field strength for better characterization of micro-structure.

[Short interspersed repetitive sequences (SINEs) and their use as a phylogenetic tool].

PubMed

Kramerov, D A; Vasetskiĭ, N S

2009-01-01

The data on one of the most common repetitive elements of eukaryotic genomes, short interspersed elements (SINEs), are reviewed. Their structure, origin, and functioning in the genome are discussed. The variation and abundance of these neutral genomic markers makes them a convenient and reliable tool for phylogenetic analysis. The main methods of such analysis are presented, and the potential and limitations of this approach are discussed using specific examples.

Geometric Variational Methods for Controlled Active Vision

DTIC Science & Technology

2006-08-01

Haker , L. Zhu, and A. Tannenbaum, ``Optimal mass transport for registration and warping’’ Int. Journal Computer Vision, volume 60, 2004, pp. 225-240. G...pp. 119-142. A. Angenent, S. Haker , and A. Tannenbaum, ``Minimizing flows for the Monge-Kantorovich problem,’’ SIAM J. Math. Analysis, volume 35...Shape analysis of structures using spherical wavelets’’ (with S. Haker and D. Nain), Proceeedings of MICCAI, 2005. ``Affine surface evolution for 3D

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.

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

Variation analysis of transcriptome changes reveals cochlear genes and their associated functions in cochlear susceptibility to acoustic overstimulation.

PubMed

Yang, Shuzhi; Cai, Qunfeng; Bard, Jonathan; Jamison, Jennifer; Wang, Jianmin; Yang, Weiping; Hu, Bo Hua

2015-12-01

Individual variation in the susceptibility of the auditory system to acoustic overstimulation has been well-documented at both the functional and structural levels. However, the molecular mechanism responsible for this variation is unclear. The current investigation was designed to examine the variation patterns of cochlear gene expression using RNA-seq data and to identify the genes with expression variation that increased following acoustic trauma. This study revealed that the constitutive expressions of cochlear genes displayed diverse levels of gene-specific variation. These variation patterns were altered by acoustic trauma; approximately one-third of the examined genes displayed marked increases in their expression variation. Bioinformatics analyses revealed that the genes that exhibited increased variation were functionally related to cell death, biomolecule metabolism, and membrane function. In contrast, the stable genes were primarily related to basic cellular processes, including protein and macromolecular syntheses and transport. There was no functional overlap between the stable and variable genes. Importantly, we demonstrated that glutamate metabolism is related to the variation in the functional response of the cochlea to acoustic overstimulation. Taken together, the results indicate that our analyses of the individual variations in transcriptome changes of cochlear genes provide important information for the identification of genes that potentially contribute to the generation of individual variation in cochlear responses to acoustic overstimulation. Copyright © 2015 Elsevier B.V. All rights reserved.

Deciphering the shape and deformation of secondary structures through local conformation analysis

PubMed Central

2011-01-01

Background Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation. Results Using a structural alphabet, we translated the 3 D structures of large sets of protein-protein complexes into sequences of structural letters. The shape of the secondary structures can be assessed by the structural letters that modeled them in the structural sequences. The distribution analysis of the structural letters in the three protein compartments (surface, core and interface) reveals that secondary structures tend to adopt preferential conformations that differ among the compartments. The local description of secondary structures highlights that curved conformations are preferred on the surface while straight ones are preferred in the core. Interfaces display a mixture of local conformations either preferred in core or surface. The analysis of the structural letters transition occurring between protein-bound and unbound conformations shows that the deformation of secondary structure is tightly linked to the compartment preference of the local conformations. Conclusion The conformation of secondary structures can be further analysed and detailed thanks to a structural alphabet which allows a better description of protein surface, core and interface in terms of secondary structures' shape and deformation. Induced-fit modification tendencies described here should be valuable information to identify and characterize regions under strong structural constraints for functional reasons. PMID:21284872

Deciphering the shape and deformation of secondary structures through local conformation analysis.

PubMed

Baussand, Julie; Camproux, Anne-Claude

2011-02-01

Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation. Using a structural alphabet, we translated the 3 D structures of large sets of protein-protein complexes into sequences of structural letters. The shape of the secondary structures can be assessed by the structural letters that modeled them in the structural sequences. The distribution analysis of the structural letters in the three protein compartments (surface, core and interface) reveals that secondary structures tend to adopt preferential conformations that differ among the compartments. The local description of secondary structures highlights that curved conformations are preferred on the surface while straight ones are preferred in the core. Interfaces display a mixture of local conformations either preferred in core or surface. The analysis of the structural letters transition occurring between protein-bound and unbound conformations shows that the deformation of secondary structure is tightly linked to the compartment preference of the local conformations. The conformation of secondary structures can be further analysed and detailed thanks to a structural alphabet which allows a better description of protein surface, core and interface in terms of secondary structures' shape and deformation. Induced-fit modification tendencies described here should be valuable information to identify and characterize regions under strong structural constraints for functional reasons.

Sensitivity Analysis of earth and environmental models: a systematic review to guide scientific advancement

NASA Astrophysics Data System (ADS)

Wagener, Thorsten; Pianosi, Francesca

2016-04-01

Sensitivity Analysis (SA) investigates how the variation in the output of a numerical model can be attributed to variations of its input factors. SA is increasingly being used in earth and environmental modelling for a variety of purposes, including uncertainty assessment, model calibration and diagnostic evaluation, dominant control analysis and robust decision-making. Here we provide some practical advice regarding best practice in SA and discuss important open questions based on a detailed recent review of the existing body of work in SA. Open questions relate to the consideration of input factor interactions, methods for factor mapping and the formal inclusion of discrete factors in SA (for example for model structure comparison). We will analyse these questions using relevant examples and discuss possible ways forward. We aim at stimulating the discussion within the community of SA developers and users regarding the setting of good practices and on defining priorities for future research.

Thermography Inspection for Early Detection of Composite Damage in Structures During Fatigue Loading

NASA Technical Reports Server (NTRS)

Zalameda, Joseph N.; Burke, Eric R.; Parker, F. Raymond; Seebo, Jeffrey P.; Wright, Christopher W.; Bly, James B.

2012-01-01

Advanced composite structures are commonly tested under controlled loading. Understanding the initiation and progression of composite damage under load is critical for validating design concepts and structural analysis tools. Thermal nondestructive evaluation (NDE) is used to detect and characterize damage in composite structures during fatigue loading. A difference image processing algorithm is demonstrated to enhance damage detection and characterization by removing thermal variations not associated with defects. In addition, a one-dimensional multilayered thermal model is used to characterize damage. Lastly, the thermography results are compared to other inspections such as non-immersion ultrasonic inspections and computed tomography X-ray.

Inherent Conservatism in Deterministic Quasi-Static Structural Analysis

NASA Technical Reports Server (NTRS)

Verderaime, V.

1997-01-01

The cause of the long-suspected excessive conservatism in the prevailing structural deterministic safety factor has been identified as an inherent violation of the error propagation laws when reducing statistical data to deterministic values and then combining them algebraically through successive structural computational processes. These errors are restricted to the applied stress computations, and because mean and variations of the tolerance limit format are added, the errors are positive, serially cumulative, and excessively conservative. Reliability methods circumvent these errors and provide more efficient and uniform safe structures. The document is a tutorial on the deficiencies and nature of the current safety factor and of its improvement and transition to absolute reliability.

Internal Tooth Structure and Burial Practices: Insights into the Neolithic Necropolis of Gurgy (France, 5100-4000 cal. BC).

PubMed

Le Luyer, Mona; Coquerelle, Michael; Rottier, Stéphane; Bayle, Priscilla

2016-01-01

Variations in the dental crown form are widely studied to interpret evolutionary changes in primates as well as to assess affinities among human archeological populations. Compared to external metrics of dental crown size and shape, variables including the internal structures such as enamel thickness, tissue proportions, and the three-dimensional shape of enamel-dentin junction (EDJ), have been described as powerful measurements to study taxonomy, phylogenetic relationships, dietary, and/or developmental patterns. In addition to providing good estimate of phenotypic distances within/across archeological samples, these internal tooth variables may help to understand phylogenetic, functional, and developmental underlying causes of variation. In this study, a high resolution microtomographic-based record of upper permanent second molars from 20 Neolithic individuals of the necropolis of Gurgy (France) was applied to evaluate the intrasite phenotypic variation in crown tissue proportions, thickness and distribution of enamel, and EDJ shape. The study aims to compare interindividual dental variations with burial practices and chronocultural parameters, and suggest underlying causes of these dental variations. From the non-invasive characterization of internal tooth structure, differences have been found between individuals buried in pits with alcove and those buried in pits with container and pits with wattling. Additionally, individuals from early and recent phases of the necropolis have been distinguished from those of the principal phase from their crown tissue proportions and EDJ shape. The results suggest that the internal tooth structure may be a reliable proxy to track groups sharing similar chronocultural and burial practices. In particular, from the EDJ shape analysis, individuals buried in an alcove shared a reduction of the distolingual dentin horn tip (corresponding to the hypocone). Environmental, developmental and/or functional underlying causes might be suggested for the origin of phenotypic differences shared by these individuals buried in alcoves.

Invertebrate Metacommunity Structure and Dynamics in an Andean Glacial Stream Network Facing Climate Change

PubMed Central

Cauvy-Fraunié, Sophie; Espinosa, Rodrigo; Andino, Patricio; Jacobsen, Dean; Dangles, Olivier

2015-01-01

Under the ongoing climate change, understanding the mechanisms structuring the spatial distribution of aquatic species in glacial stream networks is of critical importance to predict the response of aquatic biodiversity in the face of glacier melting. In this study, we propose to use metacommunity theory as a conceptual framework to better understand how river network structure influences the spatial organization of aquatic communities in glacierized catchments. At 51 stream sites in an Andean glacierized catchment (Ecuador), we sampled benthic macroinvertebrates, measured physico-chemical and food resource conditions, and calculated geographical, altitudinal and glaciality distances among all sites. Using partial redundancy analysis, we partitioned community variation to evaluate the relative strength of environmental conditions (e.g., glaciality, food resource) vs. spatial processes (e.g., overland, watercourse, and downstream directional dispersal) in organizing the aquatic metacommunity. Results revealed that both environmental and spatial variables significantly explained community variation among sites. Among all environmental variables, the glacial influence component best explained community variation. Overland spatial variables based on geographical and altitudinal distances significantly affected community variation. Watercourse spatial variables based on glaciality distances had a unique significant effect on community variation. Within alpine catchment, glacial meltwater affects macroinvertebrate metacommunity structure in many ways. Indeed, the harsh environmental conditions characterizing glacial influence not only constitute the primary environmental filter but also, limit water-borne macroinvertebrate dispersal. Therefore, glacier runoff acts as an aquatic dispersal barrier, isolating species in headwater streams, and preventing non-adapted species to colonize throughout the entire stream network. Under a scenario of glacier runoff decrease, we expect a reduction in both environmental filtering and dispersal limitation, inducing a taxonomic homogenization of the aquatic fauna in glacierized catchments as well as the extinction of specialized species in headwater groundwater and glacier-fed streams, and consequently an irreversible reduction in regional diversity. PMID:26308853

Genetic Architecture of Aluminum Tolerance in Rice (Oryza sativa) Determined through Genome-Wide Association Analysis and QTL Mapping

PubMed Central

Famoso, Adam N.; Zhao, Keyan; Clark, Randy T.; Tung, Chih-Wei; Wright, Mark H.; Bustamante, Carlos; Kochian, Leon V.; McCouch, Susan R.

2011-01-01

Aluminum (Al) toxicity is a primary limitation to crop productivity on acid soils, and rice has been demonstrated to be significantly more Al tolerant than other cereal crops. However, the mechanisms of rice Al tolerance are largely unknown, and no genes underlying natural variation have been reported. We screened 383 diverse rice accessions, conducted a genome-wide association (GWA) study, and conducted QTL mapping in two bi-parental populations using three estimates of Al tolerance based on root growth. Subpopulation structure explained 57% of the phenotypic variation, and the mean Al tolerance in Japonica was twice that of Indica. Forty-eight regions associated with Al tolerance were identified by GWA analysis, most of which were subpopulation-specific. Four of these regions co-localized with a priori candidate genes, and two highly significant regions co-localized with previously identified QTLs. Three regions corresponding to induced Al-sensitive rice mutants (ART1, STAR2, Nrat1) were identified through bi-parental QTL mapping or GWA to be involved in natural variation for Al tolerance. Haplotype analysis around the Nrat1 gene identified susceptible and tolerant haplotypes explaining 40% of the Al tolerance variation within the aus subpopulation, and sequence analysis of Nrat1 identified a trio of non-synonymous mutations predictive of Al sensitivity in our diversity panel. GWA analysis discovered more phenotype–genotype associations and provided higher resolution, but QTL mapping identified critical rare and/or subpopulation-specific alleles not detected by GWA analysis. Mapping using Indica/Japonica populations identified QTLs associated with transgressive variation where alleles from a susceptible aus or indica parent enhanced Al tolerance in a tolerant Japonica background. This work supports the hypothesis that selectively introgressing alleles across subpopulations is an efficient approach for trait enhancement in plant breeding programs and demonstrates the fundamental importance of subpopulation in interpreting and manipulating the genetics of complex traits in rice. PMID:21829395

Genetic variation and population structure of Cucumber green mottle mosaic virus.

PubMed

Rao, Li-Xia; Guo, Yushuang; Zhang, Li-Li; Zhou, Xue-Ping; Hong, Jian; Wu, Jian-Xiang

2017-05-01

Cucumber green mottle mosaic virus (CGMMV) is a single-stranded, positive sense RNA virus infecting cucurbitaceous plants. In recent years, CGMMV has become an important pathogen of cucurbitaceous crops including watermelon, pumpkin, cucumber and bottle gourd in China, causing serious losses to their production. In this study, we surveyed CGMMV infection in various cucurbitaceous crops grown in Zhejiang Province and in several seed lots purchased from local stores with the dot enzyme-linked immunosorbent assay (dot-ELISA), using a CGMMV specific monoclonal antibody. Seven CGMMV isolates obtained from watermelon, grafted watermelon or oriental melon samples were cloned and sequenced. Identity analysis showed that the nucleotide identities of the seven complete genome sequences ranged from 99.2 to 100%. Phylogenetic analysis of seven CGMMV isolates as well as 24 other CGMMV isolates from the GenBank database showed that all CGMMV isolates could be grouped into two distinct monophyletic clades according to geographic distribution, i.e. Asian isolates for subtype I and European isolates for subtype II, indicating that population diversification of CGMMV isolates may be affected by geographical distribution. Site variation rate analysis of CGMMV found that the overall variation rate was below 8% and mainly ranged from 2 to 5%, indicating that the CGMMV genomic sequence was conservative. Base substitution type analysis of CGMMV showed a mutational bias, with more transitions (A↔G and C↔T) than transversions (A↔C, A↔T, G↔C and G↔T). Most of the variation occurring in the CGMMV genome resulted in non-synonymous substitutions, and the variation rate of some sites was higher than 30% because of this mutational bias. Selection constraint analysis of CGMMV ORFs showed strong negative selection acting on the replication-associated protein, similar to what occurs for other plant RNA viruses. Finally, potential recombination analysis identified isolate Ec as a recombinant with a low degree of confidence.

Tuning and Freezing Disorder in Photonic Crystals using Percolation Lithography

PubMed Central

Burgess, Ian B.; Abedzadeh, Navid; Kay, Theresa M.; Shneidman, Anna V.; Cranshaw, Derek J.; Lončar, Marko; Aizenberg, Joanna

2016-01-01

Although common in biological systems, synthetic self-assembly routes to complex 3D photonic structures with tailored degrees of disorder remain elusive. Here we show how liquids can be used to finely control disorder in porous 3D photonic crystals, leading to complex and hierarchical geometries. In these optofluidic crystals, dynamically tunable disorder is superimposed onto the periodic optical structure through partial wetting or evaporation. In both cases, macroscopic symmetry breaking is driven by subtle sub-wavelength variations in the pore geometry. These variations direct site-selective infiltration of liquids through capillary interactions. Incorporating cross-linkable resins into our liquids, we developed methods to freeze in place the filling patterns at arbitrary degrees of partial wetting and intermediate stages of drying. These percolation lithography techniques produced permanent photonic structures with adjustable disorder. By coupling strong changes in optical properties to subtle differences in fluid behavior, optofluidic crystals may also prove useful in rapid analysis of liquids. PMID:26790372

Chemical Speciation and Bond Lengths of Organic Solutes by Core-Level Spectroscopy: pH and Solvent Influence on p-Aminobenzoic Acid.

PubMed

Stevens, Joanna S; Gainar, Adrian; Suljoti, Edlira; Xiao, Jie; Golnak, Ronny; Aziz, Emad F; Schroeder, Sven L M

2015-05-04

Through X-ray absorption and emission spectroscopies, the chemical, electronic and structural properties of organic species in solution can be observed. Near-edge X-ray absorption fine structure (NEXAFS) and resonant inelastic X-ray scattering (RIXS) measurements at the nitrogen K-edge of para-aminobenzoic acid reveal both pH- and solvent-dependent variations in the ionisation potential (IP), 1s→π* resonances and HOMO-LUMO gap. These changes unequivocally identify the chemical species (neutral, cationic or anionic) present in solution. It is shown how this incisive chemical state sensitivity is further enhanced by the possibility of quantitative bond length determination, based on the analysis of chemical shifts in IPs and σ* shape resonances in the NEXAFS spectra. This provides experimental access to detecting even minor variations in the molecular structure of solutes in solution, thereby providing an avenue to examining computational predictions of solute properties and solute-solvent interactions. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An overview of reliability assessment and control for design of civil engineering structures

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

Field, R.V. Jr.; Grigoriadis, K.M.; Bergman, L.A.

1998-06-01

Random variations, whether they occur in the input signal or the system parameters, are phenomena that occur in nearly all engineering systems of interest. As a result, nondeterministic modeling techniques must somehow account for these variations to ensure validity of the solution. As might be expected, this is a difficult proposition and the focus of many current research efforts. Controlling seismically excited structures is one pertinent application of nondeterministic analysis and is the subject of the work presented herein. This overview paper is organized into two sections. First, techniques to assess system reliability, in a context familiar to civil engineers,more » are discussed. Second, and as a consequence of the first, active control methods that ensure good performance in this random environment are presented. It is the hope of the authors that these discussions will ignite further interest in the area of reliability assessment and design of controlled civil engineering structures.« less

Chemical Speciation and Bond Lengths of Organic Solutes by Core-Level Spectroscopy: pH and Solvent Influence on p -Aminobenzoic Acid

DOE PAGES

Stevens, Joanna S.; Gainar, Adrian; Suljoti, Edlira; ...

2015-03-18

Through X-ray absorption and emission spectroscopies, the chemical, electronic and structural properties of organic species in solution can be observed. Near-edge X-ray absorption fine structure (NEXAFS) and resonant inelastic X-ray scattering (RIXS) measurements at the nitrogen K-edge of para-aminobenzoic acid reveal both pH- and solvent-dependent variations in the ionisation potential (IP), 1s→π* resonances and HOMO–LUMO gap. These changes unequivocally identify the chemical species (neutral, cationic or anionic) present in solution. It is shown how this incisive chemical state sensitivity is further enhanced by the possibility of quantitative bond length determination, based on the analysis of chemical shifts in IPs andmore » σ* shape resonances in the NEXAFS spectra. Finally, this provides experimental access to detecting even minor variations in the molecular structure of solutes in solution, thereby providing an avenue to examining computational predictions of solute properties and solute–solvent interactions.« less

Refining and defining riverscape genetics: How rivers influence population genetic structure

Treesearch

Chanté D. Davis; Clinton W. Epps; Rebecca L. Flitcroft; Michael A. Banks

2018-01-01

Traditional analysis in population genetics evaluates differences among groups of individuals and, in some cases, considers the effects of distance or potential barriers to gene flow. Genetic variation of organisms in complex landscapes, seascapes, or riverine systems, however, may be shaped by many forces. Recent research has linked habitat heterogeneity and landscape...

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...

What Has Natural Variation Taught Us about Plant Development, Physiology, and Adaptation?

PubMed Central

Alonso-Blanco, Carlos; Aarts, Mark G.M.; Bentsink, Leonie; Keurentjes, Joost J.B.; Reymond, Matthieu; Vreugdenhil, Dick; Koornneef, Maarten

2009-01-01

Nearly 100 genes and functional polymorphisms underlying natural variation in plant development and physiology have been identified. In crop plants, these include genes involved in domestication traits, such as those related to plant architecture, fruit and seed structure and morphology, as well as yield and quality traits improved by subsequent crop breeding. In wild plants, comparable traits have been dissected mainly in Arabidopsis thaliana. In this review, we discuss the major contributions of the analysis of natural variation to our understanding of plant development and physiology, focusing in particular on the timing of germination and flowering, plant growth and morphology, primary metabolism, and mineral accumulation. Overall, functional polymorphisms appear in all types of genes and gene regions, and they may have multiple mutational causes. However, understanding this diversity in relation to adaptation and environmental variation is a challenge for which tools are now available. PMID:19574434

Historical changes in the structure and functioning of the benthic community in the lagoon of Venice

NASA Astrophysics Data System (ADS)

Pranovi, Fabio; Da Ponte, Filippo; Torricelli, Patrizia

2008-03-01

One of the main challenges in environmental management is how to manage the dynamics of natural environments. In this context, having information about historical changes of the structure of the biological communities could represent a useful tool to improve management strategies, contributing to refine the policy objectives, since it gives reference states with which to compare the present. The Venice lagoon represents an interesting case study, since it is a highly dynamic, but sensitive, environment which requires the adoption of prudent management. In its recent history the lagoon ecosystem has been exposed to different kinds of disturbance, from the discharge of pollutants and nutrients, to the invasion of alien species and the exploitation of its biological resources by using highly impacting fishing gears. The analysis of available data about the macro-benthic community, from 1935 to 2004, allows the description of changes of the community structure over almost 70 years, showing a sharp decrease in its diversity. In order to obtain information about its functioning, it is necessary to know how these changes have affected processes at the community and system level. In shallow water ecosystems, as the control is mainly due to the benthic compartment, variations in the structure of the benthic community can induce modifications in processes at different hierarchical levels. The trophic structure analysis has revealed major changes during the period; from a well-assorted structure in 1935, to an herbivore-detritivore dominated one in the 1990s, and finally to a filter feeder dominated structure during the last decade. This has produced variations in the secondary production and it has induced modifications in the type of the ecosystem control. These changes are discussed in the light of the dynamics of the main driving forces.

Modeling Chinese ionospheric layer parameters based on EOF analysis

NASA Astrophysics Data System (ADS)

Yu, You; Wan, Weixing; Xiong, Bo; Ren, Zhipeng; Zhao, Biqiang; Zhang, Yun; Ning, Baiqi; Liu, Libo

2015-05-01

Using 24-ionosonde observations in and around China during the 20th solar cycle, an assimilative model is constructed to map the ionospheric layer parameters (foF2, hmF2, M(3000)F2, and foE) over China based on empirical orthogonal function (EOF) analysis. First, we decompose the background maps from the International Reference Ionosphere model 2007 (IRI-07) into different EOF modes. The obtained EOF modes consist of two factors: the EOF patterns and the corresponding EOF amplitudes. These two factors individually reflect the spatial distributions (e.g., the latitudinal dependence such as the equatorial ionization anomaly structure and the longitude structure with east-west difference) and temporal variations on different time scales (e.g., solar cycle, annual, semiannual, and diurnal variations) of the layer parameters. Then, the EOF patterns and long-term observations of ionosondes are assimilated to get the observed EOF amplitudes, which are further used to construct the Chinese Ionospheric Maps (CIMs) of the layer parameters. In contrast with the IRI-07 model, the mapped CIMs successfully capture the inherent temporal and spatial variations of the ionospheric layer parameters. Finally, comparison of the modeled (EOF and IRI-07 model) and observed values reveals that the EOF model reproduces the observation with smaller root-mean-square errors and higher linear correlation coefficients. In addition, IRI discrepancy at the low latitude especially for foF2 is effectively removed by EOF model.

Modeling Chinese ionospheric layer parameters based on EOF analysis

NASA Astrophysics Data System (ADS)

Yu, You; Wan, Weixing

2016-04-01

Using 24-ionosonde observations in and around China during the 20th solar cycle, an assimilative model is constructed to map the ionospheric layer parameters (foF2, hmF2, M(3000)F2, and foE) over China based on empirical orthogonal function (EOF) analysis. First, we decompose the background maps from the International Reference Ionosphere model 2007 (IRI-07) into different EOF modes. The obtained EOF modes consist of two factors: the EOF patterns and the corresponding EOF amplitudes. These two factors individually reflect the spatial distributions (e.g., the latitudinal dependence such as the equatorial ionization anomaly structure and the longitude structure with east-west difference) and temporal variations on different time scales (e.g., solar cycle, annual, semiannual, and diurnal variations) of the layer parameters. Then, the EOF patterns and long-term observations of ionosondes are assimilated to get the observed EOF amplitudes, which are further used to construct the Chinese Ionospheric Maps (CIMs) of the layer parameters. In contrast with the IRI-07 model, the mapped CIMs successfully capture the inherent temporal and spatial variations of the ionospheric layer parameters. Finally, comparison of the modeled (EOF and IRI-07 model) and observed values reveals that the EOF model reproduces the observation with smaller root-mean-square errors and higher linear correlation co- efficients. In addition, IRI discrepancy at the low latitude especially for foF2 is effectively removed by EOF model.

Relationships between soil and leaf mineral composition are element-specific, environment-dependent and geographically structured in the emerging model Arabidopsis halleri.

PubMed

Stein, Ricardo J; Höreth, Stephan; de Melo, J Romário F; Syllwasschy, Lara; Lee, Gwonjin; Garbin, Mário L; Clemens, Stephan; Krämer, Ute

2017-02-01

Leaf mineral composition, the leaf ionome, reflects the complex interaction between a plant and its environment including local soil composition, an influential factor that can limit species distribution and plant productivity. Here we addressed within-species variation in plant-soil interactions and edaphic adaptation using Arabidopsis halleri, a well-suited model species as a facultative metallophyte and metal hyperaccumulator. We conducted multi-element analysis of 1972 paired leaf and soil samples from 165 European populations of A. halleri, at individual resolution to accommodate soil heterogeneity. Results were further confirmed under standardized conditions upon cultivation of 105 field-collected genotypes on an artificially metal-contaminated soil in growth chamber experiments. Soil-independent between- and within-population variation set apart leaf accumulation of zinc, cadmium and lead from all other nutrient and nonessential elements, concurring with differential hypothesized ecological roles in either biotic interaction or nutrition. For these metals, soil-leaf relationships were element-specific, differed between metalliferous and nonmetalliferous soils and were geographically structured both in the field and under standardized growth conditions, implicating complex scenarios of recent ecological adaptation. Our study provides an example and a reference for future related work and will serve as a basis for the molecular-genetic dissection and ecological analysis of the observed phenotypic variation. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Crack propagation analysis and fatigue life prediction for structural alloy steel based on metal magnetic memory testing

NASA Astrophysics Data System (ADS)

Ni, Chen; Hua, Lin; Wang, Xiaokai

2018-09-01

To monitor the crack propagation and predict the fatigue life of ferromagnetic material, the metal magnetic memory (MMM) testing was carried out to the single edge notched specimen made from structural alloy steel under three-point bending fatigue experiment in this paper. The variation of magnetic memory signal Hp (y) in process of fatigue crack propagation was investigated. The gradient K of Hp (y) was investigated and compared with the stress of specimen obtained by finite element analysis. It indicated that the gradient K can qualitatively reflect the distribution and variation of stress. The maximum gradient Kmax and crack size showed a good linear relationship, which indicated that the crack propagation can be estimated by MMM testing. Furthermore, the damage model represented by magnetic memory characteristic was created and a fatigue life prediction method was developed. The fatigue life can be evaluated by the relationship between damage parameter and normalized life. The method was also verified by another specimen. Because of MMM testing, it provided a new approach for predicting fatigue life.

COSMOS: accurate detection of somatic structural variations through asymmetric comparison between tumor and normal samples.

PubMed

Yamagata, Koichi; Yamanishi, Ayako; Kokubu, Chikara; Takeda, Junji; Sese, Jun

2016-05-05

An important challenge in cancer genomics is precise detection of structural variations (SVs) by high-throughput short-read sequencing, which is hampered by the high false discovery rates of existing analysis tools. Here, we propose an accurate SV detection method named COSMOS, which compares the statistics of the mapped read pairs in tumor samples with isogenic normal control samples in a distinct asymmetric manner. COSMOS also prioritizes the candidate SVs using strand-specific read-depth information. Performance tests on modeled tumor genomes revealed that COSMOS outperformed existing methods in terms of F-measure. We also applied COSMOS to an experimental mouse cell-based model, in which SVs were induced by genome engineering and gamma-ray irradiation, followed by polymerase chain reaction-based confirmation. The precision of COSMOS was 84.5%, while the next best existing method was 70.4%. Moreover, the sensitivity of COSMOS was the highest, indicating that COSMOS has great potential for cancer genome analysis. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Litter quality versus soil microbial community controls over decomposition: a quantitative analysis

USGS Publications Warehouse

Cleveland, Cory C.; Reed, Sasha C.; Keller, Adrienne B.; Nemergut, Diana R.; O'Neill, Sean P.; Ostertag, Rebecca; Vitousek, Peter M.

2014-01-01

The possible effects of soil microbial community structure on organic matter decomposition rates have been widely acknowledged, but are poorly understood. Understanding these relationships is complicated by the fact that microbial community structure and function are likely to both affect and be affected by organic matter quality and chemistry, thus it is difficult to draw mechanistic conclusions from field studies. We conducted a reciprocal soil inoculum × litter transplant laboratory incubation experiment using samples collected from a set of sites that have similar climate and plant species composition but vary significantly in bacterial community structure and litter quality. The results showed that litter quality explained the majority of variation in decomposition rates under controlled laboratory conditions: over the course of the 162-day incubation, litter quality explained nearly two-thirds (64 %) of variation in decomposition rates, and a smaller proportion (25 %) was explained by variation in the inoculum type. In addition, the relative importance of inoculum type on soil respiration increased over the course of the experiment, and was significantly higher in microcosms with lower litter quality relative to those with higher quality litter. We also used molecular phylogenetics to examine the relationships between bacterial community composition and soil respiration in samples through time. Pyrosequencing revealed that bacterial community composition explained 32 % of the variation in respiration rates. However, equal portions (i.e., 16 %) of the variation in bacterial community composition were explained by inoculum type and litter quality, reflecting the importance of both the meta-community and the environment in bacterial assembly. Taken together, these results indicate that the effects of changing microbial community composition on decomposition are likely to be smaller than the potential effects of climate change and/or litter quality changes in response to increasing atmospheric CO2 concentrations or atmospheric nutrient deposition.

Neocortical malformation as consequence of nonadaptive regulation of neuronogenetic sequence

NASA Technical Reports Server (NTRS)

Caviness, V. S. Jr; Takahashi, T.; Nowakowski, R. S.

2000-01-01

Variations in the structure of the neocortex induced by single gene mutations may be extreme or subtle. They differ from variations in neocortical structure encountered across and within species in that these "normal" structural variations are adaptive (both structurally and behaviorally), whereas those associated with disorders of development are not. Here we propose that they also differ in principle in that they represent disruptions of molecular mechanisms that are not normally regulatory to variations in the histogenetic sequence. We propose an algorithm for the operation of the neuronogenetic sequence in relation to the overall neocortical histogenetic sequence and highlight the restriction point of the G1 phase of the cell cycle as the master regulatory control point for normal coordinate structural variation across species and importantly within species. From considerations based on the anatomic evidence from neocortical malformation in humans, we illustrate in principle how this overall sequence appears to be disrupted by molecular biological linkages operating principally outside the control mechanisms responsible for the normal structural variation of the neocortex. MRDD Research Reviews 6:22-33, 2000. Copyright 2000 Wiley-Liss, Inc.

Temporal variation in bat-fruit interactions: Foraging strategies influence network structure over time

NASA Astrophysics Data System (ADS)

Zapata-Mesa, Natalya; Montoya-Bustamante, Sebastián; Murillo-García, Oscar E.

2017-11-01

Mutualistic interactions, such as seed dispersal, are important for the maintenance of structure and stability of tropical communities. However, there is a lack of information about spatial and temporal variation in plant-animal interaction networks. Thus, our goal was to assess the effect of bat's foraging strategies on temporal variation in the structure and robustness of bat-fruit networks in both a dry and a rain tropical forest. We evaluated monthly variation in bat-fruit networks by using seven structure metrics: network size, average path length, nestedness, modularity, complementary specialization, normalized degree and betweenness centrality. Seed dispersal networks showed variations in size, species composition and modularity; did not present nested structures and their complementary specialization was high compared to other studies. Both networks presented short path lengths, and a constantly high robustness, despite their monthly variations. Sedentary bat species were recorded during all the study periods and occupied more central positions than nomadic species. We conclude that foraging strategies are important structuring factors that affect the dynamic of networks by determining the functional roles of frugivorous bats over time; thus sedentary bats are more important than nomadic species for the maintenance of the network structure, and their conservation is a must.

Chromospheric Variability: Analysis of 36 years of Time Series from the National Solar Observatory/Sacramento Peak Ca II K-line Monitoring Program

NASA Technical Reports Server (NTRS)

Scargle, Jeffrey D.; Keil, Stephen L.; Worden, Simon P.

2014-01-01

Analysis of more than 36 years of time series of seven parameters measured in the NSO/AFRL/Sac Peak K-line monitoring program elucidates five elucidates five components of the variation: (1) the solar cycle (period approx. 11 years), (2) quasi-periodic variations (periods approx 100 days), (3) a broad band stochastic process (wide range of periods), (4) rotational modulation, and (5) random observational errors. Correlation and power spectrum analyses elucidate periodic and aperiodic variation of the chromospheric parameters. Time-frequency analysis illuminates periodic and quasi periodic signals, details of frequency modulation due to differential rotation, and in particular elucidates the rather complex harmonic structure (1) and (2) at time scales in the range approx 0.1 - 10 years. These results using only full-disk data 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 (3) consists of variations over a range of timescales, in the manner of a 1/f random noise process. A timedependent Wilson-Bappu effect appears to be present in the solar cycle variations (1), but not in the stochastic process (3). Component (4) characterizes differential rotation of the active regions, and (5) is of course not characteristic of solar variability, but the fact that the observational errors are quite small greatly facilitates the analysis of the other components. The recent data suggest that the current cycle is starting late and may be relatively weak. The data analyzed in this paper can be found at the National Solar Observatory web site http://nsosp.nso.edu/cak_mon/, or by file transfer protocol at ftp://ftp.nso.edu/idl/cak.parameters.

Spatial variation of natural radiation and childhood leukaemia incidence in Great Britain.

PubMed

Richardson, S; Monfort, C; Green, M; Draper, G; Muirhead, C

This paper describes an analysis of the geographical variation of childhood leukaemia incidence in Great Britain over a 15 year period in relation to natural radiation (gamma and radon). Data at the level of the 459 district level local authorities in England, Wales and regional districts in Scotland are analysed in two complementary ways: first, by Poisson regressions with the inclusion of environmental covariates and a smooth spatial structure; secondly, by a hierarchical Bayesian model in which extra-Poisson variability is modelled explicitly in terms of spatial and non-spatial components. From this analysis, we deduce a strong indication that a main part of the variability is accounted for by a local neighbourhood 'clustering' structure. This structure is furthermore relatively stable over the 15 year period for the lymphocytic leukaemias which make up the majority of observed cases. We found no evidence of a positive association of childhood leukaemia incidence with outdoor or indoor gamma radiation levels. There is no consistent evidence of any association with radon levels. Indeed, in the Poisson regressions, a significant positive association was only observed for one 5-year period, a result which is not compatible with a stable environmental effect. Moreover, this positive association became clearly non-significant when over-dispersion relative to the Poisson distribution was taken into account.

Conformation and Stability of Intramolecular Telomeric G-Quadruplexes: Sequence Effects in the Loops

PubMed Central

Sattin, Giovanna; Artese, Anna; Nadai, Matteo; Costa, Giosuè; Parrotta, Lucia; Alcaro, Stefano; Palumbo, Manlio; Richter, Sara N.

2013-01-01

Telomeres are guanine-rich sequences that protect the ends of chromosomes. These regions can fold into G-quadruplex structures and their stabilization by G-quadruplex ligands has been employed as an anticancer strategy. Genetic analysis in human telomeres revealed extensive allelic variation restricted to loop bases, indicating that the variant telomeric sequences maintain the ability to fold into G-quadruplex. To assess the effect of mutations in loop bases on G-quadruplex folding and stability, we performed a comprehensive analysis of mutant telomeric sequences by spectroscopic techniques, molecular dynamics simulations and gel electrophoresis. We found that when the first position in the loop was mutated from T to C or A the resulting structure adopted a less stable antiparallel topology; when the second position was mutated to C or A, lower thermal stability and no evident conformational change were observed; in contrast, substitution of the third position from A to C induced a more stable and original hybrid conformation, while mutation to T did not significantly affect G-quadruplex topology and stability. Our results indicate that allelic variations generate G-quadruplex telomeric structures with variable conformation and stability. This aspect needs to be taken into account when designing new potential anticancer molecules. PMID:24367632

Fungicidal activities of soil humic/fulvic acids as related to their chemical structures in greenhouse vegetable fields with cultivation chronosequence

NASA Astrophysics Data System (ADS)

Wu, Meng; Song, Mengya; Liu, Ming; Jiang, Chunyu; Li, Zhongpei

2016-09-01

In the background of rapid expansion of plastic greenhouse vegetable production in China, many environmental risks have emerged in recent years. In this study, the soils with a chronosequence in greenhouse vegetable fields were collected and the soil humic acids (HAs) and fluvic acids (FAs) were extracted and purified. The soil HAs and FAs were found to show inhibition activities against phytopathogenic fungi for the first time. Fourier transform infrared spectroscopy was performed to investigate the chemical structures of HAs and FAs. The variation of relative peak areas indicated the chemical structure of HAs become more complex and stable under continuous cultivation. The PCA analysis showed HAs and FAs could be distinctly separated from each other and cultivation years mainly determined the variation. Mantel test and RDA analysis indicated the active components (aliphatic peaks for HAs and COOH, OH peaks for FAs) had positive correlation with the inhibition rates of HAs and FAs against phytopathogenic fungi. According to our research, the active fungicidal components in soil HAs and FAs decreased along with the extension of cultivation years, which made the soil suffer more risk to phytopathogenic fugi. So we believe continuous cultivation too many years in PGVP systems is inadvisable.

Fungicidal activities of soil humic/fulvic acids as related to their chemical structures in greenhouse vegetable fields with cultivation chronosequence

PubMed Central

Wu, Meng; Song, Mengya; Liu, Ming; Jiang, Chunyu; Li, Zhongpei

2016-01-01

In the background of rapid expansion of plastic greenhouse vegetable production in China, many environmental risks have emerged in recent years. In this study, the soils with a chronosequence in greenhouse vegetable fields were collected and the soil humic acids (HAs) and fluvic acids (FAs) were extracted and purified. The soil HAs and FAs were found to show inhibition activities against phytopathogenic fungi for the first time. Fourier transform infrared spectroscopy was performed to investigate the chemical structures of HAs and FAs. The variation of relative peak areas indicated the chemical structure of HAs become more complex and stable under continuous cultivation. The PCA analysis showed HAs and FAs could be distinctly separated from each other and cultivation years mainly determined the variation. Mantel test and RDA analysis indicated the active components (aliphatic peaks for HAs and COOH, OH peaks for FAs) had positive correlation with the inhibition rates of HAs and FAs against phytopathogenic fungi. According to our research, the active fungicidal components in soil HAs and FAs decreased along with the extension of cultivation years, which made the soil suffer more risk to phytopathogenic fugi. So we believe continuous cultivation too many years in PGVP systems is inadvisable. PMID:27597259

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.

Risk of Resource Failure and Toolkit Variation in Small-Scale Farmers and Herders

PubMed Central

Collard, Mark; Ruttle, April; Buchanan, Briggs; O’Brien, Michael J.

2012-01-01

Recent work suggests that global variation in toolkit structure among hunter-gatherers is driven by risk of resource failure such that as risk of resource failure increases, toolkits become more diverse and complex. Here we report a study in which we investigated whether the toolkits of small-scale farmers and herders are influenced by risk of resource failure in the same way. In the study, we applied simple linear and multiple regression analysis to data from 45 small-scale food-producing groups to test the risk hypothesis. Our results were not consistent with the hypothesis; none of the risk variables we examined had a significant impact on toolkit diversity or on toolkit complexity. It appears, therefore, that the drivers of toolkit structure differ between hunter-gatherers and small-scale food-producers. PMID:22844421

CFD simulations of a wind turbine for analysis of tip vortex breakdown

NASA Astrophysics Data System (ADS)

Kimura, K.; Tanabe, Y.; Aoyama, T.; Matsuo, Y.; Arakawa, C.; Iida, M.

2016-09-01

This paper discusses about the wake structure of wind turbine via the use of URANS and Quasi-DNS, focussing on the tip vortex breakdown. The moving overlapped structured grids CFD Solver based on a fourth-order reconstruction and an all-speed scheme, rFlow3D is used for capturing the characteristics of tip vortices. The results from the Model Experiments in Controlled Conditions project (MEXICO) was accordingly selected for executing wake simulations through the variation of tip speed ratio (TSR); in an operational wind turbine, TSR often changes in value. Therefore, it is important to assess the potential effects of TSR on wake characteristics. The results obtained by changing TSR show the variations of the position of wake breakdown and wake expansion. The correspondence between vortices and radial/rotational flow is also confirmed.

Genetic Variation and Geographic Differentiation Among Populations of the Nonmigratory Agricultural Pest Oedaleus infernalis (Orthoptera: Acridoidea) in China

PubMed Central

Sun, Wei; Dong, Hui; Gao, Yue-Bo; Su, Qian-Fu; Qian, Hai-Tao; Bai, Hong-Yan; Zhang, Zhu-Ting; Cong, Bin

2015-01-01

The nonmigratory grasshopper Oedaleus infernalis Saussure (Orthoptera : Acridoidea) is an agricultural pest to crops and forage grasses over a wide natural geographical distribution in China. The genetic diversity and genetic variation among 10 geographically separated populations of O. infernalis was assessed using polymerase chain reaction-based molecular markers, including the intersimple sequence repeat and mitochondrial cytochrome oxidase sequences. A high level of genetic diversity was detected among these populations from the intersimple sequence repeat (H: 0.2628, I: 0.4129, Hs: 0.2130) and cytochrome oxidase analyses (Hd: 0.653). There was no obvious geographical structure based on an unweighted pair group method analysis and median-joining network. The values of FST, θII, and Gst estimated in this study are low, and the gene flow is high (Nm > 4). Analysis of the molecular variance suggested that most of the genetic variation occurs within populations, whereas only a small variation takes place between populations. No significant correlation was found between the genetic distance and geographical distance. Overall, our results suggest that the geographical distance plays an unimpeded role in the gene flow among O. infernalis populations. PMID:26496789

The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data

PubMed Central

Clarke, Laura; Fairley, Susan; Zheng-Bradley, Xiangqun; Streeter, Ian; Perry, Emily; Lowy, Ernesto; Tassé, Anne-Marie; Flicek, Paul

2017-01-01

The International Genome Sample Resource (IGSR; http://www.internationalgenome.org) expands in data type and population diversity the resources from the 1000 Genomes Project. IGSR represents the largest open collection of human variation data and provides easy access to these resources. IGSR was established in 2015 to maintain and extend the 1000 Genomes Project data, which has been widely used as a reference set of human variation and by researchers developing analysis methods. IGSR has mapped all of the 1000 Genomes sequence to the newest human reference (GRCh38), and will release updated variant calls to ensure maximal usefulness of the existing data. IGSR is collecting new structural variation data on the 1000 Genomes samples from long read sequencing and other technologies, and will collect relevant functional data into a single comprehensive resource. IGSR is extending coverage with new populations sequenced by collaborating groups. Here, we present the new data and analysis that IGSR has made available. We have also introduced a new data portal that increases discoverability of our data—previously only browseable through our FTP site—by focusing on particular samples, populations or data sets of interest. PMID:27638885

Free vibration Analysis of Sandwich Plates with cutout

NASA Astrophysics Data System (ADS)

Mishra, N.; Basa, B.; Sarangi, S. K.

2016-09-01

This paper presents the free vibration analysis of sandwich plates with cutouts. Cutouts are inevitable in structural applications and the presence of these cutouts in the structures greatly influences their dynamic characteristics. A finite element model has been developed here using the ANSYS 15.0 software to study the free vibration characteristics of sandwich plates in the presence of cutouts. Shell 281 element, an 8-noded element with six degrees of freedom suited for analyzing thin to moderately thick structures is considered in the development of the model. Block Lanczose method is adopted to extract the mode shapes to obtain the natural frequency corresponding to free vibration of the plate. The effects of parametric variation on the natural frequency of the sandwich plates with cutout are studied and results are presented.

Derivatives of buckling loads and vibration frequencies with respect to stiffness and initial strain parameters

NASA Technical Reports Server (NTRS)

Haftka, Raphael T.; Cohen, Gerald A.; Mroz, Zenon

1990-01-01

A uniform variational approach to sensitivity analysis of vibration frequencies and bifurcation loads of nonlinear structures is developed. Two methods of calculating the sensitivities of bifurcation buckling loads and vibration frequencies of nonlinear structures, with respect to stiffness and initial strain parameters, are presented. A direct method requires calculation of derivatives of the prebuckling state with respect to these parameters. An adjoint method bypasses the need for these derivatives by using instead the strain field associated with the second-order postbuckling state. An operator notation is used and the derivation is based on the principle of virtual work. The derivative computations are easily implemented in structural analysis programs. This is demonstrated by examples using a general purpose, finite element program and a shell-of-revolution program.

Seismic imaging of Q structures by a trans-dimensional coda-wave analysis

NASA Astrophysics Data System (ADS)

Takahashi, Tsutomu

2017-04-01

Wave scattering and intrinsic attenuation are important processes to describe incoherent and complex wave trains of high frequency seismic wave (>1Hz). The multiple lapse time window analysis (MLTWA) has been used to estimate scattering and intrinsic Q values by assuming constant Q in a study area (e.g., Hoshiba 1993). This study generalizes this MLTWA to estimate lateral variations of Q values under the Bayesian framework in dimension variable space. Study area is partitioned into small areas by means of the Voronoi tessellation. Scattering and intrinsic Q in each small area are constant. We define a misfit function for spatiotemporal variations of wave energy as with the original MLTWA, and maximize the posterior probability with changing not only Q values but the number and spatial layout of the Voronoi cells. This maximization is conducted by means of the reversible jump Markov chain Monte Carlo (rjMCMC) (Green 1995) since the number of unknown parameters (i.e., dimension of posterior probability) is variable. After a convergence to the maximum posterior, we estimate Q structures from the ensemble averages of MCMC samples around the maximum posterior probability. Synthetic tests showed stable reconstructions of input structures with reasonable error distributions. We applied this method for seismic waveform data recorded by ocean bottom seismograms at the outer-rise area off Tohoku, and estimated Q values at 4-8Hz, 8-16Hz and 16-32Hz. Intrinsic Q are nearly constant at all frequency bands, and scattering Q shows two distinct strong scattering regions at petit spot area and high seismicity area. These strong scattering are probably related to magma inclusions and fractured structure, respectively. Difference between these two areas becomes clear at high frequencies. It means that scale dependences of inhomogeneities or smaller scale inhomogeneity is important to discuss medium property and origins of structural variations. While the generalized MLTWA is based on a classical waveform modeling in constant Q medium, this method can be a fundamental basis for Q structure imaging in the crust.

Sensory trait variation in an echolocating bat suggests roles for both selection and plasticity

PubMed Central

2014-01-01

Background Across heterogeneous environments selection and gene flow interact to influence the rate and extent of adaptive trait evolution. This complex relationship is further influenced by the rarely considered role of phenotypic plasticity in the evolution of adaptive population variation. Plasticity can be adaptive if it promotes colonization and survival in novel environments and in doing so may increase the potential for future population differentiation via selection. Gene flow between selectively divergent environments may favour the evolution of phenotypic plasticity or conversely, plasticity itself may promote gene flow, leading to a pattern of trait differentiation in the presence of gene flow. Variation in sensory traits is particularly informative in testing the role of environment in trait and population differentiation. Here we test the hypothesis of ‘adaptive differentiation with minimal gene flow’ in resting echolocation frequencies (RF) of Cape horseshoe bats (Rhinolophus capensis) across a gradient of increasingly cluttered habitats. Results Our analysis reveals a geographically structured pattern of increasing RF from open to highly cluttered habitats in R. capensis; however genetic drift appears to be a minor player in the processes influencing this pattern. Although Bayesian analysis of population structure uncovered a number of spatially defined mitochondrial groups and coalescent methods revealed regional-scale gene flow, phylogenetic analysis of mitochondrial sequences did not correlate with RF differentiation. Instead, habitat discontinuities between biomes, and not genetic and geographic distances, best explained echolocation variation in this species. We argue that both selection for increased detection distance in relatively less cluttered habitats and adaptive phenotypic plasticity may have influenced the evolution of matched echolocation frequencies and habitats across different populations. Conclusions Our study reveals significant sensory trait differentiation in the presence of historical gene flow and suggests roles for both selection and plasticity in the evolution of echolocation variation in R. capensis. These results highlight the importance of population level analyses to i) illuminate the subtle interplay between selection, plasticity and gene flow in the evolution of adaptive traits and ii) demonstrate that evolutionary processes may act simultaneously and that their relative influence may vary across different environments. PMID:24674227

Multiscale 3-D shape representation and segmentation using spherical wavelets.

PubMed

Nain, Delphine; Haker, Steven; Bobick, Aaron; Tannenbaum, Allen

2007-04-01

This paper presents a novel multiscale shape representation and segmentation algorithm based on the spherical wavelet transform. This work is motivated by the need to compactly and accurately encode variations at multiple scales in the shape representation in order to drive the segmentation and shape analysis of deep brain structures, such as the caudate nucleus or the hippocampus. Our proposed shape representation can be optimized to compactly encode shape variations in a population at the needed scale and spatial locations, enabling the construction of more descriptive, nonglobal, nonuniform shape probability priors to be included in the segmentation and shape analysis framework. In particular, this representation addresses the shortcomings of techniques that learn a global shape prior at a single scale of analysis and cannot represent fine, local variations in a population of shapes in the presence of a limited dataset. Specifically, our technique defines a multiscale parametric model of surfaces belonging to the same population using a compact set of spherical wavelets targeted to that population. We further refine the shape representation by separating into groups wavelet coefficients that describe independent global and/or local biological variations in the population, using spectral graph partitioning. We then learn a prior probability distribution induced over each group to explicitly encode these variations at different scales and spatial locations. Based on this representation, we derive a parametric active surface evolution using the multiscale prior coefficients as parameters for our optimization procedure to naturally include the prior for segmentation. Additionally, the optimization method can be applied in a coarse-to-fine manner. We apply our algorithm to two different brain structures, the caudate nucleus and the hippocampus, of interest in the study of schizophrenia. We show: 1) a reconstruction task of a test set to validate the expressiveness of our multiscale prior and 2) a segmentation task. In the reconstruction task, our results show that for a given training set size, our algorithm significantly improves the approximation of shapes in a testing set over the Point Distribution Model, which tends to oversmooth data. In the segmentation task, our validation shows our algorithm is computationally efficient and outperforms the Active Shape Model algorithm, by capturing finer shape details.

Multiscale 3-D Shape Representation and Segmentation Using Spherical Wavelets

PubMed Central

Nain, Delphine; Haker, Steven; Bobick, Aaron

2013-01-01

This paper presents a novel multiscale shape representation and segmentation algorithm based on the spherical wavelet transform. This work is motivated by the need to compactly and accurately encode variations at multiple scales in the shape representation in order to drive the segmentation and shape analysis of deep brain structures, such as the caudate nucleus or the hippocampus. Our proposed shape representation can be optimized to compactly encode shape variations in a population at the needed scale and spatial locations, enabling the construction of more descriptive, nonglobal, nonuniform shape probability priors to be included in the segmentation and shape analysis framework. In particular, this representation addresses the shortcomings of techniques that learn a global shape prior at a single scale of analysis and cannot represent fine, local variations in a population of shapes in the presence of a limited dataset. Specifically, our technique defines a multiscale parametric model of surfaces belonging to the same population using a compact set of spherical wavelets targeted to that population. We further refine the shape representation by separating into groups wavelet coefficients that describe independent global and/or local biological variations in the population, using spectral graph partitioning. We then learn a prior probability distribution induced over each group to explicitly encode these variations at different scales and spatial locations. Based on this representation, we derive a parametric active surface evolution using the multiscale prior coefficients as parameters for our optimization procedure to naturally include the prior for segmentation. Additionally, the optimization method can be applied in a coarse-to-fine manner. We apply our algorithm to two different brain structures, the caudate nucleus and the hippocampus, of interest in the study of schizophrenia. We show: 1) a reconstruction task of a test set to validate the expressiveness of our multiscale prior and 2) a segmentation task. In the reconstruction task, our results show that for a given training set size, our algorithm significantly improves the approximation of shapes in a testing set over the Point Distribution Model, which tends to oversmooth data. In the segmentation task, our validation shows our algorithm is computationally efficient and outperforms the Active Shape Model algorithm, by capturing finer shape details. PMID:17427745

Sensory trait variation in an echolocating bat suggests roles for both selection and plasticity.

PubMed

Odendaal, Lizelle J; Jacobs, David S; Bishop, Jacqueline M

2014-03-27

Across heterogeneous environments selection and gene flow interact to influence the rate and extent of adaptive trait evolution. This complex relationship is further influenced by the rarely considered role of phenotypic plasticity in the evolution of adaptive population variation. Plasticity can be adaptive if it promotes colonization and survival in novel environments and in doing so may increase the potential for future population differentiation via selection. Gene flow between selectively divergent environments may favour the evolution of phenotypic plasticity or conversely, plasticity itself may promote gene flow, leading to a pattern of trait differentiation in the presence of gene flow. Variation in sensory traits is particularly informative in testing the role of environment in trait and population differentiation. Here we test the hypothesis of 'adaptive differentiation with minimal gene flow' in resting echolocation frequencies (RF) of Cape horseshoe bats (Rhinolophus capensis) across a gradient of increasingly cluttered habitats. Our analysis reveals a geographically structured pattern of increasing RF from open to highly cluttered habitats in R. capensis; however genetic drift appears to be a minor player in the processes influencing this pattern. Although Bayesian analysis of population structure uncovered a number of spatially defined mitochondrial groups and coalescent methods revealed regional-scale gene flow, phylogenetic analysis of mitochondrial sequences did not correlate with RF differentiation. Instead, habitat discontinuities between biomes, and not genetic and geographic distances, best explained echolocation variation in this species. We argue that both selection for increased detection distance in relatively less cluttered habitats and adaptive phenotypic plasticity may have influenced the evolution of matched echolocation frequencies and habitats across different populations. Our study reveals significant sensory trait differentiation in the presence of historical gene flow and suggests roles for both selection and plasticity in the evolution of echolocation variation in R. capensis. These results highlight the importance of population level analyses to i) illuminate the subtle interplay between selection, plasticity and gene flow in the evolution of adaptive traits and ii) demonstrate that evolutionary processes may act simultaneously and that their relative influence may vary across different environments.

Phonetically Irregular Word Pronunciation and Cortical Thickness in the Adult Brain

PubMed Central

Blackmon, Karen; Barr, William B.; Kuzniecky, Ruben; DuBois, Jonathan; Carlson, Chad; Quinn, Brian T.; Blumberg, Mark; Halgren, Eric; Hagler, Donald J.; Mikhly, Mark; Devinsky, Orrin; McDonald, Carrie R.; Dale, Anders M.; Thesen, Thomas

2010-01-01

Accurate pronunciation of phonetically irregular words (exception words) requires prior exposure to unique relationships between orthographic and phonemic features. Whether such word knowledge is accompanied by structural variation in areas associated with orthographic-to-phonemic transformations has not been investigated. We used high resolution MRI to determine whether performance on a visual word-reading test composed of phonetically irregular words, the Wechsler Test of Adult Reading (WTAR), is associated with regional variations in cortical structure. A sample of 60 right-handed, neurologically intact individuals were administered the WTAR and underwent 3T volumetric MRI. Using quantitative, surface-based image analysis, cortical thickness was estimated at each vertex on the cortical mantle and correlated with WTAR scores while controlling for age. Higher scores on the WTAR were associated with thicker cortex in bilateral anterior superior temporal gyrus, bilateral angular gyrus/posterior superior temporal gyrus, and left hemisphere intraparietal sulcus. Higher scores were also associated with thinner cortex in left hemisphere posterior fusiform gyrus and central sulcus, bilateral inferior frontal gyrus, and right hemisphere lingual gyrus and supramarginal gyrus. These results suggest that the ability to correctly pronounce phonetically irregular words is associated with structural variations in cortical areas that are commonly activated in functional neuroimaging studies of word reading, including areas associated with grapheme-to–phonemic conversion. PMID:20302944

A worldwide analysis of within-canopy variations in leaf structural, chemical and physiological traits across plant functional types

PubMed Central

Niinemets, Ülo; Keenan, Trevor F.; Hallik, Lea

2018-01-01

Summary Extensive within-canopy light gradients importantly affect photosynthetic productivity of leaves in different canopy positions and lead to light-dependent increases in foliage photosynthetic capacity per area (AA). However, the controls on AA variations by changes in underlying traits are poorly known. We constructed an unprecedented worldwide database including 831 within-canopy gradients with standardized light estimates for 304 species belonging to major vascular plant functional types, and analyzed within-canopy variations in 12 key foliage structural, chemical and physiological traits by quantitatively separating the contributions of different traits to photosynthetic acclimation. Although the light-dependent increase in AA is surprisingly similar in different plant functional types, they fundamentally differ in the share of the controls on AA by constituent traits. Species with high rates of canopy development and leaf turnover exhibiting highly dynamic light environments, actively change AA by nitrogen reallocation among and partitioning within leaves. In contrast, species with slow leaf turnover exhibit a passive AA acclimation response primarily determined by acclimation of leaf structure to growth light. This review emphasizes that different combinations of traits are responsible for within-canopy photosynthetic acclimation in different plant functional types and solves an old enigma of the role of mass- vs. area-based traits in vegetation acclimation. PMID:25318596

Automation method to identify the geological structure of seabed using spatial statistic analysis of echo sounding data

NASA Astrophysics Data System (ADS)

Kwon, O.; Kim, W.; Kim, J.

2017-12-01

Recently construction of subsea tunnel has been increased globally. For safe construction of subsea tunnel, identifying the geological structure including fault at design and construction stage is more than important. Then unlike the tunnel in land, it's very difficult to obtain the data on geological structure because of the limit in geological survey. This study is intended to challenge such difficulties in a way of developing the technology to identify the geological structure of seabed automatically by using echo sounding data. When investigation a potential site for a deep subsea tunnel, there is the technical and economical limit with borehole of geophysical investigation. On the contrary, echo sounding data is easily obtainable while information reliability is higher comparing to above approaches. This study is aimed at developing the algorithm that identifies the large scale of geological structure of seabed using geostatic approach. This study is based on theory of structural geology that topographic features indicate geological structure. Basic concept of algorithm is outlined as follows; (1) convert the seabed topography to the grid data using echo sounding data, (2) apply the moving window in optimal size to the grid data, (3) estimate the spatial statistics of the grid data in the window area, (4) set the percentile standard of spatial statistics, (5) display the values satisfying the standard on the map, (6) visualize the geological structure on the map. The important elements in this study include optimal size of moving window, kinds of optimal spatial statistics and determination of optimal percentile standard. To determine such optimal elements, a numerous simulations were implemented. Eventually, user program based on R was developed using optimal analysis algorithm. The user program was designed to identify the variations of various spatial statistics. It leads to easy analysis of geological structure depending on variation of spatial statistics by arranging to easily designate the type of spatial statistics and percentile standard. This research was supported by the Korea Agency for Infrastructure Technology Advancement under the Ministry of Land, Infrastructure and Transport of the Korean government. (Project Number: 13 Construction Research T01)

Solar Cycle Variability and Surface Differential Rotation from Ca II K-line Time Series Data

NASA Astrophysics Data System (ADS)

Scargle, Jeffrey D.; Keil, Stephen L.; Worden, Simon P.

2013-07-01

Analysis of over 36 yr of time series data from the NSO/AFRL/Sac Peak K-line monitoring program elucidates 5 components of the variation of the 7 measured chromospheric parameters: (a) the solar cycle (period ~ 11 yr), (b) quasi-periodic variations (periods ~ 100 days), (c) a broadband stochastic process (wide range of periods), (d) rotational modulation, and (e) random observational errors, independent of (a)-(d). Correlation and power spectrum analyses elucidate periodic and aperiodic variation of these parameters. Time-frequency analysis illuminates periodic and quasi-periodic signals, details of frequency modulation due to differential rotation, and in particular elucidates the rather complex harmonic structure (a) and (b) at timescales in the range ~0.1-10 yr. These results using only full-disk data suggest that similar analyses will be useful for detecting and characterizing differential rotation in stars from stellar light curves such as those being produced by NASA's Kepler observatory. Component (c) consists of variations over a range of timescales, in the manner of a 1/f random process with a power-law slope index that varies in a systematic way. A time-dependent Wilson-Bappu effect appears to be present in the solar cycle variations (a), but not in the more rapid variations of the stochastic process (c). Component (d) characterizes differential rotation of the active regions. Component (e) is of course not characteristic of solar variability, but the fact that the observational errors are quite small greatly facilitates the analysis of the other components. The data analyzed in this paper can be found at the National Solar Observatory Web site http://nsosp.nso.edu/cak_mon/, or by file transfer protocol at ftp://ftp.nso.edu/idl/cak.parameters.

Cloudy Skies over AGN: Observations with Simbol-X

NASA Astrophysics Data System (ADS)

Salvati, M.; Risaliti, G.

2009-05-01

Recent time-resolved spectroscopic X-ray studies of bright obscured AGN show that column density variability on time scales of hours/days may be common, at least for sources with NH>1023 cm-2. This opens new oppurtunities in the analysis of the structure of the circumnuclear medium and of the X-ray source: resolving the variations due to single clouds covering/uncovering the X-ray source provides tight constraints on the source size, the clouds' size and distance, and their average number, density and column density. We show how Simbol-X will provide a breakthrough in this field, thanks to its broad band coverage, allowing (a) to precisely disentangle the continuum and NH variations, and (2) to extend the NH variability analysis to column densities >1023 cm-2.

[IR study on a series of tungsten clusters].

PubMed

Yu, R; Chen, J; Lu, S

2000-10-01

In this paper, the IR study on a series of tungsten clusters which contain a [W2S4]2+ or [W2MM'S4]4+ (M,M'=Cu,Ag) core is reported. According to the results of X-ray structural analysis and the IR spectra of the clusters, some characteristic IR absorptions of the clusters were assigned. The study of IR spectra of these clusters shows that the variation of structure can reflect on the IR spectra significantly.

Bringing diffuse X-ray scattering into focus

DOE PAGES

Wall, Michael E.; Wolff, Alexander M.; Fraser, James S.

2018-02-16

X-ray crystallography is experiencing a renaissance as a method for probing the protein conformational ensemble. The inherent limitations of Bragg analysis, however, which only reveals the mean structure, have given way to a surge in interest in diffuse scattering, which is caused by structure variations. Diffuse scattering is present in all macromolecular crystallography experiments. Recent studies are shedding light on the origins of diffuse scattering in protein crystallography, and provide clues for leveraging diffuse scattering to model protein motions with atomic detail.

Bringing diffuse X-ray scattering into focus

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

Wall, Michael E.; Wolff, Alexander M.; Fraser, James S.

X-ray crystallography is experiencing a renaissance as a method for probing the protein conformational ensemble. The inherent limitations of Bragg analysis, however, which only reveals the mean structure, have given way to a surge in interest in diffuse scattering, which is caused by structure variations. Diffuse scattering is present in all macromolecular crystallography experiments. Recent studies are shedding light on the origins of diffuse scattering in protein crystallography, and provide clues for leveraging diffuse scattering to model protein motions with atomic detail.

Development, fabrication and evaluation of composite thermal engine insulation

NASA Technical Reports Server (NTRS)

1973-01-01

Foil enclosure configurations of 10 variations were fabricated and evaluated. A discussion of the thermal protection system panel design includes: (1) description of 3DSX/foil concept, (2) design environment, (3) material selection, (4) fabrication enclosure, (5) structural design, (6) thermal sizing, and (7) weight analysis. The structural design study includes foil evaluation, venting pressure loads, thermomechanical behavior, and enclosure venting (burst) pressure tests. Results of experimental demonstrations of performance and reuse capabilities are given for both thermal and acoustic testing.

Probabilistic structural analysis to quantify uncertainties associated with turbopump blades

NASA Technical Reports Server (NTRS)

Nagpal, Vinod K.; Rubinstein, Robert; Chamis, Christos C.

1988-01-01

A probabilistic study of turbopump blades has been in progress at NASA Lewis Research Center for over the last two years. The objectives of this study are to evaluate the effects of uncertainties in geometry and material properties on the structural response of the turbopump blades to evaluate the tolerance limits on the design. A methodology based on probabilistic approach was developed to quantify the effects of the random uncertainties. The results indicate that only the variations in geometry have significant effects.

Whole genomes redefine the mutational landscape of pancreatic cancer

PubMed Central

Waddell, Nicola; Pajic, Marina; Patch, Ann-Marie; Chang, David K.; Kassahn, Karin S.; Bailey, Peter; Johns, Amber L.; Miller, David; Nones, Katia; Quek, Kelly; Quinn, Michael C. J.; Robertson, Alan J.; Fadlullah, Muhammad Z. H.; Bruxner, Tim J. C.; Christ, Angelika N.; Harliwong, Ivon; Idrisoglu, Senel; Manning, Suzanne; Nourse, Craig; Nourbakhsh, Ehsan; Wani, Shivangi; Wilson, Peter J; Markham, Emma; Cloonan, Nicole; Anderson, Matthew J.; Fink, J. Lynn; Holmes, Oliver; Kazakoff, Stephen H.; Leonard, Conrad; Newell, Felicity; Poudel, Barsha; Song, Sarah; Taylor, Darrin; Waddell, Nick; Wood, Scott; Xu, Qinying; Wu, Jianmin; Pinese, Mark; Cowley, Mark J.; Lee, Hong C.; Jones, Marc D.; Nagrial, Adnan M.; Humphris, Jeremy; Chantrill, Lorraine A.; Chin, Venessa; Steinmann, Angela M.; Mawson, Amanda; Humphrey, Emily S.; Colvin, Emily K.; Chou, Angela; Scarlett, Christopher J.; Pinho, Andreia V.; Giry-Laterriere, Marc; Rooman, Ilse; Samra, Jaswinder S.; Kench, James G.; Pettitt, Jessica A.; Merrett, Neil D.; Toon, Christopher; Epari, Krishna; Nguyen, Nam Q.; Barbour, Andrew; Zeps, Nikolajs; Jamieson, Nigel B.; Graham, Janet S.; Niclou, Simone P.; Bjerkvig, Rolf; Grützmann, Robert; Aust, Daniela; Hruban, Ralph H.; Maitra, Anirban; Iacobuzio-Donahue, Christine A.; Wolfgang, Christopher L.; Morgan, Richard A.; Lawlor, Rita T.; Corbo, Vincenzo; Bassi, Claudio; Falconi, Massimo; Zamboni, Giuseppe; Tortora, Giampaolo; Tempero, Margaret A.; Gill, Anthony J.; Eshleman, James R.; Pilarsky, Christian; Scarpa, Aldo; Musgrove, Elizabeth A.; Pearson, John V.; Biankin, Andrew V.; Grimmond, Sean M.

2015-01-01

Pancreatic cancer remains one of the most lethal of malignancies and a major health burden. We performed whole-genome sequencing and copy number variation (CNV) analysis of 100 pancreatic ductal adenocarcinomas (PDACs). Chromosomal rearrangements leading to gene disruption were prevalent, affecting genes known to be important in pancreatic cancer (TP53, SMAD4, CDKN2A, ARID1A and ROBO2) and new candidate drivers of pancreatic carcinogenesis (KDM6A and PREX2). Patterns of structural variation (variation in chromosomal structure) classified PDACs into 4 subtypes with potential clinical utility: the subtypes were termed stable, locally rearranged, scattered and unstable. A significant proportion harboured focal amplifications, many of which contained druggable oncogenes (ERBB2, MET, FGFR1, CDK6, PIK3R3 and PIK3CA), but at low individual patient prevalence. Genomic instability co-segregated with inactivation of DNA maintenance genes (BRCA1, BRCA2 or PALB2) and a mutational signature of DNA damage repair deficiency. Of 8 patients who received platinum therapy, 4 of 5 individuals with these measures of defective DNA maintenance responded. PMID:25719666

Whole genomes redefine the mutational landscape of pancreatic cancer.

PubMed

Waddell, Nicola; Pajic, Marina; Patch, Ann-Marie; Chang, David K; Kassahn, Karin S; Bailey, Peter; Johns, Amber L; Miller, David; Nones, Katia; Quek, Kelly; Quinn, Michael C J; Robertson, Alan J; Fadlullah, Muhammad Z H; Bruxner, Tim J C; Christ, Angelika N; Harliwong, Ivon; Idrisoglu, Senel; Manning, Suzanne; Nourse, Craig; Nourbakhsh, Ehsan; Wani, Shivangi; Wilson, Peter J; Markham, Emma; Cloonan, Nicole; Anderson, Matthew J; Fink, J Lynn; Holmes, Oliver; Kazakoff, Stephen H; Leonard, Conrad; Newell, Felicity; Poudel, Barsha; Song, Sarah; Taylor, Darrin; Waddell, Nick; Wood, Scott; Xu, Qinying; Wu, Jianmin; Pinese, Mark; Cowley, Mark J; Lee, Hong C; Jones, Marc D; Nagrial, Adnan M; Humphris, Jeremy; Chantrill, Lorraine A; Chin, Venessa; Steinmann, Angela M; Mawson, Amanda; Humphrey, Emily S; Colvin, Emily K; Chou, Angela; Scarlett, Christopher J; Pinho, Andreia V; Giry-Laterriere, Marc; Rooman, Ilse; Samra, Jaswinder S; Kench, James G; Pettitt, Jessica A; Merrett, Neil D; Toon, Christopher; Epari, Krishna; Nguyen, Nam Q; Barbour, Andrew; Zeps, Nikolajs; Jamieson, Nigel B; Graham, Janet S; Niclou, Simone P; Bjerkvig, Rolf; Grützmann, Robert; Aust, Daniela; Hruban, Ralph H; Maitra, Anirban; Iacobuzio-Donahue, Christine A; Wolfgang, Christopher L; Morgan, Richard A; Lawlor, Rita T; Corbo, Vincenzo; Bassi, Claudio; Falconi, Massimo; Zamboni, Giuseppe; Tortora, Giampaolo; Tempero, Margaret A; Gill, Anthony J; Eshleman, James R; Pilarsky, Christian; Scarpa, Aldo; Musgrove, Elizabeth A; Pearson, John V; Biankin, Andrew V; Grimmond, Sean M

2015-02-26

Pancreatic cancer remains one of the most lethal of malignancies and a major health burden. We performed whole-genome sequencing and copy number variation (CNV) analysis of 100 pancreatic ductal adenocarcinomas (PDACs). Chromosomal rearrangements leading to gene disruption were prevalent, affecting genes known to be important in pancreatic cancer (TP53, SMAD4, CDKN2A, ARID1A and ROBO2) and new candidate drivers of pancreatic carcinogenesis (KDM6A and PREX2). Patterns of structural variation (variation in chromosomal structure) classified PDACs into 4 subtypes with potential clinical utility: the subtypes were termed stable, locally rearranged, scattered and unstable. A significant proportion harboured focal amplifications, many of which contained druggable oncogenes (ERBB2, MET, FGFR1, CDK6, PIK3R3 and PIK3CA), but at low individual patient prevalence. Genomic instability co-segregated with inactivation of DNA maintenance genes (BRCA1, BRCA2 or PALB2) and a mutational signature of DNA damage repair deficiency. Of 8 patients who received platinum therapy, 4 of 5 individuals with these measures of defective DNA maintenance responded.

Midsagittal brain variation and MRI shape analysis of the precuneus in adult individuals.

PubMed

Bruner, Emiliano; Rangel de Lázaro, Gizéh; de la Cuétara, José Manuel; Martín-Loeches, Manuel; Colom, Roberto; Jacobs, Heidi I L

2014-04-01

Recent analyses indicate that the precuneus is one of the main centres of integration in terms of functional and structural processes within the human brain. This neuroanatomical element is formed by different subregions, involved in visuo-spatial integration, memory and self-awareness. We analysed the midsagittal brain shape in a sample of adult humans (n = 90) to evidence the patterns of variability and geometrical organization of this area. Interestingly, the major brain covariance pattern within adult humans is strictly associated with the relative proportions of the precuneus. Its morphology displays a marked individual variation, both in terms of geometry (mostly in its longitudinal dimensions) and anatomy (patterns of convolution). No patent differences are evident between males and females, and the allometric effect of size is minimal. However, in terms of morphology, the precuneus does not represent an individual module, being influenced by different neighbouring structures. Taking into consideration the apparent involvement of the precuneus in higher-order human brain functions and evolution, its wide variation further stresses the important role of these deep parietal areas in modern neuroanatomical organization. © 2014 Anatomical Society.

Calculation of flight vibration levels of the AH-1G helicopter and correlation with existing flight vibration measurements

NASA Technical Reports Server (NTRS)

Sopher, R.; Twomey, W. J.

1990-01-01

NASA-Langley is sponsoring a rotorcraft structural dynamics program with the objective to establish in the U.S. a superior capability to utilize finite element analysis models for calculations to support industrial design of helicopter airframe structures. In the initial phase of the program, teams from the major U.S. manufacturers of helicopter airframes will apply extant finite element analysis methods to calculate loads and vibrations of helicopter airframes, and perform correlations between analysis and measurements. The aforementioned rotorcraft structural dynamics program was given the acronym DAMVIBS (Design Analysis Method for Vibrations). Sikorsky's RDYNE Rotorcraft Dynamics Analysis used for the correlation study, the specifics of the application of RDYNE to the AH-1G, and comparisons of the predictions of the method with flight data for loads and vibrations on the AH-1G are described. RDYNE was able to predict trends of variations of loads and vibrations with airspeed, but in some instances magnitudes differed from measured results by factors of two or three to one. Sensitivities were studied of predictions to rotor inflow modeling, effects of torsional modes, number of blade bending modes, fuselage structural damping, and hub modal content.

Computational Methods to Work as First-Pass Filter in Deleterious SNP Analysis of Alkaptonuria

PubMed Central

Magesh, R.; George Priya Doss, C.

2012-01-01

A major challenge in the analysis of human genetic variation is to distinguish functional from nonfunctional SNPs. Discovering these functional SNPs is one of the main goals of modern genetics and genomics studies. There is a need to effectively and efficiently identify functionally important nsSNPs which may be deleterious or disease causing and to identify their molecular effects. The prediction of phenotype of nsSNPs by computational analysis may provide a good way to explore the function of nsSNPs and its relationship with susceptibility to disease. In this context, we surveyed and compared variation databases along with in silico prediction programs to assess the effects of deleterious functional variants on protein functions. In other respects, we attempted these methods to work as first-pass filter to identify the deleterious substitutions worth pursuing for further experimental research. In this analysis, we used the existing computational methods to explore the mutation-structure-function relationship in HGD gene causing alkaptonuria. PMID:22606059

"Ladder" structure in tonal noise generated by laminar flow around an airfoil.

PubMed

Chong, Tze Pei; Joseph, Phillip

2012-06-01

The presence of a "ladder" structure in the airfoil tonal noise was discovered in the 1970s, but its mechanism hitherto remains a subject of continual investigation in the research community. Based on the measured noise results and some numerical analysis presented in this letter, the variations of four types of airfoil tonal noise frequencies with the flow velocity were analyzed individually. The ladder structure is proposed to be caused by the acoustic/hydrodynamic frequency lag between the scattering of the boundary layer instability noise and the discrete noise produced by an aeroacoustic feedback loop.

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

Caliandro, Rocco; Sibillano, Teresa; Belviso, B. Danilo

In this study, we have developed a general X-ray powder diffraction (XPD) methodology for the simultaneous structural and compositional characterization of inorganic nanomaterials. The approach is validated on colloidal tungsten oxide nanocrystals (WO 3-x NCs), as a model polymorphic nanoscale material system. Rod-shaped WO 3-x NCs with different crystal structure and stoichiometry are comparatively investigated under an inert atmosphere and after prolonged air exposure. An initial structural model for the as-synthesized NCs is preliminarily identified by means of Rietveld analysis against several reference crystal phases, followed by atomic pair distribution function (PDF) refinement of the best-matching candidates (static analysis). Subtlemore » stoichiometry deviations from the corresponding bulk standards are revealed. NCs exposed to air at room temperature are monitored by XPD measurements at scheduled time intervals. The static PDF analysis is complemented with an investigation into the evolution of the WO 3-x NC structure, performed by applying the modulation enhanced diffraction technique to the whole time series of XPD profiles (dynamical analysis). Prolonged contact with ambient air is found to cause an appreciable increase in the static disorder of the O atoms in the WO 3-x NC lattice, rather than a variation in stoichiometry. Finally, the time behavior of such structural change is identified on the basis of multivariate analysis.« less

Integrated Modeling Activities for the James Webb Space Telescope (JWST): Structural-Thermal-Optical Analysis

NASA Technical Reports Server (NTRS)

Johnston, John D.; Parrish, Keith; Howard, Joseph M.; Mosier, Gary E.; McGinnis, Mark; Bluth, Marcel; Kim, Kevin; Ha, Hong Q.

2004-01-01

This is a continuation of a series of papers on modeling activities for JWST. The structural-thermal- optical, often referred to as "STOP", analysis process is used to predict the effect of thermal distortion on optical performance. The benchmark STOP analysis for JWST assesses the effect of an observatory slew on wavefront error. The paper begins an overview of multi-disciplinary engineering analysis, or integrated modeling, which is a critical element of the JWST mission. The STOP analysis process is then described. This process consists of the following steps: thermal analysis, structural analysis, and optical analysis. Temperatures predicted using geometric and thermal math models are mapped to the structural finite element model in order to predict thermally-induced deformations. Motions and deformations at optical surfaces are input to optical models and optical performance is predicted using either an optical ray trace or WFE estimation techniques based on prior ray traces or first order optics. Following the discussion of the analysis process, results based on models representing the design at the time of the System Requirements Review. In addition to baseline performance predictions, sensitivity studies are performed to assess modeling uncertainties. Of particular interest is the sensitivity of optical performance to uncertainties in temperature predictions and variations in metal properties. The paper concludes with a discussion of modeling uncertainty as it pertains to STOP analysis.

Basin-wide variations in Amazon forest structure and function are mediated by both soils and climate

NASA Astrophysics Data System (ADS)

Quesada, C. A.; Phillips, O. L.; Schwarz, M.; Czimczik, C. I.; Baker, T. R.; Patiño, S.; Fyllas, N. M.; Hodnett, M. G.; Herrera, R.; Almeida, S.; Alvarez Dávila, E.; Arneth, A.; Arroyo, L.; Chao, K. J.; Dezzeo, N.; Erwin, T.; di Fiore, A.; Higuchi, N.; Honorio Coronado, E.; Jimenez, E. M.; Killeen, T.; Lezama, A. T.; Lloyd, G.; López-González, G.; Luizão, F. J.; Malhi, Y.; Monteagudo, A.; Neill, D. A.; Núñez Vargas, P.; Paiva, R.; Peacock, J.; Peñuela, M. C.; Peña Cruz, A.; Pitman, N.; Priante Filho, N.; Prieto, A.; Ramírez, H.; Rudas, A.; Salomão, R.; Santos, A. J. B.; Schmerler, J.; Silva, N.; Silveira, M.; Vásquez, R.; Vieira, I.; Terborgh, J.; Lloyd, J.

2012-06-01

Forest structure and dynamics vary across the Amazon Basin in an east-west gradient coincident with variations in soil fertility and geology. This has resulted in the hypothesis that soil fertility may play an important role in explaining Basin-wide variations in forest biomass, growth and stem turnover rates. Soil samples were collected in a total of 59 different forest plots across the Amazon Basin and analysed for exchangeable cations, carbon, nitrogen and pH, with several phosphorus fractions of likely different plant availability also quantified. Physical properties were additionally examined and an index of soil physical quality developed. Bivariate relationships of soil and climatic properties with above-ground wood productivity, stand-level tree turnover rates, above-ground wood biomass and wood density were first examined with multivariate regression models then applied. Both forms of analysis were undertaken with and without considerations regarding the underlying spatial structure of the dataset. Despite the presence of autocorrelated spatial structures complicating many analyses, forest structure and dynamics were found to be strongly and quantitatively related to edaphic as well as climatic conditions. Basin-wide differences in stand-level turnover rates are mostly influenced by soil physical properties with variations in rates of coarse wood production mostly related to soil phosphorus status. Total soil P was a better predictor of wood production rates than any of the fractionated organic- or inorganic-P pools. This suggests that it is not only the immediately available P forms, but probably the entire soil phosphorus pool that is interacting with forest growth on longer timescales. A role for soil potassium in modulating Amazon forest dynamics through its effects on stand-level wood density was also detected. Taking this into account, otherwise enigmatic variations in stand-level biomass across the Basin were then accounted for through the interacting effects of soil physical and chemical properties with climate. A hypothesis of self-maintaining forest dynamic feedback mechanisms initiated by edaphic conditions is proposed. It is further suggested that this is a major factor determining endogenous disturbance levels, species composition, and forest productivity across the Amazon Basin.

Coupled rotor/airframe vibration analysis

NASA Technical Reports Server (NTRS)

Sopher, R.; Studwell, R. E.; Cassarino, S.; Kottapalli, S. B. R.

1982-01-01

A coupled rotor/airframe vibration analysis developed as a design tool for predicting helicopter vibrations and a research tool to quantify the effects of structural properties, aerodynamic interactions, and vibration reduction devices on vehicle vibration levels is described. The analysis consists of a base program utilizing an impedance matching technique to represent the coupled rotor/airframe dynamics of the system supported by inputs from several external programs supplying sophisticated rotor and airframe aerodynamic and structural dynamic representation. The theoretical background, computer program capabilities and limited correlation results are presented in this report. Correlation results using scale model wind tunnel results show that the analysis can adequately predict trends of vibration variations with airspeed and higher harmonic control effects. Predictions of absolute values of vibration levels were found to be very sensitive to modal characteristics and results were not representative of measured values.

Spatial variations of bacterial community and its relationship with water chemistry in Sanya Bay, South China Sea as determined by DGGE fingerprinting and multivariate analysis.

PubMed

Ling, Juan; Zhang, Yan-Ying; Dong, Jun-De; Wang, You-Shao; Feng, Jing-Bing; Zhou, Wei-Hua

2015-10-01

Bacteria play important roles in the structure and function of marine food webs by utilizing nutrients and degrading the pollutants, and their distribution are determined by surrounding water chemistry to a certain extent. It is vital to investigate the bacterial community's structure and identifying the significant factors by controlling the bacterial distribution in the paper. Flow cytometry showed that the total bacterial abundance ranged from 5.27 × 10(5) to 3.77 × 10(6) cells/mL. Molecular fingerprinting technique, denaturing gradient gel electrophoresis (DGGE) followed by DNA sequencing has been employed to investigate the bacterial community composition. The results were then interpreted through multivariate statistical analysis and tended to explain its relationship to the environmental factors. A total of 270 bands at 83 different positions were detected in DGGE profiles and 29 distinct DGGE bands were sequenced. The predominant bacteria were related to Phyla Protebacteria species (31 %, nine sequences), Cyanobacteria (37.9 %, eleven sequences) and Actinobacteria (17.2 %, five sequences). Other phylogenetic groups identified including Firmicutes (6.9 %, two sequences), Bacteroidetes (3.5 %, one sequences) and Verrucomicrobia (3.5 %, one sequences). Conical correspondence analysis was used to elucidate the relationships between the bacterial community compositions and environmental factors. The results showed that the spatial variations in the bacterial community composition was significantly related to phosphate (P = 0.002, P < 0.01), dissolved organic carbon (P = 0.004, P < 0.01), chemical oxygen demand (P = 0.010, P < 0.05) and nitrite (P = 0.016, P < 0.05). This study revealed the spatial variations of bacterial community and significant environmental factors driving the bacterial composition shift. These results may be valuable for further investigation on the functional microbial structure and expression quantitatively under the polluted environments in the world.

Twoplex 12/13 C6 aniline stable isotope and linkage-specific sialic acid labeling 2D-LC-MS workflow for quantitative N-glycomics.

PubMed

Albrecht, Simone; Mittermayr, Stefan; Smith, Josh; Martín, Silvia Millán; Doherty, Margaret; Bones, Jonathan

2017-01-01

Quantitative glycomics represents an actively expanding research field ranging from the discovery of disease-associated glycan alterations to the quantitative characterization of N-glycans on therapeutic proteins. Commonly used analytical platforms for comparative relative quantitation of complex glycan samples include MALDI-TOF-MS or chromatographic glycan profiling with subsequent data alignment and statistical evaluation. Limitations of such approaches include run-to-run technical variation and the potential introduction of subjectivity during data processing. Here, we introduce an offline 2D LC-MS E workflow for the fractionation and relative quantitation of twoplex isotopically labeled N-linked oligosaccharides using neutral 12 C 6 and 13 C 6 aniline (Δmass = 6 Da). Additional linkage-specific derivatization of sialic acids using 4-(4,6-dimethoxy-1,3,5-trizain-2-yl)-4-methylmorpholinium chloride offered simultaneous and advanced in-depth structural characterization. The potential of the method was demonstrated for the differential analysis of structurally defined N-glycans released from serum proteins of patients diagnosed with various stages of colorectal cancer. The described twoplex 12 C 6 / 13 C 6 aniline 2D LC-MS platform is ideally suited for differential glycomic analysis of structurally complex N-glycan pools due to combination and analysis of samples in a single LC-MS injection and the associated minimization in technical variation. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Application of the Probabilistic Dynamic Synthesis Method to the Analysis of a Realistic Structure

NASA Technical Reports Server (NTRS)

Brown, Andrew M.; Ferri, Aldo A.

1998-01-01

The Probabilistic Dynamic Synthesis method is a new technique for obtaining the statistics of a desired response engineering quantity for a structure with non-deterministic parameters. The method uses measured data from modal testing of the structure as the input random variables, rather than more "primitive" quantities like geometry or material variation. This modal information is much more comprehensive and easily measured than the "primitive" information. The probabilistic analysis is carried out using either response surface reliability methods or Monte Carlo simulation. A previous work verified the feasibility of the PDS method on a simple seven degree-of-freedom spring-mass system. In this paper, extensive issues involved with applying the method to a realistic three-substructure system are examined, and free and forced response analyses are performed. The results from using the method are promising, especially when the lack of alternatives for obtaining quantitative output for probabilistic structures is considered.

Low-frequency nondestructive analysis of cracks in multilayer structures using a scanning magnetic microscope

NASA Astrophysics Data System (ADS)

Adamo, M.; Nappi, C.; Sarnelli, E.

2010-09-01

The use of a scanning magnetic microscope (SMM) with a high temperature superconducting quantum interference device (SQUID) for quantitative measurements in eddy current nondestructive analysis (NDA) is presented. The SQUID has been used to detect the weak magnetic field variations around a small defect, close to a structural part generating an intensive magnetic field. The experimental data for a deep crack close to a rivet in a multilayer conducting plate have been taken in a RF-shielded environment and discussed in the light of the theoretical predictions. The results show that eddy current NDA can distinguish subsurface crack signals from wider structural signals, with defects located 10 mm below the surface. Moreover, in order to visualize the structure of the probing current when a circular induction coil is used, the simulation of eddy currents in a thick unflawed conducting plate has been carried out.

Effect of element size on the solution accuracies of finite-element heat transfer and thermal stress analyses of space shuttle orbiter

NASA Technical Reports Server (NTRS)

Ko, William L.; Olona, Timothy

1987-01-01

The effect of element size on the solution accuracies of finite-element heat transfer and thermal stress analyses of space shuttle orbiter was investigated. Several structural performance and resizing (SPAR) thermal models and NASA structural analysis (NASTRAN) structural models were set up for the orbiter wing midspan bay 3. The thermal model was found to be the one that determines the limit of finite-element fineness because of the limitation of computational core space required for the radiation view factor calculations. The thermal stresses were found to be extremely sensitive to a slight variation of structural temperature distributions. The minimum degree of element fineness required for the thermal model to yield reasonably accurate solutions was established. The radiation view factor computation time was found to be insignificant compared with the total computer time required for the SPAR transient heat transfer analysis.

Impact of Parental Bos taurus and Bos indicus Origins on Copy Number Variation in Traditional Chinese Cattle Breeds.

PubMed

Zhang, Liangzhi; Jia, Shangang; Plath, Martin; Huang, Yongzhen; Li, Congjun; Lei, Chuzhao; Zhao, Xin; Chen, Hong

2015-08-10

Copy number variation (CNV) is an important component of genomic structural variation and plays a role not only in evolutionary diversification but also in domestication. Chinese cattle were derived from Bos taurus and Bos indicus, and several breeds presumably are of hybrid origin, but the evolution of CNV regions (CNVRs) has not yet been examined in this context. Here, we of CNVRs, mtDNA D-loop sequence variation, and Y-chromosomal single nucleotide polymorphisms to assess the impact of maternal and paternal B. taurus and B. indicus origins on the distribution of CNVRs in 24 Chinese domesticated bulls. We discovered 470 genome-wide CNVRs, only 72 of which were shared by all three Y-lineages (B. taurus: Y1, Y2; B. indicus: Y3), whereas 265 were shared by inferred taurine or indicine paternal lineages, and 228 when considering their maternal taurine or indicine origins. Phylogenetic analysis uncovered eight taurine/indicine hybrids, and principal component analysis on CNVs corroborated genomic exchange during hybridization. The distribution patterns of CNVRs tended to be lineage-specific, and correlation analysis revealed significant positive or negative co-occurrences of CNVRs across lineages. Our study suggests that CNVs in Chinese cattle partly result from selective breeding during domestication, but also from hybridization and introgression. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Temperature dependence of attitude sensor coalignments on the Solar Maximum Mission (SMM)

NASA Technical Reports Server (NTRS)

Pitone, D. S.; Eudell, A. H.; Patt, F. S.

1989-01-01

Results are presented on the temperature correlation of the relative coalignment between the fine pointing sun sensor (FPSS) and fixed head star trackers (FHSTs) on the Solar Maximum Mission (SMM). This correlation can be caused by spacecraft electronic and mechanical effects. Routine daily measurements reveal a time dependent sensor coalignment variation. The magnitude of the alignment variation is on the order of 120 arc seconds (arc sec), which greatly exceeds the prelaunch thermal structural analysis estimate of 15 acr sec. Differences between FPSS-only and FHST-only yaw solutions as a function of mission day are correlated with the relevant spacecraft temperature. If unaccounted for, the sensor misalignments due to thermal effects are a significant source of error in attitude determination accuracy. Prominent sources of temperature variation are identified and correlated with the temperature profile observed on the SMM. It was determined that even relatively small changes in spacecraft temperature can affect the coalignments between the attitude hardware on the SMM and the science instrument support plate and that frequent recalibration of sensor alignments is necessary to compensate for this effect. An alterntive to frequent recalibration is to model the variation of alignments as a function of temperature and use this to maintain accurate ground or onboard alignment estimates. These flight data analysis results may be important consierations for prelaunch analysis of future missions.

Child Development and Structural Variation in the Human Genome

ERIC Educational Resources Information Center

Zhang, Ying; Haraksingh, Rajini; Grubert, Fabian; Abyzov, Alexej; Gerstein, Mark; Weissman, Sherman; Urban, Alexander E.

2013-01-01

Structural variation of the human genome sequence is the insertion, deletion, or rearrangement of stretches of DNA sequence sized from around 1,000 to millions of base pairs. Over the past few years, structural variation has been shown to be far more common in human genomes than previously thought. Very little is currently known about the effects…

Epigenetic differentiation and relationship to adaptive genetic divergence in discrete populations of the violet Viola cazorlensis.

PubMed

Herrera, Carlos M; Bazaga, Pilar

2010-08-01

*In plants, epigenetic variations based on DNA methylation are often heritable and could influence the course of evolution. Before this hypothesis can be assessed, fundamental questions about epigenetic variation remain to be addressed in a real-world context, including its magnitude, structuring within and among natural populations, and autonomy in relation to the genetic context. *Extent and patterns of cytosine methylation, and the relationship to adaptive genetic divergence between populations, were investigated for wild populations of the southern Spanish violet Viola cazorlensis (Violaceae) using the methylation-sensitive amplified polymorphism (MSAP) technique, a modification of the amplified fragment length polymorphism method (AFLP) based on the differential sensitivity of isoschizomeric restriction enzymes to site-specific cytosine methylation. *The genome of V. cazorlensis plants exhibited extensive levels of methylation, and methylation-based epigenetic variation was structured into distinct between- and within- population components. Epigenetic differentiation of populations was correlated with adaptive genetic divergence revealed by a Bayesian population-genomic analysis of AFLP data. Significant associations existed at the individual genome level between adaptive AFLP loci and the methylation state of methylation-susceptible MSAP loci. *Population-specific, divergent patterns of correlated selection on epigenetic and genetic individual variation could account for the coordinated epigenetic-genetic adaptive population differentiation revealed by this study.

The effect of individual variation on the structure and function of interaction networks in harvester ants

PubMed Central

Pinter-Wollman, Noa; Wollman, Roy; Guetz, Adam; Holmes, Susan; Gordon, Deborah M.

2011-01-01

Social insects exhibit coordinated behaviour without central control. Local interactions among individuals determine their behaviour and regulate the activity of the colony. Harvester ants are recruited for outside work, using networks of brief antennal contacts, in the nest chamber closest to the nest exit: the entrance chamber. Here, we combine empirical observations, image analysis and computer simulations to investigate the structure and function of the interaction network in the entrance chamber. Ant interactions were distributed heterogeneously in the chamber, with an interaction hot-spot at the entrance leading further into the nest. The distribution of the total interactions per ant followed a right-skewed distribution, indicating the presence of highly connected individuals. Numbers of ant encounters observed positively correlated with the duration of observation. Individuals varied in interaction frequency, even after accounting for the duration of observation. An ant's interaction frequency was explained by its path shape and location within the entrance chamber. Computer simulations demonstrate that variation among individuals in connectivity accelerates information flow to an extent equivalent to an increase in the total number of interactions. Individual variation in connectivity, arising from variation among ants in location and spatial behaviour, creates interaction centres, which may expedite information flow. PMID:21490001

Geometric morphometric analysis of allometric variation in the mandibular morphology of the hominids of Atapuerca, Sima de los Huesos site.

PubMed

Rosas, Antonio; Bastir, Markus

2004-06-01

Allometry is an important factor of morphological integration that contributes to the organization of the phenotype and its variation. Variation in the allometric shape of the mandible is particularly important in hominid evolution because the mandible carries important taxonomic traits. Some of these traits are known to covary with size, particularly the retromolar space, symphyseal curvature, and position of the mental foramen. The mandible is a well studied system in the context of the evolutionary development of complex morphological structures because it is composed of different developmental units that are integrated within a single bone. In the present study, we investigated the allometric variation of two important developmental units that are separated by the inferior nerve (a branch of CN V3). We tested the null hypothesis that there would be no difference in allometric variation between the two components. Procrustes-based geometric morphometrics of 20 two-dimensional (2D) landmarks were analyzed by multivariate regressions of shape on size in samples from 121 humans, 48 chimpanzees, and 50 gorillas (all recent specimens), eight fossil hominids from Atapuerca, Sima de los Huesos (AT-SH), and 17 Neandertals. The findings show that in all of the examined species, there was significantly greater allometric variation in the supra-nerve unit than in the infra-nerve unit. The formation of the retromolar space exhibited an allometric relationship with the supra-nerve unit in all of the species studied. The formation of the chin-like morphology is an "apodynamic" feature of the infra-nerve unit in the AT-SH hominids. The results of this study support the hypothesis that allometry contributes to the organization of variation in complex morphological structures. Copyright 2004 Wiley-Liss, Inc.

Spatial and temporal variation of the gill rakers of gizzard shad and silver carp in three Midwestern rivers

USGS Publications Warehouse

Walleser, Liza R.; Sandheinrich, Mark B.; Howard, David R.; Gaikowski, Mark P.; Amberg, Jon J.

2014-01-01

Improved management of invasive Silver Carp Hypophthalmichthys molitrix in the upper Mississippi River basin may be possible by better understanding the feeding abilities of this population. Food collection for filter-feeding fishes, such as Silver Carp, is influenced by the species-specific structure of their gill rakers. To investigate structural variation in gill rakers of Silver Carp, the morphology of gill rakers was quantified and compared with that of a native filter-feeding fish species which may compete with Silver Carp for food resources, Gizzard Shad Dorosoma cepedianum. Intra- and interspecies variation of gill rakers was examined in both species collected from three locations among four months. Interspecies analysis indicated the size of pores in gill rakers of Silver Carp were much larger than the interraker spacings of Gizzard Shad (95% CI ranged from 80.69 to 185.75 μm versus 16.72 to 47.36 μm, respectively). Intraspecies variation of gill rakers from Silver Carp was related to the overall size of fish and occurred only among sites where dissimilar sizes of fish were collected. This suggested the size of particles filtered by Silver Carp may be dependent upon ontogenic development rather than phenotypic plasticity in response to spatial or temporal factors. Intraspecies variation of gill rakers from Gizzard Shad occurred among site and monthly sampling data; however, variation was only attributable to overall size of fish for monthly sampling data. This suggested ontogeny may influence the filter-feeding ability of this species within a habitat. However, variation noted among sites, which was not attributable to size of fish, may indicate gill rakers are phenotypically plastic among Gizzard Shad populations of various river systems of the upper Mississippi River basin.

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.

Static and Dynamical Structural Investigations of Metal-Oxide Nanocrystals by Powder X-ray Diffraction: Colloidal Tungsten Oxide as a Case Study

DOE PAGES

Caliandro, Rocco; Sibillano, Teresa; Belviso, B. Danilo; ...

2016-02-02

In this study, we have developed a general X-ray powder diffraction (XPD) methodology for the simultaneous structural and compositional characterization of inorganic nanomaterials. The approach is validated on colloidal tungsten oxide nanocrystals (WO 3-x NCs), as a model polymorphic nanoscale material system. Rod-shaped WO 3-x NCs with different crystal structure and stoichiometry are comparatively investigated under an inert atmosphere and after prolonged air exposure. An initial structural model for the as-synthesized NCs is preliminarily identified by means of Rietveld analysis against several reference crystal phases, followed by atomic pair distribution function (PDF) refinement of the best-matching candidates (static analysis). Subtlemore » stoichiometry deviations from the corresponding bulk standards are revealed. NCs exposed to air at room temperature are monitored by XPD measurements at scheduled time intervals. The static PDF analysis is complemented with an investigation into the evolution of the WO 3-x NC structure, performed by applying the modulation enhanced diffraction technique to the whole time series of XPD profiles (dynamical analysis). Prolonged contact with ambient air is found to cause an appreciable increase in the static disorder of the O atoms in the WO 3-x NC lattice, rather than a variation in stoichiometry. Finally, the time behavior of such structural change is identified on the basis of multivariate analysis.« less

Quantifying Mass Transfer Processes in Groundwater as a Function of Molecular Structure Variation for Multicomponent NAPL Sources

NASA Astrophysics Data System (ADS)

Abbott, J. B., III; Tick, G. R.; Greenberg, R. R.; Carroll, K. C.

2017-12-01

The remediation of nonaqueous liquid (NAPL) contamination sources in groundwater has been shown to be challenging and have limited success in the field. The presence of multicomponent NAPL sources further complicates the remediation due to variability of mass-transfer (dissolution) behavior as a result of compositional and molecular structure variations between the different compounds within the NAPL phase. This study investigates the effects of the contaminant of concern (COC) composition and the bulk-NAPL components molecular structure (i.e. carbon chain length, aliphatic and aromatic) on dissolution and aqueous phase concentrations in groundwater. The specific COCs tested include trichloroethene (TCE), toluene (TOL), and perfluorooctanoic acid (PFOA). Each COC was tested in a series of binary batch experiments using insoluble bulk NAPL including n-hexane (HEX), n-decane (DEC), and n-hexadecane (HEXDEC). These equilibrium batch tests were performed to understand how different carbon-chain-length (NAPL) systems affect resulting COC aqueous phase concentrations. The experiments were conducted with four different COC mole fractions mixed within the bulk-NAPL derivatives (0.1:0.9, 0.05:0.95, 0.01:0.99, 0.001:0.999). Raoult's Law was used to assess the relative ideality of the mass transfer processes for each binary equilibrium dissolution experiment. Preliminary results indicate that as mole fraction of the COC decreases (composition effects), greater deviance from dissolution ideality occurs. It was also shown that greater variation in molecular structure (i.e. greater carbon chain length of bulk-NAPL with COC and aromatic COC presence) exhibited greater dissolution nonideality via Raoult's Law analysis. For instance, TOL (aromatic structure) showed greater nonideality than TCE (aliphatic structure) in the presence of the different bulk-NAPL derivatives (i.e. of various aliphatic carbon chains lengths). The results suggest that the prediction of aqueous phase concentration, from complex multicomponent NAPL sources, is highly dependent upon both composition and molecular structure variations of COC-NAPL mixtures, and such impacts should be taken into account when designing and evaluating a remediation strategy and/or predicting COC concentrations from a source zone region.

Accurate interlaminar stress recovery from finite element analysis

NASA Technical Reports Server (NTRS)

Tessler, Alexander; Riggs, H. Ronald

1994-01-01

The accuracy and robustness of a two-dimensional smoothing methodology is examined for the problem of recovering accurate interlaminar shear stress distributions in laminated composite and sandwich plates. The smoothing methodology is based on a variational formulation which combines discrete least-squares and penalty-constraint functionals in a single variational form. The smoothing analysis utilizes optimal strains computed at discrete locations in a finite element analysis. These discrete strain data are smoothed with a smoothing element discretization, producing superior accuracy strains and their first gradients. The approach enables the resulting smooth strain field to be practically C1-continuous throughout the domain of smoothing, exhibiting superconvergent properties of the smoothed quantity. The continuous strain gradients are also obtained directly from the solution. The recovered strain gradients are subsequently employed in the integration o equilibrium equations to obtain accurate interlaminar shear stresses. The problem is a simply-supported rectangular plate under a doubly sinusoidal load. The problem has an exact analytic solution which serves as a measure of goodness of the recovered interlaminar shear stresses. The method has the versatility of being applicable to the analysis of rather general and complex structures built of distinct components and materials, such as found in aircraft design. For these types of structures, the smoothing is achieved with 'patches', each patch covering the domain in which the smoothed quantity is physically continuous.

Advanced numerical technique for analysis of surface and bulk acoustic waves in resonators using periodic metal gratings

NASA Astrophysics Data System (ADS)

Naumenko, Natalya F.

2014-09-01

A numerical technique characterized by a unified approach for the analysis of different types of acoustic waves utilized in resonators in which a periodic metal grating is used for excitation and reflection of such waves is described. The combination of the Finite Element Method analysis of the electrode domain with the Spectral Domain Analysis (SDA) applied to the adjacent upper and lower semi-infinite regions, which may be multilayered and include air as a special case of a dielectric material, enables rigorous simulation of the admittance in resonators using surface acoustic waves, Love waves, plate modes including Lamb waves, Stonely waves, and other waves propagating along the interface between two media, and waves with transient structure between the mentioned types. The matrix formalism with improved convergence incorporated into SDA provides fast and robust simulation for multilayered structures with arbitrary thickness of each layer. The described technique is illustrated by a few examples of its application to various combinations of LiNbO3, isotropic silicon dioxide and silicon with a periodic array of Cu electrodes. The wave characteristics extracted from the admittance functions change continuously with the variation of the film and plate thicknesses over wide ranges, even when the wave nature changes. The transformation of the wave nature with the variation of the layer thicknesses is illustrated by diagrams and contour plots of the displacements calculated at resonant frequencies.

Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays.

PubMed

Mak, Angel C Y; Lai, Yvonne Y Y; Lam, Ernest T; Kwok, Tsz-Piu; Leung, Alden K Y; Poon, Annie; Mostovoy, Yulia; Hastie, Alex R; Stedman, William; Anantharaman, Thomas; Andrews, Warren; Zhou, Xiang; Pang, Andy W C; Dai, Heng; Chu, Catherine; Lin, Chin; Wu, Jacob J K; Li, Catherine M L; Li, Jing-Woei; Yim, Aldrin K Y; Chan, Saki; Sibert, Justin; Džakula, Željko; Cao, Han; Yiu, Siu-Ming; Chan, Ting-Fung; Yip, Kevin Y; Xiao, Ming; Kwok, Pui-Yan

2016-01-01

Comprehensive whole-genome structural variation detection is challenging with current approaches. With diploid cells as DNA source and the presence of numerous repetitive elements, short-read DNA sequencing cannot be used to detect structural variation efficiently. In this report, we show that genome mapping with long, fluorescently labeled DNA molecules imaged on nanochannel arrays can be used for whole-genome structural variation detection without sequencing. While whole-genome haplotyping is not achieved, local phasing (across >150-kb regions) is routine, as molecules from the parental chromosomes are examined separately. In one experiment, we generated genome maps from a trio from the 1000 Genomes Project, compared the maps against that derived from the reference human genome, and identified structural variations that are >5 kb in size. We find that these individuals have many more structural variants than those published, including some with the potential of disrupting gene function or regulation. Copyright © 2016 by the Genetics Society of America.

A survey of tools for variant analysis of next-generation genome sequencing data

PubMed Central

Pabinger, Stephan; Dander, Andreas; Fischer, Maria; Snajder, Rene; Sperk, Michael; Efremova, Mirjana; Krabichler, Birgit; Speicher, Michael R.; Zschocke, Johannes

2014-01-01

Recent advances in genome sequencing technologies provide unprecedented opportunities to characterize individual genomic landscapes and identify mutations relevant for diagnosis and therapy. Specifically, whole-exome sequencing using next-generation sequencing (NGS) technologies is gaining popularity in the human genetics community due to the moderate costs, manageable data amounts and straightforward interpretation of analysis results. While whole-exome and, in the near future, whole-genome sequencing are becoming commodities, data analysis still poses significant challenges and led to the development of a plethora of tools supporting specific parts of the analysis workflow or providing a complete solution. Here, we surveyed 205 tools for whole-genome/whole-exome sequencing data analysis supporting five distinct analytical steps: quality assessment, alignment, variant identification, variant annotation and visualization. We report an overview of the functionality, features and specific requirements of the individual tools. We then selected 32 programs for variant identification, variant annotation and visualization, which were subjected to hands-on evaluation using four data sets: one set of exome data from two patients with a rare disease for testing identification of germline mutations, two cancer data sets for testing variant callers for somatic mutations, copy number variations and structural variations, and one semi-synthetic data set for testing identification of copy number variations. Our comprehensive survey and evaluation of NGS tools provides a valuable guideline for human geneticists working on Mendelian disorders, complex diseases and cancers. PMID:23341494

Lithologic Control on the Form of Soil Mantled Hillslopes

NASA Astrophysics Data System (ADS)

Johnstone, S. A.; Hilley, G. E.

2014-12-01

Slopes on steady-state soil-mantled hillslopes tend to increase downslope in a way that balances local transport capacity with the sediment supplied from progressively larger source areas. Most predictions for the transport of soil depend purely on topographic slope and constants. Thus, soil mantled topography should evolve toward smooth forms in which soils act to buffer these forms from the underlying geologic structure. However, in the Gabilan Mesa, CA, oscillations in the slope of soil-mantled hillslopes mirror oscillations in the underlying stratigraphy. Using field measurements of stratigraphy and soil depths, topographic analysis, and numerical modeling, we demonstrate that variations in rock type can impact the form of soil-mantled hillslopes. Specifically, variations in the properties of underlying rocks may yield different soil thicknesses. Balancing transport rates across these variations in thickness requires slopes to change when soil transport depends on both soil thickness and slope. A compilation of published data on the variation in activity with depth of various transport processes provides the basis for a geomorphic transport law (GTL) that generalizes the depth dependence of various transport processes. While this GTL is explicitly depth dependent, it is also capable of describing situations in which hillslope transport is relatively insensitive to variations in thickness and therefore essentially equivalent to existing formulations. We use dimensional analysis and numerical modeling to demonstrate the conditions under which transport on soil mantled slopes, and consequently topographic forms, may be sensitive to variations in soil thickness and therefore lithology.

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.

A variational image-based approach to the correction of susceptibility artifacts in the alignment of diffusion weighted and structural MRI.

PubMed

Tao, Ran; Fletcher, P Thomas; Gerber, Samuel; Whitaker, Ross T

2009-01-01

This paper presents a method for correcting the geometric and greyscale distortions in diffusion-weighted MRI that result from inhomogeneities in the static magnetic field. These inhomogeneities may due to imperfections in the magnet or to spatial variations in the magnetic susceptibility of the object being imaged--so called susceptibility artifacts. Echo-planar imaging (EPI), used in virtually all diffusion weighted acquisition protocols, assumes a homogeneous static field, which generally does not hold for head MRI. The resulting distortions are significant, sometimes more than ten millimeters. These artifacts impede accurate alignment of diffusion images with structural MRI, and are generally considered an obstacle to the joint analysis of connectivity and structure in head MRI. In principle, susceptibility artifacts can be corrected by acquiring (and applying) a field map. However, as shown in the literature and demonstrated in this paper, field map corrections of susceptibility artifacts are not entirely accurate and reliable, and thus field maps do not produce reliable alignment of EPIs with corresponding structural images. This paper presents a new, image-based method for correcting susceptibility artifacts. The method relies on a variational formulation of the match between an EPI baseline image and a corresponding T2-weighted structural image but also specifically accounts for the physics of susceptibility artifacts. We derive a set of partial differential equations associated with the optimization, describe the numerical methods for solving these equations, and present results that demonstrate the effectiveness of the proposed method compared with field-map correction.

Molecular Modeling of the Structural and Dynamical Changes in Calcium Channel TRPV5 Induced by the African-Specific A563T Variation.

PubMed

Wang, Lingyun; Holmes, Ross P; Peng, Ji-Bin

2016-03-01

Transient receptor potential cation channels, vanilloid subfamily, member 5 (TRPV5) plays a key role in active Ca(2+) reabsorption in the kidney. Variations in TRPV5 occur at high frequency in African populations and may contribute to their higher efficiency of Ca(2+) reabsorption. One of the African specific variations, A563T, exhibits increased Ca(2+) transport ability. However, it is unclear how this variation influences the channel pore. On the basis of the structure of TRPV1, a TRPV5 model was generated to simulate the structural and dynamical changes induced by the A563T variation. On the basis of this model, amino acid residue 563 interacts with V540, which is one residue away from the key residue, D542, involved in Ca(2+) selectivity and Mg(2+) blockade. The A563T variation increases secondary structure stability and reduces dynamical motion of D542. In addition, the A563T variation alters the electrostatic potential of the outer surface of the pore. Differences in contact between selective filter residues and residue 563 and in electrostatic potential between the two TRPV5 variants were also observed in another model derived from an alternative alignment in the selective filters between TRPV5 and TRPV1. These findings indicate that the A563T variation induces structural, dynamical, and electrostatic changes in the TRPV5 pore, providing structural insight into the functional alterations associated with the A563T variation.

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.

Colombia a Source of Cacao Genetic Diversity As Revealed by the Population Structure Analysis of Germplasm Bank of Theobroma cacao L.

PubMed

Osorio-Guarín, Jaime A; Berdugo-Cely, Jhon; Coronado, Roberto Antonio; Zapata, Yeny Patricia; Quintero, Constanza; Gallego-Sánchez, Gerardo; Yockteng, Roxana

2017-01-01

Beans of the species Theobroma cacao L., also known as cacao, are the raw material to produce chocolate. Colombian cacao has been classified as a fine flavor cacao that represents the 5% of cacao world's production. Colombian genetic resources from this species are conserved in ex situ and in-field germplasm banks, since T. cacao has recalcitrant seeds to desication and long-term storage. Currently, the collection of T. cacao of the Colombian Corporation of Agricultural Research (CORPOICA) has approximately 700 germplasm accessions. We conducted a molecular analysis of Corpoica's cacao collection and a morphological characterization of some accessions with the goal to study its genetic diversity and population structure and, to select interesting accessions for the cacao's breeding program. Phenotypic evaluation was performed based on 18 morphological traits and 4 biochemical traits. PCA analysis of morphological traits explained 60.6% of the total variation in seven components and 100% of the total variation of biochemical traits in four components, grouping the collection in 4 clusters for both variables. We explored 565 accessions from Corpoica's germplasm and 252 accessions from reference populations using 96 single nucleotide polymorphism (SNP) molecular markers. Molecular patterns of cacao Corpoica's collection were obtained amplifying specific alleles in a Fluidigm platform that used integrated circuits of fluids. Corpoica's collection showed highest genetic diversity [Expected Heterozygosity ( H E = 0.314), Observed Heterozygosity ( H O = 0.353)] that is reduced when reference populations were included in the dataset ( H E = 0.294, H O = 0.261). The collection was divided into four clusters based on population structure analysis. Cacao accessions from distinct groups showed some taxonomic concordance and reflected their geographic origins. For instance, accessions classified as Criollo were clearly differentiated in one group and we identified two new Colombian genetic groups. Using a number of allelic variations based on 87 SNP markers and 22 different morphological/biochemical traits, a core collection with a total of 232 accessions was selected as a primary genetic resource for cacao breeders.

Colombia a Source of Cacao Genetic Diversity As Revealed by the Population Structure Analysis of Germplasm Bank of Theobroma cacao L.

PubMed Central

Osorio-Guarín, Jaime A.; Berdugo-Cely, Jhon; Coronado, Roberto Antonio; Zapata, Yeny Patricia; Quintero, Constanza; Gallego-Sánchez, Gerardo; Yockteng, Roxana

2017-01-01

Beans of the species Theobroma cacao L., also known as cacao, are the raw material to produce chocolate. Colombian cacao has been classified as a fine flavor cacao that represents the 5% of cacao world’s production. Colombian genetic resources from this species are conserved in ex situ and in-field germplasm banks, since T. cacao has recalcitrant seeds to desication and long-term storage. Currently, the collection of T. cacao of the Colombian Corporation of Agricultural Research (CORPOICA) has approximately 700 germplasm accessions. We conducted a molecular analysis of Corpoica’s cacao collection and a morphological characterization of some accessions with the goal to study its genetic diversity and population structure and, to select interesting accessions for the cacao’s breeding program. Phenotypic evaluation was performed based on 18 morphological traits and 4 biochemical traits. PCA analysis of morphological traits explained 60.6% of the total variation in seven components and 100% of the total variation of biochemical traits in four components, grouping the collection in 4 clusters for both variables. We explored 565 accessions from Corpoica’s germplasm and 252 accessions from reference populations using 96 single nucleotide polymorphism (SNP) molecular markers. Molecular patterns of cacao Corpoica’s collection were obtained amplifying specific alleles in a Fluidigm platform that used integrated circuits of fluids. Corpoica’s collection showed highest genetic diversity [Expected Heterozygosity (HE = 0.314), Observed Heterozygosity (HO = 0.353)] that is reduced when reference populations were included in the dataset (HE = 0.294, HO = 0.261). The collection was divided into four clusters based on population structure analysis. Cacao accessions from distinct groups showed some taxonomic concordance and reflected their geographic origins. For instance, accessions classified as Criollo were clearly differentiated in one group and we identified two new Colombian genetic groups. Using a number of allelic variations based on 87 SNP markers and 22 different morphological/biochemical traits, a core collection with a total of 232 accessions was selected as a primary genetic resource for cacao breeders. PMID:29209353

Moderate climate signature in cranial anatomy of late holocene human populations from Southern South America.

PubMed

Paula Menéndez, Lumila

2018-02-01

The aim of this study is to analyze the association between cranial variation and climate in order to discuss their role during the diversification of southern South American populations. Therefore, the specific objectives are: (1) to explore the spatial pattern of cranial variation with regard to the climatic diversity of the region, and (2) to evaluate the differential impact that the climatic factors may have had on the shape and size of the diverse cranial structures studied. The variation in shape and size of 361 crania was studied, registering 62 3D landmarks that capture shape and size variation in the face, cranial vault, and base. Mean, minimum, and maximum annual temperature, as well as mean annual precipitation, but also diet and altitude, were matched for each population sample. A PCA, as well as spatial statistical techniques, including kriging, regression, and multimodel inference were employed. The facial skeleton size presents a latitudinal pattern which is partially associated with temperature diversity. Both diet and altitude are the variables that mainly explain the skull shape variation, although mean annual temperature also plays a role. The association between climate factors and cranial variation is low to moderate, mean annual temperature explains almost 40% of the entire skull, facial skeleton and cranial vault shape variation, while annual precipitation and minimum annual temperature only contribute to the morphological variation when considered together with maximum annual temperature. The cranial base is the structure less associated with climate diversity. These results suggest that climate factors may have had a partial impact on the facial and vault shape, and therefore contributed moderately to the diversification of southern South American populations, while diet and altitude might have had a stronger impact. Therefore, cranial variation at the southern cone has been shaped both by random and nonrandom factors. Particularly, the influence of climate on skull shape has probably been the result of directional selection. This study supports that, although cranial vault is the cranial structure more associated to mean annual temperature, the impact of climate signature on morphology decreases when populations from extreme cold environments are excluded from the analysis. Additionally, it shows that the extent of the geographical scales analyzed, as well as differential sampling may lead to different results regarding the role of ecological factors and evolutionary processes on cranial morphology. © 2017 Wiley Periodicals, Inc.

Robust inference of population structure for ancestry prediction and correction of stratification in the presence of relatedness.

PubMed

Conomos, Matthew P; Miller, Michael B; Thornton, Timothy A

2015-05-01

Population structure inference with genetic data has been motivated by a variety of applications in population genetics and genetic association studies. Several approaches have been proposed for the identification of genetic ancestry differences in samples where study participants are assumed to be unrelated, including principal components analysis (PCA), multidimensional scaling (MDS), and model-based methods for proportional ancestry estimation. Many genetic studies, however, include individuals with some degree of relatedness, and existing methods for inferring genetic ancestry fail in related samples. We present a method, PC-AiR, for robust population structure inference in the presence of known or cryptic relatedness. PC-AiR utilizes genome-screen data and an efficient algorithm to identify a diverse subset of unrelated individuals that is representative of all ancestries in the sample. The PC-AiR method directly performs PCA on the identified ancestry representative subset and then predicts components of variation for all remaining individuals based on genetic similarities. In simulation studies and in applications to real data from Phase III of the HapMap Project, we demonstrate that PC-AiR provides a substantial improvement over existing approaches for population structure inference in related samples. We also demonstrate significant efficiency gains, where a single axis of variation from PC-AiR provides better prediction of ancestry in a variety of structure settings than using 10 (or more) components of variation from widely used PCA and MDS approaches. Finally, we illustrate that PC-AiR can provide improved population stratification correction over existing methods in genetic association studies with population structure and relatedness. © 2015 WILEY PERIODICALS, INC.

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.

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

Transtensional deformation of Montserrat revealed by shear wave splitting

NASA Astrophysics Data System (ADS)

Baird, Alan F.; Kendall, J.-Michael; Sparks, R. Stephen J.; Baptie, Brian

2015-09-01

Here we investigate seismic anisotropy of the upper crust in the vicinity of Soufrière Hills volcano using shear wave splitting (SWS) analysis from volcano-tectonic (VT) events. Soufrière Hills, which is located on the island of Montserrat in the Lesser Antilles, became active in 1995 and has been erupting ever since with five major phases of extrusive activity. We use data recorded on a network of seismometers between 1996 and 2007 partially spanning three extrusive phases. Shear-wave splitting in the crust is often assumed to be controlled either by structural features, or by stress aligned cracks. In such a case the polarization of the fast shear wave (ϕ) would align parallel to the strike of the structure, or to the maximum compressive stress direction. Previous studies analyzing SWS in the region using regional earthquakes observed temporal variations in ϕ which were interpreted as being caused by stress perturbations associated with pressurization of a dyke. Our analysis, which uses much shallower sources and thus only samples the anisotropy of the upper few kilometres of the crust, shows no clear temporal variation. However, temporal effects cannot be ruled out, as large fluctuations in the rate of VT events over the course of the study period as well as changes in the seismic network configuration make it difficult to assess. Average delay times of approximately 0.2 s, similar in magnitude to those reported for much deeper slab events, suggest that the bulk of the anisotropy is in the shallow crust. We observe clear spatial variations in anisotropy which we believe are consistent with structurally controlled anisotropy resulting from a left-lateral transtensional array of faults which crosses the volcanic complex.

Extensive copy number variations in admixed Indian population of African ancestry: potential involvement in adaptation.

PubMed

Narang, Ankita; Jha, Pankaj; Kumar, Dhirendra; Kutum, Rintu; Mondal, Anupam Kumar; Dash, Debasis; Mukerji, Mitali

2014-11-13

Admixture mapping has been enormously resourceful in identifying genetic variations linked to phenotypes, adaptation, and diseases. In this study through analysis of copy number variable regions (CNVRs), we report extensive restructuring in the genomes of the recently admixed African-Indian population (OG-W-IP) that inhabits a highly saline environment in Western India. The study included subjects from OG-W-IP (OG), five different Indian and three HapMap populations that were genotyped using Affymetrix version 6.0 arrays. Copy number variations (CNVs) detected using Birdsuite were used to define CNVRs. Population structure with respect to CNVRs was delineated using random forest approach. OG genomes have a surprising excess of CNVs in comparison to other studied populations. Individual ancestry proportions computed using STRUCTURE also reveals a unique genetic component in OGs. Population structure analysis with CNV genotypes indicates OG to be distant from both the African and Indian ancestral populations. Interestingly, it shows genetic proximity with respect to CNVs to only one Indian population IE-W-LP4, which also happens to reside in the same geographical region. We also observe a significant enrichment of molecular processes related to ion binding and receptor activity in genes encompassing OG-specific CNVRs. Our results suggest that retention of CNVRs from ancestral natives and de novo acquisition of CNVRs could accelerate the process of adaptation especially in an extreme environment. Additionally, this population would be enormously useful for dissecting genes and delineating the involvement of CNVs in salt adaptation. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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.

Large Scale Comparative Visualisation of Regulatory Networks with TRNDiff

DOE PAGES

Chua, Xin-Yi; Buckingham, Lawrence; Hogan, James M.; ...

2015-06-01

The advent of Next Generation Sequencing (NGS) technologies has seen explosive growth in genomic datasets, and dense coverage of related organisms, supporting study of subtle, strain-specific variations as a determinant of function. Such data collections present fresh and complex challenges for bioinformatics, those of comparing models of complex relationships across hundreds and even thousands of sequences. Transcriptional Regulatory Network (TRN) structures document the influence of regulatory proteins called Transcription Factors (TFs) on associated Target Genes (TGs). TRNs are routinely inferred from model systems or iterative search, and analysis at these scales requires simultaneous displays of multiple networks well beyond thosemore » of existing network visualisation tools [1]. In this paper we describe TRNDiff, an open source system supporting the comparative analysis and visualization of TRNs (and similarly structured data) from many genomes, allowing rapid identification of functional variations within species. The approach is demonstrated through a small scale multiple TRN analysis of the Fur iron-uptake system of Yersinia, suggesting a number of candidate virulence factors; and through a larger study exploiting integration with the RegPrecise database (http://regprecise.lbl.gov; [2]) - a collection of hundreds of manually curated and predicted transcription factor regulons drawn from across the entire spectrum of prokaryotic organisms.« less

Static aeroelastic analysis and tailoring of missile control fins

NASA Technical Reports Server (NTRS)

Mcintosh, S. C., Jr.; Dillenius, M. F. E.

1989-01-01

A concept for enhancing the design of control fins for supersonic tactical missiles is described. The concept makes use of aeroelastic tailoring to create fin designs (for given planforms) that limit the variations in hinge moments that can occur during maneuvers involving high load factors and high angles of attack. It combines supersonic nonlinear aerodynamic load calculations with finite-element structural modeling, static and dynamic structural analysis, and optimization. The problem definition is illustrated. The fin is at least partly made up of a composite material. The layup is fixed, and the orientations of the material principal axes are allowed to vary; these are the design variables. The objective is the magnitude of the difference between the chordwise location of the center of pressure and its desired location, calculated for a given flight condition. Three types of constraints can be imposed: upper bounds on static displacements for a given set of load conditions, lower bounds on specified natural frequencies, and upper bounds on the critical flutter damping parameter at a given set of flight speeds and altitudes. The idea is to seek designs that reduce variations in hinge moments that would otherwise occur. The block diagram describes the operation of the computer program that accomplishes these tasks. There is an option for a single analysis in addition to the optimization.

Comparative analyses of genetic/epigenetic diversities and structures in a wild barley species (Hordeum brevisubulatum) using MSAP, SSAP and AFLP.

PubMed

Shan, X H; Li, Y D; Liu, X M; Wu, Y; Zhang, M Z; Guo, W L; Liu, B; Yuan, Y P

2012-08-17

We analyzed genetic diversity and population genetic structure of four artificial populations of wild barley (Hordeum brevisubulatum); 96 plants collected from the Songnen Prairie in northeastern China were analyzed using amplified fragment length polymorphism (AFLP), specific-sequence amplified polymorphism (SSAP) and methylation-sensitive amplified polymorphism (MSAP) markers. Indices of (epi-)genetic diversity, (epi-)genetic distance, gene flow, genotype frequency, cluster analysis, PCA analysis and AMOVA analysis generated from MSAP, AFLP and SSAP markers had the same trend. We found a high level of correlation in the artificial populations between MSAP, SSAP and AFLP markers by the Mantel test (r > 0.8). This is incongruent with previous findings showing that there is virtually no correlation between DNA methylation polymorphism and classical genetic variation; the high level of genetic polymorphism could be a result of epigenetic regulation. We compared our results with data from natural populations. The population diversity of the artificial populations was lower. However, different from what was found using AFLP and SSAP, based on MSAP results the methylation polymorphism of the artificial populations was not significantly reduced. This leads us to suggest that the DNA methylation pattern change in H. brevisubulatum populations is not only related to DNA sequence variation, but is also regulated by other controlling systems.

Comparative evaluation of differential laser-induced perturbation spectroscopy as a technique to discriminate emerging skin pathology

NASA Astrophysics Data System (ADS)

Kozikowski, Raymond T.; Smith, Sarah E.; Lee, Jennifer A.; Castleman, William L.; Sorg, Brian S.; Hahn, David W.

2012-06-01

Fluorescence spectroscopy has been widely investigated as a technique for identifying pathological tissue; however, unrelated subject-to-subject variations in spectra complicate data analysis and interpretation. We describe and evaluate a new biosensing technique, differential laser-induced perturbation spectroscopy (DLIPS), based on deep ultraviolet (UV) photochemical perturbation in combination with difference spectroscopy. This technique combines sequential fluorescence probing (pre- and post-perturbation) with sub-ablative UV perturbation and difference spectroscopy to provide a new spectral dimension, facilitating two improvements over fluorescence spectroscopy. First, the differential technique eliminates significant variations in absolute fluorescence response within subject populations. Second, UV perturbations alter the extracellular matrix (ECM), directly coupling the DLIPS response to the biological structure. Improved biosensing with DLIPS is demonstrated in vivo in a murine model of chemically induced skin lesion development. Component loading analysis of the data indicates that the DLIPS technique couples to structural proteins in the ECM. Analysis of variance shows that DLIPS has a significant response to emerging pathology as opposed to other population differences. An optimal likelihood ratio classifier for the DLIPS dataset shows that this technique holds promise for improved diagnosis of epithelial pathology. Results further indicate that DLIPS may improve diagnosis of tissue by augmenting fluorescence spectra (i.e. orthogonal sensing).

Stability analysis of magnetized neutron stars - a semi-analytic approach

NASA Astrophysics Data System (ADS)

Herbrik, Marlene; Kokkotas, Kostas D.

2017-04-01

We implement a semi-analytic approach for stability analysis, addressing the ongoing uncertainty about stability and structure of neutron star magnetic fields. Applying the energy variational principle, a model system is displaced from its equilibrium state. The related energy density variation is set up analytically, whereas its volume integration is carried out numerically. This facilitates the consideration of more realistic neutron star characteristics within the model compared to analytical treatments. At the same time, our method retains the possibility to yield general information about neutron star magnetic field and composition structures that are likely to be stable. In contrast to numerical studies, classes of parametrized systems can be studied at once, finally constraining realistic configurations for interior neutron star magnetic fields. We apply the stability analysis scheme on polytropic and non-barotropic neutron stars with toroidal, poloidal and mixed fields testing their stability in a Newtonian framework. Furthermore, we provide the analytical scheme for dropping the Cowling approximation in an axisymmetric system and investigate its impact. Our results confirm the instability of simple magnetized neutron star models as well as a stabilization tendency in the case of mixed fields and stratification. These findings agree with analytical studies whose spectrum of model systems we extend by lifting former simplifications.

Chromosomal aneuploidies and copy number variations in posterior fossa abnormalities diagnosed by prenatal ultrasonography.

PubMed

Lei, Ting; Feng, Jie-Ling; Xie, Ying-Jun; Xie, Hong-Ning; Zheng, Ju; Lin, Mei-Fang

2017-11-01

To explore the genetic aetiology of fetal posterior fossa abnormalities (PFAs). This study involved cases of PFAs that were identified by prenatal ultrasonographic screening and confirmed postnatally between January 2012 and January 2016. Conventional cytogenetic analyses and chromosomal microarray analysis were performed, and chromosomal aneuploidies and copy number variations (CNVs) were identified. Among 74 cases included in this study, 8 were of Blake's pouch cyst; 7, Dandy-Walker malformation; 11, vermian hypoplasia; 32, enlarged cisterna magna; and 16, cerebellar hypoplasia. The rates of nonbenign chromosomal aberrations (including chromosomal aneuploidies, pathogenic CNVs, and variants of unknown significance) were 2/8 (25.0%), 2/7 (28.5%), 8/11 (72.7%), 7/32 (21.9%), and 6/16 (37.5%), respectively. Cases were also classified as isolated PFAs (30/74), PFAs with other central nervous system (CNS) abnormalities (13/74), or PFAs with extra-CNS structural abnormalities (31/74). No fetuses with isolated PFAs or PFAs accompanied by other CNS abnormalities exhibited chromosomal aneuploidies or pathogenic CNVs. The rate of pathogenic chromosomal aberrations in the remaining fetuses was 17/31 (22.9%). The combined use of chromosomal microarray analysis and karyotype analysis might assist the prenatal diagnosis and management of PFAs, with extra-CNS structural abnormalities being detected by ultrasonography. © 2017 John Wiley & Sons, Ltd.

Statistical Significance of Optical Map Alignments

PubMed Central

Sarkar, Deepayan; Goldstein, Steve; Schwartz, David C.

2012-01-01

Abstract The Optical Mapping System constructs ordered restriction maps spanning entire genomes through the assembly and analysis of large datasets comprising individually analyzed genomic DNA molecules. Such restriction maps uniquely reveal mammalian genome structure and variation, but also raise computational and statistical questions beyond those that have been solved in the analysis of smaller, microbial genomes. We address the problem of how to filter maps that align poorly to a reference genome. We obtain map-specific thresholds that control errors and improve iterative assembly. We also show how an optimal self-alignment score provides an accurate approximation to the probability of alignment, which is useful in applications seeking to identify structural genomic abnormalities. PMID:22506568

In silico approach to explore the disruption in the molecular mechanism of human hyaluronidase 1 by mutant E268K that directs Natowicz syndrome.

PubMed

Meshach Paul, D; Rajasekaran, R

2017-03-01

Natowicz syndrome (mucopolysaccharidoses type 9) is a lysosomal storage disorder caused by deficient or defective human hyaluronidase 1. The disorder is not well studied at the molecular level. Therefore, a new in silico approach was proposed to study the molecular basis on which one clinically observed mutation, Glu268Lys, results in a defective enzyme. The native and mutant structures were subjected to comparative analyses using a conformational sampling approach for geometrical variables viz, RMSF, RMSD, and Ramachandran plot. In addition, the strength of a Cys207-Cys221 disulfide bond and electrostatic interaction between Arg265 and Asp206 were studied, as they are known to be involved in the catalytic activity of the enzyme. Native and mutant E268K showed statistically significant variations with p < 0.05 in RMSD, Ramachandran plot, strengths of disulfide bond, and electrostatic interactions. Further, single model analysis showed variations between native and mutant structures in terms of intra-protein interactions, hydrogen bond dilution, secondary structure, and dihedral angles. Docking analysis predicted the mutant to have a less favorable substrate binding energy compared to the native protein. Additionally, steered MD analysis indicated that the substrate should have more affinity to the native than mutant enzymes. The observed changes theoretically explain the less favorable binding energy of substrate towards mutant E268K, thereby providing a structural basis for its reduced catalytic activity. Hence, our study provides a basis for understanding the disruption in the molecular mechanism of human hyaluronidase 1 by mutation E268K, which may prove useful for the development of synthetic chaperones as a treatment option for Natowicz syndrome.

Improving Structural and Functional Agreement in Patients with Glaucoma by Using Customized Perimetric Locations and Images of the Retinal Nerve Fiber Bundles

NASA Astrophysics Data System (ADS)

Alluwimi, Muhammed Saad

Glaucoma is the second leading cause of the blindness worldwide. It is a group of chronic, progressive, and potentially blinding optic neuropathies characterized by abnormalities of the optic nerve head and/or retinal nerve fiber layer (RNFL) associated with visual field abnormality. When diagnosing and managing patients with glaucoma, clinicians evaluate the agreement between structural and functional measures. However, it has been widely recognized that there is often a discordance between structural and functional (e.g., perimetry) measures in glaucoma, posing a challenge for clinicians to make their decisions. As explained in the literature, this discordance may relate to high normal between-subject variation, insufficient knowledge of the RNFL bundle organization, sparse spacing of the perimetric locations used to measure the functional performance of ganglion cells, high test-retest variation for the most commonly used stimulus for perimetry, and poor perimetric sampling of the macula. The aim of this thesis was to overcome this discordance by conducting three experiments: First, asymmetry analysis was used to reduce between-subject variation of the macular thickness and ganglion cell thickness measurements with OCT. This variation was decreased at particular regions of the macula. Outside the macula, the variation remained high leading to the second experiment in which customized closely-spaced perimetric locations were presented at wedge defects, guided by the OCT en face images of the RNFL bundles. A rapid suprathreshold perimetric strategy was used and perimetric defect was, in most cases, in correspondence with the structural defect. To threshold perimetric defects, an elongated blur-resistant stimulus was oriented within damaged RNFL bundles. It was found that contrast sensitivities were below the 95% normal limit in 37 of 44 locations. The latter experiment focused on wedge defects outside the macula, which led to the third experiment in which the goal was to investigate the feasibility of a basis to individualize perimetric locations within the macula guided by structural damage seen on OCT en face images. In preliminary data, it was feasible to individualize perimetric locations within the macula. In this thesis, the agreement between structural and functional measures was improved in glaucoma, by developing methods and techniques that provided a framework to help overcome challenges in clinical decision making.

Comparative Population Genomics Analysis of the Mammalian Fungal Pathogen Pneumocystis.

PubMed

Cissé, Ousmane H; Ma, Liang; Wei Huang, Da; Khil, Pavel P; Dekker, John P; Kutty, Geetha; Bishop, Lisa; Liu, Yueqin; Deng, Xilong; Hauser, Philippe M; Pagni, Marco; Hirsch, Vanessa; Lempicki, Richard A; Stajich, Jason E; Cuomo, Christina A; Kovacs, Joseph A

2018-05-08

Pneumocystis species are opportunistic mammalian pathogens that cause severe pneumonia in immunocompromised individuals. These fungi are highly host specific and uncultivable in vitro Human Pneumocystis infections present major challenges because of a limited therapeutic arsenal and the rise of drug resistance. To investigate the diversity and demographic history of natural populations of Pneumocystis infecting humans, rats, and mice, we performed whole-genome and large-scale multilocus sequencing of infected tissues collected in various geographic locations. Here, we detected reduced levels of recombination and variations in historical demography, which shape the global population structures. We report estimates of evolutionary rates, levels of genetic diversity, and population sizes. Molecular clock estimates indicate that Pneumocystis species diverged before their hosts, while the asynchronous timing of population declines suggests host shifts. Our results have uncovered complex patterns of genetic variation influenced by multiple factors that shaped the adaptation of Pneumocystis populations during their spread across mammals. IMPORTANCE Understanding how natural pathogen populations evolve and identifying the determinants of genetic variation are central issues in evolutionary biology. Pneumocystis , a fungal pathogen which infects mammals exclusively, provides opportunities to explore these issues. In humans, Pneumocystis can cause a life-threatening pneumonia in immunosuppressed individuals. In analysis of different Pneumocystis species infecting humans, rats, and mice, we found that there are high infection rates and that natural populations maintain a high level of genetic variation despite low levels of recombination. We found no evidence of population structuring by geography. Our comparisons of the times of divergence of these species to their respective hosts suggest that Pneumocystis may have undergone recent host shifts. The results demonstrate that Pneumocystis strains are widely disseminated geographically and provide a new understanding of the evolution of these pathogens.

Joint association discovery and diagnosis of Alzheimer's disease by supervised heterogeneous multiview learning.

PubMed

Zhe, Shandian; Xu, Zenglin; Qi, Yuan; Yu, Peng

2014-01-01

A key step for Alzheimer's disease (AD) study is to identify associations between genetic variations and intermediate phenotypes (e.g., brain structures). At the same time, it is crucial to develop a noninvasive means for AD diagnosis. Although these two tasks-association discovery and disease diagnosis-have been treated separately by a variety of approaches, they are tightly coupled due to their common biological basis. We hypothesize that the two tasks can potentially benefit each other by a joint analysis, because (i) the association study discovers correlated biomarkers from different data sources, which may help improve diagnosis accuracy, and (ii) the disease status may help identify disease-sensitive associations between genetic variations and MRI features. Based on this hypothesis, we present a new sparse Bayesian approach for joint association study and disease diagnosis. In this approach, common latent features are extracted from different data sources based on sparse projection matrices and used to predict multiple disease severity levels based on Gaussian process ordinal regression; in return, the disease status is used to guide the discovery of relationships between the data sources. The sparse projection matrices not only reveal the associations but also select groups of biomarkers related to AD. To learn the model from data, we develop an efficient variational expectation maximization algorithm. Simulation results demonstrate that our approach achieves higher accuracy in both predicting ordinal labels and discovering associations between data sources than alternative methods. We apply our approach to an imaging genetics dataset of AD. Our joint analysis approach not only identifies meaningful and interesting associations between genetic variations, brain structures, and AD status, but also achieves significantly higher accuracy for predicting ordinal AD stages than the competing methods.

Spatial and Temporal Comparison of DNRA Communities in New River Estuary, USA

NASA Astrophysics Data System (ADS)

Song, B.; Lisa, J.; Tobias, C. R.

2016-02-01

Dissimilatory nitrate reduction to ammonium (DNRA) is an important nitrate respiring pathway, competing with denitrification, in various ecosystems. Studies examining the diversity and composition of DNRA communities are limited and their link to DNRA activity is unknown. We conducted a multidisciplinary investigation of sediment communities in the upper reaches of a eutrophic estuary to examine spatial and temporal variation of DNRA community structures and determine their linkage to activities. Sediment samples were collected seasonally from two study sites (AA2 and JAX) in the New River Estuary, North Carolina, USA. 15N-nitrate tracer experiments were conducted to measure potential DNRA rates while abundance of DNRA communities was measured using quantitative PCR of cytochrome C nitrite reductase genes (nrfA). Composition and diversity of DNRA communities were also examined based on next generation sequencing (NGS) of nrfA genes using an Ion Torrent PGM. Bioinformatic analysis was conducted using the FunGene pipeline and Mothur program. Higher DNRA activities were measured at JAX and associated with higher abundance of nrfA genes. Seasonal variation in DNRA rates and nrfA gene abundance was more evident at JAX than AA2. Nitrate concentration and dissolved oxygen in bottom water were significantly and positively correlated with activities and abundance of DNRA communities. The nrfA NGS analysis revealed that spatial variation of DNRA communities was much greater than temporal variation with salinity, dissolved organic carbon, and nitrate as the most important environmental variables affecting these communities. Diversity of DNRA communities was negative correlated with the DNRA rates and nrfA gene abundance, which suggests that dominant members of the DNRA community are responsible for higher rates. Thus, our multidisciplinary study clearly demonstrates the linkage between structure and activities of DNRA communities in the upper reaches of New River Estuary.

Spectroscopic Analysis of Temporal Changes in Leaf Moisture and Dry Matter Content

NASA Astrophysics Data System (ADS)

Qi, Y.; Dennison, P. E.; Brewer, S.; Jolly, W. M.; Kropp, R.

2013-12-01

Live fuel moisture (LFM), the ratio of water content to dry matter content (DMC) in live fuel, is critical for determining fire danger and behavior. Remote sensing estimation of LFM often relies on an assumption of changing water content and stable DMC over time. In order to advance understanding of temporal variation in LFM and DMC, we collected field samples and spectroscopic data for two species, lodgepole pine (Pinus contorta) and big sagebrush (Artemisia tridentata), to explore seasonal trends and spectral expression of these trends. New and old needles were measured separately for lodgepole pine. All samples were measured using a visible/NIR/SWIR spectrometer, and coincident samples were processed to provide LFM, DMC, water content and chemical components including structural and non-structural carbohydrates. New needles initially exhibited higher LFM and a smaller proportion of DMC, but differences between new and old needles converged as the new needles hardened. DMC explained more variation in LFM than water content for new pine needles and sagebrush leaves. Old pine needles transported non-structural carbohydrates to new needles to accumulate DMC during the growth season, resulting decreasing LFM in new needles. DMC and water content co-varied with vegetation chemical components and physical structure. Spectral variation in response to changing DMC is difficulty to isolate from the spectral signatures of multiple chemical components. Partial least square regression combined with hyperspectral data may increase modeling performance in LFM estimation.

Genetic diversity of calcareous grassland plant species depends on historical landscape configuration.

PubMed

Reisch, Christoph; Schmidkonz, Sonja; Meier, Katrin; Schöpplein, Quirin; Meyer, Carina; Hums, Christian; Putz, Christina; Schmid, Christoph

2017-04-24

Habitat fragmentation is considered to be a main reason for decreasing genetic diversity of plant species. However, the results of many fragmentation studies are inconsistent. This may be due to the influence of habitat conditions, having an indirect effect on genetic variation via reproduction. Consequently we took a comparative approach to analyse the impact of habitat fragmentation and habitat conditions on the genetic diversity of calcareous grassland species in this study. We selected five typical grassland species (Primula veris, Dianthus carthusianorum, Medicago falcata, Polygala comosa and Salvia pratensis) occurring in 18 fragments of calcareous grasslands in south eastern Germany. We sampled 1286 individuals in 87 populations and analysed genetic diversity using amplified fragment length polymorphisms. Additionally, we collected data concerning habitat fragmentation (historical and present landscape structure) and habitat conditions (vegetation structure, soil conditions) of the selected study sites. The whole data set was analysed using Bayesian multiple regressions. Our investigation indicated a habitat loss of nearly 80% and increasing isolation between grasslands since 1830. Bayesian analysis revealed a significant impact of the historical landscape structure, whereas habitat conditions played no important role for the present-day genetic variation of the studied plant species. Our study indicates that the historical landscape structure may be more important for genetic diversity than present habitat conditions. Populations persisting in abandoned grassland fragments may contribute significantly to the species' variability even under deteriorating habitat conditions. Therefore, these populations should be included in approaches to preserve the genetic variation of calcareous grassland species.

Analysis of genetic diversity and population structure of peanut cultivars and breeding lines from China, India and USA

USDA-ARS?s Scientific Manuscript database

Peanut (Arachis hypogaea L.) is an important source for edible oil and protein. It is important to identify genetic diversity of peanut for cultivar development. In this study, 111 SSR markers with high polymorphic information content (PIC) were used to assess the genetic variation of 79 peanut cult...

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...

Phylogeographic analysis of the Douglas-fir beetle Dendroctonus pseudotsugae Hopkins (Coleoptera: Curculionidae: Scolytinae)

Treesearch

Enrico A. Ruíz; Jane L. Hayes; John E. Rinehart; G. Zúñiga

2007-01-01

Population genetic structure studies made in genus Dendroctonus have been conducted from the perspectives of allopatric and sympatric models. In the first case, host effect and historical contingency were not recognized as a source of variation, while the later considered the host itself as a source of reproductive isolation. Nevertheless, both...

Semi-automated separation of the epimeric dehydropyrrolizidine alkaloids lycopsamine and intermedine: Preparation of their N-oxides and NMR comparison with diastereoisomeric rinderine and echinatine

USDA-ARS?s Scientific Manuscript database

Introduction – The diversity of structure and, particularly,stereochemical variation of the dehydropyrrolizidine alkaloids can present challenges for analysis and the isolation of pure compounds for the preparation of analytical standards and for toxicology studies. Objective – To investigate method...

Learning from Tutorials: A Qualitative Study of Approaches to Learning and Perceptions of Tutorial Interaction

ERIC Educational Resources Information Center

Herrmann, Kim Jesper

2014-01-01

This study examines differences in university students' approaches to learning when attending tutorials as well as variation in students' perceptions of tutorials as an educational arena. In-depth qualitative analysis of semi-structured interviews with undergraduates showed how surface and deep approaches to learning were revealed in the…

Genetic structure of wild boar (Sus scrofa) populations from East Asia based on microsatellite loci analyses

PubMed Central

2014-01-01

Background Wild boar, Sus scrofa, is an extant wild ancestor of the domestic pig as an agro-economically important mammal. Wild boar has a worldwide distribution with its geographic origin in Southeast Asia, but genetic diversity and genetic structure of wild boar in East Asia are poorly understood. To characterize the pattern and amount of genetic variation and population structure of wild boar in East Asia, we genotyped and analyzed microsatellite loci for a total of 238 wild boar specimens from ten locations across six countries in East and Southeast Asia. Results Our data indicated that wild boar populations in East Asia are genetically diverse and structured, showing a significant correlation of genetic distance with geographic distance and implying a low level of gene flow at a regional scale. Bayesian-based clustering analysis was indicative of seven inferred genetic clusters in which wild boars in East Asia are geographically structured. The level of genetic diversity was relatively high in wild boars from Southeast Asia, compared with those from Northeast Asia. This gradient pattern of genetic diversity is consistent with an assumed ancestral population of wild boar in Southeast Asia. Genetic evidences from a relationship tree and structure analysis suggest that wild boar in Jeju Island, South Korea have a distinct genetic background from those in mainland Korea. Conclusions Our results reveal a diverse pattern of genetic diversity and the existence of genetic differentiation among wild boar populations inhabiting East Asia. This study highlights the potential contribution of genetic variation of wild boar to the high genetic diversity of local domestic pigs during domestication in East Asia. PMID:25034725

Sequence-structure correlations in silk: Poly-Ala repeat of N. clavipes MaSp1 is naturally optimized at a critical length scale.

PubMed

Bratzel, Graham; Buehler, Markus J

2012-03-01

Spider silk is a self-assembling biopolymer that outperforms many known materials in terms of its mechanical performance despite being constructed from simple and inferior building blocks. While experimental studies have shown that the molecular structure of silk has a direct influence on the stiffness, toughness, and failure strength of silk, few molecular-level analyses of the nanostructure of silk assemblies in particular under variations of genetic sequences have been reported. Here we report atomistic-level structures of the MaSp1 protein from the Nephila Clavipes spider dragline silk sequence, obtained using an in silico approach based on replica exchange molecular dynamics (REMD) and explicit water molecular dynamics. We apply this method to study the effects of a systematic variation of the poly-alanine repeat lengths, a parameter controlled by the genetic makeup of silk, on the resulting molecular structure of silk at the nanoscale. Confirming earlier experimental and computational work, a structural analysis reveals that poly-alanine regions in silk predominantly form distinct and orderly β-sheet crystal domains while disorderly regions are formed by glycine-rich repeats that consist of 3(10)-helix type structures and β-turns. Our predictions are directly validated against experimental data based on dihedral angle pair calculations presented in Ramachandran plots combined with an analysis of the secondary structure content. The key result of our study is our finding of a strong dependence of the resulting silk nanostructure depending on the poly-alanine length. We observe that the wildtype poly-alanine repeat length of six residues defines a critical minimum length that consistently results in clearly defined β-sheet nanocrystals. For poly-alanine lengths below six, the β-sheet nanocrystals are not well-defined or not visible at all, while for poly-alanine lengths at and above six, the characteristic nanocomposite structure of silk emerges with no significant improvement of the quality of the β-sheet nanocrystal geometry. We present a simple biophysical model that explains these computational observations based on the mechanistic insight gained from the molecular simulations. Our findings set the stage for understanding how variations in the spidroin sequence can be used to engineer the structure and thereby functional properties of this biological superfiber, and present a design strategy for the genetic optimization of spidroins for enhanced mechanical properties. The approach used here may also find application in the design of other self-assembled molecular structures and fibers and in particular biologically inspired or completely synthetic systems. Copyright © 2011 Elsevier Ltd. All rights reserved.

Factors associated with plant species richness in a coastal tall-grass prairie

USGS Publications Warehouse

Grace, James B.; Allain, Larry K.; Allen, Charles

2000-01-01

In this study we examine the factors associated with variations in species richness within a remnant tall-grass prairie in order to gain insight into the relative importance of controlling variables. The study area was a small, isolated prairie surrounded by wetlands and located within the coastal prairie region, which occurs along the northwestern Gulf of Mexico coastal plain. Samples were taken along three transects that spanned the prairie. Parameters measured included micro-elevation, soil characteristics, indications of recent disturbance, above-ground biomass (including litter), light penetration through the plant canopy, and species richness. Species richness was found to correlate with micro-elevation, certain soil parameters, and light penetration through the canopy, but not with above-ground biomass. Structural equation analysis was used to assess the direct and indirect effects of micro-elevation, soil properties, disturbance, and indicators of plant abundance on species richness. The results of this analysis showed that observed variations in species richness were primarily associated with variations in environmental effects (from soil and microtopography) and were largely unrelated to variations in measures of plant abundance (biomass and light penetration). These findings suggest that observed variations in species richness in this system primarily resulted from environmental effects on the species pool. These results fit with a growing body of information that suggests that environmental effects on species richness are of widespread importance.

Association mapping unveils favorable alleles for grain iron and zinc concentrations in lentil (Lens culinaris subsp. culinaris)

PubMed Central

Singh, Akanksha; Sharma, Vinay; Dikshit, Harsh Kumar; Aski, Muraleedhar; Kumar, Harish; Thirunavukkarasu, Nepolean; Patil, Basavanagouda S.; Kumar, Shiv; Sarker, Ashutosh

2017-01-01

Lentil is a major cool-season grain legume grown in South Asia, West Asia, and North Africa. Populations in developing countries of these regions have micronutrient deficiencies; therefore, breeding programs should focus more on improving the micronutrient content of food. In the present study, a set of 96 diverse germplasm lines were evaluated at three different locations in India to examine the variation in iron (Fe) and zinc (Zn) concentration and identify simple sequence repeat (SSR) markers that associate with the genetic variation. The genetic variation among genotypes of the association mapping (AM) panel was characterized using a genetic distance-based and a general model-based clustering method. The model-based analysis identified six subpopulations, which satisfactorily explained the genetic structure of the AM panel. AM analysis identified three SSRs (PBALC 13, PBALC 206, and GLLC 563) associated with grain Fe concentration explaining 9% to 11% of phenotypic variation and four SSRs (PBALC 353, SSR 317–1, PLC 62, and PBALC 217) were associated with grain Zn concentration explaining 14%, to 21% of phenotypic variation. These identified SSRs exhibited consistent performance across locations. These candidate SSRs can be used in marker-assisted genetic improvement for developing Fe and Zn fortified lentil varieties. Favorable alleles and promising genotypes identified in this study can be utilized for lentil biofortification. PMID:29161321

Transcriptome analysis of the sea cucumber (Apostichopus japonicus) with variation in individual growth.

PubMed

Gao, Lei; He, Chongbo; Bao, Xiangbo; Tian, Meilin; Ma, Zhen

2017-01-01

The sea cucumber (Apostichopus japonicus) is an economically important aquaculture species in China. However, the serious individual growth variation often caused financial losses to farmers and the genetic mechanisms are poorly understood. In the present study, the extensively analysis at the transcriptome level for individual growth variation in sea cucumber was carried out. A total of 118946 unigenes were assembled from 255861 transcripts, with N50 of 1700. Of all unigenes, about 23% were identified with at least one significant match to known databases. In all four pair of comparison, 1840 genes were found to be expressed differently. Global hypometabolism was found to be occurred in the slow growing population, based on which the hypothesis was raised that growth retardation in individual growth variation of sea cucumber is one type of dormancy which is used to be against to adverse circumstances. Besides, the pathways such as ECM-receptor interaction and focal adhesion were enriched in the maintenance of cell and tissue structure and communication. Further, 76645 SSRs, 765242 SNPs and 146886 ins-dels were detected in the current study providing an extensive set of data for future studies of genetic mapping and selective breeding. In summary, these results will provides deep insight into the molecular basis of individual growth variation in marine invertebrates, and be valuable for understanding the physiological differences of growth process.

Changes of Water Hydrogen Bond Network with Different Externalities

PubMed Central

Zhao, Lin; Ma, Kai; Yang, Zi

2015-01-01

It is crucial to uncover the mystery of water cluster and structural motif to have an insight into the abundant anomalies bound to water. In this context, the analysis of influence factors is an alternative way to shed light on the nature of water clusters. Water structure has been tentatively explained within different frameworks of structural models. Based on comprehensive analysis and summary of the studies on the response of water to four externalities (i.e., temperature, pressure, solutes and external fields), the changing trends of water structure and a deduced intrinsic structural motif are put forward in this work. The variations in physicochemical and biological effects of water induced by each externality are also discussed to emphasize the role of water in our daily life. On this basis, the underlying problems that need to be further studied are formulated by pointing out the limitations attached to current study techniques and to outline prominent studies that have come up recently. PMID:25884333

Impact of anthropogenic pressure on the formation of population structure and genetic diversity of raccoon dog Nyctereutes procyonoides

PubMed Central

Griciuvienė, Loreta; Paulauskas, Algimantas; Radzijevskaja, Jana; Žukauskienė, Judita; Pūraitė, Irma

2016-01-01

Abstract The raccoon dog Nyctereutes procyonoides experienced an active introduction and acclimatization in the European part of Russia followed by its migration to and colonization in the neighboring countries. Eventually, it has spread rapidly into many European countries. N. procyonoides probably invaded Lithuania from the neighboring countries of Belarus and Latvia where the species was introduced. However, the data on genetic diversity and population structure of the raccoon dogs in the recently invaded territories are still scarce. The objectives of this study were to investigate genetic diversity of N. procyonoides in Lithuania after acclimatization, and to assess the impact of anthropogenic pressure on the formation of population structure. A total of 147 N. procyonoides individuals collected from different regions of Lithuania were genotyped using 17 microsatellite markers. The microsatellite analysis of raccoon dogs indicated high levels of genetic diversity within the population. The Bayesian clustering analysis in STRUCTURE identified 4 genetic clusters among sampled raccoon dogs that could not reveal a clear separation between subpopulations. The widespread distribution of raccoon dogs in Lithuania, high level of genetic variation observed within subpopulations, and low level of variation portioned among subpopulations suggest migration and gene flow among locations. The significant correlation between genetic and geographic distances indicated isolation that reflected the distance between locations. The fencing of highways and very intensive traffic could be barriers to gene flow between the western and eastern sampling areas of raccoon dogs. PMID:29491930