Effects of mass variation on structures of differentially rotating polytropic stars

NASA Astrophysics Data System (ADS)

Kumar, Sunil; Saini, Seema; Singh, Kamal Krishan

2018-07-01

A method is proposed for determining equilibrium structures and various physical parameters of differentially rotating polytropic models of stars, taking into account the effect of mass variation inside the star and on its equipotential surfaces. The law of differential rotation has been assumed to be the form of ω2(s) =b1 +b2s2 +b3s4 . The proposed method utilizes the averaging approach of Kippenhahn and Thomas and concepts of Roche-equipotential to incorporate the effects of differential rotation on the equilibrium structures of polytropic stellar models. Mathematical expressions of determining the equipotential surfaces, volume, surface area and other physical parameters are also obtained under the effects of mass variation inside the stars. Some significant conclusions are also drawn.

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.

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.

Population genetic structure and its implications for adaptive variation in memory and the hippocampus on a continental scale in food-caching black-capped chickadees.

PubMed

Pravosudov, V V; Roth, T C; Forister, M L; Ladage, L D; Burg, T M; Braun, M J; Davidson, B S

2012-09-01

Food-caching birds rely on stored food to survive the winter, and spatial memory has been shown to be critical in successful cache recovery. Both spatial memory and the hippocampus, an area of the brain involved in spatial memory, exhibit significant geographic variation linked to climate-based environmental harshness and the potential reliance on food caches for survival. Such geographic variation has been suggested to have a heritable basis associated with differential selection. Here, we ask whether population genetic differentiation and potential isolation among multiple populations of food-caching black-capped chickadees is associated with differences in memory and hippocampal morphology by exploring population genetic structure within and among groups of populations that are divergent to different degrees in hippocampal morphology. Using mitochondrial DNA and 583 AFLP loci, we found that population divergence in hippocampal morphology is not significantly associated with neutral genetic divergence or geographic distance, but instead is significantly associated with differences in winter climate. These results are consistent with variation in a history of natural selection on memory and hippocampal morphology that creates and maintains differences in these traits regardless of population genetic structure and likely associated gene flow. Published 2012. This article is a US Government work and is in the public domain in the USA.

Short-range phenotypic divergence among genetically distinct parapatric populations of an Australian funnel-web spider.

PubMed

Wong, Mark K L; Woodman, James D; Rowell, David M

2017-07-01

Speciation involves divergence at genetic and phenotypic levels. Where substantial genetic differentiation exists among populations, examining variation in multiple phenotypic characters may elucidate the mechanisms by which divergence and speciation unfold. Previous work on the Australian funnel-web spider Atrax sutherlandi Gray (2010; Records of the Australian Museum 62 , 285-392; Mygalomorphae: Hexathelidae: Atracinae) has revealed a marked genetic structure along a 110-kilometer transect, with six genetically distinct, parapatric populations attributable to past glacial cycles. In the present study, we explore variation in three classes of phenotypic characters (metabolic rate, water loss, and morphological traits) within the context of this phylogeographic structuring. Variation in metabolic and water loss rates shows no detectable association with genetic structure; the little variation observed in these rates may be due to the spiders' behavioral adaptations (i.e., burrowing), which buffer the effects of climatic gradients across the landscape. However, of 17 morphological traits measured, 10 show significant variation among genetic populations, in a disjunct manner that is clearly not latitudinal. Moreover, patterns of variation observed for morphological traits serving different organismic functions (e.g., prey capture, burrowing, and locomotion) are dissimilar. In contrast, a previous study of an ecologically similar sympatric spider with little genetic structure indicated a strong latitudinal response in 10 traits over the same range. The congruence of morphological variation with deep phylogeographic structure in Tallaganda's A. sutherlandi populations, as well as the inconsistent patterns of variation across separate functional traits, suggest that the spiders are likely in early stages of speciation, with parapatric populations independently responding to local selective forces.

Major Variations in HIV-1 Capsid Assembly Morphologies Involve Minor Variations in Molecular Structures of Structurally Ordered Protein Segments*

PubMed Central

Lu, Jun-Xia; Bayro, Marvin J.; Tycko, Robert

2016-01-01

We present the results of solid state nuclear magnetic resonance (NMR) experiments on HIV-1 capsid protein (CA) assemblies with three different morphologies, namely wild-type CA (WT-CA) tubes with 35–60 nm diameters, planar sheets formed by the Arg18-Leu mutant (R18L-CA), and R18L-CA spheres with 20–100 nm diameters. The experiments are intended to elucidate molecular structural variations that underlie these variations in CA assembly morphology. We find that multidimensional solid state NMR spectra of 15N,13C-labeled CA assemblies are remarkably similar for the three morphologies, with only small differences in 15N and 13C chemical shifts, no significant differences in NMR line widths, and few differences in the number of detectable NMR cross-peaks. Thus, the pronounced differences in morphology do not involve major differences in the conformations and identities of structurally ordered protein segments. Instead, morphological variations are attributable to variations in conformational distributions within disordered segments, which do not contribute to the solid state NMR spectra. Variations in solid state NMR signals from certain amino acid side chains are also observed, suggesting differences in the intermolecular dimerization interface between curved and planar CA lattices, as well as possible differences in intramolecular helix-helix packing. PMID:27129282

Density Effects on Post-shock Turbulence Structure

NASA Astrophysics Data System (ADS)

Tian, Yifeng; Jaberi, Farhad; Livescu, Daniel; Li, Zhaorui; Michigan State University Collaboration; Los Alamos National Laboratory Collaboration; Texas A&M University-Corpus Christi Collaboration

2017-11-01

The effects of density variations due to mixture composition on post-shock turbulence structure are studied using turbulence-resolving shock-capturing simulations. This work extends the canonical Shock-Turbulence Interaction (STI) problem to involve significant variable density effects. The numerical method has been verified using a series of grid and LIA convergence tests, and is used to generate accurate post-shock turbulence data for a detailed flow study. Density effects on post-shock turbulent statistics are shown to be significant, leading to an increased amplification of turbulent kinetic energy (TKE). Eulerian and Lagrangian analyses show that the increase in the post-shock correlation between rotation and strain is weakened in the case with significant density variations (referred to as the ``multi-fluid'' case). Similar to previous single-fluid results and LIA predictions, the shock wave significantly changes the topology of the turbulent structures, exhibiting a symmetrization of the joint PDF of second and third invariant of the deviatoric part of velocity gradient tensor. In the multi-fluid case, this trend is more significant and mainly manifested in the heavy fluid regions. Lagrangian data are also used to study the evolution of turbulence structure away from the shock wave and assess the accuracy of Lagrangian dynamical models.

Robustness and optimal use of design principles of arthropod exoskeletons studied by ab initio-based multiscale simulations.

PubMed

Nikolov, S; Fabritius, H; Petrov, M; Friák, M; Lymperakis, L; Sachs, C; Raabe, D; Neugebauer, J

2011-02-01

Recently, we proposed a hierarchical model for the elastic properties of mineralized lobster cuticle using (i) ab initio calculations for the chitin properties and (ii) hierarchical homogenization performed in a bottom-up order through all length scales. It has been found that the cuticle possesses nearly extremal, excellent mechanical properties in terms of stiffness that strongly depend on the overall mineral content and the specific microstructure of the mineral-protein matrix. In this study, we investigated how the overall cuticle properties changed when there are significant variations in the properties of the constituents (chitin, amorphous calcium carbonate (ACC), proteins), and the volume fractions of key structural elements such as chitin-protein fibers. It was found that the cuticle performance is very robust with respect to variations in the elastic properties of chitin and fiber proteins at a lower hierarchy level. At higher structural levels, variations of design parameters such as the volume fraction of the chitin-protein fibers have a significant influence on the cuticle performance. Furthermore, we observed that among the possible variations in the cuticle ingredients and volume fractions, the experimental data reflect an optimal use of the structural variations regarding the best possible performance for a given composition due to the smart hierarchical organization of the cuticle design. Copyright © 2011. Elsevier Ltd. All rights reserved.

The effect of the presence of the accessory maxillary ostium on the maxillary sinus.

PubMed

Yenigun, Alper; Fazliogullari, Zeliha; Gun, Cihat; Uysal, Ismihan Ilknur; Nayman, Alaaddin; Karabulut, Ahmet Kagan

2016-12-01

This study was conducted to investigate the presence of the accessory maxillary ostium and its effects on the maxillary sinus, and the concurrent occurrence of morphological variations of neighboring anatomical structures. This study was performed in a tertiary referral center. This is a cross-sectional retrospective study that evaluated coronal CTs of patients to determine the frequency of the accessory maxillary ostium and investigated any simultaneous morphological variations in neighboring anatomical structures. The presence of the accessory maxillary ostium (AMO) plus any concurrent morphological variations of neighboring structures were investigated in 377 patients, with 754 sides. AMO was found to be present in 19.1 % (72/377) of the patients. A concurrent mucus retention cyst was found to be statistically significant on both sides (right side: p = 0.00, left side: p = 0.00), as well as mucosal thickening (right side: p = 0.00, left side: p = 0.00), and maxillary sinusitis (right side: p = 0.04, left side: p = 0.03). No other concurrent variations of statistical significance were detected in the neighboring structures. Our study demonstrated that with the presence of AMO, the likelihood of encountering a mucus retention cyst (48.6 %) had an approximately threefold increase, and that of encountering mucosal thickening (43.0 %) and maxillary sinusitis (29.1 %) had a twofold increase.

Copy number variation of human AMY1 is a minor contributor to variation in salivary amylase expression and activity.

PubMed

Carpenter, Danielle; Mitchell, Laura M; Armour, John A L

2017-02-20

Salivary amylase in humans is encoded by the copy variable gene AMY1 in the amylase gene cluster on chromosome 1. Although the role of salivary amylase is well established, the consequences of the copy number variation (CNV) at AMY1 on salivary amylase protein production are less well understood. The amylase gene cluster is highly structured with a fundamental difference between odd and even AMY1 copy number haplotypes. In this study, we aimed to explore, in samples from 119 unrelated individuals, not only the effects of AMY1 CNV on salivary amylase protein expression and amylase enzyme activity but also whether there is any evidence for underlying difference between the common haplotypes containing odd numbers of AMY1 and even copy number haplotypes. AMY1 copy number was significantly correlated with the variation observed in salivary amylase production (11.7% of variance, P < 0.0005) and enzyme activity (13.6% of variance, P < 0.0005) but did not explain the majority of observed variation between individuals. AMY1-odd and AMY1-even haplotypes showed a different relationship between copy number and expression levels, but the difference was not statistically significant (P = 0.052). Production of salivary amylase is correlated with AMY1 CNV, but the majority of interindividual variation comes from other sources. Long-range haplotype structure may affect expression, but this was not significant in our data.

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

PubMed

Growns, Ivor; Astles, Karen; Gehrke, Peter

2006-03-01

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

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.

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.

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

Pixel structures to compensate nonuniform threshold voltage and mobility of polycrystalline silicon thin-film transistors using subthreshold current for large-size active matrix organic light-emitting diode displays

NASA Astrophysics Data System (ADS)

Na, Jun-Seok; Kwon, Oh-Kyong

2014-01-01

We propose pixel structures for large-size and high-resolution active matrix organic light-emitting diode (AMOLED) displays using a polycrystalline silicon (poly-Si) thin-film transistor (TFT) backplane. The proposed pixel structures compensate the variations of the threshold voltage and mobility of the driving TFT using the subthreshold current. The simulated results show that the emission current error of the proposed pixel structure B ranges from -2.25 to 2.02 least significant bit (LSB) when the variations of the threshold voltage and mobility of the driving TFT are ±0.5 V and ±10%, respectively.

Environmental and spatial drivers of taxonomic, functional, and phylogenetic characteristics of bat communities in human-modified landscapes.

PubMed

Cisneros, Laura M; Fagan, Matthew E; Willig, Michael R

2016-01-01

Assembly of species into communities following human disturbance (e.g., deforestation, fragmentation) may be governed by spatial (e.g., dispersal) or environmental (e.g., niche partitioning) mechanisms. Variation partitioning has been used to broadly disentangle spatial and environmental mechanisms, and approaches utilizing functional and phylogenetic characteristics of communities have been implemented to determine the relative importance of particular environmental (or niche-based) mechanisms. Nonetheless, few studies have integrated these quantitative approaches to comprehensively assess the relative importance of particular structuring processes. We employed a novel variation partitioning approach to evaluate the relative importance of particular spatial and environmental drivers of taxonomic, functional, and phylogenetic aspects of bat communities in a human-modified landscape in Costa Rica. Specifically, we estimated the amount of variation in species composition (taxonomic structure) and in two aspects of functional and phylogenetic structure (i.e., composition and dispersion) along a forest loss and fragmentation gradient that are uniquely explained by landscape characteristics (i.e., environment) or space to assess the importance of competing mechanisms. The unique effects of space on taxonomic, functional and phylogenetic structure were consistently small. In contrast, landscape characteristics (i.e., environment) played an appreciable role in structuring bat communities. Spatially-structured landscape characteristics explained 84% of the variation in functional or phylogenetic dispersion, and the unique effects of landscape characteristics significantly explained 14% of the variation in species composition. Furthermore, variation in bat community structure was primarily due to differences in dispersion of species within functional or phylogenetic space along the gradient, rather than due to differences in functional or phylogenetic composition. Variation among bat communities was related to environmental mechanisms, especially niche-based (i.e., environmental) processes, rather than spatial mechanisms. High variation in functional or phylogenetic dispersion, as opposed to functional or phylogenetic composition, suggests that loss or gain of niche space is driving the progressive loss or gain of species with particular traits from communities along the human-modified gradient. Thus, environmental characteristics associated with landscape structure influence functional or phylogenetic aspects of bat communities by effectively altering the ways in which species partition niche space.

Environmental and spatial drivers of taxonomic, functional, and phylogenetic characteristics of bat communities in human-modified landscapes

PubMed Central

Fagan, Matthew E.; Willig, Michael R.

2016-01-01

Background Assembly of species into communities following human disturbance (e.g., deforestation, fragmentation) may be governed by spatial (e.g., dispersal) or environmental (e.g., niche partitioning) mechanisms. Variation partitioning has been used to broadly disentangle spatial and environmental mechanisms, and approaches utilizing functional and phylogenetic characteristics of communities have been implemented to determine the relative importance of particular environmental (or niche-based) mechanisms. Nonetheless, few studies have integrated these quantitative approaches to comprehensively assess the relative importance of particular structuring processes. Methods We employed a novel variation partitioning approach to evaluate the relative importance of particular spatial and environmental drivers of taxonomic, functional, and phylogenetic aspects of bat communities in a human-modified landscape in Costa Rica. Specifically, we estimated the amount of variation in species composition (taxonomic structure) and in two aspects of functional and phylogenetic structure (i.e., composition and dispersion) along a forest loss and fragmentation gradient that are uniquely explained by landscape characteristics (i.e., environment) or space to assess the importance of competing mechanisms. Results The unique effects of space on taxonomic, functional and phylogenetic structure were consistently small. In contrast, landscape characteristics (i.e., environment) played an appreciable role in structuring bat communities. Spatially-structured landscape characteristics explained 84% of the variation in functional or phylogenetic dispersion, and the unique effects of landscape characteristics significantly explained 14% of the variation in species composition. Furthermore, variation in bat community structure was primarily due to differences in dispersion of species within functional or phylogenetic space along the gradient, rather than due to differences in functional or phylogenetic composition. Discussion Variation among bat communities was related to environmental mechanisms, especially niche-based (i.e., environmental) processes, rather than spatial mechanisms. High variation in functional or phylogenetic dispersion, as opposed to functional or phylogenetic composition, suggests that loss or gain of niche space is driving the progressive loss or gain of species with particular traits from communities along the human-modified gradient. Thus, environmental characteristics associated with landscape structure influence functional or phylogenetic aspects of bat communities by effectively altering the ways in which species partition niche space. PMID:27761338

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.

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

PubMed Central

2013-01-01

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

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...

Intergroup Variation of Social Relationships in Wild Vervet Monkeys: A Dynamic Network Approach.

PubMed

Borgeaud, Christèle; Sosa, Sebastian; Bshary, Redouan; Sueur, Cédric; van de Waal, Erica

2016-01-01

Social network analysis is a powerful tool that enables us to describe and quantify relationships between individuals. So far most of the studies rely on the analyses of various network snapshots, but do not capture changes over time. Here we use a stochastic actor-oriented model (SAOM) to test both the structure and the dynamics of relationships of three groups of wild vervet monkeys. We found that triadic closure (i.e., the friend of a friend is a friend) was significant in all three groups while degree popularity (i.e., the willingness to associate with individuals with high degree of connections) was significant in only two groups (AK, BD). The structure and dynamics of relationships according to the attributes of sex, matrilineand age differed significantly among groups. With respect to the structure, when analyzing the likelihood of bonds according to the different attributes, we found that individuals associate themselves preferably to individuals of the same sex only in two groups (AK, NH), while significant results for attachment to individuals of the same matriline were found also in two groups (BD, NH). With respect to the dynamics, i.e., how quickly relationships are modified, we found in two groups (AK, BD) that females' relationships were more prone to variation than males.' In the BD group, relationships within high-ranking matrilines were less stable than low-ranking ones while in the NH group, juveniles' relationships were also less stable than adults' ones. The intergroup variation indicates that establishing species-specific or even population specific characteristics of social networks for later between-species comparisons will be challenging. Although, such variation could also indicate some methodological issue, we are quite confident that data was collected similarly within the different groups. Our study therefore provides a potential new method to quantify social complexity according to natural demographic variation.

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.

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.

Spectral Structure of Temperature Variations in the Midlatitude Mesopause Region

NASA Astrophysics Data System (ADS)

Perminov, V. I.; Semenov, A. I.; Medvedeva, I. V.; Pertsev, N. N.; Sukhodoev, V. A.

2018-01-01

Long-term series of midnight temperature in the mesopause region have been obtained from spectral observations of hydroxyl airglow emission (OH(6-2) λ840 nm band) at the Tory station (52° N, 103° E) in 2008-2016 and Zvenigorod (56° N, 37° E) station in 2000-2016. On their basis, the Lomb-Scargle spectra of the variations in the period range from 12 days to 11 years have been determined. Estimates of the amplitudes of statistically significant temperature fluctuations are made. The dominant oscillations are the first and second harmonics of the annual variation, the amplitudes of which are 23-24 K and 4-7 K, respectively. The remaining variations, the number of which was 16 for the Tory and 22 for Zvenigorod stations, have small amplitudes (0.5-3 K). Oscillations with combinational frequencies, which arise from modulation of the annual variation harmonics, are observed in a structure of the variation spectra in addition to interannual oscillations (periods from 2 to 11 years) and harmonics of the annual variation (up to its tenth harmonic).

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.

Soil phosphorus depletion and shifts in plant communities change bacterial community structure in a long-term grassland management trial.

PubMed

Adair, Karen L; Wratten, Steve; Lear, Gavin

2013-06-01

Agricultural systems rely on healthy soils and their sustainability requires understanding the long-term impacts of agricultural practices on soils, including microbial communities. We examined the impact of 17 years of land management on soil bacterial communities in a New Zealand randomized-block pasture trial. Significant variation in bacterial community structure related to mowing and plant biomass removal, while nitrogen fertilizer had no effect. Changes in soil chemistry and legume abundance described 52% of the observed variation in the bacterial community structure. Legumes (Trifolium species) were absent in unmanaged plots but increased in abundance with management intensity; 11% of the variation in soil bacterial community structure was attributed to this shift in the plant community. Olsen P explained 10% of the observed heterogeneity, which is likely due to persistent biomass removal resulting in P limitation; Olsen P was significantly lower in plots with biomass removed (14 mg kg(-1) ± 1.3SE) compared with plots that were not mown, or where biomass was left after mowing (32 mg kg(-1) ± 1.6SE). Our results suggest that removal of plant biomass and associated phosphorus, as well as shifts in the plant community, have greater long-term impacts on soil bacterial community structure than application of nitrogen fertilizers. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

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.

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

PubMed

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

2010-09-17

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

Untangling individual variation in natural populations: ecological, genetic and epigenetic correlates of long-term inequality in herbivory.

PubMed

Herrera, C M; Bazaga, P

2011-04-01

Individual variation in ecologically important features of organisms is a crucial element in ecology and evolution, yet disentangling its underlying causes is difficult in natural populations. We applied a genomic scan approach using amplified fragment length polymorphism (AFLP) markers to quantify the genetic basis of long-term individual differences in herbivory by mammals at a wild population of the violet Viola cazorlensis monitored for two decades. In addition, methylation-sensitive amplified polymorphism (MSAP) analyses were used to investigate the association between browsing damage and epigenetic characteristics of individuals, an aspect that has been not previously explored for any wild plant. Structural equation modelling was used to identify likely causal structures linking genotypes, epigenotypes and herbivory. Individuals of V. cazorlensis differed widely in the incidence of browsing mammals over the 20-year study period. Six AFLP markers (1.6% of total) were significantly related to herbivory, accounting altogether for 44% of population-wide variance in herbivory levels. MSAP analyses revealed considerable epigenetic variation among individuals, and differential browsing damage was significantly related to variation in multilocus epigenotypes. In addition, variation across plants in epigenetic characteristics was related to variation in several herbivory-related AFLP markers. Statistical comparison of alternative causal models suggested that individual differences in herbivory are the outcome of a complex causal structure where genotypes and epigenotypes are interconnected and have direct and indirect effects on herbivory. Insofar as methylation states of MSAP markers influential on herbivory are transgenerationally heritable, herbivore-driven evolutionary changes at the study population will involve correlated changes in genotypic and epigenotypic distributions. © 2011 Blackwell Publishing Ltd.

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.

Spatio-temporal variation in age structure and abundance of the endangered snail kite: Pooling across regions masks a declining and aging population

USGS Publications Warehouse

Reichert, Brian E.; Kendall, William L.; Fletcher, Robert J.; Kitchens, Wiley M.

2016-01-01

While variation in age structure over time and space has long been considered important for population dynamics and conservation, reliable estimates of such spatio-temporal variation in age structure have been elusive for wild vertebrate populations. This limitation has arisen because of problems of imperfect detection, the potential for temporary emigration impacting assessments of age structure, and limited information on age. However, identifying patterns in age structure is important for making reliable predictions of both short- and long-term dynamics of populations of conservation concern. Using a multistate superpopulation estimator, we estimated region-specific abundance and age structure (the proportion of individuals within each age class) of a highly endangered population of snail kites for two separate regions in Florida over 17 years (1997–2013). We find that in the southern region of the snail kite—a region known to be critical for the long-term persistence of the species—the population has declined significantly since 1997, and during this time, it has increasingly become dominated by older snail kites (> 12 years old). In contrast, in the northern region—a region historically thought to serve primarily as drought refugia—the population has increased significantly since 2007 and age structure is more evenly distributed among age classes. Given that snail kites show senescence at approximately 13 years of age, where individuals suffer higher mortality rates and lower breeding rates, these results reveal an alarming trend for the southern region. Our work illustrates the importance of accounting for spatial structure when assessing changes in abundance and age distribution and the need for monitoring of age structure in imperiled species.

Variability and similarities in the structural properties of two related Laminaria kelp species

NASA Astrophysics Data System (ADS)

Henry, Pierre-Yves

2018-01-01

Kelps of the genus Laminaria have long been studied and shown to exhibit a seasonal shift in growth and morphology, as nutrients and light levels change during the year. However, the variation of kelp biomechanical properties has been little explored despite the importance of these properties for the interaction of kelp with the flow. Previous research showed that aging does influence the algae biomechanical properties, so this study further investigates the variability of kelp biomechanical properties and morphological characteristics at a given site as a function of the season (growth phase), species, and different kelp parts. Mechanical parameters and morphological characteristics were measured on kelps sampled in winter and summer, and DNA sequencing was used to identify the two related species, L. digitata and L. hyperborea. Descriptive statistics and statistical analysis were used to detect trends in the modulation of kelp mechanical design. Although two distinct species were identified, only minor structural differences were observed between them. The biomechanical properties varied significantly along the kelp, and significant seasonal shifts occurred at the blade level, in relation to the different morphological changes during blade renewal. In general, the variations of the structural properties were mostly linked to the blade growth activity. The absence of significant variation in the mechanical design of the two species highlights the significance of the adaptation to the same local environmental conditions, this adaptation being a key process in vegetation-flow interactions and having implications on the interaction between kelp and hydrodynamics.

Limit on the temporal variation of the fine-structure constant using atomic dysprosium.

PubMed

Cingöz, A; Lapierre, A; Nguyen, A-T; Leefer, N; Budker, D; Lamoreaux, S K; Torgerson, J R

2007-01-26

Over 8 months, we monitored transition frequencies between nearly degenerate, opposite-parity levels in two isotopes of atomic dysprosium (Dy). These frequencies are sensitive to variation of the fine-structure constant (alpha) due to relativistic corrections of opposite sign for the opposite-parity levels. In this unique system, in contrast to atomic-clock comparisons, the difference of the electronic energies of the opposite-parity levels can be monitored directly utilizing a rf electric-dipole transition between them. Our measurements show that the frequency variation of the 3.1-MHz transition in (163)Dy and the 235-MHz transition in (162)Dy are 9.0+/-6.7 Hz/yr and -0.6+/-6.5 Hz/yr, respectively. These results provide a rate of fractional variation of alpha of (-2.7+/-2.6) x 10(-15) yr(-1) (1 sigma) without assumptions on constancy of other fundamental constants, indicating absence of significant variation at the present level of sensitivity.

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.

Environmental Variables Explain Genetic Structure in a Beetle-Associated Nematode

PubMed Central

McGaughran, Angela; Morgan, Katy; Sommer, Ralf J.

2014-01-01

The distribution of a species is a complex expression of its ecological and evolutionary history and integrating population genetic, environmental, and ecological data can provide new insights into the effects of the environment on the population structure of species. Previous work demonstrated strong patterns of genetic differentiation in natural populations of the hermaphroditic nematode Pristionchus pacificus in its La Réunion Island habitat, but gave no clear understanding of the role of the environment in structuring this variation. Here, we present what is to our knowledge the first study to statistically evaluate the role of the environment in shaping the structure and distribution of nematode populations. We test the hypothesis that genetic structure in P. pacificus is influenced by environmental variables, by combining population genetic analyses of microsatellite data from 18 populations and 370 strains, with multivariate statistics on environmental data, and species distribution modelling. We assess and quantify the relative importance of environmental factors (geographic distance, altitude, temperature, precipitation, and beetle host) on genetic variation among populations. Despite the fact that geographic populations of P. pacificus comprise vast genetic diversity sourced from multiple ancestral lineages, we find strong evidence for local associations between environment and genetic variation. Further, we show that significantly more genetic variation in P. pacificus populations is explained by environmental variation than by geographic distances. This supports a strong role for environmental heterogeneity vs. genetic drift in the divergence of populations, which we suggest may be influenced by adaptive forces. PMID:24498073

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.

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.

Geographic variation and genetic structure in Spotted Owls

USGS Publications Warehouse

Haig, Susan M.; Wagner, R.S.; Forsman, E.D.; Mullins, Thomas D.

2001-01-01

We examined genetic variation, population structure, and definition of conservation units in Spotted Owls (Strix occidentalis). Spotted Owls are mostly non-migratory, long-lived, socially monogamous birds that have decreased population viability due to their occupation of highly-fragmented late successional forests in western North America. To investigate potential effects of habitat fragmentation on population structure, we used random amplified polymorphic DNA (RAPD) to examine genetic variation hierarchically among local breeding areas, subregional groups, regional groups, and subspecies via sampling of 21 breeding areas (276 individuals) among the three subspecies of Spotted Owls. Data from 11 variable bands suggest a significant relationship between geographic distance among local breeding groups and genetic distance (Mantel r = 0.53, P < 0.02) although multi-dimensional scaling of three significant axes did not identify significant grouping at any hierarchical level. Similarly, neighbor-joining clustering of Manhattan distances indicated geographic structure at all levels and identified Mexican Spotted Owls as a distinct clade. RAPD analyses did not clearly differentiate Northern Spotted Owls from California Spotted Owls. Among Northern Spotted Owls, estimates of population differentiation (FST) ranged from 0.27 among breeding areas to 0.11 among regions. Concordantly, within-group agreement values estimated via multi-response permutation procedures of Jaccarda??s distances ranged from 0.22 among local sites to 0.11 among regions. Pairwise comparisons of FST and geographic distance within regions suggested only the Klamath region was in equilibrium with respect to gene flow and genetic drift. Merging nuclear data with recent mitochondrial data provides support for designation of an Evolutionary Significant Unit for Mexican Spotted Owls and two overlapping Management Units for Northern and California Spotted Owls.

Microsatellite variation reveals weak genetic structure and retention of genetic variability in threatened Chinook salmon (Oncorhynchus tshawytcha) within a Snake River watershed

Treesearch

Helen Neville; Daniel Isaak; Russell Thurow; Jason Dunham; Bruce Rieman

2007-01-01

Pacific salmon (Oncorhynchus spp.) have been central to the development of management concepts associated with evolutionarily significant units (ESUs), yet there are still relatively few studies of genetic diversity within threatened and endangered ESUs for salmon or other species. We analyzed genetic variation at 10 microsatellite loci to evaluate...

Moral values are associated with individual differences in regional brain volume

PubMed Central

Lewis, G. J.; Kanai, R.; Bates, T. C.; Rees, G.

2012-01-01

Moral sentiment has been hypothesized to reflect evolved adaptations to social living. If so, individual differences in moral values may relate to regional variation in brain structure. We tested this hypothesis in a sample of 70 young, healthy adults examining whether differences on two major dimensions of moral values were significantly associated with regional gray matter volume. The two clusters of moral values assessed were “individualizing” (values of harm/care and fairness), and “binding” (deference to authority, in-group loyalty, and purity/sanctity). Individualizing was positively associated with left dorsomedial prefrontal cortex volume, and negatively associated with bilateral precuneus volume. For binding, a significant positive association was found for bilateral subcallosal gyrus and a trend to significance for the left anterior insula volume. These findings demonstrate that variation in moral sentiment reflects individual differences in brain structure and suggest a biological basis for moral sentiment, distributed across multiple brain regions. PMID:22571458

Moral values are associated with individual differences in regional brain volume.

PubMed

Lewis, Gary J; Kanai, Ryota; Bates, Timothy C; Rees, Geraint

2012-08-01

Moral sentiment has been hypothesized to reflect evolved adaptations to social living. If so, individual differences in moral values may relate to regional variation in brain structure. We tested this hypothesis in a sample of 70 young, healthy adults examining whether differences on two major dimensions of moral values were significantly associated with regional gray matter volume. The two clusters of moral values assessed were "individualizing" (values of harm/care and fairness) and "binding" (deference to authority, in-group loyalty, and purity/sanctity). Individualizing was positively associated with left dorsomedial pFC volume and negatively associated with bilateral precuneus volume. For binding, a significant positive association was found for bilateral subcallosal gyrus and a trend to significance for the left anterior insula volume. These findings demonstrate that variation in moral sentiment reflects individual differences in brain structure and suggest a biological basis for moral sentiment, distributed across multiple brain regions.

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.

Historical explanation of genetic variation in the Mediterranean horseshoe bat Rhinolophus euryale (Chiroptera: Rhinolophidae) inferred from mitochondrial cytochrome-b and D-loop genes in Iran.

PubMed

Najafi, Nargess; Akmali, Vahid; Sharifi, Mozafar

2018-04-26

Molecular phylogeography and species distribution modelling (SDM) suggest that late Quaternary glacial cycles have portrayed a significant role in structuring current population genetic structure and diversity. Based on phylogenetic relationships using Bayesian inference and maximum likelihood of 535 bp mtDNA (D-loop) and 745 bp mtDNA (Cytb) in 62 individuals of the Mediterranean Horseshoe Bat, Rhinolophus euryale, from 13 different localities in Iran we identified two subspecific populations with differing population genetic structure distributed in southern Zagros Mts. and northern Elburz Mts. Analysis of molecular variance (AMOVA) obtained from D-loop sequences indicates that 21.18% of sequence variation is distributed among populations and 10.84% within them. Moreover, a degree of genetic subdivision, mainly attributable to the existence of significant variance among the two regions is shown (θCT = 0.68, p = .005). The positive and significant correlation between geographic and genetic distances (R 2  = 0.28, r = 0.529, p = .000) is obtained following controlling for environmental distance. Spatial distribution of haplotypes indicates that marginal population of the species in southern part of the species range have occupied this section as a glacial refugia. However, this genetic variation, in conjunction with results of the SDM shows a massive postglacial range expansion for R. euryale towards higher latitudes in Iran.

Community structure of aquatic insects in the Esparza River, Costa Rica.

PubMed

Herrera-Vásquez, Jonathan

2009-01-01

This study focused on the structure of the aquatic insect community in spatial and temporal scales in the Esparza River. The river was sampled for one full year throughout 2007. During the dry season low flow months, five sampling points were selected in two different habitats (currents and pools), with five replicates per sample site. During the wet season with peak rain, only the data in the "current habitat" were sampled at each site. Specimens present in the different substrates were collected and preserved in situ. A nested ANOVA was then applied to the data to determine richness and density as the response variables. The variations in temporal and spatial scales were analyzed using width, depth and discharge of the river, and then analyzed using a nested ANOVA. Only a correlation of 51% similarity in richness was found, while in spatial scale, richness showed significant variation between sampling sites, but not between habitats. However, the temporal scale showed significant differences between habitats. Density showed differences between sites and habitats during the dry season in the spatial scale, while in the temporal scale significant variation was found between sampling sites. Width varied between habitats during the dry season, but not between sampling points. Depth showed differences between sampling sites and season. This work studies the importance of community structure of aquatic insects in rivers, and its relevance for the quality of water in rivers and streams.

Suicide by Industry and Occupation: A Structural-change Approach.

ERIC Educational Resources Information Center

Reinhart, George R.; Linden, Leonard L.

1982-01-01

Examined data on suicide rates for males age 20 to 64 by occupation and industry for 1950. Results indicated variations in suicide are related to changes in the size of the group from which significant others are selected. Conclusions support a structural change approach to suicide. (Author)

Spatial variation in mandibular bone elastic modulus and its effect on structural bending stiffness: A test case using the Taï Forest monkeys.

PubMed

Le, Kim N; Marsik, Matthew; Daegling, David J; Duque, Ana; McGraw, William Scott

2017-03-01

We investigated how heterogeneity in material stiffness affects structural stiffness in the cercopithecid mandibular cortical bone. We assessed (1) whether this effect changes the interpretation of interspecific structural stiffness variation across four primate species, (2) whether the heterogeneity is random, and (3) whether heterogeneity mitigates bending stress in the jaw associated with food processing. The sample consisted of Taï Forest, Cote d'Ivoire, monkeys: Cercocebus atys, Piliocolobus badius, Colobus polykomos, and Cercopithecus diana. Vickers indentation hardness samples estimated elastic moduli throughout the cortical bone area of each coronal section of postcanine corpus. For each section, we calculated maximum area moment of inertia, I max (structural mechanical property), under three models of material heterogeneity, as well as spatial autocorrelation statistics (Moran's I, I MORAN ). When the model considered material stiffness variation and spatial patterning, I max decreased and individual ranks based on structural stiffness changed. Rank changes were not significant across models. All specimens showed positive (nonrandom) spatial autocorrelation. Differences in I MORAN were not significant among species, and there were no discernable patterns of autocorrelation within species. Across species, significant local I MORAN was often attributed to proximity of low moduli in the alveolar process and high moduli in the basal process. While our sample did not demonstrate species differences in the degree of spatial autocorrelation of elastic moduli, there may be mechanical effects of heterogeneity (relative strength and rigidity) that do distinguish at the species or subfamilial level (i.e., colobines vs. cercopithecines). The potential connections of heterogeneity to diet and/or taxonomy remain to be discovered. © 2016 Wiley Periodicals, Inc.

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

PubMed

Saroop, Shveta; Kaul, Veenu

2015-07-01

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

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.

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.

Relative contributions of neutral and non-neutral processes to clinal variation in calyx lobe length in the series Sakawanum (Asarum: Aristolochiaceae).

PubMed

Takahashi, Daiki; Teramine, Tsutomu; Sakaguchi, Shota; Setoguchi, Hiroaki

2018-01-25

Clines, the gradual variation in measurable traits along a geographical axis, play a major role in evolution and can contribute to our understanding of the relative roles of selective and neutral process in trait variation. Using genetic and morphological analyses, the relative contributions of neutral and non-neutral processes were explored to infer the evolutionary history of species of the series Sakawanum (genus Asarum), which shows significant clinal variation in calyx lobe length. A total of 27 populations covering the natural geographical distribution of the series Sakawanum were sampled. Six nuclear microsatellite markers were used to investigate genetic structure and genetic diversity. The lengths of calyx lobes of multiple populations were measured to quantify their geographical and taxonomic differentiation. To detect the potential impact of selective pressure, morphological differentiation was compared with genetic differentiation (QCT-FST comparison). Average calyx lobe length of A. minamitanianum was 124.11 mm, while that of A. costatum was 13.80 mm. Though gradually changing along the geographical axis within series, calyx lobe lengths were significantly differentiated among the taxa. Genetic differentiation between taxa was low (FST = 0.099), but a significant geographical structure along the morphological cline was detected. Except for one taxon pair, pairwise QCT values were significantly higher than the neutral genetic measures of FST and G'ST. Divergent selection may have driven the calyx lobe length variation in series Sakawanum taxa, although the underlying mechanism is still not clear. The low genetic differentiation indicates recent divergence and/or gene flows between geographically close taxa. These neutral processes would also affect the clinal variation in calyx lobe lengths. Overall, this study implies the roles of population history and divergent selection in shaping the current cline of a flower trait in the series Sakawanum. © The Author(s) 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Effects of Microstructure Variations on Macroscopic Terahertz Metafilm Properties

DOE PAGES

O'Hara, John F.; Smirnova, Evgenya; Azad, Abul K.; ...

2007-01-01

The properties of planar, single-layer metamaterials, or metafilms, are studied by varying the structural components of the split-ring resonators used to comprise the overall medium. Measurements and simulations reveal how minor design variations in split-ring resonator structures can result in significant changes in the macroscopic properties of the metafilm. A transmission-line/circuit model is also used to clarify some of the behavior and design limitations of the metafilms. Though our results are illustrated in the terahertz frequency range, the work has broader implications, particularly with respect to filtering, modulation, and switching devices.

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

PubMed

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

2005-08-01

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

Metacommunity composition of web-spiders in a fragmented neotropical forest: relative importance of environmental and spatial effects.

PubMed

Baldissera, Ronei; Rodrigues, Everton N L; Hartz, Sandra M

2012-01-01

The distribution of beta diversity is shaped by factors linked to environmental and spatial control. The relative importance of both processes in structuring spider metacommunities has not yet been investigated in the Atlantic Forest. The variance explained by purely environmental, spatially structured environmental, and purely spatial components was compared for a metacommunity of web spiders. The study was carried out in 16 patches of Atlantic Forest in southern Brazil. Field work was done in one landscape mosaic representing a slight gradient of urbanization. Environmental variables encompassed plot- and patch-level measurements and a climatic matrix, while principal coordinates of neighbor matrices (PCNMs) acted as spatial variables. A forward selection procedure was carried out to select environmental and spatial variables influencing web-spider beta diversity. Variation partitioning was used to estimate the contribution of pure environmental and pure spatial effects and their shared influence on beta-diversity patterns, and to estimate the relative importance of selected environmental variables. Three environmental variables (bush density, land use in the surroundings of patches, and shape of patches) and two spatial variables were selected by forward selection procedures. Variation partitioning revealed that 15% of the variation of beta diversity was explained by a combination of environmental and PCNM variables. Most of this variation (12%) corresponded to pure environmental and spatially environmental structure. The data indicated that (1) spatial legacy was not important in explaining the web-spider beta diversity; (2) environmental predictors explained a significant portion of the variation in web-spider composition; (3) one-third of environmental variation was due to a spatial structure that jointly explains variation in species distributions. We were able to detect important factors related to matrix management influencing the web-spider beta-diversity patterns, which are probably linked to historical deforestation events.

Genetic diversity and population structure of Prunus mira (Koehne) from the Tibet plateau in China and recommended conservation strategies

PubMed Central

Bao, Wenquan; Li, Tiezhu; Liu, Huimin; Jiang, Zhongmao; Zhu, Xuchun; Du, Hongyan; Bai, Yu-e

2017-01-01

Prunus mira Koehne, an important economic fruit crop with high breeding and medicinal values, and an ancestral species of many cultivated peach species, has recently been declared an endangered species. However, basic information about genetic diversity, population structure, and morphological variation is still limited for this species. In this study, we sampled 420 P. mira individuals from 21 wild populations in the Tibet plateau to conduct a comprehensive analysis of genetic and morphological characteristics. The results of molecular analyses based on simple sequence repeat (SSR) markers indicated moderate genetic diversity and inbreeding (A = 3.8, Ae = 2.5, He = 0.52, Ho = 0.44, I = 0.95, FIS = 0.17) within P. mira populations. STRUCTURE, GENELAND, and phylogenetic analyses assigned the 21 populations to three genetic clusters that were moderately correlated with geographic altitudes, and this may have resulted from significantly different climatic and environmental factors at different altitudinal ranges. Significant isolation-by-distance was detected across the entire distribution of P. mira populations, but geographic altitude might have more significant effects on genetic structure than geographic distance in partial small-scale areas. Furthermore, clear genetic structure, high genetic differentiation, and restricted gene flow were detected between pairwise populations from different geographic groups, indicating that geographic barriers and genetic drift have significant effects on P. mira populations. Analyses of molecular variance based on the SSR markers indicated high variation (83.7% and 81.7%), whereas morphological analyses revealed low variation (1.30%–36.17%) within the populations. Large and heavy fruits were better adapted than light fruits and nutlets to poor climate and environmental conditions at high altitudes. Based on the results of molecular and morphological analyses, we classified the area into three conservation units and proposed several conservation strategies for wild P. mira populations in the Tibet plateau. PMID:29186199

Genetic diversity and population structure of Prunus mira (Koehne) from the Tibet plateau in China and recommended conservation strategies.

PubMed

Bao, Wenquan; Wuyun, Tana; Li, Tiezhu; Liu, Huimin; Jiang, Zhongmao; Zhu, Xuchun; Du, Hongyan; Bai, Yu-E

2017-01-01

Prunus mira Koehne, an important economic fruit crop with high breeding and medicinal values, and an ancestral species of many cultivated peach species, has recently been declared an endangered species. However, basic information about genetic diversity, population structure, and morphological variation is still limited for this species. In this study, we sampled 420 P. mira individuals from 21 wild populations in the Tibet plateau to conduct a comprehensive analysis of genetic and morphological characteristics. The results of molecular analyses based on simple sequence repeat (SSR) markers indicated moderate genetic diversity and inbreeding (A = 3.8, Ae = 2.5, He = 0.52, Ho = 0.44, I = 0.95, FIS = 0.17) within P. mira populations. STRUCTURE, GENELAND, and phylogenetic analyses assigned the 21 populations to three genetic clusters that were moderately correlated with geographic altitudes, and this may have resulted from significantly different climatic and environmental factors at different altitudinal ranges. Significant isolation-by-distance was detected across the entire distribution of P. mira populations, but geographic altitude might have more significant effects on genetic structure than geographic distance in partial small-scale areas. Furthermore, clear genetic structure, high genetic differentiation, and restricted gene flow were detected between pairwise populations from different geographic groups, indicating that geographic barriers and genetic drift have significant effects on P. mira populations. Analyses of molecular variance based on the SSR markers indicated high variation (83.7% and 81.7%), whereas morphological analyses revealed low variation (1.30%-36.17%) within the populations. Large and heavy fruits were better adapted than light fruits and nutlets to poor climate and environmental conditions at high altitudes. Based on the results of molecular and morphological analyses, we classified the area into three conservation units and proposed several conservation strategies for wild P. mira populations in the Tibet plateau.

Soil respiration across a permafrost transition zone: spatial structure and environmental correlates

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

Stegen, James C.; Anderson, Carolyn G.; Bond-Lamberty, Ben

Soil respiration is a key ecosystem function whereby shifts in respiration rates can shift systems from carbon sinks to sources. Soil respiration in permafrost-associated systems is particularly important given climate change driven permafrost thaw that leads to significant uncertainty in resulting ecosystem carbon dynamics. Here we characterize the spatial structure and environmental drivers of soil respiration across a permafrost transition zone. We find that soil respiration is characterized by a non-linear threshold that occurs at active-layer depths greater than 140 cm. We also find that within each season, tree basal area is a dominant driver of soil respiration regardless of spatial scale, but onlymore » in spatial domains with significant spatial variability in basal area. Our analyses further show that spatial variation (the coefficient of variation) and mean-variance power-law scaling of soil respiration in our boreal system are consistent with previous work in other ecosystems (e.g., tropical forests) and in population ecology, respectively. Comparing our results to those in other ecosystems suggests that temporally stable features such as tree-stand structure are often primary drivers of spatial variation in soil respiration. If so, this provides an opportunity to better estimate the magnitude and spatial variation in soil respiration through remote sensing. Finally, combining such an approach with broader knowledge of thresholding behavior – here related to active layer depth – would provide empirical constraints on models aimed at predicting ecosystem responses to ongoing permafrost thaw.« less

Soil respiration across a permafrost transition zone: spatial structure and environmental correlates

DOE PAGES

Stegen, James C.; Anderson, Carolyn G.; Bond-Lamberty, Ben; ...

2017-09-28

Soil respiration is a key ecosystem function whereby shifts in respiration rates can shift systems from carbon sinks to sources. Soil respiration in permafrost-associated systems is particularly important given climate change driven permafrost thaw that leads to significant uncertainty in resulting ecosystem carbon dynamics. Here we characterize the spatial structure and environmental drivers of soil respiration across a permafrost transition zone. We find that soil respiration is characterized by a non-linear threshold that occurs at active-layer depths greater than 140 cm. We also find that within each season, tree basal area is a dominant driver of soil respiration regardless of spatial scale, but onlymore » in spatial domains with significant spatial variability in basal area. Our analyses further show that spatial variation (the coefficient of variation) and mean-variance power-law scaling of soil respiration in our boreal system are consistent with previous work in other ecosystems (e.g., tropical forests) and in population ecology, respectively. Comparing our results to those in other ecosystems suggests that temporally stable features such as tree-stand structure are often primary drivers of spatial variation in soil respiration. If so, this provides an opportunity to better estimate the magnitude and spatial variation in soil respiration through remote sensing. Finally, combining such an approach with broader knowledge of thresholding behavior – here related to active layer depth – would provide empirical constraints on models aimed at predicting ecosystem responses to ongoing permafrost thaw.« less

Population genetic studies of the polar bear (Ursus maritimus): A summary of available data and interpretation of results

USGS Publications Warehouse

Scribner, Kim T.; Garner, G.W.; Amstrup, Steven C.; Cronin, M.A.; Dizon, Andrew E.; Chivers, Susan J.; Perrin, William F.

1997-01-01

A summary of existing population genetics literature is presented for polar bears (Ursus maritimus) and interpreted in the context of the species' life-history characteristics and regional heterogeneity in environmental regimes and movement patterns. Several nongenetic data sets including morphology, contaminant levels, geographic variation in reproductive characteristics, and the location and distribution of open-water foraging habitat suggest some degree of spatial structuring. Eleven populations are recognized by the IUCN Polar Bear Specialist Group. Few genetics studies exist for polar bears. Interpretation and generalizations of regional variation in intra- and interpopulation levels of genetic variability are confounded by the paucity of data from many regions and by the fact that no single informative genetic marker has been employed in multiple regions. Early allozyme studies revealed comparatively low levels of genetic variability and no compelling evidence of spatial structuring. Studies employing mitochondrial DNA (mtDNA) also found low levels of genetic variation, a lack of phylogenetic structure, and no significant evidence for spatial variation in haplotype frequency. In contrast, microsatellite variable number of tandem repeat (VNTR) loci have revealed significant heterogeneity in allele frequency among populations in the Canadian Arctic. These regions are characterized by archipelgic patterns of sea-ice movements. Further studies using highly polymorphic loci are needed in regions characterized by greater polar bear dependency on pelagic sea-ice movements and in regions for which no data currently exist (i.e., Laptev and Novaya Zemlya/Franz Josef).

Soil respiration across a permafrost transition zone: spatial structure and environmental correlates

NASA Astrophysics Data System (ADS)

Stegen, James C.; Anderson, Carolyn G.; Bond-Lamberty, Ben; Crump, Alex R.; Chen, Xingyuan; Hess, Nancy

2017-09-01

Soil respiration is a key ecosystem function whereby shifts in respiration rates can shift systems from carbon sinks to sources. Soil respiration in permafrost-associated systems is particularly important given climate change driven permafrost thaw that leads to significant uncertainty in resulting ecosystem carbon dynamics. Here we characterize the spatial structure and environmental drivers of soil respiration across a permafrost transition zone. We find that soil respiration is characterized by a non-linear threshold that occurs at active-layer depths greater than 140 cm. We also find that within each season, tree basal area is a dominant driver of soil respiration regardless of spatial scale, but only in spatial domains with significant spatial variability in basal area. Our analyses further show that spatial variation (the coefficient of variation) and mean-variance power-law scaling of soil respiration in our boreal system are consistent with previous work in other ecosystems (e.g., tropical forests) and in population ecology, respectively. Comparing our results to those in other ecosystems suggests that temporally stable features such as tree-stand structure are often primary drivers of spatial variation in soil respiration. If so, this provides an opportunity to better estimate the magnitude and spatial variation in soil respiration through remote sensing. Combining such an approach with broader knowledge of thresholding behavior - here related to active layer depth - would provide empirical constraints on models aimed at predicting ecosystem responses to ongoing permafrost thaw.

Environmental heterogeneity explains the genetic structure of Continental and Mediterranean populations of Fraxinus angustifolia Vahl.

PubMed

Temunović, Martina; Franjić, Jozo; Satovic, Zlatko; Grgurev, Marin; Frascaria-Lacoste, Nathalie; Fernández-Manjarrés, Juan F

2012-01-01

Tree species with wide distributions often exhibit different levels of genetic structuring correlated to their environment. However, understanding how environmental heterogeneity influences genetic variation is difficult because the effects of gene flow, drift and selection are confounded. We investigated the genetic variation and its ecological correlates in a wind-pollinated Mediterranean tree species, Fraxinus angustifolia Vahl, within a recognised glacial refugium in Croatia. We sampled 11 populations from environmentally divergent habitats within the Continental and Mediterranean biogeographical regions. We combined genetic data analyses based on nuclear microsatellite loci, multivariate statistics on environmental data and ecological niche modelling (ENM). We identified a geographic structure with a high genetic diversity and low differentiation in the Continental region, which contrasted with the significantly lower genetic diversity and higher population divergence in the Mediterranean region. The positive and significant correlation between environmental and genetic distances after controlling for geographic distance suggests an important influence of ecological divergence of the sites in shaping genetic variation. The ENM provided support for niche differentiation between the populations from the Continental and Mediterranean regions, suggesting that contemporary populations may represent two divergent ecotypes. Ecotype differentiation was also supported by multivariate environmental and genetic distance analyses. Our results suggest that despite extensive gene flow in continental areas, long-term stability of heterogeneous environments have likely promoted genetic divergence of ashes in this region and can explain the present-day genetic variation patterns of these ancient populations.

Environmental Heterogeneity Explains the Genetic Structure of Continental and Mediterranean Populations of Fraxinus angustifolia Vahl

PubMed Central

Temunović, Martina; Franjić, Jozo; Satovic, Zlatko; Grgurev, Marin; Frascaria-Lacoste, Nathalie; Fernández-Manjarrés, Juan F.

2012-01-01

Tree species with wide distributions often exhibit different levels of genetic structuring correlated to their environment. However, understanding how environmental heterogeneity influences genetic variation is difficult because the effects of gene flow, drift and selection are confounded. We investigated the genetic variation and its ecological correlates in a wind-pollinated Mediterranean tree species, Fraxinus angustifolia Vahl, within a recognised glacial refugium in Croatia. We sampled 11 populations from environmentally divergent habitats within the Continental and Mediterranean biogeographical regions. We combined genetic data analyses based on nuclear microsatellite loci, multivariate statistics on environmental data and ecological niche modelling (ENM). We identified a geographic structure with a high genetic diversity and low differentiation in the Continental region, which contrasted with the significantly lower genetic diversity and higher population divergence in the Mediterranean region. The positive and significant correlation between environmental and genetic distances after controlling for geographic distance suggests an important influence of ecological divergence of the sites in shaping genetic variation. The ENM provided support for niche differentiation between the populations from the Continental and Mediterranean regions, suggesting that contemporary populations may represent two divergent ecotypes. Ecotype differentiation was also supported by multivariate environmental and genetic distance analyses. Our results suggest that despite extensive gene flow in continental areas, long-term stability of heterogeneous environments have likely promoted genetic divergence of ashes in this region and can explain the present-day genetic variation patterns of these ancient populations. PMID:22905171

On Three-dimensional Structures in Relativistic Hydrodynamic Jets

NASA Astrophysics Data System (ADS)

Hardee, Philip E.

2000-04-01

The appearance of wavelike helical structures on steady relativistic jets is studied using a normal mode analysis of the linearized fluid equations. Helical structures produced by the normal modes scale relative to the resonant (most unstable) wavelength and not with the absolute wavelength. The resonant wavelength of the normal modes can be less than the jet radius even on highly relativistic jets. High-pressure regions helically twisted around the jet beam may be confined close to the jet surface, penetrate deeply into the jet interior, or be confined to the jet interior. The high-pressure regions range from thin and ribbon-like to thick and tubelike depending on the mode and wavelength. The wave speeds can be significantly different at different wavelengths but are less than the flow speed. The highest wave speed for the jets studied has a Lorentz factor somewhat more than half that of the underlying flow speed. A maximum pressure fluctuation criterion found through comparison between theory and a set of relativistic axisymmetric jet simulations is applied to estimate the maximum amplitudes of the helical, elliptical, and triangular normal modes. Transverse velocity fluctuations for these asymmetric modes are up to twice the amplitude of those associated with the axisymmetric pinch mode. The maximum amplitude of jet distortions and the accompanying velocity fluctuations at, for example, the resonant wavelength decreases as the Lorentz factor increases. Long-wavelength helical surface mode and shorter wavelength helical first body mode generated structures should be the most significant. Emission from high-pressure regions as they twist around the jet beam can vary significantly as a result of angular variation in the flow direction associated with normal mode structures if they are viewed at about the beaming angle θ=1/γ. Variation in the Doppler boost factor can lead to brightness asymmetries by factors up to 6 as long-wavelength helical structure produced by the helical surface mode winds around the jet. Higher order surface modes and first body modes produce less variation. Angular variation in the flow direction associated with the helical mode appears consistent with precessing jet models that have been proposed to explain the variability in 3C 273 and BL Lac object AO 0235+164. In particular, cyclic angular variation in the flow direction produced by the normal modes could produce the activity seen in BL Lac object OJ 287. Jet precession provides a mechanism for triggering the helical modes on multiple length scales, e.g., the galactic superluminal GRO J1655-40.

Climate and Edaphic Controls on Humid Tropical Forest Tree Height

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

Genetics of Central Valley O. mykiss populations: drainage and watershed scale analyses

USGS Publications Warehouse

Nielsen, Jennifer L.; Pavey, Scott A.; Wiacek, Talia; Williams, Ian S.

2005-01-01

Genetic variation at 11 microsatellite loci described population genetic structure for Oncorhynchus mykiss in the Central Valley, California. Spatial and temporal variation was examined as well as relationships between hatchery and putative natural spawning anadromous stocks. Genetic diversity was analyzed at two distinct spatial scales: fine-scale within drainage for five populations on Clear Creek; between and among drainage diversity for 23 populations. Significant regional spatial structure was apparent, both within Clear Creek and among rainbow trout populations throughout the Central Valley. Significant differences in allelic frequencies were found among most river or drainage systems. Less than 1% of the molecular variance could be attributed to differences found between drainages. Hatchery populations were shown to carry similar genetic diversity to geographically proximate wild populations. Central Valley M = 0.626 (below the M < 0.68 threshold) supported recent population reductions within the Central Valley. However, average estimated effective population size was relatively high (Ne = 5066). Significant allelic differences were found in rainbow trout collected above and below impassable dams on the American, Yuba, Stanislaus and Tuolumne rivers. Rainbow trout sampled in Spring Creek were extremely bottlenecked with allelic variation at only two loci and an estimated effective population size of 62, suggesting some local freshwater O. mykiss stocks may be declining rapidly. These data support significant genetic population structure for steelhead and rainbow trout populations within the Central Valley across multiple scales. Careful consideration of this genetic diversity and its distribution across the landscape should be part of future conservation and restoration efforts. 

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.

Genetic and epigenetic differences associated with environmental gradients in replicate populations of two salt marsh perennials.

PubMed

Foust, C M; Preite, V; Schrey, A W; Alvarez, M; Robertson, M H; Verhoeven, K J F; Richards, C L

2016-04-01

While traits and trait plasticity are partly genetically based, investigating epigenetic mechanisms may provide more nuanced understanding of the mechanisms underlying response to environment. Using AFLP and methylation-sensitive AFLP, we tested the hypothesis that differentiation to habitats along natural salt marsh environmental gradients occurs at epigenetic, but not genetic loci in two salt marsh perennials. We detected significant genetic and epigenetic structure among populations and among subpopulations, but we found multilocus patterns of differentiation to habitat type only in epigenetic variation for both species. In addition, more epigenetic than genetic loci were correlated with habitat in both species. When we analysed genetic and epigenetic variation simultaneously with partial Mantel, we found no correlation between genetic variation and habitat and a significant correlation between epigenetic variation and habitat in Spartina alterniflora. In Borrichia frutescens, we found significant correlations between epigenetic and/or genetic variation and habitat in four of five populations when populations were analysed individually, but there was no significant correlation between genetic or epigenetic variation and habitat when analysed jointly across the five populations. These analyses suggest that epigenetic mechanisms are involved in the response to salt marsh habitats, but also that the relationships among genetic and epigenetic variation and habitat vary by species. Site-specific conditions may also cloud our ability to detect response in replicate populations with similar environmental gradients. Future studies analysing sequence data and the correlation between genetic variation and DNA methylation will be powerful to identify the contributions of genetic and epigenetic response to environmental gradients. © 2016 John Wiley & Sons Ltd.

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.

The Earth's Gravity and Its Geological Significance.

ERIC Educational Resources Information Center

Cook, A. H.

1980-01-01

Discussed is the earth's gravity and its geological significance. Variations of gravity around the earth can be produced by a great variety of possible distributions of density within the earth. Topics discussed include isostasy, local structures, geological exploration, change of gravity in time, and gravity on the moon and planets. (DS)

Effects of population succession on demographic and genetic processes: predictions and tests in the daylily Hemerocallis thunbergii (Liliaceae).

PubMed

Chung, Mi Yoon; Nason, John D; Chung, Myong Gi

2007-07-01

Spatial genetic structure within plant populations is influenced by variation in demographic processes through space and time, including a population's successional status. To determine how demographic structure and fine-scale genetic structure (FSGS) change with stages in a population's successional history, we studied Hemerocallis thunbergii (Liliaceae), a nocturnal flowering and hawkmoth-pollinated herbaceous perennial with rapid population turnover dynamics. We examined nine populations assigned to three successive stages of population succession: expansion, maturation, and senescence. We developed stage-specific expectations for within-population demographic and genetic structure, and then for each population quantified the spatial aggregation of individuals and genotypes using spatial autocorrelation methods (nonaccumulative O-ring and kinship statistics, respectively), and at the landscape level measured inbreeding and genetic structure using Wright's F-statistics. Analyses using the O-ring statistic revealed significant aggregation of individuals at short spatial scales in expanding and senescing populations, in particular, which may reflect restricted seed dispersal around maternal individuals combined with relatively low local population densities at these stages. Significant FSGS was found for three of four expanding, no mature, and only one senescing population, a pattern generally consistent with expectations of successional processes. Although allozyme genetic diversity was high within populations (mean %P = 78.9 and H(E) = 0.281), landscape-level differentiation among sites was also high (F(ST) = 0.166) and all populations exhibited a significant deficit of heterozygotes relative to Hardy-Weinberg expectations (range F = 0.201-0.424, mean F(IS) = 0.321). Within populations, F was not correlated with the degree of FSGS, thus suggesting inbreeding due primarily to selfing as opposed to mating among close relatives in spatially structured populations. Our results demonstrate considerable variation in the spatial distribution of individuals and patterns and magnitude of FSGS in H. thunbergii populations across the landscape. This variation is generally consistent with succession-stage-specific differences in ecological processes operating within these populations.

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

NASA Technical Reports Server (NTRS)

Wilson, G. R.

1991-01-01

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

An experimental test of the contributions and condition dependence of microstructure and carotenoids in yellow plumage coloration

PubMed Central

Shawkey, Matthew D; Hill, Geoffrey E; McGraw, Kevin J; Hood, Wendy R; Huggins, Kristal

2006-01-01

A combination of structural and pigmentary components is responsible for many of the colour displays of animals. Despite the ubiquity of this type of coloration, neither the relative contribution of structures and pigments to variation in such colour displays nor the relative effects of extrinsic factors on the structural and pigment-based components of such colour has been determined. Understanding the sources of colour variation is important because structures and pigments may convey different information to conspecifics. In an experiment on captive American goldfinches Carduelis tristis, we manipulated two parameters, carotenoid availability and food availability, known to affect the expression of carotenoid pigments in a full-factorial design. Yellow feathers from these birds were then analysed in two ways. First, we used full-spectrum spectrometry and high-performance liquid chromatography to examine the extent to which variation in white structural colour and total carotenoid content was associated with variation in colour properties of feathers. The carotenoid content of yellow feathers predicted two colour parameters (principal component 1—representing high values of ultraviolet and yellow chroma and low values of violet–blue chroma—and hue). Two different colour parameters (violet–blue and yellow chroma) from white de-pigmented feathers, as well as carotenoid content, predicted reflectance measurements from yellow feathers. Second, we determined the relative effects of our experimental manipulations on white structural colour and yellow colour. Carotenoid availability directly affected yellow colour, while food availability affected it only in combination with carotenoid availability. None of our manipulations had significant effects on the expression of white structural colour. Our results suggest that the contribution of microstructures to variation in the expression of yellow coloration is less than the contribution of carotenoid content, and that carotenoid deposition is more dependent on extrinsic variability than is the production of white structural colour. PMID:17015356

An experimental test of the contributions and condition dependence of microstructure and carotenoids in yellow plumage coloration.

PubMed

Shawkey, Matthew D; Hill, Geoffrey E; McGraw, Kevin J; Hood, Wendy R; Huggins, Kristal

2006-12-07

A combination of structural and pigmentary components is responsible for many of the colour displays of animals. Despite the ubiquity of this type of coloration, neither the relative contribution of structures and pigments to variation in such colour displays nor the relative effects of extrinsic factors on the structural and pigment-based components of such colour has been determined. Understanding the sources of colour variation is important because structures and pigments may convey different information to conspecifics. In an experiment on captive American goldfinches Carduelis tristis, we manipulated two parameters, carotenoid availability and food availability, known to affect the expression of carotenoid pigments in a full-factorial design. Yellow feathers from these birds were then analysed in two ways. First, we used full-spectrum spectrometry and high-performance liquid chromatography to examine the extent to which variation in white structural colour and total carotenoid content was associated with variation in colour properties of feathers. The carotenoid content of yellow feathers predicted two colour parameters (principal component 1--representing high values of ultraviolet and yellow chroma and low values of violet-blue chroma-and hue). Two different colour parameters (violet-blue and yellow chroma) from white de-pigmented feathers, as well as carotenoid content, predicted reflectance measurements from yellow feathers. Second, we determined the relative effects of our experimental manipulations on white structural colour and yellow colour. Carotenoid availability directly affected yellow colour, while food availability affected it only in combination with carotenoid availability. None of our manipulations had significant effects on the expression of white structural colour. Our results suggest that the contribution of microstructures to variation in the expression of yellow coloration is less than the contribution of carotenoid content, and that carotenoid deposition is more dependent on extrinsic variability than is the production of white structural colour.

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.

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

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.

Effects of bioaugmentation in para-nitrophenol-contaminated soil on the abundance and community structure of ammonia-oxidizing bacteria and archaea.

PubMed

Chi, Xiang-Qun; Liu, Kun; Zhou, Ning-Yi

2015-07-01

Pseudomonas sp. strain WBC-3 mineralizes the priority pollutant para-nitrophenol (PNP) and releases nitrite (NO2 (-)), which is probably involved in the nitrification. In this study, the rate of PNP removal in soil bioaugmented with strain WBC-3 was more accelerated with more NO2 (-) accumulation than in uninoculated soils. Strain WBC-3 survived well and remained stable throughout the entire period. Real-time polymerase chain reaction (real-time PCR) indicated a higher abundance of ammonia-oxidizing bacteria (AOB) than ammonia-oxidizing archaea (AOA), suggesting that AOB played a greater role in nitrification in the original sampled soil. Real-time PCR and multivariate analysis based on the denaturing gradient gel electrophoresis showed that PNP contamination did not significantly alter the abundance and community structure of ammonia oxidizers except for inhibiting the AOB abundance. Bioaugmentation of PNP-contaminated soil showed a significant effect on AOB populations and community structure as well as AOA populations. In addition, ammonium (NH4 (+)) variation was found to be the primary factor affecting the AOB community structure, as determined by the correlation between the community structures of ammonia oxidizers and environmental factors. It is here proposed that the balance between archaeal and bacterial ammonia oxidation could be influenced significantly by the variation in NH4 (+) levels as caused by bioaugmentation of contaminated soil by a pollutant containing nitrogen.

Effects of grazing on spatiotemporal variations in community structure and ecosystem function on the grasslands of Inner Mongolia, China.

PubMed

Su, Rina; Cheng, Junhui; Chen, Dima; Bai, Yongfei; Jin, Hua; Chao, Lumengqiqige; Wang, Zhijun; Li, Junqing

2017-02-28

Grasslands worldwide are suffering from overgrazing, which greatly alters plant community structure and ecosystem functioning. However, the general effects of grazing on community structure and ecosystem function at spatial and temporal scales has rarely been examined synchronously in the same grassland. Here, during 2011-2013, we investigated community structure (cover, height, and species richness) and aboveground biomass (AGB) using 250 paired field sites (grazed vs. fenced) across three vegetation types (meadow, typical, and desert steppes) on the Inner Mongolian Plateau. Grazing, vegetation type, and year all had significant effects on cover, height, species richness, and AGB, although the primary factor influencing variations in these variables was vegetation type. Spatially, grazing significantly reduced the measured variables in meadow and typical steppes, whereas no changes were observed in desert steppe. Temporally, both linear and quadratic relationships were detected between growing season precipitation and cover, height, richness, or AGB, although specific relationships varied among observation years and grazing treatments. In each vegetation type, the observed community properties were significantly correlated with each other, and the shape of the relationship was unaffected by grazing treatment. These findings indicate that vegetation type is the most important factor to be considered in grazing management for this semi-arid grassland.

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

PubMed

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

2018-05-18

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

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.

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

PubMed

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

2017-05-04

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

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

Patterns of Individual Variation in Visual Pathway Structure and Function in the Sighted and Blind

PubMed Central

Datta, Ritobrato; Benson, Noah C.; Prasad, Sashank; Jacobson, Samuel G.; Cideciyan, Artur V.; Bridge, Holly; Watkins, Kate E.; Butt, Omar H.; Dain, Aleksandra S.; Brandes, Lauren; Gennatas, Efstathios D.

2016-01-01

Many structural and functional brain alterations accompany blindness, with substantial individual variation in these effects. In normally sighted people, there is correlated individual variation in some visual pathway structures. Here we examined if the changes in brain anatomy produced by blindness alter the patterns of anatomical variation found in the sighted. We derived eight measures of central visual pathway anatomy from a structural image of the brain from 59 sighted and 53 blind people. These measures showed highly significant differences in mean size between the sighted and blind cohorts. When we examined the measurements across individuals within each group we found three clusters of correlated variation, with V1 surface area and pericalcarine volume linked, and independent of the thickness of V1 cortex. These two clusters were in turn relatively independent of the volumes of the optic chiasm and lateral geniculate nucleus. This same pattern of variation in visual pathway anatomy was found in the sighted and the blind. Anatomical changes within these clusters were graded by the timing of onset of blindness, with those subjects with a post-natal onset of blindness having alterations in brain anatomy that were intermediate to those seen in the sighted and congenitally blind. Many of the blind and sighted subjects also contributed functional MRI measures of cross-modal responses within visual cortex, and a diffusion tensor imaging measure of fractional anisotropy within the optic radiations and the splenium of the corpus callosum. We again found group differences between the blind and sighted in these measures. The previously identified clusters of anatomical variation were also found to be differentially related to these additional measures: across subjects, V1 cortical thickness was related to cross-modal activation, and the volume of the optic chiasm and lateral geniculate was related to fractional anisotropy in the visual pathway. Our findings show that several of the structural and functional effects of blindness may be reduced to a smaller set of dimensions. It also seems that the changes in the brain that accompany blindness are on a continuum with normal variation found in the sighted. PMID:27812129

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.

Fine-scale genetic structure of bull trout at the southern limit of their distribution

Treesearch

A. Whiteley; P. Spruell; B. Rieman; F. Allendorf

2006-01-01

We used six polymorphic microsatellite loci to analyze the population genetic structure of bull trout Salvelinus confluentus in the Boise River, Idaho, and we compared our results with previous data from similarly sized river systems in western North America. Within the Boise River, we found low genetic variation within and significant...

Distribution of Chironomidae in a semiarid intermittent river of Brazil.

PubMed

Farias, R L; Carvalho, L K; Medeiros, E S F

2012-12-01

The effects of the intermittency of water flow on habitat structure and substrate composition have been reported to create a patch dynamics for the aquatic fauna, mostly for that associated with the substrate. This study aims to describe the spatial distribution of Chironomidae in an intermittent river of semiarid Brazil and to associate assemblage composition with environmental variables. Benthic invertebrates were sampled during the wet and dry seasons using a D-shaped net (40 cm wide and 250 μm mesh), and the Chironomidae were identified to genus level. The most abundant genera were Tanytarsus, Polypedilum, and Saetheria with important contributions of the genera Procladius, Aedokritus, and Dicrotendipes. Richness and density were not significantly different between the study sites, and multiple regression showed that the variation in richness and density explained by the environmental variables was significant only for substrate composition. The composition of genera showed significant spatial segregation across the study sites. Canonical Correspondence Analysis showed significant correspondence between Chironomidae composition and the environmental variables, with submerged vegetation, elevation, and leaf litter being important predictors of the Chironomidae fauna. This study showed that Chironomidae presented important spatial variation along the river and that this variation was substantially explained by environmental variables associated with the habitat structure and river hierarchy. We suggest that the observed spatial segregation in the fauna results in the high diversity of this group of organisms in intermittent streams.

Application of Nitrogen and Carbon Stable Isotopes (δ15N and δ13C) to Quantify Food Chain Length and Trophic Structure

PubMed Central

Perkins, Matthew J.; McDonald, Robbie A.; van Veen, F. J. Frank; Kelly, Simon D.; Rees, Gareth; Bearhop, Stuart

2014-01-01

Increasingly, stable isotope ratios of nitrogen (δ15N) and carbon (δ13C) are used to quantify trophic structure, though relatively few studies have tested accuracy of isotopic structural measures. For laboratory-raised and wild-collected plant-invertebrate food chains spanning four trophic levels we estimated nitrogen range (NR) using δ15N, and carbon range (CR) using δ13C, which are used to quantify food chain length and breadth of trophic resources respectively. Across a range of known food chain lengths we examined how NR and CR changed within and between food chains. Our isotopic estimates of structure are robust because they were calculated using resampling procedures that propagate variance in sample means through to quantified uncertainty in final estimates. To identify origins of uncertainty in estimates of NR and CR, we additionally examined variation in discrimination (which is change in δ15N or δ13C from source to consumer) between trophic levels and among food chains. δ15N discrimination showed significant enrichment, while variation in enrichment was species and system specific, ranged broadly (1.4‰ to 3.3‰), and importantly, propagated variation to subsequent estimates of NR. However, NR proved robust to such variation and distinguished food chain length well, though some overlap between longer food chains infers a need for awareness of such limitations. δ13C discrimination was inconsistent; generally no change or small significant enrichment was observed. Consequently, estimates of CR changed little with increasing food chain length, showing the potential utility of δ13C as a tracer of energy pathways. This study serves as a robust test of isotopic quantification of food chain structure, and given global estimates of aquatic food chains approximate four trophic levels while many food chains include invertebrates, our use of four trophic level plant-invertebrate food chains makes our findings relevant for a majority of ecological systems. PMID:24676331

Among-Population Variation in Microbial Community Structure in the Floral Nectar of the Bee-Pollinated Forest Herb Pulmonaria officinalis L

PubMed Central

Jacquemyn, Hans; Lenaerts, Marijke; Brys, Rein; Willems, Kris; Honnay, Olivier; Lievens, Bart

2013-01-01

Background Microbial communities in floral nectar have been shown to be characterized by low levels of species diversity, yet little is known about among-plant population variation in microbial community composition. Methodology/Principal Findings We investigated the microbial community structure (yeasts and bacteria) in floral nectar of ten fragmented populations of the bee-pollinated forest herb Pulmonaria officinalis. We also explored possible relationships between plant population size and microbial diversity in nectar, and related microbial community composition to the distance separating plant populations. Culturable bacteria and yeasts occurring in the floral nectar of a total of 100 plant individuals were isolated and identified by partially sequencing the 16S rRNA gene and D1/D2 domains of the 26S rRNA gene, respectively. A total of 9 and 11 yeast and 28 and 39 bacterial OTUs was found, taking into account a 3% (OTU0.03) and 1% sequence dissimilarity cut-off (OTU0.01). OTU richness at the plant population level (i.e. the number of OTUs per population) was low for yeasts (mean: 1.7, range: 0–4 OTUs0.01/0.03 per population), whereas on average 6.9 (range: 2–13) OTUs0.03 and 7.9 (range 2–16) OTUs0.01 per population were found for bacteria. Both for yeasts and bacteria, OTU richness was not significantly related to plant population size. Similarity in community composition among populations was low (average Jaccard index: 0.14), and did not decline with increasing distance between populations. Conclusions/Significance We found low similarity in microbial community structure among populations, suggesting that the assembly of nectar microbiota is to a large extent context-dependent. Although the precise factors that affect variation in microbial community structure in floral nectar require further study, our results indicate that both local and regional processes may contribute to among-population variation in microbial community structure in nectar. PMID:23536759

Variation in Age and Size in Fennoscandian Three-Spined Sticklebacks (Gasterosteus aculeatus)

PubMed Central

DeFaveri, Jacquelin; Merilä, Juha

2013-01-01

Average age and maximum life span of breeding adult three-spined sticklebacks (Gasterosteus aculeatus) were determined in eight Fennoscandian localities with the aid of skeletochronology. The average age varied from 1.8 to 3.6 years, and maximum life span from three to six years depending on the locality. On average, fish from marine populations were significantly older than those from freshwater populations, but variation within habitat types was large. We also found significant differences in mean body size among different habitat types and populations, but only the population differences remained significant after accounting for variation due to age effects. These results show that generation length and longevity in three-spined sticklebacks can vary significantly from one locality to another, and that population differences in mean body size cannot be explained as a simple consequence of differences in population age structure. We also describe a nanistic population from northern Finland exhibiting long life span and small body size. PMID:24260496

Variation in age and size in Fennoscandian three-spined sticklebacks (Gasterosteus aculeatus).

PubMed

DeFaveri, Jacquelin; Merilä, Juha

2013-01-01

Average age and maximum life span of breeding adult three-spined sticklebacks (Gasterosteus aculeatus) were determined in eight Fennoscandian localities with the aid of skeletochronology. The average age varied from 1.8 to 3.6 years, and maximum life span from three to six years depending on the locality. On average, fish from marine populations were significantly older than those from freshwater populations, but variation within habitat types was large. We also found significant differences in mean body size among different habitat types and populations, but only the population differences remained significant after accounting for variation due to age effects. These results show that generation length and longevity in three-spined sticklebacks can vary significantly from one locality to another, and that population differences in mean body size cannot be explained as a simple consequence of differences in population age structure. We also describe a nanistic population from northern Finland exhibiting long life span and small body size.

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

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.

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.

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

PubMed

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

2014-11-29

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

SINGLE INSTITUTION VARIABILITY IN INTENSITY MODULATED RADIATION TARGET DELINEATION FOR CANINE NASAL NEOPLASIA.

PubMed

Christensen, Neil I; Forrest, Lisa J; White, Pamela J; Henzler, Margaret; Turek, Michelle M

2016-11-01

Contouring variability is a significant barrier to the accurate delivery and reporting of radiation therapy. The aim of this descriptive study was to determine the variation in contouring radiation targets and organs at risk by participants within our institution. Further, we also aimed to determine if all individuals contoured the same normal tissues. Two canine nasal tumor datasets were selected and contoured by two ACVR-certified radiation oncologists and two radiation oncology residents from the same institution. Eight structures were consistently contoured including the right and left eye, the right and left lens, brain, the gross tumor volume (GTV), clinical target volume (CTV), and planning target volume (PTV). Spinal cord, hard and soft palate, and bulla were contoured on 50% of datasets. Variation in contouring occurred in both targets and normal tissues at risk and was particularly significant for the GTV, CTV, and PTV. The mean metric score and dice similarity coefficient were below the threshold criteria in 37.5-50% and 12.5-50% of structures, respectively, quantitatively indicating contouring variation. This study refutes our hypothesis that minimal variation in target and normal tissue delineation occurs. The variation in contouring may contribute to different tumor response and toxicity for any given patient. Our results also highlight the difficulty associated with replication of published radiation protocols or treatments, as even with replete contouring description the outcome of treatment is still fundamentally influenced by the individual contouring the patient. © 2016 American College of Veterinary Radiology.

Anatomical variations of uncinate process observed in chronic sinusitis.

PubMed

Tuli, Isha Preet; Sengupta, Subhabrata; Munjal, Sudeep; Kesari, Santosh Prasad; Chakraborty, Suvamoy

2013-04-01

Chronic Sinusitis, an extremely persistent illness, is surgically best treated by Functional Endoscopic Sinus Surgery. The ostiomeatal complex is the main area targeted and within it uncinate process is the first anatomical structure encountered. The significance of anatomical variations concerning age and sex of uncinate process in chronic sinusitis were evaluated. A prospective study on 50 patients of chronic sinusitis (100 uncinate processes) was done. The results were tabulated and analyzed using Statistical Package for Social Science (SPSS) 16.0. Type I superior attachment of uncinate process (67 %) was the most common variety in all ages and both sexes and a statistically significant relationship between Type I superior attachment of uncinate process and sex was found (p < 0.05). The typical uncinate process was most common (70 %) followed by medial deviation of the uncinate (24 %). This difference in occurrence was significant with respect to both age and sex (p < 0.05). Anatomical variations of uncinate process are not responsible for causing chronic sinusitis. Mere presence of these variations of uncinate is not an indication for FESS.

Responses of Bacterial Communities in Arable Soils in a Rice-Wheat Cropping System to Different Fertilizer Regimes and Sampling Times

PubMed Central

Zhao, Jun; Ni, Tian; Li, Yong; Xiong, Wu; Ran, Wei; Shen, Biao; Shen, Qirong; Zhang, Ruifu

2014-01-01

Soil physicochemical properties, soil microbial biomass and bacterial community structures in a rice-wheat cropping system subjected to different fertilizer regimes were investigated in two seasons (June and October). All fertilizer regimes increased the soil microbial biomass carbon and nitrogen. Both fertilizer regime and time had a significant effect on soil physicochemical properties and bacterial community structure. The combined application of inorganic fertilizer and manure organic-inorganic fertilizer significantly enhanced the bacterial diversity in both seasons. The bacterial communities across all samples were dominated by Proteobacteria, Acidobacteria and Chloroflexi at the phylum level. Permutational multivariate analysis confirmed that both fertilizer treatment and season were significant factors in the variation of the composition of the bacterial community. Hierarchical cluster analysis based on Bray-Curtis distances further revealed that bacterial communities were separated primarily by season. The effect of fertilizer treatment is significant (P = 0.005) and accounts for 7.43% of the total variation in bacterial community. Soil nutrients (e.g., available K, total N, total P and organic matter) rather than pH showed significant correlation with the majority of abundant taxa. In conclusion, both fertilizer treatment and seasonal changes affect soil properties, microbial biomass and bacterial community structure. The application of NPK plus manure organic-inorganic fertilizer may be a sound fertilizer practice for sustainable food production. PMID:24465530

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.

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.

Structural analysis of determinants of histo-blood group antigen binding specificity in genogroup I noroviruses.

PubMed

Shanker, Sreejesh; Czako, Rita; Sankaran, Banumathi; Atmar, Robert L; Estes, Mary K; Prasad, B V Venkataram

2014-06-01

Human noroviruses (NoVs) cause acute epidemic gastroenteritis. Susceptibility to the majority of NoV infections is determined by genetically controlled secretor-dependent expression of histo-blood group antigens (HBGAs), which are also critical for NoV attachment to host cells. Human NoVs are classified into two major genogroups (genogroup I [GI] and GII), with each genogroup further divided into several genotypes. GII NoVs are more prevalent and exhibit periodic emergence of new variants, suggested to be driven by altered HBGA binding specificities and antigenic drift. Recent epidemiological studies show increased activity among GI NoVs, with some members showing the ability to bind nonsecretor HBGAs. NoVs bind HBGAs through the protruding (P) domain of the major capsid protein VP1. GI NoVs, similar to GII, exhibit significant sequence variations in the P domain; it is unclear how these variations affect HBGA binding specificities. To understand the determinants of possible strain-specific HBGA binding among GI NoVs, we determined the structure of the P domain of a GI.7 clinical isolate and compared it to the previously determined P domain structures of GI.1 and GI.2 strains. Our crystallographic studies revealed significant structural differences, particularly in the loop regions of the GI.7 P domain, altering its surface topography and electrostatic landscape and potentially indicating antigenic variation. The GI.7 strain bound to H- and A-type, Lewis secretor, and Lewis nonsecretor families of HBGAs, allowing us to further elucidate the structural determinants of nonsecretor HBGA binding among GI NoVs and to infer several contrasting and generalizable features of HBGA binding in the GI NoVs. Human noroviruses (NoVs) cause acute epidemic gastroenteritis. Recent epidemiological studies have shown increased prevalence of genogroup I (GI) NoVs. Although secretor-positive status is strongly correlated with NoV infection, cases of NoV infection associated with secretor-negative individuals are reported. Biochemical studies have shown that GI NoVs exhibit genotype-dependent binding to nonsecretor histo-blood group antigens (HBGAs). From our crystallographic studies of a GI.7 NoV, in comparison with previous studies on GI.1 and GI.2 NoVs, we show that genotypic differences translate to extensive structural changes in the loop regions that significantly alter the surface topography and electrostatic landscape of the P domain; these features may be indicative of antigenic variations contributing to serotypic differentiation in GI NoVs and also differential modulation of the HBGA binding characteristics. A significant finding is that the threshold length and the structure of one of the loops are critical determinants in the binding of GI NoVs to nonsecretor HBGAs.

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

Network Ecology and Adolescent Social Structure

PubMed Central

McFarland, Daniel A.; Moody, James; Diehl, David; Smith, Jeffrey A.; Thomas, Reuben J.

2014-01-01

Adolescent societies—whether arising from weak, short-term classroom friendships or from close, long-term friendships—exhibit various levels of network clustering, segregation, and hierarchy. Some are rank-ordered caste systems and others are flat, cliquish worlds. Explaining the source of such structural variation remains a challenge, however, because global network features are generally treated as the agglomeration of micro-level tie-formation mechanisms, namely balance, homophily, and dominance. How do the same micro-mechanisms generate significant variation in global network structures? To answer this question we propose and test a network ecological theory that specifies the ways features of organizational environments moderate the expression of tie-formation processes, thereby generating variability in global network structures across settings. We develop this argument using longitudinal friendship data on schools (Add Health study) and classrooms (Classroom Engagement study), and by extending exponential random graph models to the study of multiple societies over time. PMID:25535409

Network Ecology and Adolescent Social Structure.

PubMed

McFarland, Daniel A; Moody, James; Diehl, David; Smith, Jeffrey A; Thomas, Reuben J

2014-12-01

Adolescent societies-whether arising from weak, short-term classroom friendships or from close, long-term friendships-exhibit various levels of network clustering, segregation, and hierarchy. Some are rank-ordered caste systems and others are flat, cliquish worlds. Explaining the source of such structural variation remains a challenge, however, because global network features are generally treated as the agglomeration of micro-level tie-formation mechanisms, namely balance, homophily, and dominance. How do the same micro-mechanisms generate significant variation in global network structures? To answer this question we propose and test a network ecological theory that specifies the ways features of organizational environments moderate the expression of tie-formation processes, thereby generating variability in global network structures across settings. We develop this argument using longitudinal friendship data on schools (Add Health study) and classrooms (Classroom Engagement study), and by extending exponential random graph models to the study of multiple societies over time.

Improved Nazca slab structure from teleseismic P-wave tomography along the Andean margin

NASA Astrophysics Data System (ADS)

Portner, D. E.; Beck, S. L.; Scire, A. C.; Zandt, G.

2017-12-01

South America marks the longest continuous ocean-continent subduction zone. As such, there is significant along-strike variability in the subducting Nazca slab structure and the tectonics of the South American margin. Most notably two gaps in the otherwise continuous volcanic arc are correlated with regions of flat slab subduction, indicating that the structure of the Nazca slab plays a controlling role in South American tectonics. Traditionally in subduction zones, our knowledge of slab structure is defined by Wadati-Benioff zone earthquakes. While this method allows for the determination of large-scale variations in Nazca slab structure such as regions of flat slab subduction, a scarcity of intermediate-depth earthquakes hinders our ability to observe the smaller-scale structural variations in the slab that may be critical to our understanding of the geologic record. We use an updated, larger dataset for finite-frequency teleseismic P-wave tomography including relative arrival times from >700 seismic stations along the Andean margin to image the detailed Nazca slab structure throughout the upper mantle and uppermost lower mantle between latitudes 5°S and 45°S. Our results show prominent variations in slab character along the margin. Slab dip varies significantly, from sub-vertical inboard of the Peruvian flat slab segment to 30° dip south of the Pampean flat slab, while the slab's velocity anomaly amplitude changes dramatically near the Pampean flat slab region. High slab velocities north of the Pampean region relative to the south indicate variable slab thermal structures that correspond roughly with the locations of deep (>500 km depth) earthquakes that also occur exclusively north of the Pampean region. Additionally, a wider regional footprint increases our sampling of the upper-lower mantle boundary, improving constraints on the slab's interaction with the 660 km discontinuity along strike. We see that the Nazca slab appears to penetrate into the lower mantle along the majority of the margin.

Genetic and environmental influences on structural variability of the brain in pediatric twin: deformation based morphometry.

PubMed

Yoon, Uicheul; Perusse, Daniel; Lee, Jong-Min; Evans, Alan C

2011-04-08

Twin studies are one of the most powerful study designs for estimating the relative contribution of genetic and environmental influences on phenotypic variation inhuman brain morphology. In this study, we applied deformation based morphometry, a technique that provides a voxel-wise index of local tissue growth or atrophy relative to a template brain, combined with univariate ACE model, to investigate the genetic and environmental effects on the human brain structural variations in a cohort of homogeneously aged healthy pediatric twins. In addition, anatomical regions of interest (ROIs) were defined in order to explore global and regional genetic effects. ROI results showed that the influence of genetic factors on cerebrum (h(2)=0.70), total gray matter (0.67), and total white matter (0.73) volumes were significant. In particular, structural variability of left-side lobar volumes showed a significant heritability. Several subcortical structures such as putamen (h(ROI)(2)=0.79/0.77(L/R),h(MAX)(2)=0.82/0.79) and globus pallidus (0.81/0.76, 0.88/0.82) were also significantly heritable in both voxel-wise and ROI-based results. In the voxel-wise results, lateral parts of right cerebellum (c(2)=0.68) and the posterior portion of the corpus callosum (0.63) were rather environmentally determined, but it failed to reach statistical significance. Pediatric twin studies are important because they can discriminate several influences on developmental brain trajectories and identify relationships between gene and behavior. Several brain structures showed significant genetic effects and might therefore serve as biological markers for inherited traits, or as targets for genetic linkage and association studies. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Partitioning the impact of environment and spatial structure on alpha and beta components of taxonomic, functional, and phylogenetic diversity in European ants.

PubMed

Arnan, Xavier; Cerdá, Xim; Retana, Javier

2015-01-01

We analyze the relative contribution of environmental and spatial variables to the alpha and beta components of taxonomic (TD), phylogenetic (PD), and functional (FD) diversity in ant communities found along different climate and anthropogenic disturbance gradients across western and central Europe, in order to assess the mechanisms structuring ant biodiversity. To this aim we calculated alpha and beta TD, PD, and FD for 349 ant communities, which included a total of 155 ant species; we examined 10 functional traits and phylogenetic relatedness. Variation partitioning was used to examine how much variation in ant diversity was explained by environmental and spatial variables. Autocorrelation in diversity measures and each trait's phylogenetic signal were also analyzed. We found strong autocorrelation in diversity measures. Both environmental and spatial variables significantly contributed to variation in TD, PD, and FD at both alpha and beta scales; spatial structure had the larger influence. The different facets of diversity showed similar patterns along environmental gradients. Environment explained a much larger percentage of variation in FD than in TD or PD. All traits demonstrated strong phylogenetic signals. Our results indicate that environmental filtering and dispersal limitations structure all types of diversity in ant communities. Strong dispersal limitations appear to have led to clustering of TD, PD, and FD in western and central Europe, probably because different historical and evolutionary processes generated different pools of species. Remarkably, these three facets of diversity showed parallel patterns along environmental gradients. Trait-mediated species sorting and niche conservatism appear to structure ant diversity, as evidenced by the fact that more variation was explained for FD and that all traits had strong phylogenetic signals. Since environmental variables explained much more variation in FD than in PD, functional diversity should be a better indicator of community assembly processes than phylogenetic diversity.

Plant Biodiversity Drivers in Brazilian Campos Rupestres: Insights from Phylogenetic Structure

PubMed Central

Zappi, Daniela C.; Moro, Marcelo F.; Meagher, Thomas R.; Nic Lughadha, Eimear

2017-01-01

Old, climate-buffered infertile landscapes (Ocbils) have attracted increasing levels of interest in recent years because of their exceptionally diverse plant communities. Brazil’s campos rupestres (rupestrian grasslands) are home to almost 15% of Brazil’s native flora in less than 0.8% of Brazil’s territory: an ideal study system for exploring variation in floristic diversity and phylogenetic structure in sites differing in geology and phytophysiognomy. We found significant differences in floristic diversity and phylogenetic structure across a range of study sites encompassing open vegetation and forest on quartzite (FQ) and on ironstone substrates, commonly termed canga. Substrate and physiognomy were key in structuring floristic diversity in the Espinhaço and physiognomy was more important than substrate in structuring phylogenetic diversity, with neither substrate nor its interaction with physiognomy accounting for significant variation in phylogenetic structure. Phylogenetic clustering was significant in open vegetation on both canga and quartzite, reflecting the potential role of environmental filtering in these exposed montane communities adapted to multiple environmental stressors. In forest communities, phylogenetic clustering was significant only at relatively deep nodes of the phylogeny in FQ while no significant phylogenetic clustering was detected across forest on canga (FC), which may be attributable to proximity to the megadiverse Atlantic forest biome and/or comparatively benign environmental conditions in FC with relatively deep, nutrient-rich soils and access to edaphic water reliable in comparison to those for open vegetation on canga and open or forest communities on quartzite. Clades representing relatively old lineages are significantly over-represented in campos rupestres on quartzite, consistent with the Gondwanan Heritage Hypothesis of Ocbil theory. In contrast, forested sites on canga are recognized as Yodfels. To be effective, conservation measures must take account of the distinct communities which are encompassed within the broad term campos rupestres, and the differing vulnerabilities of Ocbils and Yodfels. PMID:29312396

Plant Biodiversity Drivers in Brazilian Campos Rupestres: Insights from Phylogenetic Structure.

PubMed

Zappi, Daniela C; Moro, Marcelo F; Meagher, Thomas R; Nic Lughadha, Eimear

2017-01-01

Old, climate-buffered infertile landscapes (Ocbils) have attracted increasing levels of interest in recent years because of their exceptionally diverse plant communities. Brazil's campos rupestres (rupestrian grasslands) are home to almost 15% of Brazil's native flora in less than 0.8% of Brazil's territory: an ideal study system for exploring variation in floristic diversity and phylogenetic structure in sites differing in geology and phytophysiognomy. We found significant differences in floristic diversity and phylogenetic structure across a range of study sites encompassing open vegetation and forest on quartzite (FQ) and on ironstone substrates, commonly termed canga . Substrate and physiognomy were key in structuring floristic diversity in the Espinhaço and physiognomy was more important than substrate in structuring phylogenetic diversity, with neither substrate nor its interaction with physiognomy accounting for significant variation in phylogenetic structure. Phylogenetic clustering was significant in open vegetation on both canga and quartzite, reflecting the potential role of environmental filtering in these exposed montane communities adapted to multiple environmental stressors. In forest communities, phylogenetic clustering was significant only at relatively deep nodes of the phylogeny in FQ while no significant phylogenetic clustering was detected across forest on canga (FC), which may be attributable to proximity to the megadiverse Atlantic forest biome and/or comparatively benign environmental conditions in FC with relatively deep, nutrient-rich soils and access to edaphic water reliable in comparison to those for open vegetation on canga and open or forest communities on quartzite. Clades representing relatively old lineages are significantly over-represented in campos rupestres on quartzite, consistent with the Gondwanan Heritage Hypothesis of Ocbil theory. In contrast, forested sites on canga are recognized as Yodfels. To be effective, conservation measures must take account of the distinct communities which are encompassed within the broad term campos rupestres , and the differing vulnerabilities of Ocbils and Yodfels.

Human activities as a driver of spatial variation in the trophic structure of fish communities on Pacific coral reefs.

PubMed

Ruppert, Jonathan L W; Vigliola, Laurent; Kulbicki, Michel; Labrosse, Pierre; Fortin, Marie-Josée; Meekan, Mark G

2018-01-01

Anthropogenic activities such as land-use change, pollution and fishing impact the trophic structure of coral reef fishes, which can influence ecosystem health and function. Although these impacts may be ubiquitous, they are not consistent across the tropical Pacific Ocean. Using an extensive database of fish biomass sampled using underwater visual transects on coral reefs, we modelled the impact of human activities on food webs at Pacific-wide and regional (1,000s-10,000s km) scales. We found significantly lower biomass of sharks and carnivores, where there were higher densities of human populations (hereafter referred to as human activity); however, these patterns were not spatially consistent as there were significant differences in the trophic structures of fishes among biogeographic regions. Additionally, we found significant changes in the benthic structure of reef environments, notably a decline in coral cover where there was more human activity. Direct human impacts were the strongest in the upper part of the food web, where we found that in a majority of the Pacific, the biomass of reef sharks and carnivores were significantly and negatively associated with human activity. Finally, although human-induced stressors varied in strength and significance throughout the coral reef food web across the Pacific, socioeconomic variables explained more variation in reef fish trophic structure than habitat variables in a majority of the biogeographic regions. Notably, economic development (measured as GDP per capita) did not guarantee healthy reef ecosystems (high coral cover and greater fish biomass). Our results indicate that human activities are significantly shaping patterns of trophic structure of reef fishes in a spatially nonuniform manner across the Pacific Ocean, by altering processes that organize communities in both "top-down" (fishing of predators) and "bottom-up" (degradation of benthic communities) contexts. © 2017 John Wiley & Sons Ltd.

Determination of the structural damping coefficients of six full-scale helicopter rotor blades of different materials and methods of construction

NASA Technical Reports Server (NTRS)

Gibson, Frederick W

1956-01-01

Results of an experimental investigation of the structural damping of six full-scale helicopter rotor blades, made to determine the variation of structural damping with materials and methods of construction, are presented. The damping of the blades was determined for the first three flapwise bending modes, first chordwise bending mode, and first torsion mode. The contribution of structural damping to the total damping of the blades is discussed for several aerodynamic conditions in order to point out situations where structural damping is significant.

The Effects of Presentation Modality, Task Demand, and Content Structure on Age-Related Memory Differences for Prose.

ERIC Educational Resources Information Center

Corgiat, Mark D.; And Others

1989-01-01

Evaluated contributions of age, presentation modality, task demand, and content structure to prose recall variation among adults. Tested 60 young and 60 older adults for recall of ideas in 641-word prose passage. Found recall for total number of idea units was significantly lower for older participants and for auditory presentation across both age…

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.

[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.

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

NASA Astrophysics Data System (ADS)

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

2006-07-01

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

Bacterial community structure and function shift along a successional series of tidal flats in the Yellow River Delta

PubMed Central

Lv, Xiaofei; Ma, Bin; Yu, Junbao; Chang, Scott X.; Xu, Jianming; Li, Yunzhao; Wang, Guangmei; Han, Guangxuan; Bo, Guan; Chu, Xiaojing

2016-01-01

Coastal ecosystems play significant ecological and economic roles but are threatened and facing decline. Microbes drive various biogeochemical processes in coastal ecosystems. Tidal flats are critical components of coastal ecosystems; however, the structure and function of microbial communities in tidal flats are poorly understood. Here we investigated the seasonal variations of bacterial communities along a tidal flat series (subtidal, intertidal and supratidal flats) and the factors affecting the variations. Bacterial community composition and diversity were analyzed over four seasons by 16S rRNA genes using the Ion Torrent PGM platform. Bacterial community composition differed significantly along the tidal flat series. Bacterial phylogenetic diversity increased while phylogenetic turnover decreased from subtidal to supratidal flats. Moreover, the bacterial community structure differed seasonally. Canonical correspondence analysis identified salinity as a major environmental factor structuring the microbial community in the sediment along the successional series. Meanwhile, temperature and nitrite concentration were major drivers of seasonal microbial changes. Despite major compositional shifts, nitrogen, methane and energy metabolisms predicted by PICRUSt were inhibited in the winter. Taken together, this study indicates that bacterial community structure changed along the successional tidal flat series and provides new insights on the characteristics of bacterial communities in coastal ecosystems. PMID:27824160

Bacterial community structure and function shift along a successional series of tidal flats in the Yellow River Delta.

PubMed

Lv, Xiaofei; Ma, Bin; Yu, Junbao; Chang, Scott X; Xu, Jianming; Li, Yunzhao; Wang, Guangmei; Han, Guangxuan; Bo, Guan; Chu, Xiaojing

2016-11-08

Coastal ecosystems play significant ecological and economic roles but are threatened and facing decline. Microbes drive various biogeochemical processes in coastal ecosystems. Tidal flats are critical components of coastal ecosystems; however, the structure and function of microbial communities in tidal flats are poorly understood. Here we investigated the seasonal variations of bacterial communities along a tidal flat series (subtidal, intertidal and supratidal flats) and the factors affecting the variations. Bacterial community composition and diversity were analyzed over four seasons by 16S rRNA genes using the Ion Torrent PGM platform. Bacterial community composition differed significantly along the tidal flat series. Bacterial phylogenetic diversity increased while phylogenetic turnover decreased from subtidal to supratidal flats. Moreover, the bacterial community structure differed seasonally. Canonical correspondence analysis identified salinity as a major environmental factor structuring the microbial community in the sediment along the successional series. Meanwhile, temperature and nitrite concentration were major drivers of seasonal microbial changes. Despite major compositional shifts, nitrogen, methane and energy metabolisms predicted by PICRUSt were inhibited in the winter. Taken together, this study indicates that bacterial community structure changed along the successional tidal flat series and provides new insights on the characteristics of bacterial communities in coastal ecosystems.

Threshold voltage variation depending on single grain boundary and stored charges in an adjacent cell for vertical silicon–oxide–nitride–oxide–silicon NAND flash memory

NASA Astrophysics Data System (ADS)

Oh, Hyeongwan; Kim, Jiwon; Baek, Rock-Hyun; Lee, Jeong-Soo

2018-04-01

The effects of single grain boundary (SGB) position and stored electron charges in an adjacent cell in silicon–oxide–nitride–oxide–silicon (SONOS) structures on the variations of threshold voltage (V th) were investigated using technology computer-aided design (TCAD) simulation. As the bit line voltage increases, the SGB position causing the maximum V th variation was shifted from the center to the source side in the channel, owing to the drain-induced grain barrier lowering effect. When the SGB is located in the spacer region, the potential interaction from both the SGB and the stored electron charges in the adjacent cell becomes significant and thus resulting in larger V th variation. In contrast, when the SGB is located at the center of the channel, the peak position of potential barrier is shifted to the center, so that the influence of the adjacent cell is diminished. As the gate length is scaled down to 20 nm, the influence of stored charges in adjacent cells becomes significant, resulting in larger V th variations.

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.

Assessing the dependency of the fine structure constant on gravity using hot DA white dwarfs

NASA Astrophysics Data System (ADS)

Barstow, Martin

2016-10-01

Variation of fundamental constants is a common theme of many theories of quantum gravity and Grand Unification. Using spectra obtained with the Hubble Space Telescope, it has been shown by Berengut et al. (2013), and Bagdonaite et al. (2014), that it is possible to place strong constraints on gravitational variations of the fine structure constant (alpha), and the proton to electron mass ratio (mu) in white dwarf stars.As part of the UV initiative, we propose to observe four hot DA white dwarf stars using STIS with the E140H grating, totalling 12 orbits. These four stars have been chosen so as to have a wide range of masses, allowing a full exploration of the compactness parameter space (M/R). We will measure several absorption features of Fe V and Ni V, and extract any potential variation in alpha in a manner similar to Berengut et al. (2013).This proposal will be a significant advance in the effort to detect gravitational variations in alpha. A confirmed detection of alpha variation would have extensive consequences for fundamental physics, cosmology, and would also signal the breakdown of Einstein's Equivalence principle, and hence, general relativity. Furthermore, a null detection would also allow strong limits to be placed on any potential alpha variation in a strong gravitational field.

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

Kennedy, R.P.; Kincaid, R.H.; Short, S.A.

This report presents the results of part of a two-task study on the engineering characterization of earthquake ground motion for nuclear power plant design. Task I of the study, which is presented in NUREG/CR-3805, Vol. 1, developed a basis for selecting design response spectra taking into account the characteristics of free-field ground motion found to be significant in causing structural damage. Task II incorporates additional considerations of effects of spatial variations of ground motions and soil-structure interaction on foundation motions and structural response. The results of Task II are presented in four parts: (1) effects of ground motion characteristics onmore » structural response of a typical PWR reactor building with localized nonlinearities and soil-structure interaction effects; (2) empirical data on spatial variations of earthquake ground motion; (3) soil-structure interaction effects on structural response; and (4) summary of conclusions and recommendations based on Tasks I and II studies. This report presents the results of the first part of Task II. The results of the other parts will be presented in NUREG/CR-3805, Vols. 3 to 5.« less

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

PubMed Central

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

2015-01-01

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

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

PubMed

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

2015-01-01

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

Residue-level global and local ensemble-ensemble comparisons of protein domains.

PubMed

Clark, Sarah A; Tronrud, Dale E; Karplus, P Andrew

2015-09-01

Many methods of protein structure generation such as NMR-based solution structure determination and template-based modeling do not produce a single model, but an ensemble of models consistent with the available information. Current strategies for comparing ensembles lose information because they use only a single representative structure. Here, we describe the ENSEMBLATOR and its novel strategy to directly compare two ensembles containing the same atoms to identify significant global and local backbone differences between them on per-atom and per-residue levels, respectively. The ENSEMBLATOR has four components: eePREP (ee for ensemble-ensemble), which selects atoms common to all models; eeCORE, which identifies atoms belonging to a cutoff-distance dependent common core; eeGLOBAL, which globally superimposes all models using the defined core atoms and calculates for each atom the two intraensemble variations, the interensemble variation, and the closest approach of members of the two ensembles; and eeLOCAL, which performs a local overlay of each dipeptide and, using a novel measure of local backbone similarity, reports the same four variations as eeGLOBAL. The combination of eeGLOBAL and eeLOCAL analyses identifies the most significant differences between ensembles. We illustrate the ENSEMBLATOR's capabilities by showing how using it to analyze NMR ensembles and to compare NMR ensembles with crystal structures provides novel insights compared to published studies. One of these studies leads us to suggest that a "consistency check" of NMR-derived ensembles may be a useful analysis step for NMR-based structure determinations in general. The ENSEMBLATOR 1.0 is available as a first generation tool to carry out ensemble-ensemble comparisons. © 2015 The Protein Society.

Residue-level global and local ensemble-ensemble comparisons of protein domains

PubMed Central

Clark, Sarah A; Tronrud, Dale E; Andrew Karplus, P

2015-01-01

Many methods of protein structure generation such as NMR-based solution structure determination and template-based modeling do not produce a single model, but an ensemble of models consistent with the available information. Current strategies for comparing ensembles lose information because they use only a single representative structure. Here, we describe the ENSEMBLATOR and its novel strategy to directly compare two ensembles containing the same atoms to identify significant global and local backbone differences between them on per-atom and per-residue levels, respectively. The ENSEMBLATOR has four components: eePREP (ee for ensemble-ensemble), which selects atoms common to all models; eeCORE, which identifies atoms belonging to a cutoff-distance dependent common core; eeGLOBAL, which globally superimposes all models using the defined core atoms and calculates for each atom the two intraensemble variations, the interensemble variation, and the closest approach of members of the two ensembles; and eeLOCAL, which performs a local overlay of each dipeptide and, using a novel measure of local backbone similarity, reports the same four variations as eeGLOBAL. The combination of eeGLOBAL and eeLOCAL analyses identifies the most significant differences between ensembles. We illustrate the ENSEMBLATOR's capabilities by showing how using it to analyze NMR ensembles and to compare NMR ensembles with crystal structures provides novel insights compared to published studies. One of these studies leads us to suggest that a “consistency check” of NMR-derived ensembles may be a useful analysis step for NMR-based structure determinations in general. The ENSEMBLATOR 1.0 is available as a first generation tool to carry out ensemble-ensemble comparisons. PMID:26032515

Prediction of functionally significant single nucleotide polymorphisms in PTEN tumor suppressor gene: An in silico approach.

PubMed

Khan, Imran; Ansari, Irfan A; Singh, Pratichi; Dass J, Febin Prabhu

2017-09-01

The phosphatase and tensin homolog (PTEN) gene plays a crucial role in signal transduction by negatively regulating the PI3K signaling pathway. It is the most frequent mutated gene in many human-related cancers. Considering its critical role, a functional analysis of missense mutations of PTEN gene was undertaken in this study. Thirty five nonsynonymous single nucleotide polymorphisms (nsSNPs) within the coding region of the PTEN gene were selected for our in silico investigation, and five nsSNPs (G129E, C124R, D252G, H61D, and R130G) were found to be deleterious based on combinatorial predictions of different computational tools. Moreover, molecular dynamics (MD) simulation was performed to investigate the conformational variation between native and all the five mutant PTEN proteins having predicted deleterious nsSNPs. The results of MD simulation of all mutant models illustrated variation in structural attributes such as root-mean-square deviation, root-mean-square fluctuation, radius of gyration, and total energy; which depicts the structural stability of PTEN protein. Furthermore, mutant PTEN protein structures also showed a significant variation in the solvent accessible surface area and hydrogen bond frequencies from the native PTEN structure. In conclusion, results of this study have established the deleterious effect of the all the five predicted nsSNPs on the PTEN protein structure. Thus, results of the current study can pave a new platform to sort out nsSNPs that can be undertaken for the confirmation of their phenotype and their correlation with diseased status in case of control studies. © 2016 International Union of Biochemistry and Molecular Biology, Inc.

Variations in the structure of nexuses in the myocardium of the golden hamster Mesocricetus auratus.

PubMed Central

Skepper, J N; Navaratnam, V

1986-01-01

The structure of nexuses in the atrioventricular node of the golden hamster was studied with the transmission electron microscope, using thin sections and freeze-fracture replicas, and was compared with that of nexuses in the working myocardium of the right ventricular wall. Whereas ventricular myocardium contained macular nexuses only, nodal tissue contained annular and linear configurations as well as maculae of varying size. The significance of such variations in nexus pattern is not clear although several hypotheses are discussed in the literature. Measurements made on electron micrographs, after allowing for tilt of the specimen, yielded a particle diameter of 10.59 nm for nodal myocardium and 10.95 nm for ventricular myocardium, both measurements being substantially higher than figures generally cited in the literature. In each area the measurements had a normal distribution suggesting a single type of particle. The small but significant difference in particle size between the two areas is more likely to be caused by dissimilarities in packing arrangement rather than by differences in intrinsic structure or in functional state. Images Fig. 1 Fig. 3 PMID:3693102

Quantification and Visualization of Variation in Anatomical Trees

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

Amenta, Nina; Datar, Manasi; Dirksen, Asger

This paper presents two approaches to quantifying and visualizing variation in datasets of trees. The first approach localizes subtrees in which significant population differences are found through hypothesis testing and sparse classifiers on subtree features. The second approach visualizes the global metric structure of datasets through low-distortion embedding into hyperbolic planes in the style of multidimensional scaling. A case study is made on a dataset of airway trees in relation to Chronic Obstructive Pulmonary Disease.

Maternal effects and Symbiodinium community composition drive differential patterns in juvenile survival in the coral Acropora tenuis

PubMed Central

Willis, Bette L.; Bay, Line K.

2016-01-01

Coral endosymbionts in the dinoflagellate genus Symbiodinium are known to impact host physiology and have led to the evolution of reef-building, but less is known about how symbiotic communities in early life-history stages and their interactions with host parental identity shape the structure of coral communities on reefs. Differentiating the roles of environmental and biological factors driving variation in population demographic processes, particularly larval settlement, early juvenile survival and the onset of symbiosis is key to understanding how coral communities are structured and to predicting how they are likely to respond to climate change. We show that maternal effects (that here include genetic and/or effects related to the maternal environment) can explain nearly 24% of variation in larval settlement success and 5–17% of variation in juvenile survival in an experimental study of the reef-building scleractinian coral, Acropora tenuis. After 25 days on the reef, Symbiodinium communities associated with juvenile corals differed significantly between high mortality and low mortality families based on estimates of taxonomic richness, composition and relative abundance of taxa. Our results highlight that maternal and familial effects significantly explain variation in juvenile survival and symbiont communities in a broadcast-spawning coral, with Symbiodinium type A3 possibly a critical symbiotic partner during this early life stage. PMID:27853562

Identifying with fictive characters: structural brain correlates of the personality trait ‘fantasy’

PubMed Central

Hänggi, Jürgen; Jancke, Lutz

2014-01-01

The perception of oneself as absorbed in the thoughts, feelings and happenings of a fictive character (e.g. in a novel or film) as if the character’s experiences were one’s own is referred to as identification. We investigated whether individual variation in the personality trait of identification is associated with individual variation in the structure of specific brain regions, using surface and volume-based morphometry. The hypothesized regions of interest were selected on the basis of their functional role in subserving the cognitive processing domains considered important for identification (i.e. mental imagery, empathy, theory of mind and merging) and for the immersive experience called ‘presence’. Controlling for age, sex, whole-brain volume and other traits, identification covaried significantly with the left hippocampal volume, cortical thickness in the right anterior insula and the left dorsal medial prefrontal cortex, and with gray matter volume in the dorsolateral prefrontal cortex. These findings show that trait identification is associated with structural variation in specific brain regions. The findings are discussed in relation to the potential functional contribution of these regions to identification. PMID:24464847

Contact networks structured by sex underpin sex-specific epidemiology of infection.

PubMed

Silk, Matthew J; Weber, Nicola L; Steward, Lucy C; Hodgson, David J; Boots, Mike; Croft, Darren P; Delahay, Richard J; McDonald, Robbie A

2018-02-01

Contact networks are fundamental to the transmission of infection and host sex often affects the acquisition and progression of infection. However, the epidemiological impacts of sex-related variation in animal contact networks have rarely been investigated. We test the hypothesis that sex-biases in infection are related to variation in multilayer contact networks structured by sex in a population of European badgers Meles meles naturally infected with Mycobacterium bovis. Our key results are that male-male and between-sex networks are structured at broader spatial scales than female-female networks and that in male-male and between-sex contact networks, but not female-female networks, there is a significant relationship between infection and contacts with individuals in other groups. These sex differences in social behaviour may underpin male-biased acquisition of infection and may result in males being responsible for more between-group transmission. This highlights the importance of sex-related variation in host behaviour when managing animal diseases. © 2017 The Authors. Ecology Letters published by CNRS and John Wiley & Sons Ltd.

Detecting significant change in stream benthic macroinvertebrate communities in wilderness areas

USGS Publications Warehouse

Milner, Alexander M.; Woodward, Andrea; Freilich, Jerome E.; Black, Robert W.; Resh, Vincent H.

2016-01-01

Within a region, both MDS analyses typically identified similar years as exceeding reference condition variation, illustrating the utility of the approach for identifying wider spatial scale effects that influence more than one stream. MDS responded to both simulated water temperature stress and a pollutant event, and generally outlying years on MDS plots could be explained by environmental variables, particularly higher precipitation. Multivariate control charts successfully identified whether shifts in community structure identified by MDS were significant and whether the shift represented a press disturbance (long-term change) or a pulse disturbance. We consider a combination of TD and MDS with control charts to be a potentially powerful tool for determining years significantly outside of a reference condition variation.

Magnetic field-driven lateral photovoltaic effect in the Fe/SiO2/p-Si hybrid structure with the Schottky barrier

NASA Astrophysics Data System (ADS)

Volkov, N. V.; Rautskii, M. V.; Tarasov, A. S.; Yakovlev, I. A.; Bondarev, I. A.; Lukyanenko, A. V.; Varnakov, S. N.; Ovchinnikov, S. G.

2018-07-01

We demonstrate that the lateral photovoltaic effect in the Fe/SiO2/p-Si structure not only strongly depends on the optical radiation wavelength and temperature, but is also sensitive to external magnetic fields. The magnetic field lowers the absolute value of photovoltage regardless of the wavelength and temperature; however, the relative photovoltage variation significantly depends on these parameters. The lateral photovoltage is observed both on the Fe film and Si substrate sides and results from separation of photoinduced electrons and holes in a built-in electric field of the Schottky barrier with their subsequent diffusion to the structure in the lateral direction from the illuminated area. The observed features in the behavior of the lateral photovoltaic effect originate from the variation in the light absorption coefficient of the semiconductor and the related quantum efficiency upon light wavelength variation. In addition, an important role is played by the change in the characteristics of the Schottky barrier at the redistribution of optically generated carriers and temperature variation. The effect of the magnetic field is attributed to the Lorentz force, which bends trajectories of carriers drifting under the action of the Schottky barrier field and, consequently, suppresses the lateral photovoltaic effect.

Habitat fragmentation causes bottlenecks and inbreeding in the European tree frog (Hyla arborea).

PubMed Central

Andersen, Liselotte W.; Fog, Kåre; Damgaard, Christian

2004-01-01

A genetic study of the European tree frog, Hyla arborea, in Denmark was undertaken to examine the population structure on mainland Jutland and the island of Lolland after a period of reduction in suitable habitat and population sizes. The two regions have experienced the same rate of habitat loss but fragmentation has been more severe on Lolland. Genetic variation based on 12 polymorphic DNA microsatellites was analysed in 494 tree frogs sampled from two ponds in Jutland and 10 ponds on Lolland. A significant overall deviation from Hardy-Weinberg expectations could be attributed to three ponds, all on Lolland. This was most probably caused by an inbreeding effect reducing fitness, which was supported by the observed significant negative correlation between larva survival and mean F(IS) value and mean individual inbreeding coefficient. A significant reduction in genetic variation (bottleneck) was detected in most of the ponds on Lolland. Population-structure analysis suggested the existence of at least 11 genetically different populations, corresponding to most of the sampled population units. The results indicated that the populations were unique genetic units and could be used to illustrate the migration pattern between newly established ponds arisen either by natural colonization of tree frogs or by artificial introduction. A high degree of pond fidelity in the tree frogs was suggested. A severe fragmentation process reducing population size and fitness within some of the populations probably caused the significant reduction in genetic variation of tree frog populations on Lolland. PMID:15306354

Spatio-temporal variability of airborne bacterial communities and their correlation with particulate matter chemical composition across two urban areas.

PubMed

Gandolfi, I; Bertolini, V; Bestetti, G; Ambrosini, R; Innocente, E; Rampazzo, G; Papacchini, M; Franzetti, A

2015-06-01

The study of spatio-temporal variability of airborne bacterial communities has recently gained importance due to the evidence that airborne bacteria are involved in atmospheric processes and can affect human health. In this work, we described the structure of airborne microbial communities in two urban areas (Milan and Venice, Northern Italy) through the sequencing, by the Illumina platform, of libraries containing the V5-V6 hypervariable regions of the 16S rRNA gene and estimated the abundance of airborne bacteria with quantitative PCR (qPCR). Airborne microbial communities were dominated by few taxa, particularly Burkholderiales and Actinomycetales, more abundant in colder seasons, and Chloroplasts, more abundant in warmer seasons. By partitioning the variation in bacterial community structure, we could assess that environmental and meteorological conditions, including variability between cities and seasons, were the major determinants of the observed variation in bacterial community structure, while chemical composition of atmospheric particulate matter (PM) had a minor contribution. Particularly, Ba, SO4 (2-) and Mg(2+) concentrations were significantly correlated with microbial community structure, but it was not possible to assess whether they simply co-varied with seasonal shifts of bacterial inputs to the atmosphere, or their variation favoured specific taxa. Both local sources of bacteria and atmospheric dispersal were involved in the assembling of airborne microbial communities, as suggested, to the one side by the large abundance of bacteria typical of lagoon environments (Rhodobacterales) observed in spring air samples from Venice and to the other by the significant effect of wind speed in shaping airborne bacterial communities at all sites.

Multidimensional structure-function relationships in human β-cardiac myosin from population-scale genetic variation

PubMed Central

Homburger, Julian R.; Green, Eric M.; Caleshu, Colleen; Sunitha, Margaret S.; Taylor, Rebecca E.; Ruppel, Kathleen M.; Metpally, Raghu Prasad Rao; Colan, Steven D.; Michels, Michelle; Day, Sharlene M.; Olivotto, Iacopo; Bustamante, Carlos D.; Dewey, Frederick E.; Ho, Carolyn Y.; Spudich, James A.; Ashley, Euan A.

2016-01-01

Myosin motors are the fundamental force-generating elements of muscle contraction. Variation in the human β-cardiac myosin heavy chain gene (MYH7) can lead to hypertrophic cardiomyopathy (HCM), a heritable disease characterized by cardiac hypertrophy, heart failure, and sudden cardiac death. How specific myosin variants alter motor function or clinical expression of disease remains incompletely understood. Here, we combine structural models of myosin from multiple stages of its chemomechanical cycle, exome sequencing data from two population cohorts of 60,706 and 42,930 individuals, and genetic and phenotypic data from 2,913 patients with HCM to identify regions of disease enrichment within β-cardiac myosin. We first developed computational models of the human β-cardiac myosin protein before and after the myosin power stroke. Then, using a spatial scan statistic modified to analyze genetic variation in protein 3D space, we found significant enrichment of disease-associated variants in the converter, a kinetic domain that transduces force from the catalytic domain to the lever arm to accomplish the power stroke. Focusing our analysis on surface-exposed residues, we identified a larger region significantly enriched for disease-associated variants that contains both the converter domain and residues on a single flat surface on the myosin head described as the myosin mesa. Notably, patients with HCM with variants in the enriched regions have earlier disease onset than patients who have HCM with variants elsewhere. Our study provides a model for integrating protein structure, large-scale genetic sequencing, and detailed phenotypic data to reveal insight into time-shifted protein structures and genetic disease. PMID:27247418

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

DOE PAGES

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

2010-01-01

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

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.

Quantifying heterogeneity in human tumours using MRI and PET.

PubMed

Asselin, Marie-Claude; O'Connor, James P B; Boellaard, Ronald; Thacker, Neil A; Jackson, Alan

2012-03-01

Most tumours, even those of the same histological type and grade, demonstrate considerable biological heterogeneity. Variations in genomic subtype, growth factor expression and local microenvironmental factors can result in regional variations within individual tumours. For example, localised variations in tumour cell proliferation, cell death, metabolic activity and vascular structure will be accompanied by variations in oxygenation status, pH and drug delivery that may directly affect therapeutic response. Documenting and quantifying regional heterogeneity within the tumour requires histological or imaging techniques. There is increasing evidence that quantitative imaging biomarkers can be used in vivo to provide important, reproducible and repeatable estimates of tumoural heterogeneity. In this article we review the imaging methods available to provide appropriate biomarkers of tumour structure and function. We also discuss the significant technical issues involved in the quantitative estimation of heterogeneity and the range of descriptive metrics that can be derived. Finally, we have reviewed the existing clinical evidence that heterogeneity metrics provide additional useful information in drug discovery and development and in clinical practice. Copyright © 2012 Elsevier Ltd. All rights reserved.

Consistent individual differences in the social phenotypes of wild great tits, Parus major

PubMed Central

Aplin, L.M.; Firth, J.A.; Farine, D.R.; Voelkl, B.; Crates, R.A.; Culina, A.; Garroway, C.J.; Hinde, C.A.; Kidd, L.R.; Psorakis, I.; Milligan, N.D.; Radersma, R.; Verhelst, B.L.; Sheldon, B.C.

2015-01-01

Despite growing interest in animal social networks, surprisingly little is known about whether individuals are consistent in their social network characteristics. Networks are rarely repeatedly sampled; yet an assumption of individual consistency in social behaviour is often made when drawing conclusions about the consequences of social processes and structure. A characterization of such social phenotypes is therefore vital to understanding the significance of social network structure for individual fitness outcomes, and for understanding the evolution and ecology of individual variation in social behaviour more broadly. Here, we measured foraging associations over three winters in a large PIT-tagged population of great tits, and used a range of social network metrics to quantify individual variation in social behaviour. We then examined repeatability in social behaviour over both short (week to week) and long (year to year) timescales, and investigated variation in repeatability across age and sex classes. Social behaviours were significantly repeatable across all timescales, with the highest repeatability observed in group size choice and unweighted degree, a measure of gregariousness. By conducting randomizations to control for the spatial and temporal distribution of individuals, we further show that differences in social phenotypes were not solely explained by within-population variation in local densities, but also reflected fine-scale variation in social decision making. Our results provide rare evidence of stable social phenotypes in a wild population of animals. Such stable social phenotypes can be targets of selection and may have important fitness consequences, both for individuals and for their social-foraging associates. PMID:26512142

Spatial changes in acid secretion from isolated stomach tissue using a pH-histamine sensing microarray.

PubMed

Bitziou, Eleni; O'Hare, Danny; Patel, Bhavik Anil

2010-03-01

The acid secretion mechanism can be studied by measuring a series of metabolic markers and neurotransmitters from in vitro isolated tissue. A microelectrode array was used to monitor proton concentration and histamine levels from isolated guinea pig stomach tissue. The device was partially modified using iridium oxide to form a series of pH sensors, whereas unmodified gold microelectrodes were used to measure the level of histamine in the gut. Real-time measurements in the presence of the H2-receptor antagonist ranitidine produced significant decreases in the overall Delta pH response, as expected. Also, a significant variation in the Delta pH response in between pH sensors was observed in the presence of pharmacological treatment due to structural features of the tissue. No significant differences in Delta i(H) were detected in the presence of ranitidine as expected. More significantly, clear variations in Delta pH responses between animals in control conditions and those in the presence of ranitidine was observed highlighting possible variation in parietal cell density and/or variations in tissue activity. These results identify great possibilities in applying these multi-sensing devices as a long-term stable personalised diagnostic tool for pharmacological screening and disease status.

Discriminating Natural Variation from Legacies of Disturbance in Semi-Arid Forests, Southwestern USA

NASA Astrophysics Data System (ADS)

Swetnam, T. L.; Lynch, A. M.; Falk, D. A.; Yool, S. R.; Guertin, D. P.

2014-12-01

Characterizing differences in existing vegetation driven by natural variation versus disturbance legacies could become a critical component of applied forest management practice with important implications for monitoring ecologic succession and eco-hydrological interactions within the critical zone. Here we characterize variations in aerial LiDAR derived forest structure at individual tree scale in Arizona and New Mexico. Differences in structure result from both topographic and climatological variations and from natural and human related disturbances. We chose a priori undisturbed and disturbed sites that included preservation, development, logging and wildfire as exemplars. We compare two topographic indices, the topographic position index (TPI) and topographic wetness index (TWI), to two local indicators of spatial association (LISA): the Getis-Ord Gi and Anselin's Moran I. We found TPI and TWI correlate well to positive z-scores (tall trees in tall neighborhoods) in undisturbed areas and that disturbed areas are clearly defined by negative z-scores, in some cases better than what is visible from traditional orthophotography and existing GIS maps. These LISA methods also serve as a robust technique for creating like-clustered stands, i.e. common stands used in forest inventory monitoring. This research provides a significant advancement in the ability to (1) quantity variation in forest structure across topographically complex landscapes, (2) identify and map previously unrecorded disturbance locations, and (3) quantify the different impacts of disturbance within the perimeter of a stand or event at ecologically relevant scale.

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

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

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

2012-07-01

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

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.

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.

The Hyperfine Structure of the Ground State in the Muonic Helium Atoms

NASA Astrophysics Data System (ADS)

Aznabayev, D. T.; Bekbaev, A. K.; Korobov, V. I.

2018-05-01

Non-relativistic ionization energies 3He2+μ-e- and 4He2+μ-e- of helium-muonic atoms are calculated for ground states. The calculations are based on the variational method of the exponential expansion. Convergence of the variational energies is studied by an increasing of a number of the basis functions N. This allows to claim that the obtained energy values have 26 significant digits for ground states. With the obtained results we calculate hyperfine splitting of the muonic helium atoms.

Genetic and Epigenetic Variations Induced by Wheat-Rye 2R and 5R Monosomic Addition Lines

PubMed Central

Fu, Shulan; Sun, Chuanfei; Yang, Manyu; Fei, Yunyan; Tan, Feiqun; Yan, Benju; Ren, Zhenglong; Tang, Zongxiang

2013-01-01

Background Monosomic alien addition lines (MAALs) can easily induce structural variation of chromosomes and have been used in crop breeding; however, it is unclear whether MAALs will induce drastic genetic and epigenetic alterations. Methodology/Principal Findings In the present study, wheat-rye 2R and 5R MAALs together with their selfed progeny and parental common wheat were investigated through amplified fragment length polymorphism (AFLP) and methylation-sensitive amplification polymorphism (MSAP) analyses. The MAALs in different generations displayed different genetic variations. Some progeny that only contained 42 wheat chromosomes showed great genetic/epigenetic alterations. Cryptic rye chromatin has introgressed into the wheat genome. However, one of the progeny that contained cryptic rye chromatin did not display outstanding genetic/epigenetic variation. 78 and 49 sequences were cloned from changed AFLP and MSAP bands, respectively. Blastn search indicated that almost half of them showed no significant similarity to known sequences. Retrotransposons were mainly involved in genetic and epigenetic variations. Genetic variations basically affected Gypsy-like retrotransposons, whereas epigenetic alterations affected Copia-like and Gypsy-like retrotransposons equally. Genetic and epigenetic variations seldom affected low-copy coding DNA sequences. Conclusions/Significance The results in the present study provided direct evidence to illustrate that monosomic wheat-rye addition lines could induce different and drastic genetic/epigenetic variations and these variations might not be caused by introgression of rye chromatins into wheat. Therefore, MAALs may be directly used as an effective means to broaden the genetic diversity of common wheat. PMID:23342073

Recovery and fine structure variability of RGII sub-domains in wine (Vitis vinifera Merlot)

PubMed Central

Buffetto, F.; Ropartz, D.; Zhang, X. J.; Gilbert, H. J.; Guillon, F.; Ralet, M.-C.

2014-01-01

Background and Aims Rhamnogalacturonan II (RGII) is a structurally complex pectic sub-domain composed of more than 12 different sugars and 20 different linkages distributed in five side chains along a homogalacturonan backbone. Although RGII has long been described as highly conserved over plant evolution, recent studies have revealed variations in the structure of the polysaccharide. This study examines the fine structure variability of RGII in wine, focusing on the side chains A and B obtained after sequential mild acid hydrolysis. Specifically, this study aims to differentiate intrinsic structural variations in these RGII side chains from structural variations due to acid hydrolysis. Methods RGII from wine (Vitis vinifera Merlot) was sequentially hydrolysed with trifluoroacetic acid (TFA) and the hydrolysis products were separated by anion-exchange chromatography (AEC). AEC fractions or total hydrolysates were analysed by MALDI-TOF mass spectrometry. Key Results The optimal conditions to recover non-degraded side chain B, side chain A and RGII backbone were 0·1 m TFA at 40 °C for 16 h, 0·48 m TFA at 40 °C for 16 h (or 0·1 m TFA at 60 °C for 8 h) and 0·1 m TFA at 60 °C for 16 h, respectively. Side chain B was particularly prone to acid degradation. Side chain A and the RGII GalA backbone were partly degraded by 0·1 m TFA at 80 °C for 1–4 h. AEC allowed separation of side chain B, methyl-esterified side chain A and non-methyl-esterified side chain A. The structure of side chain A and the GalA backbone were highly variable. Conclusions Several modifications to the RGII structure of wine were identified. The observed dearabinosylation and deacetylation were primarily the consequence of acidic treatment, while variation in methyl-esterification, methyl-ether linkages and oxidation reflect natural diversity. The physiological significance of this variability, however, remains to be determined. PMID:24908680

Computed parameters : moisture content for unbound materials at seasonal monitoring program sites

DOT National Transportation Integrated Search

2000-01-01

Moisture content plays a significant role in the performance of pavements. Variation in the amount of moisture in the subgrade can change the volume of swelling soil, which may result in detrimental deformation of the pavement structure. An increase ...

Regional variation in smoking among African Americans.

PubMed

King, G; Polednak, A P; Bendel, R

1999-08-01

The impact of geographic region and metropolitan residence on smoking prevalence among African Americans has not been adequately examined. This study analyzed 5 years of data from the National Health Interview Survey (1990-1994) on current smoking and regional variation among 16,738 African Americans. Results. Respondents in the West had the lowest unadjusted smoking prevalence rates and Midwest residents had the highest. Current smoking was lower among African Americans living in non-central cities than in central cities even after adjusting for several sociodemographic covariates. Multivariate logistic regression analysis revealed that black women in the South were significantly less likely to be smokers compared with any other gender/region group. These findings suggest the significance of gender and regional factors such as the social history of migration, social stress and racism, exposure to tobacco advertisement, variations in cultural influences, community structures, and coping strategies in under standing African American smoking behavior. Copyright 1999 American Health Foundation and Academic Press.

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

Miller, James Christopher; Rennie, John Alan; Toevs, James Waldo

The introduction points out that radiation backgrounds fluctuate across very short distances: factors include geology, soil composition, altitude, building structures, topography, and other manmade structures; and asphalt and concrete can vary significantly over short distances. Brief descriptions are given of the detection system, experimental setup, and background variation measurements. It is concluded that positive and negative gradients can greatly reduce the detection sensitivity of an MDS: negative gradients create opportunities for false negatives (nondetection), and positive gradients create a potentially unacceptable FAR (above 1%); the location of use for mobile detection is important to understand; spectroscopic systems provide more informationmore » for screening out false alarms and may be preferred for mobile use; and mobile monitor testing at LANL accounts for expected variations in the background.« less

Relative impacts of environmental variation and evolutionary history on the nestedness and modularity of tree–herbivore networks

PubMed Central

Robinson, Kathryn M; Hauzy, Céline; Loeuille, Nicolas; Albrectsen, Benedicte R

2015-01-01

Nestedness and modularity are measures of ecological networks whose causative effects are little understood. We analyzed antagonistic plant–herbivore bipartite networks using common gardens in two contrasting environments comprised of aspen trees with differing evolutionary histories of defence against herbivores. These networks were tightly connected owing to a high level of specialization of arthropod herbivores that spend a large proportion of the life cycle on aspen. The gardens were separated by ten degrees of latitude with resultant differences in abiotic conditions. We evaluated network metrics and reported similar connectance between gardens but greater numbers of links per species in the northern common garden. Interaction matrices revealed clear nestedness, indicating subsetting of the bipartite interactions into specialist divisions, in both the environmental and evolutionary aspen groups, although nestedness values were only significant in the northern garden. Variation in plant vulnerability, measured as the frequency of herbivore specialization in the aspen population, was significantly partitioned by environment (common garden) but not by evolutionary origin of the aspens. Significant values of modularity were observed in all network matrices. Trait-matching indicated that growth traits, leaf morphology, and phenolic metabolites affected modular structure in both the garden and evolutionary groups, whereas extra-floral nectaries had little influence. Further examination of module configuration revealed that plant vulnerability explained considerable variance in web structure. The contrasting conditions between the two gardens resulted in bottom-up effects of the environment, which most strongly influenced the overall network architecture, however, the aspen groups with dissimilar evolutionary history also showed contrasting degrees of nestedness and modularity. Our research therefore shows that, while evolution does affect the structure of aspen–herbivore bipartite networks, the role of environmental variations is a dominant constraint. PMID:26306175

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

Contrasting genetic structure between mitochondrial and nuclear markers in the dengue fever mosquito from Rio de Janeiro: implications for vector control

PubMed Central

Rašić, Gordana; Schama, Renata; Powell, Rosanna; Maciel-de Freitas, Rafael; Endersby-Harshman, Nancy M; Filipović, Igor; Sylvestre, Gabriel; Máspero, Renato C; Hoffmann, Ary A

2015-01-01

Dengue is the most prevalent global arboviral disease that affects over 300 million people every year. Brazil has the highest number of dengue cases in the world, with the most severe epidemics in the city of Rio de Janeiro (Rio). The effective control of dengue is critically dependent on the knowledge of population genetic structuring in the primary dengue vector, the mosquito Aedes aegypti. We analyzed mitochondrial and nuclear genomewide single nucleotide polymorphism markers generated via Restriction-site Associated DNA sequencing, as well as traditional microsatellite markers in Ae. aegypti from Rio. We found four divergent mitochondrial lineages and a strong spatial structuring of mitochondrial variation, in contrast to the overall nuclear homogeneity across Rio. Despite a low overall differentiation in the nuclear genome, we detected strong spatial structure for variation in over 20 genes that have a significantly altered expression in response to insecticides, xenobiotics, and pathogens, including the novel biocontrol agent Wolbachia. Our results indicate that high genetic diversity, spatially unconstrained admixing likely mediated by male dispersal, along with locally heterogeneous genetic variation that could affect insecticide resistance and mosquito vectorial capacity, set limits to the effectiveness of measures to control dengue fever in Rio. PMID:26495042

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

PubMed

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

2015-01-01

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

Comparative population genomics of latitudinal variation in Drosophila simulans and Drosophila melanogaster

PubMed Central

MACHADO, HEATHER E.; BERGLAND, ALAN O.; O’BRIEN, KATHERINE R.; BEHRMAN, EMILY L.; SCHMIDT, PAUL S.; PETROV, DMITRI A.

2016-01-01

Examples of clinal variation in phenotypes and genotypes across latitudinal transects have served as important models for understanding how spatially varying selection and demographic forces shape variation within species. Here, we examine the selective and demographic contributions to latitudinal variation through the largest comparative genomic study to date of Drosophila simulans and Drosophila melanogaster, with genomic sequence data from 382 individual fruit flies, collected across a spatial transect of 19 degrees latitude and at multiple time points over 2 years. Consistent with phenotypic studies, we find less clinal variation in D. simulans than D. melanogaster, particularly for the autosomes. Moreover, we find that clinally varying loci in D. simulans are less stable over multiple years than comparable clines in D. melanogaster. D. simulans shows a significantly weaker pattern of isolation by distance than D. melanogaster and we find evidence for a stronger contribution of migration to D. simulans population genetic structure. While population bottlenecks and migration can plausibly explain the differences in stability of clinal variation between the two species, we also observe a significant enrichment of shared clinal genes, suggesting that the selective forces associated with climate are acting on the same genes and phenotypes in D. simulans and D. melanogaster. PMID:26523848

Vortex wakes generated by robins Erithacus rubecula during free flight in a wind tunnel.

PubMed

Hedenström, A; Rosén, M; Spedding, G R

2006-04-22

The wakes of two individual robins were measured in digital particle image velocimetry (DPIV) experiments conducted in the Lund wind tunnel. Wake measurements were compared with each other, and with previous studies in the same facility. There was no significant individual variation in any of the measured quantities. Qualitatively, the wake structure and its gradual variation with flight speed were exactly as previously measured for the thrush nightingale. A procedure that accounts for the disparate sources of circulation spread over the complex wake structure nevertheless can account for the vertical momentum flux required to support the weight, and an example calculation is given for estimating drag from the components of horizontal momentum flux (whose net value is zero). The measured circulations of the largest structures in the wake can be predicted quite well by simple models, and expressions are given to predict these and other measurable quantities in future bird flight experiments.

Thermal structure of the Kanto region, Japan

NASA Astrophysics Data System (ADS)

Wada, Ikuko; He, Jiangheng

2017-07-01

Using a 3-D numerical thermal model, we investigate the thermal structure of the Kanto region of Japan where two oceanic plates subduct. In a typical subduction setting with one subducting slab, the motion of the slab drives solid-state mantle flow in the overlying mantle wedge, bringing in hot mantle from the back-arc toward the forearc. Beneath Kanto, however, the presence of the subducting Philippine Sea plate between the overlying North American plate and the subducting Pacific plate prevents a typical mantle wedge flow pattern, resulting in a cooler condition. Further, frictional heating and the along-margin variation in the maximum depth of slab-mantle decoupling along the Pacific slab surface affect the thermal structure significantly. The model provides quantitative estimates of spatial variations in the temperature condition that are consistent with the observed surface heat flow pattern and distributions of interplate seismicity and arc volcanoes in Kanto.

Transposable elements generate population-specific insertional patterns and allelic variation in genes of wild emmer wheat (Triticum turgidum ssp. dicoccoides).

PubMed

Domb, Katherine; Keidar, Danielle; Yaakov, Beery; Khasdan, Vadim; Kashkush, Khalil

2017-10-27

Natural populations of the tetraploid wild emmer wheat (genome AABB) were previously shown to demonstrate eco-geographically structured genetic and epigenetic diversity. Transposable elements (TEs) might make up a significant part of the genetic and epigenetic variation between individuals and populations because they comprise over 80% of the wild emmer wheat genome. In this study, we performed detailed analyses to assess the dynamics of transposable elements in 50 accessions of wild emmer wheat collected from 5 geographically isolated sites. The analyses included: the copy number variation of TEs among accessions in the five populations, population-unique insertional patterns, and the impact of population-unique/specific TE insertions on structure and expression of genes. We assessed the copy numbers of 12 TE families using real-time quantitative PCR, and found significant copy number variation (CNV) in the 50 wild emmer wheat accessions, in a population-specific manner. In some cases, the CNV difference reached up to 6-fold. However, the CNV was TE-specific, namely some TE families showed higher copy numbers in one or more populations, and other TE families showed lower copy numbers in the same population(s). Furthermore, we assessed the insertional patterns of 6 TE families using transposon display (TD), and observed significant population-specific insertional patterns. The polymorphism levels of TE-insertional patterns reached 92% among all wild emmer wheat accessions, in some cases. In addition, we observed population-specific/unique TE insertions, some of which were located within or close to protein-coding genes, creating allelic variations in a population-specific manner. We also showed that those genes are differentially expressed in wild emmer wheat. For the first time, this study shows that TEs proliferate in wild emmer wheat in a population-specific manner, creating new alleles of genes, which contribute to the divergent evolution of homeologous genes from the A and B subgenomes.

The collagen structure of equine articular cartilage, characterized using polarization-sensitive optical coherence tomography

NASA Astrophysics Data System (ADS)

Ugryumova, Nadya; Attenburrow, Don P.; Winlove, C. Peter; Matcher, Stephen J.

2005-08-01

Optical coherence tomography and polarization-sensitive optical coherence tomography images of equine articular cartilage are presented. Measurements were made on intact joint surfaces. Significant (e.g. × 2) variations in the intrinsic birefringence were found over spatial scales of a few millimetres, even on samples taken from young (18 month) animals that appeared visually homogeneous. A comparison of data obtained on a control tissue (equine flexor tendon) further suggests that significant variations in the orientation of the collagen fibres relative to the plane of the joint surface exist. Images of visually damaged cartilage tissue show characteristic features both in terms of the distribution of optical scatterers and of the birefringent components.

Significance of Dynamic Pore Pressure Variations - Comparison of Observations on Mud Volcanoes on the Costa Rica Margin and in the Gulf of Cadiz

NASA Astrophysics Data System (ADS)

Brueckmann, W.; Linke, P.; Pieper, M.; Hensen, C.; Tuerk, M.

2006-12-01

Research in the cooperative research center (SFB) 574 "Volatiles and Fluids in Subduction Zones" at the University Kiel focuses on volatile and fluid exchange processes at subduction zones. These have a significant impact on the long-term geochemical evolution of the hydrosphere and atmosphere. In the SFB 574 working area off Central America more than 120 mud volcanoes, mud diapirs and cold seeps have been identified and sampled. To better understand the internal dynamics of these structures and the temporal variability of fluid expulsion an in-situ tool for monitoring shallow pore pressure variations was devised. The tool (PWPL) monitors pore pressure variations along a 2m profile in the shallow subsurface using a stinger with 4 pressure ports. Positioned with a video-guided lander the stinger is gently pushed into the seafloor where it remains for several weeks or months in autonomous mode before being retrieved. While particular emphasis was placed on the convergent margin of Central America, mud volcanoes in other tectonic settings suitable for long-term observations of fluid flux are used for comparison. Here we will present data and interpretations from two mud volcanoes off Costa Rica and in the Gulf of Cadiz where we have conducted successful tests. Pore pressure data from short-term tests on Mound 11 on the continental slope off Costa Rica are compared with new results from a long-term (3-month) campaign on the Captain Arutjunov deep water mud volcano in the Gulf of Cadiz. Rates of fluid flow at both structures have been thoroughly characterized and quantified with geochemical methods providing a frame of reference for judging the significance of dynamic pore pressure variations.

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.

Prevalence and variations of the median maxillary labial frenum in children, adolescents, and adults in a diverse population.

PubMed

Townsend, Janice A; Brannon, Robert B; Cheramie, Toby; Hagan, Joseph

2013-01-01

The median maxillary labial frenum (MMLF) is a normal anatomic structure with inherent morphologic variations. This study sought to evaluate the prevalence of those variations in a diverse ethnic population and to educate practitioners about the prevalence of MMLF variations to prevent unnecessary biopsies. This study included adult, adolescent, and child patients at the Louisiana State University Health Science Center School of Dentistry. Among the 284 subjects examined, frenum normale was the most common frenum classification, followed by frenum with nodule and frenum with appendix. Most nodules were found in the intermediate third of the MMLF, while appendices were mainly found in the labial third. The prevalence of an appendix was significantly higher (P < 0.001) in Caucasians compared to African-Americans. The prevalence of nodules was marginally higher (P = 0.096) in Caucasians than in African-Americans. No other statistically significant differences were found with regard to ethnicity. Additionally, nodules and appendices on the MMLF were identified in all age groups, and may become more common with increasing age. The authors determined that variations of the MMLF are inherent and do not represent a pathologic condition, nor do they require biopsy for diagnostic purposes.

Regional Variation in the Structural Response and Geometrical Properties of Human Ribs

PubMed Central

Cormier, Joseph M.; Stitzel, Joel D.; Duma, Stefan M.; Matsuoka, Fumio

2005-01-01

By incorporating material and geometrical properties into a model of the human thorax one can develop an injury criterion that is a function of stress and strain of the material and not a function of the global response of the thorax. Previous research on the mechanical properties of ribs has focused on a limited set of specific ribs. For this study a total of 52 rib specimens were removed from four cadaver subjects. Variation in peak moment by thoracic region was significant (p < 0.01) with average values of 2, 2.9 and 3.9 N-m for the anterior, lateral and posterior regions respectively. Two geometrical properties, radius of gyration and distance from the neutral axis, showed significant variation by region (p < 0.0001) as well as by rib level (p = < 0.01, 0.05). The results of this study can be used to update current models of the human thorax to account for the variation in strength and geometrical properties throughout the rib cage. Accounting for the variation in rib properties by region will improve injury predictive measures and, therefore, the ability to design systems to prevent thoracic injury. PMID:16179146

Statistical behavior of the longitudinal variations of daytime electron density in the topside ionosphere at middle latitudes

NASA Astrophysics Data System (ADS)

Su, Fanfan; Wang, Wenbin; Burns, Alan G.; Yue, Xinan; Zhu, Fuying; Lin, Jian

2016-11-01

Electron density in the topside ionosphere has significant variations with latitude, longitude, altitude, local time, season, and solar cycle. This paper focuses on the global and seasonal features of longitudinal structures of daytime topside electron density (Ne) at middle latitudes and their possible causes. We used in situ Ne measured by DEMETER and F2 layer peak height (hmF2) and peak density (NmF2) from COSMIC. The longitudinal variations of the daytime topside Ne show a wave number 2-type structure in the Northern Hemisphere, whereas those in the Southern Hemisphere are dominated by a wave number 1 structure and are much larger than those in the Northern Hemisphere. The patterns around December solstice (DS) in the Northern Hemisphere (winter) are different from other seasons, whereas the patterns in the Southern Hemisphere are similar in each season. Around March equinox (ME), June solstice (JS), and September equinox (SE) in the Northern Hemisphere and around ME, SE, and DS in the Southern Hemisphere, the longitudinal variations of topside Ne have similar patterns to hmF2. Around JS in the Southern Hemisphere (winter), the topside Ne has similar patterns to NmF2 and hmF2 does not change much with longitude. Thus, the topside variations may be explained intuitively in terms of hmF2 and NmF2. This approach works reasonably well in most of the situations except in the northern winter in the topside not too far from the F2 peak. In this sense, understanding variations in hmF2 and NmF2 becomes an important and relevant subject for this topside ionospheric study.

Tuning up mind's pattern to nature's own idea: Eddington's early twenties case for variational derivatives

NASA Astrophysics Data System (ADS)

Smadja, Ivahn

This paper sets out to show how Eddington's early twenties case for variational derivatives significantly bears witness to a steady and consistent shift in focus from a resolute striving for objectivity towards "selective subjectivism" and structuralism. While framing his so-called "Hamiltonian derivatives" along the lines of previously available variational methods allowing to derive gravitational field equations from an action principle, Eddington assigned them a theoretical function of his own devising in The Mathematical Theory of Relativity (1923). I make clear that two stages should be marked out in Eddington's train of thought if the meaning of such variational derivatives is to be adequately assessed. As far as they were originally intended to embody the mind's collusion with nature by linking atomicity of matter with atomicity of action, variational derivatives were at first assigned a dual role requiring of them not only to express mind's craving for permanence but also to tune up mind's privileged pattern to "Nature's own idea". Whereas at a later stage, as affine field theory would provide a framework for world-building, such "Hamiltonian differentiation" would grow out of tune through gauge-invariance and, by disregarding how mathematical theory might precisely come into contact with actual world, would be turned into a mere heuristic device for structural knowledge.

Nanoporous structures on ZnO thin films

NASA Astrophysics Data System (ADS)

Gür, Emre; Kılıç, Bayram; Coşkun, C.; Tüzemen, S.; Bayrakçeken, Fatma

2010-01-01

Porous structures were formed on ZnO thin films which were grown by an electrochemical deposition (ECD) method. The growth processes were carried out in a solution of dimethylsulfoxide (DMSO) zinc perchlorate, Zn(ClO 4) 2, at 120 ∘C on indium tin oxide (ITO) substrates. Optical and structural characterizations of electrochemically grown ZnO thin films have shown that the films possess high (0002) c-axis orientation, high nucleation, high intensity and low FWHM of UV emission at the band edge region and a sharp UV absorption edge. Nanoporous structures were formed via self-assembled monolayers (SAMs) of hexanethiol (C 6SH) and dodecanethiol (C 12SH). Scanning electron microscope (SEM) measurements showed that while a nanoporous structure (pore radius 20 nm) is formed on the ZnO thin films by hexanathiol solution, a macroporous structure (pore radius 360 nm) is formed by dodecanethiol solution. No significant variation is observed in X-ray diffraction (XRD) measurements on the ZnO thin films after pore formation. However, photoluminescence (PL) measurements showed that green emission is observed as the dominant emission for the macroporous structures, while no variation is observed for the thin film nanoporous ZnO sample.

Interrelated chemical-microstructural-nanomechanical variations in the structural units of the cuttlebone of Sepia officinalis

NASA Astrophysics Data System (ADS)

North, L.; Labonte, D.; Oyen, M. L.; Coleman, M. P.; Caliskan, H. B.; Johnston, R. E.

2017-11-01

"Cuttlebone," the internalized shell found in all members of the cephalopod family Sepiidae, is a sophisticated buoyancy device combining high porosity with considerable strength. Using a complementary suite of characterization tools, we identified significant structural, chemical, and mechanical variations across the different structural units of the cuttlebone: the dorsal shield consists of two stiff and hard layers with prismatic mineral organization which encapsulate a more ductile and compliant layer with a lamellar structure, enriched with organic matter. A similar organization is found in the chambers, which are separated by septa, and supported by meandering plates ("pillars"). Like the dorsal shield, septa contain two layers with lamellar and prismatic organization, respectively, which differ significantly in their mechanical properties: layers with prismatic organization are a factor of three stiffer and up to a factor of ten harder than those with lamellar organization. The combination of stiff and hard, and compliant and ductile components may serve to reduce the risk of catastrophic failure, and reflect the role of organic matter for the growth process of the cuttlebone. Mechanically "weaker" units may function as sacrificial structures, ensuring a stepwise failure of the individual chambers in cases of overloading, allowing the animals to retain near-neutral buoyancy even with partially damaged cuttlebones. Our findings have implications for our understanding of the structure-property-function relationship of cuttlebone, and may help to identify novel bioinspired design strategies for light-weight yet high-strength foams.

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

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

PubMed

Momany, Cory; Neidle, Ellen L

2012-02-01

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

Homogeneous Nanodiamonds Are Different in Reality

NASA Astrophysics Data System (ADS)

Wu, Chi-Chin; Gottfried, Jennifer; Pesce-Rodriguez, Rose; Advanced Energetic Materials Team

Commercial detonation nanodiamonds (ND) have been investigated for many applications. They consist of carbon nanoparticles with diamond cores surrounded by onion-like graphitic shells. Unfortunately, variations in the purity and carbon structure between commercial ND samples due to variations in synthesis and purification conditions is an ongoing issue, since these differences can affect the resulting application-dependent ND behavior. Via characterization with transmission electron microscopy, this work investigates the structural and chemical differences among nominally homologous commercial detonation ND sold by a single vendor under the same item number. Significant discrepancies in the carbon structure and crystallinity between different batches with similar sizes and shapes were identified. The ND containing more non-carbon entities as impurities and oxygen-containing surface functional groups were found to possess thicker graphitic shells surrounding an unstable diamond core which quickly transforms to graphite under electron beam irradiation. However, the structure of ND with higher purities and thin onion shells remain unchanged over extended exposure to electron beams. This study demonstrates the structural and chemical differences between nominally identical commercial detonation ND samples and reveals their influence on the decomposition behavior of the particles.

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

Impact of Acoustic Standing Waves on Structural Responses: Reverberant Acoustic Testing (RAT) vs. Direct Field Acoustic Testing (DFAT)

NASA Technical Reports Server (NTRS)

Kolaini, Ali R.; Doty, Benjamin; Chang, Zensheu

2012-01-01

Loudspeakers have been used for acoustic qualification of spacecraft, reflectors, solar panels, and other acoustically responsive structures for more than a decade. Limited measurements from some of the recent speaker tests used to qualify flight hardware have indicated significant spatial variation of the acoustic field within the test volume. Also structural responses have been reported to differ when similar tests were performed using reverberant chambers. To address the impact of non-uniform acoustic field on structural responses, a series of acoustic tests were performed using a flat panel and a 3-ft cylinder exposed to the field controlled by speakers and repeated in a reverberant chamber. The speaker testing was performed using multi-input-single-output (MISO) and multi-input-multi-output (MIMO) control schemes with and without the test articles. In this paper the spatial variation of the acoustic field due to acoustic standing waves and their impacts on the structural responses in RAT and DFAT (both using MISO and MIMO controls for DFAT) are discussed in some detail.

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.

Genomic variation among populations of threatened coral: Acropora cervicornis.

PubMed

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

2016-04-13

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

The evolution of the Piedemonte Llanero petroleum system, Cordillera Oriental, Colombia (2) Reservoir petrography & petroleum geochemistry

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

Piggott, N.; Vear, A.; Warren, E.A.

1996-08-01

Detailed quantification of cements and rock texture, fluid inclusion microthermometry, thermal maturity data, oil-source rock correlations and structural restorations have been integrated to reveal the porosity and hydrocarbon charge evolution of reservoirs in the Piedemonte Llanero thrustbelt of Colombia. Active exploration of deeply buried structures in different thrust sheets of the Piedemonte Llanero has encountered quartz arenites of widely varying average porosities (4-15%). Porosity has been reduced by mechanical compaction and quartz cementation during burial, and by pressure solution during structural deformation. The relative importance and timing of these processes varies between thrust sheets controlling the observed porosity variation. Thermalmore » maturity data indicate that all thrust sheets have been deeply buried and uplifted in several stages of compression. Detailed structural restorations indicate significant differences in the burial histories of individual thrust sheets. Oil-source rock correlations suggest two major hydrocarbon components in the thrustbelt: a Late Cretaceous oil-prone source and a Tertiary oil- and gas-prone source. Initial generation charged early structures leading to partial inhibition of quartz cementation. For most structures quartz cementation predated major hydrocarbon migration. Average quartz cementation temperature is uniform within a structure, but varies between thrust sheets. These variations appear to reflect differences in burial depths during quartz cementation rather than variations in timing. Integration of all data reveals a complex but predictable evolution of porosity and hydrocarbon charge in both space and time which is being applied to current exploration in the Piedemonte Llanero and is relevant to thrustbelt exploration elsewhere.« less

Parametric Dielectric Model of Comet Churyumov-Gerasimenko

NASA Astrophysics Data System (ADS)

Heggy, E.; Palmer, E. M.; Kofman, W. W.; Clifford, S. M.; Righter, K.; Herique, A.

2012-12-01

In 2014, the European Space Agency's Rosetta mission is scheduled to rendezvous with Comet 67P/Churyumov-Gerasimenko (Comet 67P). Rosetta's CONSERT experiment aims to explore the cometary nucleus' geophysical properties using radar tomography. The expected scientific return and inversion algorithms are mainly dependent on our understanding of the dielectric properties of the comet nucleus and how they vary with the spatial distribution of geophysical parameters. Using observations of comets 9P/Tempel 1 and 81P/Wild 2 in combination with dielectric laboratory measurements of temperature, porosity, and dust-to-ice mass ratio dependencies for cometary analog material, we have constructed two hypothetical three-dimensional parametric dielectric models of Comet 67P's nucleus to assess different dielectric scenarios of the inner structure. Our models suggest that dust-to-ice mass ratios and porosity variations generate the most significant measurable dielectric contrast inside the comet nucleus, making it possible to explore the structural and compositional hypotheses of cometary nuclei. Surface dielectric variations, resulting from temperature changes induced by solar illumination of the comet's faces, have also been modeled and suggest that the real part of the dielectric constant varies from 1.9 to 3.0, hence changing the surface radar reflectivity. For CONSERT, this variation could be significant at low incidence angles, when the signal propagates through a length of dust mantle comparable to the wavelength. The overall modeled dielectric permittivity spatial and temporal variations are therefore consistent with the expected deep penetration of CONSERT's transmitted wave through the nucleus. It is also clear that changes in the physical properties of the nucleus induce sufficient variation in the dielectric properties of cometary material to allow their inversion from radar tomography.

Regional variation in the mechanical properties of the vertebral column during lateral bending in Morone saxatilis

PubMed Central

Nowroozi, B. N.; Brainerd, E. L.

2012-01-01

Unlike mammalian, disc-shaped intervertebral joints (IVJs), the IVJs in fishes are biconid structures, filled with fluid and thought to act as hydrostatic hinge joints during swimming. However, it remains unclear which IVJ structures are dominant in mechanical resistance to forces in fishes, and whether variation in these tissues might impact the function of the vertebral column along its length. Here, we measured the dynamic mechanical behaviour of IVJs from striped bass, Morone saxatilis. During lateral bending, angular stiffness was significantly lower in the caudal and cervical regions, relative to the abdominal region. The neutral zone, defined as the range of motion (ROM) at bending moments less than 0.001 Nm, was longer in the caudal relative to the abdominal IVJs. Hysteresis was 30–40% in all regions, suggesting that IVJs may play a role in energy dissipation during swimming. Cutting the vertical septum had no statistically significant effect, but cutting the encapsulating tissues caused a sharp decline in angular stiffness and a substantial increase in ROM and hysteresis. We conclude that stiffness decreases and ROM increases from cranial to caudal in striped bass, and that the encapsulating tissues play a prominent role in mechanical variation along the length of the vertebral column. PMID:22552920

Regional variation in the mechanical properties of the vertebral column during lateral bending in Morone saxatilis.

PubMed

Nowroozi, B N; Brainerd, E L

2012-10-07

Unlike mammalian, disc-shaped intervertebral joints (IVJs), the IVJs in fishes are biconid structures, filled with fluid and thought to act as hydrostatic hinge joints during swimming. However, it remains unclear which IVJ structures are dominant in mechanical resistance to forces in fishes, and whether variation in these tissues might impact the function of the vertebral column along its length. Here, we measured the dynamic mechanical behaviour of IVJs from striped bass, Morone saxatilis. During lateral bending, angular stiffness was significantly lower in the caudal and cervical regions, relative to the abdominal region. The neutral zone, defined as the range of motion (ROM) at bending moments less than 0.001 Nm, was longer in the caudal relative to the abdominal IVJs. Hysteresis was 30-40% in all regions, suggesting that IVJs may play a role in energy dissipation during swimming. Cutting the vertical septum had no statistically significant effect, but cutting the encapsulating tissues caused a sharp decline in angular stiffness and a substantial increase in ROM and hysteresis. We conclude that stiffness decreases and ROM increases from cranial to caudal in striped bass, and that the encapsulating tissues play a prominent role in mechanical variation along the length of the vertebral column.

Impact of Human Management on the Genetic Variation of Wild Pepper, Capsicum annuum var. glabriusculum

PubMed Central

González-Jara, Pablo; Moreno-Letelier, Alejandra; Fraile, Aurora; Piñero, Daniel; García-Arenal, Fernando

2011-01-01

Management of wild peppers in Mexico has occurred for a long time without clear phenotypic signs of domestication. However, pre-domestication management could have implications for the population's genetic richness. To test this hypothesis we analysed 27 wild (W), let standing (LS) and cultivated (C) populations, plus 7 samples from local markets (LM), with nine polymorphic microsatellite markers. Two hundred and fifty two alleles were identified, averaging 28 per locus. Allele number was higher in W, and 15 and 40% less in LS and C populations, respectively. Genetic variation had a significant population structure. In W populations, structure was associated with ecological and geographic areas according to isolation by distance. When LM and C populations where included in the analysis, differentiation was no longer apparent. Most LM were related to distant populations from Sierra Madre Oriental, which represents their probable origin. Historical demography shows a recent decline in all W populations. Thus, pre-domestication human management is associated with a significant reduction of genetic diversity and with a loss of differentiation suggesting movement among regions by man. Measures to conserve wild and managed populations should be implemented to maintain the source and the architecture of genetic variation in this important crop relative. PMID:22163053

Effect of temperature on the permeability of gas adsorbed coal under triaxial stress conditions

NASA Astrophysics Data System (ADS)

Li, Xiangchen; Yan, Xiaopeng; Kang, Yili

2018-04-01

The combined effects of gas sorption, stress and temperature play a significant role in the changing behavior of gas permeability in coal seams. The effect of temperature on nitrogen and methane permeability of naturally fractured coal is investigated. Coal permeability, P-wave velocity and axial strain were simultaneously measured under two effective stresses and six different temperatures. The results showed that the behavior of nitrogen and methane permeability presented nonmonotonic changes with increasing temperature. The variation in the P-wave velocity and axial strain showed a good correspondence with coal permeability. A higher effective stress limited the bigger deformation and caused the small change in permeability. Methane adsorption and desorption significantly influence the mechanical properties of coal and play an important role in the variations in coal permeability. The result of coal permeability during a complete stress-strain process showed that the variation in permeability is determined by the evolution of the internal structure. The increase in the temperature of the gas saturated coal causes the complex interaction between matrix swelling, matrix shrinkage and micro-fracture generation, which leads to the complex changes in coal structure and permeability. These results are helpful to understand the gas transport mechanism for exploiting coal methane by heat injection.

Association of MTHFR polymorphisms and chromosomal abnormalities in leukemia.

PubMed

Sinthuwiwat, Thivaratana; Poowasanpetch, Phanasit; Wongngamrungroj, Angsana; Soonklang, Kamonwan; Promso, Somying; Auewarakul, Chirayu; Tocharoentanaphol, Chintana

2012-01-01

Genetic variation in MTHFR gene might explain the interindividual differences in the reduction of DNA repaired and the increase of chromosome breakage and damage. Nowadays, chromosomal rearrangement is recognized as a major cause of lymphoid malignancies. In addition, the association of MTHFR polymorphisms with aneuploidy was found in several studies, making the MTHFR gene as a good candidate for leukemia etiology. Therefore, in this study, we investigated the common sequence variation, 677C>T and 1298A>C in the MTHFR gene of 350 fixed cell specimens archived after chromosome analysis. The distribution of the MTHFR polymorphisms frequency was compared in leukemic patients with structural chromosome abnormality and chromosome aneuploidy, as well as in those with no evidence of chromosome abnormalities. We observed a significant decrease in the distribution of T allele in 677C>T polymorphisms among patients with chromosomal abnormalities including both structural aberration and aneuploidy. The same significance result also found in patients with structural aberration when compare with the normal karyotype patients. Suggesting that polymorphism in the MTHFR gene was involved in chromosome abnormalities of leukemia. However, further investigation on the correlation with the specific types of chromosomal aberrations is needed.

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

NASA Astrophysics Data System (ADS)

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

2009-07-01

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

RAPD variation and population genetic structure of Physalaemus cuvieri (Anura: Leptodactylidae) in Central Brazil.

PubMed

Telles, Mariana Pires de Campos; Bastos, Rogério Pereira; Soares, Thannya Nascimento; Resende, Lucileide Vilela; Diniz-Filho, José Alexandre Felizola

2006-01-01

Studies about the organization of the genetic variability and population structure in natural populations are used either to understand microevolutionary processes or the effects of isolation by human-inducted landscape modifications. In this paper, we analyzed patterns of genetic population structure using 126 RAPD loci scored for 214 individuals of Physalaemus cuvieri, sampled from 18 local populations. Around 97% of these loci were polymorphic. The among-population variation component (Phi(ST)) obtained by AMOVA was equal to 0.101 and theta B obtained using a Bayesian approach for dominant markers was 0.103. Genetic divergence, analyzed by Mantel spatial correlogram, revealed only a short-distance significant correlation between genetic and geographic distances. This is expected if low levels of population differentiation, due to high abundance buffering the effect of stochastic processes, are combined with low spatially restricted gene flow. Although this may be consistent with the current knowledge of species' biology, the spatial distribution of local populations observed in this study also suggest that, at least in part, recent human occupation and habitat fragmentation may also explain part of the interpopulational component of the genetic variation.

Concerted and mosaic evolution of functional modules in songbird brains

PubMed Central

DeVoogd, Timothy J.

2017-01-01

Vertebrate brains differ in overall size, composition and functional capacities, but the evolutionary processes linking these traits are unclear. Two leading models offer opposing views: the concerted model ascribes major dimensions of covariation in brain structures to developmental events, whereas the mosaic model relates divergent structures to functional capabilities. The models are often cast as incompatible, but they must be unified to explain how adaptive changes in brain structure arise from pre-existing architectures and developmental mechanisms. Here we show that variation in the sizes of discrete neural systems in songbirds, a species-rich group exhibiting diverse behavioural and ecological specializations, supports major elements of both models. In accordance with the concerted model, most variation in nucleus volumes is shared across functional domains and allometry is related to developmental sequence. Per the mosaic model, residual variation in nucleus volumes is correlated within functional systems and predicts specific behavioural capabilities. These comparisons indicate that oscine brains evolved primarily as a coordinated whole but also experienced significant, independent modifications to dedicated systems from specific selection pressures. Finally, patterns of covariation between species and brain areas hint at underlying developmental mechanisms. PMID:28490627

Estimating Carcass Persistence and Scavenging Bias in a Human Influenced Landscape

USGS Publications Warehouse

Flint, Paul L.; Lance, Ellen W.; Sowl, Kristine M.; Donnelly, Tyrone F.

2010-01-01

We examined variation in persistence rates of waterfowl carcasses placed along a series of transects in tundra habitats in western Alaska. This study was designed to assess the effects of existing tower structures and was replicated with separate trials in winter, summer and fall as both the resident avian population and the suite of potential scavengers varied seasonally. Carcass persistence rates were uniformly low, with <50% of carcasses persisting for more than a day on average. Persistence rate varied by carcass age, carcass size, among transects and was lowest in the fall and highest in the summer. We found little support for models where persistence varied in relation to the presence of tower structures. We interpret this as evidence that scavengers were not habituated to searching for carcasses near these structures. Our data demonstrate that only a small fraction of bird carcasses are likely to persist between searches, and if not appropriately accounted for, scavenging bias could significantly influence bird mortality estimates. The variation that we documented suggests that persistence rates should not be extrapolated among tower locations or across time periods as the variation in carcass persistence will result in biased estimates of total bird strike mortality.

Identifying with fictive characters: structural brain correlates of the personality trait 'fantasy'.

PubMed

Cheetham, Marcus; Hänggi, Jürgen; Jancke, Lutz

2014-11-01

The perception of oneself as absorbed in the thoughts, feelings and happenings of a fictive character (e.g. in a novel or film) as if the character's experiences were one's own is referred to as identification. We investigated whether individual variation in the personality trait of identification is associated with individual variation in the structure of specific brain regions, using surface and volume-based morphometry. The hypothesized regions of interest were selected on the basis of their functional role in subserving the cognitive processing domains considered important for identification (i.e. mental imagery, empathy, theory of mind and merging) and for the immersive experience called 'presence'. Controlling for age, sex, whole-brain volume and other traits, identification covaried significantly with the left hippocampal volume, cortical thickness in the right anterior insula and the left dorsal medial prefrontal cortex, and with gray matter volume in the dorsolateral prefrontal cortex. These findings show that trait identification is associated with structural variation in specific brain regions. The findings are discussed in relation to the potential functional contribution of these regions to identification. © The Author (2014). Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

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.

Macro and micro structures in the dorsal anterior cingulate cortex contribute to individual differences in self-monitoring.

PubMed

Yang, Junyi; Tian, Xue; Wei, Dongtao; Liu, Huijuan; Zhang, Qinglin; Wang, Kangcheng; Chen, Qunlin; Qiu, Jiang

2016-06-01

Individual differences in self-monitoring, which are the capability to adjust behavior to adapt to social situations, influence a wide range of social behaviors. However, understanding of focal differences in brain structures related to individual self-monitoring is minimal, particularly when micro and macro structures are considered simultaneously. The present study investigates the relationship between self-monitoring and brain structure in a relatively large sample of young adults. Voxel-based morphometry (VBM) revealed a significant positive correlation between self-monitoring and gray matter volume in the dorsal cingulate anterior cortex (dACC), dorsal lateral prefrontal cortex (DLPFC), and bilateral ventral striatum (VS). Further analysis revealed a significant negative correlation between self-monitoring and white matter (WM) integrity, as indexed by fractional anisotropy (FA) in the anterior cingulum (ACG) bundle. Moreover, there was a significant positive correlation between self-monitoring and mean radius diffusion (RD). These results shed light on the structural neural basis of variation in self-monitoring.

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.

[Spatial heterogeneity and influencing factors of soil phosphorus concentration in a mid-subtropical Choerospondias axillaris deciduous broad-leaved forest, China.

PubMed

Hu, Rui Bin; Fang, Xi; Xiang, Wen Hua; Jiang, Fang; Lei, Pi Feng; Zhao, Li Juan; Zhu, Wen Juan; Deng, Xiang Wen

2016-03-01

In order to investigate spatial variations in soil phosphorus (P) concentration and the influencing factors, one permanent plot of 1 hm 2 was established and stand structure was surveyed in Choerospondias axillaries deciduous broadleaved forest in Dashanchong Forest Park in Changsha County, Hunan Province, China. Soil samples were collected with equidistant grid point sampling method and soil P concentration and its spatial variation were analyzed by using geo-statistics and geographical information system (GIS) techniques. The results showed that the variations of total P and available P concentrations in humus layer and in the soil profile at depth of 0-10, 10-20 and 20-30 cm were moderate and the available P showed higher variability in a specific soil layer compared with total P. Concentrations of total P and available P in soil decreased, while the variations increased with the increase in soil depth. The total P and available P showed high spatial autocorrelation, primarily resulted from the structural factors. The spatial heterogeneity of available P was stronger than that of total P, and the spatial autocorrelation ranges of total P and available P varied from 92.80 to 168.90 m and from 79.43 to 106.20 m in different soil layers, respectively. At the same soil depth, fractal dimensions of total P were higher than that of available P, with more complex spatial pattern, while available P showed stronger spatial correlation with stronger spatial structure. In humus layer and soil depths of 0-10, 10-20 and 20-30 cm, the spatial variation pattern of total P and available P concentrations showed an apparent belt-shaped and spot massive gradient change. The high value appeared at low elevation and valley position, and the low value appeared in the high elevation and ridge area. The total P and available P concentrations showed significantly negative correlation with elevation and litter, but the relationship with convexity, species, numbers and soil pH was not significant. The total P and available P exhibited significant positive correlations with soil organic carbon (SOC), total nitrogen concentration, indicating the leaching characteristics of soil P. Its spatial variability was affected by many interactive factors.

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

Individual differences in migratory behavior shape population genetic structure and microhabitat choice in sympatric blackcaps (Sylvia atricapilla)

PubMed Central

Rolshausen, Gregor; Segelbacher, Gernot; Hermes, Claudia; Hobson, Keith A; Schaefer, H Martin

2013-01-01

In migratory birds, traits such as orientation and distance are known to have a strong genetic background, and they often exhibit considerable within-population variation. How this variation relates to evolutionary responses to ongoing selection is unknown because the underlying mechanisms that translate environmental changes into population genetic changes are unclear. We show that within-population genetic structure in southern German blackcaps (Sylvia atricapilla) is related to individual differences in migratory behavior. Our 3-year study revealed a positive correlation between individual migratory origins, denoted via isotope (δ2H) values, and genetic distances. Genetic diversity and admixture differed not only across a recently established migratory polymorphism with NW- and SW-migrating birds but also across δ2H clusters within the same migratory route. Our results suggest assortment based on individual migratory origins which would facilitate evolutionary responses. We scrutinized arrival times and microhabitat choice as potential mechanisms mediating between individual variation in migratory behavior and assortment. We found significant support that microhabitat choice, rather than timing of arrival, is associated with individual variation in migratory origins. Moreover, examining genetic diversity across the migratory divide, we found migrants following the NW route to be genetically more distinct from each other compared with migrants following the traditional SW route. Our study suggests that migratory behavior shapes population genetic structure in blackcaps not only across the migratory divide but also on an individual level independent of the divide. Thus, within-population variation in migratory behavior might play an important role in translating environmental change into genetic change. PMID:24324877

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.

Design Methodology for Scarf Repairs to Composite Structures

DTIC Science & Technology

2006-08-01

particularly for laminates containing unidirectional ( tape ) plies, where the variation in stiffness along the scarf is significant. (a) A scarf...London. p. 610-666. 5. Lubkin, J.L., A theory of adhesive scarf joints. Journal of Applied Mechanics, 1956. July 1957: p. 255-260. 6. Erdogan , F

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.

Microsatellite variation reveals weak genetic structure and retention of genetic variability in threatened Chinook salmon (Oncorhynchus tshawytscha) within a Snake River watershed

USGS Publications Warehouse

Neville, Helen; Issacs, Frank B.; Thurow, Russel; Dunham, J.B.; Rieman, B.

2007-01-01

Pacific salmon (Oncorhynchus spp.) have been central to the development of management concepts associated with evolutionarily significant units (ESUs), yet there are still relatively few studies of genetic diversity within threatened and endangered ESUs for salmon or other species. We analyzed genetic variation at 10 microsatellite loci to evaluate spatial population structure and genetic variability in indigenous Chinook salmon (Oncorhynchus tshawytscha) across a large wilderness basin within a Snake River ESU. Despite dramatic 20th century declines in abundance, these populations retained robust levels of genetic variability. No significant genetic bottlenecks were found, although the bottleneck metric (M ratio) was significantly correlated with average population size and variability. Weak but significant genetic structure existed among tributaries despite evidence of high levels of gene flow, with the strongest genetic differentiation mirroring the physical segregation of fish from two sub-basins. Despite the more recent colonization of one sub-basin and differences between sub-basins in the natural level of fragmentation, gene diversity and genetic differentiation were similar between sub-basins. Various factors, such as the (unknown) genetic contribution of precocial males, genetic compensation, lack of hatchery influence, and high levels of current gene flow may have contributed to the persistence of genetic variability in this system in spite of historical declines. This unique study of indigenous Chinook salmon underscores the importance of maintaining natural populations in interconnected and complex habitats to minimize losses of genetic diversity within ESUs.

Ants of three adjacent habitats of a transition region between the cerrado and caatinga biomes: the effects of heterogeneity and variation in canopy cover.

PubMed

Neves, F S; Queiroz-Dantas, K S; da Rocha, W D; Delabie, J H C

2013-06-01

Habitat heterogeneity and complexity associated with variations in climatic conditions are important factors determining the structure of ant communities in different terrestrial ecosystems. The objective of this study was to describe the horizontal and vertical distribution patterns of the ant community associated with three adjacent habitats in a transition area between the Cerrado and Caatinga biomes at the Pandeiros River, state of Minas Gerais, Brazil. We tested the following hypotheses: (1) the richness and composition of ant species and functional group structure changes between different habitats and strata; (2) habitats with higher tree species richness and density support higher ant species richness; and (3) habitats with lower variation in canopy cover support higher ant species richness. Sampling was conducted in three adjacent habitats and at three vertical strata. Ant species richness was significantly different among vertical strata. Ant species composition was different among both habitats and vertical strata and functional group structure was divergent among habitats. Partitioning of the diversity revealed that the diversity for the three components was statistically different from the one expected by the null model; α and β 2 were higher and β 1 was lower than the values expected by chance. Tree density and variation in canopy cover negatively affected ant species richness. The occurrence of different species and the changing of functional group structures in different habitats and strata suggest an ecological-evolutionary relationship between ants and their habitats and emphasize the need to implement local conservation strategies in the ecotones between biomes.

Quality of care indicators for the structure and organization of inpatient rehabilitation care of children with traumatic brain injury.

PubMed

Zumsteg, Jennifer M; Ennis, Stephanie K; Jaffe, Kenneth M; Mangione-Smith, Rita; MacKenzie, Ellen J; Rivara, Frederick P

2012-03-01

To develop evidence-based and expert-driven quality indicators for measuring variations in the structure and organization of acute inpatient rehabilitation for children after traumatic brain injury (TBI) and to survey centers across the United States to determine the degree of variation in care. Quality indicators were developed using the RAND/UCLA modified Delphi method. Adherence to these indicators was determined from a survey of rehabilitation facilities. Inpatient rehabilitation units in the United States. A sample of rehabilitation programs identified using data from the National Association of Children's Hospitals and Related Institutions, Uniform Data System for Medical Rehabilitation, and the Commission on Accreditation of Rehabilitation Facilities yielded 74 inpatient units treating children with TBI. Survey respondents comprised 31 pediatric and 28 all age units. Not applicable. Variations in structure and organization of care among institutions providing acute inpatient rehabilitation for children with TBI. Twelve indicators were developed. Pediatric inpatient rehabilitation units and units with higher volumes of children with TBI were more likely to have: a census of at least 1 child admitted with a TBI for at least 90% of the time; adequate specialized equipment; a classroom; a pediatric subspecialty trained medical director; and more than 75% of therapists with pediatric training. There were clinically and statistically significant variations in the structure and organization of acute pediatric rehabilitation based on the pediatric focus of the unit and volume of children with TBI. Copyright © 2012 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Metacommunity ecology meets biogeography: effects of geographical region, spatial dynamics and environmental filtering on community structure in aquatic organisms.

PubMed

Heino, Jani; Soininen, Janne; Alahuhta, Janne; Lappalainen, Jyrki; Virtanen, Risto

2017-01-01

Metacommunity patterns and underlying processes in aquatic organisms have typically been studied within a drainage basin. We examined variation in the composition of six freshwater organismal groups across various drainage basins in Finland. We first modelled spatial structures within each drainage basin using Moran eigenvector maps. Second, we partitioned variation in community structure among three groups of predictors using constrained ordination: (1) local environmental variables, (2) spatial variables, and (3) dummy variable drainage basin identity. Third, we examined turnover and nestedness components of multiple-site beta diversity, and tested the best fit patterns of our datasets using the "elements of metacommunity structure" analysis. Our results showed that basin identity and local environmental variables were significant predictors of community structure, whereas within-basin spatial effects were typically negligible. In half of the organismal groups (diatoms, bryophytes, zooplankton), basin identity was a slightly better predictor of community structure than local environmental variables, whereas the opposite was true for the remaining three organismal groups (insects, macrophytes, fish). Both pure basin and local environmental fractions were, however, significant after accounting for the effects of the other predictor variable sets. All organismal groups exhibited high levels of beta diversity, which was mostly attributable to the turnover component. Our results showed consistent Clementsian-type metacommunity structures, suggesting that subgroups of species responded similarly to environmental factors or drainage basin limits. We conclude that aquatic communities across large scales are mostly determined by environmental and basin effects, which leads to high beta diversity and prevalence of Clementsian community types.

Isostatic models and isostatic gravity anomalies of the Arabian plate and surroundings

NASA Astrophysics Data System (ADS)

Kaban, Mikhail K.; El Khrepy, Sami; Al-Arifi, Nassir

2015-04-01

Isostaic anomalies represent one of the most useful "geological" reduction of the gravity field. With the isostatic correction it is possible to remove a significant part of the effect of deep density heterogeneity, which dominates in the Bouguer gravity anomalies. This correction is based on the fact that a major part of the near-surface load is compensated by variations of the lithosphere boundaries (chiefly the Moho and LAB) and by density variations within the crust and upper mantle. It is usually supposed that it is less important to a first order, what is the actual compensation model when reducing the effect of compensating masses, since their total weight is exactly opposite to the near-surface load. We compare several compensating models for the Arabian plate and surrounding area. The Airy model gives very significant regional isostatic anomalies, which can not be explained by the upper crust structure or disturbances of the isostatic equilibrium. Also the predicted "isostatic" Moho is very different from the existing observations. The second group of the isostatic models includes the Moho, which is based on existing seismic determinations. Additional compensation is provided by density variations within the lithosphere (chiefly in the upper mantle). In this way we minimize regional anomalies over the Arabian plate. The residual local anomalies well correspond to tectonic structure of the plate. Still very significant anomalies are associated with the Zagros fold belt, the collision zone of the Arabian and Eurasian plates.

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.

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.

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.

Population structure and cultural geography of a folktale in Europe

PubMed Central

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

2013-01-01

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

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.

Macrophytes shape trophic niche variation among generalist fishes.

PubMed

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

2017-01-01

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

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.

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

NASA Astrophysics Data System (ADS)

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

1997-05-01

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

Structural studies and band gap tuning of Cr doped ZnO nanoparticles

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

Srinet, Gunjan, E-mail: gunjansrinet@gmail.com; Kumar, Ravindra, E-mail: gunjansrinet@gmail.com; Sajal, Vivek, E-mail: gunjansrinet@gmail.com

2014-04-24

Structural and optical properties of Cr doped ZnO nanoparticles prepared by the thermal decomposition method are presented. X-ray diffraction studies confirmed the substitution of Cr on Zn sites without changing the wurtzite structure of ZnO. Modified form of W-H equations was used to calculate various physical parameters and their variation with Cr doping is discussed. Significant red shift was observed in band gap, i.e., a band gap tuning is achieved by Cr doping which could eventually be useful for optoelectronic applications.

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Mineral Ecology: Surface Specific Colonization and Geochemical Drivers of Biofilm Accumulation, Composition, and Phylogeny

PubMed Central

Jones, Aaron A.; Bennett, Philip C.

2017-01-01

This study tests the hypothesis that surface composition influences microbial community structure and growth of biofilms. We used laboratory biofilm reactors (inoculated with a diverse subsurface community) to explore the phylogenetic and taxonomic variability in microbial communities as a function of surface type (carbonate, silicate, aluminosilicate), media pH, and carbon and phosphate availability. Using high-throughput pyrosequencing, we found that surface type significantly controlled ~70–90% of the variance in phylogenetic diversity regardless of environmental pressures. Consistent patterns also emerged in the taxonomy of specific guilds (sulfur-oxidizers/reducers, Gram-positives, acidophiles) due to variations in media chemistry. Media phosphate availability was a key property associated with variation in phylogeny and taxonomy of whole reactors and was negatively correlated with biofilm accumulation and α-diversity (species richness and evenness). However, mineral-bound phosphate limitations were correlated with less biofilm. Carbon added to the media was correlated with a significant increase in biofilm accumulation and overall α-diversity. Additionally, planktonic communities were phylogenetically distant from those in biofilms. All treatments harbored structurally (taxonomically and phylogenetically) distinct microbial communities. Selective advantages within each treatment encouraged growth and revealed the presence of hundreds of additional operational taxonomix units (OTU), representing distinct consortiums of microorganisms. Ultimately, these results provide evidence that mineral/rock composition significantly influences microbial community structure, diversity, membership, phylogenetic variability, and biofilm growth in subsurface communities. PMID:28400754

Variation in tooth morphology of Gorilla gorilla.

PubMed

Uchida, A

1998-01-01

Gorilla gorilla exemplifies a species that shows considerable variation in habitat, behaviour, genetic structure and morphology. This study examines variation of dental morphology in gorillas. Despite the marked size dimorphism, there are no significant shape differences between the sexes within subspecies. Differences in dental morphology, including tooth cusp proportions between the western G. g. gorilla and the eastern G. g. beringei are considerable. Although more similar to G. g. beringei than to the western G. g. gorilla, G. g. graueri also shows distinct morphological features. This indicates that the morphology of G. g. graueri is not merely intermediate, and genetic isolation between the two eastern subspecies could have had a substantial influence. Such extensive variation in dental morphology in Gorilla gorilla can be considered to be the result of an interesting combination of factors, including local dietary adaptations.

Influence of structural variations in push-pull zinc porphyrins on photovoltaic performance of dye-sensitized solar cells.

PubMed

Yi, Chenyi; Giordano, Fabrizio; Cevey-Ha, Ngoc-Le; Tsao, Hoi Nok; Zakeeruddin, Shaik M; Grätzel, Michael

2014-04-01

We designed and synthesized two new zinc porphyrin dyes for dye-sensitized solar cells (DSCs). Subtle molecular structural variation in the dyes significantly influenced the performance of the DSC devices. By utilizing these dyes in combination with a cobalt-based redox electrolyte using a photoanode made of mesoporous TiO2 , we achieved a power conversion efficiency (PCE) of up to 12.0 % under AM 1.5 G (100 mW cm(-2)) simulated solar light. Moreover, we obtained a high PCE of 6.4 % for solid-state dye-sensitized solar cells by using 2,2',7,7'-tetrakis-(N,N-di-p-methoxyphenylamine)-9,9'-spirobifluorene as a hole-transporting material. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Homology models of main proteinase from coronavirus associated with SARS

NASA Astrophysics Data System (ADS)

Liu, Hsuan-Liang; Lin, Jin-Chung; Ho, Yih; Chen, Chin-Wen

2005-01-01

In this study, two homology models of the main proteinase (M pro) from the novel coronavirus associated with severe acute respiratory syndrome (SARS-CoV) were constructed. These models reveal three distinct functional domains, in which an intervening loop connecting domains II and III as well as a catalytic cleft containing the substrate binding subsites S1 and S2 between domains I and II are observed. S2 exhibits structural variations more significantly than S1 during the 200 ps molecular dynamics simulations because it is located at the open mouth of the catalytic cleft and the amino acid residues lining up this subsite are least conserved. In addition, the higher structural variation of S2 makes it flexible enough to accommodate a bulky hydrophobic residue from the substrate.

Assessing intraspecific variation in effective dispersal along an altitudinal gradient: a test in two Mediterranean high-mountain plants.

PubMed

Lara-Romero, Carlos; Robledo-Arnuncio, Juan J; García-Fernández, Alfredo; Iriondo, Jose M

2014-01-01

Plant recruitment depends among other factors on environmental conditions and their variation at different spatial scales. Characterizing dispersal in contrasting environments may thus be necessary to understand natural intraspecific variation in the processes underlying recruitment. Silene ciliata and Armeria caespitosa are two representative species of cryophilic pastures above the tree line in Mediterranean high mountains. No explicit estimations of dispersal kernels have been made so far for these or other high-mountain plants. Such data could help to predict their dispersal and recruitment patterns in a context of changing environments under ongoing global warming. We used an inverse modelling approach to analyse effective seed dispersal patterns in five populations of both Silene ciliata and Armeria caespitosa along an altitudinal gradient in Sierra de Guadarrama (Madrid, Spain). We considered four commonly employed two-dimensional seedling dispersal kernels exponential-power, 2Dt, WALD and log-normal. No single kernel function provided the best fit across all populations, although estimated mean dispersal distances were short (<1 m) in all cases. S. ciliata did not exhibit significant among-population variation in mean dispersal distance, whereas significant differences in mean dispersal distance were found in A. caespitosa. Both S. ciliata and A. caespitosa exhibited among-population variation in the fecundity parameter and lacked significant variation in kernel shape. This study illustrates the complexity of intraspecific variation in the processes underlying recruitment, showing that effective dispersal kernels can remain relatively invariant across populations within particular species, even if there are strong variations in demographic structure and/or physical environment among populations, while the invariant dispersal assumption may not hold for other species in the same environment. Our results call for a case-by-case analysis in a wider range of plant taxa and environments to assess the prevalence and magnitude of intraspecific dispersal variation.

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.                   

Ecological correlates of group-size variation in a resource-defense ungulate, the sedentary guanaco.

PubMed

Marino, Andrea; Baldi, Ricardo

2014-01-01

For large herbivores, predation-risk, habitat structure and population density are often reported as major determinants of group size variation within and between species. However, whether the underlying causes of these relationships imply an ecological adaptation or are the result of a purely mechanistic process in which fusion and fragmentation events only depend on the rate of group meeting, is still under debate. The aim of this study was to model guanaco family and bachelor group sizes in contrasting ecological settings in order to test hypotheses regarding the adaptive significance of group-size variation. We surveyed guanaco group sizes within three wildlife reserves located in eastern Patagonia where guanacos occupy a mosaic of grasslands and shrublands. Two of these reserves have been free from predators for decades while in the third, pumas often prey on guanacos. All locations have experienced important changes in guanaco abundance throughout the study offering the opportunity to test for density effects. We found that bachelor group size increased with increasing density, as expected by the mechanistic approach, but was independent of habitat structure or predation risk. In contrast, the smaller and territorial family groups were larger in the predator-exposed than in the predator-free locations, and were larger in open grasslands than in shrublands. However, the influence of population density on these social units was very weak. Therefore, family group data supported the adaptive significance of group-size variation but did not support the mechanistic idea. Yet, the magnitude of the effects was small and between-population variation in family group size after controlling for habitat and predation was negligible, suggesting that plasticity of these social units is considerably low. Our results showed that different social units might respond differentially to local ecological conditions, supporting two contrasting hypotheses in a single species, and highlight the importance of taking into account the proximate interests and constraints to which group members may be exposed to when deriving predictions about group-size variation.

Size Variation under Domestication: Conservatism in the inner ear shape of wolves, dogs and dingoes.

PubMed

Schweizer, Anita V; Lebrun, Renaud; Wilson, Laura A B; Costeur, Loïc; Schmelzle, Thomas; Sánchez-Villagra, Marcelo R

2017-10-17

A broad sample of wolves, dingoes, and domesticated dogs of different kinds and time periods was used to identify changes in size and shape of the organs of balance and hearing related to domestication and to evaluate the potential utility of uncovered patterns as markers of domestication. Using geometric morphometrics coupled with non-invasive imaging and three-dimensional reconstructions, we exposed and compared complex structures that remain largely conserved. There is no statistically significant difference in the levels of shape variation between prehistoric and modern dogs. Shape variance is slightly higher for the different components of the inner ear in modern dogs than in wolves, but these differences are not significant. Wolves express a significantly greater level of variance in the angle between the lateral and the posterior canal than domestic dog breeds. Wolves have smaller levels of size variation than dogs. In terms of the shape of the semicircular canals, dingoes reflect the mean shape in the context of variation in the sample. This mirrors the condition of feral forms in other organs, in which there is an incomplete return to the characteristics of the ancestor. In general, morphological diversity or disparity in the inner ear is generated by scaling.

Comparative morphology among northern populations of breeding Cooper's Hawks

USGS Publications Warehouse

Rosenfield, Robert N.; Rosenfield, Laura J.; Bielefeldt, John; Murphy, Robert K.; Stewart, Andrew C.; Stout, William E.; Driscoll, Timothy G.; Bozek, Michael A.

2010-01-01

Few studies at a broad geographical scale have characterized intraspecific variation in morphology of woodland hawks in the genus Accipiter. From 1999 to 2007 we investigated morphological variation in large samples of live Cooper's Hawks (A. cooperii) nesting in four study areas: coniferous woodland around Victoria, British Columbia, Canada, isolated deciduous woodlands in short-grass prairies of northwestern North Dakota, towns and rural deciduous woodlands along the border of North Dakota and Minnesota, and urban and rural mixed deciduous and coniferous landscapes of Wisconsin. These sites span 2660 km across the northern part of the species' breeding range. We measured body mass (i.e., size), wing chord, tail length, tarsus diameter, hallux length, and culmen length of breeding adults, finding significant and clinal variation in body mass (or size). The smallest and most similar-sized birds occurred in British Columbia and western North Dakota, larger birds along the border between North Dakota and Minnesota, and the largest birds in Wisconsin. Several other characters varied significantly when mass was used as a covariate. Variation by study site in mean indices of sexual size dimorphism was negligible and not significant. We speculate that the morphological differences we found, in part, are the result of geographic isolation, where diets, migratory behavior, and structural characteristics of nesting habitats vary across landscape types.

Mothers' Work Hours and Marital Quality: Variations by Family Structure and Family Size.

ERIC Educational Resources Information Center

Rogers, Stacy J.

1996-01-01

Investigated the association between married mothers' (n=1,502) employment and their reports of marital conflict and marital happiness in continuously married families with children and in mother-stepfather families. Found significant difference between types of families. Discusses findings and calls for additional research. (RB)

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

PubMed

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

2017-09-01

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

Epigenetic Variation in Mangrove Plants Occurring in Contrasting Natural Environment

PubMed Central

Lira-Medeiros, Catarina Fonseca; Parisod, Christian; Fernandes, Ricardo Avancini; Mata, Camila Souza; Cardoso, Monica Aires; Ferreira, Paulo Cavalcanti Gomes

2010-01-01

Background Epigenetic modifications, such as cytosine methylation, are inherited in plant species and may occur in response to biotic or abiotic stress, affecting gene expression without changing genome sequence. Laguncularia racemosa, a mangrove species, occurs in naturally contrasting habitats where it is subjected daily to salinity and nutrient variations leading to morphological differences. This work aims at unraveling how CpG-methylation variation is distributed among individuals from two nearby habitats, at a riverside (RS) or near a salt marsh (SM), with different environmental pressures and how this variation is correlated with the observed morphological variation. Principal Findings Significant differences were observed in morphological traits such as tree height, tree diameter, leaf width and leaf area between plants from RS and SM locations, resulting in smaller plants and smaller leaf size in SM plants. Methyl-Sensitive Amplified Polymorphism (MSAP) was used to assess genetic and epigenetic (CpG-methylation) variation in L. racemosa genomes from these populations. SM plants were hypomethylated (14.6% of loci had methylated samples) in comparison to RS (32.1% of loci had methylated samples). Within-population diversity was significantly greater for epigenetic than genetic data in both locations, but SM also had less epigenetic diversity than RS. Frequency-based (GST) and multivariate (βST) methods that estimate population structure showed significantly greater differentiation among locations for epigenetic than genetic data. Co-Inertia analysis, exploring jointly the genetic and epigenetic data, showed that individuals with similar genetic profiles presented divergent epigenetic profiles that were characteristic of the population in a particular environment, suggesting that CpG-methylation changes may be associated with environmental heterogeneity. Conclusions In spite of significant morphological dissimilarities, individuals of L. racemosa from salt marsh and riverside presented little genetic but abundant DNA methylation differentiation, suggesting that epigenetic variation in natural plant populations has an important role in helping individuals to cope with different environments. PMID:20436669

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

NASA Astrophysics Data System (ADS)

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

2016-11-01

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

Big mountains but small barriers: population genetic structure of the Chinese wood frog (Rana chensinensis) in the Tsinling and Daba Mountain region of northern China.

PubMed

Zhan, Aibin; Li, Cheng; Fu, Jinzhong

2009-04-09

Amphibians in general are poor dispersers and highly philopatric, and landscape features often have important impacts on their population genetic structure and dispersal patterns. Numerous studies have suggested that genetic differentiation among amphibian populations are particularly pronounced for populations separated by mountain ridges. The Tsinling Mountain range of northern China is a major mountain chain that forms the boundary between the Oriental and Palearctic zoogeographic realms. We studied the population structure of the Chinese wood frog (Rana chensinensis) to test whether the Tsinling Mountains and the nearby Daba Mountains impose major barriers to gene flow. Using 13 polymorphic microsatellite DNA loci, 523 individuals from 12 breeding sites with geographical distances ranging from 2.6 to 422.8 kilometers were examined. Substantial genetic diversity was detected at all sites with an average of 25.5 alleles per locus and an expected heterozygosity ranging from 0.504 to 0.855, and two peripheral populations revealed significantly lower genetic diversity than the central populations. In addition, the genetic differentiation among the central populations was statistically significant, with pairwise FST values ranging from 0.0175 to 0.1625 with an average of 0.0878. Furthermore, hierarchical AMOVA analysis attributed most genetic variation to the within-population component, and the between-population variation can largely be explained by isolation-by-distance. None of the putative barriers detected from genetic data coincided with the location of the Tsinling Mountains. The Tsinling and Daba Mountains revealed no significant impact on the population genetic structure of R. chensinensis. High population connectivity and extensive juvenile dispersal may account for the significant, but moderate differentiation between populations. Chinese wood frogs are able to use streams as breeding sites at high elevations, which may significantly contribute to the diminishing barrier effect of mountain ridges. Additionally, a significant decrease in genetic diversity in the peripheral populations supports Mayr's central-peripheral population hypothesis.

Sapling structure and regeneration strategy in 18 Shorea species co-occurring in a tropical rainforest.

PubMed

Aiba, Masahiro; Nakashizuka, Tohru

2005-08-01

Inevitable trade-offs in structure may be a basis for differentiation in plant strategies. Juvenile trees in different functional groups are characterized by specific suites of structural traits such as crown architecture and biomass distribution. The relationship between juvenile tree structure and function was tested to find out if it is robust among functionally and taxonomically similar species of the genus Shorea that coexist sympatrically in a tropical rain forest in Borneo. The sapling structures of 18 species were compared for standardized dry masses of 5 and 30 g. Pairwise simple correlation and multiple correlation patterns among structural traits of juveniles (0.1-1.5 m in height) of 18 Shorea species were examined using Pearson's correlation and principal component analysis (PCA), respectively. The correlation was then tested between the PCA results and three indices of shade tolerance: the net photosynthetic rate, the wood density of mature trees and seed size. The structural variation in saplings of the genus Shorea was as large as that found in sets of species with much more diverse origins. The PCA showed that both crown architecture and allocation to leaves are major sources of variation in the structures of the 18 species investigated. Of these two axes, allocation to leaves was significantly correlated with wood density and showed a limited correlation with photosynthetic rate, whereas crown architecture was significantly correlated to seed size. Overall, the results suggest that an allocation trade-off between leaves and other organs, which co-varied with wood density and to a certain extent with photosynthetic capacity, accounts for the difference in shade tolerance among congeneric, functionally similar species. In contrast, the relationship between the architecture and regeneration strategy differed from the pattern found between functional groups, and the function of crown architecture was ambiguous.

Spatiotemporal variation in survival rates: implications for population dynamics of yellow-bellied marmots.

PubMed

Ozgul, Arpat; Armitage, Kenneth B; Blumstein, Daniel T; Oli, Madan K

2006-04-01

Spatiotemporal variation in age-specific survival rates can profoundly influence population dynamics, but few studies of vertebrates have thoroughly investigated both spatial and temporal variability in age-specific survival rates. We used 28 years (1976-2003) of capture-mark-recapture (CMR) data from 17 locations to parameterize an age-structured Cormack-Jolly-Seber model, and investigated spatial and temporal variation in age-specific annual survival rates of yellow-bellied marmots (Marmota flaviventris). Survival rates varied both spatially and temporally, with survival of younger animals exhibiting the highest degree of variation. Juvenile survival rates varied from 0.52 +/- 0.05 to 0.78 +/- 0.10 among sites and from 0.15 +/- 0.14 to 0.89 +/- 0.06 over time. Adult survival rates varied from 0.62 +/- 0.09 to 0.80 +/- 0.03 among sites, but did not vary significantly over time. We used reverse-time CMR models to estimate the realized population growth rate (lamda), and to investigate the influence of the observed variation in age-specific survival rates on lamda. The realized growth rate of the population closely covaried with, and was significantly influenced by, spatiotemporal variation in juvenile survival rate. High variability in juvenile survival rates over space and time clearly influenced the dynamics of our study population and is also likely to be an important determinant of the spatiotemporal variation in the population dynamics of other mammals with similar life history characteristics.

New inorganic/organic copolymers (ORMOCER{reg_sign}s) for dental applications

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

Wolter, H.; Storch, W.; Ott, H.

1994-12-31

Urethane and thioether (meth)acrylate alkoxysilanes have been used, as sol-gel precursors, for the preparation of a special family of inorganic/organic copolymers (ORMOCER{reg_sign}s). The basic silane type offers the following structural and synthetic possibilities for modifying the properties of the resulting copolymers: variation of the number of alkoxy groups, combination with other, different, sol-gel precursors, variation of the number of attached (meth)acrylate groups (1--5), and variation within the molecular segment (kind, structure and length) connecting the inorganic with the organic polymer structure. To achieve the additional organic polymer structure in the cured copolymer the use of different radically induced polymerization approachesmore » (UV-, visible light-, thermal- and redox induced) is possible. Taking the incorporation of fillers into account, the Young`s modulus of these copolymers is adjustable in a range of 1--17,000 MPa, and the thermal expansion coefficient in a range of 17--250{center_dot}10{sup {minus}6}{center_dot}K{sup {minus}1} (5--50 C). Other advantages are the low shrinkage (1--2,8 vol.-%), the high flexural strength (up to 160 MPa), and the high abrasion resistance. This new copolymer type seems to have significant potential for medical applications, especially as dental filling material to replace the currently used controversial amalgam fillings.« less

Phylogenetic, functional, and structural components of variation in bone growth rate of amniotes.

PubMed

Cubo, Jorge; Legendre, Pierre; de Ricqlès, Armand; Montes, Laëtitia; de Margerie, Emmanuel; Castanet, Jacques; Desdevises, Yves

2008-01-01

The biological features observed in every living organism are the outcome of three sets of factors: historical (inherited by homology), functional (biological adaptation), and structural (properties inherent to the materials with which organs are constructed, and the morphogenetic rules by which they grow). Integrating them should bring satisfactory causal explanations of empirical data. However, little progress has been accomplished in practice toward this goal, because a methodologically efficient tool was lacking. Here we use a new statistical method of variation partitioning to analyze bone growth in amniotes. (1) Historical component. The variation of bone growth rates contains a significant phylogenetic signal, suggesting that the observed patterns are partly the outcome of shared ancestry. (2) Functional causation. High growth rates, although energy costly, may be adaptive (i.e., they may increase survival rates) in taxa showing short growth periods (e.g., birds). In ectothermic amniotes, low resting metabolic rates may limit the maximum possible growth rates. (3) Structural constraint. Whereas soft tissues grow through a multiplicative process, growth of mineralized tissues is accretionary (additive, i.e., mineralization fronts occur only at free surfaces). Bone growth of many amniotes partially circumvents this constraint: it is achieved not only at the external surface of the bone shaft, but also within cavities included in the bone cortex as it grows centrifugally. Our approach contributes to the unification of historicism, functionalism, and structuralism toward a more integrated evolutionary biology.

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

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

Life between tides: Spatial and temporal variations of an intertidal macroalgal community at Potter Peninsula, South Shetland Islands, Antarctica

NASA Astrophysics Data System (ADS)

Marcías, María Laura; Deregibus, Dolores; Saravia, Leonardo Ariel; Campana, Gabriela Laura; Quartino, María Liliana

2017-03-01

Intertidal zones are one of the most studied habitats in the world. However, in Antarctica, further studies are needed for a more complete understanding of these systems. When conspicuous Antarctic intertidal communities occur, macroalgae are a key component. Given that intertidal communities have a fast response to variations in environmental conditions and could reflect climate fluctuations, we conducted a non-destructive study with photographic transects in an intertidal zone at Potter Peninsula, Isla 25 de Mayo/King George Island, over four years and during five months of the warm season. We tested the general hypothesis that macroalgal intertidal communities are mainly structured by the vertical stress gradient and that changes in temperature between seasons and between years have a great influence in the macroalgal community structure. Spatial, seasonal and inter-annual variations were studied using GLM, quantile regression and NMDS ordinations. The vertical stress gradient was the main factor that explained macroalgal cover. The Low and the Middle level shared similarities, but the latter was more variable. The High level had the lowest cover, richness and diversity. The dominant species here was the endemic red alga Pyropia endiviifolia, which is strongly adapted to extreme conditions. At the Middle level, there was a significant increase in macroalgal cover during spring months, and it stabilized in summer. Inter-annual variations showed that there is a strong variation in the total macroalgal cover and community structure over the studied years. Environmental conditions have a significant effect in shaping the studied intertidal community, which is very sensitive to climate oscillations. An increase in temperature produced a decrease of annual ice foot cover, number of snow days and - as a result - an increase in macroalgal cover. In a global climate-change scenario, a shift in species composition could also occur. Species with wide physiological tolerance that grow in warmer conditions, like Palmaria decipiens, could benefit, while other species will be discriminated. More detailed studies are necessary to predict future changes in Antarctic intertidal communities.

Strain induced enhancement of magnetization in Ba{sub 2}FeMoO{sub 6} based heterostructure with (Ba{sub x}Sr{sub 1-x})TiO{sub 3}

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

Kim, Kyeong-Won; Norton, David P.; Ghosh, Siddhartha, E-mail: ghoshsid@gmail.com

2016-05-14

High quality epitaxial Ba{sub 2}FeMoO{sub 6} thin films and Ba{sub 2}FeMoO{sub 6}–(Ba{sub x}Sr{sub 1−x})TiO{sub 3} bi-layer (BL) and superlattice (SL) structures were grown via pulsed laser deposition under low oxygen pressure, and their structural, magnetic, and magneto-transport properties were examined. Superlattice and bi-layer structures were confirmed by X-ray diffraction patterns. Low temperature magnetic measurement shows that the saturation magnetization (M{sub S}) is significantly higher for SLs and almost similar or lower for BLs, when compared to phase pure Ba{sub 2}FeMoO{sub 6} thin films. The variation of the coercive field (H{sub C}) follows exact opposite trend, where BL samples have highermore » H{sub C} and SL samples have lower H{sub C} than pure Ba{sub 2}FeMoO{sub 6} thin films. Also, a significant decrease of the Curie temperature is found in both BL and SL structures compared to pure Ba{sub 2}FeMoO{sub 6} thin films. Negative magneto-resistance is seen in all the BL and SL structures as well as in pure Ba{sub 2}FeMoO{sub 6} thin films. In contrast to the magnetic properties, the magneto-transport properties do not show much variation with induced strain.« less

Slow-freezing-induced changes of birefringent structures in human oocytes are related to responsiveness to ovulation induction.

PubMed

Molinari, Emanuela; Revelli, Alberto; Racca, Cinzia; Delle Piane, Luisa; Massobrio, Marco

2010-05-01

The slow-freezing method is widely used to freeze human oocytes, both for fertility preservation and in routine IVF programmes. Slow freezing damages some of the cell's structures, including the meiotic spindle (MS) and the zona pellucida (ZP). Polarized light microscopy was used to study the variations induced by slow freezing on the MS and the ZP of human oocytes and to analyse the relationship between slow-freezing effects on the gamete and some clinical characteristics, such as age, body mass index and ovarian responsiveness to ovulation induction (expressed as total follicle-stimulating hormone dose/retrieved oocyte). Both the MS and the ZP (particularly its inner layer) underwent significant changes during slow-freezing procedure. The MS became thinner and structurally less organized (lower retardance) (P<0.001 and P<0.05, respectively), whereas the ZP became thicker and its inner layer lost structural organization (both P<0.05). These morphological changes were unrelated to the patient's age or body mass index, but ZP variations in thickness and retardance were significantly related to ovarian responsiveness (P=0.033 and P=0.026, respectively), suggesting that patients with a higher response to gonadotrophins produce oocytes better able to preserve their characteristics after freezing-thawing. Copyright (c) 2010 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.

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.

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

NASA Astrophysics Data System (ADS)

Li, Mingming; Zhong, Shijie; Olson, Peter

2018-04-01

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

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

Diel and seasonal variation of a molluscan taxocoenosis associated with a Zostera marina bed in southern Spain (Alboran Sea)

NASA Astrophysics Data System (ADS)

Rueda, Jose L.; Urra, Javier; Salas, Carmen

2008-09-01

The diel and seasonal variation of molluscs living in a Zostera marina bed (12-14 m depth) from southern Spain have been studied for one year using a small Agassiz trawl for collecting the samples (222 m2). The frequent and dominant species were very similar in both diurnal and nocturnal samples, including mainly gastropods such as Jujubinus striatus, Nassarius pygmaeus, Mitrella minor, Calliostoma planatum, Rissoa membranacea or Smaragdia viridis. Nevertheless, a significant increase of abundance of scavengers (e.g. Nassarius spp.) and carnivores (e.g. cephalopods) was registered in nocturnal samples. The abundance was maximal in spring and summer in diurnal and nocturnal samples and also in autumn for nocturnal ones, displaying significantly higher values in nocturnal samples. The species richness, diversity and evenness displayed a similar seasonal trend for diurnal and nocturnal samples, with maximum values during summer months. Monthly variation of the molluscan composition (species presence-absence data) was more acute than diel variation, according to the Cluster, MDS and ANOSIM results. Nevertheless, both monthly and diel changes in the structure (species abundance data) of the molluscan taxocoenosis were important throughout the year. Diel changes in the structure of the molluscan fauna are related to an increase of abundance of some species at nighttime due to vertical movements from the sediment to the shoots or along them (e.g. J. striatus, Nassarius spp.) or due to horizontal movements from adjacent habitats (e.g. cephalopods). Nevertheless, some species such as Rissoa spp. or Bittium spp. stay on the leaves of Z. marina during day as well as nighttime.

Corallite skeletal morphological variation in Hawaiian Porites lobata

NASA Astrophysics Data System (ADS)

Tisthammer, Kaho H.; Richmond, Robert H.

2018-06-01

Due to their high morphological plasticity and complex evolutionary history, the species boundaries of many reef-building corals are poorly understood. The skeletal structures of corals have traditionally been used for species identification, but these structures can be highly variable, and currently we lack knowledge regarding the extent of morphological variation within species. Porites species are notorious for their taxonomic difficulties, both morphologically and genetically, and currently there are several unresolved species complexes in the Pacific. Despite its ubiquitous presence and broad use in coral research, Porites lobata belongs to one such unresolved species complex. To understand the degree of intraspecific variation in skeletal morphology, 120 corallites from the Hawaiian P. lobata were examined. A subset of samples from two genetically differentiated populations from contrasting high- and low-stress environments in Maunalua Bay, Hawaii, were then quantitatively analyzed using multivariate morphometrics. Our observations revealed high intraspecific variation in corallite morphology, as well as significant morphological differences between the two populations of P. lobata. Additionally, significant correlation was found between the morphological and genetic distances calculated from approximately 18,000 loci generated from restriction site-associated DNA sequencing. The unique morphological characters observed from the genetically differentiated population under environmental stress suggest that these characters may have adaptive values, but how such traits relate to fitness and how much plasticity they can exhibit remain to be determined by future studies. Relatively simple morphometric analyses used in our study can be useful in clarifying the existing ambiguity in skeletal architecture, thus contributing to resolving species issues in corals.

Variations of bacteria and fungi in PM2.5 in Beijing, China

NASA Astrophysics Data System (ADS)

Du, Pengrui; Du, Rui; Ren, Weishan; Lu, Zedong; Zhang, Yang; Fu, Pingqing

2018-01-01

Bacteria and fungi present in the airborne fine particulate matter (PM2.5) play important roles in the atmosphere and provide significant impacts on human health. However, variations in the species composition and community structure have not been well understood. In this study, we sampled PM2.5 in suburban Beijing and analyzed the bacterial and fungal composition during different seasons and at different air pollution levels using gene sequencing methods. The results showed that the species richness and diversity of bacterial communities displayed a downtrend with the aggravation of air pollution. Additionally, the bacterial communities in spring samples showed the highest species richness, with average richness estimators, ACE and Chao 1, up to 14,649 and 7608, respectively, followed by winter samples (7690 and 5031, respectively) and autumn samples (4368 and 3438, respectively), whereas summer samples exhibited the lowest average ACE and Chao 1 indexes (2916 and 1900, respectively). The species richness of fungal communities followed the same seasonal pattern. The community structure of bacteria and the species composition of fungi in PM2.5 showed significant seasonal variations. The dominant bacteria were Actinobacteria (33.89%), Proteobacteria (25.72%), Firmicutes (19.87%), Cyanobacteria/Chloroplast (15.34%), and Bacteroidetes (3.19%), and Ascomycota, with an average abundance of 74.68% of all sequences, were the most abundant fungi. At the genus level, as many as 791 bacterial genera and 517 fungal genera were identified in PM2.5. The results advance our understanding of the distribution and variation of airborne microorganisms in the metropolitan surrounding areas.

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

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

Spatial and temporal variation in proportional stock density and relative weight of smallmouth bass in a reservoir

USGS Publications Warehouse

Mesa, Matthew G.; Duke, S.D.; Ward, David L.

1990-01-01

Population data for smallmouth bass Micropterus dolomieui in 20,235 ha John Day Reservoir on the Columbia River were used to (1) determine whether Proportional Stock Density (PSD) and Relative Weight (Wr) varied spatially and temporally in two areas of the reservoir with established smallmouth bass fisheries; (2) explore possible causes of any observed variation; and (3) discuss some management implications and recommendations. Both PSD and Wr varied spatially and monthly in all years examined. On an annual basis, PSD varied at one area but not at the other, whereas Wr showed little variation. Possible explanations for the variation in PSD and Wr are differences in growth, mortality, recruitment, and exploitation. Our data suggested that regulations established or changed on a reservoir-wide basis may have different effects on the fishery, depending on location in the reservoir. Also, pooling data from various areas within a reservoir to yield point estimates of structural indices may not represent the variation present in the population as a whole. The significant temporal variability reflects the importance of determining the proper time to sample fish to yield representative estimates of the variable of interest. In areas with valuable fisheries or markedly different population structures, we suggest that an area-specific approach be made to reservoir fishery management, and that efforts be made toward effecting consistent harvest regulations in interstate waters.

Age-related variation in limb bone diaphyseal structure among Inuit foragers from Point Hope, northern Alaska.

PubMed

Wallace, I J; Nesbitt, A; Mongle, C; Gould, E S; Grine, F E

2014-01-01

Age-related deterioration of limb bone diaphyseal structure is documented among precontact Inuit foragers from northern Alaska. These findings challenge the concept that bone loss and fracture susceptibility among modern Inuit stem from their transition away from a physically demanding traditional lifestyle toward a more sedentary Western lifestyle. Skeletal fragility is rare among foragers and other traditional-living societies, likely due to their high physical activity levels. Among modern Inuit, however, severe bone loss and fractures are apparently common. This is possibly because of recent Western influences and increasing sedentism. To determine whether compromised bone structure and strength among the Inuit are indeed aberrant for a traditional-living group, data were collected on age-related variation in limb bone diaphyseal structure from a group predating Western influences. Skeletons of 184 adults were analyzed from the Point Hope archaeological site. Mid-diaphyseal structure was measured in the humerus, radius, ulna, femur, and tibia using CT. Structural differences were assessed between young, middle-aged, and old individuals. In all bones examined, both females and males exhibited significant age-related reductions in bone quantity. With few exceptions, total bone (periosteal) area did not significantly increase between young and old age in either sex, nor did geometric components of bending rigidity (second moments of area). While the physically demanding lifestyles of certain traditional-living groups may protect against bone loss and fracture susceptibility, this is not the case among the Inuit. It remains possible, however, that Western characteristics of the modern Inuit lifestyle exacerbate age-related skeletal deterioration.

Influence of overpressure on formation velocity evaluation of Neogene strata from the eastern Bengal Basin, Bangladesh

NASA Astrophysics Data System (ADS)

Zahid, Khandaker M.; Uddin, Ashraf

2005-06-01

Interpretation of sonic log data of anticlinal structures from eastern Bangladesh reveals significant variations of acoustic velocity of subsurface strata. The amount of variation in velocity is 32% from Miocene to Pliocene stratigraphic units in Titas and Bakhrabad structure, whereas 21% in Rashidpur structure. Velocity fluctuations are influenced by the presence of gas-bearing horizons, with velocities of gas-producing strata 3-7% lower than laterally equivalent strata at similar depth. Average velocities of Miocene Boka Bil and Bhuban formations are, respectively, 2630 and 3480 m/s at Titas structure; 2820 and 3750 m/s at Bakhrabad; and 3430 and 3843 m/s at the Rashidpur structure. From the overall velocity-depth distribution for a common depth range of 915-3000 m, the Titas, Bakhrabad and Rashidpur structures show a gradual increase in velocity with depth. In contrast, the Sitakund anticline in SE Bangladesh reveals a decrease in velocity with depth from 3000 to 4000 m, probably due to the presence of overpressured mudrocks of the Bhuban Formation. Tectonic compression, associated with the Indo-Burmese plate convergence likely contributed the most toward formation of subsurface overpressure in the Sitakund structure situated in the Chittagong-Tripura Fold Belt of the eastern Bengal basin, Bangladesh.

Salaries in histology.

PubMed

Buesa, René J

2008-04-01

An analysis of histology salaries from the last 4 national surveys conducted by the American Society of Clinical Pathologists is presented. The regional variations within and between years for histology salaries presented in the last 4 national surveys of medical laboratory specialties are not statistically significant. Local variations greater than the national variations reflect the preponderant effect of local supply and demand over regional characteristics. Salaries by hospitals are significantly different only between 2 size categories and the supervisors' salary. There is no correlation between the salary increase for any histology position in any one year and the vacancy level in the previous year. On the other hand, the correlation between histotechnicians' salaries and both the cost of living and the median income are significant, as well as between the latter and the supervisors' salary. The histotechnologists' salaries are significantly correlated with the consumer price index but not with the inflation rate. A survey of histology salaries in foreign countries was also undertaken and compared with salaries in the United States. National salaries rank close to the general average for 10 foreign countries when expressed as ratios with the personal gross domestic product or with the countries' minimum wage. For the midpoint salary ranges, the United States ranks fourth after Canada, the United Kingdom, and Australia, the latter 3 countries with structured pay rates adjusted to local costs of living in contrast with United States' salary characteristics. Histology salaries rest on negotiations within each employer's salary structure and fluctuate according to license level, documented studies, special training(s), years of experience, references, and the ability to negotiate, where each side tries to take advantage of the other. The result is a heterogeneous and chaotic salary situation driven by personal and local needs, where the histology worker usually ends underpaid, especially in nonmedical settings.

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

Elevational patterns of genetic variation in the cosmopolitan moss Bryum argenteum (Bryaceae).

PubMed

Pisa, Sergio; Werner, Olaf; Vanderpoorten, Alain; Magdy, Mahmoud; Ros, Rosa M

2013-10-01

The Baas Becking tenet posits that 'everything is everywhere, but the environment selects' to explain cosmopolitan distributions in highly vagile taxa. Bryophyte species show wider distributions than vascular plants and include examples of truly cosmopolitan ranges, which have been interpreted as a result of high dispersal capacities and ecological plasticity. In the current study, we documented patterns of genetic structure and diversity in the cosmopolitan moss Bryum argenteum along an elevational gradient to determine if genetic diversity and structure is homogenized by intense migrations in the lack of ecological differentiation. • 60 specimens were collected in the Sierra Nevada Mountains (Spain) between 100 and 2870 m and sequenced for ITS and rps4. Comparative analyses, genetic diversity estimators, and Mantel's tests were employed to determine the relationship between genetic variation, elevation, and geographic distance and to look for signs of demographic shifts. • Genetic diversity peaked above 1900 m and no signs of demographic shifts were detected at any elevation. There was a strong phylogenetic component in elevational variation. Genetic variation was significantly correlated with elevation, but not with geographic distance. • The results point to the long-term persistence of Bryum argenteum in a range that was glaciated during the Late Pleistocene. Evidence for an environmentally driven pattern of genetic differentiation suggests adaptive divergence. This supports the Baas Becking tenet and indicates that ecological specialization might play a key role in explaining patterns of genetic structure in cosmopolitan mosses.

Genetic variation for leaf morphology, leaf structure and leaf carbon isotope discrimination in European populations of black poplar (Populus nigra L.).

PubMed

Guet, Justine; Fabbrini, Francesco; Fichot, Régis; Sabatti, Maurizio; Bastien, Catherine; Brignolas, Franck

2015-08-01

To buffer against the high spatial and temporal heterogeneity of the riparian habitat, riparian tree species, such as black poplar (Populus nigra L.), may display a high level of genetic variation and phenotypic plasticity for functional traits. Using a multisite common garden experiment, we estimated the relative contribution of genetic and environmental effects on the phenotypic variation expressed for individual leaf area, leaf shape, leaf structure and leaf carbon isotope discrimination (Δ(13)C) in natural populations of black poplar. Twenty-four to 62 genotypes were sampled in nine metapopulations covering a latitudinal range from 48 °N to 42 °N in France and in Italy and grown in two common gardens at Orléans (ORL) and at Savigliano (SAV). In the two common gardens, substantial genetic variation was expressed for leaf traits within all metapopulations, but its expression was modulated by the environment, as attested by the genotype × environment (G × E) interaction variance being comparable to or even greater than genetic effects. For LA, G × E interactions were explained by both changes in genotype ranking between common gardens and increased variation in SAV, while these interactions were mainly attributed to changes in genotype ranking for Δ(13)C. The nine P. nigra metapopulations were highly differentiated for LA, as attested by the high coefficient of genetic differentiation (QST = 0.50 at ORL and 0.51 at SAV), and the pattern of metapopulation differentiation was highly conserved between the two common gardens. In contrast, they were moderately differentiated for Δ(13)C (QST = 0.24 at ORL and 0.25 at SAV) and the metapopulation clustering changed significantly between common gardens. Our results evidenced that the nine P. nigra metapopulations present substantial genetic variation and phenotypic plasticity for leaf traits, which both represent potentially significant determinants of populations' capacities to respond, on a short-term basis and over generations, to environmental variations. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Ultra-deep sequencing reveals high prevalence and broad structural diversity of hepatitis B surface antigen mutations in a global population

PubMed Central

Gencay, Mikael; Hübner, Kirsten; Gohl, Peter; Seffner, Anja; Weizenegger, Michael; Neofytos, Dionysios; Batrla, Richard; Woeste, Andreas; Kim, Hyon-suk; Westergaard, Gaston; Reinsch, Christine; Brill, Eva; Thu Thuy, Pham Thi; Hoang, Bui Huu; Sonderup, Mark; Spearman, C. Wendy; Pabinger, Stephan; Gautier, Jérémie; Brancaccio, Giuseppina; Fasano, Massimo; Santantonio, Teresa; Gaeta, Giovanni B.; Nauck, Markus; Kaminski, Wolfgang E.

2017-01-01

The diversity of the hepatitis B surface antigen (HBsAg) has a significant impact on the performance of diagnostic screening tests and the clinical outcome of hepatitis B infection. Neutralizing or diagnostic antibodies against the HBsAg are directed towards its highly conserved major hydrophilic region (MHR), in particular towards its “a” determinant subdomain. Here, we explored, on a global scale, the genetic diversity of the HBsAg MHR in a large, multi-ethnic cohort of randomly selected subjects with HBV infection from four continents. A total of 1553 HBsAg positive blood samples of subjects originating from 20 different countries across Africa, America, Asia and central Europe were characterized for amino acid variation in the MHR. Using highly sensitive ultra-deep sequencing, we found 72.8% of the successfully sequenced subjects (n = 1391) demonstrated amino acid sequence variation in the HBsAg MHR. This indicates that the global variation frequency in the HBsAg MHR is threefold higher than previously reported. The majority of the amino acid mutations were found in the HBV genotypes B (28.9%) and C (25.4%). Collectively, we identified 345 distinct amino acid mutations in the MHR. Among these, we report 62 previously unknown mutations, which extends the worldwide pool of currently known HBsAg MHR mutations by 22%. Importantly, topological analysis identified the “a” determinant upstream flanking region as the structurally most diverse subdomain of the HBsAg MHR. The highest prevalence of “a” determinant region mutations was observed in subjects from Asia, followed by the African, American and European cohorts, respectively. Finally, we found that more than half (59.3%) of all HBV subjects investigated carried multiple MHR mutations. Together, this worldwide ultra-deep sequencing based genotyping study reveals that the global prevalence and structural complexity of variation in the hepatitis B surface antigen have, to date, been significantly underappreciated. PMID:28472040

Ultra-deep sequencing reveals high prevalence and broad structural diversity of hepatitis B surface antigen mutations in a global population.

PubMed

Gencay, Mikael; Hübner, Kirsten; Gohl, Peter; Seffner, Anja; Weizenegger, Michael; Neofytos, Dionysios; Batrla, Richard; Woeste, Andreas; Kim, Hyon-Suk; Westergaard, Gaston; Reinsch, Christine; Brill, Eva; Thu Thuy, Pham Thi; Hoang, Bui Huu; Sonderup, Mark; Spearman, C Wendy; Pabinger, Stephan; Gautier, Jérémie; Brancaccio, Giuseppina; Fasano, Massimo; Santantonio, Teresa; Gaeta, Giovanni B; Nauck, Markus; Kaminski, Wolfgang E

2017-01-01

The diversity of the hepatitis B surface antigen (HBsAg) has a significant impact on the performance of diagnostic screening tests and the clinical outcome of hepatitis B infection. Neutralizing or diagnostic antibodies against the HBsAg are directed towards its highly conserved major hydrophilic region (MHR), in particular towards its "a" determinant subdomain. Here, we explored, on a global scale, the genetic diversity of the HBsAg MHR in a large, multi-ethnic cohort of randomly selected subjects with HBV infection from four continents. A total of 1553 HBsAg positive blood samples of subjects originating from 20 different countries across Africa, America, Asia and central Europe were characterized for amino acid variation in the MHR. Using highly sensitive ultra-deep sequencing, we found 72.8% of the successfully sequenced subjects (n = 1391) demonstrated amino acid sequence variation in the HBsAg MHR. This indicates that the global variation frequency in the HBsAg MHR is threefold higher than previously reported. The majority of the amino acid mutations were found in the HBV genotypes B (28.9%) and C (25.4%). Collectively, we identified 345 distinct amino acid mutations in the MHR. Among these, we report 62 previously unknown mutations, which extends the worldwide pool of currently known HBsAg MHR mutations by 22%. Importantly, topological analysis identified the "a" determinant upstream flanking region as the structurally most diverse subdomain of the HBsAg MHR. The highest prevalence of "a" determinant region mutations was observed in subjects from Asia, followed by the African, American and European cohorts, respectively. Finally, we found that more than half (59.3%) of all HBV subjects investigated carried multiple MHR mutations. Together, this worldwide ultra-deep sequencing based genotyping study reveals that the global prevalence and structural complexity of variation in the hepatitis B surface antigen have, to date, been significantly underappreciated.

Scaling up functional traits for ecosystem services with remote sensing: concepts and methods.

PubMed

Abelleira Martínez, Oscar J; Fremier, Alexander K; Günter, Sven; Ramos Bendaña, Zayra; Vierling, Lee; Galbraith, Sara M; Bosque-Pérez, Nilsa A; Ordoñez, Jenny C

2016-07-01

Ecosystem service-based management requires an accurate understanding of how human modification influences ecosystem processes and these relationships are most accurate when based on functional traits. Although trait variation is typically sampled at local scales, remote sensing methods can facilitate scaling up trait variation to regional scales needed for ecosystem service management. We review concepts and methods for scaling up plant and animal functional traits from local to regional spatial scales with the goal of assessing impacts of human modification on ecosystem processes and services. We focus our objectives on considerations and approaches for (1) conducting local plot-level sampling of trait variation and (2) scaling up trait variation to regional spatial scales using remotely sensed data. We show that sampling methods for scaling up traits need to account for the modification of trait variation due to land cover change and species introductions. Sampling intraspecific variation, stratification by land cover type or landscape context, or inference of traits from published sources may be necessary depending on the traits of interest. Passive and active remote sensing are useful for mapping plant phenological, chemical, and structural traits. Combining these methods can significantly improve their capacity for mapping plant trait variation. These methods can also be used to map landscape and vegetation structure in order to infer animal trait variation. Due to high context dependency, relationships between trait variation and remotely sensed data are not directly transferable across regions. We end our review with a brief synthesis of issues to consider and outlook for the development of these approaches. Research that relates typical functional trait metrics, such as the community-weighted mean, with remote sensing data and that relates variation in traits that cannot be remotely sensed to other proxies is needed. Our review narrows the gap between functional trait and remote sensing methods for ecosystem service management.

Large-scale properties of the interplanetary magnetic field

NASA Technical Reports Server (NTRS)

Schatten, K. H.

1972-01-01

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

Chemical variations among L-chondrites. IV - Analyses, with petrographic notes, of 13 L-group and 3 LL-group chondrites

NASA Astrophysics Data System (ADS)

Jarosewich, E.; Dodd, R. T.

1985-03-01

Procedures are reviewed for selecting, preparing and analyzing meteorite samples, present new analyses of 16 ordinary chondrites, and discuss variations of Fe, S and Si in the L-group. A tendency for Fe/Mg, S/Mg and Si/Mg to be low in L chondrites of facies d to f testifies that post-metamorphic shock melting played a significant role in the chemical diversification of the L-group. However, these ratios also vary widely and sympathetically in melt-free chondrites, indicating that much of the L-group's chemical variation arose prior to thermal metamorphism and is in that sense primary. If all L chondrites come from one parent body, type-correlated chemical trends suggest: (1) that the body had a tradiational 'onion skin' structure, with metamorphic intensity increasing with depth; and (2) that it formed from material that became more homogeneous, slightly poorer in iron, and significantly richer in sulfur as accretion proceeded.

Chemical Variations Among L-Chondrites--IV. Analyses, with Petrographic Notes, of 13 L-group and 3 LL-group Chondrites

NASA Astrophysics Data System (ADS)

Jarosewich, E.; Dodd, R. T.

1985-03-01

We review our procedures for selecting, preparing and analyzing meteorite samples, present new analyses of 16 ordinary chondrites, and discuss variations of Fe, S and Si in the L-group. A tendency for Fe/Mg, S/Mg and Si/Mg to be low in L chondrites of facies d to f testifies that post-metamorphic shock melting played a significant role in the chemical diversification of the L-group. However, these ratios also vary widely and sympathetically in melt-free chondrites, indicating that much of the L-group's chemical variation arose prior to thermal metamorphism and is in that sense primary. If all L chondrites come from one parent body, type-correlated chemical trends suggest: 1) that the body had a traditional "onion skin" structure, with metamorphic intensity increasing with depth; and 2) that it formed from material that became more homogeneous, slightly poorer in iron, and significantly richer in sulfur as accretion proceeded.

A method for reducing misclassification in the extended Glasgow Outcome Score.

PubMed

Lu, Juan; Marmarou, Anthony; Lapane, Kate; Turf, Elizabeth; Wilson, Lindsay

2010-05-01

The eight-point extended Glasgow Outcome Scale (GOSE) is commonly used as the primary outcome measure in traumatic brain injury (TBI) clinical trials. The outcome is conventionally collected through a structured interview with the patient alone or together with a caretaker. Despite the fact that using the structured interview questionnaires helps reach agreement in GOSE assessment between raters, significant variation remains among different raters. We introduce an alternate GOSE rating system as an aid in determining GOSE scores, with the objective of reducing inter-rater variation in the primary outcome assessment in TBI trials. Forty-five trauma centers were randomly assigned to three groups to assess GOSE scores on sample cases, using the alternative GOSE rating system coupled with central quality control (Group 1), the alternative system alone (Group 2), or conventional structured interviews (Group 3). The inter-rater variation between an expert and untrained raters was assessed for each group and reported through raw agreement and with weighted kappa (kappa) statistics. Groups 2 and 3 without central review yielded inter-rater agreements of 83% (weighted kappa = 0.81; 95% CI 0.69, 0.92) and 83% (weighted kappa = 0.76, 95% CI 0.63, 0.89), respectively, in GOS scores. In GOSE, the groups had an agreement of 76% (weighted kappa = 0.79; 95% CI 0.69, 0.89), and 63% (weighted kappa = 0.70; 95% CI 0.60, 0.81), respectively. The group using the alternative rating system coupled with central monitoring yielded the highest inter-rater agreement among the three groups in rating GOS (97%; weighted kappa = 0.95; 95% CI 0.89, 1.00), and GOSE (97%; weighted kappa = 0.97; 95% CI 0.91, 1.00). The alternate system is an improved GOSE rating method that reduces inter-rater variations and provides for the first time, source documentation and structured narratives that allow a thorough central review of information. The data suggest that a collective effort can be made to minimize inter-rater variation.

Genotype-Specific Variation in the Structure of Root Fungal Communities Is Related to Chickpea Plant Productivity

PubMed Central

Hamel, Chantal; Gan, Yantai; Tar'an, Bunyamin; Knight, Joan Diane

2015-01-01

Increasing evidence supports the existence of variations in the association of plant roots with symbiotic fungi that can improve plant growth and inhibit pathogens. However, it is unclear whether intraspecific variations in the symbiosis exist among plant cultivars and if they can be used to improve crop productivity. In this study, we determined genotype-specific variations in the association of chickpea roots with soil fungal communities and evaluated the effect of root mycota on crop productivity. A 2-year field experiment was conducted in southwestern Saskatchewan, the central zone of the chickpea growing region of the Canadian prairie. The effects of 13 cultivars of chickpea, comprising a wide range of phenotypes and genotypes, were tested on the structure of root-associated fungal communities based on internal transcribed spacer (ITS) and 18S rRNA gene markers using 454 amplicon pyrosequencing. Chickpea cultivar significantly influenced the structure of the root fungal community. The magnitude of the effect varied with the genotypes evaluated, and effects were consistent across years. For example, the roots of CDC Corrine, CDC Cory, and CDC Anna hosted the highest fungal diversity and CDC Alma and CDC Xena the lowest. Fusarium sp. was dominant in chickpea roots but was less abundant in CDC Corrine than the other cultivars. A bioassay showed that certain of these fungal taxa, including Fusarium species, can reduce the productivity of chickpea, whereas Trichoderma harzianum can increase chickpea productivity. The large variation in the profile of chickpea root mycota, which included growth-promoting and -inhibiting species, supports the possibility of improving the productivity of chickpea by improving its root mycota in chickpea genetic improvement programs using traditional breeding techniques. PMID:25616789

The influence of age and gender on skin-associated microbial communities in urban and rural human populations

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

Ying, Shi; Zeng, Dan -Ning; Chi, Liang

Differences in the bacterial community structure associated with 7 skin sites in 71 healthy people over five days showed significant correlations with age, gender, physical skin parameters, and whether participants lived in urban or rural locations in the same city. While body site explained the majority of the variance in bacterial community structure, the composition of the skin-associated bacterial communities were predominantly influenced by whether the participants were living in an urban or rural environment, with a significantly greater relative abundance of Trabulsiella in urban populations. Adults maintained greater overall microbial diversity than adolescents or the elderly, while the intragroupmore » variation among the elderly and rural populations was significantly greater. Lastly, skin-associated bacterial community structure and composition could predict whether a sample came from an urban or a rural resident ~ 5x greater than random.« less

Metagenomic analysis reveals significant changes of microbial compositions and protective functions during drinking water treatment.

PubMed

Chao, Yuanqing; Ma, Liping; Yang, Ying; Ju, Feng; Zhang, Xu-Xiang; Wu, Wei-Min; Zhang, Tong

2013-12-19

The metagenomic approach was applied to characterize variations of microbial structure and functions in raw (RW) and treated water (TW) in a drinking water treatment plant (DWTP) at Pearl River Delta, China. Microbial structure was significantly influenced by the treatment processes, shifting from Gammaproteobacteria and Betaproteobacteria in RW to Alphaproteobacteria in TW. Further functional analysis indicated the basic metabolic functions of microorganisms in TW did not vary considerably. However, protective functions, i.e. glutathione synthesis genes in 'oxidative stress' and 'detoxification' subsystems, significantly increased, revealing the surviving bacteria may have higher chlorine resistance. Similar results were also found in glutathione metabolism pathway, which identified the major reaction for glutathione synthesis and supported more genes for glutathione metabolism existed in TW. This metagenomic study largely enhanced our knowledge about the influences of treatment processes, especially chlorination, on bacterial community structure and protective functions (e.g. glutathione metabolism) in ecosystems of DWTPs.

The influence of age and gender on skin-associated microbial communities in urban and rural human populations

DOE PAGES

Ying, Shi; Zeng, Dan -Ning; Chi, Liang; ...

2015-10-28

Differences in the bacterial community structure associated with 7 skin sites in 71 healthy people over five days showed significant correlations with age, gender, physical skin parameters, and whether participants lived in urban or rural locations in the same city. While body site explained the majority of the variance in bacterial community structure, the composition of the skin-associated bacterial communities were predominantly influenced by whether the participants were living in an urban or rural environment, with a significantly greater relative abundance of Trabulsiella in urban populations. Adults maintained greater overall microbial diversity than adolescents or the elderly, while the intragroupmore » variation among the elderly and rural populations was significantly greater. Lastly, skin-associated bacterial community structure and composition could predict whether a sample came from an urban or a rural resident ~ 5x greater than random.« less

Vortex wakes generated by robins Erithacus rubecula during free flight in a wind tunnel

PubMed Central

Hedenström, A; Rosén, M; Spedding, G.R

2005-01-01

The wakes of two individual robins were measured in digital particle image velocimetry (DPIV) experiments conducted in the Lund wind tunnel. Wake measurements were compared with each other, and with previous studies in the same facility. There was no significant individual variation in any of the measured quantities. Qualitatively, the wake structure and its gradual variation with flight speed were exactly as previously measured for the thrush nightingale. A procedure that accounts for the disparate sources of circulation spread over the complex wake structure nevertheless can account for the vertical momentum flux required to support the weight, and an example calculation is given for estimating drag from the components of horizontal momentum flux (whose net value is zero). The measured circulations of the largest structures in the wake can be predicted quite well by simple models, and expressions are given to predict these and other measurable quantities in future bird flight experiments. PMID:16849236

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…

Structural Variation in the Bacterial Community Associated with Airborne Particulate Matter in Beijing, China, during Hazy and Nonhazy Days.

PubMed

Yan, Dong; Zhang, Tao; Su, Jing; Zhao, Li-Li; Wang, Hao; Fang, Xiao-Mei; Zhang, Yu-Qin; Liu, Hong-Yu; Yu, Li-Yan

2018-05-01

The structural variation of the bacterial community associated with particulate matter (PM) was assessed in an urban area of Beijing during hazy and nonhazy days. Sampling for different PM fractions (PM 2.5 [<2.5 μm], PM 10 [<10 μm], and total suspended particulate) was conducted using three portable air samplers from September 2014 to February 2015. The airborne bacterial community in these samples was analyzed using the Illumina MiSeq platform with bacterium-specific primers targeting the 16S rRNA gene. A total of 1,707,072 reads belonging to 6,009 operational taxonomic units were observed. The airborne bacterial community composition was significantly affected by PM fractions ( R = 0.157, P < 0.01). In addition, the relative abundances of several genera significantly differed between samples with various haze levels; for example, Methylobacillus , Tumebacillus , and Desulfurispora spp. increased in heavy-haze days. Canonical correspondence analysis and permutation tests showed that temperature, SO 2 concentration, relative humidity, PM 10 concentration, and CO concentration were significant factors that associated with airborne bacterial community composition. Only six genera increased across PM 10 samples ( Dokdonella , Caenimonas , Geminicoccus , and Sphingopyxis ) and PM 2.5 samples ( Cellulomonas and Rhizobacter ), while a large number of taxa significantly increased in total suspended particulate samples, such as Paracoccus , Kocuria , and Sphingomonas Network analysis indicated that Paracoccus , Rubellimicrobium , Kocuria , and Arthrobacter were the key genera in the airborne PM samples. Overall, the findings presented here suggest that diverse airborne bacterial communities are associated with PM and provide further understanding of bacterial community structure in the atmosphere during hazy and nonhazy days. IMPORTANCE The results presented here represent an analysis of the airborne bacterial community associated with particulate matter (PM) and advance our understanding of the structural variation of these communities. We observed a shift in bacterial community composition with PM fractions but no significant difference with haze levels. This may be because the bacterial differences are obscured by high bacterial diversity in the atmosphere. However, we also observed that a few genera (such as Methylobacillus , Tumebacillus , and Desulfurispora ) increased significantly on heavy-haze days. In addition, Paracoccus , Rubellimicrobium , Kocuria , and Arthrobacter were the key genera in the airborne PM samples. Accurate and real-time techniques, such as metagenomics and metatranscriptomics, should be developed for a future survey of the relationship of airborne bacteria and haze. Copyright © 2018 American Society for Microbiology.

Clinical Significance of an Unusual Variation

PubMed Central

Murugan, M. Senthil; Sudha, R.; Bhargavan, Rajesh

2016-01-01

The infrahyoid muscles are involved in vocalisation and swallowing; among these, the sternothyroid muscle is derived from the common primitive sheet. The improper differentiation of this muscle may therefore result in morphological variations. We report an unusual variation found during the dissection of a 65-year-old male cadaver at the Sri Manakula Vinayagar Medical College, Madagadipet, Pondicherry, India, in 2015. An anomalous belly of the right sternothyroid muscle was observed between the internal jugular (IJ) vein and the internal carotid artery with an additional insertion into the tympanic plate and petrous part of the temporal bone and the presence of a levator glandulae thyroideae muscle. The anomalous muscle may compress the IJ vein if it is related to the neurovascular structures of neck; hence, knowledge of variations of the infrahyoid muscles can aid in the evaluation of IJ vein compression among patients with idiopathic symptoms resulting from venous congestion. PMID:28003898

Significant population genetic structure detected in the rock bream Oplegnathus fasciatus (Temminck & Schlegel, 1844) inferred from fluorescent-AFLP analysis

NASA Astrophysics Data System (ADS)

Xiao, Yongshuang; Ma, Daoyuan; Xu, Shihong; Liu, Qinghua; Wang, Yanfeng; Xiao, Zhizhong; Li, Jun

2016-05-01

Oplegnathus fasciatus (rock bream) is a commercial rocky reef fish species in East Asia that has been considered for aquaculture. We estimated the population genetic diversity and population structure of the species along the coastal waters of China using fluorescent-amplified fragment length polymorphisms technology. Using 53 individuals from three populations and four pairs of selective primers, we amplified 1 264 bands, 98.73% of which were polymorphic. The Zhoushan population showed the highest Nei's genetic diversity and Shannon genetic diversity. The results of analysis of molecular variance (AMOVA) showed that 59.55% of genetic variation existed among populations and 40.45% occurred within populations, which indicated that a significant population genetic structure existed in the species. The pairwise fixation index F st ranged from 0.20 to 0.63 and were significant after sequential Bonferroni correction. The topology of an unweighted pair group method with arithmetic mean tree showed two significant genealogical branches corresponding to the sampling locations of North and South China. The AMOVA and STRUCTURE analyses suggested that the O. fasciatus populations examined should comprise two stocks.

Molecular dynamics simulations indicate that deoxyhemoglobin, oxyhemoglobin, carboxyhemoglobin, and glycated hemoglobin under compression and shear exhibit an anisotropic mechanical behavior.

PubMed

Yesudasan, Sumith; Wang, Xianqiao; Averett, Rodney D

2018-05-01

We developed a new mechanical model for determining the compression and shear mechanical behavior of four different hemoglobin structures. Previous studies on hemoglobin structures have focused primarily on overall mechanical behavior; however, this study investigates the mechanical behavior of hemoglobin, a major constituent of red blood cells, using steered molecular dynamics (SMD) simulations to obtain anisotropic mechanical behavior under compression and shear loading conditions. Four different configurations of hemoglobin molecules were considered: deoxyhemoglobin (deoxyHb), oxyhemoglobin (HbO 2 ), carboxyhemoglobin (HbCO), and glycated hemoglobin (HbA 1C ). The SMD simulations were performed on the hemoglobin variants to estimate their unidirectional stiffness and shear stiffness. Although hemoglobin is structurally denoted as a globular protein due to its spherical shape and secondary structure, our simulation results show a significant variation in the mechanical strength in different directions (anisotropy) and also a strength variation among the four different hemoglobin configurations studied. The glycated hemoglobin molecule possesses an overall higher compressive mechanical stiffness and shear stiffness when compared to deoxyhemoglobin, oxyhemoglobin, and carboxyhemoglobin molecules. Further results from the models indicate that the hemoglobin structures studied possess a soft outer shell and a stiff core based on stiffness.

Developmental mechanisms underlying variation in craniofacial disease and evolution.

PubMed

Fish, Jennifer L

2016-07-15

Craniofacial disease phenotypes exhibit significant variation in penetrance and severity. Although many genetic contributions to phenotypic variation have been identified, genotype-phenotype correlations remain imprecise. Recent work in evolutionary developmental biology has exposed intriguing developmental mechanisms that potentially explain incongruities in genotype-phenotype relationships. This review focuses on two observations from work in comparative and experimental animal model systems that highlight how development structures variation. First, multiple genetic inputs converge on relatively few developmental processes. Investigation of when and how variation in developmental processes occurs may therefore help predict potential genetic interactions and phenotypic outcomes. Second, genetic mutation is typically associated with an increase in phenotypic variance. Several models outlining developmental mechanisms underlying mutational increases in phenotypic variance are discussed using Satb2-mediated variation in jaw size as an example. These data highlight development as a critical mediator of genotype-phenotype correlations. Future research in evolutionary developmental biology focusing on tissue-level processes may help elucidate the "black box" between genotype and phenotype, potentially leading to novel treatment, earlier diagnoses, and better clinical consultations for individuals affected by craniofacial anomalies. Copyright © 2015 Elsevier Inc. All rights reserved.

Coparenting and Relationship Quality Effects on Father Engagement: Variations by Residence, Romance

ERIC Educational Resources Information Center

Fagan, Jay; Palkovitz, Rob

2011-01-01

We focused on coparenting support, partner relationship quality, and father engagement in families with young children that did not change structurally over 4 years of participation in the Fragile Families and Child Wellbeing study (N = 1,756). There was a significantly stronger and more robust positive association between fathers' perceived…

Southern pine beetles in central hardwood forests: frequency, spatial extent, and changes to forest structure

Treesearch

John Nowak; Kier Klepzig; D R Coyle; William Carothers; Kamal J K Gandhi

2015-01-01

EXCERPT FROM: Natural Disturbances and Historic Range Variation 2015. The southern pine beetle (SPB) is a major disturbance in pine forests throughout the range of southern yellow pines, and is a significant influence on forests throughout several Central Hardwood Region (CHR) ecoregions...

Variations in killer whale food-associated calls produced during different prey behavioural contexts.

PubMed

Samarra, Filipa I P

2015-07-01

Killer whales produce herding calls to increase herring school density but previous studies suggested that these calls were made only when feeding upon spawning herring. Herring schools less densely when spawning compared to overwintering; therefore, producing herding calls may be advantageous only when feeding upon less dense spawning schools. To investigate if herding calls were produced across different prey behavioural contexts and whether structural variants occurred and correlated with prey behaviour, this study recorded killer whales when feeding upon spawning and overwintering herring. Herding calls were produced by whales feeding on both spawning and overwintering herring, however, calls recorded during overwintering had significantly different duration and peak frequency to those recorded during spawning. Calls recorded in herring overwintering grounds were more variable and sometimes included nonlinear phenomena. Thus, herding calls were not produced exclusively when feeding upon spawning herring, likely because the call increases feeding efficiency regardless of herring school density or behaviour. Variations in herding call structure were observed between prey behavioural contexts and did not appear to be adapted to prey characteristics. Herding call structural variants may be more likely a result of individual or group variation rather than a reflection of properties of the food source. Copyright © 2015. Published by Elsevier B.V.

Drivers of protogynous sex change differ across spatial scales.

PubMed

Taylor, Brett M

2014-01-22

The influence of social demography on sex change schedules in protogynous reef fishes is well established, yet effects across spatial scales (in particular, the magnitude of natural variation relative to size-selective fishing effects) are poorly understood. Here, I examine variation in timing of sex change for exploited parrotfishes across a range of environmental, anthropogenic and geographical factors. Results were highly dependent on spatial scale. Fishing pressure was the most influential factor determining length at sex change at the within-island scale where a wide range of anthropogenic pressure existed. Sex transition occurred at smaller sizes where fishing pressure was high. Among islands, however, differences were overwhelmingly predicted by reefal-scale structural features, a pattern evident for all species examined. For the most abundant species, Chlorurus spilurus, length at sex change increased at higher overall densities and greater female-to-male sex ratios at all islands except where targeted by fishermen; here the trend was reversed. This implies differing selective pressures on adult individuals can significantly alter sex change dynamics, highlighting the importance of social structure, demography and the selective forces structuring populations. Considerable life-history responses to exploitation were observed, but results suggest potential fishing effects on demography may be obscured by natural variation at biogeographic scales.

Populations of weedy crop–wild hybrid beets show contrasting variation in mating system and population genetic structure

PubMed Central

Arnaud, Jean-François; Fénart, Stéphane; Cordellier, Mathilde; Cuguen, Joël

2010-01-01

Reproductive traits are key parameters for the evolution of invasiveness in weedy crop–wild hybrids. In Beta vulgaris, cultivated beets hybridize with their wild relatives in the seed production areas, giving rise to crop–wild hybrid weed beets. We investigated the genetic structure, the variation in first-year flowering and the variation in mating system among weed beet populations occurring within sugar beet production fields. No spatial genetic structure was found for first-year populations composed of F1 crop–wild hybrid beets. In contrast, populations composed of backcrossed weed beets emerging from the seed bank showed a strong isolation-by-distance pattern. Whereas gametophytic self-incompatibility prevents selfing in wild beet populations, all studied weed beet populations had a mixed-mating system, plausibly because of the introgression of the crop-derived Sf gene that disrupts self-incompatibility. No significant relationship between outcrossing rate and local weed beet density was found, suggesting no trends for a shift in the mating system because of environmental effects. We further reveal that increased invasiveness of weed beets may stem from positive selection on first-year flowering induction depending on the B gene inherited from the wild. Finally, we discuss the practical and applied consequences of our findings for crop-weed management. PMID:25567926

Measurement of admixture proportions and description of admixture structure in different US populations

PubMed Central

Halder, Indrani; Yang, Bao-Zhu; Kranzler, Henry R.; Stein, Murray B.; Shriver, Mark D.; Gelernter, Joel

2010-01-01

Variation in individual admixture proportions leads to heterogeneity within populations. Though novel methods and marker panels have been developed to quantify individual admixture, empirical data describing individual admixture distributions are limited. We investigated variation in individual admixture in four US populations [European American (EA), African American (AA) and Hispanics from Connecticut (EC) and California (WC)] assuming three-way intermixture among Europeans, Africans and Indigenous Americans. Admixture estimates were inferred using a panel of 36 microsatellites and 1 SNP, which have significant allele frequency differences between ancestral populations, and by using both a maximum likelihood (ML) based method and a Bayesian method implemented in the program STRUCTURE. Simulation studies showed that estimates obtained with this marker panel are within 96% of expected values. EAs had the lowest non-European admixture with both methods, but showed greater homogeneity with STRUCTURE than with ML. All other samples showed a high degree of variation in admixture estimates with both methods, were highly concordant and showed evidence of admixture stratification. With both methods, AA subjects had 16% European and <10% Indigenous American admixture on average. EC Hispanics had higher mean African admixture and the WC Hispanics higher mean Indigenous American admixture, possibly reflecting their different continental origins. PMID:19572378

Variations in the ultrastructure of human nasal cilia including abnormalities found in retinitis pigmentosa.

PubMed Central

Fox, B; Bull, T B; Arden, G B

1980-01-01

The electron microscopic structure of cilia from the inferior turbinate of the nose was studied in 12 adults, four with chronic sinusitis, one with allergic rhinitis, two with bronchiectasis, three with deviated nasal septum, and two normals. The changes are compared with those found in nasal cilia in 14 patients with retinitis pigmentosa. There were compound cilia in the seven cases with chronic sinusitis, allergic rhinitis, and bronchiectasis but, apart from this, the structure of the cilia was similar in all 12 cases. There were variations in the microtubular pattern in about 4% of cilia, dynein arms were not seen in 4%, and in the rest an average of 5-6 dynein arms were seen in each cilium. The orientation of the cilia was 0 to 90 degrees. In the retinitis pigmentosa patients there was a highly significant increase in cilial abnormalities. The establishment on a quantitative basis of the variations in normal structure of nasal cilila facilitated the recognition of an association between cilial abnormalities and retinitis pigmentosa and should help in the identification of associations that may exist between cilial abnormalities and other diseases. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 Fig. 5 Fig. 7 Fig. 8 PMID:7400333

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

PubMed

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

2017-05-01

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

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

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

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

2014-12-10

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

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

Effect of annealing on optical properties and structure of the vanadium dioxide thin films

NASA Astrophysics Data System (ADS)

Zhu, Huiqun; Li, Yi; Li, Yuming; Huang, Yize; Tong, Guoxiang; Fang, Baoying; Zheng, Qiuxin; Li, Liu; Shen, Yujian

2012-10-01

VO2 thin films were prepared on soda-lime glass substrates by DC magnetron sputtering at room temperature using vanadium target and post annealing in air. X-ray diffraction and FTIR spectroscopy analyses showed that the films obtained at the optimized parameters have high VO2 (011) orientation. Both low temperature deposition and post annealing method were beneficial to grow the nano-films with pure VO2 phase-structure and composition. Metalinsulator transition properties of the VO2 films in terms of infrared transmittance, transmittance variation and film thickness were investigated under varying annealing temperature. Results showed that infrared transmittance variation and transition temperature of the nano-films were significantly improved and reduced respectively. Therefore, this study was able to develop practical low-cost preparation methods for high-performance intelligent energy-saving thin films.

Stochastic Nonlinear Response of Woven CMCs

NASA Technical Reports Server (NTRS)

Kuang, C. Liu; Arnold, Steven M.

2013-01-01

It is well known that failure of a material is a locally driven event. In the case of ceramic matrix composites (CMCs), significant variations in the microstructure of the composite exist and their significance on both deformation and life response need to be assessed. Examples of these variations include changes in the fiber tow shape, tow shifting/nesting and voids within and between tows. In the present work, the influence of scale specific architectural features of woven ceramic composite are examined stochastically at both the macroscale (woven repeating unit cell (RUC)) and structural scale (idealized using multiple RUCs). The recently developed MultiScale Generalized Method of Cells methodology is used to determine the overall deformation response, proportional elastic limit (first matrix cracking), and failure under tensile loading conditions and associated probability distribution functions. Prior results showed that the most critical architectural parameter to account for is weave void shape and content with other parameters being less in severity. Current results show that statistically only the post-elastic limit region (secondary hardening modulus and ultimate tensile strength) is impacted by local uncertainties both at the macro and structural level.

Genetic evaluation of the breeding population of a valuable reforestation conifer Platycladus orientalis (Cupressaceae)

NASA Astrophysics Data System (ADS)

Jin, Yuqing; Ma, Yongpeng; Wang, Shun; Hu, Xian-Ge; Huang, Li-Sha; Li, Yue; Wang, Xiao-Ru; Mao, Jian-Feng

2016-10-01

Platycladus orientalis, a widespread conifer with long lifespan and significant adaptability. It is much used in reforestation in north China and commonly planted in central Asia. With the increasing demand for plantation forest in central to north China, breeding programs are progressively established for this species. Efficient use of breeding resources requires good understanding of the genetic value of the founder breeding materials. This study investigated the distribution of genetic variation in 192 elite trees collected for the breeding program for the central range of the species. We developed first set of 27 polymorphic EST-derived SSR loci for the species from transcriptome/genome data. After examination of amplification quality, 10 loci were used to evaluate the genetic variation in the breeding population. We found moderate genetic diversity (average He = 0.348) and low population differentiation (Fst = 0.011). Extensive admixture and no significant geographic population structure characterized this set of collections. Our analyses of the diversity and population structure are important steps toward a long-term sustainable deployment of the species and provide valuable genetic information for conservation and breeding applications.

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.

Population genetic structure of traditional populations in the Peruvian Central Andes and implications for South American population history.

PubMed

Cabana, Graciela S; Lewis, Cecil M; Tito, Raúl Y; Covey, R Alan; Cáceres, Angela M; Cruz, Augusto F De La; Durand, Diana; Housman, Genevieve; Hulsey, Brannon I; Iannacone, Gian Carlo; López, Paul W; Martínez, Rolando; Medina, Ángel; Dávila, Olimpio Ortega; Pinto, Karla Paloma Osorio; Santillán, Susan I Polo; Domínguez, Percy Rojas; Rubel, Meagan; Smith, Heather F; Smith, Silvia E; Massa, Verónica Rubín de Celis; Lizárraga, Beatriz; Stone, Anne C

2014-01-01

Molecular-based characterizations of Andean peoples are traditionally conducted in the service of elucidating continent-level evolutionary processes in South America. Consequently, genetic variation among "western" Andean populations is often represented in relation to variation among "eastern" Amazon and Orinoco River Basin populations. This west-east contrast in patterns of population genetic variation is typically attributed to large-scale phenomena, such as dual founder colonization events or differing long-term microevolutionary histories. However, alternative explanations that consider the nature and causes of population genetic diversity within the Andean region remain underexplored. Here we examine population genetic diversity in the Peruvian Central Andes using data from the mtDNA first hypervariable region and Y-chromosome short tandem repeats among 17 newly sampled populations and 15 published samples. Using this geographically comprehensive data set, we first reassessed the currently accepted pattern of western versus eastern population genetic structure, which our results ultimately reject: mtDNA population diversities were lower, rather than higher, within Andean versus eastern populations, and only highland Y-chromosomes exhibited significantly higher within-population diversities compared with eastern groups. Multiple populations, including several highland samples, exhibited low genetic diversities for both genetic systems. Second, we explored whether the implementation of Inca state and Spanish colonial policies starting at about ad 1400 could have substantially restructured population genetic variation and consequently constitute a primary explanation for the extant pattern of population diversity in the Peruvian Central Andes. Our results suggest that Peruvian Central Andean population structure cannot be parsimoniously explained as the sole outcome of combined Inca and Spanish policies on the region's population demography: highland populations differed from coastal and lowland populations in mtDNA genetic structure only; highland groups also showed strong evidence of female-biased gene flow and/or effective sizes relative to other Peruvian ecozones. Taken together, these findings indicate that population genetic structure in the Peruvian Central Andes is considerably more complex than previously reported and that characterizations of and explanations for genetic variation may be best pursued within more localized regions and defined time periods.

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.

Regional variations in the density and arrangement of elastic fibres in the anulus fibrosus of the human lumbar disc

PubMed Central

Smith, Lachlan J; Fazzalari, Nicola L

2006-01-01

Elastic fibres are critical components of the extracellular matrix in dynamic biological structures that undergo extension and recoil. Their presence has been demonstrated in the anulus fibrosus of the human lumbar intervertebral disc; however, a detailed regional analysis of their density and arrangement has not been undertaken, limiting our understanding of their structural and functional roles. In this investigation we have quantitatively described regional variations in elastic fibre density in the anulus fibrosus of the human L3–L4 intervertebral disc using histochemistry and light microscopy. Additionally, a multiplanar comparison of patterns of elastic fibre distribution in the intralamellar and interlamellar zones was undertaken. Novel imaging techniques were developed to facilitate the visualization of elastic fibres otherwise masked by dense surrounding matrix. Elastic fibre density was found to be significantly higher in the lamellae of the posterolateral region of the anulus than the anterolateral, and significantly higher in the outer regions than the inner, suggesting that elastic fibre density in each region of the anulus is commensurate with the magnitude of the tensile deformations experienced in bending and torsion. Elastic fibre arrangments in intralamellar and interlamellar zones were shown to be architecturally distinct, suggesting that they perform multiple functional roles within the anulus matrix structural hierarchy. PMID:16928204

Uranus' and Neptune's Clouds as Revealed by UKIRT/UIST Observations

NASA Astrophysics Data System (ADS)

Irwin, Patrick G. J.; Teanby, N. A.; Davis, G. R.

2009-09-01

In 2006, 2007 and 2008 observations of the near-infrared spectrum of Uranus were made with the UIST instrument of the UK Infrared Telescope, covering the period of Uranus’ Northern Spring Equinox. A significant change in the visible appearance of Uranus occurred during this time with the southern polar zone at 45°S fading, while a corresponding zone at 45°N began to form. In addition the visibility of the equatorial zone increased. The observed spectra were fitted using the NEMESIS optimal estimation retrieval model to determine the variation in the latitudinal and vertical cloud structure during this time. Retrievals were conducted using both the methane absorption coefficients used in our previous analyses and also a newly available revised set of methane coefficients and significant differences were seen, which will be reported. During the Uranus observations in 2007, corresponding observations were also made of Neptune's near-infrared spectrum, albeit with substantially less spatial resolution. The spectra were nevertheless sufficient to retrieve the gross variation in Neptune's latitudinal-vertical cloud structure using both sets of methane absorption coefficients. The retrieved vertical-latitudinal cloud structure on Uranus and Neptune, observed with identical instrument setups, are directly compared and the similarities and differences will be presented and discussed.

The American Quarter Horse: Population Structure and Relationship to the Thoroughbred

PubMed Central

2014-01-01

A breed known for its versatility, the American Quarter Horse (QH), is increasingly bred for performance in specific disciplines. The impact of selective breeding on the diversity and structure of the QH breed was evaluated using pedigree analysis and genome-wide SNP data from horses representing 6 performance groups (halter, western pleasure, reining, working cow, cutting, and racing). Genotype data (36 037 single nucleotide polymorphisms [SNPs]) from 36 Thoroughbreds were also evaluated with those from the 132 performing QHs to evaluate the Thoroughbred’s influence on QH diversity. Results showed significant population structure among all QH performance groups excepting the comparison between the cutting and working cow horses; divergence was greatest between the cutting and racing QHs, the latter of which had a large contribution of Thoroughbred ancestry. Significant coancestry and the potential for inbreeding exist within performance groups, especially when considering the elite performers. Relatedness within performance groups is increasing with popular sires contributing disproportionate levels of variation to each discipline. Expected heterozygosity, inbreeding, F ST, cluster, and haplotype analyses suggest these QHs can be broadly classified into 3 categories: stock, racing, and pleasure/halter. Although the QH breed as a whole contains substantial genetic diversity, current breeding practices have resulted in this variation being sequestered into subpopulations. PMID:24293614

Investigation of the foundations of a Byzantine church by three-dimensional seismic tomography

NASA Astrophysics Data System (ADS)

Polymenakos, L.; Papamarinopoulos, S.; Miltiadou, A.; Charkiolakis, N.

2005-02-01

Byzantine public buildings are of high historical and cultural value. Churches, in particular, are of high architectural and artistic value because they are built using various materials and construction techniques and may contain significant frescoes and mosaics. The knowledge of the state of foundations and ground material conditions is important for their proper restoration and preservation. Seismic tomography is employed to investigate the foundation structure and ground material of a Byzantine church. Energy sources are placed across the floor of the church and surrounding courts, while recorders are placed in a subterranean crypt. Travel time data are analyzed and processed with a three-dimensional (3D) tomographic inversion software in order to construct seismic velocity images at the foundation and below foundation level. Velocity variations are known to correlate well with the lithological character of the earth materials, thus providing important structural and lithological information. A case study from a Byzantine church of 11th c. A.D. in the suburbs of Athens, Greece, is presented. The objective of this research is the nondestructive investigation of unknown underground structures or void spaces, mainly under the floor of the building. The results are interpreted in terms of the foundation elements as well as of significant variations in the earth material character.

Structural basis of glycan specificity in neonate-specific bovine-human reassortant rotavirus

DOE PAGES

Hu, Liya; Ramani, Sasirekha; Czako, Rita; ...

2015-09-30

We report that strain-dependent variation of glycan recognition during initial cell attachment of viruses is a critical determinant of host specificity, tissue-tropism and zoonosis. Rotaviruses (RVs), which cause life-threatening gastroenteritis in infants and children, display significant genotype-dependent variations in glycan recognition resulting from sequence alterations in the VP8* domain of the spike protein VP4. The structural basis of this genotype-dependent glycan specificity, particularly in human RVs, remains poorly understood. Here, from crystallographic studies, we show how genotypic variations configure a novel binding site in the VP8* of a neonate-specific bovine-human reassortant to uniquely recognize either type I or type IImore » precursor glycans, and to restrict type II glycan binding in the bovine counterpart. In conclusion, such a distinct glycan-binding site that allows differential recognition of the precursor glycans, which are developmentally regulated in the neonate gut and abundant in bovine and human milk provides a basis for age-restricted tropism and zoonotic transmission of G10P[11] rotaviruses.« less

Structural basis of glycan specificity in neonate-specific bovine-human reassortant rotavirus

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

Hu, Liya; Ramani, Sasirekha; Czako, Rita

We report that strain-dependent variation of glycan recognition during initial cell attachment of viruses is a critical determinant of host specificity, tissue-tropism and zoonosis. Rotaviruses (RVs), which cause life-threatening gastroenteritis in infants and children, display significant genotype-dependent variations in glycan recognition resulting from sequence alterations in the VP8* domain of the spike protein VP4. The structural basis of this genotype-dependent glycan specificity, particularly in human RVs, remains poorly understood. Here, from crystallographic studies, we show how genotypic variations configure a novel binding site in the VP8* of a neonate-specific bovine-human reassortant to uniquely recognize either type I or type IImore » precursor glycans, and to restrict type II glycan binding in the bovine counterpart. In conclusion, such a distinct glycan-binding site that allows differential recognition of the precursor glycans, which are developmentally regulated in the neonate gut and abundant in bovine and human milk provides a basis for age-restricted tropism and zoonotic transmission of G10P[11] rotaviruses.« 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.

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.

Nomenclature of Vertebral Laminae in Lizards, with Comments on Ontogenetic and Serial Variation in Lacertini (Squamata, Lacertidae)

PubMed Central

Tschopp, Emanuel

2016-01-01

Vertebral laminae are bony ridges or sheets that connect important morphological landmarks on the vertebrae, like diapophyses or zygapophyses. They usually exhibit some serial variation throughout the column. A consistent terminology facilitates the morphological description of this variation, and the recognition of patterns that could be taxonomically significant and could serve as phylogenetic characters. Such a terminology was designed for saurischian dinosaurs, and has also been applied to other members of Archosauriformes. Herein, this terminology is applied for the first time to lizards (Squamata). Probably due to their generally smaller size compared to saurischian dinosaurs, lizards have less developed vertebral laminae. Some laminae could not be recognized in this group and others require new names to account for differences in basic vertebral morphology. For instance, the fusion of diapophysis and parapophysis in lacertids into a structure called synapophysis necessitates the creation of the new term synapophyseal laminae for both diapophyseal and parapophyseal laminae. An assessment of occurrence and serial variation in a number of lacertid species shows that some laminae develop throughout ontogeny or only occur in large-sized species, whereas the distribution of other laminae might prove to be taxonomically significant in future. PMID:26907769

Nomenclature of Vertebral Laminae in Lizards, with Comments on Ontogenetic and Serial Variation in Lacertini (Squamata, Lacertidae).

PubMed

Tschopp, Emanuel

2016-01-01

Vertebral laminae are bony ridges or sheets that connect important morphological landmarks on the vertebrae, like diapophyses or zygapophyses. They usually exhibit some serial variation throughout the column. A consistent terminology facilitates the morphological description of this variation, and the recognition of patterns that could be taxonomically significant and could serve as phylogenetic characters. Such a terminology was designed for saurischian dinosaurs, and has also been applied to other members of Archosauriformes. Herein, this terminology is applied for the first time to lizards (Squamata). Probably due to their generally smaller size compared to saurischian dinosaurs, lizards have less developed vertebral laminae. Some laminae could not be recognized in this group and others require new names to account for differences in basic vertebral morphology. For instance, the fusion of diapophysis and parapophysis in lacertids into a structure called synapophysis necessitates the creation of the new term synapophyseal laminae for both diapophyseal and parapophyseal laminae. An assessment of occurrence and serial variation in a number of lacertid species shows that some laminae develop throughout ontogeny or only occur in large-sized species, whereas the distribution of other laminae might prove to be taxonomically significant in future.

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.

Time-dependent seismic tomography of the Coso geothermal area, 1996-2004

USGS Publications Warehouse

Julian, B.R.; Foulger, G.R.

2005-01-01

The permanent 18-station network of three-component digital seismometers at the seismically active Coso geothermal area, California, provides high-quality microearthquake (MEQ) data that are well suited to investigating temporal variations in structure related to processes within the geothermal reservoir. A preliminary study [Julian, et al., 2003; Julian, et al., 2004] comparing data from 1996 and 2003 found significant variations in the ratio of the seismic wave-speeds, Vp/Vs, at shallow depths over this time interval. This report describes results of a more detailed study of each year from 1996 through 2004.

[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.

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.

Primary Productivity and Precipitation-Use Efficiency in Temperate Grassland in the Loess Plateau of China

PubMed Central

Jia, Xiaoxu; Xie, Baoni; Shao, Ming’an; Zhao, Chunlei

2015-01-01

Clarifying spatial variations in aboveground net primary productivity (ANPP) and precipitation-use efficiency (PUE) of grasslands is critical for effective prediction of the response of terrestrial ecosystem carbon and water cycle to future climate change. Though the combination use of remote sensing products and in situ ANPP measurements, we quantified the effects of climatic [mean annual precipitation (MAP) and precipitation seasonal distribution (PSD)], biotic [leaf area index (LAI)] and abiotic [slope gradient, aspect, soil water storage (SWS) and other soil physical properties] factors on the spatial variations in ANPP and PUE across different grassland types (i.e., meadow steppe, typical steppe and desert steppe) in the Loess Plateau. Based on the study, ANPP increased exponentially with MAP for the entire temperate grassland; suggesting that PUE increased with increasing MAP. Also PSD had a significant effect on ANPP and PUE; where more even PSD favored higher ANPP and PUE. Then MAP, more than PSD, explained spatial variations in typical steppe and desert steppe. However, PSD was the dominant driving factor of spatial variations in ANPP of meadow steppe. This suggested that in terms of spatial variations in ANPP of meadow steppe, change in PSD due to climate change was more important than that in total annual precipitation. LAI explained 78% of spatial PUE in the entire Loess Plateau temperate grassland. As such, LAI was the primary driving factor of spatial variations in PUE. Although the effect of SWS on ANPP and PUE was significant, it was nonetheless less than that of precipitation and vegetation. We therefore concluded that changes in vegetation structure and consequently in LAI and/or altered pattern of seasonal distribution of rainfall due to global climate change could significantly influence ecosystem carbon and water cycle in temperate grasslands. PMID:26295954

Primary Productivity and Precipitation-Use Efficiency in Temperate Grassland in the Loess Plateau of China.

PubMed

Jia, Xiaoxu; Xie, Baoni; Shao, Ming'an; Zhao, Chunlei

2015-01-01

Clarifying spatial variations in aboveground net primary productivity (ANPP) and precipitation-use efficiency (PUE) of grasslands is critical for effective prediction of the response of terrestrial ecosystem carbon and water cycle to future climate change. Though the combination use of remote sensing products and in situ ANPP measurements, we quantified the effects of climatic [mean annual precipitation (MAP) and precipitation seasonal distribution (PSD)], biotic [leaf area index (LAI)] and abiotic [slope gradient, aspect, soil water storage (SWS) and other soil physical properties] factors on the spatial variations in ANPP and PUE across different grassland types (i.e., meadow steppe, typical steppe and desert steppe) in the Loess Plateau. Based on the study, ANPP increased exponentially with MAP for the entire temperate grassland; suggesting that PUE increased with increasing MAP. Also PSD had a significant effect on ANPP and PUE; where more even PSD favored higher ANPP and PUE. Then MAP, more than PSD, explained spatial variations in typical steppe and desert steppe. However, PSD was the dominant driving factor of spatial variations in ANPP of meadow steppe. This suggested that in terms of spatial variations in ANPP of meadow steppe, change in PSD due to climate change was more important than that in total annual precipitation. LAI explained 78% of spatial PUE in the entire Loess Plateau temperate grassland. As such, LAI was the primary driving factor of spatial variations in PUE. Although the effect of SWS on ANPP and PUE was significant, it was nonetheless less than that of precipitation and vegetation. We therefore concluded that changes in vegetation structure and consequently in LAI and/or altered pattern of seasonal distribution of rainfall due to global climate change could significantly influence ecosystem carbon and water cycle in temperate grasslands.

Thermal control requirements for large space structures

NASA Technical Reports Server (NTRS)

Manoff, M.

1978-01-01

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

Circular electrodes to reduce the current variation of OTFTs with the drop-casted semiconducting layer

NASA Astrophysics Data System (ADS)

Dipu Kabir, H. M.; Ahmed, Zubair; Kariyadan, Remashan; Zhang, Lining; Chan, Mansun

2018-06-01

Circular organic thin film transistor (OTFT) structures are proposed to reduce the impact of variable grain alignment on the drive current of the polycrystalline organic thin film transistor (OTFT). As the circular structure is planar symmetric, the orientation of the grain cannot affect the drive current of the circular OTFT. Thus, circular electrodes expected to provide a lower variation. Top-gate, bottom-contact circular and conventional OTFTs with drop-casted polycrystalline 6,13-Bis(triisopropyl-silylethynyl) (TIPS)-Pentacene organic semiconducting layer (OSC) are fabricated to verify the theoretical variation reduction. The relative standard deviation (RSD), defined as the ratio of standard deviation and the average of drive current is used as the degree of variations in different structures. According to our fabrication result, circular transistors have a significantly lower variation (20% RSD), compared to the variation of conventional OTFTs (61% RSD). His research interests include Organic Electronics, VLSI Design, Embedded System, Neural Networks, and Solid-state devices. Between July 2001 and December 2002, he was a Visiting Professor at University of California at Berkeley and the Co-director of the BSIM program. He is currently still consulting on the development of the next generation compact models. He has been actively contributing to the professional community and hold many positions. He was a Board of Governor, Chair of the Education Committee, the Chair of the Region 10 subcommittee and a Distinguished lecturer of the IEEE Electron Device Society. He has also chaired many international conferences and acting as editors for a number of technical journals. In addition, he has received many awards including the UC Regents Fellowship, Golden Keys Scholarship for Academic Excellence, SRC Inventor Recognition Award, Rockwell Research Fellowship, R&D 100 award (for the BSIM3v3 project), Distinguished Teaching Award, the Shenzhen Science and Technology Innovation awards, and EDS Education Award etc. He is a Fellow of HKIE, IET and IEEE.

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

PubMed Central

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

2016-01-01

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

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.

Body size and pubertal development explain ethnic differences in structural geometry at the femur in Asian, Hispanic, and white early adolescent girls living in the U.S.

PubMed Central

Osborne, D.L.; Weaver, C.M.; McCabe, L.D.; McCabe, G.M.; Novotny, R.; Van Loan, M.D.; Going, S.; Matkovic, V.; Boushey, C.J.; Savaiano, D.A.

2012-01-01

Variation in structural geometry is present in adulthood, but when this variation arises and what influences this variation prior to adulthood remains poorly understood. Ethnicity is commonly the focus of research of skeletal integrity and appears to explain some of the variation in quantification of bone tissue. However, why ethnicity explains variation in skeletal integrity is unclear. Methods Here we examine predictors of bone cross sectional area (CSA) and section modulus (Z), measured using dual-energy X-ray absorptiometry (DXA) and the Advanced Hip Analysis (AHA) program at the narrow neck of the femur in adolescent (9–14 yr) girls (n=479) living in the United States who were classified as Asian, Hispanic, or white if the subject was 75% of a given group based on parental reported ethnicity. Protocols for measuring height and weight follow standardized procedures. Total body lean mass (LM) and total body fat mass (FM) were quantified in kilograms using DXA. Total dietary and total dairy calcium intakes from the previous month were estimated by the use of an electronic semi-quantitative food frequency questionnaire (eFFQ). Physical activity was estimated for the previous year by a validated self-administered modifiable activity questionnaire for adolescents with energy expenditure calculated from the metabolic equivalent (MET) values from the Compendium of Physical Activities. Multiple regression models were developed to predict CSA and Z. Results Age, time from menarche, total body lean mass (LM), total body fat mass (FM), height, total calcium, and total dairy calcium all shared a significant (p<0.05), positive relationship with CSA. Age, time from menarche, LM, FM, and height shared significant (p<0.05), positive relationships with Z. For both CSA and Z, LM was the most important covariate. Physical activity was not a significant predictor of geometry at the femoral neck (p≥0.339), even after removing LM as a covariate. After adjusting for covariates, ethnicity was not a significant predictor in regression models for CSA and Z. Conclusion Variability in bone geometry at the narrow neck of the femur is best explained by body size and pubertal maturation. After controlling for these covariates there were no differences in bone geometry between ethnic groups. PMID:22944607

Body size and pubertal development explain ethnic differences in structural geometry at the femur in Asian, Hispanic, and white early adolescent girls living in the U.S.

PubMed

Osborne, D L; Weaver, C M; McCabe, L D; McCabe, G P; Novotny, R; Van Loan, M D; Going, S; Matkovic, V; Boushey, C J; Savaiano, D A

2012-11-01

Variation in structural geometry is present in adulthood, but when this variation arises and what influences this variation prior to adulthood remains poorly understood. Ethnicity is commonly the focus of research of skeletal integrity and appears to explain some of the variation in quantification of bone tissue. However, why ethnicity explains variation in skeletal integrity is unclear. Here we examine predictors of bone cross sectional area (CSA) and section modulus (Z), measured using dual-energy X-ray absorptiometry (DXA) and the Advanced Hip Analysis (AHA) program at the narrow neck of the femur in adolescent (9-14 years) girls (n=479) living in the United States who were classified as Asian, Hispanic, or white if the subject was 75% of a given group based on parental reported ethnicity. Protocols for measuring height and weight follow standardized procedures. Total body lean mass (LM) and total body fat mass (FM) were quantified in kilograms using DXA. Total dietary and total dairy calcium intakes from the previous month were estimated by the use of an electronic semi-quantitative food frequency questionnaire (eFFQ). Physical activity was estimated for the previous year by a validated self-administered modifiable activity questionnaire for adolescents with energy expenditure calculated from the metabolic equivalent (MET) values from the Compendium of Physical Activities. Multiple regression models were developed to predict CSA and Z. Age, time from menarche, total body lean mass (LM), total body fat mass (FM), height, total calcium, and total dairy calcium all shared a significant (p<0.05), positive relationship with CSA. Age, time from menarche, LM, FM, and height shared significant (p<0.05), positive relationships with Z. For both CSA and Z, LM was the most important covariate. Physical activity was not a significant predictor of geometry at the femoral neck (p≥0.339), even after removing LM as a covariate. After adjusting for covariates, ethnicity was not a significant predictor in regression models for CSA and Z. Variability in bone geometry at the narrow neck of the femur is best explained by body size and pubertal maturation. After controlling for these covariates there were no differences in bone geometry between ethnic groups. Published by Elsevier Inc.

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.

Consumer trait variation influences tritrophic interactions in salt marsh communities.

PubMed

Hughes, Anne Randall; Hanley, Torrance C; Orozco, Nohelia P; Zerebecki, Robyn A

2015-07-01

The importance of intraspecific variation has emerged as a key question in community ecology, helping to bridge the gap between ecology and evolution. Although much of this work has focused on plant species, recent syntheses have highlighted the prevalence and potential importance of morphological, behavioral, and life history variation within animals for ecological and evolutionary processes. Many small-bodied consumers live on the plant that they consume, often resulting in host plant-associated trait variation within and across consumer species. Given the central position of consumer species within tritrophic food webs, such consumer trait variation may play a particularly important role in mediating trophic dynamics, including trophic cascades. In this study, we used a series of field surveys and laboratory experiments to document intraspecific trait variation in a key consumer species, the marsh periwinkle Littoraria irrorata, based on its host plant species (Spartina alterniflora or Juncus roemerianus) in a mixed species assemblage. We then conducted a 12-week mesocosm experiment to examine the effects of Littoraria trait variation on plant community structure and dynamics in a tritrophic salt marsh food web. Littoraria from different host plant species varied across a suite of morphological and behavioral traits. These consumer trait differences interacted with plant community composition and predator presence to affect overall plant stem height, as well as differentially alter the density and biomass of the two key plant species in this system. Whether due to genetic differences or phenotypic plasticity, trait differences between consumer types had significant ecological consequences for the tritrophic marsh food web over seasonal time scales. By altering the cascading effects of the top predator on plant community structure and dynamics, consumer differences may generate a feedback over longer time scales, which in turn influences the degree of trait divergence in subsequent consumer populations.

Genetic mechanisms underlying the methylation level of anthocyanins in grape (Vitis vinifera L.)

PubMed Central

2011-01-01

Background Plant color variation is due not only to the global pigment concentration but also to the proportion of different types of pigment. Variation in the color spectrum may arise from secondary modifications, such as hydroxylation and methylation, affecting the chromatic properties of pigments. In grapes (Vitis vinifera L.), the level of methylation modifies the stability and reactivity of anthocyanin, which directly influence the color of the berry. Anthocyanin methylation, as a complex trait, is controlled by multiple molecular factors likely to involve multiple regulatory steps. Results In a Syrah × Grenache progeny, two QTLs were detected for variation in level of anthocyanin methylation. The first one, explaining up to 27% of variance, colocalized with a cluster of Myb-type transcription factor genes. The second one, explaining up to 20% of variance, colocalized with a cluster of O-methyltransferase coding genes (AOMT). In a collection of 32 unrelated cultivars, MybA and AOMT expression profiles correlated with the level of methylated anthocyanin. In addition, the newly characterized AOMT2 gene presented two SNPs associated with methylation level. These mutations, probably leading to a structural change of the AOMT2 protein significantly affected the enzyme specific catalytic efficiency for the 3'-O-methylation of delphinidin 3-glucoside. Conclusion We demonstrated that variation in methylated anthocyanin accumulation is susceptible to involve both transcriptional regulation and structural variation. We report here the identification of novel AOMT variants likely to cause methylated anthocyanin variation. The integration of QTL mapping and molecular approaches enabled a better understanding of how variation in gene expression and catalytic efficiency of the resulting enzyme may influence the grape anthocyanin profile. PMID:22171701

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.

Two worlds collide: Image analysis methods for quantifying structural variation in cluster molecular dynamics

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

Steenbergen, K. G., E-mail: kgsteen@gmail.com; Gaston, N.

2014-02-14

Inspired by methods of remote sensing image analysis, we analyze structural variation in cluster molecular dynamics (MD) simulations through a unique application of the principal component analysis (PCA) and Pearson Correlation Coefficient (PCC). The PCA analysis characterizes the geometric shape of the cluster structure at each time step, yielding a detailed and quantitative measure of structural stability and variation at finite temperature. Our PCC analysis captures bond structure variation in MD, which can be used to both supplement the PCA analysis as well as compare bond patterns between different cluster sizes. Relying only on atomic position data, without requirement formore » a priori structural input, PCA and PCC can be used to analyze both classical and ab initio MD simulations for any cluster composition or electronic configuration. Taken together, these statistical tools represent powerful new techniques for quantitative structural characterization and isomer identification in cluster MD.« less

Two worlds collide: image analysis methods for quantifying structural variation in cluster molecular dynamics.

PubMed

Steenbergen, K G; Gaston, N

2014-02-14

Inspired by methods of remote sensing image analysis, we analyze structural variation in cluster molecular dynamics (MD) simulations through a unique application of the principal component analysis (PCA) and Pearson Correlation Coefficient (PCC). The PCA analysis characterizes the geometric shape of the cluster structure at each time step, yielding a detailed and quantitative measure of structural stability and variation at finite temperature. Our PCC analysis captures bond structure variation in MD, which can be used to both supplement the PCA analysis as well as compare bond patterns between different cluster sizes. Relying only on atomic position data, without requirement for a priori structural input, PCA and PCC can be used to analyze both classical and ab initio MD simulations for any cluster composition or electronic configuration. Taken together, these statistical tools represent powerful new techniques for quantitative structural characterization and isomer identification in cluster MD.

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.

Impacts of Edaphic Factors on Communities of Ammonia-Oxidizing Archaea, Ammonia-Oxidizing Bacteria and Nitrification in Tropical Soils

PubMed Central

de Gannes, Vidya; Eudoxie, Gaius; Hickey, William J.

2014-01-01

Nitrification is a key process in soil nitrogen (N) dynamics, but relatively little is known about it in tropical soils. In this study, we examined soils from Trinidad to determine the edaphic drivers affecting nitrification levels and community structure of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in non-managed soils. The soils were naturally vegetated, ranged in texture from sands to clays and spanned pH 4 to 8. The AOA were detected by qPCR in all soils (ca. 105 to 106 copies archaeal amoA g−1 soil), but AOB levels were low and bacterial amoA was infrequently detected. AOA abundance showed a significant negative correlation (p<0.001) with levels of soil organic carbon, clay and ammonium, but was not correlated to pH. Structures of AOA and AOB communities, as determined by amoA terminal restriction fragment (TRF) analysis, differed significantly between soils (p<0.001). Variation in AOA TRF profiles was best explained by ammonium-N and either Kjeldahl N or total N (p<0.001) while variation in AOB TRF profiles was best explained by phosphorus, bulk density and iron (p<0.01). In clone libraries, phylotypes of archaeal amoA (predominantly Nitrososphaera) and bacterial amoA (predominanatly Nitrosospira) differed between soils, but variation was not correlated with pH. Nitrification potential was positively correlated with clay content and pH (p<0.001), but not to AOA or AOB abundance or community structure. Collectively, the study showed that AOA and AOB communities were affected by differing sets of edaphic factors, notably that soil N characteristics were significant for AOA, but not AOB, and that pH was not a major driver for either community. Thus, the effect of pH on nitrification appeared to mainly reflect impacts on AOA or AOB activity, rather than selection for AOA or AOB phylotypes differing in nitrifying capacity. PMID:24586878

Genetic variation, multiple paternity, and measures of reproductive success in the critically endangered hawksbill turtle (Eretmochelys imbricata).

PubMed

González-Garza, Blanca Idalia; Stow, Adam; Sánchez-Teyer, Lorenzo Felipe; Zapata-Pérez, Omar

2015-12-01

The Yucatán Peninsula in Mexico contains some of the largest breeding groups of the globally distributed and critically endangered hawksbill turtle (Eretmochelys imbricata). An improved understanding of the breeding system of this species and how its genetic variation is structured among nesting areas is required before the threats to its survival can be properly evaluated. Here, we genotype 1195 hatchlings and 41 nesting females at 12 microsatellite loci to assess levels of multiple paternity, genetic variation and whether individual levels of homozygosity are associated with reproductive success. Of the 50 clutches analyzed, only 6% have multiple paternity. The distribution of pairwise relatedness among nesting localities (rookeries) was not random with elevated within-rookery relatedness, and declining relatedness with geographic distance indicating some natal philopatry. Although there was no strong evidence that particular rookeries had lost allelic variation via drift, younger turtles had significantly lower levels of genetic variation than older turtles, suggesting some loss of genetic variation. At present there is no indication that levels of genetic variation are associated with measures of reproductive success such as clutch size, hatching success, and frequency of infertile eggs.

Regional deep hyperthermia: impact of observer variability in CT-based manual tissue segmentation on simulated temperature distribution

NASA Astrophysics Data System (ADS)

Aklan, Bassim; Hartmann, Josefin; Zink, Diana; Siavooshhaghighi, Hadi; Merten, Ricarda; Putz, Florian; Ott, Oliver; Fietkau, Rainer; Bert, Christoph

2017-06-01

The aim of this study was to systematically investigate the influence of the inter- and intra-observer segmentation variation of tumors and organs at risk on the simulated temperature coverage of the target. CT scans of six patients with tumors in the pelvic region acquired for radiotherapy treatment planning were used for hyperthermia treatment planning. To study the effect of inter-observer variation, three observers manually segmented in the CT images of each patient the following structures: fat, muscle, bone and the bladder. The gross tumor volumes (GTV) were contoured by three radiation oncology residents and used as the hyperthermia target volumes. For intra-observer variation, one of the observers of each group contoured the structures of each patient three times with a time span of one week between the segmentations. Moreover, the impact of segmentation variations in organs at risk (OARs) between the three inter-observers was investigated on simulated temperature distributions using only one GTV. The spatial overlap between individual segmentations was assessed by the Dice similarity coefficient (DSC) and the mean surface distance (MSD). Additionally, the temperatures T90/T10 delivered to 90%/10% of the GTV, respectively, were assessed for each observer combination. The results of the segmentation similarity evaluation showed that the DSC of the inter-observer variation of fat, muscle, the bladder, bone and the target was 0.68  ±  0.12, 0.88  ±  0.05, 0.73  ±  0.14, 0.91  ±  0.04 and 0.64  ±  0.11, respectively. Similar results were found for the intra-observer variation. The MSD results were similar to the DSCs for both observer variations. A statistically significant difference (p  <  0.05) was found for T90 and T10 in the predicted target temperature due to the observer variability. The conclusion is that intra- and inter-observer variations have a significant impact on the temperature coverage of the target. Furthermore, OARs, such as bone and the bladder, may essentially influence the homogeneity of the simulated target temperature distribution.

Relationship of uranium and other trace elements to post-Cretaceous vulcanism

USGS Publications Warehouse

Coats, Robert R.

1955-01-01

A regional study of the distribution of uranium, boron, tin, beryllium, niobium, lanthanum, lead, zirconium, lithium, and fluorine in 112 samples of Cenozoic volcanic rocks of predominately rhyolitic and dacitic composition has shown that the content of uranium has a significantly high positive correlation with that of niobium, beryllium, and fluorine, a lower but still significant positive correlation with lithium and tin, a significant negative correlation with boron and lanthanum, and no significant correlation with zirconium and lead. A study of the relation of content of the several elements to the geographic provenance shows significant variation with provenance for all these elements, except tin and lanthanum. On the basis of these variations and on patterns of consistency, five comagmatic provinces, one of which is divided into three sub-provinces, have been delimited, in part, on a map of the western United States. The patter of distribution of boron is significantly different from that of the other elements. The regional difference are perhaps best explained by structural control of the effectiveness of vertical transport.

Relationships between Host Phylogeny, Host Type and Bacterial Community Diversity in Cold-Water Coral Reef Sponges

PubMed Central

Schöttner, Sandra; Hoffmann, Friederike; Cárdenas, Paco; Rapp, Hans Tore; Boetius, Antje; Ramette, Alban

2013-01-01

Cold-water coral reefs are known to locally enhance the diversity of deep-sea fauna as well as of microbes. Sponges are among the most diverse faunal groups in these ecosystems, and many of them host large abundances of microbes in their tissues. In this study, twelve sponge species from three cold-water coral reefs off Norway were investigated for the relationship between sponge phylogenetic classification (species and family level), as well as sponge type (high versus low microbial abundance), and the diversity of sponge-associated bacterial communities, taking also geographic location and water depth into account. Community analysis by Automated Ribosomal Intergenic Spacer Analysis (ARISA) showed that as many as 345 (79%) of the 437 different bacterial operational taxonomic units (OTUs) detected in the dataset were shared between sponges and sediments, while only 70 (16%) appeared purely sponge-associated. Furthermore, changes in bacterial community structure were significantly related to sponge species (63% of explained community variation), sponge family (52%) or sponge type (30%), whereas mesoscale geographic distances and water depth showed comparatively small effects (<5% each). In addition, a highly significant, positive relationship between bacterial community dissimilarity and sponge phylogenetic distance was observed within the ancient family of the Geodiidae. Overall, the high diversity of sponges in cold-water coral reefs, combined with the observed sponge-related variation in bacterial community structure, support the idea that sponges represent heterogeneous, yet structured microbial habitats that contribute significantly to enhancing bacterial diversity in deep-sea ecosystems. PMID:23393586

Evidence of weak genetic structure and recent gene flow between Bactrocera dorsalis s.s. and B. papayae, across Southern Thailand and West Malaysia, supporting a single target pest for SIT applications

PubMed Central

2014-01-01

Background Bactrocera dorsalis s.s. (Hendel) and B. papayae Drew & Hancock, are invasive pests belonging to the B. dorsalis complex. Their species status, based on morphology, is sometimes arguable. Consequently, the existence of cryptic species and/or population isolation may decrease the effectiveness of the sterile insect technique (SIT) due to an unknown degree of sexual isolation between released sterile flies and wild counterparts. To evaluate the genetic relationship and current demography in wild populations for guiding the application of area-wide integrated pest management using SIT, seven microsatellite-derived markers from B. dorsalis s.s. and another five from B. papayae were used for surveying intra- and inter-specific variation, population structure, and recent migration among sympatric and allopatric populations of the two morphological forms across Southern Thailand and West Malaysia. Results Basic genetic variations were not significantly different among forms, populations, and geographical areas (P > 0.05). Nonetheless, two sets of microsatellite markers showed significantly different levels of polymorphisms. Genetic differentiation between intra- and inter-specific differences was significant, but low. Seventeen populations revealed three hypothetical genetic clusters (K = 3) regardless of forms and geographical areas. The genetic structure of sympatric populations slightly changed during the different years of collection. Recent gene flow (m ≥ 0.10) was frequently detected whether samples were sympatric or allopatric. Ninety-five of 379 individuals distributed across the given area were designated as recent migrants or of admixed ancestry. As a consequence of substantial migration, no significant correlation between genetic and geographic distances was detected (R2 = 0.056, P = 0.650). Conclusions According to the 12 microsatellite variations, weak population structure and recent gene flow suggest that there is no status for cryptic species between B. dorsalis s.s. and B. papayae forms in Southern Thailand and West Malaysia. Both forms can be treated as a single target pest for the SIT program in an area-wide sense. Additionally, the result of species identification based on molecular data and morphological character are not congruent. The use of independent, multiple approaches in the characterization of the target population may ensure the effectiveness and feasibility of SIT-based control in the target area. PMID:24929425

Evidence of weak genetic structure and recent gene flow between Bactrocera dorsalis s.s. and B. papayae, across Southern Thailand and West Malaysia, supporting a single target pest for SIT applications.

PubMed

Aketarawong, Nidchaya; Isasawin, Siriwan; Thanaphum, Sujinda

2014-06-14

Bactrocera dorsalis s.s. (Hendel) and B. papayae Drew & Hancock, are invasive pests belonging to the B. dorsalis complex. Their species status, based on morphology, is sometimes arguable. Consequently, the existence of cryptic species and/or population isolation may decrease the effectiveness of the sterile insect technique (SIT) due to an unknown degree of sexual isolation between released sterile flies and wild counterparts. To evaluate the genetic relationship and current demography in wild populations for guiding the application of area-wide integrated pest management using SIT, seven microsatellite-derived markers from B. dorsalis s.s. and another five from B. papayae were used for surveying intra- and inter-specific variation, population structure, and recent migration among sympatric and allopatric populations of the two morphological forms across Southern Thailand and West Malaysia. Basic genetic variations were not significantly different among forms, populations, and geographical areas (P > 0.05). Nonetheless, two sets of microsatellite markers showed significantly different levels of polymorphisms. Genetic differentiation between intra- and inter-specific differences was significant, but low. Seventeen populations revealed three hypothetical genetic clusters (K = 3) regardless of forms and geographical areas. The genetic structure of sympatric populations slightly changed during the different years of collection. Recent gene flow (m ≥ 0.10) was frequently detected whether samples were sympatric or allopatric. Ninety-five of 379 individuals distributed across the given area were designated as recent migrants or of admixed ancestry. As a consequence of substantial migration, no significant correlation between genetic and geographic distances was detected (R2 = 0.056, P = 0.650). According to the 12 microsatellite variations, weak population structure and recent gene flow suggest that there is no status for cryptic species between B. dorsalis s.s. and B. papayae forms in Southern Thailand and West Malaysia. Both forms can be treated as a single target pest for the SIT program in an area-wide sense. Additionally, the result of species identification based on molecular data and morphological character are not congruent. The use of independent, multiple approaches in the characterization of the target population may ensure the effectiveness and feasibility of SIT-based control in the target area.

Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sands.

PubMed

Böer, Simone I; Hedtkamp, Stefanie I C; van Beusekom, Justus E E; Fuhrman, Jed A; Boetius, Antje; Ramette, Alban

2009-07-01

Bacterial community structure and microbial activity were determined together with a large number of contextual environmental parameters over 2 years in subtidal sands of the German Wadden Sea in order to identify the main factors shaping microbial community structure and activity in this habitat. Seasonal changes in temperature were directly reflected in bacterial activities and total community respiration, but could not explain variations in the community structure. Strong sediment depth-related patterns were observed for bacterial abundances, carbon production rates and extracellular enzymatic activities. Bacterial community structure also showed a clear vertical variation with higher operational taxonomic unit (OTU) numbers at 10-15 cm depth than in the top 10 cm, probably because of the decreasing disturbance by hydrodynamic forces with sediment depth. The depth-related variations in bacterial community structure could be attributed to vertical changes in bacterial abundances, chlorophyll a and NO(3)(-), indicating that spatial patterns of microbes are partially environmentally controlled. Time was the most important single factor affecting microbial community structure with an OTU replacement of up to 47% over 2 years and a contribution of 34% to the total variation. A large part of this variation was not related to any environmental parameters, suggesting that temporal variations in bacterial community structure are caused by yet unknown environmental drivers and/or by stochastic events in coastal sand habitats. Principal ecosystem functions such as benthic oxygen consumption and extracellular hydrolysis of organic matter were, however, at a high level at all times, indicating functional redundancy in the microbial communities.

Dispersion Measure Variation of Repeating Fast Radio Burst Sources

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

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

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

Fractual interrelationships in field and seismic data. Final report

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

NONE

1997-01-07

Fractals provide a description of physical patterns over a range of scales in both time and space. Studies presented herein examine the fractal characteristics of various geological variables such as deformed bed-lengths, fold relief, seismic reflection arrival time variations, drainage and topographic patterns, and fracture systems. The studies are also extended to consider the possibility that the fractal characteristics of these variables are interrelated. Fractal interrelationships observed in these studies provide a method for relating variations in the fractal characteristics of seismic reflection events from reservoir intervals to the fractal characteristics of reservoir fracture systems, faults, and fold distributions. Themore » work is motivated by current exploration and development interests to detect fractured reservoirs and to accurately predict flow rates and flow patterns within the fractured reservoir. Accurate prediction requires an understanding of several reservoir properties including the fractal geometry of the reservoir fracture network. Results of these studies provide a method to remotely assess the fractal characteristics of a fractured reservoir, and help guide field development activities. The most significant outgrowth of this research is that the fractal properties of structural relief inferred from seismic data and structural cross sections provide a quantitative means to characterize and compare complex structural patterns. Production from fractured reservoirs is the result of complex structural and stratigraphic controls; hence, the import of fractal characterization to the assessment of fractured reservoirs lies in its potential to quantitatively define interrelationships between subtle structural variation and production. The potential uses are illustrated using seismic data from the Granny Creek oil field in the Appalachian Plateau.« less

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.

Local topography shapes fine-scale spatial genetic structure in the Arkansas Valley evening primrose, Oenothera harringtonii (Onagraceae).

PubMed

Rhodes, Matthew K; Fant, Jeremie B; Skogen, Krissa A

2014-01-01

Identifying factors that shape the spatial distribution of genetic variation is crucial to understanding many population- and landscape-level processes. In this study, we explore fine-scale spatial genetic structure in Oenothera harringtonii (Onagraceae), an insect-pollinated, gravity-dispersed herb endemic to the grasslands of south-central and southeastern Colorado, USA. We genotyped 315 individuals with 11 microsatellite markers and utilized a combination of spatial autocorrelation analyses and landscape genetic models to relate life history traits and landscape features to dispersal processes. Spatial genetic structure was consistent with theoretical expectations of isolation by distance, but this pattern was weak (Sp = 0.00374). Anisotropic analyses indicated that spatial genetic structure was markedly directional, in this case consistent with increased dispersal along prominent slopes. Landscape genetic models subsequently confirmed that spatial genetic variation was significantly influenced by local topographic heterogeneity, specifically that geographic distance, elevation and aspect were important predictors of spatial genetic structure. Among these variables, geographic distance was ~68% more important than elevation in describing spatial genetic variation, and elevation was ~42% more important than aspect after removing the effect of geographic distance. From these results, we infer a mechanism of hydrochorous seed dispersal along major drainages aided by seasonal monsoon rains. Our findings suggest that landscape features may shape microevolutionary processes at much finer spatial scales than typically considered, and stress the importance of considering how particular dispersal vectors are influenced by their environmental context. © The American Genetic Association 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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.

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

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.

Seismic velocity variation along the Izu-Bonin arc estaimated from traveltime tomography using OBS data

NASA Astrophysics Data System (ADS)

Obana, K.; Tamura, Y.; Takahashi, T.; Kodaira, S.

2014-12-01

The Izu-Bonin (Ogasawara) arc is an intra-oceanic island arc along the convergent plate boundary between the subducting Pacific and overriding Philippine Sea plates. Recent active seismic studies in the Izu-Bonin arc reveal significant along-arc variations in crustal structure [Kodaira et al., 2007]. The thickness of the arc crust shows a remarkable change between thicker Izu (~30 km) and thinner Bonin (~10 km) arcs. In addition to this, several geological and geophysical contrasts, such as seafloor topography and chemical composition of volcanic rocks, between Izu and Bonin arc have been reported [e.g., Yuasa 1992]. We have conducted earthquake observations using ocean bottom seismographs (OBSs) to reveal seismic velocity structure of the crust and mantle wedge in the Izu-Bonin arc and to investigate origin of the along-arc structure variations. We deployed 40 short-period OBSs in Izu and Bonin area in 2006 and 2009, respectively. The OBS data were processed with seismic data recorded at routine seismic stations on Hachijo-jima, Aoga-shima, and Chichi-jima operated by National Research Institute for Earth Science and Disaster Prevention (NIED). More than 5000 earthquakes were observed during about three-months observation period in each experiment. We conducted three-dimensional seismic tomography using manually picked P- and S-wave arrival time data. The obtained image shows a different seismic velocity structures in the mantle beneath the volcanic front between Izu and Bonin arcs. Low P-wave velocity anomalies in the mantle beneath the volcanic front in the Izu arc are limited at depths deeper than those in the Bonin arc. On the other hand, P-wave velocity in the low velocity anomalies beneath volcanic front in the Bonin arc is slower than that in the Izu arc. These large-scale along-arc structure variations in the mantle could relate to the geological and geophysical contrasts between Izu and Bonin arcs.

Among-population variation in microbial community structure in the floral nectar of the bee-pollinated forest herb Pulmonaria officinalis L.

PubMed

Jacquemyn, Hans; Lenaerts, Marijke; Brys, Rein; Willems, Kris; Honnay, Olivier; Lievens, Bart

2013-01-01

Microbial communities in floral nectar have been shown to be characterized by low levels of species diversity, yet little is known about among-plant population variation in microbial community composition. We investigated the microbial community structure (yeasts and bacteria) in floral nectar of ten fragmented populations of the bee-pollinated forest herb Pulmonaria officinalis. We also explored possible relationships between plant population size and microbial diversity in nectar, and related microbial community composition to the distance separating plant populations. Culturable bacteria and yeasts occurring in the floral nectar of a total of 100 plant individuals were isolated and identified by partially sequencing the 16S rRNA gene and D1/D2 domains of the 26S rRNA gene, respectively. A total of 9 and 11 yeast and 28 and 39 bacterial OTUs was found, taking into account a 3% (OTU0.03) and 1% sequence dissimilarity cut-off (OTU0.01). OTU richness at the plant population level (i.e. the number of OTUs per population) was low for yeasts (mean: 1.7, range: 0-4 OTUs0.01/0.03 per population), whereas on average 6.9 (range: 2-13) OTUs0.03 and 7.9 (range 2-16) OTUs0.01 per population were found for bacteria. Both for yeasts and bacteria, OTU richness was not significantly related to plant population size. Similarity in community composition among populations was low (average Jaccard index: 0.14), and did not decline with increasing distance between populations. We found low similarity in microbial community structure among populations, suggesting that the assembly of nectar microbiota is to a large extent context-dependent. Although the precise factors that affect variation in microbial community structure in floral nectar require further study, our results indicate that both local and regional processes may contribute to among-population variation in microbial community structure in nectar.

The color of sea level: Importance of spatial variations in spectral shape for assessing the significance of trends

NASA Astrophysics Data System (ADS)

Hughes, Chris W.; Williams, Simon D. P.

2010-10-01

We investigate spatial variations in the shape of the spectrum of sea level variability based on a homogeneously sampled 12 year gridded altimeter data set. We present a method of plotting spectral information as color, focusing on periods between 2 and 24 weeks, which shows that significant spatial variations in the spectral shape exist and contain useful dynamical information. Using the Bayesian Information Criterion, we determine that, typically, a fifth-order autoregressive model is needed to capture the structure in the spectrum. Using this model, we show that statistical errors in fitted local trends range between less than 1 and more than 5 times of what would be calculated assuming "white" noise and that the time needed to detect a 1 mm/yr trend ranges between about 5 years and many decades. For global mean sea level, the statistical error reduces to 0.1 mm/yr over 12 years, with only 2 years needed to detect a 1 mm/yr trend. We find significant regional differences in trend from the global mean. The patterns of these regional differences are indicative of a sea level trend dominated by dynamical ocean processes over this period.

Dissection of complex adult traits in a mouse synthetic population.

PubMed

Burke, David T; Kozloff, Kenneth M; Chen, Shu; West, Joshua L; Wilkowski, Jodi M; Goldstein, Steven A; Miller, Richard A; Galecki, Andrzej T

2012-08-01

Finding the causative genetic variations that underlie complex adult traits is a significant experimental challenge. The unbiased search strategy of genome-wide association (GWAS) has been used extensively in recent human population studies. These efforts, however, typically find only a minor fraction of the genetic loci that are predicted to affect variation. As an experimental model for the analysis of adult polygenic traits, we measured a mouse population for multiple phenotypes and conducted a genome-wide search for effector loci. Complex adult phenotypes, related to body size and bone structure, were measured as component phenotypes, and each subphenotype was associated with a genomic spectrum of candidate effector loci. The strategy successfully detected several loci for the phenotypes, at genome-wide significance, using a single, modest-sized population (N = 505). The effector loci each explain 2%-10% of the measured trait variation and, taken together, the loci can account for over 25% of a trait's total population variation. A replicate population (N = 378) was used to confirm initially observed loci for one trait (femur length), and, when the two groups were merged, the combined population demonstrated increased power to detect loci. In contrast to human population studies, our mouse genome-wide searches find loci that individually explain a larger fraction of the observed variation. Also, the additive effects of our detected mouse loci more closely match the predicted genetic component of variation. The genetic loci discovered are logical candidates for components of the genetic networks having evolutionary conservation with human biology.

Determining the effects of dams on subdaily variation in river flows at a whole-basin scale

USGS Publications Warehouse

Zimmerman, J.K.H.; Letcher, B.H.; Nislow, K.H.; Lutz, K.A.; Magilligan, F.J.

2010-01-01

River regulation can alter the frequency and magnitude of subdaily flow variations causing major impacts on ecological structure and function. We developed an approach to quantify subdaily flow variation for multiple sites across a large watershed to assess the potential impacts of different dam operations (flood control, run-of-river hydropower and peaking hydropower) on natural communities. We used hourly flow data over a 9-year period from 30 stream gages throughout the Connecticut River basin to calculate four metrics of subdaily flow variation and to compare sites downstream of dams with unregulated sites. Our objectives were to (1) determine the temporal scale of data needed to characterize subdaily variability; (2) compare the frequency of days with high subdaily flow variation downstream of dams and unregulated sites; (3) analyse the magnitude of subdaily variation at all sites and (4) identify individual sites that had subdaily variation significantly higher than unregulated locations. We found that estimates of flow variability based on daily mean flow data were not sufficient to characterize subdaily flow patterns. Alteration of subdaily flows was evident in the number of days natural ranges of variability were exceeded, rather than in the magnitude of subdaily variation, suggesting that all rivers may exhibit highly variable subdaily flows, but altered rivers exhibit this variability more frequently. Peaking hydropower facilities had the most highly altered subdaily flows; however, we observed significantly altered ranges of subdaily variability downstream of some flood-control and run-of-river hydropower dams. Our analysis can be used to identify situations where dam operating procedures could be modified to reduce the level of hydrologic alteration. ?? 2009 John Wiley & Sons, Ltd.

Assemblage organization in stream fishes: effects of environmental variation and interspecific interactions

USGS Publications Warehouse

Grossman, G.D.; Ratajczak, R.E.; Crawford, M. M.; Freeman, Mary C.

1998-01-01

We assessed the relative importance of environmental variation, interspecific competition for space, and predator abundance on assemblage structure and microhabitat use in a stream fish assemblage inhabiting Coweeta Creek, North Carolina, USA. Our study encompassed a ten year time span (1983-1992) and included some of the highest and lowest flows in the last 58 years. We collected 16 seasonal samples which included data on: 1) habitat availability (total and microhabitat) and microhabitat diversity, 2) assemblage structure (i.e., the number and abundances of species comprising a subset of the community), and 3) microhabitat use and overlap. We classified habitat availability data on the basis of year, season, and hydrologic period. Hydrologic period (i.e., pre-drought [PR], drought [D], and post-drought [PO]) represented the temporal location of a sample with respect to a four-year drought that occurred during the study. Hydrologic period explained a greater amount of variance in habitat availability data than either season or year. Total habitat availability was significantly greater during PO than in PR or D, although microhabitat diversity did not differ among either seasons or hydrologic periods. There were significantly fewer high-flow events (i.e., > 2.1 m3/s) during D than in either PR or PO periods. We observed a total of 16 species during our investigation, and the total number of species was significantly higher in D than in PR samples. Correlation analyses between the number of species present (total and abundant species) and environmental data yielded limited results, although the total number of species was inversely correlated with total habitat availability. A cluster analysis grouped assemblage structure samples by hydrologic period rather than season or year, supporting the contention that variation in annual flow had a strong impact on this assemblage. The drought had little effect on the numerical abundance of benthic species in this assemblage; however, a majority of water-column species increased in abundance. The increased abundances or water-column species may have been related to the decrease in high flow events observed during the D. Such high flow events are known to cause mortality in stream fishes. Microhabitat use data showed that species belonged to one of three microhabitat guilds: benthic, lower water-column, and mid-water-column. In general, species within the same guild did not exhibit statistically distinguishable patterns of microhabitat use, and most significant differences occurred between members of different guilds. However, lower water-column guild species frequently were not separable from all members of either benthic or mid-water-column guilds. Variations in the abundance of potential competitors or predators did not produce strong shifts in microhabitat use by assemblage members. Predators were present in the site in only 9 of 16 seasonal samples and never were abundant (maximum number observed per day was 2). In conclusion, our results demonstrate that variability in both mean and peak flows had a much stronger effect on the structure and use of spatial resources within this assemblage than either interspecific competition for space or predation. Consequently, we suspect that the patterns in both assemblage structure and resource use displayed by fishes in Coweeta Creek arose from the interaction between environmental variation and species-specific evolutionary constraints on behavior, morphology and physiology.

Environmental characteristics drive variation in Amazonian understorey bird assemblages

PubMed Central

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

2017-01-01

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

Control of the Lithospheric Mantle on intracontinental Deformation: Revival of Eastern U.S. Tectonism

NASA Astrophysics Data System (ADS)

Biryol, C. B.; Wagner, L. S.; Fischer, K. M.; Hawman, R. B.

2016-12-01

The present tectonic configuration of the southeastern United States is a product of earlier episodes of arc accretion, continental collision and breakup. This region is located in the interior of the North American Plate, some 1500 km away from closest active plate margin. However, there is ongoing tectonism across the area with multiple zones of seismicity, rejuvenation of the Appalachians of North Carolina, Virginia, and Pennsylvania, and Cenozoic intraplate volcanism. The mechanisms controlling this activity and the modern-day state of stress remain enigmatic. Two factors often regarded as major contributors are plate strength and preexisting inherited structures. Recent improvements in broadband seismic data coverage in the region associated with the South Eastern Suture of the Appalachian Margin Experiment (SESAME) and EarthScope Transportable Array make it possible to obtain detailed information on the structure of the lithosphere in the region. Here we present new tomographic images of the upper mantle beneath the Southeastern United States, revealing large-scale structural variations in the upper mantle. Our results indicate fast seismic velocity patterns that can be interpreted as ongoing lithospheric foundering. We observe an agreement between the locations of these upper mantle anomalies and the location of major zones of tectonism, volcanism and seismicity, providing a viable explanation for modern-day activity in this plate interior setting long after it became a passive margin. Based on distinct variations in the geometry and thickness of the lithospheric mantle and foundered lithosphere, we propose that piecemeal delamination has occurred beneath the region throughout the Cenozoic, removing a significant amount of reworked/deformed mantle lithosphere. Ongoing lithospheric foundering beneath the eastern margin of stable North America explains significant variations in thickness of lithospheric mantle across the former Grenville deformation front.

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

PubMed Central

Ekdale, Eric G.

2013-01-01

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

Body size and pubertal development explain ethnic differences in structural geometry at the femur in Asian, Hispanic and white early adolescent girls living in the US

USDA-ARS?s Scientific Manuscript database

Variation in structural geometry is present in adulthood, but when this variation arises and what influences this variation prior to adulthood remains poorly understood. Ethnicity is commonly the focus of research of skeletal integrity and appears to explain some of the variation in quantification o...

Thinned crustal structure and tectonic boundary of the Nansha Block, southern South China Sea

NASA Astrophysics Data System (ADS)

Dong, Miao; Wu, Shi-Guo; Zhang, Jian

2016-12-01

The southern South China Sea margin consists of the thinned crustal Nansha Block and a compressional collision zone. The Nansha Block's deep structure and tectonic evolution contains critical information about the South China Sea's rifting. Multiple geophysical data sets, including regional magnetic, gravity and reflection seismic data, reveal the deep structure and rifting processes. Curie point depth (CPD), estimated from magnetic anomalies using a windowed wavenumber-domain algorithm, enables us to image thermal structures. To derive a 3D Moho topography and crustal thickness model, we apply Oldenburg algorithm to the gravity anomaly, which was extracted from the observed free air gravity anomaly data after removing the gravity effect of density variations of sediments, and temperature and pressure variations of the lithospheric mantle. We found that the Moho depth (20 km) is shallower than the CPD (24 km) in the Northwest Borneo Trough, possibly caused by thinned crust, low heat flow and a low vertical geothermal gradient. The Nansha Block's northern boundary is a narrow continent-ocean transition zone constrained by magnetic anomalies, reflection seismic data, gravity anomalies and an interpretation of Moho depth (about 13 km). The block extends southward beneath a gravity-driven deformed sediment wedge caused by uplift on land after a collision, with a contribution from deep crustal flow. Its southwestern boundary is close to the Lupar Line defined by a significant negative reduction to the pole (RTP) of magnetic anomaly and short-length-scale variation in crustal thickness, increasing from 18 to 26 km.

Water vapour condensation in a partly closed structure. Comparison between results obtained with an inside wet or dry bottom wall

NASA Astrophysics Data System (ADS)

Batina, Jean; Peyrous, René

2018-04-01

We are interested in the determination of the more significant parameters acting on the water vapour condensation in a partly closed structure, submitted to external constraints (temperature and humidity), in view to recover the generated droplets as an additional source of potable water. External temperature variations, by inducing temperature differences between outside and inside of the structure, lead to convective movements and thermal variations inside this structure. Through an orifice, these movements permit a renewing of the humid inner air and can lead to the condensation of the water vapour initially contained in the inner air volume and/or on the walls. With the above hypotheses, and by using a numerical simulation [1] based on the ambient air characteristics and a finite volumes method, it appears that condensed water quantities are mainly depending on the boundary conditions imposed. These conditions are: 1) dimensions of the structure; 2) external temperature and relative hygrometry; 3) the phase φ (T/RH) linking thermal and hydrometric conditions; 4) the air renewing and its hygrometry for each phase; and 5) for each case, the fact that the inside bottom wall can be wet or dry. The resulting condensed water vapour quantities obtained, for the width section, point out clearly that they are very depending on this phase φ (T/RH) which appears as the more significant parameter and can be modified by the presence or not of a thin layer of water vapour on the inside bottom wall. Condensation phenomenon could be increased if φ could be optimized.

Effects of Phenylalanine Substitutions in Gramicidin A on the Kinetics of Channel Formation in Vesicles and Channel Structure in SDS Micelles

PubMed Central

Jordan, J. B.; Easton, P. L.; Hinton, J. F.

2005-01-01

The common occurrence of Trp residues at the aqueous-lipid interface region of transmembrane channels is thought to be indicative of its importance for insertion and stabilization of the channel in membranes. To further investigate the effects of Trp→Phe substitution on the structure and function of the gramicidin channel, four analogs of gramicidin A have been synthesized in which the tryptophan residues at positions 9, 11, 13, and 15 are sequentially replaced with phenylalanine. The three-dimensional structure of each viable analog has been determined using a combination of two-dimensional NMR techniques and distance geometry-simulated annealing structure calculations. These phenylalanine analogs adopt a homodimer motif, consisting of two β6.3 helices joined by six hydrogen bonds at their NH2-termini. The replacement of the tryptophan residues does not have a significant effect on the backbone structure of the channels when compared to native gramicidin A, and only small effects are seen on side-chain conformations. Single-channel conductance measurements have shown that the conductance and lifetime of the channels are significantly affected by the replacement of the tryptophan residues (Wallace, 2000; Becker et al., 1991). The variation in conductance appears to be caused by the sequential removal of a tryptophan dipole, thereby removing the ion-dipole interaction at the channel entrance and at the ion binding site. Channel lifetime variations appear to be related to changing side chain-lipid interactions. This is supported by data relating to transport and incorporation kinetics. PMID:15501932

Effects of phenylalanine substitutions in gramicidin A on the kinetics of channel formation in vesicles and channel structure in SDS micelles.

PubMed

Jordan, J B; Easton, P L; Hinton, J F

2005-01-01

The common occurrence of Trp residues at the aqueous-lipid interface region of transmembrane channels is thought to be indicative of its importance for insertion and stabilization of the channel in membranes. To further investigate the effects of Trp-->Phe substitution on the structure and function of the gramicidin channel, four analogs of gramicidin A have been synthesized in which the tryptophan residues at positions 9, 11, 13, and 15 are sequentially replaced with phenylalanine. The three-dimensional structure of each viable analog has been determined using a combination of two-dimensional NMR techniques and distance geometry-simulated annealing structure calculations. These phenylalanine analogs adopt a homodimer motif, consisting of two beta6.3 helices joined by six hydrogen bonds at their NH2-termini. The replacement of the tryptophan residues does not have a significant effect on the backbone structure of the channels when compared to native gramicidin A, and only small effects are seen on side-chain conformations. Single-channel conductance measurements have shown that the conductance and lifetime of the channels are significantly affected by the replacement of the tryptophan residues (Wallace, 2000; Becker et al., 1991). The variation in conductance appears to be caused by the sequential removal of a tryptophan dipole, thereby removing the ion-dipole interaction at the channel entrance and at the ion binding site. Channel lifetime variations appear to be related to changing side chain-lipid interactions. This is supported by data relating to transport and incorporation kinetics.

Trade-offs with stability modulate innate and mutationally acquired drug-resistance in bacterial dihydrofolate reductase enzymes.

PubMed

Matange, Nishad; Bodkhe, Swapnil; Patel, Maitri; Shah, Pooja

2018-06-05

Structural stability is a major constraint on the evolution of protein sequences. However, under strong directional selection, mutations that confer novel phenotypes but compromise structural stability of proteins may be permissible. During the evolution of antibiotic resistance, mutations that confer drug resistance often have pleiotropic effects on the structure and function of antibiotic-target proteins, usually essential metabolic enzymes. In this study, we show that trimethoprim-resistant alleles of dihydrofolate reductase from Escherichia coli (EcDHFR) harbouring the Trp30Gly, Trp30Arg or Trp30Cys mutations are significantly less stable than the wild type making them prone to aggregation and proteolysis. This destabilization is associated with lower expression level resulting in a fitness cost and negative epistasis with other TMP-resistant mutations in EcDHFR. Using structure-based mutational analysis we show that perturbation of critical stabilizing hydrophobic interactions in wild type EcDHFR enzyme explains the phenotypes of Trp30 mutants. Surprisingly, though crucial for the stability of EcDHFR, significant sequence variation is found at this site among bacterial DHFRs. Mutational and computational analyses in EcDHFR as well as in DHFR enzymes from Staphylococcus aureus and Mycobacterium tuberculosis demonstrate that natural variation at this site and its interacting hydrophobic residues, modulates TMP-resistance in other bacterial DHFRs as well, and may explain the different susceptibilities of bacterial pathogens to trimethoprim. Our study demonstrates that trade-offs between structural stability and function can influence innate drug resistance as well as the potential for mutationally acquired drug resistance of an enzyme. ©2018 The Author(s).

Population Genomics of the Euryhaline Teleost Poecilia latipinna

PubMed Central

Hoover, D.; Travis, J.; Oleksiak, M. F.; Crawford, D. L.

2015-01-01

Global climate change and increases in sea levels will affect coastal marine communities. The conservation of these ecologically important areas will be a challenge because of their wide geographic distribution, ecological diversity and species richness. To address this problem, we need to better understand how the genetic variation of the species in these communities is distributed within local populations, among populations and between distant regions. In this study we apply genotyping by sequencing (GBS) and examine 955 SNPs to determine Sailfin molly (Poecilia latipinna) genetic diversity among three geographically close mangrove salt marsh flats in the Florida Keys compared to populations in southern and northern Florida. The questions we are asking are whether there is sufficient genetic variation among isolated estuarine fish within populations and whether there are significant divergences among populations. Additionally, we want to know if GBS approaches agree with previous studies using more traditional molecular approaches. We are able to identify large genetic diversity within each saltmarsh community (π ≈ 36%). Additionally, among the Florida Key populations and the mainland or between southern and northern Florida regions, there are significant differences in allele frequencies seen in population structure and evolutionary relationships among individuals. Surprisingly, even though the cumulative FST value using all 955 SNPs within the three Florida Key populations is small, there are 29 loci with significant FST values, and 11 of these were outliers suggestive of adaptive divergence. These data suggest that among the salt marsh flats surveyed here, there is significant genetic diversity within each population and small but significant differences among populations. Much of the genetic variation within and among populations found here with GBS is very similar to previous studies using allozymes and microsatellites. However, the meaningful difference between GBS and these previous measures of genetic diversity is the number of loci examined, which allows more precise delineations of population structure as well as facilitates identifying loci with excessive FST values that could indicate adaptive divergence. PMID:26335684

Population Genomics of the Euryhaline Teleost Poecilia latipinna.

PubMed

Nunez, J C B; Seale, T P; Fraser, M A; Burton, T L; Fortson, T N; Hoover, D; Travis, J; Oleksiak, M F; Crawford, D L

2015-01-01

Global climate change and increases in sea levels will affect coastal marine communities. The conservation of these ecologically important areas will be a challenge because of their wide geographic distribution, ecological diversity and species richness. To address this problem, we need to better understand how the genetic variation of the species in these communities is distributed within local populations, among populations and between distant regions. In this study we apply genotyping by sequencing (GBS) and examine 955 SNPs to determine Sailfin molly (Poecilia latipinna) genetic diversity among three geographically close mangrove salt marsh flats in the Florida Keys compared to populations in southern and northern Florida. The questions we are asking are whether there is sufficient genetic variation among isolated estuarine fish within populations and whether there are significant divergences among populations. Additionally, we want to know if GBS approaches agree with previous studies using more traditional molecular approaches. We are able to identify large genetic diversity within each saltmarsh community (π ≈ 36%). Additionally, among the Florida Key populations and the mainland or between southern and northern Florida regions, there are significant differences in allele frequencies seen in population structure and evolutionary relationships among individuals. Surprisingly, even though the cumulative FST value using all 955 SNPs within the three Florida Key populations is small, there are 29 loci with significant FST values, and 11 of these were outliers suggestive of adaptive divergence. These data suggest that among the salt marsh flats surveyed here, there is significant genetic diversity within each population and small but significant differences among populations. Much of the genetic variation within and among populations found here with GBS is very similar to previous studies using allozymes and microsatellites. However, the meaningful difference between GBS and these previous measures of genetic diversity is the number of loci examined, which allows more precise delineations of population structure as well as facilitates identifying loci with excessive FST values that could indicate adaptive divergence.

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

PubMed Central

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

2016-01-01

We examined the abundance, diversity and community composition of airborne fungi in swine houses during winter and summer seasons by using quantitative PCR and Illumina HiSeq sequencing of ITS1 region. The abundance of airborne fungi varied significantly only between seasons, while fungal diversity varied significantly both within and between seasons, with both abundance and diversity peaked in winter. The fungal OTU composition was largely structured by the swine house unit and season as well as by their interactions. Of the measured microclimate variables, relative humidity, particulate matters (PMs), ammonia, and stocking density were significantly correlated with fungal OTU composition. The variation in beta diversity was higher within swine houses during summer, which indicates that the airborne fungal community composition was more heterogeneous in summer compared to winter. We also identified several potential allergen/pathogen related fungal genera in swine houses. The total relative abundance of potential allergen/pathogen related fungal genera varied between swine houses in both seasons, and showed positive correlation with PM2.5. Overall, our findings show that the abundance, diversity and composition of airborne fungi are highly variable in swine houses and to a large extent structured by indoor microclimate variables of swine houses. PMID:27892507

Influence of LOD variations on seismic energy release

NASA Astrophysics Data System (ADS)

Riguzzi, F.; Krumm, F.; Wang, K.; Kiszely, M.; Varga, P.

2009-04-01

Tidal friction causes significant time variations of geodynamical parameters, among them geometrical flattening. The axial despinning of the Earth due to tidal friction through the change of flattening generates incremental meridional and azimuthal stresses. The stress pattern in an incompressible elastic upper mantle and crust is symmetric to the equator and has its inflection points at the critical latitude close to ±45°. Consequently the distribution of seismic energy released by strong, shallow focus earthquakes should have also sharp maxima at this latitude. To investigate the influence of length of day (LOD) variations on earthquake activity an earthquake catalogue of strongest seismic events (M>7.0) was completed for the period 1900-2007. It is shown with the use of this catalogue that for the studied time-interval the catalogue is complete and consists of the seismic events responsible for more than 90% of released seismic energy. Study of the catalogue for earthquakes M>7.0 shows that the seismic energy discharged by the strongest seismic events has significant maxima at ±45°, what renders probably that the seismic activity of our planet is influenced by an external component, i.e. by the tidal friction, which acts through the variation of the hydrostatic figure of the Earth caused by it. Distribution along the latitude of earthquake numbers and energies was investigated also for the case of global linear tectonic structures, such as mid ocean ridges and subduction zones. It can be shown that the number of the shallow focus shocks has a repartition along the latitude similar to the distribution of the linear tectonic structures. This means that the position of foci of seismic events is mainly controlled by the tectonic activity.

Ultrafast laser-induced modifications of energy bands of non-metal crystals

NASA Astrophysics Data System (ADS)

Gruzdev, Vitaly

2009-10-01

Ultrafast laser-induced variations of electron energy bands of transparent solids significantly influence ionization and conduction-band electron absorption driving the initial stage of laser-induced damage (LID). The mechanisms of the variations are attributed to changing electron functions from bonding to anti-bonding configuration via laser-induced ionization; laser-driven electron oscillations in quasi-momentum space; and direct distortion of the inter-atomic potential by electric field of laser radiation. The ionization results in the band-structure modification via accumulation of broken chemical bonds between atoms and provides significant contribution to the overall modification only when enough excited electrons are accumulated in the conduction band. The oscillations are associated with modification of electron energy by pondermotive potential of the oscillations. The direct action of radiation's electric field leads to specific high-frequency Franz-Keldysh effect (FKE) spreading the allowed electron states into the bands of forbidden energy. Those processes determine the effective band gap that is a laser-driven energy gap between the modified electron energy bands. Among those mechanisms, the latter two provide reversible band-structure modification that takes place from the beginning of the ionization and are, therefore, of special interest due to their strong influence on the initial stage of the ionization. The pondermotive potential results either in monotonous increase or oscillatory variations of the effective band gap that has been taken into account in some ionization models. The classical FKE provides decrease of the band gap. We analyzing the competition between those two opposite trends of the effective-band-gap variations and discuss applications of those effects for considerations of the laser-induced damage and its threshold in transparent solids.

Local time, seasonal, and solar cycle dependency of longitudinal variations of TEC along the crest of EIA over India

NASA Astrophysics Data System (ADS)

Sunda, Surendra; Vyas, B. M.

2013-10-01

global wave number 4 structure in the Indian longitudinal region spanning from ~70 to 95°E forming the upward slope of the peak in the total electron content (TEC) are reported along the crest of equatorial ionization anomaly (EIA). The continuous and simultaneous measurements from five GPS stations of GPS Aided Geo Augmented Navigation (GAGAN) network are used in this study. The long-term database (2004-2012) is utilized for examining the local time, seasonal, and solar cycle dependency on the longitudinal variations of TEC. Our results confirm the existence of longitudinal variations of TEC in accordance with wave number 4 longitudinal structure including its strength. The results suggest that these variations, in general, start to develop at ~09 LT, achieve maximum strength at 12-15 LT, and decay thereafter, the decay rate depending on the season. They are more pronounced in equinoctial season followed by summer and winter. The longitudinal variations persist beyond midnight in equinox seasons, whereas in winter, they are conspicuously absent. Interestingly, they also exhibit significant solar cycle dependence in the solstices, whereas in the equinoxes, they are independent of solar activity. The comparison of crest-to-trough ratio (CTR) in the eastern (92°E) and western (72°E) extreme longitudes reveals higher CTR on the eastern side than over the western extreme, suggesting the role of nonmigrating tides in modulating the ExB vertical drift and the consequential EIA crest formation.

Genome-Wide Survey on Genomic Variation, Expression Divergence, and Evolution in Two Contrasting Rice Genotypes under High Salinity Stress

PubMed Central

Jiang, Shu-Ye; Ma, Ali; Ramamoorthy, Rengasamy; Ramachandran, Srinivasan

2013-01-01

Expression profiling is one of the most important tools for dissecting biological functions of genes and the upregulation or downregulation of gene expression is sufficient for recreating phenotypic differences. Expression divergence of genes significantly contributes to phenotypic variations. However, little is known on the molecular basis of expression divergence and evolution among rice genotypes with contrasting phenotypes. In this study, we have implemented an integrative approach using bioinformatics and experimental analyses to provide insights into genomic variation, expression divergence, and evolution between salinity-sensitive rice variety Nipponbare and tolerant rice line Pokkali under normal and high salinity stress conditions. We have detected thousands of differentially expressed genes between these two genotypes and thousands of up- or downregulated genes under high salinity stress. Many genes were first detected with expression evidence using custom microarray analysis. Some gene families were preferentially regulated by high salinity stress and might play key roles in stress-responsive biological processes. Genomic variations in promoter regions resulted from single nucleotide polymorphisms, indels (1–10 bp of insertion/deletion), and structural variations significantly contributed to the expression divergence and regulation. Our data also showed that tandem and segmental duplication, CACTA and hAT elements played roles in the evolution of gene expression divergence and regulation between these two contrasting genotypes under normal or high salinity stress conditions. PMID:24121498

Cost variation in a laparoscopic cholecystectomy and the association with outcomes across a single health system: implications for standardization and improved resource utilization.

PubMed

Brauer, David G; Hawkins, William G; Strasberg, Steven M; Brunt, L Michael; Jaques, David P; Mercurio, Nicholas R; Hall, Bruce L; Fields, Ryan C

2015-12-01

Payers and regulatory bodies are increasingly placing emphasis on cost containment, quality/outcome measurement and transparent reporting. Significant cost variation occurs in many operative procedures without a clear relationship with outcomes. Clear cost-benefit associations will be necessary to justify expenditures in the era of bundled payment structures. All laparoscopic cholecystectomies (LCCKs) performed within a single health system over a 1-year period were analysed for operating room (OR) supply cost. The cost was correlated with American College of Surgeons National Surgical Quality Improvement Program (ACS NSQIP) outcomes. From July 2013 to June 2014, 2178 LCCKs were performed by 55 surgeons at seven hospitals. The median case OR supply cost was $513 ± 156. There was variation in cost between individual surgeons and within an individual surgeon's practice. There was no correlation between cost and ACS NSQIP outcomes. The majority of cost variation was explained by selection of trocar and clip applier constructs. Significant case OR cost variation is present in LCCK across a single health system, and there is no clear association between increased cost and NSQIP outcomes. Placed within the larger context of overall cost, the opportunity exists for improved resource utilization with no obvious risk for a reduction in the quality of care. © 2015 International Hepato-Pancreato-Biliary Association.

Cost variation in a laparoscopic cholecystectomy and the association with outcomes across a single health system: implications for standardization and improved resource utilization

PubMed Central

Brauer, David G; Hawkins, William G; Strasberg, Steven M; Brunt, L Michael; Jaques, David P; Mercurio, Nicholas R; Hall, Bruce L; Fields, Ryan C

2015-01-01

Background Payers and regulatory bodies are increasingly placing emphasis on cost containment, quality/outcome measurement and transparent reporting. Significant cost variation occurs in many operative procedures without a clear relationship with outcomes. Clear cost-benefit associations will be necessary to justify expenditures in the era of bundled payment structures. Methods All laparoscopic cholecystectomies (LCCKs) performed within a single health system over a 1-year period were analysed for operating room (OR) supply cost. The cost was correlated with American College of Surgeons National Surgical Quality Improvement Program (ACS NSQIP) outcomes. Results From July 2013 to June 2014, 2178 LCCKs were performed by 55 surgeons at seven hospitals. The median case OR supply cost was $513 ± 156. There was variation in cost between individual surgeons and within an individual surgeon's practice. There was no correlation between cost and ACS NSQIP outcomes. The majority of cost variation was explained by selection of trocar and clip applier constructs. Conclusions Significant case OR cost variation is present in LCCK across a single health system, and there is no clear association between increased cost and NSQIP outcomes. Placed within the larger context of overall cost, the opportunity exists for improved resource utilization with no obvious risk for a reduction in the quality of care. PMID:26345351

Genetic diversity and population structure of Eleutheronema rhadinum in the East and South China Seas revealed in mitochondrial COI sequences

NASA Astrophysics Data System (ADS)

Sun, Xinxu; Xu, Dongdong; Lou, Bao; Zhang, Tao; Xin, Jian; Guo, Yaoshi; Ma, Shilei

2013-11-01

Eleutheronema rhadinum is a potential commercial fisheries species and is subject to intense exploitation in China. Knowledge on the population structure of E. rhadinum in Chinese coastal waters, which is important for sustainable exploitation and proper resource management, is lacking. In the present study, the genetic diversity and population structure of E. rhadinum were evaluated using a 564-base pair fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene. A total of 76 specimens were collected from three localities around the East (Qidong and Zhoushan) and South China Seas (Zhuhai). Among these individuals, nine polymorphic sites were detected and 11 distinct haplotypes were defined. High levels of haplotype diversity ( h =0.759±0.035) and low levels of nucleotide diversity ( π= 0.001 98±0.003 26) were observed in these populations. Hierarchical analysis of molecular variance (AMOVA) indicated that 96.72% of the genetic variation occurred within the populations, whereas 3.28% occurred among populations. No significant genealogical branches or clusters were recognized on the neighbor-joining tree. Intra-group variation among populations was significant ( φ st=0.032 85, P<0.01). These results suggest that E. rhadinum populations in the East and South China Seas have developed divergent genetic structures. Tests of neutral evolution and mismatch distribution suggest that E. rhadinum may have experienced a population expansion. The present study provides basic information for the conservation and sustainable exploitation of this species.

Tianeptine, olanzapine and fluoxetine show similar restoring effects on stress induced molecular changes in mice brain: An FT-IR study

NASA Astrophysics Data System (ADS)

Türker-Kaya, Sevgi; Mutlu, Oğuz; Çelikyurt, İpek K.; Akar, Furuzan; Ulak, Güner

2016-05-01

Chronic stress which can cause a variety of disorders and illness ranging from metabolic and cardiovascular to mental leads to alterations in content, structure and dynamics of biomolecules in brain. The determination of stress-induced changes along with the effects of antidepressant treatment on these parameters might bring about more effective therapeutic strategies. In the present study, we investigated unpredictable chronic mild stress (UCMS)-induced changes in biomolecules in mouse brain and the restoring effects of tianeptine (TIA), olanzapine (OLZ) and fluoxetine (FLX) on these variations, by Fourier transform infrared (FT-IR) spectroscopy. The results revealed that chronic stress causes different membrane packing and an increase in lipid peroxidation, membrane fluidity. A significant increment for lipid/protein, Cdbnd O/lipid, CH3/lipid, CH2/lipid, PO-2/lipid, COO-/lipid and RNA/protein ratios but a significant decrease for lipid/protein ratios were also obtained. Additionally, altered protein secondary structure components were estimated, such as increment in random coils and beta structures. The administration of TIA, OLZ and FLX drugs restored these stress-induced variations except for alterations in protein structure and RNA/protein ratio. This may suggest that these drugs have similar restoring effects on the consequences of stress activity in brain, in spite of the differences in their action mechanisms. All findings might have importance in understanding molecular mechanisms underlying chronic stress and contribute to studies aimed for drug development.

Practice variation in the structure of stroke rehabilitation in four rehabilitation centres in the Netherlands.

PubMed

Groeneveld, Iris F; Meesters, Jorit J L; Arwert, Henk J; Roux-Otter, Nienke; Ribbers, Gerard M; van Bennekom, Coen A M; Goossens, Paulien H; Vliet Vlieland, Thea P M

2016-03-01

To describe practice variation in the structure of stroke rehabilitation in 4 specialized multidisciplinary rehabilitation centres in the Netherlands. A multidisciplinary expert group formulated a set of 23 elements concerning the structure of inpatient and outpatient stroke rehabilitation, categorized into 4 domains: admission-related (n = 7), treatment-related (n = 10), client involvement-related (n = 2), and facilities-related (n = 4). In a cross-sectional study in 4 rehabilitation centres data on the presence and content of these elements were abstracted from treatment programmes and protocols. In a structured expert meeting consensus was reached on the presence of practice variation per element. Practice variation was observed in 22 of the 23 structure elements. The element "strategies for patient involvement" appeared similar in all rehabilitation centres, whereas differences were found in the elements regarding admission, exclusion and discharge criteria, patient subgroups, care pathways, team meetings, clinical assessments, maximum time to admission, aftercare and return to work modules, health professionals, treatment facilities, and care-giver involvement. Practice variation was found in a wide range of aspects of the structure of stroke rehabilitation.

Facile preparation of porous carbon from coffee bean waste using low temperature solvothermal method

NASA Astrophysics Data System (ADS)

Baroroh, L. A. Al; Fitria, D.; Amal, M. I.; Wismogroho, A. S.; Widayatno, W. B.

2018-03-01

In this study, porous carbon made from coffee bean waste (CBW) was carbonized at 500 °C, 600 °C, and 700 °C to find effective temperature. It is verified from the IR spectrum that carbonization process at certain temperature can effectively break cellulose bonding and make aromatics functional group while preserving its carbon structure. The TG-DTA curve shows four stages of decomposition process and confirms most effective carbonization temperature. Activation process of as-carbonized CBW was carried out using solvothermal method in KOH and NH4OH steam environment at 200 °C with variation of 30%, 40%, and 50% solvothermal volume. Scanning electron micrographs reveals significant increase of porosity on the carbon surface and differences of structural pores between the variations. The results show the possible potential of utilizing low temperature-solvothermal method for nanoporous carbon material.

Scale Dependence of the Mechanical Properties and Microstructure of Crustaceans Thin Films as Biomimetic Materials

NASA Astrophysics Data System (ADS)

Verma, Devendra; Qu, Tao; Tomar, Vikas

2015-04-01

The exoskeletons of crustacean species in the form of thin films have been investigated by several researchers to better understand the role played by the exoskeletal structure in affecting the functioning of species such as shrimps, crabs, and lobsters. These species exhibit similar designs in their exoskeleton microstructure, such as a Bouligand pattern (twisted plywood structure), layers of different thickness across cross section, change in mineral content through the layers, etc. Different parts of crustaceans exhibit a significant variation in mechanical properties based on the variation in the above-mentioned parameters. This change in mechanical properties has been analyzed by using imaging techniques such as scanning electron microscopy and energy-dispersive x-ray spectroscopy, and by using mechanical characterization techniques such as nanoindentation and atomic force microscopy. In this article, the design principles of these biological composites are discussed based on two shrimp species: Rimicaris exoculata and Pandalus platyceros.

A climate-associated multispecies cryptic cline in the northwest Atlantic

PubMed Central

DiBacco, Claudio; Lowen, Ben; Beiko, Robert G.; Bentzen, Paul; Brickman, David; Johnson, Catherine; Wang, Zeliang; Wringe, Brendan F.; Bradbury, Ian R.

2018-01-01

The spatial genetic structure of most species in the open marine environment remains largely unresolved. This information gap creates uncertainty in the sustainable management, recovery, and associated resilience of marine communities and our capacity to extrapolate beyond the few species for which such information exists. We document a previously unidentified multispecies biogeographic break aligned with a steep climatic gradient and driven by seasonal temperature minima in the northwest Atlantic. The coherence of this genetic break across our five study species with contrasting life histories suggests a pervasive macroecological phenomenon. The integration of this genetic structure with habitat suitability models and climate forecasts predicts significant variation in northward distributional shifts among populations and availability of suitable habitat in future oceans. The results of our integrated approach provide new perspective on how cryptic intraspecific diversity associated with climatic variation influences species and community response to climate change beyond simple poleward shifts. PMID:29600272

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

A Quantitative Analysis of the Effects of Human Activities and Climate Change on Rainfall-Runoff in Xiaoqing River Basin

NASA Astrophysics Data System (ADS)

Yang, Y.; Cao, S.; Liu, C.; Liu, Y.

2017-12-01

It is a hot topic to study the effects of human activities on the rainfall-runoff relationship and quantitatively analyze the influencing factors. According to the flexibility of Copula function to capture multivariate interdependent structure, the Copula structure between rainfall and runoff was analyzed by using the rainfall-runoff variation test method based on Archimedean Copula function to diagnose the variation of rainfall-runoff relationship. The correlation of rainfall-runoff relationship could be directly analyzed by Copula function, which could intuitively display the change of runoff in the same rainfall before and after the mutation period. The statistical method was used to simulate the underlying surface conditions before the abrupt point, and the effects of climate change and human activities on runoff changes were calculated. It can finally figure out the effects of human activities on the rainfall-runoff relationship. Taking xiaoqing river for example, the results showed that the rainfall-runoff relationship in the Xiaoqing River Basin variated in 1996 mainly due to the continuous increase of water consumption in the watershed and the change of the runoff attenuation caused by the large-scale water conservancy projects. And interannual or annual change of rainfall was not obvious; compared with the year before the variation , the runoff capacity of the basin was weakened under the same rainfall conditions after the variation ; Rainfall and runoff distribution were significantly changed and the same magnitude of rainfall and probability of runoff change were significantly different in different periods; The statistical method was used to simulate the runoff from 1996 to 2016. Compared with that from 1960 to 1995, the result showed that the contribution rate of human activities to runoff reduction was 46.8% and that of climate change was 53.2%. By relevant reference, rainfall-runoff correlation and analysis of human activities, the result was verified to be reasonable. The study can be applied to other watersheds, or used to diagnose the variation of the relationship between meteorological elements and hydrological elements so as to provide scientific basis for rational exploitation and utilization of river water resources, as well as soil and water conservation.

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.

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.

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.

Magnon Splitting Induced by Charge Transfer in the Three-Orbital Hubbard Model

NASA Astrophysics Data System (ADS)

Wang, Yao; Huang, Edwin W.; Moritz, Brian; Devereaux, Thomas P.

2018-06-01

Understanding spin excitations and their connection to unconventional superconductivity have remained central issues since the discovery of cuprates. Direct measurement of the dynamical spin structure factor in the parent compounds can provide key information on important interactions relevant in the doped regime, and variations in the magnon dispersion have been linked closely to differences in crystal structure between families of cuprate compounds. Here, we elucidate the relationship between spin excitations and various controlling factors thought to be significant in high-Tc materials by systematically evaluating the dynamical spin structure factor for the three-orbital Hubbard model, revealing differences in the spin dispersion along the Brillouin zone axis and the diagonal. Generally, we find that the absolute energy scale and momentum dependence of the excitations primarily are sensitive to the effective charge-transfer energy, while changes in the on-site Coulomb interactions have little effect on the details of the dispersion. In particular, our result highlights the splitting between spin excitations along the axial and diagonal directions in the Brillouin zone. This splitting decreases with increasing charge-transfer energy and correlates with changes in the apical oxygen position, and general structural variations, for different cuprate families.

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

NASA Astrophysics Data System (ADS)

Drolet, David; Barbeau, Myriam A.

2012-05-01

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

Moire interferometry patterns for rotational alignment of structures

NASA Astrophysics Data System (ADS)

Heidari, Esmaeil; Harding, Kevin

2016-08-01

In some manufacturing applications the alignment of fine structures formed on the surface of a part such as micro-scribed patterns on solar panels can be critical to the panel performance. Variations in pattern uniformity may degrade the efficiency of the solar panel if the pattern deviates significantly from designed parameters. This paper will explore the use of moire patterns to interpret the angular alignment of such structures on 3 dimensional non-planar shapes. The moire interferometry pattern creates a beat between the scribed pattern and a reference pattern that is a function of both the shape of the part as well as the shape of the scribed pattern. Both the part shape variations and the patterns of interest are typically much smaller than can be seen visually. Similar challenges exist when inspecting specular models or testing low quality optics. The moire effect allows small displacements to be measured from patterns that are well below the resolution of the camera systems that are used to view the patterns. Issues such as the separation of the shape of the part from the alignment of the fine structure as well as resolution and robustness of the technique will be explored in this paper.

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

Structural correlates of Openness and Intellect: Implications for the contribution of personality to creativity.

PubMed

Vartanian, Oshin; Wertz, Christopher J; Flores, Ranee A; Beatty, Erin L; Smith, Ingrid; Blackler, Kristen; Lam, Quan; Jung, Rex E

2018-04-15

Openness/Intellect (i.e., openness to experience) is the Big Five personality factor most consistently associated with individual differences in creativity. Recent psychometric evidence has demonstrated that this factor consists of two distinct aspects-Intellect and Openness. Whereas Intellect reflects perceived intelligence and intellectual engagement, Openness reflects engagement with fantasy, perception, and aesthetics. We investigated the extent to which Openness and Intellect are associated with variations in brain structure as measured by cortical thickness, area, and volume (N = 185). Our results demonstrated that Openness was correlated inversely with cortical thickness and volume in left middle frontal gyrus (BA 6), middle temporal gyrus (MTG, BA 21), and superior temporal gyrus (BA 41), and exclusively with cortical thickness in left inferior parietal lobule (BA 40), right inferior frontal gyrus (IFG, BA 45), and MTG (BA 37). When age and sex were statistically controlled for, the inverse correlations between Openness and cortical thickness remained statistically significant for all regions except left MTG, whereas the correlations involving cortical volume remained statistically significant only for left middle frontal gyrus. There was no statistically significant correlation between Openness and cortical area, and no statistically significant correlation between Intellect and cortical thickness, area, or volume. Our results demonstrate that individual differences in Openness are correlated with variation in brain structure-particularly as indexed by cortical thickness. Given the involvement of the above regions in processes related to memory and cognitive control, we discuss the implications of our findings for the possible contribution of personality to creative cognition. © 2018 Her Majesty the Queen in Right of Canada 2018. Reproduced with permission of the Minister of Health, Canada. Human Brain Mapping.

Age-associated patterns in gray matter volume, cerebral perfusion and BOLD oscillations in children and adolescents.

PubMed

Bray, Signe

2017-05-01

Healthy brain development involves changes in brain structure and function that are believed to support cognitive maturation. However, understanding how structural changes such as grey matter thinning relate to functional changes is challenging. To gain insight into structure-function relationships in development, the present study took a data driven approach to define age-related patterns of variation in gray matter volume (GMV), cerebral blood flow (CBF) and blood-oxygen level dependent (BOLD) signal variation (fractional amplitude of low-frequency fluctuations; fALFF) in 59 healthy children aged 7-18 years, and examined relationships between modalities. Principal components analysis (PCA) was applied to each modality in parallel, and participant scores for the top components were assessed for age associations. We found that decompositions of CBF, GMV and fALFF all included components for which scores were significantly associated with age. The dominant patterns in GMV and CBF showed significant (GMV) or trend level (CBF) associations with age and a strong spatial overlap, driven by increased signal intensity in default mode network (DMN) regions. GMV, CBF and fALFF additionally showed components accounting for 3-5% of variability with significant age associations. However, these patterns were relatively spatially independent, with small-to-moderate overlap between modalities. Independence of age effects was further demonstrated by correlating individual subject maps between modalities: CBF was significantly less correlated with GMV and fALFF in older children relative to younger. These spatially independent effects of age suggest that the parallel decline observed in global GMV and CBF may not reflect spatially synchronized processes. Hum Brain Mapp 38:2398-2407, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Tree root dynamics in montane and sub-alpine mixed forest patches.

PubMed

Wang, Y; Kim, J H; Mao, Z; Ramel, M; Pailler, F; Perez, J; Rey, H; Tron, S; Jourdan, C; Stokes, A

2018-02-28

The structure of heterogeneous forests has consequences for their biophysical environment. Variations in the local climate significantly affect tree physiological processes. We hypothesize that forest structure also alters tree root elongation and longevity through temporal and spatial variations in soil temperature and water potential. We installed rhizotrons in paired vegetation communities of closed forest (tree islands) and open patches (canopy gaps), along a soil temperature gradient (elevations of 1400, 1700 and 2000 m) in a heterogeneous mixed forest. We measured the number of growing tree roots, elongation and mortality every month over 4 years. The results showed that the mean daily root elongation rate (RER) was not correlated with soil water potential but was significantly and positively correlated with soil temperature between 0 and 8 °C only. The RER peaked in spring, and a smaller peak was usually observed in the autumn. Root longevity was dependent on altitude and the season in which roots were initiated, and root diameter was a significant factor explaining much of the variability observed. The finest roots usually grew faster and had a higher risk of mortality in gaps than in closed forest. At 2000 m, the finest roots had a higher risk of mortality compared with the lower altitudes. The RER was largely driven by soil temperature and was lower in cold soils. At the treeline, ephemeral fine roots were more numerous, probably in order to compensate for the shorter growing season. Differences in soil climate and root dynamics between gaps and closed forest were marked at 1400 and 1700 m, but not at 2000 m, where canopy cover was more sparse. Therefore, heterogeneous forest structure and situation play a significant role in determining root demography in temperate, montane forests, mostly through impacts on soil temperature.

SPATIAL VARIATION OF THE EVOLUTION AND STRUCTURE OF THE URBAN BOUNDARY LAYER

EPA Science Inventory

The spatial variation of the nocturnal urban boundary layer structure and the time variation of the mixing height, the nocturnal inversion top and strength after sunrise are presented for urban sites located upwind, downwind, and near the center of the heat island and for upwind ...

Structure of the Sumatra-Andaman subduction zone

NASA Astrophysics Data System (ADS)

Pesicek, Jeremy Dale

We have conducted studies of the Sumatra-Andaman subduction zone using newly available teleseismic data resulting from the aftershock sequences of the 2004, 2005, and 2007 great earthquakes that occurred offshore of the island of Sumatra. In order to better exploit the new data, existing methodologies have been adapted and advanced in several ways to obtain results at a level of precision not previously possible from teleseismic data. Seismic tomography studies of the mantle were conducted using an improved iterative technique that accounts for fine-scale three-dimensional (3-D) velocity variations inside the study region and coarser global velocity variations outside the region. More precise earthquake locations were determined using a double-difference technique that has been extended to teleseismic distances using spherical ray tracing through the nested 3-D regional-global velocity models. Earthquake relocation was included in the iterative tomography scheme and was found to significantly enhance the recovery of slab velocity anomalies. Finally, because crustal structure is poorly constrained by the teleseismic data, 3-D density modeling of the crust was conducted using newly available satellite gravity data and a spherical prism gravity algorithm. The results of these studies better constrain the structure of the Sumatra-Andaman subduction zone, including the geometry of the mantle slab, position of the megathrust, and structural features of the downgoing plate. Tomography results reveal continuous upper mantle slab anomalies with significant variations in dip throughout the region. Broad curvature of the fast anomalies beneath northern Sumatra, similar to curvature of the trench and volcanic arc at the surface, is interpreted as folding of the upper mantle slab. Earthquake relocations show systematic shifts of the hypocenters to the northeast and to shallower depths, each with average changes of 5 km. Reduced scatter in the relocations better constrain the megathrust plate boundary and the regions of coseismic slip during the 2004 and 2005 great earthquakes. In addition, the relocations reveal discrete seismic features on the downgoing plate not previously visible in teleseismic catalogs. The new velocity model and earthquake locations provide the most comprehensive view of the deep structure of the Sumatra-Andaman subduction zone yet available.

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.

A Hymen Epiphany.

PubMed

Jarral, Farrah

2015-01-01

The hymen is a structure of the female genitalia that is poorly understood even by many medical professionals. Despite the significant anatomical variation in the hymen and no guarantee that rupture or bleeding will occur at first coitus, it has come to hold major cultural significance around the world as a perceived biological indicator of virginity. The persistence of such myths around the hymen causes real harm, including the increase in so-called revirgination surgical procedures. Copyright 2015 The Journal of Clinical Ethics. All rights reserved.

Isostatic Model and Isostatic Gravity Anomalies of the Arabian Plate and Surroundings

NASA Astrophysics Data System (ADS)

Kaban, Mikhail K.; El Khrepy, Sami; Al-Arifi, Nassir

2016-04-01

The isostatic modeling represents one of the most useful "geological" reduction methods of the gravity field. With the isostatic correction, it is possible to remove a significant part of the effect of deep density heterogeneity, which dominates in the Bouguer gravity anomalies. Although there exist several isostatic compensation schemes, it is usually supposed that a choice of the model is not an important factor to first order, since the total weight of compensating masses remains the same. We compare two alternative models for the Arabian plate and surrounding area. The Airy model gives very significant regional isostatic anomalies, which cannot be explained by the upper crust structure or disturbances of the isostatic equilibrium. Also, the predicted "isostatic" Moho is very different from existing seismic observations. The second isostatic model includes the Moho, which is based on seismic determinations. Additional compensation is provided by density variations within the lithosphere (chiefly in the upper mantle). According to this model, the upper mantle under the Arabian Shield is less dense than under the Platform. In the Arabian platform, the maximum density coincides with the Rub' al Khali, one of the richest oil basin in the world. This finding agrees with previous studies, showing that such basins are often underlain by dense mantle, possibly related to an eclogite layer that has caused their subsidence. The mantle density variations might be also a result of variations of the lithosphere thickness. With the combined isostatic model, it is possible to minimize regional anomalies over the Arabian plate. The residual local anomalies correspond well to tectonic structure of the plate. Still very significant anomalies, showing isostatic disturbances of the lithosphere, are associated with the Zagros fold belt, the collision zone of the Arabian and Eurasian plates.

Variational tricomplex of a local gauge system, Lagrange structure and weak Poisson bracket

NASA Astrophysics Data System (ADS)

Sharapov, A. A.

2015-09-01

We introduce the concept of a variational tricomplex, which is applicable both to variational and nonvariational gauge systems. Assigning this tricomplex with an appropriate symplectic structure and a Cauchy foliation, we establish a general correspondence between the Lagrangian and Hamiltonian pictures of one and the same (not necessarily variational) dynamics. In practical terms, this correspondence allows one to construct the generating functional of a weak Poisson structure starting from that of a Lagrange structure. As a byproduct, a covariant procedure is proposed for deriving the classical BRST charge of the BFV formalism by a given BV master action. The general approach is illustrated by the examples of Maxwell’s electrodynamics and chiral bosons in two dimensions.

Heritability of the structures and 13C fractionation in tomato leaf wax alkanes: a genetic model system to inform paleoenvironmental reconstructions

NASA Astrophysics Data System (ADS)

Bender, Amanda L. D.; Chitwood, Daniel H.; Bradley, Alexander S.

2017-06-01

Leaf wax n-alkanes are broadly used to reconstruct paleoenvironmental information. However, the utility of n-alkanes as a paleoenvironmental proxy may be modulated by the extent to which biological as well as environmental factors influence the structural and isotopic variability of leaf waxes. In paleoclimate applications, there is usually an implicit assumption that most variation of leaf wax traits through a time series can be attributed to environmental change and that biological sources of variability within plant communities are small. For example, changes in hydrology affect the δ2H of waxes via rainwater and the δ13C of leaf waxes by changing plant communities. We measured the degree of genetic control over δ13C variation in leaf waxes within closely related species with an experimental greenhouse growth study. We measured the proportion of variability in structural and isotopic leaf wax traits that is attributable to genetic variation using a set of 76 introgression lines (ILs) between two interfertile Solanum (tomato) species: S. lycopersicum cv M82 (hereafter cv M82) and S. pennellii. Leaves of S. pennellii, a wild desert tomato relative, produced significantly more iso-alkanes than cv M82, a domesticated tomato cultivar adapted to water-replete conditions. We report a methylation index to summarize the ratio of branched (iso- and anteiso-) to total alkanes. Between S. pennellii and cv M82, the iso-alkanes were found to be enriched in 13C by 1.2-1.4‰ over n-alkanes. The broad-sense heritability values (H2) of leaf wax traits describe the degree to which genetic variation contributes to variation of these traits. Variation of individual carbon isotopic compositions of alkanes were of low heritability (H2 = 0.13-0.19), suggesting that most variation in δ13C of leaf waxes in this study can be attributed to environmental variance. This supports the interpretation that variation in the δ13C of wax compounds recorded in sediments reflects paleoenvironmental and vegetation changes. Average chain length (ACL) values of n-alkanes were of intermediate heritability (H2 = 0.30), suggesting that ACL values are more strongly influenced by genetic cues.

Bird-landscape relations in the Chihuahuan Desert: Coping with uncertainties about predictive models

USGS Publications Warehouse

Gutzwiller, K.J.; Barrow, W.C.

2001-01-01

During the springs of 1995-1997, we studied birds and landscapes in the Chihuahuan Desert along part of the Texas-Mexico border. Our objectives were to assess bird-landscape relations and their interannual consistency and to identify ways to cope with associated uncertainties that undermine confidence in using such relations in conservation decision processes. Bird distributions were often significantly associated with landscape features, and many bird-landscape models were valid and useful for predictive purposes. Differences in early spring rainfall appeared to influence bird abundance, but there was no evidence that annual differences in bird abundance affected model consistency. Model consistency for richness (42%) was higher than mean model consistency for 26 focal species (mean 30%, range 0-67%), suggesting that relations involving individual species are, on average, more subject to factors that cause variation than are richness-landscape relations. Consistency of bird-landscape relations may be influenced by such factors as plant succession, exotic species invasion, bird species' tolerances for environmental variation, habitat occupancy patterns, and variation in food density or weather. The low model consistency that we observed for most species indicates the high variation in bird-landscape relations that managers and other decision makers may encounter. The uncertainty of interannual variation in bird-landscape relations can be reduced by using projections of bird distributions from different annual models to determine the likely range of temporal and spatial variation in a species' distribution. Stochastic simulation models can be used to incorporate the uncertainty of random environmental variation into predictions of bird distributions based on bird-landscape relations and to provide probabilistic projections with which managers can weigh the costs and benefits of various decisions, Uncertainty about the true structure of bird-landscape relations (structural uncertainty) can be reduced by ensuring that models meet important statistical assumptions, designing studies with sufficient statistical power, validating the predictive ability of models, and improving model accuracy through continued field sampling and model fitting. Un certainty associated with sampling variation (partial observability) can be reduced by ensuring that sample sizes are large enough to provide precise estimates of both bird and landscape parameters. By decreasing the uncertainty due to partial observability, managers will improve their ability to reduce structural uncertainty.

Oxygen-17 and molybdenum-95 coupling in spectroscopic models of molybdoenzymes

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

Wilson, G.L.; Kony, M.; Tiekink, E.R.

1988-09-28

Assignment of (Mo/sup V/OS) and cis-(Mo/sup V/O(SH)) centers in active xanthine oxidase (very rapid and rapid ESR signals) are supported by generation of these species in solution. The ESR parameters were measured using /sup 17/O and /sup 95/Mo and are reported herein. The data revealed variations in relative magnitudes of the hyperfine components, and the different patterns of angles reflect significant differences in electronic structure. The same electronic differences appear to be responsible for the variations in magnitude and anisotropy of the /sup 17/O coupling, assigned to bound product Mo-/sup 17/OR in both enzyme signals.

Compositional zoning and its significance in pyroxenes from three coarse-grained lunar samples.

PubMed

Hargraves, R B; Hollister, L S; Otalora, G

1970-01-30

The calcium-rich pyroxenes in lunar samples 10047, 10058, and 10062 show pronounced sectoral and radial compositional variations which correlate with sharp to gradual variations in color and optical properties. The pyroxenes apparently grew as nearly euhedral crystals from melts of approximately the same composition as that of the samples. The coupled substitutions determined across sector boundaries suggest that Al is predominantly in the tetrahedral site and that Ti is predominantly quadrivalent. The pyroxene differentiation trend (unknown in terrestrial pyroxenes) is toward extreme enrichment in the ferrosilite molecule. The iron-enriched portions of the pyroxene grains may have grown with a triclinic pyroxenoid structure.

Full genome sequence of Rocio virus reveal substantial variations from the prototype Rocio virus SPH 34675 sequence.

PubMed

Setoh, Yin Xiang; Amarilla, Alberto A; Peng, Nias Y; Slonchak, Andrii; Periasamy, Parthiban; Figueiredo, Luiz T M; Aquino, Victor H; Khromykh, Alexander A

2018-01-01

Rocio virus (ROCV) is an arbovirus belonging to the genus Flavivirus, family Flaviviridae. We present an updated sequence of ROCV strain SPH 34675 (GenBank: AY632542.4), the only available full genome sequence prior to this study. Using next-generation sequencing of the entire genome, we reveal substantial sequence variation from the prototype sequence, with 30 nucleotide differences amounting to 14 amino acid changes, as well as significant changes to predicted 3'UTR RNA structures. Our results present an updated and corrected sequence of a potential emerging human-virulent flavivirus uniquely indigenous to Brazil (GenBank: MF461639).

Genetic structure and isolation by distance in a landrace of Thai rice

PubMed Central

Pusadee, Tonapha; Jamjod, Sansanee; Chiang, Yu-Chung; Rerkasem, Benjavan; Schaal, Barbara A.

2009-01-01

Rice is among the 3 most important crops worldwide. While much of the world's rice harvest is based on modern high-yield varieties, traditional varieties of rice grown by indigenous groups have great importance as a resource for future crop improvement. These local landraces represent an intermediate stage of domestication between a wild ancestor and modern varieties and they serve as reservoirs of genetic variation. Such genetic variation is influenced both by natural processes such as selection and drift, and by the agriculture practices of local farmers. How these processes interact to shape and change the population genetics of landrace rice is unknown. Here, we determine the population genetic structure of a single variety of landrace rice, Bue Chomee, cultivated by Karen people of Thailand. Microsatellite markers reveal high level of genetic variation despite predominant inbreeding in the crop. Bue Chomee rice shows slight but significant genetic differentiation among Karen villages. Moreover, genetically determined traits such as flowering time can vary significantly among villages. An unanticipated result was the overall pattern of genetic differentiation across villages which conforms to an isolation by distance model of differentiation. Isolation by distance is observed in natural plant species where the likelihood of gene flow is inversely related to distance. In Karen rice, gene flow is the result of farmers' seed sharing networks. Taken together, these data suggest that landrace rice is a dynamic genetic system that responds to evolutionary forces, both natural and those imposed by humans. PMID:19651617

Normal variation in fronto-occipital circuitry and cerebellar structure with an autism-associated polymorphism of CNTNAP2

PubMed Central

Tan, Geoffrey C.Y.; Doke, Thomas F.; Ashburner, John; Wood, Nicholas W.; Frackowiak, Richard S.J.

2010-01-01

Recent genetic studies have implicated a number of candidate genes in the pathogenesis of Autism Spectrum Disorder (ASD). Polymorphisms of CNTNAP2 (contactin-associated like protein-2), a member of the neurexin family, have already been implicated as a susceptibility gene for autism by at least 3 separate studies. We investigated variation in white and grey matter morphology using structural MRI and diffusion tensor imaging. We compared volumetric differences in white and grey matter and fractional anisotropy values in control subjects characterised by genotype at rs7794745, a single nucleotide polymorphism in CNTNAP2. Homozygotes for the risk allele showed significant reductions in grey and white matter volume and fractional anisotropy in several regions that have already been implicated in ASD, including the cerebellum, fusiform gyrus, occipital and frontal cortices. Male homozygotes for the risk alleles showed greater reductions in grey matter in the right frontal pole and in FA in the right rostral fronto-occipital fasciculus compared to their female counterparts who showed greater reductions in FA of the anterior thalamic radiation. Thus a risk allele for autism results in significant cerebral morphological variation, despite the absence of overt symptoms or behavioural abnormalities. The results are consistent with accumulating evidence of CNTNAP2's function in neuronal development. The finding suggests the possibility that the heterogeneous manifestations of ASD can be aetiologically characterised into distinct subtypes through genetic-morphological analysis. PMID:20176116

Structural studies of zirconium doped Ba{sub 0.70}Sr{sub 0.30}TiO{sub 3} lead free ferroelectric thin films

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

Sharma, Sarita, E-mail: sss.sharmasarita@gmail.com; Ram, Mast; Thakur, Shilpa

2016-05-06

Ba{sub 0.7}Sr{sub 0.3}(Zr{sub x}Ti{sub 1-x})O{sub 3}(BSZT, x=0,0.05,0.10,0.15,0.20) thin films were prepared by using sol gel method. Structural and microstructural properties were studied by using XRD, Raman Spectroscopy and atomic force microscopy (AFM) respectively. XRD and Raman Spectroscopy show the presence of tetragonal phase in multilayer BSZT thin film. The experimental results demonstrate that structural and microstructural properties of BSZT thin film were significantly dependent on variation of Zr content.

Buried anti resonant reflecting optical waveguide based on porous silicon material for an integrated Mach Zehnder structure

NASA Astrophysics Data System (ADS)

Hiraoui, M.; Guendouz, M.; Lorrain, N.; Haji, L.; Oueslati, M.

2012-11-01

A buried anti resonant reflecting optical waveguide for an integrated Mach Zehnder structure based on porous silicon material is achieved using a classical photolithography process. Three distinct porous silicon layers are then elaborated in a single step, by varying the porosity (thus the refractive index) and the thickness while respecting the anti-resonance conditions. Simulations and experimental results clearly show the antiresonant character of the buried waveguides. Significant variation of the reflectance and light propagation with different behavior depending on the polarization and the Mach Zehnder dimensions is obtained. Finally, we confirm the feasibility of this structure for sensing applications.

Relating microstructure to rheology of a bundled and cross-linked F-actin network in vitro

NASA Astrophysics Data System (ADS)

Shin, J. H.; Gardel, M. L.; Mahadevan, L.; Matsudaira, P.; Weitz, D. A.

2004-06-01

The organization of individual actin filaments into higher-order structures is controlled by actin-binding proteins (ABPs). Although the biological significance of the ABPs is well documented, little is known about how bundling and cross-linking quantitatively affect the microstructure and mechanical properties of actin networks. Here we quantify the effect of the ABP scruin on actin networks by using imaging techniques, cosedimentation assays, multiparticle tracking, and bulk rheology. We show how the structure of the actin network is modified as the scruin concentration is varied, and we correlate these structural changes to variations in the resultant network elasticity.

Large-scale variability in marine stratocumulus clouds defined from simultaneous aircraft and satellite measurements

NASA Technical Reports Server (NTRS)

Albrecht, Bruce A.; Barlow, Roy W.

1990-01-01

Satellite images often show significant variations in the structure of marine stratocumulus clouds on scales ranging from 10 to 1000 km. This is illustrated where a GOES West satellite image shows a well-defined variation in cloud structure near 32 N, 122 W on 30 June 1987. Aircraft measurements were made with the UK C-130 and the NCAR Electra on this day as part of the FIRE Marine Stratocumulus Intensive Field Observations (IFO). The mean, turbulent, and the microphysical structure of the clouds sampled in these two areas are compared an an attempt is made to explain the differences in cloud structure. In an attempt to identify any systematic differences between the measurements made with the two aircraft, data were analyzed that were collected on 14 July 1987 with the C-130 and the Electra flying in close formation at an altitude of 250 m. The microphysical and turbulence data are being compared in an attempt to explain the differences in the cloud liquid water content obtained with the two aircraft and the differences in cloud structure shown by the GOES image. In addition, data are being analyzed for three other days during the experiment when coordinated downstream flights were made with the Electra and the C-130.

Admittance of MIS-Structures Based on HgCdTe with a Double-Layer CdTe/Al2O3 Insulator

NASA Astrophysics Data System (ADS)

Dzyadukh, S. M.; Voitsekhovskii, A. V.; Nesmelov, S. N.; Sidorov, G. Yu.; Varavin, V. S.; Vasil'ev, V. V.; Dvoretsky, S. A.; Mikhailov, N. N.; Yakushev, M. V.

2018-03-01

Admittance of MIS structures based on n( p)- Hg1-xCdxTe (at x from 0.22 to 0.40) with SiO2/Si3N4, Al2O3, and CdTe/Al2O3 insulators is studied experimentally at 77 K. Growth of an intermediate CdTe layer during epitaxy results in the almost complete disappearance of the hysteresis of electrophysical characteristics of MIS structures based on graded-gap n-HgCdTe for a small range of the voltage variation. For a wide range of the voltage variation, the hysteresis of the capacitance-voltage characteristics appears for MIS structures based on n-HgCdTe with the CdTe/Al2O3 insulator. However, the hysteresis mechanism differs from that in case of a single-layer Al2O3 insulator. For MIS structures based on p-HgCdTe, introduction of an additional CdTe layer does not lead to a significant decrease of the hysteresis phenomena, which may be due to the degradation of the interface properties when mercury leaves the film as a result of low-temperature annealing changing the conductivity type of the semiconductor.

Phenotypic diversity, population structure and stress protein-based capacitoring in populations of Xeropicta derbentina, a heat-tolerant land snail species.

PubMed

Di Lellis, Maddalena A; Sereda, Sergej; Geißler, Anna; Picot, Adrien; Arnold, Petra; Lang, Stefanie; Troschinski, Sandra; Dieterich, Andreas; Hauffe, Torsten; Capowiez, Yvan; Mazzia, Christophe; Knigge, Thomas; Monsinjon, Tiphaine; Krais, Stefanie; Wilke, Thomas; Triebskorn, Rita; Köhler, Heinz-R

2014-11-01

The shell colour of many pulmonate land snail species is highly diverse. Besides a genetic basis, environmentally triggered epigenetic mechanisms including stress proteins as evolutionary capacitors are thought to influence such phenotypic diversity. In this study, we investigated the relationship of stress protein (Hsp70) levels with temperature stress tolerance, population structure and phenotypic diversity within and among different populations of a xerophilic Mediterranean snail species (Xeropicta derbentina). Hsp70 levels varied considerably among populations, and were significantly associated with shell colour diversity: individuals in populations exhibiting low diversity expressed higher Hsp70 levels both constitutively and under heat stress than those of phenotypically diverse populations. In contrast, population structure (cytochrome c oxidase subunit I gene) did not correlate with phenotypic diversity. However, genetic parameters (both within and among population differences) were able to explain variation in Hsp70 induction at elevated but non-pathologic temperatures. Our observation that (1) population structure had a high explanatory potential for Hsp70 induction and that (2) Hsp70 levels, in turn, correlated with phenotypic diversity while (3) population structure and phenotypic diversity failed to correlate provides empirical evidence for Hsp70 to act as a mediator between genotypic variation and phenotype and thus for chaperone-driven evolutionary capacitance in natural populations.

Flow Structure and Force Variation with Aspect Ratio for a Two-Degree-of-Freedom Flapping Wing

NASA Astrophysics Data System (ADS)

Burge, Matthew; Favale, James; Ringuette, Matthew

2014-11-01

We investigate experimentally the effect of aspect ratio (AR) on the flow structure and forces of a two-degree-of-freedom flapping wing. Flapping wings are known to produce complex and unsteady vortex loop structures, and the objective is to characterize their variation with AR and how this influences the lift force. Previous results on rotating wings demonstrated that changes in AR significantly affect the three-dimensional flow structure and lift coefficient. This is primarily due to the relatively greater influence of the tip vortex for lower AR. At Reynolds number of order O(103) we test wings of AR = 2-4, values typically found in nature, with simplified planform shapes. The lift force is measured using a submersible transducer at the base of the wing in a glycerin-water mixture. The qualitative, three-dimensional vortex loop structure for different ARs is obtained using multi-color dye flow visualization. Guided by this, quantitative three-component flow information, namely vorticity, the Q-criterion, and circulation, is acquired from stereoscopic particle image velocimetry in key planes. Of interest is how these parameters and the vortex loop topology vary with AR, and their connection to features in the unsteady force signal. This work is supported by the National Science Foundation, Award Number 1336548, supervised by Dr. Dimitrios Papavassiliou.

Association of GSK3beta polymorphisms with brain structural changes in major depressive disorder.

PubMed

Inkster, Becky; Nichols, Thomas E; Saemann, Philipp G; Auer, Dorothee P; Holsboer, Florian; Muglia, Pierandrea; Matthews, Paul M

2009-07-01

Indirect evidence suggests that the glycogen synthase kinase-3beta (GSK3beta) gene might be implicated in major depressive disorder (MDD). We evaluated 15 GSK3beta single-nucleotide polymorphisms (SNPs) to test for associations with regional gray matter (GM) volume differences in patients with recurrent MDD. We then used the defined regions of interest based on significant associations to test for MDD x genotype interactions by including a matched control group without any psychiatric disorder, including MDD. General linear model with nonstationary cluster-based inference. Munich, Germany. Patients with recurrent MDD (n = 134) and age-, sex-, and ethnicity-matched healthy controls (n = 143). Associations between GSK3beta polymorphisms and regional GM volume differences. Variation in GM volume was associated with GSK3beta polymorphisms; the most significant associations were found for rs6438552, a putative functional intronic SNP that showed 3 significant GM clusters in the right and left superior temporal gyri and the right hippocampus (P < .001, P = .02, and P = .02, respectively, corrected for multiple comparisons across the whole brain). Similar results were obtained with rs12630592, an SNP in high linkage disequilibrium. A significant SNP x MDD status interaction was observed for the effect on GM volumes in the right hippocampus and superior temporal gyri (P < .001 and P = .01, corrected, respectively). The GSK3beta gene may have a role in determining regional GM volume differences of the right hippocampus and bilateral superior temporal gyri. The association between genotype and brain structure was specific to the patients with MDD, suggesting that GSK3beta genotypes might interact with MDD status. We speculate that this is a consequence of regional neocortical, glial, or neuronal growth or survival. In considering core cognitive features of MDD, the association of GSK3beta polymorphisms with structural variation in the temporal lobe and hippocampus is of particular interest in the context of other evidence for structural and functional abnormalities in the hippocampi of patients with MDD.

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

PubMed

Cardew, P T

2009-03-01

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

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.

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.

Mantle shear-wave tomography and the fate of subducted slabs.

PubMed

Grand, Steven P

2002-11-15

A new seismic model of the three-dimensional variation in shear velocity throughout the Earth's mantle is presented. The model is derived entirely from shear bodywave travel times. Multibounce shear waves, core-reflected waves and SKS and SKKS waves that travel through the core are used in the analysis. A unique aspect of the dataset used in this study is the use of bodywaves that turn at shallow depths in the mantle, some of which are triplicated. The new model is compared with other global shear models. Although competing models show significant variations, several large-scale structures are common to most of the models. The high-velocity anomalies are mostly associated with subduction zones. In some regions the anomalies only extend into the shallow lower mantle, whereas in other regions tabular high-velocity structures seem to extend to the deepest mantle. The base of the mantle shows long-wavelength high-velocity zones also associated with subduction zones. The heterogeneity seen in global tomography models is difficult to interpret in terms of mantle flow due to variations in structure from one subduction zone to another. The simplest interpretation of the seismic images is that slabs in general penetrate to the deepest mantle, although the flow is likely to be sporadic. The interruption in slab sinking is likely to be associated with the 660 km discontinuity.

Colony social structure in native and invasive populations of the social wasp Vespula pensylvanica

USGS Publications Warehouse

Hanna, Cause; Cook, Erin D.; Thompson, Ariel R.; Dare, Lyndzey E.; Palaski, Amanda L.; Foote, David; Goodisman, Michael A. D.

2014-01-01

Social insects rank among the most invasive of terrestrial species. The success of invasive social insects stems, in part, from the flexibility derived from their social behaviors. We used genetic markers to investigate if the social system of the invasive wasp, Vespula pensylvanica, differed in its introduced and native habitats in order to better understand variation in social phenotype in invasive social species. We found that (1) nestmate workers showed lower levels of relatedness in introduced populations than native populations, (2) introduced colonies contained workers produced by multiple queens whereas native colonies contained workers produced by only a single queen, (3) queen mate number did not differ significantly between introduced and native colonies, and (4) workers from introduced colonies were frequently produced by queens that originated from foreign nests. Thus, overall, native and introduced colonies differed substantially in social phenotype because introduced colonies more frequently contained workers produced by multiple, foreign queens. In addition, the similarity in levels of genetic variation in introduced and native habitats, as well as observed variation in colony social phenotype in native populations, suggest that colony structure in invasive populations may be partially associated with social plasticity. Overall, the differences in social structure observed in invasive V. pensylvanica parallel those in other, distantly related invasive social insects, suggesting that insect societies often develop similar social phenotypes upon introduction into new habitats.

3D mechanical stratigraphy of a deformed multi-layer: Linking sedimentary architecture and strain partitioning

NASA Astrophysics Data System (ADS)

Cawood, Adam J.; Bond, Clare E.

2018-01-01

Stratigraphic influence on structural style and strain distribution in deformed sedimentary sequences is well established, in models of 2D mechanical stratigraphy. In this study we attempt to refine existing models of stratigraphic-structure interaction by examining outcrop scale 3D variations in sedimentary architecture and the effects on subsequent deformation. At Monkstone Point, Pembrokeshire, SW Wales, digital mapping and virtual scanline data from a high resolution virtual outcrop have been combined with field observations, sedimentary logs and thin section analysis. Results show that significant variation in strain partitioning is controlled by changes, at a scale of tens of metres, in sedimentary architecture within Upper Carboniferous fluvio-deltaic deposits. Coupled vs uncoupled deformation of the sequence is defined by the composition and lateral continuity of mechanical units and unit interfaces. Where the sedimentary sequence is characterized by gradational changes in composition and grain size, we find that deformation structures are best characterized by patterns of distributed strain. In contrast, distinct compositional changes vertically and in laterally equivalent deposits results in highly partitioned deformation and strain. The mechanical stratigraphy of the study area is inherently 3D in nature, due to lateral and vertical compositional variability. Consideration should be given to 3D variations in mechanical stratigraphy, such as those outlined here, when predicting subsurface deformation in multi-layers.

Effects of mistuning and matrix structure on the topology of frequency response curves

NASA Technical Reports Server (NTRS)

Afolabi, Dare

1989-01-01

The stability of a frequency response curve under mild perturbations of the system's matrix is investigated. Using recent developments in the theory of singularities of differentiable maps, it is shown that the stability of a response curve depends on the structure of the system's matrix. In particular, the frequency response curves of a cylic system are shown to be unstable. Consequently, slight parameter variations engendered by mistuning will induce a significant difference in the topology of the forced response curves, if the mistuning transformation crosses the bifurcation set.

Probabilistic structural analysis to quantify uncertainties associated with turbopump blades

NASA Technical Reports Server (NTRS)

Nagpal, Vinod K.; Rubinstein, Robert; Chamis, Christos C.

1987-01-01

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 has been developed to quantify the effects of the random uncertainties. The results of this study indicate that only the variations in geometry have significant effects.

Gas and Dust Structures of the Protoplanetary Disk around HD 142527

NASA Astrophysics Data System (ADS)

Momose, M.; Muto, T.; Hanawa, T.; Fukagawa, M.; Tsukagoshi, T.; Saigo, K.; Kataoka, A.; Nomura, H.; Takeuchi, T.; Akiyama, E.; Ohashi, N.; Fujiwara, H.; Shibai, H.; Kitamura, Y.; Inutsuka, S.; Kobayashi, H.; Honda, M.; Aso, Y.; Takahashi, S. Z.

2015-12-01

HD142527 is a Herbig Fe star accompanied by a disk with ring-like structure. We derive the distributions of dust and gas separately by model fitting and discuss the spatial variation of gas-to-dust mass ratio in the disk. The radial distribution of dust is well approximated by a Gaussian function, while the gas is roughly followed by a power-law distribution between 110 and 400 AU in radius, which is significantly more extended than dust. G/d may reach the order of unity at the northern peak.

Balancing Selection on a Regulatory Region Exhibiting Ancient Variation That Predates Human–Neandertal Divergence

PubMed Central

Iskow, Rebecca C.; Austermann, Christian; Scharer, Christopher D.; Raj, Towfique; Boss, Jeremy M.; Sunyaev, Shamil; Price, Alkes; Stranger, Barbara; Simon, Viviana; Lee, Charles

2013-01-01

Ancient population structure shaping contemporary genetic variation has been recently appreciated and has important implications regarding our understanding of the structure of modern human genomes. We identified a ∼36-kb DNA segment in the human genome that displays an ancient substructure. The variation at this locus exists primarily as two highly divergent haplogroups. One of these haplogroups (the NE1 haplogroup) aligns with the Neandertal haplotype and contains a 4.6-kb deletion polymorphism in perfect linkage disequilibrium with 12 single nucleotide polymorphisms (SNPs) across diverse populations. The other haplogroup, which does not contain the 4.6-kb deletion, aligns with the chimpanzee haplotype and is likely ancestral. Africans have higher overall pairwise differences with the Neandertal haplotype than Eurasians do for this NE1 locus (p<10−15). Moreover, the nucleotide diversity at this locus is higher in Eurasians than in Africans. These results mimic signatures of recent Neandertal admixture contributing to this locus. However, an in-depth assessment of the variation in this region across multiple populations reveals that African NE1 haplotypes, albeit rare, harbor more sequence variation than NE1 haplotypes found in Europeans, indicating an ancient African origin of this haplogroup and refuting recent Neandertal admixture. Population genetic analyses of the SNPs within each of these haplogroups, along with genome-wide comparisons revealed significant FST (p = 0.00003) and positive Tajima's D (p = 0.00285) statistics, pointing to non-neutral evolution of this locus. The NE1 locus harbors no protein-coding genes, but contains transcribed sequences as well as sequences with putative regulatory function based on bioinformatic predictions and in vitro experiments. We postulate that the variation observed at this locus predates Human–Neandertal divergence and is evolving under balancing selection, especially among European populations. PMID:23593015

Morphometric Variations in the Skin Layers of Frogs: An Exploration Into Their Relation With Ecological Parameters in Leptodactylus (Anura, Leptodactylidae), With an Emphasis on the Eberth-Kastschenko Layer.

PubMed

Ponssa, María Laura; Barrionuevo, J Sebastián; Pucci Alcaide, Franco; Pucci Alcaide, Ana

2017-10-01

Leptodactylus is a genus of frogs known to live in diverse habitats and to show both aquatic and terrestrial breeding habits. We studied 21 species of Leptodactylus to explore whether skin structure specialization relates to habitats and habit variation. Morphometric analyses of the skin thickness revealed that phylogeny has a strong influence on variations in the thickness of the epidermis, stratum spongiosum, Eberth-Kastschenko layer, and stratum compactum, while habitat and habits display no significant correlation. The optimization of the phylogenetic hypothesis suggested that a pattern of intermediate values for skin layer thickness are plesiomorphic for this group. Anat Rec, 2017. © 2017 Wiley Periodicals, Inc. Anat Rec, 300:1895-1909, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Anatomic variation of depth-dependent mechanical properties in neonatal bovine articular cartilage.

PubMed

Silverberg, Jesse L; Dillavou, Sam; Bonassar, Lawrence; Cohen, Itai

2013-05-01

Articular cartilage has well known depth-dependent structure and has recently been shown to have similarly non-uniform depth-dependent mechanical properties. Here, we study anatomic variation of the depth-dependent shear modulus and energy dissipation rate in neonatal bovine knees. The regions we specifically focus on are the patellofemoral groove, trochlea, femoral condyle, and tibial plateau. In every sample, we find a highly compliant region within the first 500 µm of tissue measured from the articular surface, where the local shear modulus is reduced by up to two orders of magnitude. Comparing measurements taken from different anatomic sites, we find statistically significant differences localized within the first 50 µm. Histological images reveal these anatomic variations are associated with differences in collagen density and fiber organization. Copyright © 2012 Orthopaedic Research Society.

Leaf water relations during summer water deficit: differential responses in turgor maintenance and variation in leaf structure among different plant communities in south-western Australia.

PubMed

Mitchell, Patrick J; Veneklaas, Erik J; Lambers, Hans; Burgess, Stephen S O

2008-12-01

We measured leaf water relations and leaf structural traits of 20 species from three communities growing along a topographical gradient. Our aim was to assess variation in seasonal responses in leaf water status and leaf tissue physiology between sites and among species in response to summer water deficit. Species from a ridge-top heath community showed the greatest reductions in pre-dawn leaf water potentials (Psi(leaf)) and stomatal conductance during summer; species from a valley-floor woodland and a midslope mallee community showed less reductions in these parameters. Heath species also displayed greater seasonal reduction in turgor-loss point (Psi(TLP)) than species from woodland or mallee communities. In general, species that had larger reductions in Psi(leaf) during summer showed significant shifts in either their osmotic potential at full turgor (Psi(pi 100); osmotic adjustment) or in tissue elasticity (epsilon(max)). Psi(pi 100) and epsilon(max) were negatively correlated, during both spring and summer, suggesting a trade-off between these different mechanisms to cope with water stress. Specific leaf area varied greatly among species, and was significantly correlated with seasonal changes in Psi(TLP) and pre-dawn Psi(leaf). These correlations suggest that leaf structure is a prerequisite for cellular mechanisms to be effective in adjusting to water deficit.

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.

Intraspecific differences in plant chemotype determine the structure of arthropod food webs.

PubMed

Bálint, János; Zytynska, Sharon E; Salamon, Rozália Veronika; Mehrparvar, Mohsen; Weisser, Wolfgang W; Schmitz, Oswald J; Benedek, Klára; Balog, Adalbert

2016-03-01

It is becoming increasingly appreciated that the structure and functioning of ecological food webs are controlled by the nature and level of plant chemicals. It is hypothesized that intraspecific variation in plant chemical resistance, in which individuals of a host-plant population exhibit genetic differences in their chemical contents (called 'plant chemotypes'), may be an important determinant of variation in food web structure and functioning. We evaluated this hypothesis using field assessments and plant chemical assays in the tansy plant Tanacetum vulgare L. (Asteraceae). We examined food webs in which chemotypes of tansy plants are the resource for two specialized aphids, their predators and mutualistic ants. The density of the ant-tended aphid Metopeurum fuscoviride was significantly higher on particular chemotypes (borneol) than others. Clear chemotype preferences between predators were also detected. Aphid specialist seven-spotted ladybird beetles (Coccinella septempunctata) were more often found on camphor plants, while significantly higher numbers of the polyphagous nursery web spider (Pisaura mirabilis) were observed on borneol plants. The analysis of plant chemotype effects on the arthropod community clearly demonstrates a range of possible outcomes between plant-aphid-predator networks. The findings help to offer a deeper insight into how one important factor--plant chemical content--influences which species coexist within a food web on a particular host plant and the nature of their trophic linkages.

Effects of the magnetic field variation on the spin wave interference in a magnetic cross junction

NASA Astrophysics Data System (ADS)

Balynskiy, M.; Chiang, H.; Kozhevnikov, A.; Dudko, G.; Filimonov, Y.; Balandin, A. A.; Khitun, A.

2018-05-01

This article reports results of the investigation of the effect of the external magnetic field variation on the spin wave interference in a magnetic cross junction. The experiments were performed using a micrometer scale Y3Fe5O12 cross structure with a set of micro-antennas fabricated on the edges of the cross arms. Two of the antennas were used for the spin wave excitation while a third antenna was used for detecting the inductive voltage produced by the interfering spin waves. It was found that a small variation of the bias magnetic field may result in a significant change of the output inductive voltage. The effect is most prominent under the destructive interference condition. The maximum response exceeds 30 dB per 0.1 Oe at room temperature. It takes a relatively small bias magnetic field variation of about 1 Oe to drive the system from the destructive to the constructive interference conditions. The switching is accompanied by a significant, up to 50 dB, change in the output voltage. The obtained results demonstrate a feasibility of the efficient spin wave interference control by an external magnetic field, which may be utilized for engineering novel type of magnetometers and magnonic logic devices.

STELLAR STRUCTURE AND TESTS OF MODIFIED GRAVITY

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

Chang, Philip; Hui, Lam, E-mail: pchang@cita.utoronto.ca, E-mail: lhui@astro.columbia.edu

2011-05-01

Theories that attempt to explain cosmic acceleration by modifying gravity typically introduces a long-range scalar force that needs to be screened on small scales. One common screening mechanism is the chameleon, where the scalar force is screened in environments with a sufficiently deep gravitational potential, but acts unimpeded in regions with a shallow gravitational potential. This leads to a variation in the overall gravitational G with environment. We show that such a variation can occur within a star itself, significantly affecting its evolution and structure, provided that the host galaxy is unscreened. The effect is most pronounced for red giants,more » which would be smaller by a factor of tens of percent and thus hotter by hundreds of Kelvin, depending on the parameters of the underlying scalar-tensor theory. Careful measurements of these stars in suitable environments (nearby dwarf galaxies not associated with groups or clusters) would provide constraints on the chameleon mechanism that are four orders of magnitude better than current large-scale structure limits and two orders of magnitude better than present solar system tests.« less

SNR improvement by variation of recording and media parameters for a HAMR exchange coupled composite media

NASA Astrophysics Data System (ADS)

Natekar, N. A.; Liu, Zengyuan; Hernandez, Stephanie; Victora, R. H.

2018-05-01

An exchange coupled composite media structure proposed previously seems to address both the issue of Tc variation in FePt as well as poor SNR/User Density during the HAMR process. Here we examine a thinner 3-6 nm structure that is likely easier to fabricate than the previous 13.5 nm thick structure. We find that increasing the damping within the write (superparamagnetic) layer and introducing intergranular exchange within the grains in the write layer are both successful approaches to improve the recorded SNR. Ensemble waveform analysis that allows the breakdown of the total SNR into transition SNR (due to AC noise) and remanence SNR (due to DC noise) helps identify the leading causes for this SNR improvement. Further studies indicate that varying the peak heat spot temperature in the HAMR write process is also a successful approach for improving the recorded SNR. This lends credence to the idea that a thinner composite media may still be used successfully to realize significant enhancements of SNR and the corresponding user density.

Galaxy clusters, type Ia supernovae and the fine structure constant

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

Holanda, R.F.L.; Busti, V.C.; Colaço, L.R.

2016-08-01

As is well known, measurements of the Sunyaev-Zeldovich effect can be combined with observations of the X-ray surface brightness of galaxy clusters to estimate the angular diameter distance to these structures. In this paper, we show that this technique depends on the fine structure constant, α. Therefore, if α is a time-dependent quantity, e.g., α = α{sub 0}φ( z ), where φ is a function of redshift, we argue that current data do not provide the real angular diameter distance, D {sub A}( z ), to the cluster, but instead D {sub A}{sup data}( z ) = φ( z ){supmore » 2} D {sub A}( z ). We use this result to derive constraints on a possible variation of α for a class of dilaton runaway models considering a sample of 25 measurements of D {sub A}{sup data}( z ) in redshift range 0.023 < z < 0.784 and estimates of D {sub A}( z ) from current type Ia supernovae observations. We find no significant indication of variation of α with the present data.« less

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

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

A detection method of subrecent to recent tectonic activity in the anticlinal system of the northern Negev, Israel

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

Zilberman, E.; Wachs, D.

Geomorphological and geophysical methods combined with borehole information were employed to search for possible subrecent small-scale vertical movement along the anticlinal fold belt of the central Negev, Israel. Such tectonic deformation might indicate displacement on the buried reverse faults underneath the anticlines. Variations in the thickness of the alluvial fill in the study area, which are in accordance with the fold structures, could be an indication of recent folding activity along the anticlinal system. In order to detect these thickness variations in the alluvial fill, seismic refraction and electrical resistivity measurements were carries out along the valley of Nahal Besor,more » which crosses the anticlinal belt. The thickness variations of the alluvial fill along the valley were not found to indicate any significant tectonic movement along the anticlines during the Pleistocene. The thickest alluvium was found overlying a karst bedrock, hence karst relief is suggested to be responsible for these variations.« less

The response of epiphytic microbes to habitat and growth status of Potamogeton malaianus Miq. in Lake Taihu.

PubMed

Cai, Xianlei; Gao, Guang; Tang, Xiangming; Dong, Baili; Dai, Jiangyu; Chen, Dan; Song, Yuzhi

2013-10-01

To investigate the effects of different habitats and plant growth status on abundance, biomass and community structure of epiphytic microbes, Potamogeton malaianus Miq. at two different habitats (Gonghu Bay and East Taihu) in Lake Taihu were collected in June, August and November (corresponding to the period of development of submerged macrophytes). The relative abundance of major epiphytic algae groups was determined with high performance liquid chromatography (HPLC), and the structures and dynamics of epiphytic bacteria were assessed by terminal restriction fragment length polymorphism (T-RFLP) analysis. Results showed that the biomass of epiphytic microbes was not significant difference between the two sites, and the analysis of similarity found no significant intra-lake heterogeneity in community structure, but the temporal heterogeneity of epiphytic microbes was significant, which linked to the growth state of submerged macrophytes and water temperature. The difference in community structure between June and August was larger than that between August and November at each site, indicating that the growth status of submerged macrophytes has a greater impact on the community structure of epiphytic microbes than the seasonal variation of environmental conditions. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Genetic Structure and Diversity of the Endangered Fir Tree of Lebanon (Abies cilicica Carr.): Implications for Conservation

PubMed Central

Awad, Lara; Fady, Bruno; Khater, Carla; Roig, Anne; Cheddadi, Rachid

2014-01-01

The threatened conifer Abies cilicica currently persists in Lebanon in geographically isolated forest patches. The impact of demographic and evolutionary processes on population genetic diversity and structure were assessed using 10 nuclear microsatellite loci. All remnant 15 local populations revealed a low genetic variation but a high recent effective population size. FST-based measures of population genetic differentiation revealed a low spatial genetic structure, but Bayesian analysis of population structure identified a significant Northeast-Southwest population structure. Populations showed significant but weak isolation-by-distance, indicating non-equilibrium conditions between dispersal and genetic drift. Bayesian assignment tests detected an asymmetric Northeast-Southwest migration involving some long-distance dispersal events. We suggest that the persistence and Northeast-Southwest geographic structure of Abies cilicica in Lebanon is the result of at least two demographic processes during its recent evolutionary history: (1) recent migration to currently marginal populations and (2) local persistence through altitudinal shifts along a mountainous topography. These results might help us better understand the mechanisms involved in the species response to expected climate change. PMID:24587219

Structure and seasonal variations of the nocturnal mesospheric K layer at Arecibo

NASA Astrophysics Data System (ADS)

Yue, Xianchang; Friedman, Jonathan S.; Wu, Xiongbin; Zhou, Qihou H.

2017-07-01

We present the seasonal variations of the nocturnal mesospheric potassium (K) layer at Arecibo, Puerto Rico (18.35°N, 66.75°W) from 160 nights of K Doppler lidar observations between December 2003 and January 2010, during which the solar activity is mostly low. The background temperature is also measured simultaneously by the lidar and shows a strong semiannual oscillation with maxima occurring during equinoxes at all altitudes. The annual mean K density profile is approximately Gaussian with a peak altitude of 91.7 km. The K column abundance and the centroid height have strong semiannual variations, with maxima at the solstices. Both parameters are negatively correlated to the mean background temperature with a correlation coefficient < -0.5. The root-mean-square (RMS) width has a distinct annual oscillation with the largest width occurring in May. The seasonal variation of the centroid height is similar to that of the Fe layer at the same site. The seasonal temperature variation indicates significant enhanced wave-induced downward transport for both species during spring and autumn. This explains the metal layer centroid height and column abundance variations at Arecibo and provides a general mechanism to account for the seasonal variations in the centroid height of all metal species measured at low-latitude and midlatitude sites.

Impact of the variation in dynamic vehicle load on flexible pavement responses

NASA Astrophysics Data System (ADS)

Ahsanuzzaman, Md

The purpose of this research was to evaluate the dynamic variation in asphalt pavement critical responses due to dynamic tire load variations. An attempt was also made to develop generalized regression equations to predict the dynamic response variation in flexible pavement under various dynamic load conditions. The study used an extensive database of computed pavement response histories for five different types of sites (smooth, rough, medium rough, very rough and severely rough), two different asphalt pavement structures (thin and thick) at two temperatures (70 °F and 104 °F), subjected to a tandem axle dual tire at three speeds 25, 37 and 50 mph (40, 60 and 80 km/h). All pavement responses were determined using the 3D-Move Analysis program (Version 1.2) developed by University of Nevada, Reno. A new term called Dynamic Response Coefficient (DRC) was introduced in this study to address the variation in critical pavement responses due to dynamic loads as traditionally measured by the Dynamic Load Coefficient (DLC). While DLC represents the additional varying component of the tire load, DRC represents the additional varying component of the response value (standard deviation divided by mean response). In this study, DRC was compared with DLC for five different sites based on the roughness condition of the sites. Previous studies showed that DLC varies with vehicle speed and suspension types, and assumes a constant value for the whole pavement structure (lateral and vertical directions). On the other hand, in this study, DRC was found to be significantly varied with the asphalt pavement and function of pavement structure, road roughness conditions, temperatures, vehicle speeds, suspension types, and locations of the point of interest in the pavement. A major contribution of the study is that the variation of pavement responses due to dynamic load in a flexible pavement system can be predicted with generalized regression equations. Fitting parameters (R2) in the rage of 0.60 to 0.87 were observed the DRC predictive equations. In addition, verification of those generalized equations was evaluated using different sets of asphalt pavement structures and pavement materials. The differences between calculated and predicted values were found to be within +/-20% for the maximum tensile strain and +/-30% for the maximum compressive strain in the asphalt layer.

Visualizing Structure and Dynamics of Disaccharide Simulations

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

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

2012-01-01

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

Discriminating disturbance from natural variation with LiDAR in semi-arid forests in the southwestern USA

Treesearch

T. L. Swetnam; A. M. Lynch; D. A. Falk; S. R. Yool; D. P. Guertin

2015-01-01

Discriminating amongst spatial configurations and climax size of trees in forests along varying physical gradients from time since last disturbance is a significant component of applied forest management. Understanding what has led to the existing vegetation’s structure has important implications for monitoring succession and eco-hydrological interactions within the...

A Method for Reducing Misclassification in the Extended Glasgow Outcome Score

PubMed Central

Marmarou, Anthony; Lapane, Kate; Turf, Elizabeth; Wilson, Lindsay

2010-01-01

Abstract The eight-point extended Glasgow Outcome Scale (GOSE) is commonly used as the primary outcome measure in traumatic brain injury (TBI) clinical trials. The outcome is conventionally collected through a structured interview with the patient alone or together with a caretaker. Despite the fact that using the structured interview questionnaires helps reach agreement in GOSE assessment between raters, significant variation remains among different raters. We introduce an alternate GOSE rating system as an aid in determining GOSE scores, with the objective of reducing inter-rater variation in the primary outcome assessment in TBI trials. Forty-five trauma centers were randomly assigned to three groups to assess GOSE scores on sample cases, using the alternative GOSE rating system coupled with central quality control (Group 1), the alternative system alone (Group 2), or conventional structured interviews (Group 3). The inter-rater variation between an expert and untrained raters was assessed for each group and reported through raw agreement and with weighted kappa (κ) statistics. Groups 2 and 3 without central review yielded inter-rater agreements of 83% (weighted κ = 0.81; 95% CI 0.69, 0.92) and 83% (weighted κ = 0.76, 95% CI 0.63, 0.89), respectively, in GOS scores. In GOSE, the groups had an agreement of 76% (weighted κ = 0.79; 95% CI 0.69, 0.89), and 63% (weighted κ = 0.70; 95% CI 0.60, 0.81), respectively. The group using the alternative rating system coupled with central monitoring yielded the highest inter-rater agreement among the three groups in rating GOS (97%; weighted κ = 0.95; 95% CI 0.89, 1.00), and GOSE (97%; weighted κ = 0.97; 95% CI 0.91, 1.00). The alternate system is an improved GOSE rating method that reduces inter-rater variations and provides for the first time, source documentation and structured narratives that allow a thorough central review of information. The data suggest that a collective effort can be made to minimize inter-rater variation. PMID:20334503

Topological methods reveal high and low functioning neuro-phenotypes within fragile X syndrome

PubMed Central

Romano, David; Nicolau, Monica; Quintin, Eve-Marie; Mazaika, Paul; Lightbody, Amy; Hazlett, Heather; Piven, Joseph; Carlsson, Gunnar; Reiss, Allan

2014-01-01

Fragile X syndrome (FXS), due to mutations of the FMR1 gene, is the most common known inherited cause of developmental disability as well as the most common single-gene risk factor for autism. Our goal was to examine variation in brain structure in FXS with topological data analysis (TDA), and to assess how such variation is associated with measures of IQ and autism-related behaviors. To this end, we analyzed imaging and behavioral data from young boys (n=52; aged 1.57-4.15 years) diagnosed with FXS. Application of topological methods to structural MRI data revealed two large subgroups within the study population. Comparison of these subgroups showed significant between-subgroup neuroanatomical differences similar to those previously reported to distinguish children with FXS from typically developing controls (e.g., enlarged caudate). In addition to neuroanatomy, the groups showed significant differences in IQ and autism severity scores. These results suggest that despite arising from a single gene mutation, fragile X syndrome may encompass two biologically and clinically separable phenotypes. In addition, these findings underscore the potential of TDA as a powerful tool in the search for biological phenotypes of neuropsychiatric disorders. PMID:24737721

Changes in tundra pond limnology: re-sampling Alaskan ponds after 40 years.

PubMed

Lougheed, Vanessa L; Butler, Malcolm G; McEwen, Daniel C; Hobbie, John E

2011-09-01

The arctic tundra ponds at the International Biological Program (IBP) site in Barrow, AK, were studied extensively in the 1970s; however, very little aquatic research has been conducted there for over three decades. Due to the rapid climate changes already occurring in northern Alaska, identifying any changes in the ponds' structure and function over the past 30-40 years can help identify any potential climate-related impacts. Current research on the IBP ponds has revealed significant changes in the physical, chemical, and biological characteristics of these ponds over time. These changes include increased water temperatures, increased water column nutrient concentrations, the presence of at least one new chironomid species, and increased macrophyte cover. However, we have also observed significant annual variation in many measured variables and caution that this variation must be taken into account when attempting to make statements about longer-term change. The Barrow IBP tundra ponds represent one of the very few locations in the Arctic where long-term data are available on freshwater ecosystem structure and function. Continued monitoring and protection of these invaluable sites is required to help understand the implications of climate change on freshwater ecosystems in the Arctic.

Study on the effect of hydrogen addition on the variation of plasma parameters of argon-oxygen magnetron glow discharge for synthesis of TiO{sub 2} films

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

Saikia, Partha, E-mail: partha.008@gmail.com; Institute of Physics, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Santiago; Saikia, Bipul Kumar

2016-04-15

We report the effect of hydrogen addition on plasma parameters of argon-oxygen magnetron glow discharge plasma in the synthesis of H-doped TiO{sub 2} films. The parameters of the hydrogen-added Ar/O{sub 2} plasma influence the properties and the structural phases of the deposited TiO{sub 2} film. Therefore, the variation of plasma parameters such as electron temperature (T{sub e}), electron density (n{sub e}), ion density (n{sub i}), degree of ionization of Ar and degree of dissociation of H{sub 2} as a function of hydrogen content in the discharge is studied. Langmuir probe and Optical emission spectroscopy are used to characterize the plasma.more » On the basis of the different reactions in the gas phase of the magnetron discharge, the variation of plasma parameters and sputtering rate are explained. It is observed that the electron and heavy ion density decline with gradual addition of hydrogen in the discharge. Hydrogen addition significantly changes the degree of ionization of Ar which influences the structural phases of the TiO{sub 2} film.« less

Variation of turbulence in a coastal thermal internal boundary layer

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

SethuRaman, S.; Raynor, G.S.; Brown, R.M.

1981-01-01

Internal boundary layers (IBL) form when an air mass encounters a change in surface characteristics. There are essentially two types of internal boundary layers - one caused by the change in surface roughness and the other by the variation in surface heating. The former is known as the aerodynamic internal boundary layer (AIBL) and the latter the thermal internal boundary layer (TIBL). Change in shear stress generally characterizes the AIBL and change in turbulence the TIBL. Results of some observations of the vertical component of turbulence made in a coastal TIBL over Long Island, New York from 1974 to 1978more » are reported. Vertical turbulence measured by a simple sail plane variometer in a thermal internal boundary layer over Long Island with onshore flows indicates the structure to depend significantly on the land-water temperature difference. The position of the vertical velocity fluctuation maximum seems to vary from one test to another but its variation could not be correlated to other parameters due to lack of a sufficient number of tests. The structure of vertical turbulence was found to be different for sea breeze flows as compared to gradient winds.« less

Structure dependent resistivity and dielectric characteristics of tantalum oxynitride thin films produced by magnetron sputtering

NASA Astrophysics Data System (ADS)

Cristea, D.; Crisan, A.; Cretu, N.; Borges, J.; Lopes, C.; Cunha, L.; Ion, V.; Dinescu, M.; Barradas, N. P.; Alves, E.; Apreutesei, M.; Munteanu, D.

2015-11-01

The main purpose of this work is to present and to interpret the change of electrical properties of TaxNyOz thin films, produced by DC reactive magnetron sputtering. Some parameters were varied during deposition: the flow of the reactive gases mixture (N2 and O2, with a constant concentration ratio of 17:3); the substrate voltage bias (grounded, -50 V or -100 V) and the substrate (glass, (1 0 0) Si or high speed steel). The obtained films exhibit significant differences. The variation of the deposition parameters induces variations of the composition, microstructure and morphology. These differences cause variation of the electrical resistivity essentially correlated with the composition and structural changes. The gradual decrease of the Ta concentration in the films induces amorphization and causes a raise of the resistivity. The dielectric characteristics of some of the high resistance TaxNyOz films were obtained in the samples with a capacitor-like design (deposited onto high speed steel, with gold pads deposited on the dielectric TaxNyOz films). Some of these films exhibited dielectric constant values higher than those reported for other tantalum based dielectric films.

Subtelomeric Rearrangements and Copy Number Variations in People with Intellectual Disabilities

ERIC Educational Resources Information Center

Christofolini, D. M.; De Paula Ramos, M. A.; Kulikowski, L. D.; Da Silva Bellucco, F. T.; Belangero, S. I. N.; Brunoni, D.; Melaragno, M. I.

2010-01-01

Background: The most prevalent type of structural variation in the human genome is represented by copy number variations that can affect transcription levels, sequence, structure and function of genes. Method: In the present study, we used the multiplex ligation-dependent probe amplification (MLPA) technique and quantitative PCR for the detection…

The Effects of Environmental Characteristics on the Structure of Hospital Clusters.

ERIC Educational Resources Information Center

Fennell, Mary L.

1980-01-01

The population ecology view that variation in sets or clusters of organizations should be isomorphic with variation in cluster environment was used to explain structural variation among hospital clusters. Cluster differentiation seems to be casually affected by range of services, average hospital size, and the periodic closing of hospitals.…

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

PubMed

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

2015-03-01

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

Interspecific variation in mitochondrial serine transfer RNA (UCN) in Euptychiina butterflies (Lepidoptera: Satyrinae): structure and alignment.

PubMed

Marín, Mario Alejandro; López, Andrés; Uribe, Sandra Inés

2012-06-01

The nucleotide variation and structural patterns of mitochondrial RNA molecule have been proposed as useful tools in molecular systematics; however, their usefulness is always subject to a proper assessment of homology in the sequence alignment. The present study describes the secondary structure of mitochondrial tRNA for the amino acid serine (UCN) on 13 Euptychiina species and the evaluation of its potential use for evolutionary studies in this group of butterflies. The secondary structure of tRNAs showed variation among the included species except between Hermeuptychia sp1 and sp2. Variation was concentrated in the ribotimidina-pseudouridine-cystosine (TψC), dihydrouridine (DHU) and variable loops and in the DHU and TψC arms. These results suggest this region as a potential marker useful for taxonomic differentiation of species in this group and also confirm the importance of including information from the secondary structure of tRNA to optimize the alignments.

Emergence of intercolonial variation in termite shelter tube patterns and prediction of its underlying mechanism

PubMed Central

2015-01-01

Building behaviours occur in various organisms from bacteria to humans. Social insects build various structures such as large nests and underground galleries, achieved by self-organization. Structures built by social insects have recently been demonstrated to vary widely in size and shape within a species, even under the same environmental conditions. However, little is known about how intraspecific variation in structures emerges from collective behaviours. Here we show that the colony variation of structures can be generated by simply changing two behavioural parameters of group members, even with the same building algorithm. Our laboratory experiment of termite shelter tube construction demonstrated clear intercolonial variation, and a two-dimensional lattice model showed that it can be attributed to the extent of positive feedback and the number of individuals engaged in building. This study contributes to explaining the great diversity of structures emerging from collective building in social insects. PMID:26715997

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

A Variational Monte Carlo Approach to Atomic Structure

ERIC Educational Resources Information Center

Davis, Stephen L.

2007-01-01

The practicality and usefulness of variational Monte Carlo calculations to atomic structure are demonstrated. It is found to succeed in quantitatively illustrating electron shielding, effective nuclear charge, l-dependence of the orbital energies, and singlet-tripetenergy splitting and ionization energy trends in atomic structure theory.

Epigenetic variation predicts regional and local intraspecific functional diversity in a perennial herb.

PubMed

Medrano, Mónica; Herrera, Carlos M; Bazaga, Pilar

2014-10-01

The ecological significance of epigenetic variation has been generally inferred from studies on model plants under artificial conditions, but the importance of epigenetic differences between individuals as a source of intraspecific diversity in natural plant populations remains essentially unknown. This study investigates the relationship between epigenetic variation and functional plant diversity by conducting epigenetic (methylation-sensitive amplified fragment length polymorphisms, MSAP) and genetic (amplified fragment length polymorphisms, AFLP) marker-trait association analyses for 20 whole-plant, leaf and regenerative functional traits in a large sample of wild-growing plants of the perennial herb Helleborus foetidus from ten sampling sites in south-eastern Spain. Plants differed widely in functional characteristics, and exhibited greater epigenetic than genetic diversity, as shown by per cent polymorphism of MSAP fragments (92%) or markers (69%) greatly exceeding that for AFLP ones (41%). After controlling for genetic structuring and possible cryptic relatedness, every functional trait considered exhibited a significant association with at least one AFLP or MSAP marker. A total of 27 MSAP (13.0% of total) and 12 AFLP (4.4%) markers were involved in significant associations, which explained on average 8.2% and 8.0% of trait variance, respectively. Individual MSAP markers were more likely to be associated with functional traits than AFLP markers. Between-site differences in multivariate functional diversity were directly related to variation in multilocus epigenetic diversity after multilocus genetic diversity was statistically accounted for. Results suggest that epigenetic variation can be an important source of intraspecific functional diversity in H. foetidus, possibly endowing this species with the capacity to exploit a broad range of ecological conditions despite its modest genetic diversity. © 2014 John Wiley & Sons Ltd.

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

PubMed

Lazim, Raudah; Mei, Ye; Zhang, Dawei

2012-03-01

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

Ion Mobility Measurements of Multianionic Metalloporphyrin Dimers: Structural Changes Induced by Countercation Exchange

NASA Astrophysics Data System (ADS)

Schneider, Erik; Brendle, Katrina; Jäger, Patrick; Weis, Patrick; Kappes, Manfred M.

2018-04-01

We present gas-phase structures of dimers of MnIII and FeIII meso-tetra(4-sulfonatophenyl)porphyrin multianions with various amounts of sodium and hydrogen counterions. The structural assignments are achieved by combining mass spectrometry, ion mobility measurements, quantum chemical calculations, and trajectory method collision cross section calculations. For a common charge state, we observe significant topological variations in the dimer structures of [(MTPPS)2+nX](6-n)- (M=MnIII, FeIII; X=H, Na; n = 1-3) induced by replacing hydrogen counterions by sodium. For sodium, the dimer structures are much more compact, a finding that can be rationalized by the stronger interactions of the sodium cations with the anionic sulfonic acid groups of the porphyrins as compared to hydrogen. [Figure not available: see fulltext.

Normal variation in early parental sensitivity predicts child structural brain development.

PubMed

Kok, Rianne; Thijssen, Sandra; Bakermans-Kranenburg, Marian J; Jaddoe, Vincent W V; Verhulst, Frank C; White, Tonya; van IJzendoorn, Marinus H; Tiemeier, Henning

2015-10-01

Early caregiving can have an impact on brain structure and function in children. The influence of extreme caregiving experiences has been demonstrated, but studies on the influence of normal variation in parenting quality are scarce. Moreover, no studies to date have included the role of both maternal and paternal sensitivity in child brain maturation. This study examined the prospective relation between mothers' and fathers' sensitive caregiving in early childhood and brain structure later in childhood. Participants were enrolled in a population-based prenatal cohort. For 191 families, maternal and paternal sensitivity was repeatedly observed when the child was between 1 year and 4 years of age. Head circumference was assessed at 6 weeks, and brain structure was assessed using magnetic resonance imaging (MRI) measurements at 8 years of age. Higher levels of parental sensitivity in early childhood were associated with larger total brain volume (adjusted β = 0.15, p = .01) and gray matter volume (adjusted β = 0.16, p = .01) at 8 years, controlling for infant head size. Higher levels of maternal sensitivity in early childhood were associated with a larger gray matter volume (adjusted β = 0.13, p = .04) at 8 years, independent of infant head circumference. Associations with maternal versus paternal sensitivity were not significantly different. Normal variation in caregiving quality is related to markers of more optimal brain development in children. The results illustrate the important role of both mothers and fathers in child brain development. Copyright © 2015 American Academy of Child and Adolescent Psychiatry. Published by Elsevier Inc. All rights reserved.

Resolvability of regional density structure and the road to direct density inversion - a principal-component approach to resolution analysis

NASA Astrophysics Data System (ADS)

Płonka, Agnieszka; Fichtner, Andreas

2017-04-01

Lateral density variations are the source of mass transport in the Earth at all scales, acting as drivers of convective motion. However, the density structure of the Earth remains largely unknown since classic seismic observables and gravity provide only weak constraints with strong trade-offs. Current density models are therefore often based on velocity scaling, making strong assumptions on the origin of structural heterogeneities, which may not necessarily be correct. Our goal is to assess if 3D density structure may be resolvable with emerging full-waveform inversion techniques. We have previously quantified the impact of regional-scale crustal density structure on seismic waveforms with the conclusion that reasonably sized density variations within the crust can leave a strong imprint on both travel times and amplitudes, and, while this can produce significant biases in velocity and Q estimates, the seismic waveform inversion for density may become feasible. In this study we perform principal component analyses of sensitivity kernels for P velocity, S velocity, and density. This is intended to establish the extent to which these kernels are linearly independent, i.e. the extent to which the different parameters may be constrained independently. We apply the method to data from 81 events around the Iberian Penninsula, registered in total by 492 stations. The objective is to find a principal kernel which would maximize the sensitivity to density, potentially allowing for as independent as possible density resolution. We find that surface (mosty Rayleigh) waves have significant sensitivity to density, and that the trade-off with velocity is negligible. We also show the preliminary results of the inversion.

Correlation between temperature variations of static and dynamic properties in glass-forming liquids

DOE PAGES

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

2016-12-29

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.

Macrofaunal Patterns in and around du Couedic and Bonney Submarine Canyons, South Australia

PubMed Central

Dittmann, Sabine; Sorokin, Shirley J.; Hendrycks, Ed

2015-01-01

Two South Australian canyons, one shelf-incising (du Couedic) and one slope-limited (Bonney) were compared for macrofaunal patterns on the shelf and slope that spanned three water masses. It was hypothesized that community structure would (H1) significantly differ by water mass, (H2) show significant regional differences and (H3) differ significantly between interior and exterior of each canyon. Five hundred and thirty-one species of macrofauna ≥1 mm were captured at 27 stations situated in depth stratified transects inside and outside the canyons from 100 to1500 m depth. The macrofauna showed a positive relationship to depth in abundance, biomass, species richness and community composition while taxonomic distinctness and evenness remained high at all depths. Biotic variation on the shelf was best defined by variation in bottom water primary production while sediment characteristics and bottom water oxygen, temperature and nutrients defined biotic variation at greater depth. Community structure differed significantly (p<0.01) among the three water masses (shelf-flowing South Australian current, upper slope Flinders current and lower slope Antarctic Intermediate Water) (H1). Although community differences between the du Couedic and Bonney regions were marginally above significance at p = 0.05 (H2), over half of the species captured were unique to each region. This supports the evidence from fish and megafaunal distributions that the du Couedic and Bonney areas are in different bioregions. Overall, the canyon interiors were not significantly different in community composition from the exterior (H3). However, both canyons had higher abundance and/or biomass, increased species dominance, different species composition and coarser sediments near the canyon heads compared to outside the canyons at the same depth (500 m), suggestive of heightened currents within the canyons that influence community composition there. At 1000–1500 m, the canyon interiors were depauperate, typical of V-shaped canyons elsewhere. The large number of species captured, given the relatively low sampling effort and focus on the larger macrofauna, support previous studies that identify the South Australian coast as a high biodiversity area. PMID:26618354

Comparative social grooming networks in captive chimpanzees and bonobos.

PubMed

Rodrigues, Michelle A; Boeving, Emily R

2018-06-21

Despite similar dispersal patterns, models of Pan sociality emphasize sex differences in social bonding between the two species. Such disparities are attributed to hypothesized differences in environmental selective pressures that structure association patterns. However, recent research documents greater within-species variation in social bonds in both species. Here, we examine grooming networks in captive chimpanzees at the North Carolina Zoo, and captive bonobos at the Columbus Zoo. We hypothesized that male-female grooming relationships would be the strongest in both species, but that males and females of both species would not significantly differ between centrality, strength, or clustering. Via Mantel tests, we found that neither bonobos (t = - 0.070, r = - 0.009, two-tailed p = 0.942) nor chimpanzees (t = - 0.495, r = - 0.0939, two-tailed p = 0.6205) had significant differences in grooming between or within sexes. Neither species had significant sex differences in centrality, strength, or clustering. To account for idiosyncratic factors affecting grooming distribution, we examined the effect of origin, kinship, and group tenure on social network position. We found that wild-born bonobos exhibited greater eigenvector centrality (t = - 2.592, df = 9, p = 0.29) and strength (t = - 2.401; df = 9, p = 0.040), and group tenure was significantly correlated with strength (r = 0.608; N = 11, p - 0 = 0.47). None of these factors varied with social network position in chimpanzees. Our findings suggest that in captive settings, idiosyncratic factors related to individual history play a greater role in structuring social networks. Such variation may point to the behavioral flexibility inherent in fission-fusion networks, and mirror between-site variation found in wild chimpanzees. However, some idiosyncratic factors shaping captive networks may be an artifact of captivity.

Tendon material properties vary and are interdependent among turkey hindlimb muscles

PubMed Central

Matson, Andrew; Konow, Nicolai; Miller, Samuel; Konow, Pernille P.; Roberts, Thomas J.

2012-01-01

SUMMARY The material properties of a tendon affect its ability to store and return elastic energy, resist damage, provide mechanical feedback and amplify or attenuate muscle power. While the structural properties of a tendon are known to respond to a variety of stimuli, the extent to which material properties vary among individual muscles remains unclear. We studied the tendons of six different muscles in the hindlimb of Eastern wild turkeys to determine whether there was variation in elastic modulus, ultimate tensile strength and resilience. A hydraulic testing machine was used to measure tendon force during quasi-static lengthening, and a stress–strain curve was constructed. There was substantial variation in tendon material properties among different muscles. Average elastic modulus differed significantly between some tendons, and values for the six different tendons varied nearly twofold, from 829±140 to 1479±106 MPa. Tendons were stretched to failure, and the stress at failure, or ultimate tensile stress, was taken as a lower-limit estimate of tendon strength. Breaking tests for four of the tendons revealed significant variation in ultimate tensile stress, ranging from 66.83±14.34 to 112.37±9.39 MPa. Resilience, or the fraction of energy returned in cyclic length changes was generally high, and one of the four tendons tested was significantly different in resilience from the other tendons (range: 90.65±0.83 to 94.02±0.71%). An analysis of correlation between material properties revealed a positive relationship between ultimate tensile strength and elastic modulus (r2=0.79). Specifically, stiffer tendons were stronger, and we suggest that this correlation results from a constrained value of breaking strain, which did not vary significantly among tendons. This finding suggests an interdependence of material properties that may have a structural basis and may explain some adaptive responses observed in studies of tendon plasticity. PMID:22771746

Tendon material properties vary and are interdependent among turkey hindlimb muscles.

PubMed

Matson, Andrew; Konow, Nicolai; Miller, Samuel; Konow, Pernille P; Roberts, Thomas J

2012-10-15

The material properties of a tendon affect its ability to store and return elastic energy, resist damage, provide mechanical feedback and amplify or attenuate muscle power. While the structural properties of a tendon are known to respond to a variety of stimuli, the extent to which material properties vary among individual muscles remains unclear. We studied the tendons of six different muscles in the hindlimb of Eastern wild turkeys to determine whether there was variation in elastic modulus, ultimate tensile strength and resilience. A hydraulic testing machine was used to measure tendon force during quasi-static lengthening, and a stress-strain curve was constructed. There was substantial variation in tendon material properties among different muscles. Average elastic modulus differed significantly between some tendons, and values for the six different tendons varied nearly twofold, from 829±140 to 1479±106 MPa. Tendons were stretched to failure, and the stress at failure, or ultimate tensile stress, was taken as a lower-limit estimate of tendon strength. Breaking tests for four of the tendons revealed significant variation in ultimate tensile stress, ranging from 66.83±14.34 to 112.37±9.39 MPa. Resilience, or the fraction of energy returned in cyclic length changes was generally high, and one of the four tendons tested was significantly different in resilience from the other tendons (range: 90.65±0.83 to 94.02±0.71%). An analysis of correlation between material properties revealed a positive relationship between ultimate tensile strength and elastic modulus (r(2)=0.79). Specifically, stiffer tendons were stronger, and we suggest that this correlation results from a constrained value of breaking strain, which did not vary significantly among tendons. This finding suggests an interdependence of material properties that may have a structural basis and may explain some adaptive responses observed in studies of tendon plasticity.

Adaptive potential of genomic structural variation in human and mammalian evolution.

PubMed

Radke, David W; Lee, Charles

2015-09-01

Because phenotypic innovations must be genetically heritable for biological evolution to proceed, it is natural to consider new mutation events as well as standing genetic variation as sources for their birth. Previous research has identified a number of single-nucleotide polymorphisms that underlie a subset of adaptive traits in organisms. However, another well-known class of variation, genomic structural variation, could have even greater potential to produce adaptive phenotypes, due to the variety of possible types of alterations (deletions, insertions, duplications, among others) at different genomic positions and with variable lengths. It is from these dramatic genomic alterations, and selection on their phenotypic consequences, that adaptations leading to biological diversification could be derived. In this review, using studies in humans and other mammals, we highlight examples of how phenotypic variation from structural variants might become adaptive in populations and potentially enable biological diversification. Phenotypic change arising from structural variants will be described according to their immediate effect on organismal metabolic processes, immunological response and physical features. Study of population dynamics of segregating structural variation can therefore provide a window into understanding current and historical biological diversification. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Variation in Biomass Composition Components among Forage, Biomass, Sorghum-Sudangrass, and Sweet Sorghum Types

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

Stefaniak, T. R.; Dahlberg, J. A.; Bean, B. W.

2012-07-01

Alternative biomass sources must be developed if the United States is to meet the goal in the U.S. Energy Security Act of 2007 to derive 30% of its petroleum from renewable sources, and several different biomass crops are currently in development. Sorghum [Sorghum bicolor (L.) Moench] is one such crop that will be an important feedstock source for biofuel production. As composition influences productivity, there exists a need to understand the range in composition observed within the crop. The goal of this research was to assess the range in dietary fiber composition observed within different types of biomass sorghums. Amore » total of 152 sorghum samples were divided into the four end-use types of sorghum: biomass, forage, sorghum-sudangrass, and sweet. These samples were analyzed chemically using dietary fiber analysis performed at the National Renewable Energy Laboratory using published protocols. Significant variation among the groups was detected for glucan and ash. Positive and highly significant correlations were detected between structural carbohydrates in the biomass and sweet sorghums while many of these correlations were negative or not significant in the forage and sorghum-sudangrass types. In addition, a wide range of variation was present within each group indicating that there is potential to manipulate the composition of the crop.« less

Effects of life history variation on size and growth in stream-dwelling Atlantic salmon

USGS Publications Warehouse

Letcher, B.H.; Gries, G.

2003-01-01

A large size variation amongst life histories for stream-dwelling Atlantic salmon Salmo salar was found and the relative effect of life histories on size varied over time. As early as December (age 0+ years), fish that later smolted at age 2+ years were significantly larger than fish that did not smolt at age 2+ years. In contrast, there were no mass differences at age 0+ years between fish that would mature or not at age 1+ years (October). The mass differences between smolts and non-smolts persisted until smolting, and differences between mature and immature fish first appeared in May (age 1+ years). Following September (age 1+ years), there was also a significant interaction between smolting and maturity. Previously mature and immature age 2+ year smolts were not significantly different in size, but immature age 2+ year non-smolts were much lighter than mature age 2+ year non-smolts. Based on mass differences, the apparent 'decision' to smolt occurred c. 5 months before (winter, age 0+ years) the decision to mature (late spring, age 1+ years). In addition to strong seasonal growth variation, sizes of freshwater Atlantic salmon were largely structured by the complex interaction between smolt-age and maturity. ?? 2003 The fisheries Society of the British Isles.

Photometric long-term variations and superhump occurrence in the Classical Nova RR Pictoris

NASA Astrophysics Data System (ADS)

Fuentes-Morales, I.; Vogt, N.; Tappert, C.; Schmidtobreick, L.; Hambsch, F.-J.; Vučković, M.

2018-02-01

We present an analysis of all available time-resolved photometry from the literature and new light curves obtained in 2013-2014 for the old nova RR Pictoris. The well-known hump light curve phased with the orbital period reveals significant variations over the last 42 yr in shape, amplitude and other details which apparently are caused by long-term variations in the disc structure. In addition, we found evidence for the presence of superhumps in 2007, with the same period ( ˜ 9 per cent longer than the orbital period), as reported earlier by other authors from observations in 2005. Possibly, superhumps arise quickly in RR Pic, but are sporadic events, because in all the other observing runs analysed no significant superhump signal was detected. We also determined an actual version of the Stolz-Schoembs relation between superhump period and orbital period, analysing separately dwarf novae, classical novae and nova-like stars, and conclude that this relation is of general validity for all superhumpers among the cataclysmic variables (CVs), in spite of small but significant differences among the sub-types mentioned above. We emphasize the importance of such a study in context with the still open question of the interrelation between the different sub-classes of CVs, crucial for our understanding of the long-term CV evolution.

Ecology Driving Genetic Variation: A Comparative Phylogeography of Jungle Cat (Felis chaus) and Leopard Cat (Prionailurus bengalensis) in India

PubMed Central

Mukherjee, Shomita; Krishnan, Anand; Tamma, Krishnapriya; Home, Chandrima; R, Navya; Joseph, Sonia; Das, Arundhati; Ramakrishnan, Uma

2010-01-01

Background Comparative phylogeography links historical population processes to current/ecological processes through congruent/incongruent patterns of genetic variation among species/lineages. Despite high biodiversity, India lacks a phylogeographic paradigm due to limited comparative studies. We compared the phylogenetic patterns of Indian populations of jungle cat (Felis chaus) and leopard cat (Prionailurus bengalensis). Given similarities in their distribution within India, evolutionary histories, body size and habits, congruent patterns of genetic variation were expected. Methodology/Principal Findings We collected scats from various biogeographic zones in India and analyzed mtDNA from 55 jungle cats (460 bp NADH5, 141 bp cytochrome b) and 40 leopard cats (362 bp NADH5, 202 bp cytochrome b). Jungle cats revealed high genetic variation, relatively low population structure and demographic expansion around the mid-Pleistocene. In contrast, leopard cats revealed lower genetic variation and high population structure with a F ST of 0.86 between North and South Indian populations. Niche-model analyses using two approaches (BIOCLIM and MaxEnt) support absence of leopard cats from Central India, indicating a climate associated barrier. We hypothesize that high summer temperatures limit leopard cat distribution and that a rise in temperature in the peninsular region of India during the LGM caused the split in leopard cat population in India. Conclusions/Significance Our results indicate that ecological variables describing a species range can predict genetic patterns. Our study has also resolved the confusion over the distribution of the leopard cat in India. The reciprocally monophyletic island population in the South mandates conservation attention. PMID:21060831

Differential contributions of cortical thickness and surface area to trait impulsivity in healthy young adults.

PubMed

Kubera, Katharina M; Schmitgen, Mike M; Maier-Hein, Klaus H; Thomann, Philipp A; Hirjak, Dusan; Wolf, Robert C

2018-05-08

Impulsivity is an essential human personality trait and highly relevant for the development of several mental disorders. There is evidence that impulsivity is heritable, yet little is known about neural correlates reflecting early brain development. Here, we address the question whether motor, attentional and non-planning components, as reflected by the Barratt Impulsiveness Scale (BIS-11), are distinctly associated with cortical thickness and surface area variations in young healthy individuals. We investigated cortical thickness and surface area in 54 healthy volunteers (m/f = 30%/70%; age mean/SD = 24.9/4.02) using structural magnetic resonance imaging at 3 T together with surface-based analysis techniques. Impulsivity was examined on the Barratt impulsiveness scale (BIS-11) and related to the two distinct cortical measurements. Higher BIS-11 total scores were negatively associated with cortical thickness variations in the left lingual gyrus, left superior temporal gyrus, right cuneus, and right superior parietal gyrus (p<0.05 cluster-wise probability [CWP] corrected). Higher BIS-11 nonplanning scores were negatively associated with cortical thickness variations in bilateral pericalcarine gyrus (p<0.05 CWP corr.). In the orbitofrontal cortex motor impulsivity associated cortical thickness differs significantly between male and female. These data suggest distinct neurodevelopmental trajectories underlying impulsivity in healthy subjects. Impulsivity total scores appear to be specifically related to cortical thickness variations, in contrast to variations of cortical surface area. Furthermore, our findings underscores the importance of better characterizing gender-specific structural correlates of impulsivity. Copyright © 2018. Published by Elsevier B.V.

Environmental and genetic correlates of allocation to sexual reproduction in the circumpolar plant Bistorta vivipara.

PubMed

Bills, John W; Roalson, Eric H; Busch, Jeremiah W; Eidesen, Pernille B

2015-07-01

• Sexual reproduction often requires more energy and time than clonal reproduction. In marginal arctic conditions, species that can reproduce both sexually and clonally dominate. Plants with this capacity may thrive because they can alter reproduction depending on environmental conditions. Bistorta vivipara is a circumpolar herb that predominately reproduces clonally, but certain environmental conditions promote higher investment in flowers (and possible sexual reproduction). Despite largely reproducing clonally, the herb has high levels of genetic variation, and the processes underlying this paradoxical pattern of variation remain unclear. Here we identified environmental factors associated with sexual investment and examined whether sexual reproduction is associated with higher levels of genetic variation.• We sampled 20 populations of B. vivipara across the high Arctic archipelago of Svalbard. In each population, we measured reproductive traits, environmental variables, and collected samples for genetic analyses. These samples permitted hypotheses to be tested regarding sexual investment and ecological and genetic correlates.• Increased soil nitrogen and organic matter content and decreased elevation were positively associated with investment in flowers. Increased investment in flowers significantly correlated with more genotypes per population. Linkage disequilibrium was consistent with predominant clonality, but several populations showed higher genetic variation and lower differentiation than expected. There was no geographical genetic structure.• In B. vivipara, sexual investment is positively associated with habitat quality. Bistorta vivipara predominantly reproduces clonally, but occasional outcrossing, efficient clonal reproduction, and dispersal by bulbils can explain the considerable genetic variation and weak genetic structure in B. vivipara. © 2015 Botanical Society of America, Inc.

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.

Evaluation of the usefulness of three-dimensional optical coherence tomography in a guinea pig model of endolymphatic hydrops induced by surgical obliteration of the endolymphatic duct

NASA Astrophysics Data System (ADS)

Cho, Nam Hyun; Lee, Jang Woo; Cho, Jin-ho; Kim, Jeehyun; Jang, Jeong Hun; Jung, Woonggyu

2015-03-01

Optical coherence tomography (OCT) has advanced significantly over the past two decades and is currently used extensively to monitor the internal structures of organs, particularly in ophthalmology and dermatology. We used ethylenediamine tetra-acetic acid (EDTA) to decalcify the bony walls of the cochlea and investigated the inner structures by deep penetration of light into the cochlear tissue using OCT on a guinea pig model of endolymphatic hydrops (EH), induced by surgical obliteration of the endolymphatic duct. The structural and functional changes associated with EH were identified using OCT and auditory brainstem response tests, respectively. We also evaluated structural alterations in the cochlea using three-dimensional reconstruction of the OCT images, which clearly showed physical changes in the cochlear structures. Furthermore, we found significant anatomical variations in the EH model and conducted graphical analysis by strial atrophy for comparison. The physical changes included damage to and flattening of the organ of Corti-evidence of Reissner's membrane distention-and thinning of the lateral wall. These results indicate that observation of EDTA-decalcified cochlea using OCT is significant in examination of gradual changes in the cochlear structures that are otherwise not depicted by hematoxylin and eosin staining.

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

PubMed

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

2014-01-01

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

Investigating the sources of variability in the dynamic response of built-up structures through a linear analytical model

NASA Astrophysics Data System (ADS)

Abolfathi, Ali; O'Boy, Dan J.; Walsh, Stephen J.; Fisher, Stephen A.

2017-01-01

It is well established that the dynamic response of a number of nominally identical built-up structures are often different and the variability increases with increasing complexity of the structure. Furthermore, the effects of the different parameters, for example the variation in joint locations or the range of the Young's modulus, on the dynamic response of the system are not the same. In this paper, the effects of different material and geometric parameters on the variability of a vibration transfer function are compared using an analytical model of a simple linear built-up structure that consist of two plates connected by a single mount. Similar results can be obtained if multiple mounts are used. The scope of this paper is limited to a low and medium frequency range where usually deterministic models are used for vibrational analysis. The effect of the mount position and also the global variation in the properties of the plate, such as modulus of elasticity or thickness, is higher on the variability of vibration transfer function than the effect of the mount properties. It is shown that the vibration transfer function between the plates is independent of the mount property if a stiff enough mount with a small mass is implemented. For a soft mount, there is a direct relationship between the mount impedance and the variation in the vibration transfer function. Furthermore, there are a range of mount stiffnesses between these two extreme cases at which the vibration transfer function is more sensitive to changes in the stiffness of the mount than when compared to a soft mount. It is found that the effect of variation in the mount damping and the mount mass on the variability is negligible. Similarly, the effect of the plate damping on the variability is not significant.

Genetic structure of coexisting wild and managed agave populations: implications for the evolution of plants under domestication

PubMed Central

Figueredo, Carmen Julia; Casas, Alejandro; González-Rodríguez, Antonio; Nassar, Jafet M.; Colunga-GarcíaMarín, Patricia; Rocha-Ramírez, Víctor

2015-01-01

Domestication is a continuous evolutionary process guided by humans. This process leads to divergence in characteristics such as behaviour, morphology or genetics, between wild and managed populations. Agaves have been important resources for Mesoamerican peoples since prehistory. Some species are domesticated and others vary in degree of domestication. Agave inaequidens Koch is used in central Mexico to produce mescal, and a management gradient from gathered wild and silvicultural populations, as well as cultivated plantations, has been documented. Significant morphological differences were reported among wild and managed populations, and a high phenotypic variation in cultivated populations composed of plants from different populations. We evaluated levels of genetic diversity and structure associated with management, hypothesizing that high morphological variation would be accompanied by high genetic diversity in populations with high gene flow and low genetic structure among managed and unmanaged populations. Wild, silvicultural and cultivated populations were studied, collecting tissue of 19–30 plants per population. Through 10 nuclear microsatellite loci, we compared population genetic parameters. We analysed partition of variation associated with management categories to estimate gene flow among populations. Agave inaequidens exhibits high levels of genetic diversity (He = 0.707) and moderate genetic structure (FST = 0.112). No differences were found in levels of genetic diversity among wild (He = 0.704), silviculturally managed (He = 0.733) and cultivated (He = 0.698) populations. Bayesian analysis indicated that five genetic clusters best fit the data, with genetic groups corresponding to habitats where populations grow rather than to management. Migration rates ranged from zero between two populations to markedly high among others (M = 0.73–35.25). Natural mechanisms of gene flow and the dynamic management of agave propagules among populations favour gene flow and the maintenance of high levels of variation within all populations. The slight differentiation associated with management indicates that domestication is in an incipient stage. PMID:26433707

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

Population structure and genetic diversity of the amphiatlantic haploid peatmoss Sphagnum affine (Sphagnopsida).

PubMed

Thingsgaard, K

2001-10-01

Nineteen populations of Sphagnum affine were included in a study of genetic diversity and structure in fragmented and less fragmented landscapes, and differentiation at intercontinental and three regional levels. Isozyme electrophoresis of eight enzyme systems revealed 12 variable loci, which could be used for haplotype identification. A hierachical analysis of variance (AMOVA) revealed no significant intercontinental differentiation, and very limited differentiation among European regions. A trend of decreasing diversity with increasing latitude was apparent. Gametic phase disequilibria was high, suggesting nonrandom mating and regionally high incidences of inbreeding. The partitioning of genetic variation within and among populations in each region varied among regions, the northernmost populations having 86% of the total variation among populations, the southernmost in Scandinavia having 25% of the variation among populations, whereas the American populations displayed 89% of the variation within populations. Fifteen alleles at eight loci occurred in the U.S.A. which were not encountered in Europe, whereas only three European alleles at one locus in three populations were not encountered in U.S.A. The differences in diversity between North America and Europe may result from loss of genetic diversity caused by founder effects during postglacial recolonization of northern Europe. In Europe, the main mountain ranges extend E-W, posing severe barriers to northwards migration of lowland species, compared to the N-S trend of mountain ranges in North America. The decline in genetic diversity and increase in population differentiation and gametic phase disequilibria towards the north in Scandinavia may be caused by a series of founder effects during postglacial migration. These may have corresponded to minor climatic oscillations that influenced the migration front/leading edge in the suboceanic lowlands of Norway. According to this model random genetic drift will be an increasingly important structuring factor with latitude.

Molecular modelling studies of kdr mutations in voltage gated sodium channel revealed significant conformational variations contributing to insecticide resistance.

PubMed

Yellapu, Nanda Kumar; Gopal, Jeyakodi; Kasinathan, Gunasekaran; Purushothaman, Jambulingam

2018-06-01

Voltage gated sodium channels (VGSC) of mosquito vectors are the primary targets of dichlorodiphenyltrichloroethane (DDT) and other synthetic pyrethroids used in public health programmes. The knockdown resistant (kdr) mutations in VGSC are associated with the insecticide resistance especially in Anophelines. The present study is aimed to emphasize and demarcate the impact of three kdr-mutations such as L1014S, L1014F and L1014H on insecticide resistance. The membrane model of sodium transport domain of VGSC (STD-VGSC) was constructed using de novo approach based on domain and trans-membrane predictions. The comparative molecular modelling studies of wild type and mutant models of STD-VGSC revealed that L1014F mutant was observed to be near native to the wild type model in all the respects, but, L1014S and L1014H mutations showed drastic variations in the energy levels, root mean square fluctuations (RMSF) that resulted in conformational variations. The predicted binding sites also showed variable cavity volumes and RMSF in L1014S and L1014H mutants. Further, DDT also found be bound in near native manner to wild type in L1014F mutant and with variable orientation and affinities in L1014S and L1014H mutants. The variations and fluctuations observed in mutant structures explained that each mutation has its specific impact on the conformation of VGSC and its binding with DDT. The study provides new insights into the structure-function-correlations of mutant STD-VGSC structures and demonstrates the role and effects of kdr mutations on insecticide resistance in mosquito vectors.

Ontogenetic variation of heritability and maternal effects in yellow-bellied marmot alarm calls.

PubMed

Blumstein, Daniel T; Nguyen, Kathy T; Martin, Julien G A

2013-05-07

Individuals of many species produce distinctive vocalizations that may relay potential information about the signaller. The alarm calls of some species have been reported to be individually specific, and this distinctiveness may allow individuals to access the reliability or kinship of callers. While not much is known generally about the heritability of mammalian vocalizations, if alarm calls were individually distinctive to permit kinship assessment, then call structure should be heritable. Here, we show conclusively for the first time that alarm call structure is heritable. We studied yellow-bellied marmots (Marmota flaviventris) and made nine quantitative measurements of their alarm calls. With a known genealogy, we used the animal model (a statistical technique) to estimate alarm call heritability. In juveniles, only one of the measured variables had heritability significantly different from zero; however, most variables had significant maternal environmental effects. By contrast, yearlings and adults had no significant maternal environmental effects, but the heritability of nearly all measured variables was significantly different from zero. Some, but not all of these heritable effects were significantly different across age classes. The presence of significantly non-zero maternal environmental effects in juveniles could reflect the impact of maternal environmental stresses on call structure. Regardless of this mechanism, maternal environmental effects could permit kinship recognition in juveniles. In older animals, the substantial genetic basis of alarm call structure suggests that calls could be used to assess kinship and, paradoxically, might also suggest a role of learning in call structure.

Ontogenetic variation of heritability and maternal effects in yellow-bellied marmot alarm calls

PubMed Central

Blumstein, Daniel T.; Nguyen, Kathy T.; Martin, Julien G. A.

2013-01-01

Individuals of many species produce distinctive vocalizations that may relay potential information about the signaller. The alarm calls of some species have been reported to be individually specific, and this distinctiveness may allow individuals to access the reliability or kinship of callers. While not much is known generally about the heritability of mammalian vocalizations, if alarm calls were individually distinctive to permit kinship assessment, then call structure should be heritable. Here, we show conclusively for the first time that alarm call structure is heritable. We studied yellow-bellied marmots (Marmota flaviventris) and made nine quantitative measurements of their alarm calls. With a known genealogy, we used the animal model (a statistical technique) to estimate alarm call heritability. In juveniles, only one of the measured variables had heritability significantly different from zero; however, most variables had significant maternal environmental effects. By contrast, yearlings and adults had no significant maternal environmental effects, but the heritability of nearly all measured variables was significantly different from zero. Some, but not all of these heritable effects were significantly different across age classes. The presence of significantly non-zero maternal environmental effects in juveniles could reflect the impact of maternal environmental stresses on call structure. Regardless of this mechanism, maternal environmental effects could permit kinship recognition in juveniles. In older animals, the substantial genetic basis of alarm call structure suggests that calls could be used to assess kinship and, paradoxically, might also suggest a role of learning in call structure. PMID:23466987

Marine Magnetic Anomalies, Oceanic Crust Magnetization, and Geomagnetic Time Variations

NASA Astrophysics Data System (ADS)

Dyment, J.; Arkani-Hamed, J.

2005-12-01

Since the classic paper of Vine and Matthews (Nature, 1963), marine magnetic anomalies are commonly used to date the ocean floor through comparison with the geomagnetic polarity time scale and proper identification of reversal sequences. As a consequence, the classical model of rectangular prisms bearing a normal / reversed magnetization has been dominant in the literature for more than 40 years. Although the model explains major characteristics of the sea-surface magnetic anomalies, it is contradicted by (1) recent advances on the geophysical and petrologic structure of the slow-spreading oceanic crust, and (2) the observation of short-term geomagnetic time variations, both of which are more complex than assumed in the classical model. Marine magnetic anomalies may also provide information on the magnetization of the oceanic crust as well as short-term temporal fluctuations of the geomagnetic field. The "anomalous skewness", a residual phase once the anomalies have been reduced to the pole, has been interpreted either in terms of geomagnetic field variations or crustal structure. The spreading-rate dependence of anomalous skewness rules out the geomagnetic hypothesis and supports a spreading-rate dependent magnetic structure of the oceanic crust, with a basaltic layer accounting for most of the anomalies at fast spreading rates and an increasing contribution of the deeper layers with decreasing spreading rate. The slow cooling of the lower crust and uppermost mantle and serpentinization, a low temperature alteration process which produces magnetite, are the likely cause of this contribution, also required to account for satellite magnetic anomalies over oceanic areas. Moreover, the "hook shape" of some sea-surface anomalies favors a time lag in the magnetization acquisition processes between upper and lower magnetic layers: extrusive basalt acquires a thermoremanent magnetization as soon as emplaced, whereas the underlying peridotite and olivine gabbro cool slowly and pass through serpentinization to bear a significant magnetization. Our analysis of the amplitude of Anomaly 25 shows a sharp threshold at the spreading rate of 30 km/Ma, which corresponds to the transition between oceanic lithosphere built at axial domes and axial valleys. The twice lower amplitudes are in agreement with a much disrupted and altered basaltic layer at slow rates and a significant contribution from the deeper layers. Oceanic lithosphere created at fast and slow spreading rates therefore exhibits contrasted magnetic structures. High resolution magnetic anomaly measurements carried out with deep tows and submersibles show that the magmatic (fast spreading and parts of the slow spreading) crust is a good recorder of short-term geomagnetic time variations, such as short polarity intervals, excursions, or paleointensity variations. Surface and deep-sea magnetic anomalies therefore help to confirm or infirm geomagnetic findings obtained by other means. Many excursions and paleointensity variations within Brunhes and Matuyama periods are confirmed, but the "saw tooth pattern" inferred from sediment cores - a possible candidate to explain the anomalous skewness - is not, which suggests a bias in the sedimentary approach.

Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm.

PubMed

Yu, Isseki; Mori, Takaharu; Ando, Tadashi; Harada, Ryuhei; Jung, Jaewoon; Sugita, Yuji; Feig, Michael

2016-11-01

Biological macromolecules function in highly crowded cellular environments. The structure and dynamics of proteins and nucleic acids are well characterized in vitro, but in vivo crowding effects remain unclear. Using molecular dynamics simulations of a comprehensive atomistic model cytoplasm we found that protein-protein interactions may destabilize native protein structures, whereas metabolite interactions may induce more compact states due to electrostatic screening. Protein-protein interactions also resulted in significant variations in reduced macromolecular diffusion under crowded conditions, while metabolites exhibited significant two-dimensional surface diffusion and altered protein-ligand binding that may reduce the effective concentration of metabolites and ligands in vivo. Metabolic enzymes showed weak non-specific association in cellular environments attributed to solvation and entropic effects. These effects are expected to have broad implications for the in vivo functioning of biomolecules. This work is a first step towards physically realistic in silico whole-cell models that connect molecular with cellular biology.

Environmental drivers of heterogeneity in the trophic-functional structure of protozoan communities during an annual cycle in a coastal ecosystem.

PubMed

Xu, Guangjian; Yang, Eun Jin; Xu, Henglong

2017-08-15

Trophic-functional groupings are an important biological trait to summarize community structure in functional space. The heterogeneity of the tropic-functional pattern of protozoan communities and its environmental drivers were studied in coastal waters of the Yellow Sea during a 1-year cycle. Samples were collected using the glass slide method at four stations within a water pollution gradient. A second-stage matrix-based analysis was used to summarize spatial variation in the annual pattern of the functional structure. A clustering analysis revealed significant variability in the trophic-functional pattern among the four stations during the 1-year cycle. The heterogeneity in the trophic-functional pattern of the communities was significantly related to changes in environmental variables, particularly ammonium-nitrogen and nitrates, alone or in combination with dissolved oxygen. These results suggest that the heterogeneity in annual patterns of protozoan trophic-functional structure may reflect water quality status in coastal ecosystems. Copyright © 2017. Published by Elsevier Ltd.

The Geography of Sexual Orientation: Structural Stigma and Sexual Attraction, Behavior, and Identity Among Men Who Have Sex with Men Across 38 European Countries.

PubMed

Pachankis, John E; Hatzenbuehler, Mark L; Mirandola, Massimo; Weatherburn, Peter; Berg, Rigmor C; Marcus, Ulrich; Schmidt, Axel J

2017-07-01

While the prevalence of sexual identities and behaviors of men who have sex with men (MSM) varies across countries, no study has examined country-level structural stigma toward sexual minorities as a correlate of this variation. Drawing on emerging support for the context-dependent nature of MSM's open sexual self-identification cross-nationally, we examined country-level structural stigma as a key correlate of the geographic variation in MSM's sexual attraction, behavior, and identity, and concordance across these factors. Data come from the European MSM Internet Survey, a multi-national dataset containing a multi-component assessment of sexual orientation administered across 38 European countries (N = 174,209). Country-level stigma was assessed using a combination of national laws and policies affecting sexual minorities and a measure of attitudes toward sexual minorities held by the citizens of each country. Results demonstrate that in more stigmatizing countries, MSM were significantly more likely to report bisexual/heterosexual attractions, behaviors, and identities, and significantly less likely to report concordance across these factors, than in less stigmatizing countries. Settlement size moderated associations between country-level structural stigma and odds of bisexual/heterosexual attraction and behavior, such that MSM living in sparsely populated locales within high-structural stigma countries were the most likely to report bisexual or heterosexual behaviors and attractions. While previous research has demonstrated associations between structural stigma and adverse physical and mental health outcomes among sexual minorities, this study was the first to show that structural stigma was also a key correlate not only of sexual orientation identification, but also of MSM's sexual behavior and even attraction. Findings have implications for understanding the ontology of MSM's sexuality and suggest that a comprehensive picture of MSM's sexuality will come from attending to the local contexts surrounding this important segment of the global population.

Microsatellite and mtDNA analysis of lake trout, Salvelinus namaycush, from Great Bear Lake, Northwest Territories: impacts of historical and contemporary evolutionary forces on Arctic ecosystems

PubMed Central

Harris, Les N; Howland, Kimberly L; Kowalchuk, Matthew W; Bajno, Robert; Lindsay, Melissa M; Taylor, Eric B

2013-01-01

Resolving the genetic population structure of species inhabiting pristine, high latitude ecosystems can provide novel insights into the post-glacial, evolutionary processes shaping the distribution of contemporary genetic variation. In this study, we assayed genetic variation in lake trout (Salvelinus namaycush) from Great Bear Lake (GBL), NT and one population outside of this lake (Sandy Lake, NT) at 11 microsatellite loci and the mtDNA control region (d-loop). Overall, population subdivision was low, but significant (global FST θ = 0.025), and pairwise comparisons indicated that significance was heavily influenced by comparisons between GBL localities and Sandy Lake. Our data indicate that there is no obvious genetic structure among the various basins within GBL (global FST = 0.002) despite the large geographic distances between sampling areas. We found evidence of low levels of contemporary gene flow among arms within GBL, but not between Sandy Lake and GBL. Coalescent analyses suggested that some historical gene flow occurred among arms within GBL and between GBL and Sandy Lake. It appears, therefore, that contemporary (ongoing dispersal and gene flow) and historical (historical gene flow and large founding and present-day effective population sizes) factors contribute to the lack of neutral genetic structure in GBL. Overall, our results illustrate the importance of history (e.g., post-glacial colonization) and contemporary dispersal ecology in shaping genetic population structure of Arctic faunas and provide a better understanding of the evolutionary ecology of long-lived salmonids in pristine, interconnected habitats. PMID:23404390

Microsatellite and mtDNA analysis of lake trout, Salvelinus namaycush, from Great Bear Lake, Northwest Territories: impacts of historical and contemporary evolutionary forces on Arctic ecosystems.

PubMed

Harris, Les N; Howland, Kimberly L; Kowalchuk, Matthew W; Bajno, Robert; Lindsay, Melissa M; Taylor, Eric B

2012-01-01

Resolving the genetic population structure of species inhabiting pristine, high latitude ecosystems can provide novel insights into the post-glacial, evolutionary processes shaping the distribution of contemporary genetic variation. In this study, we assayed genetic variation in lake trout (Salvelinus namaycush) from Great Bear Lake (GBL), NT and one population outside of this lake (Sandy Lake, NT) at 11 microsatellite loci and the mtDNA control region (d-loop). Overall, population subdivision was low, but significant (global F(ST) θ = 0.025), and pairwise comparisons indicated that significance was heavily influenced by comparisons between GBL localities and Sandy Lake. Our data indicate that there is no obvious genetic structure among the various basins within GBL (global F(ST) = 0.002) despite the large geographic distances between sampling areas. We found evidence of low levels of contemporary gene flow among arms within GBL, but not between Sandy Lake and GBL. Coalescent analyses suggested that some historical gene flow occurred among arms within GBL and between GBL and Sandy Lake. It appears, therefore, that contemporary (ongoing dispersal and gene flow) and historical (historical gene flow and large founding and present-day effective population sizes) factors contribute to the lack of neutral genetic structure in GBL. Overall, our results illustrate the importance of history (e.g., post-glacial colonization) and contemporary dispersal ecology in shaping genetic population structure of Arctic faunas and provide a better understanding of the evolutionary ecology of long-lived salmonids in pristine, interconnected habitats.

Comparative interactomics provides evidence for functional specialization of the nuclear pore complex.

PubMed

Obado, Samson O; Field, Mark C; Rout, Michael P

2017-07-04

The core architecture of the eukaryotic cell was established well over one billion years ago, and is largely retained in all extant lineages. However, eukaryotic cells also possess lineage-specific features, frequently keyed to specific functional requirements. One quintessential core eukaryotic structure is the nuclear pore complex (NPC), responsible for regulating exchange of macromolecules between the nucleus and cytoplasm as well as acting as a nuclear organizational hub. NPC architecture has been best documented in one eukaryotic supergroup, the Opisthokonts (e.g. Saccharomyces cerevisiae and Homo sapiens), which although compositionally similar, have significant variations in certain NPC subcomplex structures. The variation of NPC structure across other taxa in the eukaryotic kingdom however, remains poorly understood. We explored trypanosomes, highly divergent organisms, and mapped and assigned their NPC proteins to specific substructures to reveal their NPC architecture. We showed that the NPC central structural scaffold is conserved, likely across all eukaryotes, but more peripheral elements can exhibit very significant lineage-specific losses, duplications or other alterations in their components. Amazingly, trypanosomes lack the major components of the mRNA export platform that are asymmetrically localized within yeast and vertebrate NPCs. Concomitant with this, the trypanosome NPC is ALMOST completely symmetric with the nuclear basket being the only major source of asymmetry. We suggest these features point toward a stepwise evolution of the NPC in which a coating scaffold first stabilized the pore after which selective gating emerged and expanded, leading to the addition of peripheral remodeling machineries on the nucleoplasmic and cytoplasmic sides of the pore.

Numerical Cerebrospinal System Modeling in Fluid-Structure Interaction.

PubMed

Garnotel, Simon; Salmon, Stéphanie; Balédent, Olivier

2018-01-01

Cerebrospinal fluid (CSF) stroke volume in the aqueduct is widely used to evaluate CSF dynamics disorders. In a healthy population, aqueduct stroke volume represents around 10% of the spinal stroke volume while intracranial subarachnoid space stroke volume represents 90%. The amplitude of the CSF oscillations through the different compartments of the cerebrospinal system is a function of the geometry and the compliances of each compartment, but we suspect that it could also be impacted be the cardiac cycle frequency. To study this CSF distribution, we have developed a numerical model of the cerebrospinal system taking into account cerebral ventricles, intracranial subarachnoid spaces, spinal canal and brain tissue in fluid-structure interactions. A numerical fluid-structure interaction model is implemented using a finite-element method library to model the cerebrospinal system and its interaction with the brain based on fluid mechanics equations and linear elasticity equations coupled in a monolithic formulation. The model geometry, simplified in a first approach, is designed in accordance with realistic volume ratios of the different compartments: a thin tube is used to mimic the high flow resistance of the aqueduct. CSF velocity and pressure and brain displacements are obtained as simulation results, and CSF flow and stroke volume are calculated from these results. Simulation results show a significant variability of aqueduct stroke volume and intracranial subarachnoid space stroke volume in the physiological range of cardiac frequencies. Fluid-structure interactions are numerous in the cerebrospinal system and difficult to understand in the rigid skull. The presented model highlights significant variations of stroke volumes under cardiac frequency variations only.

Comparative genetic structure between Sedum ussuriense and S. kamtschaticum (Crassulaceae), two stonecrops co-occurring on rocky cliffs.

PubMed

Chung, Mi Yoon; López-Pujol, Jordi; Chung, Myong Gi

2014-06-01

• Premise of the study: Geographic isolation due to discontinuities of suitable habitat may have significant effects on the genetic structure of plant populations. Even within a few kilometers, physical barriers to gene flow may lead to considerable genetic differentiation among populations.• Methods: Sedum ussuriense is a boreal species that in Korea occurs only in four valleys separated by mountain ranges in Juwangsan National Park and its vicinity (a range of ∼15 km). Its congener S. kamtschaticum, by contrast, co-occurs in the four valleys but also on the intervening mountains. Using 12 allozyme loci, we comparatively assessed genetic variability and structure in 12 population pairs of the two stonecrops.• Key results: While we found high and comparable levels of within-population genetic variation for the two species, among-population divergence was significantly higher in S. ussuriense (F ST = 0.261 vs. F ST = 0.165). Sedum ussuriense also showed a much higher percentage of among-valley variation (19%) than S. kamtschaticum (4%).• Conclusions: High levels of genetic diversity in the two Sedum species are consistent with the previous hypothesis that mountains of the Korean Peninsula served as glacial refugia for many boreal species. Given that the two congeners have similar life-history traits, the lower among-population differentiation in S. kamtschaticum is attributable to its higher abundance and more continuous distribution in the study area. This study confirms the central role of geographic isolation in the genetic structure of plant species even at very small scales. © 2014 Botanical Society of America, Inc.

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.

Significant demographic and fine-scale genetic structure in expanding and senescing populations of the terrestrial orchid Cymbidium goeringii (Orchidaceae).

PubMed

Chung, Mi Yoon; Nason, John D; Chung, Myong Gi

2011-12-01

Fine-scale genetic structure (FSGS) in plants is influenced by variation in spatial and temporal demographic processes. To determine how demographic structure and FSGS change with stages of population succession, we studied replicate expanding and senescing populations of the Asian terrestrial orchid Cymbidium goeringii. We used spatial autocorrelation methods (O-ring and kinship statistics) to quantify spatial demographic structure and FSGS in two expanding and two senescing populations, also measuring genetic diversity and inbreeding in each. All populations exhibited significant aggregation of individuals and FSGS at short spatial scales. In expanding populations, this finding was associated with high recruitment rates, suggesting restricted seed dispersal. In senescing populations, recruitment was minimal, suggesting alternative mechanisms of aggregation, perhaps including spatial associations with mycorrhizal fungi. All populations had significant evidence of genetic bottlenecks, and inbreeding levels were consistently high. Our results indicate that different successional stages can generate similar patterns of spatial demographic and genetic structure, but as a consequence of different processes. These results contrast with the only other study of senescence effects on population genetic structure in an herbaceous perennial, which found little to no FSGS in senescing populations. With the exception of populations subject to mass collection by orchid sellers, significant FSGS is characteristic of the 16 terrestrial orchid species examined to date. From a conservation perspective, this result suggests that inference of orchid population history will benefit from analyses of both FSGS and demographic structure in combination with other ecological field data.

Bulk and interfacial structures of reline deep eutectic solvent: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Kaur, Supreet; Sharma, Shobha; Kashyap, Hemant K.

2017-11-01

We apply all-atom molecular dynamics simulations to describe the bulk morphology and interfacial structure of reline, a deep eutectic solvent comprising choline chloride and urea in 1:2 molar ratio, near neutral and charged graphene electrodes. For the bulk phase structural investigation, we analyze the simulated real-space radial distribution functions, X-ray/neutron scattering structure functions, and their partial components. Our study shows that both hydrogen-bonding and long-range correlations between different constituents of reline play a crucial role to lay out the bulk structure of reline. Further, we examine the variation of number density profiles, orientational order parameters, and electrostatic potentials near the neutral and charged graphene electrodes with varying electrode charge density. The present study reveals the presence of profound structural layering of not only the ionic components of reline but also urea near the electrodes. In addition, depending on the electrode charge density, the choline ions and urea molecules render different orientations near the electrodes. The simulated number density and electrostatic potential profiles for reline clearly show the presence of multilayer structures up to a distance of 1.2 nm from the respective electrodes. The observation of positive values of the surface potential at zero charge indicates the presence of significant nonelectrostatic attraction between the choline cation and graphene electrode. The computed differential capacitance (Cd) for reline exhibits an asymmetric bell-shaped curve, signifying different variation of Cd with positive and negative surface potentials.

Bulk and interfacial structures of reline deep eutectic solvent: A molecular dynamics study.

PubMed

Kaur, Supreet; Sharma, Shobha; Kashyap, Hemant K

2017-11-21

We apply all-atom molecular dynamics simulations to describe the bulk morphology and interfacial structure of reline, a deep eutectic solvent comprising choline chloride and urea in 1:2 molar ratio, near neutral and charged graphene electrodes. For the bulk phase structural investigation, we analyze the simulated real-space radial distribution functions, X-ray/neutron scattering structure functions, and their partial components. Our study shows that both hydrogen-bonding and long-range correlations between different constituents of reline play a crucial role to lay out the bulk structure of reline. Further, we examine the variation of number density profiles, orientational order parameters, and electrostatic potentials near the neutral and charged graphene electrodes with varying electrode charge density. The present study reveals the presence of profound structural layering of not only the ionic components of reline but also urea near the electrodes. In addition, depending on the electrode charge density, the choline ions and urea molecules render different orientations near the electrodes. The simulated number density and electrostatic potential profiles for reline clearly show the presence of multilayer structures up to a distance of 1.2 nm from the respective electrodes. The observation of positive values of the surface potential at zero charge indicates the presence of significant nonelectrostatic attraction between the choline cation and graphene electrode. The computed differential capacitance (C d ) for reline exhibits an asymmetric bell-shaped curve, signifying different variation of C d with positive and negative surface potentials.

Non-linear analysis and the design of Pumpkin Balloons: stress, stability and viscoelasticity

NASA Astrophysics Data System (ADS)

Rand, J. L.; Wakefield, D. S.

Tensys have a long-established background in the shape generation and load analysis of architectural stressed membrane structures Founded upon their inTENS finite element analysis suite these activities have broadened to encompass lighter than air structures such as aerostats hybrid air-vehicles and stratospheric balloons Winzen Engineering couple many years of practical balloon design and fabrication experience with both academic and practical knowledge of the characterisation of the non-linear viscoelastic response of the polymeric films typically used for high-altitude scientific balloons Both companies have provided consulting services to the NASA Ultra Long Duration Balloon ULDB Program Early implementations of pumpkin balloons have shown problems of geometric instability characterised by improper deployment and these difficulties have been reproduced numerically using inTENS The solution lies in both the shapes of the membrane lobes and also the need to generate a biaxial stress field in order to mobilise in-plane shear stiffness Balloons undergo significant temperature and pressure variations in flight The different thermal characteristics between tendons and film can lead to significant meridional stress Fabrication tolerances can lead to significant local hoop stress concentrations particularly adjacent to the base and apex end fittings The non-linear viscoelastic response of the envelope film acts positively to help dissipate stress concentrations However creep over time may produce lobe geometry variations that may

The ethical implications and religious significance of organ transplantation payment systems.

PubMed

Smith, Hunter Jackson

2016-03-01

One of the more polarizing policies proposed to alleviate the organ shortage is financial payment of donors in return for organs. A priori and empirical investigation concludes that such systems are ethically inadequate. A new methodological approach towards policy formation and implementation is proposed which places ethical concerns at its core. From a hypothetical secular origin, the optimal ethical policy structure concerning organ donation is derived. However, when applied universally, it does not yield ideal results for every culture and society due to region-specific variation. Since religion holds significant influence in the organ donation debate, three religions-Catholicism, Islam, and Shinto-were examined in order to illustrate this variation. Although secular ethical concerns should rest at the core of policy construction, certain region-specific contexts require cultural and religious competence and necessitate the adjustment of the optimal template policy accordingly to yield the best moral and practical results.

Statistical Simulation of the Performance and Degradation of a PEMFC Membrane Electrode Assembly

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

Harvey, David; Bellemare-Davis, Alexander; Karan, Kunal

2012-07-01

A 1-D MEA Performance model was developed that considered transport of liquid water, agglomerate catalyst structure, and the statistical variation of the MEA characteristic parameters. The model was validated against a low surface area carbon supported catalyst across various platinum loadings and operational conditions. The statistical variation was found to play a significant role in creating noise in the validation data and that there was a coupling effect between movement in material properties with liquid water transport. Further, in studying the low platinum loaded catalyst layers it was found that liquid water played a significant role in the increasing themore » overall transport losses. The model was then further applied to study platinum dissolution via potential cycling accelerated stress tests, in which the platinum was found to dissolve nearest the membrane effectively resulting in reaction distribution shifts within the layer.« less

Multi-path variational transition state theory for chemical reaction rates of complex polyatomic species: ethanol + OH reactions.

PubMed

Zheng, Jingjing; Truhlar, Donald G

2012-01-01

Complex molecules often have many structures (conformations) of the reactants and the transition states, and these structures may be connected by coupled-mode torsions and pseudorotations; some but not all structures may have hydrogen bonds in the transition state or reagents. A quantitative theory of the reaction rates of complex molecules must take account of these structures, their coupled-mode nature, their qualitatively different character, and the possibility of merging reaction paths at high temperature. We have recently developed a coupled-mode theory called multi-structural variational transition state theory (MS-VTST) and an extension, called multi-path variational transition state theory (MP-VTST), that includes a treatment of the differences in the multi-dimensional tunneling paths and their contributions to the reaction rate. The MP-VTST method was presented for unimolecular reactions in the original paper and has now been extended to bimolecular reactions. The MS-VTST and MP-VTST formulations of variational transition state theory include multi-faceted configuration-space dividing surfaces to define the variational transition state. They occupy an intermediate position between single-conformation variational transition state theory (VTST), which has been used successfully for small molecules, and ensemble-averaged variational transition state theory (EA-VTST), which has been used successfully for enzyme kinetics. The theories are illustrated and compared here by application to three thermal rate constants for reactions of ethanol with hydroxyl radical--reactions with 4, 6, and 14 saddle points.

Multiple regimes of robust patterns between network structure and biodiversity

NASA Astrophysics Data System (ADS)

Jover, Luis F.; Flores, Cesar O.; Cortez, Michael H.; Weitz, Joshua S.

2015-12-01

Ecological networks such as plant-pollinator and host-parasite networks have structured interactions that define who interacts with whom. The structure of interactions also shapes ecological and evolutionary dynamics. Yet, there is significant ongoing debate as to whether certain structures, e.g., nestedness, contribute positively, negatively or not at all to biodiversity. We contend that examining variation in life history traits is key to disentangling the potential relationship between network structure and biodiversity. Here, we do so by analyzing a dynamic model of virus-bacteria interactions across a spectrum of network structures. Consistent with prior studies, we find plausible parameter domains exhibiting strong, positive relationships between nestedness and biodiversity. Yet, the same model can exhibit negative relationships between nestedness and biodiversity when examined in a distinct, plausible region of parameter space. We discuss steps towards identifying when network structure could, on its own, drive the resilience, sustainability, and even conservation of ecological communities.