GENETIC ACTIVITY PROFILES AND PATTERN RECOGNITION IN TEST BATTERY SELECTION (JOURNAL VERSION)

EPA Science Inventory

Computer-generated genetic activity profiles and pairwise matching procedures may aid in the selection of the most appropriate short-term bioassays to be used in test batteries for the evaluation of the genotoxicity of a given chemical or group of chemicals. Selection of test bat...

De novo metatranscriptome assembly and coral gene expression profile of Montipora capitata with growth anomaly.

PubMed

Frazier, Monika; Helmkampf, Martin; Bellinger, M Renee; Geib, Scott M; Takabayashi, Misaki

2017-09-11

Scleractinian corals are a vital component of coral reef ecosystems, and of significant cultural and economic value worldwide. As anthropogenic and natural stressors are contributing to a global decline of coral reefs, understanding coral health is critical to help preserve these ecosystems. Growth anomaly (GA) is a coral disease that has significant negative impacts on coral biology, yet our understanding of its etiology and pathology is lacking. In this study we used RNA-seq along with de novo metatranscriptome assembly and homology assignment to identify coral genes that are expressed in three distinct coral tissue types: tissue from healthy corals ("healthy"), GA lesion tissue from diseased corals ("GA-affected") and apparently healthy tissue from diseased corals ("GA-unaffected"). We conducted pairwise comparisons of gene expression among these three tissue types to identify genes and pathways that help us to unravel the molecular pathology of this coral disease. The quality-filtered de novo-assembled metatranscriptome contained 76,063 genes, of which 13,643 were identified as putative coral genes. Overall gene expression profiles of coral genes revealed high similarity between healthy tissue samples, in contrast to high variance among diseased samples. This indicates GA has a variety of genetic effects at the colony level, including on seemingly healthy (GA-unaffected) tissue. A total of 105 unique coral genes were found differentially expressed among tissue types. Pairwise comparisons revealed the greatest number of differentially expressed genes between healthy and GA-affected tissue (93 genes), followed by healthy and GA-unaffected tissue (33 genes), and GA-affected and -unaffected tissue (7 genes). The putative function of these genes suggests GA is associated with changes in the activity of genes involved in developmental processes and activation of the immune system. This is one of the first transcriptome-level studies to investigate coral GA, and the first metatranscriptome assembly for the M. capitata holobiont. The gene expression data, metatranscriptome assembly and methodology developed through this study represent a significant addition to the molecular information available to further our understanding of this coral disease.

Community assembly of the ferns of Florida.

PubMed

Sessa, Emily B; Chambers, Sally M; Li, Daijiang; Trotta, Lauren; Endara, Lorena; Burleigh, J Gordon; Baiser, Benjamin

2018-03-01

Many ecological and evolutionary processes shape the assembly of organisms into local communities from a regional pool of species. We analyzed phylogenetic and functional diversity to understand community assembly of the ferns of Florida at two spatial scales. We built a phylogeny for 125 of the 141 species of ferns in Florida using five chloroplast markers. We calculated mean pairwise dissimilarity (MPD) and mean nearest taxon distance (MNTD) from phylogenetic distances and functional trait data for both spatial scales and compared the results to null models to assess significance. Our results for over vs. underdispersion in functional and phylogenetic diversity differed depending on spatial scale and metric considered. At the county scale, MPD revealed evidence for phylogenetic overdispersion, while MNTD revealed phylogenetic and functional underdispersion, and at the conservation area scale, MPD revealed phylogenetic and functional underdispersion while MNTD revealed evidence only of functional underdispersion. Our results are consistent with environmental filtering playing a larger role at the smaller, conservation area scale. The smaller spatial units are likely composed of fewer local habitat types that are selecting for closely related species, with the larger-scale units more likely to be composed of multiple habitat types that bring together a larger pool of species from across the phylogeny. Several aspects of fern biology, including their unique physiology and water relations and the importance of the independent gametophyte stage of the life cycle, make ferns highly sensitive to local, microhabitat conditions. © 2018 The Authors. American Journal of Botany is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America.

De novo transcriptome assembly, development of EST-SSR markers and population genetic analyses for the desert biomass willow, Salix psammophila

PubMed Central

Jia, Huixia; Yang, Haifeng; Sun, Pei; Li, Jianbo; Zhang, Jin; Guo, Yinghua; Han, Xiaojiao; Zhang, Guosheng; Lu, Mengzhu; Hu, Jianjun

2016-01-01

Salix psammophila, a sandy shrub known as desert willow, is regarded as a potential biomass feedstock and plays an important role in maintaining local ecosystems. However, a lack of genomic data and efficient molecular markers limit the study of its population evolution and genetic breeding. In this study, chromosome counts, flow cytometry and SSR analyses indicated that S. psammophila is tetraploid. A total of 6,346 EST-SSRs were detected based on 71,458 de novo assembled unigenes from transcriptome data. Twenty-seven EST-SSR markers were developed to evaluate the genetic diversity and population structure of S. psammophila from eight natural populations in Northern China. High levels of genetic diversity (mean 10.63 alleles per locus; mean HE 0.689) were dectected in S. psammophila. The weak population structure and little genetic differentiation (pairwise FST = 0.006–0.016) were found among Population 1-Population 7 (Pop1-Pop7; Inner Mongolia and Shaanxi), but Pop8 (Ningxia) was clearly separated from Pop1-Pop7 and moderate differentiation (pairwise FST = 0.045–0.055) was detected between them, which may be influenced by local habitat conditions. Molecular variance analyses indicated that most of the genetic variation (94.27%) existed within populations. These results provide valuable genetic informations for natural resource conservation and breeding programme optimisation of S. psammophila. PMID:27995985

Collective translational and rotational Monte Carlo cluster move for general pairwise interaction

NASA Astrophysics Data System (ADS)

Růžička, Štěpán; Allen, Michael P.

2014-09-01

Virtual move Monte Carlo is a cluster algorithm which was originally developed for strongly attractive colloidal, molecular, or atomistic systems in order to both approximate the collective dynamics and avoid sampling of unphysical kinetic traps. In this paper, we present the algorithm in the form, which selects the moving cluster through a wider class of virtual states and which is applicable to general pairwise interactions, including hard-core repulsion. The newly proposed way of selecting the cluster increases the acceptance probability by up to several orders of magnitude, especially for rotational moves. The results have their applications in simulations of systems interacting via anisotropic potentials both to enhance the sampling of the phase space and to approximate the dynamics.

OxfordGrid: a web interface for pairwise comparative map views.

PubMed

Yang, Hongyu; Gingle, Alan R

2005-12-01

OxfordGrid is a web application and database schema for storing and interactively displaying genetic map data in a comparative, dot-plot, fashion. Its display is composed of a matrix of cells, each representing a pairwise comparison of mapped probe data for two linkage groups or chromosomes. These are arranged along the axes with one forming grid columns and the other grid rows with the degree and pattern of synteny/colinearity between the two linkage groups manifested in the cell's dot density and structure. A mouse click over the selected grid cell launches an image map-based display for the selected cell. Both individual and linear groups of mapped probes can be selected and displayed. Also, configurable links can be used to access other web resources for mapped probe information. OxfordGrid is implemented in C#/ASP.NET and the package, including MySQL schema creation scripts, is available at ftp://cggc.agtec.uga.edu/OxfordGrid/.

Frequency-Dependent Selection: The High Potential for Permanent Genetic Variation in the Diallelic, Pairwise Interaction Model

PubMed Central

Asmussen, M. A.; Basnayake, E.

1990-01-01

A detailed analytic and numerical study is made of the potential for permanent genetic variation in frequency-dependent models based on pairwise interactions among genotypes at a single diallelic locus. The full equilibrium structure and qualitative gene-frequency dynamics are derived analytically for a symmetric model, in which pairwise fitnesses are chiefly determined by the genetic similarity of the individuals involved. This is supplemented by an extensive numerical investigation of the general model, the symmetric model, and nine other special cases. Together the results show that there is a high potential for permanent genetic diversity in the pairwise interaction model, and provide insight into the extent to which various forms of genotypic interactions enhance or reduce this potential. Technically, although two stable polymorphic equilibria are possible, the increased likelihood of maintaining both alleles, and the poor performance of protected polymorphism conditions as a measure of this likelihood, are primarily due to a greater variety and frequency of equilibrium patterns with one stable polymorphic equilibrium, in conjunction with a disproportionately large domain of attraction for stable internal equilibria. PMID:2341034

Exploring the evolutionary ecology of fungal endophytes in agricultural systems: using functional traits to reveal mechanisms in community processes

PubMed Central

Saunders, Megan; Glenn, Anthony E; Kohn, Linda M

2010-01-01

All plants, including crop species, harbor a community of fungal endophyte species, yet we know little about the biotic factors that are important in endophyte community assembly. We suggest that the most direct route to understanding the mechanisms underlying community assembly is through the study of functional trait variation in the host and its fungal consortium. We review studies on crop endophytes that investigate plant and fungal traits likely to be important in endophyte community processes. We focus on approaches that could speed detection of general trends in endophyte community assembly: (i) use of the ‘assembly rules’ concept to identify specific mechanisms that influence endophyte community dynamics, (ii) measurement of functional trait variation in plants and fungi to better understand endophyte community processes and plant–fungal interactions, and (iii) investigation of microbe–microbe interactions, and fungal traits that mediate them. This approach is well suited for research in agricultural systems, where pair-wise host–fungus interactions and mechanisms of fungal–fungal competition have frequently been described. Areas for consideration include the possibility that human manipulation of crop phenotype and deployment of fungal biocontrol species can significantly influence endophyte community assembly. Evaluation of endophyte assembly rules may help to fine-tune crop management strategies. PMID:25567944

Living network meta-analysis compared with pairwise meta-analysis in comparative effectiveness research: empirical study

PubMed Central

Nikolakopoulou, Adriani; Mavridis, Dimitris; Furukawa, Toshi A; Cipriani, Andrea; Tricco, Andrea C; Straus, Sharon E; Siontis, George C M; Egger, Matthias

2018-01-01

Abstract Objective To examine whether the continuous updating of networks of prospectively planned randomised controlled trials (RCTs) (“living” network meta-analysis) provides strong evidence against the null hypothesis in comparative effectiveness of medical interventions earlier than the updating of conventional, pairwise meta-analysis. Design Empirical study of the accumulating evidence about the comparative effectiveness of clinical interventions. Data sources Database of network meta-analyses of RCTs identified through searches of Medline, Embase, and the Cochrane Database of Systematic Reviews until 14 April 2015. Eligibility criteria for study selection Network meta-analyses published after January 2012 that compared at least five treatments and included at least 20 RCTs. Clinical experts were asked to identify in each network the treatment comparison of greatest clinical interest. Comparisons were excluded for which direct and indirect evidence disagreed, based on side, or node, splitting test (P<0.10). Outcomes and analysis Cumulative pairwise and network meta-analyses were performed for each selected comparison. Monitoring boundaries of statistical significance were constructed and the evidence against the null hypothesis was considered to be strong when the monitoring boundaries were crossed. A significance level was defined as α=5%, power of 90% (β=10%), and an anticipated treatment effect to detect equal to the final estimate from the network meta-analysis. The frequency and time to strong evidence was compared against the null hypothesis between pairwise and network meta-analyses. Results 49 comparisons of interest from 44 networks were included; most (n=39, 80%) were between active drugs, mainly from the specialties of cardiology, endocrinology, psychiatry, and rheumatology. 29 comparisons were informed by both direct and indirect evidence (59%), 13 by indirect evidence (27%), and 7 by direct evidence (14%). Both network and pairwise meta-analysis provided strong evidence against the null hypothesis for seven comparisons, but for an additional 10 comparisons only network meta-analysis provided strong evidence against the null hypothesis (P=0.002). The median time to strong evidence against the null hypothesis was 19 years with living network meta-analysis and 23 years with living pairwise meta-analysis (hazard ratio 2.78, 95% confidence interval 1.00 to 7.72, P=0.05). Studies directly comparing the treatments of interest continued to be published for eight comparisons after strong evidence had become evident in network meta-analysis. Conclusions In comparative effectiveness research, prospectively planned living network meta-analyses produced strong evidence against the null hypothesis more often and earlier than conventional, pairwise meta-analyses. PMID:29490922

Natural history matters: how biological constraints shape diversified interactions in pollination networks.

PubMed

Jordano, Pedro

2016-11-01

Species-specific traits constrain the ways organisms interact in nature. Some pairwise interactions among coexisting species simply do not occur; they are impossible to observe despite the fact that partners coexist in the same place. The author discusses these 'forbidden links' of species interaction networks. Photo: a sphingid moth, Manduca sexta visiting a flower of Tocoyena formosa (Rubiaceae) in the Brazilian Cerrado; tongue and corolla tube lengths approximately 100 mm. Courtesy of Felipe Amorim. Sazatornil, F.D., Moré, M., Benitez-Vieyra, S., Cocucci, A.A., Kitching, I.J., Schlumpberger, B.O., Oliveira, P.E., Sazima, M. & Amorim, F.W. (2016) Beyond neutral and forbidden links: morphological matches and the assembly of mutualistic hawkmoth-plant networks. Journal of Animal Ecology, 85, 1586-1594. Species-specific traits and life-history characteristics constrain the ways organisms interact in nature. For example, gape-limited predators are constrained in the sizes of prey they can handle and efficiently consume. When we consider the ubiquity of such constrains, it is evident how hard it can be to be a generalist partner in ecological interactions: a free-living animal or plant cannot simply interact with every available partner it encounters. Some pairwise interactions among coexisting species simply do not occur; they are impossible to observe despite the fact that partners coexist in the same place. Sazatornil et al. () explore the nature of such constraints in the mutualisms among hawkmoths and the plants they pollinate. In this iconic interaction, used by Darwin and Wallace to vividly illustrate the power of natural selection in shaping evolutionary change, both pollinators and plants are sharply constrained in their interaction modes and outcomes. © 2016 The Author. Journal of Animal Ecology © 2016 British Ecological Society.

Catalytically powered dynamic assembly of rod-shaped nanomotors and passive tracer particles

PubMed Central

Wang, Wei; Duan, Wentao; Sen, Ayusman; Mallouk, Thomas E.

2013-01-01

Nano- and microscale motors powered by catalytic reactions exhibit collective behavior such as swarming, predator–prey interactions, and chemotaxis that resemble those of biological microorganisms. A quantitative understanding of the catalytically generated forces between particles that lead to these behaviors has so far been lacking. Observations and numerical simulations of pairwise interactions between gold-platinum nanorods in hydrogen peroxide solutions show that attractive and repulsive interactions arise from the catalytically generated electric field. Electrokinetic effects drive the assembly of staggered doublets and triplets of nanorods that are moving in the same direction. None of these behaviors are observed with nanorods composed of a single metal. The motors also collect tracer microparticles at their head or tail, depending on the charge of the particles, actively assembling them into close-packed rafts and aggregates of rafts. These motor–tracer particle interactions can also be understood in terms of the catalytically generated electric field around the ends of the nanorod motors. PMID:24127603

Catalytically powered dynamic assembly of rod-shaped nanomotors and passive tracer particles.

PubMed

Wang, Wei; Duan, Wentao; Sen, Ayusman; Mallouk, Thomas E

2013-10-29

Nano- and microscale motors powered by catalytic reactions exhibit collective behavior such as swarming, predator-prey interactions, and chemotaxis that resemble those of biological microorganisms. A quantitative understanding of the catalytically generated forces between particles that lead to these behaviors has so far been lacking. Observations and numerical simulations of pairwise interactions between gold-platinum nanorods in hydrogen peroxide solutions show that attractive and repulsive interactions arise from the catalytically generated electric field. Electrokinetic effects drive the assembly of staggered doublets and triplets of nanorods that are moving in the same direction. None of these behaviors are observed with nanorods composed of a single metal. The motors also collect tracer microparticles at their head or tail, depending on the charge of the particles, actively assembling them into close-packed rafts and aggregates of rafts. These motor-tracer particle interactions can also be understood in terms of the catalytically generated electric field around the ends of the nanorod motors.

Evolution of genetic architecture under directional selection.

PubMed

Hansen, Thomas F; Alvarez-Castro, José M; Carter, Ashley J R; Hermisson, Joachim; Wagner, Günter P

2006-08-01

We investigate the multilinear epistatic model under mutation-limited directional selection. We confirm previous results that only directional epistasis, in which genes on average reinforce or diminish each other's effects, contribute to the initial evolution of mutational effects. Thus, either canalization or decanalization can occur under directional selection, depending on whether positive or negative epistasis is prevalent. We then focus on the evolution of the epistatic coefficients themselves. In the absence of higher-order epistasis, positive pairwise epistasis will tend to weaken relative to additive effects, while negative pairwise epistasis will tend to become strengthened. Positive third-order epistasis will counteract these effects, while negative third-order epistasis will reinforce them. More generally, gene interactions of all orders have an inherent tendency for negative changes under directional selection, which can only be modified by higher-order directional epistasis. We identify three types of nonadditive quasi-equilibrium architectures that, although not strictly stable, can be maintained for an extended time: (1) nondirectional epistatic architectures; (2) canalized architectures with strong epistasis; and (3) near-additive architectures in which additive effects keep increasing relative to epistasis.

Evaluation of a Pair-Wise Conflict Detection and Resolution Algorithm in a Multiple Aircraft Scenario

NASA Technical Reports Server (NTRS)

Carreno, Victor A.

2002-01-01

The KB3D algorithm is a pairwise conflict detection and resolution (CD&R) algorithm. It detects and generates trajectory vectoring for an aircraft which has been predicted to be in an airspace minima violation within a given look-ahead time. It has been proven, using mechanized theorem proving techniques, that for a pair of aircraft, KB3D produces at least one vectoring solution and that all solutions produced are correct. Although solutions produced by the algorithm are mathematically correct, they might not be physically executable by an aircraft or might not solve multiple aircraft conflicts. This paper describes a simple solution selection method which assesses all solutions generated by KB3D and determines the solution to be executed. The solution selection method and KB3D are evaluated using a simulation in which N aircraft fly in a free-flight environment and each aircraft in the simulation uses KB3D to maintain separation. Specifically, the solution selection method filters KB3D solutions which are procedurally undesirable or physically not executable and uses a predetermined criteria for selection.

Active constrained clustering by examining spectral Eigenvectors

NASA Technical Reports Server (NTRS)

Wagstaff, Kiri L.; desJardins, Marie; Xu, Qianjun

2005-01-01

This work focuses on the active selection of pairwise constraints for spectral clustering. We develop and analyze a technique for Active Constrained Clustering by Examining Spectral eigenvectorS (ACCESS) derived from a similarity matrix.

Structure of colloidosomes with tunable particle density: Simulation versus experiment

NASA Astrophysics Data System (ADS)

Fantoni, Riccardo; Salari, Johannes W. O.; Klumperman, Bert

2012-06-01

Colloidosomes are created in the laboratory from a Pickering emulsion of water droplets in oil. The colloidosomes have approximately the same diameter and by choosing (hairy) particles of different diameters it is possible to control the particle density on the droplets. The experiment is performed at room temperature. The radial distribution function of the assembly of (primary) particles on the water droplet is measured in the laboratory and in a computer experiment of a fluid model of particles with pairwise interactions on the surface of a sphere.

DockTrina: docking triangular protein trimers.

PubMed

Popov, Petr; Ritchie, David W; Grudinin, Sergei

2014-01-01

In spite of the abundance of oligomeric proteins within a cell, the structural characterization of protein-protein interactions is still a challenging task. In particular, many of these interactions involve heteromeric complexes, which are relatively difficult to determine experimentally. Hence there is growing interest in using computational techniques to model such complexes. However, assembling large heteromeric complexes computationally is a highly combinatorial problem. Nonetheless the problem can be simplified greatly by considering interactions between protein trimers. After dimers and monomers, triangular trimers (i.e. trimers with pair-wise contacts between all three pairs of proteins) are the most frequently observed quaternary structural motifs according to the three-dimensional (3D) complex database. This article presents DockTrina, a novel protein docking method for modeling the 3D structures of nonsymmetrical triangular trimers. The method takes as input pair-wise contact predictions from a rigid body docking program. It then scans and scores all possible combinations of pairs of monomers using a very fast root mean square deviation test. Finally, it ranks the predictions using a scoring function which combines triples of pair-wise contact terms and a geometric clash penalty term. The overall approach takes less than 2 min per complex on a modern desktop computer. The method is tested and validated using a benchmark set of 220 bound and seven unbound protein trimer structures. DockTrina will be made available at http://nano-d.inrialpes.fr/software/docktrina. Copyright © 2013 Wiley Periodicals, Inc.

Understanding co-polymerization in amyloid formation by direct observation of mixed oligomers† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc00620a Click here for additional data file.

PubMed Central

Young, Lydia M.; Tu, Ling-Hsien; Raleigh, Daniel P.; Ashcroft, Alison E.

2017-01-01

Although amyloid assembly in vitro is commonly investigated using single protein sequences, fibril formation in vivo can be more heterogeneous, involving co-assembly of proteins of different length, sequence and/or post-translational modifications. Emerging evidence suggests that co-polymerization can alter the rate and/or mechanism of aggregation and can contribute to pathogenicity. Electrospray ionization-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS) is uniquely suited to the study of these heterogeneous ensembles. Here, ESI-IMS-MS combined with analysis of fibrillation rates using thioflavin T (ThT) fluorescence, is used to track the course of aggregation of variants of islet-amyloid polypeptide (IAPP) in isolation and in pairwise mixtures. We identify a sub-population of extended monomers as the key precursors of amyloid assembly, and reveal that the fastest aggregating sequence in peptide mixtures determines the lag time of fibrillation, despite being unable to cross-seed polymerization. The results demonstrate that co-polymerization of IAPP sequences radically alters the rate of amyloid assembly by altering the conformational properties of the mixed oligomers that form. PMID:28970890

Feature Grouping and Selection Over an Undirected Graph.

PubMed

Yang, Sen; Yuan, Lei; Lai, Ying-Cheng; Shen, Xiaotong; Wonka, Peter; Ye, Jieping

2012-01-01

High-dimensional regression/classification continues to be an important and challenging problem, especially when features are highly correlated. Feature selection, combined with additional structure information on the features has been considered to be promising in promoting regression/classification performance. Graph-guided fused lasso (GFlasso) has recently been proposed to facilitate feature selection and graph structure exploitation, when features exhibit certain graph structures. However, the formulation in GFlasso relies on pairwise sample correlations to perform feature grouping, which could introduce additional estimation bias. In this paper, we propose three new feature grouping and selection methods to resolve this issue. The first method employs a convex function to penalize the pairwise l ∞ norm of connected regression/classification coefficients, achieving simultaneous feature grouping and selection. The second method improves the first one by utilizing a non-convex function to reduce the estimation bias. The third one is the extension of the second method using a truncated l 1 regularization to further reduce the estimation bias. The proposed methods combine feature grouping and feature selection to enhance estimation accuracy. We employ the alternating direction method of multipliers (ADMM) and difference of convex functions (DC) programming to solve the proposed formulations. Our experimental results on synthetic data and two real datasets demonstrate the effectiveness of the proposed methods.

Genetic diversity of Elaeis oleifera (HBK) Cortes populations using cross species SSRs: implication's for germplasm utilization and conservation.

PubMed

Ithnin, Maizura; Teh, Chee-Keng; Ratnam, Wickneswari

2017-04-19

The Elaeis oleifera genetic materials were assembled from its center of diversity in South and Central America. These materials are currently being preserved in Malaysia as ex situ living collections. Maintaining such collections is expensive and requires sizable land. Information on the genetic diversity of these collections can help achieve efficient conservation via maintenance of core collection. For this purpose, we have applied fourteen unlinked microsatellite markers to evaluate 532 E. oleifera palms representing 19 populations distributed across Honduras, Costa Rica, Panama and Colombia. In general, the genetic diversity decreased from Costa Rica towards the north (Honduras) and south-east (Colombia). Principle coordinate analysis (PCoA) showed a single cluster indicating low divergence among palms. The phylogenetic tree and STRUCTURE analysis revealed clusters based on country of origin, indicating considerable gene flow among populations within countries. Based on the values of the genetic diversity parameters, some genetically diverse populations could be identified. Further, a total of 34 individual palms that collectively captured maximum allelic diversity with reduced redundancy were also identified. High pairwise genetic differentiation (Fst > 0.250) among populations was evident, particularly between the Colombian populations and those from Honduras, Panama and Costa Rica. Crossing selected palms from highly differentiated populations could generate off-springs that retain more genetic diversity. The results attained are useful for selecting palms and populations for core collection. The selected materials can also be included into crossing scheme to generate offsprings that capture greater genetic diversity for selection gain in the future.

The role of eigenvalues in linear feature selection theory

NASA Technical Reports Server (NTRS)

Brown, D. R.; Omalley, M. J.

1976-01-01

A particular measure of pattern class distinction called the average interclass divergence, or more simply, divergence, is considered. Here divergence will be the pairwise average of the expected interclass divergence derived from Hajek's two-class divergence.

Working with Missing Values

ERIC Educational Resources Information Center

Acock, Alan C.

2005-01-01

Less than optimum strategies for missing values can produce biased estimates, distorted statistical power, and invalid conclusions. After reviewing traditional approaches (listwise, pairwise, and mean substitution), selected alternatives are covered including single imputation, multiple imputation, and full information maximum likelihood…

Selecting Soldiers and Civilians into the U.S. Army Officer Candidate School : Developing Empirical Selection Composites

DTIC Science & Technology

2014-07-01

a biographical instrument measuring personality ; (b) a Work Values instrument representing work preferences investigated in prior officer and...items used in SelectOCS Phase 2 (see Table 2.5). TAPAS uses multidimensional pairwise preference (MDPP) personality items scored using item response...presented respondents with a list of 30 traits and 30 skills (derived from leadership and personality literature) and instructed them to rate the

Scaling laws for van der Waals interactions in nanostructured materials.

PubMed

Gobre, Vivekanand V; Tkatchenko, Alexandre

2013-01-01

Van der Waals interactions have a fundamental role in biology, physics and chemistry, in particular in the self-assembly and the ensuing function of nanostructured materials. Here we utilize an efficient microscopic method to demonstrate that van der Waals interactions in nanomaterials act at distances greater than typically assumed, and can be characterized by different scaling laws depending on the dimensionality and size of the system. Specifically, we study the behaviour of van der Waals interactions in single-layer and multilayer graphene, fullerenes of varying size, single-wall carbon nanotubes and graphene nanoribbons. As a function of nanostructure size, the van der Waals coefficients follow unusual trends for all of the considered systems, and deviate significantly from the conventionally employed pairwise-additive picture. We propose that the peculiar van der Waals interactions in nanostructured materials could be exploited to control their self-assembly.

Sequential programmable self-assembly: Role of cooperative interactions

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

Jonathan D. Halverson; Tkachenko, Alexei V.

Here, we propose a general strategy of “sequential programmable self-assembly” that enables a bottom-up design of arbitrary multi-particle architectures on nano- and microscales. We show that a naive realization of this scheme, based on the pairwise additive interactions between particles, has fundamental limitations that lead to a relatively high error rate. This can be overcome by using cooperative interparticle binding. The cooperativity is a well known feature of many biochemical processes, responsible, e.g., for signaling and regulations in living systems. Here we propose to utilize a similar strategy for high precision self-assembly, and show that DNA-mediated interactions provide a convenientmore » platform for its implementation. In particular, we outline a specific design of a DNA-based complex which we call “DNA spider,” that acts as a smart interparticle linker and provides a built-in cooperativity of binding. We demonstrate versatility of the sequential self-assembly based on spider-functionalized particles by designing several mesostructures of increasing complexity and simulating their assembly process. This includes a number of finite and repeating structures, in particular, the so-called tetrahelix and its several derivatives. Due to its generality, this approach allows one to design and successfully self-assemble virtually any structure made of a “GEOMAG” magnetic construction toy, out of nanoparticles. According to our results, once the binding cooperativity is strong enough, the sequential self-assembly becomes essentially error-free.« less

Sequential programmable self-assembly: Role of cooperative interactions

DOE PAGES

Jonathan D. Halverson; Tkachenko, Alexei V.

2016-03-04

Here, we propose a general strategy of “sequential programmable self-assembly” that enables a bottom-up design of arbitrary multi-particle architectures on nano- and microscales. We show that a naive realization of this scheme, based on the pairwise additive interactions between particles, has fundamental limitations that lead to a relatively high error rate. This can be overcome by using cooperative interparticle binding. The cooperativity is a well known feature of many biochemical processes, responsible, e.g., for signaling and regulations in living systems. Here we propose to utilize a similar strategy for high precision self-assembly, and show that DNA-mediated interactions provide a convenientmore » platform for its implementation. In particular, we outline a specific design of a DNA-based complex which we call “DNA spider,” that acts as a smart interparticle linker and provides a built-in cooperativity of binding. We demonstrate versatility of the sequential self-assembly based on spider-functionalized particles by designing several mesostructures of increasing complexity and simulating their assembly process. This includes a number of finite and repeating structures, in particular, the so-called tetrahelix and its several derivatives. Due to its generality, this approach allows one to design and successfully self-assemble virtually any structure made of a “GEOMAG” magnetic construction toy, out of nanoparticles. According to our results, once the binding cooperativity is strong enough, the sequential self-assembly becomes essentially error-free.« less

Identification of landscape features influencing gene flow: How useful are habitat selection models?

USGS Publications Warehouse

Roffler, Gretchen H.; Schwartz, Michael K.; Pilgrim, Kristy L.; Talbot, Sandra L.; Sage, Kevin; Adams, Layne G.; Luikart, Gordon

2016-01-01

Understanding how dispersal patterns are influenced by landscape heterogeneity is critical for modeling species connectivity. Resource selection function (RSF) models are increasingly used in landscape genetics approaches. However, because the ecological factors that drive habitat selection may be different from those influencing dispersal and gene flow, it is important to consider explicit assumptions and spatial scales of measurement. We calculated pairwise genetic distance among 301 Dall's sheep (Ovis dalli dalli) in southcentral Alaska using an intensive noninvasive sampling effort and 15 microsatellite loci. We used multiple regression of distance matrices to assess the correlation of pairwise genetic distance and landscape resistance derived from an RSF, and combinations of landscape features hypothesized to influence dispersal. Dall's sheep gene flow was positively correlated with steep slopes, moderate peak normalized difference vegetation indices (NDVI), and open land cover. Whereas RSF covariates were significant in predicting genetic distance, the RSF model itself was not significantly correlated with Dall's sheep gene flow, suggesting that certain habitat features important during summer (rugged terrain, mid-range elevation) were not influential to effective dispersal. This work underscores that consideration of both habitat selection and landscape genetics models may be useful in developing management strategies to both meet the immediate survival of a species and allow for long-term genetic connectivity.

29 CFR 1926.1403 - Assembly/Disassembly-selection of manufacturer or employer procedures.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 29 Labor 8 2013-07-01 2013-07-01 false Assembly/Disassembly-selection of manufacturer or employer... CONSTRUCTION Cranes and Derricks in Construction § 1926.1403 Assembly/Disassembly—selection of manufacturer or... applicable to assembly and disassembly, or (b) Employer procedures for assembly and disassembly. Employer...

29 CFR 1926.1403 - Assembly/Disassembly-selection of manufacturer or employer procedures.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 29 Labor 8 2012-07-01 2012-07-01 false Assembly/Disassembly-selection of manufacturer or employer... CONSTRUCTION Cranes and Derricks in Construction § 1926.1403 Assembly/Disassembly—selection of manufacturer or... applicable to assembly and disassembly, or (b) Employer procedures for assembly and disassembly. Employer...

29 CFR 1926.1403 - Assembly/Disassembly-selection of manufacturer or employer procedures.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 29 Labor 8 2014-07-01 2014-07-01 false Assembly/Disassembly-selection of manufacturer or employer... CONSTRUCTION Cranes and Derricks in Construction § 1926.1403 Assembly/Disassembly—selection of manufacturer or... applicable to assembly and disassembly, or (b) Employer procedures for assembly and disassembly. Employer...

29 CFR 1926.1403 - Assembly/Disassembly-selection of manufacturer or employer procedures.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 29 Labor 8 2011-07-01 2011-07-01 false Assembly/Disassembly-selection of manufacturer or employer... CONSTRUCTION Cranes and Derricks in Construction § 1926.1403 Assembly/Disassembly—selection of manufacturer or... applicable to assembly and disassembly, or (b) Employer procedures for assembly and disassembly. Employer...

Memory-efficient dynamic programming backtrace and pairwise local sequence alignment.

PubMed

Newberg, Lee A

2008-08-15

A backtrace through a dynamic programming algorithm's intermediate results in search of an optimal path, or to sample paths according to an implied probability distribution, or as the second stage of a forward-backward algorithm, is a task of fundamental importance in computational biology. When there is insufficient space to store all intermediate results in high-speed memory (e.g. cache) existing approaches store selected stages of the computation, and recompute missing values from these checkpoints on an as-needed basis. Here we present an optimal checkpointing strategy, and demonstrate its utility with pairwise local sequence alignment of sequences of length 10,000. Sample C++-code for optimal backtrace is available in the Supplementary Materials. Supplementary data is available at Bioinformatics online.

Self-assembly of the yeast actomyosin contractile ring as an aggregation process: kinetics of formation and instability regimes

NASA Astrophysics Data System (ADS)

Ojkic, Nikola; Vavylonis, Dimitrios

2009-03-01

Fission yeast cells assemble an equatorial contractile ring for cytokinesis, the last step of mitosis. The ring assembles from ˜ 65 membrane-bound ``nodes''' containing myosin motors and other proteins. Actin filaments that grow out from the nodes establish transient connections among the nodes and aid in pulling them together in a process that appears as pair-wise attraction (Vavylonis et al. Science 97:319, 2008). We used scaling arguments, coarse grained stability analysis of homogeneous states, and Monte Carlo simulations of simple models, to explore the conditions that yield fast and efficient ring formation, as opposed to formation of isolated clumps. We described our results as a function of: number of nodes, rate of establishing connections, range of node interaction, distance traveled per node interaction and broad band width, w. Uniform cortical 2d distributions of nodes are stable over short times due to randomness of connections among nodes, but become unstable over long times due to fluctuations in the initial node distribution. Successful condensation of nodes into a ring requires sufficiently small w such that lateral contraction occurs faster then clump formation.

The structure and intermolecular forces of DNA condensates.

PubMed

Yoo, Jejoong; Aksimentiev, Aleksei

2016-03-18

Spontaneous assembly of DNA molecules into compact structures is ubiquitous in biological systems. Experiment has shown that polycations can turn electrostatic self-repulsion of DNA into attraction, yet the physical mechanism of DNA condensation has remained elusive. Here, we report the results of atomistic molecular dynamics simulations that elucidated the microscopic structure of dense DNA assemblies and the physics of interactions that makes such assemblies possible. Reproducing the setup of the DNA condensation experiments, we measured the internal pressure of DNA arrays as a function of the DNA-DNA distance, showing a quantitative agreement between the results of our simulations and the experimental data. Analysis of the MD trajectories determined the DNA-DNA force in a DNA condensate to be pairwise, the DNA condensation to be driven by electrostatics of polycations and not hydration, and the concentration of bridging cations, not adsorbed cations, to determine the magnitude and the sign of the DNA-DNA force. Finally, our simulations quantitatively characterized the orientational correlations of DNA in DNA arrays as well as diffusive motion of DNA and cations. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

SFESA: a web server for pairwise alignment refinement by secondary structure shifts.

PubMed

Tong, Jing; Pei, Jimin; Grishin, Nick V

2015-09-03

Protein sequence alignment is essential for a variety of tasks such as homology modeling and active site prediction. Alignment errors remain the main cause of low-quality structure models. A bioinformatics tool to refine alignments is needed to make protein alignments more accurate. We developed the SFESA web server to refine pairwise protein sequence alignments. Compared to the previous version of SFESA, which required a set of 3D coordinates for a protein, the new server will search a sequence database for the closest homolog with an available 3D structure to be used as a template. For each alignment block defined by secondary structure elements in the template, SFESA evaluates alignment variants generated by local shifts and selects the best-scoring alignment variant. A scoring function that combines the sequence score of profile-profile comparison and the structure score of template-derived contact energy is used for evaluation of alignments. PROMALS pairwise alignments refined by SFESA are more accurate than those produced by current advanced alignment methods such as HHpred and CNFpred. In addition, SFESA also improves alignments generated by other software. SFESA is a web-based tool for alignment refinement, designed for researchers to compute, refine, and evaluate pairwise alignments with a combined sequence and structure scoring of alignment blocks. To our knowledge, the SFESA web server is the only tool that refines alignments by evaluating local shifts of secondary structure elements. The SFESA web server is available at http://prodata.swmed.edu/sfesa.

Self-assembly of thin, triangular prisms into open networks at a flat air-water interface

NASA Astrophysics Data System (ADS)

Solomon, Michael; Ferrar, Joseph; Bedi, Deshpreet; Zhou, Shangnan; Mao, Xiaoming

We observe capillary-driven binding between thin, equilateral triangle microprisms at a flat air-water interface. The triangles are fabricated from epoxy resin via SU-8 photolithography. For small thickness to length (T/L) ratios, two distinct pairwise particle-particle binding events occur with roughly equal frequency, and optical and environmental scanning electron microscopy (eSEM) demonstrate that these two distinct binding events are driven by the specific manner in which the interface is pinned to the particle surface. Additionally, particle bending is observed for the lowest T/L ratios, which leads to enhanced interface curvature and thus enhanced strength of capillary-driven attractions, and may also play a pivotal role in the dichotomy in particle-particle binding. Dichotomy in particle-particle binding is not observed at thicker T/L ratios, although capillary-driven binding still occurs. Ultimately, the particles self-assemble into space-spanning open networks, and the results suggest design parameters for the fabrication of building blocks of ordered open structures, such as the Kagome lattice.

Community assembly of the worm gut microbiome

NASA Astrophysics Data System (ADS)

Gore, Jeff

It has become increasingly clear that human health is strongly influenced by the bacteria that live within the gut, known collectively as the gut microbiome. This complex community varies tremendously between individuals, but understanding the sources that lead to this heterogeneity is challenging. To address this challenge, we are using a bottom-up approach to develop a predictive understanding of how the microbiome assembles and functions within a simple and experimentally tractable gut, the gut of the worm C. elegans. We have found that stochastic community assembly in the C. elegansintestine is sufficient to produce strong inter-worm heterogeneity in community composition. When worms are fed with two neutrally-competing fluorescently labeled bacterial strains, we observe stochastically-driven bimodality in community composition, where approximately half of the worms are dominated by each bacterial strain. A simple model incorporating stochastic colonization suggests that heterogeneity between worms is driven by the low rate at which bacteria successfully establish new intestinal colonies. We can increase this rate experimentally by feeding worms at high bacterial density; in these conditions the bimodality disappears. We have also characterized all pairwise interspecies competitions among a set of eleven bacterial species, illuminating the rules governing interspecies community assembly. These results demonstrate the potential importance of stochastic processes in bacterial community formation and suggest a role for C. elegans as a model system for ecology of host-associated communities.

Active learning for semi-supervised clustering based on locally linear propagation reconstruction.

PubMed

Chang, Chin-Chun; Lin, Po-Yi

2015-03-01

The success of semi-supervised clustering relies on the effectiveness of side information. To get effective side information, a new active learner learning pairwise constraints known as must-link and cannot-link constraints is proposed in this paper. Three novel techniques are developed for learning effective pairwise constraints. The first technique is used to identify samples less important to cluster structures. This technique makes use of a kernel version of locally linear embedding for manifold learning. Samples neither important to locally linear propagation reconstructions of other samples nor on flat patches in the learned manifold are regarded as unimportant samples. The second is a novel criterion for query selection. This criterion considers not only the importance of a sample to expanding the space coverage of the learned samples but also the expected number of queries needed to learn the sample. To facilitate semi-supervised clustering, the third technique yields inferred must-links for passing information about flat patches in the learned manifold to semi-supervised clustering algorithms. Experimental results have shown that the learned pairwise constraints can capture the underlying cluster structures and proven the feasibility of the proposed approach. Copyright © 2014 Elsevier Ltd. All rights reserved.

Living network meta-analysis compared with pairwise meta-analysis in comparative effectiveness research: empirical study.

PubMed

Nikolakopoulou, Adriani; Mavridis, Dimitris; Furukawa, Toshi A; Cipriani, Andrea; Tricco, Andrea C; Straus, Sharon E; Siontis, George C M; Egger, Matthias; Salanti, Georgia

2018-02-28

To examine whether the continuous updating of networks of prospectively planned randomised controlled trials (RCTs) ("living" network meta-analysis) provides strong evidence against the null hypothesis in comparative effectiveness of medical interventions earlier than the updating of conventional, pairwise meta-analysis. Empirical study of the accumulating evidence about the comparative effectiveness of clinical interventions. Database of network meta-analyses of RCTs identified through searches of Medline, Embase, and the Cochrane Database of Systematic Reviews until 14 April 2015. Network meta-analyses published after January 2012 that compared at least five treatments and included at least 20 RCTs. Clinical experts were asked to identify in each network the treatment comparison of greatest clinical interest. Comparisons were excluded for which direct and indirect evidence disagreed, based on side, or node, splitting test (P<0.10). Cumulative pairwise and network meta-analyses were performed for each selected comparison. Monitoring boundaries of statistical significance were constructed and the evidence against the null hypothesis was considered to be strong when the monitoring boundaries were crossed. A significance level was defined as α=5%, power of 90% (β=10%), and an anticipated treatment effect to detect equal to the final estimate from the network meta-analysis. The frequency and time to strong evidence was compared against the null hypothesis between pairwise and network meta-analyses. 49 comparisons of interest from 44 networks were included; most (n=39, 80%) were between active drugs, mainly from the specialties of cardiology, endocrinology, psychiatry, and rheumatology. 29 comparisons were informed by both direct and indirect evidence (59%), 13 by indirect evidence (27%), and 7 by direct evidence (14%). Both network and pairwise meta-analysis provided strong evidence against the null hypothesis for seven comparisons, but for an additional 10 comparisons only network meta-analysis provided strong evidence against the null hypothesis (P=0.002). The median time to strong evidence against the null hypothesis was 19 years with living network meta-analysis and 23 years with living pairwise meta-analysis (hazard ratio 2.78, 95% confidence interval 1.00 to 7.72, P=0.05). Studies directly comparing the treatments of interest continued to be published for eight comparisons after strong evidence had become evident in network meta-analysis. In comparative effectiveness research, prospectively planned living network meta-analyses produced strong evidence against the null hypothesis more often and earlier than conventional, pairwise meta-analyses. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Lotka-Volterra pairwise modeling fails to capture diverse pairwise microbial interactions

PubMed Central

Momeni, Babak; Xie, Li; Shou, Wenying

2017-01-01

Pairwise models are commonly used to describe many-species communities. In these models, an individual receives additive fitness effects from pairwise interactions with each species in the community ('additivity assumption'). All pairwise interactions are typically represented by a single equation where parameters reflect signs and strengths of fitness effects ('universality assumption'). Here, we show that a single equation fails to qualitatively capture diverse pairwise microbial interactions. We build mechanistic reference models for two microbial species engaging in commonly-found chemical-mediated interactions, and attempt to derive pairwise models. Different equations are appropriate depending on whether a mediator is consumable or reusable, whether an interaction is mediated by one or more mediators, and sometimes even on quantitative details of the community (e.g. relative fitness of the two species, initial conditions). Our results, combined with potential violation of the additivity assumption in many-species communities, suggest that pairwise modeling will often fail to predict microbial dynamics. DOI: http://dx.doi.org/10.7554/eLife.25051.001 PMID:28350295

Constructing Adverse Outcome Pathways: a Demonstration of ...

EPA Pesticide Factsheets

Adverse outcome pathway (AOP) provides a conceptual framework to evaluate and integrate chemical toxicity and its effects across the levels of biological organization. As such, it is essential to develop a resource-efficient and effective approach to extend molecular initiating events (MIEs) of chemicals to their downstream phenotypes of a greater regulatory relevance. A number of ongoing public phenomics (high throughput phenotyping) efforts have been generating abundant phenotypic data annotated with ontology terms. These phenotypes can be analyzed semantically and linked to MIEs of interest, all in the context of a knowledge base integrated from a variety of ontologies for various species and knowledge domains. In such analyses, two phenotypic profiles (PPs; anchored by genes or diseases) each characterized by multiple ontology terms are compared for their semantic similarities within a common ontology graph, but across boundaries of species and knowledge domains. Taking advantage of publicly available ontologies and software tool kits, we have implemented an OS-Mapping (Ontology-based Semantics Mapping) approach as a Java application, and constructed a network of 19383 PPs as nodes with edges weighed by their pairwise semantic similarity scores. Individual PPs were assembled from public phenomics data. Out of possible 1.87×108 pairwise connections among these nodes, about 71% of them have similarity scores between 0.2 and the maximum possible of 1.0.

Pairwise diversity ranking of polychotomous features for ensemble physiological signal classifiers.

PubMed

Gupta, Lalit; Kota, Srinivas; Molfese, Dennis L; Vaidyanathan, Ravi

2013-06-01

It is well known that fusion classifiers for physiological signal classification with diverse components (classifiers or data sets) outperform those with less diverse components. Determining component diversity, therefore, is of the utmost importance in the design of fusion classifiers that are often employed in clinical diagnostic and numerous other pattern recognition problems. In this article, a new pairwise diversity-based ranking strategy is introduced to select a subset of ensemble components, which when combined will be more diverse than any other component subset of the same size. The strategy is unified in the sense that the components can be classifiers or data sets. Moreover, the classifiers and data sets can be polychotomous. Classifier-fusion and data-fusion systems are formulated based on the diversity-based selection strategy, and the application of the two fusion strategies are demonstrated through the classification of multichannel event-related potentials. It is observed that for both classifier and data fusion, the classification accuracy tends to increase/decrease when the diversity of the component ensemble increases/decreases. For the four sets of 14-channel event-related potentials considered, it is shown that data fusion outperforms classifier fusion. Furthermore, it is demonstrated that the combination of data components that yield the best performance, in a relative sense, can be determined through the diversity-based selection strategy.

Relative importance of evolutionary dynamics depends on the composition of microbial predator-prey community.

PubMed

Friman, Ville-Petri; Dupont, Alessandra; Bass, David; Murrell, David J; Bell, Thomas

2016-06-01

Community dynamics are often studied in subsets of pairwise interactions. Scaling pairwise interactions back to the community level is, however, problematic because one given interaction might not reflect ecological and evolutionary outcomes of other functionally similar species interactions or capture the emergent eco-evolutionary dynamics arising only in more complex communities. Here we studied this experimentally by exposing Pseudomonas fluorescens SBW25 prey bacterium to four different protist predators (Tetrahymena pyriformis, Tetrahymena vorax, Chilomonas paramecium and Acanthamoeba polyphaga) in all possible single-predator, two-predator and four-predator communities for hundreds of prey generations covering both ecological and evolutionary timescales. We found that only T. pyriformis selected for prey defence in single-predator communities. Although T. pyriformis selection was constrained in the presence of the intraguild predator, T. vorax, T. pyriformis selection led to evolution of specialised prey defence strategies in the presence of C. paramecium or A. polyphaga. At the ecological level, adapted prey populations were phenotypically more diverse, less stable and less productive compared with non-adapted prey populations. These results suggest that predator community composition affects the relative importance of ecological and evolutionary processes and can crucially determine when rapid evolution has the potential to change ecological properties of microbial communities.

Relative importance of evolutionary dynamics depends on the composition of microbial predator–prey community

PubMed Central

Friman, Ville-Petri; Dupont, Alessandra; Bass, David; Murrell, David J; Bell, Thomas

2016-01-01

Community dynamics are often studied in subsets of pairwise interactions. Scaling pairwise interactions back to the community level is, however, problematic because one given interaction might not reflect ecological and evolutionary outcomes of other functionally similar species interactions or capture the emergent eco-evolutionary dynamics arising only in more complex communities. Here we studied this experimentally by exposing Pseudomonas fluorescens SBW25 prey bacterium to four different protist predators (Tetrahymena pyriformis, Tetrahymena vorax, Chilomonas paramecium and Acanthamoeba polyphaga) in all possible single-predator, two-predator and four-predator communities for hundreds of prey generations covering both ecological and evolutionary timescales. We found that only T. pyriformis selected for prey defence in single-predator communities. Although T. pyriformis selection was constrained in the presence of the intraguild predator, T. vorax, T. pyriformis selection led to evolution of specialised prey defence strategies in the presence of C. paramecium or A. polyphaga. At the ecological level, adapted prey populations were phenotypically more diverse, less stable and less productive compared with non-adapted prey populations. These results suggest that predator community composition affects the relative importance of ecological and evolutionary processes and can crucially determine when rapid evolution has the potential to change ecological properties of microbial communities. PMID:26684728

Characterization of Adelphocoris suturalis (Hemiptera: Miridae) Transcriptome from Different Developmental Stages

NASA Astrophysics Data System (ADS)

Tian, Caihong; Tek Tay, Wee; Feng, Hongqiang; Wang, Ying; Hu, Yongmin; Li, Guoping

2015-06-01

Adelphocoris suturalis is one of the most serious pest insects of Bt cotton in China, however its molecular genetics, biochemistry and physiology are poorly understood. We used high throughput sequencing platform to perform de novo transcriptome assembly and gene expression analyses across different developmental stages (eggs, 2nd and 5th instar nymphs, female and male adults). We obtained 20 GB of clean data and revealed 88,614 unigenes, including 23,830 clusters and 64,784 singletons. These unigene sequences were annotated and classified by Gene Ontology, Clusters of Orthologous Groups, and Kyoto Encyclopedia of Genes and Genomes databases. A large number of differentially expressed genes were discovered through pairwise comparisons between these developmental stages. Gene expression profiles were dramatically different between life stage transitions, with some of these most differentially expressed genes being associated with sex difference, metabolism and development. Quantitative real-time PCR results confirm deep-sequencing findings based on relative expression levels of nine randomly selected genes. Furthermore, over 791,390 single nucleotide polymorphisms and 2,682 potential simple sequence repeats were identified. Our study provided comprehensive transcriptional gene expression information for A. suturalis that will form the basis to better understanding of development pathways, hormone biosynthesis, sex differences and wing formation in mirid bugs.

Characterization of Adelphocoris suturalis (Hemiptera: Miridae) Transcriptome from Different Developmental Stages

PubMed Central

Tian, Caihong; Tek Tay, Wee; Feng, Hongqiang; Wang, Ying; Hu, Yongmin; Li, Guoping

2015-01-01

Adelphocoris suturalis is one of the most serious pest insects of Bt cotton in China, however its molecular genetics, biochemistry and physiology are poorly understood. We used high throughput sequencing platform to perform de novo transcriptome assembly and gene expression analyses across different developmental stages (eggs, 2nd and 5th instar nymphs, female and male adults). We obtained 20 GB of clean data and revealed 88,614 unigenes, including 23,830 clusters and 64,784 singletons. These unigene sequences were annotated and classified by Gene Ontology, Clusters of Orthologous Groups, and Kyoto Encyclopedia of Genes and Genomes databases. A large number of differentially expressed genes were discovered through pairwise comparisons between these developmental stages. Gene expression profiles were dramatically different between life stage transitions, with some of these most differentially expressed genes being associated with sex difference, metabolism and development. Quantitative real-time PCR results confirm deep-sequencing findings based on relative expression levels of nine randomly selected genes. Furthermore, over 791,390 single nucleotide polymorphisms and 2,682 potential simple sequence repeats were identified. Our study provided comprehensive transcriptional gene expression information for A. suturalis that will form the basis to better understanding of development pathways, hormone biosynthesis, sex differences and wing formation in mirid bugs. PMID:26047353

Comparative Transcriptome Analysis Identifies Candidate Genes Related to Skin Color Differentiation in Red Tilapia.

PubMed

Zhu, Wenbin; Wang, Lanmei; Dong, Zaijie; Chen, Xingting; Song, Feibiao; Liu, Nian; Yang, Hui; Fu, Jianjun

2016-08-11

Red tilapia is becoming more popular for aquaculture production in China in recent years. However, the pigmentation differentiation in genetic breeding is the main problem limiting its development of commercial red tilapia culture and the genetic basis of skin color variation is still unknown. In this study, we conducted Illumina sequencing of transcriptome on three color variety red tilapia. A total of 224,895,758 reads were generated, resulting in 160,762 assembled contigs that were used as reference contigs. The contigs of red tilapia transcriptome had hits in the range of 53.4% to 86.7% of the unique proteins of zebrafish, fugu, medaka, three-spined stickleback and tilapia. And 44,723 contigs containing 77,423 simple sequence repeats (SSRs) were identified, with 16,646 contigs containing more than one SSR. Three skin transcriptomes were compared pairwise and the results revealed that there were 148 common significantly differentially expressed unigenes and several key genes related to pigment synthesis, i.e. tyr, tyrp1, silv, sox10, slc24a5, cbs and slc7a11, were included. The results will facilitate understanding the molecular mechanisms of skin pigmentation differentiation in red tilapia and accelerate the molecular selection of the specific strain with consistent skin colors.

Qualitative and quantitative evaluation of solvent systems for countercurrent separation.

PubMed

Friesen, J Brent; Ahmed, Sana; Pauli, Guido F

2015-01-16

Rational solvent system selection for countercurrent chromatography and centrifugal partition chromatography technology (collectively known as countercurrent separation) studies continues to be a scientific challenge as the fundamental questions of comparing polarity range and selectivity within a solvent system family and between putative orthogonal solvent systems remain unanswered. The current emphasis on metabolomic investigations and analysis of complex mixtures necessitates the use of successive orthogonal countercurrent separation (CS) steps as part of complex fractionation protocols. Addressing the broad range of metabolite polarities demands development of new CS solvent systems with appropriate composition, polarity (π), selectivity (σ), and suitability. In this study, a mixture of twenty commercially available natural products, called the GUESSmix, was utilized to evaluate both solvent system polarity and selectively characteristics. Comparisons of GUESSmix analyte partition coefficient (K) values give rise to a measure of solvent system polarity range called the GUESSmix polarity index (GUPI). Solvatochromic dye and electrical permittivity measurements were also evaluated in quantitatively assessing solvent system polarity. The relative selectivity of solvent systems were evaluated with the GUESSmix by calculating the pairwise resolution (αip), the number of analytes found in the sweet spot (Nsw), and the pairwise resolution of those sweet spot analytes (αsw). The combination of these parameters allowed for both intra- and inter-family comparison of solvent system selectivity. Finally, 2-dimensional reciprocal shifted symmetry plots (ReSS(2)) were created to visually compare both the polarities and selectivities of solvent system pairs. This study helps to pave the way to the development of new solvent systems that are amenable to successive orthogonal CS protocols employed in metabolomic studies. Copyright © 2014 Elsevier B.V. All rights reserved.

Two-stages of chiral selectivity in the molecular self-assembly of tryptophan

NASA Astrophysics Data System (ADS)

Guisinger, Nathan

Both chirality and molecular assembly are essential and key components to life. In this study we explore the molecular assembly of the amino acid tryptophan (both L- and D- chiralities) on Cu(111). Our investigation utilizes low temperature scanning tunneling microscopy to observe resulting assemblies at the molecular scale. We find that depositing a racemic mixture of both L- and D- tryptophan results in the assembly of basic 6 molecule ``Lego'' structures that are enantiopure. These enantiopure ``Legos'' further assemble into 1-dimensional chains one block at a time. These resulting chains are also enantiopure with chiral selectivity occurring at two stages of assembly. Utilizing scanning tunneling spectroscopy we are able to probe the electronic structure of the chiral Legos that give insight into the root of the observed selectivity. Two-stages of chiral selectivity in the molecular self-assembly of tryptophan.

Human Retroviruses: Methods and Protocols

PubMed Central

Zhao, Gongpu; Zhang, Peijun

2015-01-01

Summary After virus fusion with a target cell, the viral core is released into the host cell cytoplasm and undergoes a controlled disassembly process, termed uncoating, before or as reverse transcription takes place. The cellular protein TRIM5α is a host cell restriction factor that blocks HIV-1 infection in rhesus macaque cells by targeting the viral capsid and inducing premature uncoating. The molecular mechanism of the interaction between capsid and TRIM5α remains unclear. Here, we describe an approach that utilizes cryo-electron microscopy (cryoEM) to examine the structural changes exerted on HIV-1 capsid (CA) assembly by TRIM5α binding. The TRIM5α interaction sites on CA assembly were further dissected by combining cryoEM with pair-wise cysteine mutations that crosslink CA either within a CA hexamer or between CA hexamers. Based on the structural information from cryoEM and crosslinking results from in vitro CA assemblies and purified intact HIV-1 cores, we demonstrate that direct binding of TRIM5α CC-SPRY domains to the viral capsid results in disruption and fragmentation of the surface lattice of HIV-1 capsid, specifically at inter-hexamer interfaces. The method described here can be easily adopted to study other important interactions in multi-protein complexes. PMID:24158810

Constrained spectral clustering under a local proximity structure assumption

NASA Technical Reports Server (NTRS)

Wagstaff, Kiri; Xu, Qianjun; des Jardins, Marie

2005-01-01

This work focuses on incorporating pairwise constraints into a spectral clustering algorithm. A new constrained spectral clustering method is proposed, as well as an active constraint acquisition technique and a heuristic for parameter selection. We demonstrate that our constrained spectral clustering method, CSC, works well when the data exhibits what we term local proximity structure.

Learning a constrained conditional random field for enhanced segmentation of fallen trees in ALS point clouds

NASA Astrophysics Data System (ADS)

Polewski, Przemyslaw; Yao, Wei; Heurich, Marco; Krzystek, Peter; Stilla, Uwe

2018-06-01

In this study, we present a method for improving the quality of automatic single fallen tree stem segmentation in ALS data by applying a specialized constrained conditional random field (CRF). The entire processing pipeline is composed of two steps. First, short stem segments of equal length are detected and a subset of them is selected for further processing, while in the second step the chosen segments are merged to form entire trees. The first step is accomplished using the specialized CRF defined on the space of segment labelings, capable of finding segment candidates which are easier to merge subsequently. To achieve this, the CRF considers not only the features of every candidate individually, but incorporates pairwise spatial interactions between adjacent segments into the model. In particular, pairwise interactions include a collinearity/angular deviation probability which is learned from training data as well as the ratio of spatial overlap, whereas unary potentials encode a learned probabilistic model of the laser point distribution around each segment. Each of these components enters the CRF energy with its own balance factor. To process previously unseen data, we first calculate the subset of segments for merging on a grid of balance factors by minimizing the CRF energy. Then, we perform the merging and rank the balance configurations according to the quality of their resulting merged trees, obtained from a learned tree appearance model. The final result is derived from the top-ranked configuration. We tested our approach on 5 plots from the Bavarian Forest National Park using reference data acquired in a field inventory. Compared to our previous segment selection method without pairwise interactions, an increase in detection correctness and completeness of up to 7 and 9 percentage points, respectively, was observed.

Chiral recognition and selection during the self-assembly process of protein-mimic macroanions

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

Yin, Panchao; Zhang, Zhi-Ming; Lv, Hongjin

The research on chiral recognition and chiral selection is not only fundamental in resolving the puzzle of homochirality, but also instructive in chiral separation and stereoselective catalysis. Here we report the chiral recognition and chiral selection during the self-assembly process of two enantiomeric wheel-shaped macroanions, [Fe28(μ3-O)8(Tart)16(HCOO)24]20- (Tart=D- or L-tartaric acid tetra-anion). The enantiomers are observed to remain self-sorted and self-assemble into their individual assemblies in their racemic mixture solution. The addition of chiral co-anions can selectively suppress the self-assembly process of the enantiomeric macroanions, which is further used to separate the two enantiomers from their mixtures on the basis ofmore » the size difference between the monomers and the assemblies. We believe that delicate long-range electrostatic interactions could be responsible for such high-level chiral recognition and selection.« less

Building dynamic population graph for accurate correspondence detection.

PubMed

Du, Shaoyi; Guo, Yanrong; Sanroma, Gerard; Ni, Dong; Wu, Guorong; Shen, Dinggang

2015-12-01

In medical imaging studies, there is an increasing trend for discovering the intrinsic anatomical difference across individual subjects in a dataset, such as hand images for skeletal bone age estimation. Pair-wise matching is often used to detect correspondences between each individual subject and a pre-selected model image with manually-placed landmarks. However, the large anatomical variability across individual subjects can easily compromise such pair-wise matching step. In this paper, we present a new framework to simultaneously detect correspondences among a population of individual subjects, by propagating all manually-placed landmarks from a small set of model images through a dynamically constructed image graph. Specifically, we first establish graph links between models and individual subjects according to pair-wise shape similarity (called as forward step). Next, we detect correspondences for the individual subjects with direct links to any of model images, which is achieved by a new multi-model correspondence detection approach based on our recently-published sparse point matching method. To correct those inaccurate correspondences, we further apply an error detection mechanism to automatically detect wrong correspondences and then update the image graph accordingly (called as backward step). After that, all subject images with detected correspondences are included into the set of model images, and the above two steps of graph expansion and error correction are repeated until accurate correspondences for all subject images are established. Evaluations on real hand X-ray images demonstrate that our proposed method using a dynamic graph construction approach can achieve much higher accuracy and robustness, when compared with the state-of-the-art pair-wise correspondence detection methods as well as a similar method but using static population graph. Copyright © 2015 Elsevier B.V. All rights reserved.

Experimental characterization of pairwise correlations from triple quantum correlated beams generated by cascaded four-wave mixing processes

NASA Astrophysics Data System (ADS)

Wang, Wei; Cao, Leiming; Lou, Yanbo; Du, Jinjian; Jing, Jietai

2018-01-01

We theoretically and experimentally characterize the performance of the pairwise correlations from triple quantum correlated beams based on the cascaded four-wave mixing (FWM) processes. The pairwise correlations between any two of the beams are theoretically calculated and experimentally measured. The experimental and theoretical results are in good agreement. We find that two of the three pairwise correlations can be in the quantum regime. The other pairwise correlation is always in the classical regime. In addition, we also measure the triple-beam correlation which is always in the quantum regime. Such unbalanced and controllable pairwise correlation structures may be taken as advantages in practical quantum communications, for example, hierarchical quantum secret sharing. Our results also open the way for the classification and application of quantum states generated from the cascaded FWM processes.

Automated ensemble assembly and validation of microbial genomes.

PubMed

Koren, Sergey; Treangen, Todd J; Hill, Christopher M; Pop, Mihai; Phillippy, Adam M

2014-05-03

The continued democratization of DNA sequencing has sparked a new wave of development of genome assembly and assembly validation methods. As individual research labs, rather than centralized centers, begin to sequence the majority of new genomes, it is important to establish best practices for genome assembly. However, recent evaluations such as GAGE and the Assemblathon have concluded that there is no single best approach to genome assembly. Instead, it is preferable to generate multiple assemblies and validate them to determine which is most useful for the desired analysis; this is a labor-intensive process that is often impossible or unfeasible. To encourage best practices supported by the community, we present iMetAMOS, an automated ensemble assembly pipeline; iMetAMOS encapsulates the process of running, validating, and selecting a single assembly from multiple assemblies. iMetAMOS packages several leading open-source tools into a single binary that automates parameter selection and execution of multiple assemblers, scores the resulting assemblies based on multiple validation metrics, and annotates the assemblies for genes and contaminants. We demonstrate the utility of the ensemble process on 225 previously unassembled Mycobacterium tuberculosis genomes as well as a Rhodobacter sphaeroides benchmark dataset. On these real data, iMetAMOS reliably produces validated assemblies and identifies potential contamination without user intervention. In addition, intelligent parameter selection produces assemblies of R. sphaeroides comparable to or exceeding the quality of those from the GAGE-B evaluation, affecting the relative ranking of some assemblers. Ensemble assembly with iMetAMOS provides users with multiple, validated assemblies for each genome. Although computationally limited to small or mid-sized genomes, this approach is the most effective and reproducible means for generating high-quality assemblies and enables users to select an assembly best tailored to their specific needs.

Two criteria for the selection of assembly plans - Maximizing the flexibility of sequencing the assembly tasks and minimizing the assembly time through parallel execution of assembly tasks

NASA Technical Reports Server (NTRS)

Homem De Mello, Luiz S.; Sanderson, Arthur C.

1991-01-01

The authors introduce two criteria for the evaluation and selection of assembly plans. The first criterion is to maximize the number of different sequences in which the assembly tasks can be executed. The second criterion is to minimize the total assembly time through simultaneous execution of assembly tasks. An algorithm that performs a heuristic search for the best assembly plan over the AND/OR graph representation of assembly plans is discussed. Admissible heuristics for each of the two criteria introduced are presented. Some implementation issues that affect the computational efficiency are addressed.

The Influence of Higher-Order Epistasis on Biological Fitness Landscape Topography

NASA Astrophysics Data System (ADS)

Weinreich, Daniel M.; Lan, Yinghong; Jaffe, Jacob; Heckendorn, Robert B.

2018-07-01

The effect of a mutation on the organism often depends on what other mutations are already present in its genome. Geneticists refer to such mutational interactions as epistasis. Pairwise epistatic effects have been recognized for over a century, and their evolutionary implications have received theoretical attention for nearly as long. However, pairwise epistatic interactions themselves can vary with genomic background. This is called higher-order epistasis, and its consequences for evolution are much less well understood. Here, we assess the influence that higher-order epistasis has on the topography of 16 published, biological fitness landscapes. We find that on average, their effects on fitness landscape declines with order, and suggest that notable exceptions to this trend may deserve experimental scrutiny. We conclude by highlighting opportunities for further theoretical and experimental work dissecting the influence that epistasis of all orders has on fitness landscape topography and on the efficiency of evolution by natural selection.

The Influence of Higher-Order Epistasis on Biological Fitness Landscape Topography

NASA Astrophysics Data System (ADS)

Weinreich, Daniel M.; Lan, Yinghong; Jaffe, Jacob; Heckendorn, Robert B.

2018-02-01

The effect of a mutation on the organism often depends on what other mutations are already present in its genome. Geneticists refer to such mutational interactions as epistasis. Pairwise epistatic effects have been recognized for over a century, and their evolutionary implications have received theoretical attention for nearly as long. However, pairwise epistatic interactions themselves can vary with genomic background. This is called higher-order epistasis, and its consequences for evolution are much less well understood. Here, we assess the influence that higher-order epistasis has on the topography of 16 published, biological fitness landscapes. We find that on average, their effects on fitness landscape declines with order, and suggest that notable exceptions to this trend may deserve experimental scrutiny. We conclude by highlighting opportunities for further theoretical and experimental work dissecting the influence that epistasis of all orders has on fitness landscape topography and on the efficiency of evolution by natural selection.

Beyond pairwise strategy updating in the prisoner's dilemma game

NASA Astrophysics Data System (ADS)

Wang, Xiaofeng; Perc, Matjaž; Liu, Yongkui; Chen, Xiaojie; Wang, Long

2012-10-01

In spatial games players typically alter their strategy by imitating the most successful or one randomly selected neighbor. Since a single neighbor is taken as reference, the information stemming from other neighbors is neglected, which begets the consideration of alternative, possibly more realistic approaches. Here we show that strategy changes inspired not only by the performance of individual neighbors but rather by entire neighborhoods introduce a qualitatively different evolutionary dynamics that is able to support the stable existence of very small cooperative clusters. This leads to phase diagrams that differ significantly from those obtained by means of pairwise strategy updating. In particular, the survivability of cooperators is possible even by high temptations to defect and over a much wider uncertainty range. We support the simulation results by means of pair approximations and analysis of spatial patterns, which jointly highlight the importance of local information for the resolution of social dilemmas.

Surveying alignment-free features for Ortholog detection in related yeast proteomes by using supervised big data classifiers.

PubMed

Galpert, Deborah; Fernández, Alberto; Herrera, Francisco; Antunes, Agostinho; Molina-Ruiz, Reinaldo; Agüero-Chapin, Guillermin

2018-05-03

The development of new ortholog detection algorithms and the improvement of existing ones are of major importance in functional genomics. We have previously introduced a successful supervised pairwise ortholog classification approach implemented in a big data platform that considered several pairwise protein features and the low ortholog pair ratios found between two annotated proteomes (Galpert, D et al., BioMed Research International, 2015). The supervised models were built and tested using a Saccharomycete yeast benchmark dataset proposed by Salichos and Rokas (2011). Despite several pairwise protein features being combined in a supervised big data approach; they all, to some extent were alignment-based features and the proposed algorithms were evaluated on a unique test set. Here, we aim to evaluate the impact of alignment-free features on the performance of supervised models implemented in the Spark big data platform for pairwise ortholog detection in several related yeast proteomes. The Spark Random Forest and Decision Trees with oversampling and undersampling techniques, and built with only alignment-based similarity measures or combined with several alignment-free pairwise protein features showed the highest classification performance for ortholog detection in three yeast proteome pairs. Although such supervised approaches outperformed traditional methods, there were no significant differences between the exclusive use of alignment-based similarity measures and their combination with alignment-free features, even within the twilight zone of the studied proteomes. Just when alignment-based and alignment-free features were combined in Spark Decision Trees with imbalance management, a higher success rate (98.71%) within the twilight zone could be achieved for a yeast proteome pair that underwent a whole genome duplication. The feature selection study showed that alignment-based features were top-ranked for the best classifiers while the runners-up were alignment-free features related to amino acid composition. The incorporation of alignment-free features in supervised big data models did not significantly improve ortholog detection in yeast proteomes regarding the classification qualities achieved with just alignment-based similarity measures. However, the similarity of their classification performance to that of traditional ortholog detection methods encourages the evaluation of other alignment-free protein pair descriptors in future research.

Structure based alignment and clustering of proteins (STRALCP)

DOEpatents

Zemla, Adam T.; Zhou, Carol E.; Smith, Jason R.; Lam, Marisa W.

2013-06-18

Disclosed are computational methods of clustering a set of protein structures based on local and pair-wise global similarity values. Pair-wise local and global similarity values are generated based on pair-wise structural alignments for each protein in the set of protein structures. Initially, the protein structures are clustered based on pair-wise local similarity values. The protein structures are then clustered based on pair-wise global similarity values. For each given cluster both a representative structure and spans of conserved residues are identified. The representative protein structure is used to assign newly-solved protein structures to a group. The spans are used to characterize conservation and assign a "structural footprint" to the cluster.

Redshift-space distortions of group and galaxy correlations in the Updated Zwicky Catalog

NASA Astrophysics Data System (ADS)

Padilla, N. D.; Merchán, M.; García Lambas, D.; Maia, M. G.

We calculate two-point correlation functions of galaxies and groups of galaxies selected in three dimensions from the Updated Zwicky Galaxy Catalog - (UZC). The redshift space distortion of the correlation function ξ(σ,π) in the directions parallel and perpendicular to the line of sight, induced by pairwise group peculiar velocities is evaluated. Two methods are used to characterize the pairwise velocity field. The first method consists in fitting the observed ξ(σ,π) with a distorted model with an exponential pairwise velocity distribution, in fixed σ bins. The second method compares the contours of constant predicted correlation function of this model with the data. The results are consistent with a one-dimensional pairwise rms velocity dispersion of groups 1/2=250 ± 110 km/s. We find that UZC galaxy pairwise velocity dispersion is 1/2 = 460 ± 35 km/s. Such findings point towards a smoothly varying peculiar velocity field from galaxies to systems of galaxies, a expected in a hierarchical scenario of structure formation. We estimate the real-space correlation function in the power-law approximation ξ(r)=(r/r0)γ for groups and galaxies in UZC. We obtain the correlation length, r0, from the projected correlation function W(σ)=∫- ∞∞ξ(σ,π)dπ= 2 ∫0∞ ξ(σ,π) dπ using the values of γ derived from the correlation function in projected separations ω(σ). The best fitting parameters are γ=-1.89 ± 0.17 and r0=9.7 ± 4.5 Mpc h-1 for groups, and γ=-2.00 ± 0.03, r0=5.29 ± 0.21 Mpc h-1 for galaxies. We carried out an estimate of the parameter β= Ω0.6/b for groups and galaxies using the linear approximation regime relating the real and the redshift-space correlation functions. We find βgalaxies=0.51 ± 0.15 for galaxies, in agreement with previous works, while for groups we obtain a noisy estimate β < 1.5. We have tested our methods on mock UZC catalogs taken from N-body simulations. The results of these tests show that the conclusions derived from the application of our methods to the observations are reliable and provide a suitable characterization of the spatial correlation and pairwise velocities of groups and galaxies. We also find that the second method, developed in this work, provides more stable and precise results.

Advanced membrane electrode assemblies for fuel cells

DOEpatents

Kim, Yu Seung; Pivovar, Bryan S.

2012-07-24

A method of preparing advanced membrane electrode assemblies (MEA) for use in fuel cells. A base polymer is selected for a base membrane. An electrode composition is selected to optimize properties exhibited by the membrane electrode assembly based on the selection of the base polymer. A property-tuning coating layer composition is selected based on compatibility with the base polymer and the electrode composition. A solvent is selected based on the interaction of the solvent with the base polymer and the property-tuning coating layer composition. The MEA is assembled by preparing the base membrane and then applying the property-tuning coating layer to form a composite membrane. Finally, a catalyst is applied to the composite membrane.

Advanced membrane electrode assemblies for fuel cells

DOEpatents

Kim, Yu Seung; Pivovar, Bryan S

2014-02-25

A method of preparing advanced membrane electrode assemblies (MEA) for use in fuel cells. A base polymer is selected for a base membrane. An electrode composition is selected to optimize properties exhibited by the membrane electrode assembly based on the selection of the base polymer. A property-tuning coating layer composition is selected based on compatibility with the base polymer and the electrode composition. A solvent is selected based on the interaction of the solvent with the base polymer and the property-tuning coating layer composition. The MEA is assembled by preparing the base membrane and then applying the property-tuning coating layer to form a composite membrane. Finally, a catalyst is applied to the composite membrane.

Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism

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

Graham, Emily B.; Crump, Alex R.; Resch, Charles T.

Community assembly processes govern shifts in species abundances in response to environmental change, yet our understanding of assembly remains largely decoupled from ecosystem function. Here, we test hypotheses regarding assembly and function across space and time using hyporheic microbial communities as a model system. We pair sampling of two habitat types through hydrologic fluctuation with null modeling and multivariate statistics. We demonstrate that dual selective pressures assimilate to generate compositional changes at distinct timescales among habitat types, resulting in contrasting associations of Betaproteobacteria and Thaumarchaeota with selection and with seasonal changes in aerobic metabolism. Our results culminate in a conceptualmore » model in which selection from contrasting environments regulates taxon abundance and ecosystem function through time, with increases in function when oscillating selection opposes stable selective pressures. Our model is applicable within both macrobial and microbial ecology and presents an avenue for assimilating community assembly processes into predictions of ecosystem function.« less

Algorithm for selection of optimized EPR distance restraints for de novo protein structure determination

PubMed Central

Kazmier, Kelli; Alexander, Nathan S.; Meiler, Jens; Mchaourab, Hassane S.

2010-01-01

A hybrid protein structure determination approach combining sparse Electron Paramagnetic Resonance (EPR) distance restraints and Rosetta de novo protein folding has been previously demonstrated to yield high quality models (Alexander et al., 2008). However, widespread application of this methodology to proteins of unknown structures is hindered by the lack of a general strategy to place spin label pairs in the primary sequence. In this work, we report the development of an algorithm that optimally selects spin labeling positions for the purpose of distance measurements by EPR. For the α-helical subdomain of T4 lysozyme (T4L), simulated restraints that maximize sequence separation between the two spin labels while simultaneously ensuring pairwise connectivity of secondary structure elements yielded vastly improved models by Rosetta folding. 50% of all these models have the correct fold compared to only 21% and 8% correctly folded models when randomly placed restraints or no restraints are used, respectively. Moreover, the improvements in model quality require a limited number of optimized restraints, the number of which is determined by the pairwise connectivities of T4L α-helices. The predicted improvement in Rosetta model quality was verified by experimental determination of distances between spin labels pairs selected by the algorithm. Overall, our results reinforce the rationale for the combined use of sparse EPR distance restraints and de novo folding. By alleviating the experimental bottleneck associated with restraint selection, this algorithm sets the stage for extending computational structure determination to larger, traditionally elusive protein topologies of critical structural and biochemical importance. PMID:21074624

Multiple graph regularized protein domain ranking.

PubMed

Wang, Jim Jing-Yan; Bensmail, Halima; Gao, Xin

2012-11-19

Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods. To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods. The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications.

Multiple graph regularized protein domain ranking

PubMed Central

2012-01-01

Background Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods. Results To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods. Conclusion The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications. PMID:23157331

Genetic Evaluation of Natural Populations of the Endangered Conifer Thuja koraiensis Using Microsatellite Markers by Restriction-Associated DNA Sequencing

PubMed Central

Hou, Lu; Cui, Yanhong; Li, Xiang; Chen, Wu; Zhang, Zhiyong; Pang, Xiaoming; Li, Yingyue

2018-01-01

Thuja koraiensis Nakai is an endangered conifer of high economic and ecological value in Jilin Province, China. However, studies on its population structure and conservation genetics have been limited by the lack of genomic data. Here, 37,761 microsatellites (simple sequence repeat, SSR) were detected based on 875,792 de novo-assembled contigs using a restriction-associated DNA (RAD) approach. Among these SSRs, 300 were randomly selected to test for polymorphisms and 96 obtained loci were able to amplify a fragment of expected size. Twelve polymorphic SSR markers were developed to analyze the genetic diversity and population structure of three natural populations. High genetic diversity (mean NA = 5.481, HE = 0.548) and moderate population differentiation (pairwise Fst = 0.048–0.078, Nm = 2.940–4.958) were found in this species. Molecular variance analysis suggested that most of the variation (83%) existed within populations. Combining the results of STRUCTURE, principal coordinate, and neighbor-joining analysis, the 232 individuals were divided into three genetic clusters that generally correlated with their geographical distributions. Finally, appropriate conservation strategies were proposed to protect this species. This study provides genetic information for the natural resource conservation and utilization of T. koraiensis and will facilitate further studies of the evolution and phylogeography of the species. PMID:29673217

Variation simulation for compliant sheet metal assemblies with applications

NASA Astrophysics Data System (ADS)

Long, Yufeng

Sheet metals are widely used in discrete products, such as automobiles, aircraft, furniture and electronics appliances, due to their good manufacturability and low cost. A typical automotive body assembly consists of more than 300 parts welded together in more than 200 assembly fixture stations. Such an assembly system is usually quite complex, and takes a long time to develop. As the automotive customer demands products of increasing quality in a shorter time, engineers in automotive industry turn to computer-aided engineering (CAE) tools for help. Computers are an invaluable resource for engineers, not only to simplify and automate the design process, but also to share design specifications with manufacturing groups so that production systems can be tooled up quickly and efficiently. Therefore, it is beneficial to develop computerized simulation and evaluation tools for development of automotive body assembly systems. It is a well-known fact that assembly architectures (joints, fixtures, and assembly lines) have a profound impact on dimensional quality of compliant sheet metal assemblies. To evaluate sheet metal assembly architectures, a special dimensional analysis tool need be developed for predicting dimensional variation of the assembly. Then, the corresponding systematic tools can be established to help engineers select the assembly architectures. In this dissertation, a unified variation model is developed to predict variation in compliant sheet metal assemblies by considering fixture-induced rigid-body motion, deformation and springback. Based on the unified variation model, variation propagation models in multiple assembly stations with various configurations are established. To evaluate the dimensional capability of assembly architectures, quantitative indices are proposed based on the sensitivity matrix, which are independent of the variation level of the process. Examples are given to demonstrate their applications in selecting robust assembly architectures, and some useful guidelines for selection of assembly architectures are summarized. In addition, to enhance the fault diagnosis, a systematic methodology is proposed for selection of measurement configurations. Specifically, principles involved in selecting measurements are generalized first; then, the corresponding quantitative indices are developed to evaluate the measurement configurations, and finally, examples are present.

Feedbacks between community assembly and habitat selection shape variation in local colonization

USGS Publications Warehouse

Kraus, J.M.; Vonesh, J.R.

2010-01-01

1. Non-consumptive effects of predators are increasingly recognized as important drivers of community assembly and structure. Specifically, habitat selection responses to top predators during colonization and oviposition can lead to large differences in aquatic community structure, composition and diversity. 2. These differences among communities due to predators may develop as communities assemble, potentially altering the relative quality of predator vs. predator-free habitats through time. If so, community assembly would be expected to modify the subsequent behavioural responses of colonists to habitats containing top predators. Here, we test this hypothesis by manipulating community assembly and the presence of fish in experimental ponds and measuring their independent and combined effects on patterns of colonization by insects and amphibians. 3. Assembly modified habitat selection of dytscid beetles and hylid frogs by decreasing or even reversing avoidance of pools containing blue-spotted sunfish (Enneacanthus gloriosus). However, not all habitat selection responses to fish depended on assembly history. Hydrophilid beetles and mosquitoes avoided fish while chironomids were attracted to fish pools, regardless of assembly history. 4. Our results show that community assembly causes taxa-dependent feedbacks that can modify avoidance of habitats containing a top predator. Thus, non-consumptive effects of a top predator on community structure change as communities assemble and effects of competitors and other predators combine with the direct effects of top predators to shape colonization. 5. This work reinforces the importance of habitat selection for community assembly in aquatic systems, while illustrating the range of factors that may influence colonization rates and resulting community structure. Directly manipulating communities both during colonization and post-colonization is critical for elucidating how sequential processes interact to shape communities.

Method and apparatus for selectively controlling the speed of an engine

DOEpatents

Davis, Roy Inge

2001-02-27

A control assembly 12 for use within a vehicle 10 having an engine 14 and which selectively controls the speed of the engine 14 in order to increase fuel efficiency and to effect relatively smooth starting and stopping of the engine. Particularly, in one embodiment, control assembly 12 cooperatively operates with a starter/alternator assembly 20 and is adapted for use with hybrid vehicles employing a start/stop powertrain assembly, wherein fuel efficiency is increased by selectively stopping engine operation when the vehicle has stopped.

Assembly planning based on subassembly extraction

NASA Technical Reports Server (NTRS)

Lee, Sukhan; Shin, Yeong Gil

1990-01-01

A method is presented for the automatic determination of assembly partial orders from a liaison graph representation of an assembly through the extraction of preferred subassemblies. In particular, the authors show how to select a set of tentative subassemblies by decomposing a liaison graph into a set of subgraphs based on feasibility and difficulty of disassembly, how to evaluate each of the tentative subassemblies in terms of assembly cost using the subassembly selection indices, and how to construct a hierarchical partial order graph (HPOG) as an assembly plan. The method provides an approach to assembly planning by identifying spatial parallelism in assembly as a means of constructing temporal relationships among assembly operations and solves the problem of finding a cost-effective assembly plan in a flexible environment. A case study of the assembly planning of a mechanical assembly is presented.

Biological, serological and molecular typing of potato virus Y (PVY) isolates from Tunisia.

PubMed

Tayahi, M; Gharsallah, C; Khamassy, N; Fakhfakh, H; Djilani-Khouadja, F

2016-10-17

In Tunisia, potato virus Y (PVY) currently presents a significant threat to potato production, reducing tuber yield and quality. Three hundred and eighty-five potato samples (six different cultivars) collected in autumn 2007 from nine regions in Tunisia were tested for PVY infection by DAS-ELISA. The virus was detected in all regions surveyed, with an average incidence of 80.26%. Subsequently, a panel of 82 Tunisian PVY isolates (PVY-TN) was subjected to systematic biological, serological and molecular typing using immunocapture reverse-transcription polymerase chain reaction and a series of PVY OC - and PVY N -specific monoclonal antibodies. Combined analyses revealed ~67% of PVY NTN variants of which 17 were sequenced in the 5'NTR-P1 region to assess the genetic diversity and phylogenetic relationship of PVY-TN against other worldwide PVY isolates. To investigate whether selective constraints could act on viral genomic RNA, synonymous and non-synonymous substitution rates and their ratio were analyzed. Averages of all pairwise comparisons obtained in the 5'NTR-P1 region allowed more synonymous changes, suggesting selective constraint acting in this region. Selective neutrality test was significantly negative, suggesting a rapid expansion of PVY isolates. Pairwise mismatch distribution gave a bimodal pattern and pointed to an eventually early evolution characterizing these sequences. Genetic haplotype network topology provided evidence of the existence of a distinct geographical structure. This is the first report of such genetic analyses conducted on PVY isolates from Tunisia.

Which is more effective for suppressing an infectious disease: imperfect vaccination or defense against contagion?

NASA Astrophysics Data System (ADS)

Kuga, Kazuki; Tanimoto, Jun

2018-02-01

We consider two imperfect ways to protect against an infectious disease such as influenza, namely vaccination giving only partial immunity and a defense against contagion such as wearing a mask. We build up a new analytic framework considering those two cases instead of perfect vaccination, conventionally assumed as a premise, with the assumption of an infinite and well-mixed population. Our framework also considers three different strategy-updating rules based on evolutionary game theory: conventional pairwise comparison with one randomly selected agent, another concept of pairwise comparison referring to a social average, and direct alternative selection not depending on the usual copying concept. We successfully obtain a phase diagram in which vaccination coverage at equilibrium can be compared when assuming the model of either imperfect vaccination or a defense against contagion. The obtained phase diagram reveals that a defense against contagion is marginally inferior to an imperfect vaccination as long as the same coefficient value is used. Highlights - We build a new analytical framework for a vaccination game combined with the susceptible-infected-recovered (SIR) model. - Our model can evaluate imperfect provisions such as vaccination giving only partial immunity and a defense against contagion. - We obtain a phase diagram with which to compare the quantitative effects of partial vaccination and a defense against contagion.

A Generic multi-dimensional feature extraction method using multiobjective genetic programming.

PubMed

Zhang, Yang; Rockett, Peter I

2009-01-01

In this paper, we present a generic feature extraction method for pattern classification using multiobjective genetic programming. This not only evolves the (near-)optimal set of mappings from a pattern space to a multi-dimensional decision space, but also simultaneously optimizes the dimensionality of that decision space. The presented framework evolves vector-to-vector feature extractors that maximize class separability. We demonstrate the efficacy of our approach by making statistically-founded comparisons with a wide variety of established classifier paradigms over a range of datasets and find that for most of the pairwise comparisons, our evolutionary method delivers statistically smaller misclassification errors. At very worst, our method displays no statistical difference in a few pairwise comparisons with established classifier/dataset combinations; crucially, none of the misclassification results produced by our method is worse than any comparator classifier. Although principally focused on feature extraction, feature selection is also performed as an implicit side effect; we show that both feature extraction and selection are important to the success of our technique. The presented method has the practical consequence of obviating the need to exhaustively evaluate a large family of conventional classifiers when faced with a new pattern recognition problem in order to attain a good classification accuracy.

Developing approaches for linear mixed modeling in landscape genetics through landscape-directed dispersal simulations

USGS Publications Warehouse

Row, Jeffrey R.; Knick, Steven T.; Oyler-McCance, Sara J.; Lougheed, Stephen C.; Fedy, Bradley C.

2017-01-01

Dispersal can impact population dynamics and geographic variation, and thus, genetic approaches that can establish which landscape factors influence population connectivity have ecological and evolutionary importance. Mixed models that account for the error structure of pairwise datasets are increasingly used to compare models relating genetic differentiation to pairwise measures of landscape resistance. A model selection framework based on information criteria metrics or explained variance may help disentangle the ecological and landscape factors influencing genetic structure, yet there are currently no consensus for the best protocols. Here, we develop landscape-directed simulations and test a series of replicates that emulate independent empirical datasets of two species with different life history characteristics (greater sage-grouse; eastern foxsnake). We determined that in our simulated scenarios, AIC and BIC were the best model selection indices and that marginal R2 values were biased toward more complex models. The model coefficients for landscape variables generally reflected the underlying dispersal model with confidence intervals that did not overlap with zero across the entire model set. When we controlled for geographic distance, variables not in the underlying dispersal models (i.e., nontrue) typically overlapped zero. Our study helps establish methods for using linear mixed models to identify the features underlying patterns of dispersal across a variety of landscapes.

Pairwise-Comparison Software

NASA Technical Reports Server (NTRS)

Ricks, Wendell R.

1995-01-01

Pairwise comparison (PWC) is computer program that collects data for psychometric scaling techniques now used in cognitive research. It applies technique of pairwise comparisons, which is one of many techniques commonly used to acquire the data necessary for analyses. PWC administers task, collects data from test subject, and formats data for analysis. Written in Turbo Pascal v6.0.

MOX fuel arrangement for nuclear core

DOEpatents

Kantrowitz, M.L.; Rosenstein, R.G.

1998-10-13

In order to use up a stockpile of weapons-grade plutonium, the plutonium is converted into a mixed oxide (MOX) fuel form wherein it can be disposed in a plurality of different fuel assembly types. Depending on the equilibrium cycle that is required, a predetermined number of one or more of the fuel assembly types are selected and arranged in the core of the reactor in accordance with a selected loading schedule. Each of the fuel assemblies is designed to produce different combustion characteristics whereby the appropriate selection and disposition in the core enables the resulting equilibrium cycle to closely resemble that which is produced using urania fuel. The arrangement of the MOX rods and burnable absorber rods within each of the fuel assemblies, in combination with a selective control of the amount of plutonium which is contained in each of the MOX rods, is used to tailor the combustion characteristics of the assembly. 38 figs.

Mox fuel arrangement for nuclear core

DOEpatents

Kantrowitz, Mark L.; Rosenstein, Richard G.

2001-05-15

In order to use up a stockpile of weapons-grade plutonium, the plutonium is converted into a mixed oxide (MOX) fuel form wherein it can be disposed in a plurality of different fuel assembly types. Depending on the equilibrium cycle that is required, a predetermined number of one or more of the fuel assembly types are selected and arranged in the core of the reactor in accordance with a selected loading schedule. Each of the fuel assemblies is designed to produce different combustion characteristics whereby the appropriate selection and disposition in the core enables the resulting equilibrium cycle to closely resemble that which is produced using urania fuel. The arrangement of the MOX rods and burnable absorber rods within each of the fuel assemblies, in combination with a selective control of the amount of plutonium which is contained in each of the MOX rods, is used to tailor the combustion. characteristics of the assembly.

MOX fuel arrangement for nuclear core

DOEpatents

Kantrowitz, Mark L.; Rosenstein, Richard G.

2001-07-17

In order to use up a stockpile of weapons-grade plutonium, the plutonium is converted into a mixed oxide (MOX) fuel form wherein it can be disposed in a plurality of different fuel assembly types. Depending on the equilibrium cycle that is required, a predetermined number of one or more of the fuel assembly types are selected and arranged in the core of the reactor in accordance with a selected loading schedule. Each of the fuel assemblies is designed to produce different combustion characteristics whereby the appropriate selection and disposition in the core enables the resulting equilibrium cycle to closely resemble that which is produced using urania fuel. The arrangement of the MOX rods and burnable absorber rods within each of the fuel assemblies, in combination with a selective control of the amount of plutonium which is contained in each of the MOX rods, is used to tailor the combustion characteristics of the assembly.

MOX fuel arrangement for nuclear core

DOEpatents

Kantrowitz, Mark L.; Rosenstein, Richard G.

1998-01-01

In order to use up a stockpile of weapons-grade plutonium, the plutonium is converted into a mixed oxide (MOX) fuel form wherein it can be disposed in a plurality of different fuel assembly types. Depending on the equilibrium cycle that is required, a predetermined number of one or more of the fuel assembly types are selected and arranged in the core of the reactor in accordance with a selected loading schedule. Each of the fuel assemblies is designed to produce different combustion characteristics whereby the appropriate selection and disposition in the core enables the resulting equilibrium cycle to closely resemble that which is produced using urania fuel. The arrangement of the MOX rods and burnable absorber rods within each of the fuel assemblies, in combination with a selective control of the amount of plutonium which is contained in each of the MOX rods, is used to tailor the combustion characteristics of the assembly.

Effectiveness of oral hydration in preventing contrast-induced acute kidney injury in patients undergoing coronary angiography or intervention: a pairwise and network meta-analysis.

PubMed

Zhang, Weidai; Zhang, Jiawei; Yang, Baojun; Wu, Kefei; Lin, Hanfei; Wang, Yanping; Zhou, Lihong; Wang, Huatao; Zeng, Chujuan; Chen, Xiao; Wang, Zhixing; Zhu, Junxing; Songming, Chen

2018-06-01

The effectiveness of oral hydration in preventing contrast-induced acute kidney injury (CI-AKI) in patients undergoing coronary angiography or intervention has not been well established. This study aims to evaluate the efficacy of oral hydration compared with intravenous hydration and other frequently used hydration strategies. PubMed, Embase, Web of Science, and the Cochrane central register of controlled trials were searched from inception to 8 October 2017. To be eligible for analysis, studies had to evaluate the relative efficacy of different prophylactic hydration strategies. We selected and assessed the studies that fulfilled the inclusion criteria and carried out a pairwise and network meta-analysis using RevMan5.2 and Aggregate Data Drug Information System 1.16.8 software. A total of four studies (538 participants) were included in our pairwise meta-analysis and 1754 participants from eight studies with four frequently used hydration strategies were included in a network meta-analysis. Pairwise meta-analysis indicated that oral hydration was as effective as intravenous hydration for the prevention of CI-AKI (5.88 vs. 8.43%; odds ratio: 0.73; 95% confidence interval: 0.36-1.47; P>0.05), with no significant heterogeneity between studies. Network meta-analysis showed that there was no significant difference in the prevention of CI-AKI. However, the rank probability plot suggested that oral plus intravenous hydration had a higher probability (51%) of being the best strategy, followed by diuretic plus intravenous hydration (39%) and oral hydration alone (10%). Intravenous hydration alone was the strategy with the highest probability (70%) of being the worst hydration strategy. Our study shows that oral hydration is not inferior to intravenous hydration for the prevention of CI-AKI in patients with normal or mild-to-moderate renal dysfunction undergoing coronary angiography or intervention.

Genetic association with low concentrations of high density lipoprotein-cholesterol in a pediatric population of the Middle East and North Africa: the CASPIAN-III study.

PubMed

Kelishadi, Roya; Haghjooy Javanmard, Shaghayegh; Tajadini, Mohammad Hasan; Mansourian, Marjan; Motlagh, Mohammad Esmaeil; Ardalan, Gelayol; Ban, Matthew

2014-11-01

Depressed high-density lipoprotein cholesterol (HDL-C) is prevalent the Middle East and North Africa. Some studies have documented associations between HDL-C and several single nucleotide polymorphisms (SNPs) in candidate gene polymorphisms. We investigated the associations between SNP genotypes and HDL-C levels in Iranian students, aged 10-18 years. Genotyping was performed in 750 randomly selected participants among those with low HDL-C levels (below 5th percentile), intermediate HDL-C levels (5-95th) and high HDL-C levels (above the 95th percentile). Minor allele frequencies (MAFs) of the SNPs of interest were compared between the three HDL-C groups. The vast majority of pairwise comparisons of MAFs between HDL-C groups were significant. Pairwise comparisons between low and high HDL-C groups showed significant between-group differences in MAFs for all SNPs, except for APOC3 rs5128. Pairwise comparisons between low and intermediate HDL-C groups showed significant between-group differences in MAFs for all SNPs, except for APOC3 rs5128 and APOA1 rs2893157. Pairwise comparisons between intermediate and high HDL-C groups showed significant between-group differences in MAFs for all SNPs, except for ABCA1 APOC3 rs5128 and APOA1 rs2893157. After adjustment for confounding factors, including age, sex, body mass index, low physical activity, consumption of saturated fats, and socioeconomic status, ABCA1 r1587K and CETP A373P significantly increased the risk of depressed HDL-C, and CETP Taq1 had a protective role. This study replicated several associations between HDL-C levels and candidate gene SNPs from genome-wide associations with HDL-C in Iranians from the pediatric age group. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign

PubMed Central

2007-01-01

Background Joint alignment and secondary structure prediction of two RNA sequences can significantly improve the accuracy of the structural predictions. Methods addressing this problem, however, are forced to employ constraints that reduce computation by restricting the alignments and/or structures (i.e. folds) that are permissible. In this paper, a new methodology is presented for the purpose of establishing alignment constraints based on nucleotide alignment and insertion posterior probabilities. Using a hidden Markov model, posterior probabilities of alignment and insertion are computed for all possible pairings of nucleotide positions from the two sequences. These alignment and insertion posterior probabilities are additively combined to obtain probabilities of co-incidence for nucleotide position pairs. A suitable alignment constraint is obtained by thresholding the co-incidence probabilities. The constraint is integrated with Dynalign, a free energy minimization algorithm for joint alignment and secondary structure prediction. The resulting method is benchmarked against the previous version of Dynalign and against other programs for pairwise RNA structure prediction. Results The proposed technique eliminates manual parameter selection in Dynalign and provides significant computational time savings in comparison to prior constraints in Dynalign while simultaneously providing a small improvement in the structural prediction accuracy. Savings are also realized in memory. In experiments over a 5S RNA dataset with average sequence length of approximately 120 nucleotides, the method reduces computation by a factor of 2. The method performs favorably in comparison to other programs for pairwise RNA structure prediction: yielding better accuracy, on average, and requiring significantly lesser computational resources. Conclusion Probabilistic analysis can be utilized in order to automate the determination of alignment constraints for pairwise RNA structure prediction methods in a principled fashion. These constraints can reduce the computational and memory requirements of these methods while maintaining or improving their accuracy of structural prediction. This extends the practical reach of these methods to longer length sequences. The revised Dynalign code is freely available for download. PMID:17445273

Dynamic peptide libraries for the discovery of supramolecular nanomaterials

NASA Astrophysics Data System (ADS)

Pappas, Charalampos G.; Shafi, Ramim; Sasselli, Ivan R.; Siccardi, Henry; Wang, Tong; Narang, Vishal; Abzalimov, Rinat; Wijerathne, Nadeesha; Ulijn, Rein V.

2016-11-01

Sequence-specific polymers, such as oligonucleotides and peptides, can be used as building blocks for functional supramolecular nanomaterials. The design and selection of suitable self-assembling sequences is, however, challenging because of the vast combinatorial space available. Here we report a methodology that allows the peptide sequence space to be searched for self-assembling structures. In this approach, unprotected homo- and heterodipeptides (including aromatic, aliphatic, polar and charged amino acids) are subjected to continuous enzymatic condensation, hydrolysis and sequence exchange to create a dynamic combinatorial peptide library. The free-energy change associated with the assembly process itself gives rise to selective amplification of self-assembling candidates. By changing the environmental conditions during the selection process, different sequences and consequent nanoscale morphologies are selected.

Dynamic peptide libraries for the discovery of supramolecular nanomaterials.

PubMed

Pappas, Charalampos G; Shafi, Ramim; Sasselli, Ivan R; Siccardi, Henry; Wang, Tong; Narang, Vishal; Abzalimov, Rinat; Wijerathne, Nadeesha; Ulijn, Rein V

2016-11-01

Sequence-specific polymers, such as oligonucleotides and peptides, can be used as building blocks for functional supramolecular nanomaterials. The design and selection of suitable self-assembling sequences is, however, challenging because of the vast combinatorial space available. Here we report a methodology that allows the peptide sequence space to be searched for self-assembling structures. In this approach, unprotected homo- and heterodipeptides (including aromatic, aliphatic, polar and charged amino acids) are subjected to continuous enzymatic condensation, hydrolysis and sequence exchange to create a dynamic combinatorial peptide library. The free-energy change associated with the assembly process itself gives rise to selective amplification of self-assembling candidates. By changing the environmental conditions during the selection process, different sequences and consequent nanoscale morphologies are selected.

Non-random assembly of bacterioplankton communities in the subtropical north pacific ocean.

PubMed

Eiler, Alexander; Hayakawa, Darin H; Rappé, Michael S

2011-01-01

The exploration of bacterial diversity in the global ocean has revealed new taxa and previously unrecognized metabolic potential; however, our understanding of what regulates this diversity is limited. Using terminal restriction fragment length polymorphism (T-RFLP) data from bacterial small-subunit ribosomal RNA genes we show that, independent of depth and time, a large fraction of bacterioplankton co-occurrence patterns are non-random in the oligotrophic North Pacific subtropical gyre (NPSG). Pair-wise correlations of all identified operational taxonomic units (OTUs) revealed a high degree of significance, with 6.6% of the pair-wise co-occurrences being negatively correlated and 20.7% of them being positive. The most abundant OTUs, putatively identified as Prochlorococcus, SAR11, and SAR116 bacteria, were among the most correlated OTUs. As expected, bacterial community composition lacked statistically significant patterns of seasonality in the mostly stratified water column except in a few depth horizons of the sunlit surface waters, with higher frequency variations in community structure apparently related to populations associated with the deep chlorophyll maximum. Communities were structured vertically into epipelagic, mesopelagic, and bathypelagic populations. Permutation-based statistical analyses of T-RFLP data and their corresponding metadata revealed a broad range of putative environmental drivers controlling bacterioplankton community composition in the NPSG, including concentrations of inorganic nutrients and phytoplankton pigments. Together, our results suggest that deterministic forces such as environmental filtering and interactions among taxa determine bacterioplankton community patterns, and consequently affect ecosystem functions in the NPSG.

Genetic divergence and isolation by thermal environment in geothermal populations of an aquatic invertebrate.

PubMed

Johansson, M P; Quintela, M; Laurila, A

2016-09-01

Temperature is one of the most influential forces of natural selection impacting all biological levels. In the face of increasing global temperatures, studies over small geographic scales allowing investigations on the effects of gene flow are of great value for understanding thermal adaptation. Here, we investigated genetic population structure in the freshwater gastropod Radix balthica originating from contrasting thermal habitats in three areas of geothermal activity in Iceland. Snails from 32 sites were genotyped at 208 AFLP loci. Five AFLPs were identified as putatively under divergent selection in Lake Mývatn, a geothermal lake with an almost 20 °C difference in mean temperature across a distance of a few kilometres. In four of these loci, variation across all study populations was correlated with temperature. We found significant population structure in neutral markers both within and between the areas. Cluster analysis using neutral markers classified the sites mainly by geography, whereas analyses using markers under selection differentiated the sites based on temperature. Isolation by distance was stronger in the neutral than in the outlier loci. Pairwise differences based on outlier FST were significantly correlated with temperature at different spatial scales, even after correcting for geographic distance or neutral pairwise FST differences. In general, genetic variation decreased with increasing environmental temperature, possibly suggesting that natural selection had reduced the genetic diversity in the warm origin sites. Our results emphasize the influence of environmental temperature on the genetic structure of populations and suggest local thermal adaptation in these geothermal habitats. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Analysis of Geographic and Pairwise Distances among Chinese Cashmere Goat Populations

PubMed Central

Liu, Jian-Bin; Wang, Fan; Lang, Xia; Zha, Xi; Sun, Xiao-Ping; Yue, Yao-Jing; Feng, Rui-Lin; Yang, Bo-Hui; Guo, Jian

2013-01-01

This study investigated the geographic and pairwise distances of nine Chinese local Cashmere goat populations through the analysis of 20 microsatellite DNA markers. Fluorescence PCR was used to identify the markers, which were selected based on their significance as identified by the Food and Agriculture Organization of the United Nations (FAO) and the International Society for Animal Genetics (ISAG). In total, 206 alleles were detected; the average allele number was 10.30; the polymorphism information content of loci ranged from 0.5213 to 0.7582; the number of effective alleles ranged from 4.0484 to 4.6178; the observed heterozygosity was from 0.5023 to 0.5602 for the practical sample; the expected heterozygosity ranged from 0.5783 to 0.6464; and Allelic richness ranged from 4.7551 to 8.0693. These results indicated that Chinese Cashmere goat populations exhibited rich genetic diversity. Further, the Wright’s F-statistics of subpopulation within total (FST) was 0.1184; the genetic differentiation coefficient (GST) was 0.0940; and the average gene flow (Nm) was 2.0415. All pairwise FST values among the populations were highly significant (p<0.01 or p<0.001), suggesting that the populations studied should all be considered to be separate breeds. Finally, the clustering analysis divided the Chinese Cashmere goat populations into at least four clusters, with the Hexi and Yashan goat populations alone in one cluster. These results have provided useful, practical, and important information for the future of Chinese Cashmere goat breeding. PMID:25049794

Differential Item Functioning Detection across Two Methods of Defining Group Comparisons: Pairwise and Composite Group Comparisons

ERIC Educational Resources Information Center

Sari, Halil Ibrahim; Huggins, Anne Corinne

2015-01-01

This study compares two methods of defining groups for the detection of differential item functioning (DIF): (a) pairwise comparisons and (b) composite group comparisons. We aim to emphasize and empirically support the notion that the choice of pairwise versus composite group definitions in DIF is a reflection of how one defines fairness in DIF…

Metabolic network prediction through pairwise rational kernels.

PubMed

Roche-Lima, Abiel; Domaratzki, Michael; Fristensky, Brian

2014-09-26

Metabolic networks are represented by the set of metabolic pathways. Metabolic pathways are a series of biochemical reactions, in which the product (output) from one reaction serves as the substrate (input) to another reaction. Many pathways remain incompletely characterized. One of the major challenges of computational biology is to obtain better models of metabolic pathways. Existing models are dependent on the annotation of the genes. This propagates error accumulation when the pathways are predicted by incorrectly annotated genes. Pairwise classification methods are supervised learning methods used to classify new pair of entities. Some of these classification methods, e.g., Pairwise Support Vector Machines (SVMs), use pairwise kernels. Pairwise kernels describe similarity measures between two pairs of entities. Using pairwise kernels to handle sequence data requires long processing times and large storage. Rational kernels are kernels based on weighted finite-state transducers that represent similarity measures between sequences or automata. They have been effectively used in problems that handle large amount of sequence information such as protein essentiality, natural language processing and machine translations. We create a new family of pairwise kernels using weighted finite-state transducers (called Pairwise Rational Kernel (PRK)) to predict metabolic pathways from a variety of biological data. PRKs take advantage of the simpler representations and faster algorithms of transducers. Because raw sequence data can be used, the predictor model avoids the errors introduced by incorrect gene annotations. We then developed several experiments with PRKs and Pairwise SVM to validate our methods using the metabolic network of Saccharomyces cerevisiae. As a result, when PRKs are used, our method executes faster in comparison with other pairwise kernels. Also, when we use PRKs combined with other simple kernels that include evolutionary information, the accuracy values have been improved, while maintaining lower construction and execution times. The power of using kernels is that almost any sort of data can be represented using kernels. Therefore, completely disparate types of data can be combined to add power to kernel-based machine learning methods. When we compared our proposal using PRKs with other similar kernel, the execution times were decreased, with no compromise of accuracy. We also proved that by combining PRKs with other kernels that include evolutionary information, the accuracy can also also be improved. As our proposal can use any type of sequence data, genes do not need to be properly annotated, avoiding accumulation errors because of incorrect previous annotations.

Nano-encrypted Morse code: a versatile approach to programmable and reversible nanoscale assembly and disassembly.

PubMed

Wong, Ngo Yin; Xing, Hang; Tan, Li Huey; Lu, Yi

2013-02-27

While much work has been devoted to nanoscale assembly of functional materials, selective reversible assembly of components in the nanoscale pattern at selective sites has received much less attention. Exerting such a reversible control of the assembly process will make it possible to fine-tune the functional properties of the assembly and to realize more complex designs. Herein, by taking advantage of different binding affinities of biotin and desthiobiotin toward streptavidin, we demonstrate selective and reversible decoration of DNA origami tiles with streptavidin, including revealing an encrypted Morse code "NANO" and reversible exchange of uppercase letter "I" with lowercase "i". The yields of the conjugations are high (>90%), and the process is reversible. We expect this versatile conjugation technique to be widely applicable with different nanomaterials and templates.

Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism.

PubMed

Graham, Emily B; Crump, Alex R; Resch, Charles T; Fansler, Sarah; Arntzen, Evan; Kennedy, David W; Fredrickson, Jim K; Stegen, James C

2016-01-01

Community assembly processes generate shifts in species abundances that influence ecosystem cycling of carbon and nutrients, yet our understanding of assembly remains largely separate from ecosystem-level functioning. Here, we investigate relationships between assembly and changes in microbial metabolism across space and time in hyporheic microbial communities. We pair sampling of two habitat types (i.e., attached and planktonic) through seasonal and sub-hourly hydrologic fluctuation with null modeling and temporally explicit multivariate statistics. We demonstrate that multiple selective pressures-imposed by sediment and porewater physicochemistry-integrate to generate changes in microbial community composition at distinct timescales among habitat types. These changes in composition are reflective of contrasting associations of Betaproteobacteria and Thaumarchaeota with ecological selection and with seasonal changes in microbial metabolism. We present a conceptual model based on our results in which metabolism increases when oscillating selective pressures oppose temporally stable selective pressures. Our conceptual model is pertinent to both macrobial and microbial systems experiencing multiple selective pressures and presents an avenue for assimilating community assembly processes into predictions of ecosystem-level functioning.

Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA.

PubMed

Kelly, Brendan J; Gross, Robert; Bittinger, Kyle; Sherrill-Mix, Scott; Lewis, James D; Collman, Ronald G; Bushman, Frederic D; Li, Hongzhe

2015-08-01

The variation in community composition between microbiome samples, termed beta diversity, can be measured by pairwise distance based on either presence-absence or quantitative species abundance data. PERMANOVA, a permutation-based extension of multivariate analysis of variance to a matrix of pairwise distances, partitions within-group and between-group distances to permit assessment of the effect of an exposure or intervention (grouping factor) upon the sampled microbiome. Within-group distance and exposure/intervention effect size must be accurately modeled to estimate statistical power for a microbiome study that will be analyzed with pairwise distances and PERMANOVA. We present a framework for PERMANOVA power estimation tailored to marker-gene microbiome studies that will be analyzed by pairwise distances, which includes: (i) a novel method for distance matrix simulation that permits modeling of within-group pairwise distances according to pre-specified population parameters; (ii) a method to incorporate effects of different sizes within the simulated distance matrix; (iii) a simulation-based method for estimating PERMANOVA power from simulated distance matrices; and (iv) an R statistical software package that implements the above. Matrices of pairwise distances can be efficiently simulated to satisfy the triangle inequality and incorporate group-level effects, which are quantified by the adjusted coefficient of determination, omega-squared (ω2). From simulated distance matrices, available PERMANOVA power or necessary sample size can be estimated for a planned microbiome study. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Shuttle plate braiding machine

NASA Technical Reports Server (NTRS)

Huey, Jr., Cecil O. (Inventor)

1994-01-01

A method and apparatus for moving yarn in a selected pattern to form a braided article. The apparatus includes a segmented grid of stationary support elements and a plurality of shuttles configured to carry yarn. The shuttles are supported for movement on the grid assembly and each shuttle includes a retractable plunger for engaging a reciprocating shuttle plate that moves below the grid assembly. Such engagement at selected times causes the shuttles to move about the grid assembly in a selected pattern to form a braided article of a particular geometry.

Selection of a suitable method for the preparation of polymeric nanoparticles: multi-criteria decision making approach.

PubMed

Krishnamoorthy, Kannan; Mahalingam, Manikandan

2015-03-01

The present study is aimed to select the suitable method for preparation of camptothecin loaded polymeric nanoparticles by utilizing the multi-criteria decision making method. Novel approaches of drug delivery by formulation using nanotechnology are revolutionizing the future of medicine. Recent years have witnessed unprecedented growth of research and application in the area of nanotechnology. Nanoparticles have become an important area of research in the field of drug delivery because they have the ability to deliver a wide range of drug to varying areas of body. Despite of extensive research and development, polymeric nanoparticles are frequently used to improve the therapeutic effect of drugs. A number of techniques are available for the preparation of polymeric nanoparticles. The Analytical Hierarchy Process (AHP) is a method for decision making, which are derived from individual judgements for qualitative factors, using the pair-wise comparison matrix. In AHP, a decision hierarchy is constructed with a goal, criteria and alternatives. The model uses three main criteria 1) Instrument, 2) Process and Output and 3) Cost. In addition, there are eight sub-criteria's as well as eight alternatives. Pair-wise comparison matrixes are used to obtain the overall priority weight and ranking for the selection of suitable method. Nanoprecipitation technique is the most suitable method for the preparation of camptothecin loaded polymeric nanoparticles with the highest overall priority weight of 0.297 CONCLUSION: In particular, the result indicates that the priority weights obtained from AHP could be defined as a multiple output for finding out the most suitable method for preparation of camptothecin loaded polymeric nanoparticles.

Phenotyping: Using Machine Learning for Improved Pairwise Genotype Classification Based on Root Traits

PubMed Central

Zhao, Jiangsan; Bodner, Gernot; Rewald, Boris

2016-01-01

Phenotyping local crop cultivars is becoming more and more important, as they are an important genetic source for breeding – especially in regard to inherent root system architectures. Machine learning algorithms are promising tools to assist in the analysis of complex data sets; novel approaches are need to apply them on root phenotyping data of mature plants. A greenhouse experiment was conducted in large, sand-filled columns to differentiate 16 European Pisum sativum cultivars based on 36 manually derived root traits. Through combining random forest and support vector machine models, machine learning algorithms were successfully used for unbiased identification of most distinguishing root traits and subsequent pairwise cultivar differentiation. Up to 86% of pea cultivar pairs could be distinguished based on top five important root traits (Timp5) – Timp5 differed widely between cultivar pairs. Selecting top important root traits (Timp) provided a significant improved classification compared to using all available traits or randomly selected trait sets. The most frequent Timp of mature pea cultivars was total surface area of lateral roots originating from tap root segments at 0–5 cm depth. The high classification rate implies that culturing did not lead to a major loss of variability in root system architecture in the studied pea cultivars. Our results illustrate the potential of machine learning approaches for unbiased (root) trait selection and cultivar classification based on rather small, complex phenotypic data sets derived from pot experiments. Powerful statistical approaches are essential to make use of the increasing amount of (root) phenotyping information, integrating the complex trait sets describing crop cultivars. PMID:27999587

Application of whole genome re-sequencing data in the development of diagnostic DNA markers tightly linked to a disease-resistance locus for marker-assisted selection in lupin (Lupinus angustifolius).

PubMed

Yang, Huaan; Jian, Jianbo; Li, Xuan; Renshaw, Daniel; Clements, Jonathan; Sweetingham, Mark W; Tan, Cong; Li, Chengdao

2015-09-02

Molecular marker-assisted breeding provides an efficient tool to develop improved crop varieties. A major challenge for the broad application of markers in marker-assisted selection is that the marker phenotypes must match plant phenotypes in a wide range of breeding germplasm. In this study, we used the legume crop species Lupinus angustifolius (lupin) to demonstrate the utility of whole genome sequencing and re-sequencing on the development of diagnostic markers for molecular plant breeding. Nine lupin cultivars released in Australia from 1973 to 2007 were subjected to whole genome re-sequencing. The re-sequencing data together with the reference genome sequence data were used in marker development, which revealed 180,596 to 795,735 SNP markers from pairwise comparisons among the cultivars. A total of 207,887 markers were anchored on the lupin genetic linkage map. Marker mining obtained an average of 387 SNP markers and 87 InDel markers for each of the 24 genome sequence assembly scaffolds bearing markers linked to 11 genes of agronomic interest. Using the R gene PhtjR conferring resistance to phomopsis stem blight disease as a test case, we discovered 17 candidate diagnostic markers by genotyping and selecting markers on a genetic linkage map. A further 243 candidate diagnostic markers were discovered by marker mining on a scaffold bearing non-diagnostic markers linked to the PhtjR gene. Nine out from the ten tested candidate diagnostic markers were confirmed as truly diagnostic on a broad range of commercial cultivars. Markers developed using these strategies meet the requirements for broad application in molecular plant breeding. We demonstrated that low-cost genome sequencing and re-sequencing data were sufficient and very effective in the development of diagnostic markers for marker-assisted selection. The strategies used in this study may be applied to any trait or plant species. Whole genome sequencing and re-sequencing provides a powerful tool to overcome current limitations in molecular plant breeding, which will enable plant breeders to precisely pyramid favourable genes to develop super crop varieties to meet future food demands.

Nano-Encrypted Morse Code: A Versatile Approach to Programmable and Reversible Nanoscale Assembly and Disassembly

PubMed Central

Wong, Ngo Yin; Xing, Hang; Tan, Li Huey; Lu, Yi

2013-01-01

While much work has been devoted to nanoscale assembly of functional materials, selective reversible assembly of components in the nanoscale pattern at selective sites has received much less attention. Exerting such a reversible control of the assembly process will make it possible to fine-tune the functional properties of the assembly and to realize more complex designs. Herein, by taking advantage of different binding affinities of biotin and desthiobiotin toward streptavidin, we demonstrate selective and reversible decoration of DNA origami tiles with streptavidin, including revealing an encrypted Morse code “NANO” and reversible exchange of uppercase letter “I” with lowercase “i”. The yields of the conjugations are high (> 90%) and the process is reversible. We expect this versatile conjugation technique to be widely applicable with different nanomaterials and templates. PMID:23373425

Multi-layer assemblies with predetermined stress profile and method for producing same

NASA Technical Reports Server (NTRS)

Heuer, Arthur H. (Inventor); Kahn, Harold (Inventor); Yang, Jie (Inventor); Phillips, Stephen M. (Inventor)

2003-01-01

Multi-layer assemblies of polysilicon thin films having predetermined stress characteristics and techniques for forming such assemblies are disclosed. In particular, a multi-layer assembly of polysilicon thin films may be produced that has a stress level of zero, or substantially so. The multi-layer assemblies comprise at least one constituent thin film having a tensile stress and at least one constituent thin film having a compressive stress. The thin films forming the multi-layer assemblies may be disposed immediately adjacent to one another without the use of intermediate layers between the thin films. Multi-layer assemblies exhibiting selectively determinable overall bending moments are also disclosed. Selective production of overall bending moments in microstructures enables manufacture of such structures with a wide array of geometrical configurations.

Pair-Wise Trajectory Management-Oceanic (PTM-O) . [Concept of Operations—Version 3.9

NASA Technical Reports Server (NTRS)

Jones, Kenneth M.

2014-01-01

This document describes the Pair-wise Trajectory Management-Oceanic (PTM-O) Concept of Operations (ConOps). Pair-wise Trajectory Management (PTM) is a concept that includes airborne and ground-based capabilities designed to enable and to benefit from, airborne pair-wise distance-monitoring capability. PTM includes the capabilities needed for the controller to issue a PTM clearance that resolves a conflict for a specific pair of aircraft. PTM avionics include the capabilities needed for the flight crew to manage their trajectory relative to specific designated aircraft. Pair-wise Trajectory Management PTM-Oceanic (PTM-O) is a regional specific application of the PTM concept. PTM is sponsored by the National Aeronautics and Space Administration (NASA) Concept and Technology Development Project (part of NASA's Airspace Systems Program). The goal of PTM is to use enhanced and distributed communications and surveillance along with airborne tools to permit reduced separation standards for given aircraft pairs, thereby increasing the capacity and efficiency of aircraft operations at a given altitude or volume of airspace.

A pairwise maximum entropy model accurately describes resting-state human brain networks

PubMed Central

Watanabe, Takamitsu; Hirose, Satoshi; Wada, Hiroyuki; Imai, Yoshio; Machida, Toru; Shirouzu, Ichiro; Konishi, Seiki; Miyashita, Yasushi; Masuda, Naoki

2013-01-01

The resting-state human brain networks underlie fundamental cognitive functions and consist of complex interactions among brain regions. However, the level of complexity of the resting-state networks has not been quantified, which has prevented comprehensive descriptions of the brain activity as an integrative system. Here, we address this issue by demonstrating that a pairwise maximum entropy model, which takes into account region-specific activity rates and pairwise interactions, can be robustly and accurately fitted to resting-state human brain activities obtained by functional magnetic resonance imaging. Furthermore, to validate the approximation of the resting-state networks by the pairwise maximum entropy model, we show that the functional interactions estimated by the pairwise maximum entropy model reflect anatomical connexions more accurately than the conventional functional connectivity method. These findings indicate that a relatively simple statistical model not only captures the structure of the resting-state networks but also provides a possible method to derive physiological information about various large-scale brain networks. PMID:23340410

Development of a methodology for selecting criteria and indicators of sustainable forest management: a case study on participatory assessment.

PubMed

Mendoza, G A; Prabhu, R

2000-12-01

This paper describes an application of multiple criteria analysis (MCA) in assessing criteria and indicators adapted for a particular forest management unit. The methods include: ranking, rating, and pairwise comparisons. These methods were used in a participatory decision-making environment where a team representing various stakeholders and professionals used their expert opinions and judgements in assessing different criteria and indicators (C&I) on the one hand, and how suitable and applicable they are to a forest management unit on the other. A forest concession located in Kalimantan, Indonesia, was used as the site for the case study. Results from the study show that the multicriteria methods are effective tools that can be used as structured decision aids to evaluate, prioritize, and select sets of C&I for a particular forest management unit. Ranking and rating approaches can be used as a screening tool to develop an initial list of C&I. Pairwise comparison, on the other hand, can be used as a finer filter to further reduce the list. In addition to using these three MCA methods, the study also examines two commonly used group decision-making techniques, the Delphi method and the nominal group technique. Feedback received from the participants indicates that the methods are transparent, easy to implement, and provide a convenient environment for participatory decision-making.

Phenotypic covariance at species’ borders

PubMed Central

2013-01-01

Background Understanding the evolution of species limits is important in ecology, evolution, and conservation biology. Despite its likely importance in the evolution of these limits, little is known about phenotypic covariance in geographically marginal populations, and the degree to which it constrains, or facilitates, responses to selection. We investigated phenotypic covariance in morphological traits at species’ borders by comparing phenotypic covariance matrices (P), including the degree of shared structure, the distribution of strengths of pair-wise correlations between traits, the degree of morphological integration of traits, and the ranks of matricies, between central and marginal populations of three species-pairs of coral reef fishes. Results Greater structural differences in P were observed between populations close to range margins and conspecific populations toward range centres, than between pairs of conspecific populations that were both more centrally located within their ranges. Approximately 80% of all pair-wise trait correlations within populations were greater in the north, but these differences were unrelated to the position of the sampled population with respect to the geographic range of the species. Conclusions Neither the degree of morphological integration, nor ranks of P, indicated greater evolutionary constraint at range edges. Characteristics of P observed here provide no support for constraint contributing to the formation of these species’ borders, but may instead reflect structural change in P caused by selection or drift, and their potential to evolve in the future. PMID:23714580

Phenotypic covariance at species' borders.

PubMed

Caley, M Julian; Cripps, Edward; Game, Edward T

2013-05-28

Understanding the evolution of species limits is important in ecology, evolution, and conservation biology. Despite its likely importance in the evolution of these limits, little is known about phenotypic covariance in geographically marginal populations, and the degree to which it constrains, or facilitates, responses to selection. We investigated phenotypic covariance in morphological traits at species' borders by comparing phenotypic covariance matrices (P), including the degree of shared structure, the distribution of strengths of pair-wise correlations between traits, the degree of morphological integration of traits, and the ranks of matricies, between central and marginal populations of three species-pairs of coral reef fishes. Greater structural differences in P were observed between populations close to range margins and conspecific populations toward range centres, than between pairs of conspecific populations that were both more centrally located within their ranges. Approximately 80% of all pair-wise trait correlations within populations were greater in the north, but these differences were unrelated to the position of the sampled population with respect to the geographic range of the species. Neither the degree of morphological integration, nor ranks of P, indicated greater evolutionary constraint at range edges. Characteristics of P observed here provide no support for constraint contributing to the formation of these species' borders, but may instead reflect structural change in P caused by selection or drift, and their potential to evolve in the future.

Enemy targeting, trade-offs, and the evolutionary assembly of a tortoise beetle defense arsenal

USDA-ARS?s Scientific Manuscript database

In response to intense enemy selection, immature folivorous insects have evolved elaborate, multi-trait defense arsenals. How enemies foster trait diversification and arsenal assembly depends on which selective mode they impose: whether different enemies select for the same defense or exert conflict...

Air actuated clutch for four wheel drive vehicles

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

Clohessy, K.E.

1986-12-09

A control system is described for selectively engaging and disengaging a vehicle wheel and a vehicle drive mechanism comprising; a spindle having inside and outside rotative support surfaces, the spindle adapted to be mounted to a vehicle frame, an axle portion rotatably supported on the inside support surface, and drive means for selectively and rotatively driving the axle portion relative to the spindle; a wheel hub assembly adapted to carry a vehicle wheel, the hub assembly rotatively supported on the outside support surface of the spindle; a sealed expansion chamber defined in part by the spindle, the axle portion, themore » hub assembly and a movable wall carried by the hub assembly, venting means venting the outer side of the movable wall to atmospheric pressure, the clutch ring engaged by the movable wall for movement of the clutch ring with movement of the movable wall as induced by a pressure difference generated within the chamber, and pressurizing means for selectively pressurizing and depressurizing the expansion chamber to thereby selectively shift the clutch ring between the positions of interlocking the axle portion and hub assembly and unlocking the axle portion and hub assembly.« less

Target-Independent Prediction of Drug Synergies Using Only Drug Lipophilicity

PubMed Central

2015-01-01

Physicochemical properties of compounds have been instrumental in selecting lead compounds with increased drug-likeness. However, the relationship between physicochemical properties of constituent drugs and the tendency to exhibit drug interaction has not been systematically studied. We assembled physicochemical descriptors for a set of antifungal compounds (“drugs”) previously examined for interaction. Analyzing the relationship between molecular weight, lipophilicity, H-bond donor, and H-bond acceptor values for drugs and their propensity to show pairwise antifungal drug synergy, we found that combinations of two lipophilic drugs had a greater tendency to show drug synergy. We developed a more refined decision tree model that successfully predicted drug synergy in stringent cross-validation tests based on only lipophilicity of drugs. Our predictions achieved a precision of 63% and allowed successful prediction for 58% of synergistic drug pairs, suggesting that this phenomenon can extend our understanding for a substantial fraction of synergistic drug interactions. We also generated and analyzed a large-scale synergistic human toxicity network, in which we observed that combinations of lipophilic compounds show a tendency for increased toxicity. Thus, lipophilicity, a simple and easily determined molecular descriptor, is a powerful predictor of drug synergy. It is well established that lipophilic compounds (i) are promiscuous, having many targets in the cell, and (ii) often penetrate into the cell via the cellular membrane by passive diffusion. We discuss the positive relationship between drug lipophilicity and drug synergy in the context of potential drug synergy mechanisms. PMID:25026390

Why rate when you could compare? Using the "EloChoice" package to assess pairwise comparisons of perceived physical strength.

PubMed

Clark, Andrew P; Howard, Kate L; Woods, Andy T; Penton-Voak, Ian S; Neumann, Christof

2018-01-01

We introduce "EloChoice", a package for R which uses Elo rating to assess pairwise comparisons between stimuli in order to measure perceived stimulus characteristics. To demonstrate the package and compare results from forced choice pairwise comparisons to those from more standard single stimulus rating tasks using Likert (or Likert-type) items, we investigated perceptions of physical strength from images of male bodies. The stimulus set comprised images of 82 men standing on a raised platform with minimal clothing. Strength-related anthropometrics and grip strength measurements were available for each man in the set. UK laboratory participants (Study 1) and US online participants (Study 2) viewed all images in both a Likert rating task, to collect mean Likert scores, and a pairwise comparison task, to calculate Elo, mean Elo (mElo), and Bradley-Terry scores. Within both studies, Likert, Elo and Bradley-Terry scores were closely correlated to mElo scores (all rs > 0.95), and all measures were correlated with stimulus grip strength (all rs > 0.38) and body size (all rs > 0.59). However, mElo scores were less variable than Elo scores and were hundreds of times quicker to compute than Bradley-Terry scores. Responses in pairwise comparison trials were 2/3 quicker than in Likert tasks, indicating that participants found pairwise comparisons to be easier. In addition, mElo scores generated from a data set with half the participants randomly excluded produced very comparable results to those produced with Likert scores from the full participant set, indicating that researchers require fewer participants when using pairwise comparisons.

Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA

PubMed Central

Kelly, Brendan J.; Gross, Robert; Bittinger, Kyle; Sherrill-Mix, Scott; Lewis, James D.; Collman, Ronald G.; Bushman, Frederic D.; Li, Hongzhe

2015-01-01

Motivation: The variation in community composition between microbiome samples, termed beta diversity, can be measured by pairwise distance based on either presence–absence or quantitative species abundance data. PERMANOVA, a permutation-based extension of multivariate analysis of variance to a matrix of pairwise distances, partitions within-group and between-group distances to permit assessment of the effect of an exposure or intervention (grouping factor) upon the sampled microbiome. Within-group distance and exposure/intervention effect size must be accurately modeled to estimate statistical power for a microbiome study that will be analyzed with pairwise distances and PERMANOVA. Results: We present a framework for PERMANOVA power estimation tailored to marker-gene microbiome studies that will be analyzed by pairwise distances, which includes: (i) a novel method for distance matrix simulation that permits modeling of within-group pairwise distances according to pre-specified population parameters; (ii) a method to incorporate effects of different sizes within the simulated distance matrix; (iii) a simulation-based method for estimating PERMANOVA power from simulated distance matrices; and (iv) an R statistical software package that implements the above. Matrices of pairwise distances can be efficiently simulated to satisfy the triangle inequality and incorporate group-level effects, which are quantified by the adjusted coefficient of determination, omega-squared (ω2). From simulated distance matrices, available PERMANOVA power or necessary sample size can be estimated for a planned microbiome study. Availability and implementation: http://github.com/brendankelly/micropower. Contact: brendank@mail.med.upenn.edu or hongzhe@upenn.edu PMID:25819674

Directing reaction pathways by catalyst active-site selection using self-assembled monolayers.

PubMed

Pang, Simon H; Schoenbaum, Carolyn A; Schwartz, Daniel K; Medlin, J Will

2013-01-01

One key route for controlling reaction selectivity in heterogeneous catalysis is to prepare catalysts that exhibit only specific types of sites required for desired product formation. Here we show that alkanethiolate self-assembled monolayers with varying surface densities can be used to tune selectivity to desired hydrogenation and hydrodeoxygenation products during the reaction of furfural on supported palladium catalysts. Vibrational spectroscopic studies demonstrate that the selectivity improvement is achieved by controlling the availability of specific sites for the hydrogenation of furfural on supported palladium catalysts through the selection of an appropriate alkanethiolate. Increasing self-assembled monolayer density by controlling the steric bulk of the organic tail ligand restricts adsorption on terrace sites and dramatically increases selectivity to desired products furfuryl alcohol and methylfuran. This technique of active-site selection simultaneously serves both to enhance selectivity and provide insight into the reaction mechanism.

Constraints on the optical depth of galaxy groups and clusters

DOE PAGES

Flender, Samuel; Nagai, Daisuke; McDonald, Michael

2017-03-10

Here, future data from galaxy redshift surveys, combined with high-resolutions maps of the cosmic microwave background, will enable measurements of the pairwise kinematic Sunyaev–Zel'dovich (kSZ) signal with unprecedented statistical significance. This signal probes the matter-velocity correlation function, scaled by the average optical depth (τ) of the galaxy groups and clusters in the sample, and is thus of fundamental importance for cosmology. However, in order to translate pairwise kSZ measurements into cosmological constraints, external constraints on τ are necessary. In this work, we present a new model for the intracluster medium, which takes into account star formation, feedback, non-thermal pressure, and gas cooling. Our semi-analytic model is computationally efficient and can reproduce results of recent hydrodynamical simulations of galaxy cluster formation. We calibrate the free parameters in the model using recent X-ray measurements of gas density profiles of clusters, and gas masses of groups and clusters. Our observationally calibrated model predicts the averagemore » $${\\tau }_{500}$$ (i.e., the integrated τ within a disk of size R 500) to better than 6% modeling uncertainty (at 95% confidence level). If the remaining uncertainties associated with other astrophysical uncertainties and X-ray selection effects can be better understood, our model for the optical depth should break the degeneracy between optical depth and cluster velocity in the analysis of future pairwise kSZ measurements and improve cosmological constraints with the combination of upcoming galaxy and CMB surveys, including the nature of dark energy, modified gravity, and neutrino mass.« less

Delineating slowly and rapidly evolving fractions of the Drosophila genome.

PubMed

Keith, Jonathan M; Adams, Peter; Stephen, Stuart; Mattick, John S

2008-05-01

Evolutionary conservation is an important indicator of function and a major component of bioinformatic methods to identify non-protein-coding genes. We present a new Bayesian method for segmenting pairwise alignments of eukaryotic genomes while simultaneously classifying segments into slowly and rapidly evolving fractions. We also describe an information criterion similar to the Akaike Information Criterion (AIC) for determining the number of classes. Working with pairwise alignments enables detection of differences in conservation patterns among closely related species. We analyzed three whole-genome and three partial-genome pairwise alignments among eight Drosophila species. Three distinct classes of conservation level were detected. Sequences comprising the most slowly evolving component were consistent across a range of species pairs, and constituted approximately 62-66% of the D. melanogaster genome. Almost all (>90%) of the aligned protein-coding sequence is in this fraction, suggesting much of it (comprising the majority of the Drosophila genome, including approximately 56% of non-protein-coding sequences) is functional. The size and content of the most rapidly evolving component was species dependent, and varied from 1.6% to 4.8%. This fraction is also enriched for protein-coding sequence (while containing significant amounts of non-protein-coding sequence), suggesting it is under positive selection. We also classified segments according to conservation and GC content simultaneously. This analysis identified numerous sub-classes of those identified on the basis of conservation alone, but was nevertheless consistent with that classification. Software, data, and results available at www.maths.qut.edu.au/-keithj/. Genomic segments comprising the conservation classes available in BED format.

Constraints on the optical depth of galaxy groups and clusters

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

Flender, Samuel; Nagai, Daisuke; McDonald, Michael

Here, future data from galaxy redshift surveys, combined with high-resolutions maps of the cosmic microwave background, will enable measurements of the pairwise kinematic Sunyaev–Zel'dovich (kSZ) signal with unprecedented statistical significance. This signal probes the matter-velocity correlation function, scaled by the average optical depth (τ) of the galaxy groups and clusters in the sample, and is thus of fundamental importance for cosmology. However, in order to translate pairwise kSZ measurements into cosmological constraints, external constraints on τ are necessary. In this work, we present a new model for the intracluster medium, which takes into account star formation, feedback, non-thermal pressure, and gas cooling. Our semi-analytic model is computationally efficient and can reproduce results of recent hydrodynamical simulations of galaxy cluster formation. We calibrate the free parameters in the model using recent X-ray measurements of gas density profiles of clusters, and gas masses of groups and clusters. Our observationally calibrated model predicts the averagemore » $${\\tau }_{500}$$ (i.e., the integrated τ within a disk of size R 500) to better than 6% modeling uncertainty (at 95% confidence level). If the remaining uncertainties associated with other astrophysical uncertainties and X-ray selection effects can be better understood, our model for the optical depth should break the degeneracy between optical depth and cluster velocity in the analysis of future pairwise kSZ measurements and improve cosmological constraints with the combination of upcoming galaxy and CMB surveys, including the nature of dark energy, modified gravity, and neutrino mass.« less

Numerical simulation of the pairwise interaction of deformable cells during migration in a microchannel

NASA Astrophysics Data System (ADS)

Lan, Hongzhi; Khismatullin, Damir B.

2014-07-01

Leukocytes and other circulating cells deform and move relatively to the channel flow in the lateral and translational directions. Their migratory property is important in immune response, hemostasis, cancer progression, delivery of nutrients, and microfluidic technologies such as cell separation and enrichment, and flow cytometry. Using our three-dimensional computational algorithm for multiphase viscoelastic flow, we have investigated the effect of pairwise interaction on the lateral and translational migration of circulating cells in a microchannel. The numerical simulation data show that when two cells with the same size and small separation distance interact, repulsive interaction take place until they reach the same lateral equilibrium position. During this process, they undergo swapping or passing, depending on the initial separation distance between each other. The threshold value of this distance increases with cell deformation, indicating that the cells experiencing larger deformation are more likely to swap. When a series of closely spaced cells with the same size are considered, they generally undergo damped oscillation in both lateral and translational directions until they reach equilibrium positions where they become evenly distributed in the flow direction (self-assembly phenomenon). A series of cells with a large lateral separation distance could collide repeatedly with each other, eventually crossing the centerline and entering the other side of the channel. For a series of cells with different deformability, more deformable cells, upon impact with less deformable cells, move to an equilibrium position closer to the centerline. The results of our study show that the bulk deformation of circulating cells plays a key role in their migration in a microchannel.

Systematic chemical-genetic and chemical-chemical interaction datasets for prediction of compound synergism

PubMed Central

Wildenhain, Jan; Spitzer, Michaela; Dolma, Sonam; Jarvik, Nick; White, Rachel; Roy, Marcia; Griffiths, Emma; Bellows, David S.; Wright, Gerard D.; Tyers, Mike

2016-01-01

The network structure of biological systems suggests that effective therapeutic intervention may require combinations of agents that act synergistically. However, a dearth of systematic chemical combination datasets have limited the development of predictive algorithms for chemical synergism. Here, we report two large datasets of linked chemical-genetic and chemical-chemical interactions in the budding yeast Saccharomyces cerevisiae. We screened 5,518 unique compounds against 242 diverse yeast gene deletion strains to generate an extended chemical-genetic matrix (CGM) of 492,126 chemical-gene interaction measurements. This CGM dataset contained 1,434 genotype-specific inhibitors, termed cryptagens. We selected 128 structurally diverse cryptagens and tested all pairwise combinations to generate a benchmark dataset of 8,128 pairwise chemical-chemical interaction tests for synergy prediction, termed the cryptagen matrix (CM). An accompanying database resource called ChemGRID was developed to enable analysis, visualisation and downloads of all data. The CGM and CM datasets will facilitate the benchmarking of computational approaches for synergy prediction, as well as chemical structure-activity relationship models for anti-fungal drug discovery. PMID:27874849

Why rate when you could compare? Using the “EloChoice” package to assess pairwise comparisons of perceived physical strength

PubMed Central

Howard, Kate L.; Woods, Andy T.; Penton-Voak, Ian S.; Neumann, Christof

2018-01-01

We introduce “EloChoice”, a package for R which uses Elo rating to assess pairwise comparisons between stimuli in order to measure perceived stimulus characteristics. To demonstrate the package and compare results from forced choice pairwise comparisons to those from more standard single stimulus rating tasks using Likert (or Likert-type) items, we investigated perceptions of physical strength from images of male bodies. The stimulus set comprised images of 82 men standing on a raised platform with minimal clothing. Strength-related anthropometrics and grip strength measurements were available for each man in the set. UK laboratory participants (Study 1) and US online participants (Study 2) viewed all images in both a Likert rating task, to collect mean Likert scores, and a pairwise comparison task, to calculate Elo, mean Elo (mElo), and Bradley-Terry scores. Within both studies, Likert, Elo and Bradley-Terry scores were closely correlated to mElo scores (all rs > 0.95), and all measures were correlated with stimulus grip strength (all rs > 0.38) and body size (all rs > 0.59). However, mElo scores were less variable than Elo scores and were hundreds of times quicker to compute than Bradley-Terry scores. Responses in pairwise comparison trials were 2/3 quicker than in Likert tasks, indicating that participants found pairwise comparisons to be easier. In addition, mElo scores generated from a data set with half the participants randomly excluded produced very comparable results to those produced with Likert scores from the full participant set, indicating that researchers require fewer participants when using pairwise comparisons. PMID:29293615

Automatic paper sliceform design from 3D solid models.

PubMed

Le-Nguyen, Tuong-Vu; Low, Kok-Lim; Ruiz, Conrado; Le, Sang N

2013-11-01

A paper sliceform or lattice-style pop-up is a form of papercraft that uses two sets of parallel paper patches slotted together to make a foldable structure. The structure can be folded flat, as well as fully opened (popped-up) to make the two sets of patches orthogonal to each other. Automatic design of paper sliceforms is still not supported by existing computational models and remains a challenge. We propose novel geometric formulations of valid paper sliceform designs that consider the stability, flat-foldability and physical realizability of the designs. Based on a set of sufficient construction conditions, we also present an automatic algorithm for generating valid sliceform designs that closely depict the given 3D solid models. By approximating the input models using a set of generalized cylinders, our method significantly reduces the search space for stable and flat-foldable sliceforms. To ensure the physical realizability of the designs, the algorithm automatically generates slots or slits on the patches such that no two cycles embedded in two different patches are interlocking each other. This guarantees local pairwise assembility between patches, which is empirically shown to lead to global assembility. Our method has been demonstrated on a number of example models, and the output designs have been successfully made into real paper sliceforms.

Exploring contribution of intermolecular interactions in supramolecular layered assembly of naphthyridine co-crystals: Insights from Hirshfeld surface analysis of their crystalline states

NASA Astrophysics Data System (ADS)

Seth, Saikat Kumar; Das, Nirmal Kumar; Aich, Krishnendu; Sen, Debabrata; Fun, Hoong-Kun; Goswami, Shyamaprasad

2013-09-01

Co-crystals of 1a and 1b have been prepared by slow evaporation of the solutions of mixtures of 2,7-dimethyl-1,8-naphthyridine (1), urea (a) and thiourea (b). The structures of the complexes are determined by the single crystal X-ray diffraction and a detailed investigation of the crystal packing and classification of intermolecular interactions is presented by means of Hirshfeld surface analysis which is of considerable current interest in crystal engineering. The X-ray study reveals that the co-crystal formers are envisioned to produce N-H⋯N hydrogen bond as well as N-H⋯O/N-H⋯S pair-wise hydrogen bonds and also the weaker aromatic π⋯π interactions which cooperatively take part in the crystal packing. The recurring feature of the self-assembly in the compounds is the appearance of the molecular ribbon through multiple hydrogen bonding which are further stacked into molecular layers by π⋯π stacking interactions. Hirshfeld surface analysis for visually analyzing intermolecular interactions in crystal structures employing molecular surface contours and 2D Fingerprint plots have been used to examine molecular shapes. Crystal structure analysis supported with the Hirshfeld surface and fingerprint plots enabled the identification of the significant intermolecular interactions.

HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts

PubMed Central

Laffy, Patrick W.; Wood-Charlson, Elisha M.; Turaev, Dmitrij; Weynberg, Karen D.; Botté, Emmanuelle S.; van Oppen, Madeleine J. H.; Webster, Nicole S.; Rattei, Thomas

2016-01-01

Abundant bioinformatics resources are available for the study of complex microbial metagenomes, however their utility in viral metagenomics is limited. HoloVir is a robust and flexible data analysis pipeline that provides an optimized and validated workflow for taxonomic and functional characterization of viral metagenomes derived from invertebrate holobionts. Simulated viral metagenomes comprising varying levels of viral diversity and abundance were used to determine the optimal assembly and gene prediction strategy, and multiple sequence assembly methods and gene prediction tools were tested in order to optimize our analysis workflow. HoloVir performs pairwise comparisons of single read and predicted gene datasets against the viral RefSeq database to assign taxonomy and additional comparison to phage-specific and cellular markers is undertaken to support the taxonomic assignments and identify potential cellular contamination. Broad functional classification of the predicted genes is provided by assignment of COG microbial functional category classifications using EggNOG and higher resolution functional analysis is achieved by searching for enrichment of specific Swiss-Prot keywords within the viral metagenome. Application of HoloVir to viral metagenomes from the coral Pocillopora damicornis and the sponge Rhopaloeides odorabile demonstrated that HoloVir provides a valuable tool to characterize holobiont viral communities across species, environments, or experiments. PMID:27375564

Defining the Molecular Actions of Dietary Fatty Acids in Breast Cancer: Selective Modulation of Peroxisome Proliferator-Activated Receptor Gamma. Addendum

DTIC Science & Technology

2008-05-01

0.05 significance threshold. Fol- owing ANOVA, Fisher’s least significant difference, LSD , air-wise comparison was implemented post-hoc. Briefly, the SD...average absolute difference etween any two groups was greater than the LSD critical alue, then the pair-wise comparison for those two groups ere...Xu, Y., Hin- shaw , J.C., Zimmerman, G.A., Hama, K., Aoki, J., Arai, H., Prestwich, G.D., 2003. Identification of an intracellular receptor for

A Comparative Study of Pairwise Learning Methods Based on Kernel Ridge Regression.

PubMed

Stock, Michiel; Pahikkala, Tapio; Airola, Antti; De Baets, Bernard; Waegeman, Willem

2018-06-12

Many machine learning problems can be formulated as predicting labels for a pair of objects. Problems of that kind are often referred to as pairwise learning, dyadic prediction, or network inference problems. During the past decade, kernel methods have played a dominant role in pairwise learning. They still obtain a state-of-the-art predictive performance, but a theoretical analysis of their behavior has been underexplored in the machine learning literature. In this work we review and unify kernel-based algorithms that are commonly used in different pairwise learning settings, ranging from matrix filtering to zero-shot learning. To this end, we focus on closed-form efficient instantiations of Kronecker kernel ridge regression. We show that independent task kernel ridge regression, two-step kernel ridge regression, and a linear matrix filter arise naturally as a special case of Kronecker kernel ridge regression, implying that all these methods implicitly minimize a squared loss. In addition, we analyze universality, consistency, and spectral filtering properties. Our theoretical results provide valuable insights into assessing the advantages and limitations of existing pairwise learning methods.

Large area polysilicon films with predetermined stress characteristics and method for producing same

NASA Technical Reports Server (NTRS)

Heuer, Arthur H. (Inventor); Kahn, Harold (Inventor); Yang, Jie (Inventor); Phillips, Stephen M. (Inventor)

2002-01-01

Multi-layer assemblies of polysilicon thin films having predetermined stress characteristics and techniques for forming such assemblies are disclosed. In particular, a multi-layer assembly of polysilicon thin films may be produced that has a stress level of zero, or substantially so. The multi-layer assemblies comprise at least one constituent thin film having a tensile stress and at least one constituent thin film having a compressive stress. The thin films forming the multi-layer assemblies may be disposed immediately adjacent to one another without the use of intermediate layers between the thin films. Multi-layer assemblies exhibiting selectively determinable overall bending moments are also disclosed. Selective production of overall bending moments in microstructures enables manufacture of such structures with a wide array of geometrical configurations.

Fast and accurate estimation of the covariance between pairwise maximum likelihood distances.

PubMed

Gil, Manuel

2014-01-01

Pairwise evolutionary distances are a model-based summary statistic for a set of molecular sequences. They represent the leaf-to-leaf path lengths of the underlying phylogenetic tree. Estimates of pairwise distances with overlapping paths covary because of shared mutation events. It is desirable to take these covariance structure into account to increase precision in any process that compares or combines distances. This paper introduces a fast estimator for the covariance of two pairwise maximum likelihood distances, estimated under general Markov models. The estimator is based on a conjecture (going back to Nei & Jin, 1989) which links the covariance to path lengths. It is proven here under a simple symmetric substitution model. A simulation shows that the estimator outperforms previously published ones in terms of the mean squared error.

Fast and accurate estimation of the covariance between pairwise maximum likelihood distances

PubMed Central

2014-01-01

Pairwise evolutionary distances are a model-based summary statistic for a set of molecular sequences. They represent the leaf-to-leaf path lengths of the underlying phylogenetic tree. Estimates of pairwise distances with overlapping paths covary because of shared mutation events. It is desirable to take these covariance structure into account to increase precision in any process that compares or combines distances. This paper introduces a fast estimator for the covariance of two pairwise maximum likelihood distances, estimated under general Markov models. The estimator is based on a conjecture (going back to Nei & Jin, 1989) which links the covariance to path lengths. It is proven here under a simple symmetric substitution model. A simulation shows that the estimator outperforms previously published ones in terms of the mean squared error. PMID:25279263

Superior ab initio identification, annotation and characterisation of TEs and segmental duplications from genome assemblies.

PubMed

Zeng, Lu; Kortschak, R Daniel; Raison, Joy M; Bertozzi, Terry; Adelson, David L

2018-01-01

Transposable Elements (TEs) are mobile DNA sequences that make up significant fractions of amniote genomes. However, they are difficult to detect and annotate ab initio because of their variable features, lengths and clade-specific variants. We have addressed this problem by refining and developing a Comprehensive ab initio Repeat Pipeline (CARP) to identify and cluster TEs and other repetitive sequences in genome assemblies. The pipeline begins with a pairwise alignment using krishna, a custom aligner. Single linkage clustering is then carried out to produce families of repetitive elements. Consensus sequences are then filtered for protein coding genes and then annotated using Repbase and a custom library of retrovirus and reverse transcriptase sequences. This process yields three types of family: fully annotated, partially annotated and unannotated. Fully annotated families reflect recently diverged/young known TEs present in Repbase. The remaining two types of families contain a mixture of novel TEs and segmental duplications. These can be resolved by aligning these consensus sequences back to the genome to assess copy number vs. length distribution. Our pipeline has three significant advantages compared to other methods for ab initio repeat identification: 1) we generate not only consensus sequences, but keep the genomic intervals for the original aligned sequences, allowing straightforward analysis of evolutionary dynamics, 2) consensus sequences represent low-divergence, recently/currently active TE families, 3) segmental duplications are annotated as a useful by-product. We have compared our ab initio repeat annotations for 7 genome assemblies to other methods and demonstrate that CARP compares favourably with RepeatModeler, the most widely used repeat annotation package.

Superior ab initio identification, annotation and characterisation of TEs and segmental duplications from genome assemblies

PubMed Central

Zeng, Lu; Kortschak, R. Daniel; Raison, Joy M.

2018-01-01

Transposable Elements (TEs) are mobile DNA sequences that make up significant fractions of amniote genomes. However, they are difficult to detect and annotate ab initio because of their variable features, lengths and clade-specific variants. We have addressed this problem by refining and developing a Comprehensive ab initio Repeat Pipeline (CARP) to identify and cluster TEs and other repetitive sequences in genome assemblies. The pipeline begins with a pairwise alignment using krishna, a custom aligner. Single linkage clustering is then carried out to produce families of repetitive elements. Consensus sequences are then filtered for protein coding genes and then annotated using Repbase and a custom library of retrovirus and reverse transcriptase sequences. This process yields three types of family: fully annotated, partially annotated and unannotated. Fully annotated families reflect recently diverged/young known TEs present in Repbase. The remaining two types of families contain a mixture of novel TEs and segmental duplications. These can be resolved by aligning these consensus sequences back to the genome to assess copy number vs. length distribution. Our pipeline has three significant advantages compared to other methods for ab initio repeat identification: 1) we generate not only consensus sequences, but keep the genomic intervals for the original aligned sequences, allowing straightforward analysis of evolutionary dynamics, 2) consensus sequences represent low-divergence, recently/currently active TE families, 3) segmental duplications are annotated as a useful by-product. We have compared our ab initio repeat annotations for 7 genome assemblies to other methods and demonstrate that CARP compares favourably with RepeatModeler, the most widely used repeat annotation package. PMID:29538441

Mutation-selection equilibrium in games with multiple strategies.

PubMed

Antal, Tibor; Traulsen, Arne; Ohtsuki, Hisashi; Tarnita, Corina E; Nowak, Martin A

2009-06-21

In evolutionary games the fitness of individuals is not constant but depends on the relative abundance of the various strategies in the population. Here we study general games among n strategies in populations of large but finite size. We explore stochastic evolutionary dynamics under weak selection, but for any mutation rate. We analyze the frequency dependent Moran process in well-mixed populations, but almost identical results are found for the Wright-Fisher and Pairwise Comparison processes. Surprisingly simple conditions specify whether a strategy is more abundant on average than 1/n, or than another strategy, in the mutation-selection equilibrium. We find one condition that holds for low mutation rate and another condition that holds for high mutation rate. A linear combination of these two conditions holds for any mutation rate. Our results allow a complete characterization of nxn games in the limit of weak selection.

Selection of a Suitable Method for the Preparation of Polymeric Nanoparticles: Multi-Criteria Decision Making Approach

PubMed Central

Krishnamoorthy, Kannan; Mahalingam, Manikandan

2015-01-01

Purpose: The present study is aimed to select the suitable method for preparation of camptothecin loaded polymeric nanoparticles by utilizing the multi-criteria decision making method. Novel approaches of drug delivery by formulation using nanotechnology are revolutionizing the future of medicine. Recent years have witnessed unprecedented growth of research and application in the area of nanotechnology. Nanoparticles have become an important area of research in the field of drug delivery because they have the ability to deliver a wide range of drug to varying areas of body. Methods: Despite of extensive research and development, polymeric nanoparticles are frequently used to improve the therapeutic effect of drugs. A number of techniques are available for the preparation of polymeric nanoparticles. The Analytical Hierarchy Process (AHP) is a method for decision making, which are derived from individual judgements for qualitative factors, using the pair-wise comparison matrix. In AHP, a decision hierarchy is constructed with a goal, criteria and alternatives. Results: The model uses three main criteria 1) Instrument, 2) Process and Output and 3) Cost. In addition, there are eight sub-criteria’s as well as eight alternatives. Pair-wise comparison matrixes are used to obtain the overall priority weight and ranking for the selection of suitable method. Nanoprecipitation technique is the most suitable method for the preparation of camptothecin loaded polymeric nanoparticles with the highest overall priority weight of 0.297 Conclusion: In particular, the result indicates that the priority weights obtained from AHP could be defined as a multiple output for finding out the most suitable method for preparation of camptothecin loaded polymeric nanoparticles. PMID:25789220

Blood-Based Gene Expression Profiles Models for Classification of Subsyndromal Symptomatic Depression and Major Depressive Disorder

PubMed Central

Yu, Shunying; Yuan, Chengmei; Hong, Wu; Wang, Zuowei; Cui, Jian; Shi, Tieliu; Fang, Yiru

2012-01-01

Subsyndromal symptomatic depression (SSD) is a subtype of subthreshold depressive and also lead to significant psychosocial functional impairment as same as major depressive disorder (MDD). Several studies have suggested that SSD is a transitory phenomena in the depression spectrum and is thus considered a subtype of depression. However, the pathophysioloy of depression remain largely obscure and studies on SSD are limited. The present study compared the expression profile and made the classification with the leukocytes by using whole-genome cRNA microarrays among drug-free first-episode subjects with SSD, MDD, and matched controls (8 subjects in each group). Support vector machines (SVMs) were utilized for training and testing on candidate signature expression profiles from signature selection step. Firstly, we identified 63 differentially expressed SSD signatures in contrast to control (P< = 5.0E-4) and 30 differentially expressed MDD signatures in contrast to control, respectively. Then, 123 gene signatures were identified with significantly differential expression level between SSD and MDD. Secondly, in order to conduct priority selection for biomarkers for SSD and MDD together, we selected top gene signatures from each group of pair-wise comparison results, and merged the signatures together to generate better profiles used for clearly classify SSD and MDD sets in the same time. In details, we tried different combination of signatures from the three pair-wise compartmental results and finally determined 48 gene expression signatures with 100% accuracy. Our finding suggested that SSD and MDD did not exhibit the same expressed genome signature with peripheral blood leukocyte, and blood cell–derived RNA of these 48 gene models may have significant value for performing diagnostic functions and classifying SSD, MDD, and healthy controls. PMID:22348066

Latching relay switch assembly

DOEpatents

Duimstra, Frederick A.

1991-01-01

A latching relay switch assembly which includes a coil section and a switch or contact section. The coil section includes at least one permanent magnet and at least one electromagnet. The respective sections are, generally, arranged in separate locations or cavities in the assembly. The switch is latched by a permanent magnet assembly and selectively switched by an overriding electromagnetic assembly.

Electrolytic oxide reduction system

DOEpatents

Wiedmeyer, Stanley G; Barnes, Laurel A; Williamson, Mark A; Willit, James L; Berger, John F

2015-04-28

An electrolytic oxide reduction system according to a non-limiting embodiment of the present invention may include a plurality of anode assemblies, a plurality of cathode assemblies, and a lift system configured to engage the anode and cathode assemblies. The cathode assemblies may be alternately arranged with the anode assemblies such that each cathode assembly is flanked by two anode assemblies. The lift system may be configured to selectively engage the anode and cathode assemblies so as to allow the simultaneous lifting of any combination of the anode and cathode assemblies (whether adjacent or non-adjacent).

Non-pairwise additivity of the leading-order dispersion energy

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

Hollett, Joshua W., E-mail: j.hollett@uwinnipeg.ca

2015-02-28

The leading-order (i.e., dipole-dipole) dispersion energy is calculated for one-dimensional (1D) and two-dimensional (2D) infinite lattices, and an infinite 1D array of infinitely long lines, of doubly occupied locally harmonic wells. The dispersion energy is decomposed into pairwise and non-pairwise additive components. By varying the force constant and separation of the wells, the non-pairwise additive contribution to the dispersion energy is shown to depend on the overlap of density between neighboring wells. As well separation is increased, the non-pairwise additivity of the dispersion energy decays. The different rates of decay for 1D and 2D lattices of wells is explained inmore » terms of a Jacobian effect that influences the number of nearest neighbors. For an array of infinitely long lines of wells spaced 5 bohrs apart, and an inter-well spacing of 3 bohrs within a line, the non-pairwise additive component of the leading-order dispersion energy is −0.11 kJ mol{sup −1} well{sup −1}, which is 7% of the total. The polarizability of the wells and the density overlap between them are small in comparison to that of the atomic densities that arise from the molecular density partitioning used in post-density-functional theory (DFT) damped dispersion corrections, or DFT-D methods. Therefore, the nonadditivity of the leading-order dispersion observed here is a conservative estimate of that in molecular clusters.« less

Computational design of enzyme-ligand binding using a combined energy function and deterministic sequence optimization algorithm.

PubMed

Tian, Ye; Huang, Xiaoqiang; Zhu, Yushan

2015-08-01

Enzyme amino-acid sequences at ligand-binding interfaces are evolutionarily optimized for reactions, and the natural conformation of an enzyme-ligand complex must have a low free energy relative to alternative conformations in native-like or non-native sequences. Based on this assumption, a combined energy function was developed for enzyme design and then evaluated by recapitulating native enzyme sequences at ligand-binding interfaces for 10 enzyme-ligand complexes. In this energy function, the electrostatic interaction between polar or charged atoms at buried interfaces is described by an explicitly orientation-dependent hydrogen-bonding potential and a pairwise-decomposable generalized Born model based on the general side chain in the protein design framework. The energy function is augmented with a pairwise surface-area based hydrophobic contribution for nonpolar atom burial. Using this function, on average, 78% of the amino acids at ligand-binding sites were predicted correctly in the minimum-energy sequences, whereas 84% were predicted correctly in the most-similar sequences, which were selected from the top 20 sequences for each enzyme-ligand complex. Hydrogen bonds at the enzyme-ligand binding interfaces in the 10 complexes were usually recovered with the correct geometries. The binding energies calculated using the combined energy function helped to discriminate the active sequences from a pool of alternative sequences that were generated by repeatedly solving a series of mixed-integer linear programming problems for sequence selection with increasing integer cuts.

Diffusion-weighted imaging of the liver at 3 T using section-selection gradient reversal: emphasis on chemical shift artefacts and lesion conspicuity.

PubMed

Lee, J S; Kim, Y K; Jeong, W K; Choi, D; Lee, W J

2015-04-01

To assess the value of section-selection gradient reversal (SSGR) in liver diffusion-weighted imaging (DWI) by comparing it to conventional DWI with an emphasis on chemical shift artefacts and lesion conspicuity. Forty-eight patients (29 men and 19 women; age range 33-80 years) with 48 liver lesions underwent two DWI examinations using spectral presaturation with inversion recovery fat suppression with and without SSGR at 3 T. Two reviewers evaluated each DWI (b = 100 and b = 800 image) with respect to chemical shift artefacts and liver lesion conspicuity using five-point scales and performed pairwise comparisons between the two DWIs. The signal-to-noise ratio (SNR) of the liver and the lesion and the lesion-liver contrast-to-noise ratio (CNR) were also calculated. SSGR-DWI was significantly better than conventional DWI with respect to chemical shift artefacts and lesion conspicuity in both separate reviews and pairwise comparisons (p < 0.05). There were significant differences in the SNR of the liver (b = 100 and b = 800 images) and lesion (b = 800) between SSGR-DWI and conventional DWI (p < 0.05). Applying the SSGR method to DWI using SPIR fat suppression at 3 T could significantly reduce chemical shift artefacts without incurring additional acquisition time or SNR penalties, which leads to increased conspicuity of focal liver lesions. Copyright © 2014 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

Inferring Weighted Directed Association Network from Multivariate Time Series with a Synthetic Method of Partial Symbolic Transfer Entropy Spectrum and Granger Causality

PubMed Central

Hu, Yanzhu; Ai, Xinbo

2016-01-01

Complex network methodology is very useful for complex system explorer. However, the relationships among variables in complex system are usually not clear. Therefore, inferring association networks among variables from their observed data has been a popular research topic. We propose a synthetic method, named small-shuffle partial symbolic transfer entropy spectrum (SSPSTES), for inferring association network from multivariate time series. The method synthesizes surrogate data, partial symbolic transfer entropy (PSTE) and Granger causality. A proper threshold selection is crucial for common correlation identification methods and it is not easy for users. The proposed method can not only identify the strong correlation without selecting a threshold but also has the ability of correlation quantification, direction identification and temporal relation identification. The method can be divided into three layers, i.e. data layer, model layer and network layer. In the model layer, the method identifies all the possible pair-wise correlation. In the network layer, we introduce a filter algorithm to remove the indirect weak correlation and retain strong correlation. Finally, we build a weighted adjacency matrix, the value of each entry representing the correlation level between pair-wise variables, and then get the weighted directed association network. Two numerical simulated data from linear system and nonlinear system are illustrated to show the steps and performance of the proposed approach. The ability of the proposed method is approved by an application finally. PMID:27832153

Photonic-structured fibers assembled from cellulose nanocrystals with tunable polarized selective reflection.

PubMed

Meng, Xin; Pan, Hui; Lu, Tao; Chen, Zhixin; Chen, Yanru; Zhang, Di; Zhu, Shenmin

2018-08-10

Fibers with self-assembled photonic structures are of special interest due to their unique photonic properties and potential applications in the smart textile industry. Inspired by nature, the photonic-structured fibers were fabricated through the self-assembly of chiral nematic cellulose nanocrystals (CNCs) and the fibers showed tunably brilliant and selectively reflected colors under crossed-polarization. A simple wet-spinning method was applied to prepare composite fibers of the mixed CNC matrix and polyvinyl alcohol (PVA) additions. During the processing, a cholesteric CNC phase formed photonic fibers through a self-assembly process. The selective color reflection of the composite fibers in the polarized condition showed a typical red-shift tendency with an increase in the PVA content, which was attributed to the increased helical pitch of the CNC. Furthermore, the polarized angle could also alter the reflected colors. Owing to their excellent selective reflection properties under the polarized condition, CNC-based photonic fibers are promising as the next-generation of smart fibers, applied in the fields of specific display and sensing.

Intransitivity is infrequent and fails to promote annual plant coexistence without pairwise niche differences.

PubMed

Godoy, Oscar; Stouffer, Daniel B; Kraft, Nathan J B; Levine, Jonathan M

2017-05-01

Intransitive competition is often projected to be a widespread mechanism of species coexistence in ecological communities. However, it is unknown how much of the coexistence we observe in nature results from this mechanism when species interactions are also stabilized by pairwise niche differences. We combined field-parameterized models of competition among 18 annual plant species with tools from network theory to quantify the prevalence of intransitive competitive relationships. We then analyzed the predicted outcome of competitive interactions with and without pairwise niche differences. Intransitive competition was found for just 15-19% of the 816 possible triplets, and this mechanism was never sufficient to stabilize the coexistence of the triplet when the pair-wise niche differences between competitors were removed. Of the transitive and intransitive triplets, only four were predicted to coexist and these were more similar in multidimensional trait space defined by 11 functional traits than non-coexisting triplets. Our results argue that intransitive competition may be less frequent than recently posed, and that even when it does operate, pairwise niche differences may be key to possible coexistence. © 2017 by the Ecological Society of America.

Dynamics of pairwise motions in the Cosmic Web

NASA Astrophysics Data System (ADS)

Hellwing, Wojciech A.

2016-10-01

We present results of analysis of the dark matter (DM) pairwise velocity statistics in different Cosmic Web environments. We use the DM velocity and density field from the Millennium 2 simulation together with the NEXUS+ algorithm to segment the simulation volume into voxels uniquely identifying one of the four possible environments: nodes, filaments, walls or cosmic voids. We show that the PDFs of the mean infall velocities v 12 as well as its spatial dependence together with the perpendicular and parallel velocity dispersions bear a significant signal of the large-scale structure environment in which DM particle pairs are embedded. The pairwise flows are notably colder and have smaller mean magnitude in wall and voids, when compared to much denser environments of filaments and nodes. We discuss on our results, indicating that they are consistent with a simple theoretical predictions for pairwise motions as induced by gravitational instability mechanism. Our results indicate that the Cosmic Web elements are coherent dynamical entities rather than just temporal geometrical associations. In addition it should be possible to observationally test various Cosmic Web finding algorithms by segmenting available peculiar velocity data and studying resulting pairwise velocity statistics.

Competing Thermodynamic and Dynamic Factors Select Molecular Assemblies on a Gold Surface

NASA Astrophysics Data System (ADS)

Haxton, Thomas K.; Zhou, Hui; Tamblyn, Isaac; Eom, Daejin; Hu, Zonghai; Neaton, Jeffrey B.; Heinz, Tony F.; Whitelam, Stephen

2013-12-01

Controlling the self-assembly of surface-adsorbed molecules into nanostructures requires understanding physical mechanisms that act across multiple length and time scales. By combining scanning tunneling microscopy with hierarchical ab initio and statistical mechanical modeling of 1,4-substituted benzenediamine (BDA) molecules adsorbed on a gold (111) surface, we demonstrate that apparently simple nanostructures are selected by a subtle competition of thermodynamics and dynamics. Of the collection of possible BDA nanostructures mechanically stabilized by hydrogen bonding, the interplay of intermolecular forces, surface modulation, and assembly dynamics select at low temperature a particular subset: low free energy oriented linear chains of monomers and high free energy branched chains.

Dispersal-Based Microbial Community Assembly Decreases Biogeochemical Function

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

Graham, Emily B.; Stegen, James C.

Ecological mechanisms influence relationships among microbial communities, which in turn impact biogeochemistry. In particular, microbial communities are assembled by deterministic (e.g., selection) and stochastic (e.g., dispersal) processes, and the relative balance of these two process types is hypothesized to alter the influence of microbial communities over biogeochemical function. We used an ecological simulation model to evaluate this hypothesis, defining biogeochemical function generically to represent any biogeochemical reaction of interest. We assembled receiving communities under different levels of dispersal from a source community that was assembled purely by selection. The dispersal scenarios ranged from no dispersal (i.e., selection-only) to dispersal ratesmore » high enough to overwhelm selection (i.e., homogenizing dispersal). We used an aggregate measure of community fitness to infer a given community’s biogeochemical function relative to other communities. We also used ecological null models to further link the relative influence of deterministic assembly to function. We found that increasing rates of dispersal decrease biogeochemical function by increasing the proportion of maladapted taxa in a local community. Niche breadth was also a key determinant of biogeochemical function, suggesting a tradeoff between the function of generalist and specialist species. Finally, we show that microbial assembly processes exert greater influence over biogeochemical function when there is variation in the relative contributions of dispersal and selection among communities. Taken together, our results highlight the influence of spatial processes on biogeochemical function and indicate the need to account for such effects in models that aim to predict biogeochemical function under future environmental scenarios.« less

Dispersal-Based Microbial Community Assembly Decreases Biogeochemical Function

DOE PAGES

Graham, Emily B.; Stegen, James C.

2017-11-01

Ecological mechanisms influence relationships among microbial communities, which in turn impact biogeochemistry. In particular, microbial communities are assembled by deterministic (e.g., selection) and stochastic (e.g., dispersal) processes, and the relative balance of these two process types is hypothesized to alter the influence of microbial communities over biogeochemical function. We used an ecological simulation model to evaluate this hypothesis, defining biogeochemical function generically to represent any biogeochemical reaction of interest. We assembled receiving communities under different levels of dispersal from a source community that was assembled purely by selection. The dispersal scenarios ranged from no dispersal (i.e., selection-only) to dispersal ratesmore » high enough to overwhelm selection (i.e., homogenizing dispersal). We used an aggregate measure of community fitness to infer a given community’s biogeochemical function relative to other communities. We also used ecological null models to further link the relative influence of deterministic assembly to function. We found that increasing rates of dispersal decrease biogeochemical function by increasing the proportion of maladapted taxa in a local community. Niche breadth was also a key determinant of biogeochemical function, suggesting a tradeoff between the function of generalist and specialist species. Finally, we show that microbial assembly processes exert greater influence over biogeochemical function when there is variation in the relative contributions of dispersal and selection among communities. Taken together, our results highlight the influence of spatial processes on biogeochemical function and indicate the need to account for such effects in models that aim to predict biogeochemical function under future environmental scenarios.« less

Exponential series approaches for nonparametric graphical models

NASA Astrophysics Data System (ADS)

Janofsky, Eric

Markov Random Fields (MRFs) or undirected graphical models are parsimonious representations of joint probability distributions. This thesis studies high-dimensional, continuous-valued pairwise Markov Random Fields. We are particularly interested in approximating pairwise densities whose logarithm belongs to a Sobolev space. For this problem we propose the method of exponential series which approximates the log density by a finite-dimensional exponential family with the number of sufficient statistics increasing with the sample size. We consider two approaches to estimating these models. The first is regularized maximum likelihood. This involves optimizing the sum of the log-likelihood of the data and a sparsity-inducing regularizer. We then propose a variational approximation to the likelihood based on tree-reweighted, nonparametric message passing. This approximation allows for upper bounds on risk estimates, leverages parallelization and is scalable to densities on hundreds of nodes. We show how the regularized variational MLE may be estimated using a proximal gradient algorithm. We then consider estimation using regularized score matching. This approach uses an alternative scoring rule to the log-likelihood, which obviates the need to compute the normalizing constant of the distribution. For general continuous-valued exponential families, we provide parameter and edge consistency results. As a special case we detail a new approach to sparse precision matrix estimation which has statistical performance competitive with the graphical lasso and computational performance competitive with the state-of-the-art glasso algorithm. We then describe results for model selection in the nonparametric pairwise model using exponential series. The regularized score matching problem is shown to be a convex program; we provide scalable algorithms based on consensus alternating direction method of multipliers (ADMM) and coordinate-wise descent. We use simulations to compare our method to others in the literature as well as the aforementioned TRW estimator.

Analyses of Selected Automotive Parts and Assemblies for Cost and Material Impacts

DOT National Transportation Integrated Search

1979-03-01

This is a study of selected automotive parts and assemblies analyzed to determine the elements of manufacturing cost and methods of production. Parts from the 1975 Ford Pinto, 1975 Chevelle, 1976 Audi 100LS, and the VW Rabbit are included in the sele...

EASE (Experimental Assembly of Structures in EVA) overview of selected results

NASA Technical Reports Server (NTRS)

Akin, David L.

1987-01-01

Experimental Assembly of Structures in EVA (EASE) objectives, experimental protocol, neutral buoyancy simulation, task time distribution, assembly task performance, metabolic rate/biomedical readouts are summarized. This presentation is shown in charts, figures, and graphs.

SynTrack: DNA Assembly Workflow Management (SynTrack) v2.0.1

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

MENG, XIANWEI; SIMIRENKO, LISA

2016-12-01

SynTrack is a dynamic, workflow-driven data management system that tracks the DNA build process: Management of the hierarchical relationships of the DNA fragments; Monitoring of process tasks for the assembly of multiple DNA fragments into final constructs; Creations of vendor order forms with selectable building blocks. Organizing plate layouts barcodes for vendor/pcr/fusion/chewback/bioassay/glycerol/master plate maps (default/condensed); Creating or updating Pre-Assembly/Assembly process workflows with selected building blocks; Generating Echo pooling instructions based on plate maps; Tracking of building block orders, received and final assembled for delivering; Bulk updating of colony or PCR amplification information, fusion PCR and chewback results; Updating with QA/QCmore » outcome with .csv & .xlsx template files; Re-work assembly workflow enabled before and after sequencing validation; and Tracking of plate/well data changes and status updates and reporting of master plate status with QC outcomes.« less

Drive piston assembly for a valve actuator assembly

DOEpatents

Sun, Zongxuan

2010-02-23

A drive piston assembly is provided that is operable to selectively open a poppet valve. The drive piston assembly includes a cartridge defining a generally stepped bore. A drive piston is movable within the generally stepped bore and a boost sleeve is coaxially disposed with respect to the drive piston. A main fluid chamber is at least partially defined by the generally stepped bore, drive piston, and boost sleeve. First and second feedback chambers are at least partially defined by the drive piston and each are disposed at opposite ends of the drive piston. At least one of the drive piston and the boost sleeve is sufficiently configured to move within the generally stepped bore in response to fluid pressure within the main fluid chamber to selectively open the poppet valve. A valve actuator assembly and engine are also provided incorporating the disclosed drive piston assembly.

Bearing assemblies, apparatuses, and motor assemblies using the same

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

Sexton, Timothy N.; Cooley, Craig H.; Knuteson, Cody W.

2015-12-29

Various embodiments of the invention relate to bearing assemblies, apparatuses and motor assemblies that include geometric features configured to impart a selected amount of heat transfer and/or hydrodynamic film formation. In an embodiment, a bearing assembly may include a plurality of superhard bearing pads distributed circumferentially about an axis. At least some of the plurality of superhard bearing pads may include a plurality of sub-superhard bearing elements defining a bearing surface. At least some of the plurality of sub-superhard bearing elements may be spaced from one another by one or more voids to impart a selected amount of heat transfermore » and hydrodynamic film formation thereon during operation. The bearing assembly may also include a support ring that carries the plurality of superhard bearing pads. In addition, at least a portion of the sub-superhard bearing elements may extend beyond the support ring.« less

Quantitative self-assembly prediction yields targeted nanomedicines

NASA Astrophysics Data System (ADS)

Shamay, Yosi; Shah, Janki; Işık, Mehtap; Mizrachi, Aviram; Leibold, Josef; Tschaharganeh, Darjus F.; Roxbury, Daniel; Budhathoki-Uprety, Januka; Nawaly, Karla; Sugarman, James L.; Baut, Emily; Neiman, Michelle R.; Dacek, Megan; Ganesh, Kripa S.; Johnson, Darren C.; Sridharan, Ramya; Chu, Karen L.; Rajasekhar, Vinagolu K.; Lowe, Scott W.; Chodera, John D.; Heller, Daniel A.

2018-02-01

Development of targeted nanoparticle drug carriers often requires complex synthetic schemes involving both supramolecular self-assembly and chemical modification. These processes are generally difficult to predict, execute, and control. We describe herein a targeted drug delivery system that is accurately and quantitatively predicted to self-assemble into nanoparticles based on the molecular structures of precursor molecules, which are the drugs themselves. The drugs assemble with the aid of sulfated indocyanines into particles with ultrahigh drug loadings of up to 90%. We devised quantitative structure-nanoparticle assembly prediction (QSNAP) models to identify and validate electrotopological molecular descriptors as highly predictive indicators of nano-assembly and nanoparticle size. The resulting nanoparticles selectively targeted kinase inhibitors to caveolin-1-expressing human colon cancer and autochthonous liver cancer models to yield striking therapeutic effects while avoiding pERK inhibition in healthy skin. This finding enables the computational design of nanomedicines based on quantitative models for drug payload selection.

Effect of interacting second- and third-order stimulus-dependent correlations on population-coding asymmetries.

PubMed

Montangie, Lisandro; Montani, Fernando

2016-10-01

Spike correlations among neurons are widely encountered in the brain. Although models accounting for pairwise interactions have proved able to capture some of the most important features of population activity at the level of the retina, the evidence shows that pairwise neuronal correlation analysis does not resolve cooperative population dynamics by itself. By means of a series expansion for short time scales of the mutual information conveyed by a population of neurons, the information transmission can be broken down into firing rate and correlational components. In a proposed extension of this framework, we investigate the information components considering both second- and higher-order correlations. We show that the existence of a mixed stimulus-dependent correlation term defines a new scenario for the interplay between pairwise and higher-than-pairwise interactions in noise and signal correlations that would lead either to redundancy or synergy in the information-theoretic sense.

Pairwise Force Smoothed Particle Hydrodynamics model for multiphase flow: Surface tension and contact line dynamics

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

Tartakovsky, Alexandre M.; Panchenko, Alexander

2016-01-01

We present a novel formulation of the Pairwise Force Smoothed Particle Hydrodynamics Model (PF-SPH) and use it to simulate two- and three-phase flows in bounded domains. In the PF-SPH model, the Navier-Stokes equations are discretized with the Smoothed Particle Hydrodynamics (SPH) method and the Young-Laplace boundary condition at the fluid-fluid interface and the Young boundary condition at the fluid-fluid-solid interface are replaced with pairwise forces added into the Navier-Stokes equations. We derive a relationship between the parameters in the pairwise forces and the surface tension and static contact angle. Next, we demonstrate the accuracy of the model under static andmore » dynamic conditions. Finally, to demonstrate the capabilities and robustness of the model we use it to simulate flow of three fluids in a porous material.« less

Non-latching relay switch assembly

DOEpatents

Duimstra, Frederick A.

1991-01-01

A non-latching relay switch assembly which includes a coil section and a switch or contact section. The coil section includes a permanent magnet and an electromagnet. The respective sections are arranged in separate locations or cavities in the assembly. The switch has a "normal" position and is selectively switched by an overriding electromagnetic assembly. The switch returns to the "normal" position when the overriding electromagnetic assembly is inactive.

Improved de novo genomic assembly for the domestic donkey.

PubMed

Renaud, Gabriel; Petersen, Bent; Seguin-Orlando, Andaine; Bertelsen, Mads Frost; Waller, Andrew; Newton, Richard; Paillot, Romain; Bryant, Neil; Vaudin, Mark; Librado, Pablo; Orlando, Ludovic

2018-04-01

Donkeys and horses share a common ancestor dating back to about 4 million years ago. Although a high-quality genome assembly at the chromosomal level is available for the horse, current assemblies available for the donkey are limited to moderately sized scaffolds. The absence of a better-quality assembly for the donkey has hampered studies involving the characterization of patterns of genetic variation at the genome-wide scale. These range from the application of genomic tools to selective breeding and conservation to the more fundamental characterization of the genomic loci underlying speciation and domestication. We present a new high-quality donkey genome assembly obtained using the Chicago HiRise assembly technology, providing scaffolds of subchromosomal size. We make use of this new assembly to obtain more accurate measures of heterozygosity for equine species other than the horse, both genome-wide and locally, and to detect runs of homozygosity potentially pertaining to positive selection in domestic donkeys. Finally, this new assembly allowed us to identify fine-scale chromosomal rearrangements between the horse and the donkey that likely played an active role in their divergence and, ultimately, speciation.

Improved de novo genomic assembly for the domestic donkey

PubMed Central

Newton, Richard; Paillot, Romain; Bryant, Neil; Vaudin, Mark

2018-01-01

Donkeys and horses share a common ancestor dating back to about 4 million years ago. Although a high-quality genome assembly at the chromosomal level is available for the horse, current assemblies available for the donkey are limited to moderately sized scaffolds. The absence of a better-quality assembly for the donkey has hampered studies involving the characterization of patterns of genetic variation at the genome-wide scale. These range from the application of genomic tools to selective breeding and conservation to the more fundamental characterization of the genomic loci underlying speciation and domestication. We present a new high-quality donkey genome assembly obtained using the Chicago HiRise assembly technology, providing scaffolds of subchromosomal size. We make use of this new assembly to obtain more accurate measures of heterozygosity for equine species other than the horse, both genome-wide and locally, and to detect runs of homozygosity potentially pertaining to positive selection in domestic donkeys. Finally, this new assembly allowed us to identify fine-scale chromosomal rearrangements between the horse and the donkey that likely played an active role in their divergence and, ultimately, speciation. PMID:29740610

Long-life leak standard assembly

DOEpatents

Basford, James A.; Mathis, John E.; Wright, Harlan C.

1982-01-01

The present invention is directed to a portable leak standard assembly which is capable of providing a stream of high-purity reference gas at a virtually constant flow rate over an extensive period of time. The leak assembly comprises a high pressure reservoir coupled to a metal leak valve through a valve-controlled conduit. A reproducible leak valve useful in this assembly is provided by a metal tube crimped with a selected pressure loading for forming an orifice in the tube with this orifice being of a sufficient size to provide the selected flow rate. The leak valve assembly is formed of metal so that it can be "baked-out" in a vacuum furnace to rid the reservoir and attendent components of volatile impurities which reduce the efficiency of the leak standard.

Long-life leak standard assembly. [Patent application

DOEpatents

Basford, J.A.; Mathis, J.E.; Wright, H.C.

1980-11-12

The present invention is directed to a portable leak standard assembly which is capable of providing a stream of high-purity reference gas at a virtually constant flow rate over an extensive period of time. The leak assembly comprises a high pressure reservoir coupled to a metal leak valve through a valve-controlled conduit. A reproducible leak valve useful in this assembly is provided by a metal tube crimped with a selected pressure loading for forming an orifice in the tube with this orifice being of a sufficient size to provide the selected flow rate. The leak valve assembly is formed of metal so that it can be baked-out in a vacuum furnace to rid the reservoir and attendent components of volatile impurities which reduce the efficiency of the leak standard.

Selective catalyst reduction light-off strategy

DOEpatents

Gonze, Eugene V [Pinckney, MI

2011-10-18

An emissions control system includes a temperature determination module and an emissions control module. The temperature determination module determines a first temperature of a heater element of a diesel particulate filter (DPF) assembly in an exhaust system and determines a second temperature of a catalyst of the DPF assembly. The emissions control module selectively activates the heater element, selectively initiates a predefined combustion process in an engine based upon the first temperature, and selectively starts a reductant injection process based upon the second temperature.

Spatially selective assembly of quantum dot light emitters in an LED using engineered peptides.

PubMed

Demir, Hilmi Volkan; Seker, Urartu Ozgur Safak; Zengin, Gulis; Mutlugun, Evren; Sari, Emre; Tamerler, Candan; Sarikaya, Mehmet

2011-04-26

Semiconductor nanocrystal quantum dots are utilized in numerous applications in nano- and biotechnology. In device applications, where several different material components are involved, quantum dots typically need to be assembled at explicit locations for enhanced functionality. Conventional approaches cannot meet these requirements where assembly of nanocrystals is usually material-nonspecific, thereby limiting the control of their spatial distribution. Here we demonstrate directed self-assembly of quantum dot emitters at material-specific locations in a color-conversion LED containing several material components including a metal, a dielectric, and a semiconductor. We achieve a spatially selective immobilization of quantum dot emitters by using the unique material selectivity characteristics provided by the engineered solid-binding peptides as smart linkers. Peptide-decorated quantum dots exhibited several orders of magnitude higher photoluminescence compared to the control groups, thus, potentially opening up novel ways to advance these photonic platforms in applications ranging from chemical to biodetection.

Reversible Assembly of Graphitic Carbon Nitride 3D Network for Highly Selective Dyes Absorption and Regeneration.

PubMed

Zhang, Yuye; Zhou, Zhixin; Shen, Yanfei; Zhou, Qing; Wang, Jianhai; Liu, Anran; Liu, Songqin; Zhang, Yuanjian

2016-09-27

Responsive assembly of 2D materials is of great interest for a range of applications. In this work, interfacial functionalized carbon nitride (CN) nanofibers were synthesized by hydrolyzing bulk CN in sodium hydroxide solution. The reversible assemble and disassemble behavior of the as-prepared CN nanofibers was investigated by using CO2 as a trigger to form a hydrogel network at first. Compared to the most widespread absorbent materials such as active carbon, graphene and previously reported supramolecular gel, the proposed CN hydrogel not only exhibited a competitive absorbing capacity (maximum absorbing capacity of methylene blue up to 402 mg/g) but also overcame the typical deficiencies such as poor selectivity and high energy-consuming regeneration. This work would provide a strategy to construct a 3D CN network and open an avenue for developing smart assembly for potential applications ranging from environment to selective extraction.

Protein alignment algorithms with an efficient backtracking routine on multiple GPUs.

PubMed

Blazewicz, Jacek; Frohmberg, Wojciech; Kierzynka, Michal; Pesch, Erwin; Wojciechowski, Pawel

2011-05-20

Pairwise sequence alignment methods are widely used in biological research. The increasing number of sequences is perceived as one of the upcoming challenges for sequence alignment methods in the nearest future. To overcome this challenge several GPU (Graphics Processing Unit) computing approaches have been proposed lately. These solutions show a great potential of a GPU platform but in most cases address the problem of sequence database scanning and computing only the alignment score whereas the alignment itself is omitted. Thus, the need arose to implement the global and semiglobal Needleman-Wunsch, and Smith-Waterman algorithms with a backtracking procedure which is needed to construct the alignment. In this paper we present the solution that performs the alignment of every given sequence pair, which is a required step for progressive multiple sequence alignment methods, as well as for DNA recognition at the DNA assembly stage. Performed tests show that the implementation, with performance up to 6.3 GCUPS on a single GPU for affine gap penalties, is very efficient in comparison to other CPU and GPU-based solutions. Moreover, multiple GPUs support with load balancing makes the application very scalable. The article shows that the backtracking procedure of the sequence alignment algorithms may be designed to fit in with the GPU architecture. Therefore, our algorithm, apart from scores, is able to compute pairwise alignments. This opens a wide range of new possibilities, allowing other methods from the area of molecular biology to take advantage of the new computational architecture. Performed tests show that the efficiency of the implementation is excellent. Moreover, the speed of our GPU-based algorithms can be almost linearly increased when using more than one graphics card.

A novel papillomavirus in Adélie penguin (Pygoscelis adeliae) faeces sampled at the Cape Crozier colony, Antarctica.

PubMed

Varsani, Arvind; Kraberger, Simona; Jennings, Scott; Porzig, Elizabeth L; Julian, Laurel; Massaro, Melanie; Pollard, Annie; Ballard, Grant; Ainley, David G

2014-06-01

Papillomaviruses are epitheliotropic viruses that have circular dsDNA genomes encapsidated in non-enveloped virions. They have been found to infect a variety of mammals, reptiles and birds, but so far they have not been found in amphibians. Using a next-generation sequencing de novo assembly contig-informed recovery, we cloned and Sanger sequenced the complete genome of a novel papillomavirus from the faecal matter of Adélie penguins (Pygoscelis adeliae) nesting on Ross Island, Antarctica. The genome had all the usual features of a papillomavirus and an E9 ORF encoding a protein of unknown function that is found in all avian papillomaviruses to date. This novel papillomavirus genome shared ~60 % pairwise identity with the genomes of the other three known avian papillomaviruses: Fringilla coelebs papillomavirus 1 (FcPV1), Francolinus leucoscepus papillomavirus 1 (FlPV1) and Psittacus erithacus papillomavirus 1. Pairwise identity analysis and phylogenetic analysis of the major capsid protein gene clearly indicated that it represents a novel species, which we named Pygoscelis adeliae papillomavirus 1 (PaCV1). No evidence of recombination was detected in the genome of PaCV1, but we did detect a recombinant region (119 nt) in the E6 gene of FlPV1 with the recombinant region being derived from ancestral FcPV1-like sequences. Previously only paramyxoviruses, orthomyxoviruses and avian pox viruses have been genetically identified in penguins; however, the majority of penguin viral identifications have been based on serology or histology. This is the first report, to our knowledge, of a papillomavirus associated with a penguin species. © 2014 The Authors.

MC1R diversity in Northern Island Melanesia has not been constrained by strong purifying selection and cannot explain pigmentation phenotype variation in the region.

PubMed

Norton, Heather L; Werren, Elizabeth; Friedlaender, Jonathan

2015-10-19

Variation in human skin pigmentation evolved in response to the selective pressure of ultra-violet radiation (UVR). Selection to maintain darker skin in high UVR environments is expected to constrain pigmentation phenotype and variation in pigmentation loci. Consistent with this hypothesis, the gene MC1R exhibits reduced diversity in African populations from high UVR regions compared to low-UVR non-African populations. However, MC1R diversity in non-African populations that have evolved under high-UVR conditions is not well characterized. In order to test the hypothesis that MC1R variation has been constrained in Melanesians the coding region of the MC1R gene was sequenced in 188 individuals from Northern Island Melanesia. The role of purifying selection was assessed using a modified McDonald Kreitman's test. Pairwise FST was calculated between Melanesian populations and populations from the 1000 Genomes Project. The SNP rs2228479 was genotyped in a larger sample (n = 635) of Melanesians and tested for associations with skin and hair pigmentation. We observe three nonsynonymous and two synonymous mutations. A modified McDonald Kreitman's test failed to detect a significant signal of purifying selection. Pairwise FST values calculated between the four islands sampled here indicate little regional substructure in MC1R. When compared to African, European, East and South Asian populations, Melanesians do not exhibit reduced population divergence (measured as FST) or a high proportion of haplotype sharing with Africans, as one might expect if ancestral haplotypes were conserved across high UVR populations in and out of Africa. The only common nonsynonymous polymorphism observed, rs2228479, is not significantly associated with skin or hair pigmentation in a larger sample of Melanesians. The pattern of sequence diversity here does not support a model of strong selective constraint on MC1R in Northern Island Melanesia This absence of strong constraint, as well as the recent population history of the region, may explain the observed frequencies of the derived rs2228479 allele. These results emphasize the complex genetic architecture of pigmentation phenotypes, which are controlled by multiple, possibly interacting loci. They also highlight the role that population history can play in influencing phenotypic diversity in the absence of strong natural selection.

Life history traits in selfing versus outcrossing annuals: exploring the 'time-limitation' hypothesis for the fitness benefit of self-pollination

PubMed Central

Snell, Rebecca; Aarssen, Lonnie W

2005-01-01

Background Most self-pollinating plants are annuals. According to the 'time-limitation' hypothesis, this association between selfing and the annual life cycle has evolved as a consequence of strong r-selection, involving severe time-limitation for completing the life cycle. Under this model, selection from frequent density-independent mortality in ephemeral habitats minimizes time to flower maturation, with selfing as a trade-off, and / or selection minimizes the time between flower maturation and ovule fertilization, in which case selfing has a direct fitness benefit. Predictions arising from this hypothesis were evaluated using phylogenetically-independent contrasts of several life history traits in predominantly selfing versus outcrossing annuals from a data base of 118 species distributed across 14 families. Data for life history traits specifically related to maturation and pollination times were obtained by monitoring the start and completion of different stages of reproductive development in a greenhouse study of selfing and outcrossing annuals from an unbiased sample of 25 species involving five pair-wise family comparisons and four pair-wise genus comparisons. Results Selfing annuals in general had significantly shorter plant heights, smaller flowers, shorter bud development times, shorter flower longevity and smaller seed sizes compared with their outcrossing annual relatives. Age at first flower did not differ significantly between selfing and outcrossing annuals. Conclusions This is the first multi-species study to report these general life-history differences between selfers and outcrossers among annuals exclusively. The results are all explained more parsimoniously by selection associated with time-limitation than by selection associated with pollinator/mate limitation. The shorter bud development time reported here for selfing annuals is predicted explicitly by the time-limitation hypothesis for the fitness benefit of selfing (and not by the alternative 'reproductive assurance' hypothesis associated with pollinator/mate limitation). Support for the time-limitation hypothesis is also evident from published surveys: whereas selfers and outcrossers are about equally represented among annual species as a whole, selfers occur in much higher frequencies among the annual species found in two of the most severely time-limited habitats where flowering plants grow – deserts and cultivated habitats. PMID:15707481

Consistent linguistic fuzzy preference relations method with ranking fuzzy numbers

NASA Astrophysics Data System (ADS)

Ridzuan, Siti Amnah Mohd; Mohamad, Daud; Kamis, Nor Hanimah

2014-12-01

Multi-Criteria Decision Making (MCDM) methods have been developed to help decision makers in selecting the best criteria or alternatives from the options given. One of the well known methods in MCDM is the Consistent Fuzzy Preference Relation (CFPR) method, essentially utilizes a pairwise comparison approach. This method was later improved to cater subjectivity in the data by using fuzzy set, known as the Consistent Linguistic Fuzzy Preference Relations (CLFPR). The CLFPR method uses the additive transitivity property in the evaluation of pairwise comparison matrices. However, the calculation involved is lengthy and cumbersome. To overcome this problem, a method of defuzzification was introduced by researchers. Nevertheless, the defuzzification process has a major setback where some information may lose due to the simplification process. In this paper, we propose a method of CLFPR that preserves the fuzzy numbers form throughout the process. In obtaining the desired ordering result, a method of ranking fuzzy numbers is utilized in the procedure. This improved procedure for CLFPR is implemented to a case study to verify its effectiveness. This method is useful for solving decision making problems and can be applied to many areas of applications.

Strategies for informed sample size reduction in adaptive controlled clinical trials

NASA Astrophysics Data System (ADS)

Arandjelović, Ognjen

2017-12-01

Clinical trial adaptation refers to any adjustment of the trial protocol after the onset of the trial. The main goal is to make the process of introducing new medical interventions to patients more efficient. The principal challenge, which is an outstanding research problem, is to be found in the question of how adaptation should be performed so as to minimize the chance of distorting the outcome of the trial. In this paper, we propose a novel method for achieving this. Unlike most of the previously published work, our approach focuses on trial adaptation by sample size adjustment, i.e. by reducing the number of trial participants in a statistically informed manner. Our key idea is to select the sample subset for removal in a manner which minimizes the associated loss of information. We formalize this notion and describe three algorithms which approach the problem in different ways, respectively, using (i) repeated random draws, (ii) a genetic algorithm, and (iii) what we term pair-wise sample compatibilities. Experiments on simulated data demonstrate the effectiveness of all three approaches, with a consistently superior performance exhibited by the pair-wise sample compatibilities-based method.

Analyzing brain networks with PCA and conditional Granger causality.

PubMed

Zhou, Zhenyu; Chen, Yonghong; Ding, Mingzhou; Wright, Paul; Lu, Zuhong; Liu, Yijun

2009-07-01

Identifying directional influences in anatomical and functional circuits presents one of the greatest challenges for understanding neural computations in the brain. Granger causality mapping (GCM) derived from vector autoregressive models of data has been employed for this purpose, revealing complex temporal and spatial dynamics underlying cognitive processes. However, the traditional GCM methods are computationally expensive, as signals from thousands of voxels within selected regions of interest (ROIs) are individually processed, and being based on pairwise Granger causality, they lack the ability to distinguish direct from indirect connectivity among brain regions. In this work a new algorithm called PCA based conditional GCM is proposed to overcome these problems. The algorithm implements the following two procedures: (i) dimensionality reduction in ROIs of interest with principle component analysis (PCA), and (ii) estimation of the direct causal influences in local brain networks, using conditional Granger causality. Our results show that the proposed method achieves greater accuracy in detecting network connectivity than the commonly used pairwise Granger causality method. Furthermore, the use of PCA components in conjunction with conditional GCM greatly reduces the computational cost relative to the use of individual voxel time series. Copyright 2009 Wiley-Liss, Inc

Online Pairwise Learning Algorithms.

PubMed

Ying, Yiming; Zhou, Ding-Xuan

2016-04-01

Pairwise learning usually refers to a learning task that involves a loss function depending on pairs of examples, among which the most notable ones are bipartite ranking, metric learning, and AUC maximization. In this letter we study an online algorithm for pairwise learning with a least-square loss function in an unconstrained setting of a reproducing kernel Hilbert space (RKHS) that we refer to as the Online Pairwise lEaRning Algorithm (OPERA). In contrast to existing works (Kar, Sriperumbudur, Jain, & Karnick, 2013 ; Wang, Khardon, Pechyony, & Jones, 2012 ), which require that the iterates are restricted to a bounded domain or the loss function is strongly convex, OPERA is associated with a non-strongly convex objective function and learns the target function in an unconstrained RKHS. Specifically, we establish a general theorem that guarantees the almost sure convergence for the last iterate of OPERA without any assumptions on the underlying distribution. Explicit convergence rates are derived under the condition of polynomially decaying step sizes. We also establish an interesting property for a family of widely used kernels in the setting of pairwise learning and illustrate the convergence results using such kernels. Our methodology mainly depends on the characterization of RKHSs using its associated integral operators and probability inequalities for random variables with values in a Hilbert space.

Cosmology with the pairwise kinematic SZ effect: Calibration and validation using hydrodynamical simulations

NASA Astrophysics Data System (ADS)

Soergel, Bjoern; Saro, Alexandro; Giannantonio, Tommaso; Efstathiou, George; Dolag, Klaus

2018-05-01

We study the potential of the kinematic SZ effect as a probe for cosmology, focusing on the pairwise method. The main challenge is disentangling the cosmologically interesting mean pairwise velocity from the cluster optical depth and the associated uncertainties on the baryonic physics in clusters. Furthermore, the pairwise kSZ signal might be affected by internal cluster motions or correlations between velocity and optical depth. We investigate these effects using the Magneticum cosmological hydrodynamical simulations, one of the largest simulations of this kind performed to date. We produce tSZ and kSZ maps with an area of ≃ 1600 deg2, and the corresponding cluster catalogues with M500c ≳ 3 × 1013 h-1M⊙ and z ≲ 2. From these data sets we calibrate a scaling relation between the average Compton-y parameter and optical depth. We show that this relation can be used to recover an accurate estimate of the mean pairwise velocity from the kSZ effect, and that this effect can be used as an important probe of cosmology. We discuss the impact of theoretical and observational systematic effects, and find that further work on feedback models is required to interpret future high-precision measurements of the kSZ effect.

The Medicago sativa gene index 1.2: a web-accessible gene expression atlas for investigating expression differences between Medicago sativa subspecies.

PubMed

O'Rourke, Jamie A; Fu, Fengli; Bucciarelli, Bruna; Yang, S Sam; Samac, Deborah A; Lamb, JoAnn F S; Monteros, Maria J; Graham, Michelle A; Gronwald, John W; Krom, Nick; Li, Jun; Dai, Xinbin; Zhao, Patrick X; Vance, Carroll P

2015-07-07

Alfalfa (Medicago sativa L.) is the primary forage legume crop species in the United States and plays essential economic and ecological roles in agricultural systems across the country. Modern alfalfa is the result of hybridization between tetraploid M. sativa ssp. sativa and M. sativa ssp. falcata. Due to its large and complex genome, there are few genomic resources available for alfalfa improvement. A de novo transcriptome assembly from two alfalfa subspecies, M. sativa ssp. sativa (B47) and M. sativa ssp. falcata (F56) was developed using Illumina RNA-seq technology. Transcripts from roots, nitrogen-fixing root nodules, leaves, flowers, elongating stem internodes, and post-elongation stem internodes were assembled into the Medicago sativa Gene Index 1.2 (MSGI 1.2) representing 112,626 unique transcript sequences. Nodule-specific and transcripts involved in cell wall biosynthesis were identified. Statistical analyses identified 20,447 transcripts differentially expressed between the two subspecies. Pair-wise comparisons of each tissue combination identified 58,932 sequences differentially expressed in B47 and 69,143 sequences differentially expressed in F56. Comparing transcript abundance in floral tissues of B47 and F56 identified expression differences in sequences involved in anthocyanin and carotenoid synthesis, which determine flower pigmentation. Single nucleotide polymorphisms (SNPs) unique to each M. sativa subspecies (110,241) were identified. The Medicago sativa Gene Index 1.2 increases the expressed sequence data available for alfalfa by ninefold and can be expanded as additional experiments are performed. The MSGI 1.2 transcriptome sequences, annotations, expression profiles, and SNPs were assembled into the Alfalfa Gene Index and Expression Database (AGED) at http://plantgrn.noble.org/AGED/ , a publicly available genomic resource for alfalfa improvement and legume research.

The chaperonin-60 universal target is a barcode for bacteria that enables de novo assembly of metagenomic sequence data.

PubMed

Links, Matthew G; Dumonceaux, Tim J; Hemmingsen, Sean M; Hill, Janet E

2012-01-01

Barcoding with molecular sequences is widely used to catalogue eukaryotic biodiversity. Studies investigating the community dynamics of microbes have relied heavily on gene-centric metagenomic profiling using two genes (16S rRNA and cpn60) to identify and track Bacteria. While there have been criteria formalized for barcoding of eukaryotes, these criteria have not been used to evaluate gene targets for other domains of life. Using the framework of the International Barcode of Life we evaluated DNA barcodes for Bacteria. Candidates from the 16S rRNA gene and the protein coding cpn60 gene were evaluated. Within complete bacterial genomes in the public domain representing 983 species from 21 phyla, the largest difference between median pairwise inter- and intra-specific distances ("barcode gap") was found from cpn60. Distribution of sequence diversity along the ∼555 bp cpn60 target region was remarkably uniform. The barcode gap of the cpn60 universal target facilitated the faithful de novo assembly of full-length operational taxonomic units from pyrosequencing data from a synthetic microbial community. Analysis supported the recognition of both 16S rRNA and cpn60 as DNA barcodes for Bacteria. The cpn60 universal target was found to have a much larger barcode gap than 16S rRNA suggesting cpn60 as a preferred barcode for Bacteria. A large barcode gap for cpn60 provided a robust target for species-level characterization of data. The assembly of consensus sequences for barcodes was shown to be a reliable method for the identification and tracking of novel microbes in metagenomic studies.

Selected Lessons Learned through the ISS Design, Development, Assembly, and Operations: Applicability to International Cooperation for Standardization

NASA Technical Reports Server (NTRS)

Hirsch, David B.

2009-01-01

This slide presentation reviews selected lessons that were learned during the design, development, assembly and operation of the International Space Station. The critical importance of standards and common interfaces is emphasized to create a common operation environment that can lead to flexibility and adaptability.

Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families.

PubMed

Reinharz, Vladimir; Soulé, Antoine; Westhof, Eric; Waldispühl, Jérôme; Denise, Alain

2018-05-04

The wealth of the combinatorics of nucleotide base pairs enables RNA molecules to assemble into sophisticated interaction networks, which are used to create complex 3D substructures. These interaction networks are essential to shape the 3D architecture of the molecule, and also to provide the key elements to carry molecular functions such as protein or ligand binding. They are made of organised sets of long-range tertiary interactions which connect distinct secondary structure elements in 3D structures. Here, we present a de novo data-driven approach to extract automatically from large data sets of full RNA 3D structures the recurrent interaction networks (RINs). Our methodology enables us for the first time to detect the interaction networks connecting distinct components of the RNA structure, highlighting their diversity and conservation through non-related functional RNAs. We use a graphical model to perform pairwise comparisons of all RNA structures available and to extract RINs and modules. Our analysis yields a complete catalog of RNA 3D structures available in the Protein Data Bank and reveals the intricate hierarchical organization of the RNA interaction networks and modules. We assembled our results in an online database (http://carnaval.lri.fr) which will be regularly updated. Within the site, a tool allows users with a novel RNA structure to detect automatically whether the novel structure contains previously observed RINs.

Molecular docking based screening of compounds against VP40 from Ebola virus.

PubMed

M Alam El-Din, Hanaa; A Loutfy, Samah; Fathy, Nasra; H Elberry, Mostafa; M Mayla, Ahmed; Kassem, Sara; Naqvi, Asif

2016-01-01

Ebola virus causes severe and often fatal hemorrhagic fevers in humans. The 2014 Ebola epidemic affected multiple countries. The virus matrix protein (VP40) plays a central role in virus assembly and budding. Since there is no FDA-approved vaccine or medicine against Ebola viral infection, discovering new compounds with different binding patterns against it is required. Therefore, we aim to identify small molecules that target the Arg 134 RNA binding and active site of VP40 protein. 1800 molecules were retrieved from PubChem compound database based on Structure Similarity and Conformers of pyrimidine-2, 4-dione. Molecular docking approach using Lamarckian Genetic Algorithm was carried out to find the potent inhibitors for VP40 based on calculated ligand-protein pairwise interaction energies. The grid maps representing the protein were calculated using auto grid and grid size was set to 60*60*60 points with grid spacing of 0.375 Ǻ. Ten independent docking runs were carried out for each ligand and results were clustered according to the 1.0 Ǻ RMSD criteria. The post-docking analysis showed that binding energies ranged from -8.87 to 0.6 Kcal/mol. We report 7 molecules, which showed promising ADMET results, LD-50, as well as H-bond interaction in the binding pocket. The small molecules discovered could act as potential inhibitors for VP40 and could interfere with virus assembly and budding process.

Molecular docking based screening of compounds against VP40 from Ebola virus

PubMed Central

M Alam El-Din, Hanaa; A. Loutfy, Samah; Fathy, Nasra; H Elberry, Mostafa; M Mayla, Ahmed; Kassem, Sara; Naqvi, Asif

2016-01-01

Ebola virus causes severe and often fatal hemorrhagic fevers in humans. The 2014 Ebola epidemic affected multiple countries. The virus matrix protein (VP40) plays a central role in virus assembly and budding. Since there is no FDA-approved vaccine or medicine against Ebola viral infection, discovering new compounds with different binding patterns against it is required. Therefore, we aim to identify small molecules that target the Arg 134 RNA binding and active site of VP40 protein. 1800 molecules were retrieved from PubChem compound database based on Structure Similarity and Conformers of pyrimidine-2, 4-dione. Molecular docking approach using Lamarckian Genetic Algorithm was carried out to find the potent inhibitors for VP40 based on calculated ligand-protein pairwise interaction energies. The grid maps representing the protein were calculated using auto grid and grid size was set to 60*60*60 points with grid spacing of 0.375 Ǻ. Ten independent docking runs were carried out for each ligand and results were clustered according to the 1.0 Ǻ RMSD criteria. The post-docking analysis showed that binding energies ranged from -8.87 to 0.6 Kcal/mol. We report 7 molecules, which showed promising ADMET results, LD-50, as well as H-bond interaction in the binding pocket. The small molecules discovered could act as potential inhibitors for VP40 and could interfere with virus assembly and budding process. PMID:28149054

Expression, purification and re folding of a self-assembling protein nanoparticle (SAPN) malaria vaccine

PubMed Central

Guo, Qin; Dasgupta, Debleena; Doll, Tais A.P.F.; Burkhard, Peter; Lanar, David E.

2013-01-01

There are many ways to present antigens to the immune system. We have used a repetitive antigen display technology that relies on the self-assembly of 60 protein chains into a spherical self-assembling protein nanoparticle (SAPN) to develop a vaccine against Plasmodium falciparum malaria. The protein sequence contains selected B- and T-cell epitopes of the circumsporozoite protein of P. falciparum (PfCSP) and, when assembled into a nanoparticle induces strong, long-lived and protective immune responses against the PfCSP. Here we describe the conditions needed for promoting self-assembly of a P. falciparum vaccine nanoparticle, PfCSP-KMY-SAPN, and note pitfalls that may occur when determining conditions for other SAPN vaccines. Attention was paid to selecting processes that were amenable to scale up and cGMP manufacturing. PMID:23548672

Some Questions about Feature Re-Assembly

ERIC Educational Resources Information Center

White, Lydia

2009-01-01

In this commentary, differences between feature re-assembly and feature selection are discussed. Lardiere's proposals are compared to existing approaches to grammatical features in second language (L2) acquisition. Questions are raised about the predictive power of the feature re-assembly approach. (Contains 1 footnote.)

Evolutionary dynamics on any population structure

NASA Astrophysics Data System (ADS)

Allen, Benjamin; Lippner, Gabor; Chen, Yu-Ting; Fotouhi, Babak; Momeni, Naghmeh; Yau, Shing-Tung; Nowak, Martin A.

2017-03-01

Evolution occurs in populations of reproducing individuals. The structure of a population can affect which traits evolve. Understanding evolutionary game dynamics in structured populations remains difficult. Mathematical results are known for special structures in which all individuals have the same number of neighbours. The general case, in which the number of neighbours can vary, has remained open. For arbitrary selection intensity, the problem is in a computational complexity class that suggests there is no efficient algorithm. Whether a simple solution for weak selection exists has remained unanswered. Here we provide a solution for weak selection that applies to any graph or network. Our method relies on calculating the coalescence times of random walks. We evaluate large numbers of diverse population structures for their propensity to favour cooperation. We study how small changes in population structure—graph surgery—affect evolutionary outcomes. We find that cooperation flourishes most in societies that are based on strong pairwise ties.

A Meta-Assembly of Selection Signatures in Cattle

PubMed Central

Randhawa, Imtiaz A. S.; Khatkar, Mehar S.; Thomson, Peter C.; Raadsma, Herman W.

2016-01-01

Since domestication, significant genetic improvement has been achieved for many traits of commercial importance in cattle, including adaptation, appearance and production. In response to such intense selection pressures, the bovine genome has undergone changes at the underlying regions of functional genetic variants, which are termed “selection signatures”. This article reviews 64 recent (2009–2015) investigations testing genomic diversity for departure from neutrality in worldwide cattle populations. In particular, we constructed a meta-assembly of 16,158 selection signatures for individual breeds and their archetype groups (European, African, Zebu and composite) from 56 genome-wide scans representing 70,743 animals of 90 pure and crossbred cattle breeds. Meta-selection-scores (MSS) were computed by combining published results at every given locus, within a sliding window span. MSS were adjusted for common samples across studies and were weighted for significance thresholds across and within studies. Published selection signatures show extensive coverage across the bovine genome, however, the meta-assembly provides a consensus profile of 263 genomic regions of which 141 were unique (113 were breed-specific) and 122 were shared across cattle archetypes. The most prominent peaks of MSS represent regions under selection across multiple populations and harboured genes of known major effects (coat color, polledness and muscle hypertrophy) and genes known to influence polygenic traits (stature, adaptation, feed efficiency, immunity, behaviour, reproduction, beef and dairy production). As the first meta-assembly of selection signatures, it offers novel insights about the hotspots of selective sweeps in the bovine genome, and this method could equally be applied to other species. PMID:27045296

Production of solar chemicals: gaining selectivity with hybrid molecule/semiconductor assemblies.

PubMed

Hennessey, Seán; Farràs, Pau

2018-05-29

Research on the production of solar fuels and chemicals has rocketed over the past decade, with a wide variety of systems proposed to harvest solar energy and drive chemical reactions. In this Feature Article we have focused on hybrid molecule/semiconductor assemblies in both powder and supported materials, summarising recent systems and highlighting the enormous possibilities offered by such assemblies to carry out highly demanding chemical reactions with industrial impact. Of relevance is the higher selectivity obtained in visible light-driven organic transformations when using molecular catalysts compared to photocatalytic materials.

Quantitative characterization of all single amino acid variants of a viral capsid-based drug delivery vehicle.

PubMed

Hartman, Emily C; Jakobson, Christopher M; Favor, Andrew H; Lobba, Marco J; Álvarez-Benedicto, Ester; Francis, Matthew B; Tullman-Ercek, Danielle

2018-04-11

Self-assembling proteins are critical to biological systems and industrial technologies, but predicting how mutations affect self-assembly remains a significant challenge. Here, we report a technique, termed SyMAPS (Systematic Mutation and Assembled Particle Selection), that can be used to characterize the assembly competency of all single amino acid variants of a self-assembling viral structural protein. SyMAPS studies on the MS2 bacteriophage coat protein revealed a high-resolution fitness landscape that challenges some conventional assumptions of protein engineering. An additional round of selection identified a previously unknown variant (CP[T71H]) that is stable at neutral pH but less tolerant to acidic conditions than the wild-type coat protein. The capsids formed by this variant could be more amenable to disassembly in late endosomes or early lysosomes-a feature that is advantageous for delivery applications. In addition to providing a mutability blueprint for virus-like particles, SyMAPS can be readily applied to other self-assembling proteins.

Maximally informative pairwise interactions in networks

PubMed Central

Fitzgerald, Jeffrey D.; Sharpee, Tatyana O.

2010-01-01

Several types of biological networks have recently been shown to be accurately described by a maximum entropy model with pairwise interactions, also known as the Ising model. Here we present an approach for finding the optimal mappings between input signals and network states that allow the network to convey the maximal information about input signals drawn from a given distribution. This mapping also produces a set of linear equations for calculating the optimal Ising-model coupling constants, as well as geometric properties that indicate the applicability of the pairwise Ising model. We show that the optimal pairwise interactions are on average zero for Gaussian and uniformly distributed inputs, whereas they are nonzero for inputs approximating those in natural environments. These nonzero network interactions are predicted to increase in strength as the noise in the response functions of each network node increases. This approach also suggests ways for how interactions with unmeasured parts of the network can be inferred from the parameters of response functions for the measured network nodes. PMID:19905153

Threesomes destabilise certain relationships: multispecies interactions between wood decay fungi in natural resources

PubMed Central

Savoury, Melanie; Toledo, Selin; Kingscott-Edmunds, James; Bettridge, Aimee; Waili, Nasra Al; Boddy, Lynne

2017-01-01

Abstract Understanding interspecific interactions is key to explaining and modelling community development and associated ecosystem function. Most interactions research has focused on pairwise combinations, overlooking the complexity of multispecies communities. This study investigated three-way interactions between saprotrophic fungi in wood and across soil, and indicated that pairwise combinations are often inaccurate predictors of the outcomes of multispecies competition in wood block interactions. This inconsistency was especially true of intransitive combinations, resulting in increased species coexistence within the resource. Furthermore, the addition of a third competitor frequently destabilised the otherwise consistent outcomes of pairwise combinations in wood blocks, which occasionally resulted in altered resource decomposition rates, depending on the relative decay abilities of the species involved. Conversely, interaction outcomes in soil microcosms were unaffected by the presence of a third combatant. Multispecies interactions promoted species diversity within natural resources, and made community dynamics less consistent than could be predicted from pairwise interaction studies. PMID:28175239

Limiting similarity and Darwin's naturalization hypothesis: understanding the drivers of biotic resistance against invasive plant species.

PubMed

Yannelli, F A; Koch, C; Jeschke, J M; Kollmann, J

2017-03-01

Several hypotheses have been proposed to explain biotic resistance of a recipient plant community based on reduced niche opportunities for invasive alien plant species. The limiting similarity hypothesis predicts that invasive species are less likely to establish in communities of species holding similar functional traits. Likewise, Darwin's naturalization hypothesis states that invasive species closely related to the native community would be less successful. We tested both using the invasive alien Ambrosia artemisiifolia L. and Solidago gigantea Aiton, and grassland species used for ecological restoration in central Europe. We classified all plant species into groups based on functional traits obtained from trait databases and calculated the phylogenetic distance among them. In a greenhouse experiment, we submitted the two invasive species at two propagule pressures to competition with communities of ten native species from the same functional group. In another experiment, they were submitted to pairwise competition with native species selected from each functional group. At the community level, highest suppression for both invasive species was observed at low propagule pressure and not explained by similarity in functional traits. Moreover, suppression decreased asymptotically with increasing phylogenetic distance to species of the native community. When submitted to pairwise competition, suppression for both invasive species was also better explained by phylogenetic distance. Overall, our results support Darwin's naturalization hypothesis but not the limiting similarity hypothesis based on the selected traits. Biotic resistance of native communities against invasive species at an early stage of establishment is enhanced by competitive traits and phylogenetic relatedness.

Network Analysis of Protein Adaptation: Modeling the Functional Impact of Multiple Mutations

PubMed Central

Beleva Guthrie, Violeta; Masica, David L; Fraser, Andrew; Federico, Joseph; Fan, Yunfan; Camps, Manel; Karchin, Rachel

2018-01-01

Abstract The evolution of new biochemical activities frequently involves complex dependencies between mutations and rapid evolutionary radiation. Mutation co-occurrence and covariation have previously been used to identify compensating mutations that are the result of physical contacts and preserve protein function and fold. Here, we model pairwise functional dependencies and higher order interactions that enable evolution of new protein functions. We use a network model to find complex dependencies between mutations resulting from evolutionary trade-offs and pleiotropic effects. We present a method to construct these networks and to identify functionally interacting mutations in both extant and reconstructed ancestral sequences (Network Analysis of Protein Adaptation). The time ordering of mutations can be incorporated into the networks through phylogenetic reconstruction. We apply NAPA to three distantly homologous β-lactamase protein clusters (TEM, CTX-M-3, and OXA-51), each of which has experienced recent evolutionary radiation under substantially different selective pressures. By analyzing the network properties of each protein cluster, we identify key adaptive mutations, positive pairwise interactions, different adaptive solutions to the same selective pressure, and complex evolutionary trajectories likely to increase protein fitness. We also present evidence that incorporating information from phylogenetic reconstruction and ancestral sequence inference can reduce the number of spurious links in the network, whereas preserving overall network community structure. The analysis does not require structural or biochemical data. In contrast to function-preserving mutation dependencies, which are frequently from structural contacts, gain-of-function mutation dependencies are most commonly between residues distal in protein structure. PMID:29522102

Embracing Community Ecology in Plant Microbiome Research.

PubMed

Dini-Andreote, Francisco; Raaijmakers, Jos M

2018-06-01

Community assembly is mediated by selection, dispersal, drift, and speciation. Environmental selection is mostly used to date to explain patterns in plant microbiome assembly, whereas the influence of the other processes remains largely elusive. Recent studies highlight that adopting community ecology concepts provides a mechanistic framework for plant microbiome research. Copyright © 2018 Elsevier Ltd. All rights reserved.

On the Selective Packaging of Genomic RNA by HIV-1.

PubMed

Comas-Garcia, Mauricio; Davis, Sean R; Rein, Alan

2016-09-12

Like other retroviruses, human immunodeficiency virus type 1 (HIV-1) selectively packages genomic RNA (gRNA) during virus assembly. However, in the absence of the gRNA, cellular messenger RNAs (mRNAs) are packaged. While the gRNA is selected because of its cis-acting packaging signal, the mechanism of this selection is not understood. The affinity of Gag (the viral structural protein) for cellular RNAs at physiological ionic strength is not much higher than that for the gRNA. However, binding to the gRNA is more salt-resistant, implying that it has a higher non-electrostatic component. We have previously studied the spacer 1 (SP1) region of Gag and showed that it can undergo a concentration-dependent conformational transition. We proposed that this transition represents the first step in assembly, i.e., the conversion of Gag to an assembly-ready state. To explain selective packaging of gRNA, we suggest here that binding of Gag to gRNA, with its high non-electrostatic component, triggers this conversion more readily than binding to other RNAs; thus we predict that a Gag-gRNA complex will nucleate particle assembly more efficiently than other Gag-RNA complexes. New data shows that among cellular mRNAs, those with long 3'-untranslated regions (UTR) are selectively packaged. It seems plausible that the 3'-UTR, a stretch of RNA not occupied by ribosomes, offers a favorable binding site for Gag.

Bevel Gear Driver and Method Having Torque Limit Selection

NASA Technical Reports Server (NTRS)

Cook, Joseph S., Jr. (Inventor)

1997-01-01

Methods and apparatus are provided for a torque driver including an axially displaceable gear with a biasing assembly to bias the displaceable gear into an engagement position. A rotatable cap is provided with a micrometer dial to select a desired output torque. An intermediate bevel gear assembly is disposed between an input gear and an output gear. A gear tooth profile provides a separation force that overcomes the bias to limit torque at a desired torque limit. The torque limit is adjustable and may be adjusted manually or automatically depending on the type of biasing assembly provided. A clutch assembly automatically limits axial force applied to a fastener by the operator to avoid alteration of the desired torque limit.

Directed-Assembly of Carbon Nanotubes on Soft Substrates for Flexible Biosensor Array

NASA Astrophysics Data System (ADS)

Lee, Hyoung Woo; Koh, Juntae; Lee, Byung Yang; Kim, Tae Hyun; Lee, Joohyung; Hong, Seunghun; Yi, Mihye; Jhon, Young Min

2009-03-01

We developed a method to selectively assemble and align carbon nanotubes (CNTs) on soft substrates for flexible biosensors. In this strategy, thin oxide layer was deposited on soft substrates via low temperature plasma enhanced chemical vapor deposition, and linker-free assembly process was applied onto the oxide surface where the assembly of carbon nanotubes was guided by methyl-terminated molecular patterns on the oxide surface. The electrical characterization of the fabricated CNT devices exhibited typical p-type gating effect and 1/f noise behavior. The bare oxide regions near CNTs were functionalized with glutamate oxidase to fabricate selective biosensors to detect two forms of glutamate substances existing in different situations: L-glutamic acid, a neuro-transmitting material, and monosodium glutamate, a food additive.

Biomimetic self-templating optical structures fabricated by genetically engineered M13 bacteriophage.

PubMed

Kim, Won-Geun; Song, Hyerin; Kim, Chuntae; Moon, Jong-Sik; Kim, Kyujung; Lee, Seung-Wuk; Oh, Jin-Woo

2016-11-15

Here, we describe a highly sensitive and selective surface plasmon resonance sensor system by utilizing self-assembly of genetically engineered M13 bacteriophage. About 2700 copies of genetically expressed peptide copies give superior selectivity and sensitivity to M13 phage-based SPR sensor. Furthermore, the sensitivity of the M13 phage-based SPR sensor was enhanced due to the aligning of receptor matrix in specific direction. Incorporation of specific binding peptide (His Pro Gln: HPQ) gives M13 bacteriophage high selectivity for the streptavidin. Our M13 phage-based SPR sensor takes advantage of simplicity of self-assembly compared with relatively complex photolithography techniques or chemical conjugations. Additionally, designed structure which is composed of functionalized M13 bacteriophage can simultaneously improve the sensitivity and selectivity of SPR sensor evidently. By taking advantages of the genetic engineering and self-assembly, we propose the simple method for fabricating novel M13 phage-based SPR sensor system which has a high sensitivity and high selectivity. Copyright © 2016 Elsevier B.V. All rights reserved.

Fiber optic assembly and method of making same

DOEpatents

Kramer, D.P.; Beckman, T.M.

1997-09-02

There is provided an assembly having a light guiding medium sealed to a holder. Preferably the holder is a metal shell and a light guiding medium is an optical fiber of glass or sapphire whisker. The assembly includes a sealing medium which sealingly engages the metal holder to the fiber. In the formation of the assembly, the seal is essentially hermetic having a capability of minimizing leakage having a helium leak rate of less than 1{times}10{sup {minus}8} cubic centimeters per second and high strength having a capability of withstanding pressures of 100,000 psi or greater. The features of the assembly are obtained by a specific preparation method and by selection of specific starting materials. The fiber is selected to have a sufficiently high coefficient of thermal expansion which minimizes strains in the component during fabrication, as a result of fabrication, and during use. The other components are selected to be of a material having compatible coefficients of thermal expansion (TEC) where the TEC of the holder is greater than or equal to the TEC of the sealing material. The TEC of the sealing material is in turn greater than or equal to the TEC of the fiber. It is preferred that the materials be selected so that their respective coefficients of thermal expansion are as close as possible to one another and they may all be equal. 4 figs.

Fiber optic assembly and method of making same

DOEpatents

Kramer, Daniel P.; Beckman, Thomas M.

1997-09-02

There is provided an assembly having a light guiding medium sealed to a her. Preferably the holder is a metal shell and a light guiding medium is an optical fiber of glass or sapphire whisker. The assembly includes a sealing medium which sealingly engages the metal holder to the fiber. In the formation of the assembly, the seal is essentially hermetic having a capability of minimizing leakage having a helium leak rate of less than 1.times.10.sup.-8 cubic centimeters per second and high strength having a capability of withstanding pressures of 100,000 psi or greater. The features of the assembly are obtained by a specific preparation method and by selection of specific starting materials. The fiber is selected to have a sufficiently high coefficient of thermal expansion which minimizes strains in the component during fabrication, as a result of fabrication, and during use. The other components are selected to be of a material having compatible coefficients of thermal expansion (TEC) where the TEC of the holder is greater than or equal to the TEC of the sealing material. The TEC of the sealing material is in turn greater than or equal to the TEC of the fiber. It is preferred that the materials be selected so that their respective coefficients of thermal expansion are as close as possible to one another and they may all be equal.

Blazing Signature Filter: a library for fast pairwise similarity comparisons

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

Lee, Joon-Yong; Fujimoto, Grant M.; Wilson, Ryan

Identifying similarities between datasets is a fundamental task in data mining and has become an integral part of modern scientific investigation. Whether the task is to identify co-expressed genes in large-scale expression surveys or to predict combinations of gene knockouts which would elicit a similar phenotype, the underlying computational task is often a multi-dimensional similarity test. As datasets continue to grow, improvements to the efficiency, sensitivity or specificity of such computation will have broad impacts as it allows scientists to more completely explore the wealth of scientific data. A significant practical drawback of large-scale data mining is the vast majoritymore » of pairwise comparisons are unlikely to be relevant, meaning that they do not share a signature of interest. It is therefore essential to efficiently identify these unproductive comparisons as rapidly as possible and exclude them from more time-intensive similarity calculations. The Blazing Signature Filter (BSF) is a highly efficient pairwise similarity algorithm which enables extensive data mining within a reasonable amount of time. The algorithm transforms datasets into binary metrics, allowing it to utilize the computationally efficient bit operators and provide a coarse measure of similarity. As a result, the BSF can scale to high dimensionality and rapidly filter unproductive pairwise comparison. Two bioinformatics applications of the tool are presented to demonstrate the ability to scale to billions of pairwise comparisons and the usefulness of this approach.« less

The structure of pairwise correlation in mouse primary visual cortex reveals functional organization in the absence of an orientation map.

PubMed

Denman, Daniel J; Contreras, Diego

2014-10-01

Neural responses to sensory stimuli are not independent. Pairwise correlation can reduce coding efficiency, occur independent of stimulus representation, or serve as an additional channel of information, depending on the timescale of correlation and the method of decoding. Any role for correlation depends on its magnitude and structure. In sensory areas with maps, like the orientation map in primary visual cortex (V1), correlation is strongly related to the underlying functional architecture, but it is unclear whether this correlation structure is an essential feature of the system or arises from the arrangement of cells in the map. We assessed the relationship between functional architecture and pairwise correlation by measuring both synchrony and correlated spike count variability in mouse V1, which lacks an orientation map. We observed significant pairwise synchrony, which was organized by distance and relative orientation preference between cells. We also observed nonzero correlated variability in both the anesthetized (0.16) and awake states (0.18). Our results indicate that the structure of pairwise correlation is maintained in the absence of an underlying anatomical organization and may be an organizing principle of the mammalian visual system preserved by nonrandom connectivity within local networks. © The Author 2013. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Pairwise Maximum Entropy Models for Studying Large Biological Systems: When They Can Work and When They Can't

PubMed Central

Roudi, Yasser; Nirenberg, Sheila; Latham, Peter E.

2009-01-01

One of the most critical problems we face in the study of biological systems is building accurate statistical descriptions of them. This problem has been particularly challenging because biological systems typically contain large numbers of interacting elements, which precludes the use of standard brute force approaches. Recently, though, several groups have reported that there may be an alternate strategy. The reports show that reliable statistical models can be built without knowledge of all the interactions in a system; instead, pairwise interactions can suffice. These findings, however, are based on the analysis of small subsystems. Here, we ask whether the observations will generalize to systems of realistic size, that is, whether pairwise models will provide reliable descriptions of true biological systems. Our results show that, in most cases, they will not. The reason is that there is a crossover in the predictive power of pairwise models: If the size of the subsystem is below the crossover point, then the results have no predictive power for large systems. If the size is above the crossover point, then the results may have predictive power. This work thus provides a general framework for determining the extent to which pairwise models can be used to predict the behavior of large biological systems. Applied to neural data, the size of most systems studied so far is below the crossover point. PMID:19424487

Liquid rocket valve assemblies

NASA Technical Reports Server (NTRS)

1973-01-01

The design and operating characteristics of valve assemblies used in liquid propellant rocket engines are discussed. The subjects considered are as follows: (1) valve selection parameters, (2) major design aspects, (3) design integration of valve subassemblies, and (4) assembly of components and functional tests. Information is provided on engine, stage, and spacecraft checkout procedures.

Design, Implementation and Deployment of PAIRwise

ERIC Educational Resources Information Center

Knight, Allan; Almeroth, Kevin; Bimber, Bruce

2008-01-01

Increased access to the Internet has dramatically increased the sources from which students can deliberately or accidentally copy information. This article discusses our motivation to design, implement, and deploy an Internet based plagiarism detection system, called PAIRwise, to address this growing problem. We give details as to how we detect…

The OGCleaner: filtering false-positive homology clusters.

PubMed

Fujimoto, M Stanley; Suvorov, Anton; Jensen, Nicholas O; Clement, Mark J; Snell, Quinn; Bybee, Seth M

2017-01-01

Detecting homologous sequences in organisms is an essential step in protein structure and function prediction, gene annotation and phylogenetic tree construction. Heuristic methods are often employed for quality control of putative homology clusters. These heuristics, however, usually only apply to pairwise sequence comparison and do not examine clusters as a whole. We present the Orthology Group Cleaner (the OGCleaner), a tool designed for filtering putative orthology groups as homology or non-homology clusters by considering all sequences in a cluster. The OGCleaner relies on high-quality orthologous groups identified in OrthoDB to train machine learning algorithms that are able to distinguish between true-positive and false-positive homology groups. This package aims to improve the quality of phylogenetic tree construction especially in instances of lower-quality transcriptome assemblies. https://github.com/byucsl/ogcleaner CONTACT: sfujimoto@gmail.comSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

CAFE: aCcelerated Alignment-FrEe sequence analysis.

PubMed

Lu, Yang Young; Tang, Kujin; Ren, Jie; Fuhrman, Jed A; Waterman, Michael S; Sun, Fengzhu

2017-07-03

Alignment-free genome and metagenome comparisons are increasingly important with the development of next generation sequencing (NGS) technologies. Recently developed state-of-the-art k-mer based alignment-free dissimilarity measures including CVTree, $d_2^*$ and $d_2^S$ are more computationally expensive than measures based solely on the k-mer frequencies. Here, we report a standalone software, aCcelerated Alignment-FrEe sequence analysis (CAFE), for efficient calculation of 28 alignment-free dissimilarity measures. CAFE allows for both assembled genome sequences and unassembled NGS shotgun reads as input, and wraps the output in a standard PHYLIP format. In downstream analyses, CAFE can also be used to visualize the pairwise dissimilarity measures, including dendrograms, heatmap, principal coordinate analysis and network display. CAFE serves as a general k-mer based alignment-free analysis platform for studying the relationships among genomes and metagenomes, and is freely available at https://github.com/younglululu/CAFE. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Performance tuning of N-body codes on modern microprocessors: I. Direct integration with a hermite scheme on x86_64 architecture

NASA Astrophysics Data System (ADS)

Nitadori, Keigo; Makino, Junichiro; Hut, Piet

2006-12-01

The main performance bottleneck of gravitational N-body codes is the force calculation between two particles. We have succeeded in speeding up this pair-wise force calculation by factors between 2 and 10, depending on the code and the processor on which the code is run. These speed-ups were obtained by writing highly fine-tuned code for x86_64 microprocessors. Any existing N-body code, running on these chips, can easily incorporate our assembly code programs. In the current paper, we present an outline of our overall approach, which we illustrate with one specific example: the use of a Hermite scheme for a direct N2 type integration on a single 2.0 GHz Athlon 64 processor, for which we obtain an effective performance of 4.05 Gflops, for double-precision accuracy. In subsequent papers, we will discuss other variations, including the combinations of N log N codes, single-precision implementations, and performance on other microprocessors.

Selective DNA-Mediated Assembly of Gold Nanoparticles on Electroded Substrates

DTIC Science & Technology

2008-06-01

might use the Watson - Crick base-pairing of DNA as a means for ultrahigh-precision engineering is well- known.5,6 The idea is to use the highly specific...Selective DNA -Mediated Assembly of Gold Nanoparticles on Electroded Substrates K. E. Sapsford,†,‡,∇ D. Park,§ E. R. Goldman,‡ E. E. Foos,| S. A...electrodes via DNA hybridization. Protocols are demonstrated for maximizing selectivity and coverage using 15mers as the active binding agents. Detailed

Joint Feature Selection and Classification for Multilabel Learning.

PubMed

Huang, Jun; Li, Guorong; Huang, Qingming; Wu, Xindong

2018-03-01

Multilabel learning deals with examples having multiple class labels simultaneously. It has been applied to a variety of applications, such as text categorization and image annotation. A large number of algorithms have been proposed for multilabel learning, most of which concentrate on multilabel classification problems and only a few of them are feature selection algorithms. Current multilabel classification models are mainly built on a single data representation composed of all the features which are shared by all the class labels. Since each class label might be decided by some specific features of its own, and the problems of classification and feature selection are often addressed independently, in this paper, we propose a novel method which can perform joint feature selection and classification for multilabel learning, named JFSC. Different from many existing methods, JFSC learns both shared features and label-specific features by considering pairwise label correlations, and builds the multilabel classifier on the learned low-dimensional data representations simultaneously. A comparative study with state-of-the-art approaches manifests a competitive performance of our proposed method both in classification and feature selection for multilabel learning.

Model selection with multiple regression on distance matrices leads to incorrect inferences.

PubMed

Franckowiak, Ryan P; Panasci, Michael; Jarvis, Karl J; Acuña-Rodriguez, Ian S; Landguth, Erin L; Fortin, Marie-Josée; Wagner, Helene H

2017-01-01

In landscape genetics, model selection procedures based on Information Theoretic and Bayesian principles have been used with multiple regression on distance matrices (MRM) to test the relationship between multiple vectors of pairwise genetic, geographic, and environmental distance. Using Monte Carlo simulations, we examined the ability of model selection criteria based on Akaike's information criterion (AIC), its small-sample correction (AICc), and the Bayesian information criterion (BIC) to reliably rank candidate models when applied with MRM while varying the sample size. The results showed a serious problem: all three criteria exhibit a systematic bias toward selecting unnecessarily complex models containing spurious random variables and erroneously suggest a high level of support for the incorrectly ranked best model. These problems effectively increased with increasing sample size. The failure of AIC, AICc, and BIC was likely driven by the inflated sample size and different sum-of-squares partitioned by MRM, and the resulting effect on delta values. Based on these findings, we strongly discourage the continued application of AIC, AICc, and BIC for model selection with MRM.

Self-assembling amphiphilic peptides†

PubMed Central

Dehsorkhi, Ashkan; Castelletto, Valeria; Hamley, Ian W

2014-01-01

The self-assembly of several classes of amphiphilic peptides is reviewed, and selected applications are discussed. We discuss recent work on the self-assembly of lipopeptides, surfactant-like peptides and amyloid peptides derived from the amyloid-β peptide. The influence of environmental variables such as pH and temperature on aggregate nanostructure is discussed. Enzyme-induced remodelling due to peptide cleavage and nanostructure control through photocleavage or photo-cross-linking are also considered. Lastly, selected applications of amphiphilic peptides in biomedicine and materials science are outlined. © 2014 The Authors. Journal of Peptide Science published by European Peptide Society and John Wiley & Sons, Ltd. PMID:24729276

A multi-stakeholder framework for urban runoff quality management: Application of social choice and bargaining techniques.

PubMed

Ghodsi, Seyed Hamed; Kerachian, Reza; Zahmatkesh, Zahra

2016-04-15

In this paper, an integrated framework is proposed for urban runoff management. To control and improve runoff quality and quantity, Low Impact Development (LID) practices are utilized. In order to determine the LIDs' areas and locations, the Non-dominated Sorting Genetic Algorithm-II (NSGA-II), which considers three objective functions of minimizing runoff volume, runoff pollution and implementation cost of LIDs, is utilized. In this framework, the Storm Water Management Model (SWMM) is used for stream flow simulation. The non-dominated solutions provided by the NSGA-II are considered as management scenarios. To select the most preferred scenario, interactions among the main stakeholders in the study area with conflicting utilities are incorporated by utilizing bargaining models including a non-cooperative game, Nash model and social choice procedures of Borda count and approval voting. Moreover, a new social choice procedure, named pairwise voting method, is proposed and applied. Based on each conflict resolution approach, a scenario is identified as the ideal solution providing the LIDs' areas, locations and implementation cost. The proposed framework is applied for urban water quality and quantity management in the northern part of Tehran metropolitan city, Iran. Results show that the proposed pairwise voting method tends to select a scenario with a higher percentage of reduction in TSS (Total Suspended Solid) load and runoff volume, in comparison with the Borda count and approval voting methods. Besides, the Nash method presents a management scenario with the highest cost for LIDs' implementation and the maximum values for percentage of runoff volume reduction and TSS removal. The results also signify that selection of an appropriate management scenario by stakeholders in the study area depends on the available financial resources and the relative importance of runoff quality improvement in comparison with reducing the runoff volume. Copyright © 2016 Elsevier B.V. All rights reserved.

Generation of Synthetic Spike Trains with Defined Pairwise Correlations

PubMed Central

Niebur, Ernst

2008-01-01

Recent technological advances as well as progress in theoretical understanding of neural systems have created a need for synthetic spike trains with controlled mean rate and pairwise cross-correlation. This report introduces and analyzes a novel algorithm for the generation of discretized spike trains with arbitrary mean rates and controlled cross correlation. Pairs of spike trains with any pairwise correlation can be generated, and higher-order correlations are compatible with common synaptic input. Relations between allowable mean rates and correlations within a population are discussed. The algorithm is highly efficient, its complexity increasing linearly with the number of spike trains generated and therefore inversely with the number of cross-correlated pairs. PMID:17521277

Assembly flow simulation of a radar

NASA Technical Reports Server (NTRS)

Rutherford, W. C.; Biggs, P. M.

1994-01-01

A discrete event simulation model has been developed to predict the assembly flow time of a new radar product. The simulation was the key tool employed to identify flow constraints. The radar, production facility, and equipment complement were designed, arranged, and selected to provide the most manufacturable assembly possible. A goal was to reduce the assembly and testing cycle time from twenty-six weeks. A computer software simulation package (SLAM 2) was utilized as the foundation for simulating the assembly flow time. FORTRAN subroutines were incorporated into the software to deal with unique flow circumstances that were not accommodated by the software. Detailed information relating to the assembly operations was provided by a team selected from the engineering, manufacturing management, inspection, and production assembly staff. The simulation verified that it would be possible to achieve the cycle time goal of six weeks. Equipment and manpower constraints were identified during the simulation process and adjusted as required to achieve the flow with a given monthly production requirement. The simulation is being maintained as a planning tool to be used to identify constraints in the event that monthly output is increased. 'What-if' studies have been conducted to identify the cost of reducing constraints caused by increases in output requirement.

Directed assembly of carbon nanotubes on soft substrates for use as a flexible biosensor array.

PubMed

Koh, Juntae; Yi, Mihye; Yang Lee, Byung; Kim, Tae Hyun; Lee, Joohyung; Jhon, Young Min; Hong, Seunghun

2008-12-17

We have developed a method to selectively assemble and align carbon nanotubes (CNTs) on soft substrates for use as flexible biosensors. In this strategy, a thin oxide layer was deposited on soft substrates via low temperature plasma enhanced chemical vapor deposition, and a linker-free assembly process was applied on the oxide surface where the assembly of carbon nanotubes was guided by methyl-terminated molecular patterns on the oxide surface. The electrical characterization of the fabricated CNT devices exhibited a typical p-type gating effect and 1/f noise behavior. The bare oxide regions near CNTs were functionalized with glutamate oxidase to fabricate selective biosensors to detect two forms of glutamate substances existing in different situations: L-glutamic acid, a neurotransmitting material, and monosodium glutamate, a food additive.

Self-assembled near-infrared dye nanoparticles as a selective protein sensor by activation of a dormant fluorophore.

PubMed

Anees, Palapuravan; Sreejith, Sivaramapanicker; Ajayaghosh, Ayyappanpillai

2014-09-24

Design of selective sensors for a specific analyte in blood serum, which contains a large number of proteins, small molecules, and ions, is important in clinical diagnostics. While metal and polymeric nanoparticle conjugates have been used as sensors, small molecular assemblies have rarely been exploited for the selective sensing of a protein in blood serum. Herein we demonstrate how a nonspecific small molecular fluorescent dye can be empowered to form a selective protein sensor as illustrated with a thiol-sensitive near-IR squaraine (Sq) dye (λabs= 670 nm, λem= 700 nm). The dye self-assembles to form nonfluorescent nanoparticles (Dh = 200 nm) which selectively respond to human serum albumin (HSA) in the presence of other thiol-containing molecules and proteins by triggering a green fluorescence. This selective response of the dye nanoparticles allowed detection and quantification of HSA in blood serum with a sensitivity limit of 3 nM. Notably, the Sq dye in solution state is nonselective and responds to any thiol-containing proteins and small molecules. The sensing mechanism involves HSA specific controlled disassembly of the Sq nanoparticles to the molecular dye by a noncovalent binding process and its subsequent reaction with the thiol moiety of the protein, triggering the green emission of a dormant fluorophore present in the dye. This study demonstrates the power of a self-assembled small molecular fluorophore for protein sensing and is a simple chemical tool for the clinical diagnosis of blood serum.

Single nucleotide polymorphisms unravel hierarchical divergence and signatures of selection among Alaskan sockeye salmon (Oncorhynchus nerka) populations.

PubMed

Gomez-Uchida, Daniel; Seeb, James E; Smith, Matt J; Habicht, Christopher; Quinn, Thomas P; Seeb, Lisa W

2011-02-18

Disentangling the roles of geography and ecology driving population divergence and distinguishing adaptive from neutral evolution at the molecular level have been common goals among evolutionary and conservation biologists. Using single nucleotide polymorphism (SNP) multilocus genotypes for 31 sockeye salmon (Oncorhynchus nerka) populations from the Kvichak River, Alaska, we assessed the relative roles of geography (discrete boundaries or continuous distance) and ecology (spawning habitat and timing) driving genetic divergence in this species at varying spatial scales within the drainage. We also evaluated two outlier detection methods to characterize candidate SNPs responding to environmental selection, emphasizing which mechanism(s) may maintain the genetic variation of outlier loci. For the entire drainage, Mantel tests suggested a greater role of geographic distance on population divergence than differences in spawn timing when each variable was correlated with pairwise genetic distances. Clustering and hierarchical analyses of molecular variance indicated that the largest genetic differentiation occurred between populations from distinct lakes or subdrainages. Within one population-rich lake, however, Mantel tests suggested a greater role of spawn timing than geographic distance on population divergence when each variable was correlated with pairwise genetic distances. Variable spawn timing among populations was linked to specific spawning habitats as revealed by principal coordinate analyses. We additionally identified two outlier SNPs located in the major histocompatibility complex (MHC) class II that appeared robust to violations of demographic assumptions from an initial pool of eight candidates for selection. First, our results suggest that geography and ecology have influenced genetic divergence between Alaskan sockeye salmon populations in a hierarchical manner depending on the spatial scale. Second, we found consistent evidence for diversifying selection in two loci located in the MHC class II by means of outlier detection methods; yet, alternative scenarios for the evolution of these loci were also evaluated. Both conclusions argue that historical contingency and contemporary adaptation have likely driven differentiation between Kvichak River sockeye salmon populations, as revealed by a suite of SNPs. Our findings highlight the need for conservation of complex population structure, because it provides resilience in the face of environmental change, both natural and anthropogenic.

Single nucleotide polymorphisms unravel hierarchical divergence and signatures of selection among Alaskan sockeye salmon (Oncorhynchus nerka) populations

PubMed Central

2011-01-01

Background Disentangling the roles of geography and ecology driving population divergence and distinguishing adaptive from neutral evolution at the molecular level have been common goals among evolutionary and conservation biologists. Using single nucleotide polymorphism (SNP) multilocus genotypes for 31 sockeye salmon (Oncorhynchus nerka) populations from the Kvichak River, Alaska, we assessed the relative roles of geography (discrete boundaries or continuous distance) and ecology (spawning habitat and timing) driving genetic divergence in this species at varying spatial scales within the drainage. We also evaluated two outlier detection methods to characterize candidate SNPs responding to environmental selection, emphasizing which mechanism(s) may maintain the genetic variation of outlier loci. Results For the entire drainage, Mantel tests suggested a greater role of geographic distance on population divergence than differences in spawn timing when each variable was correlated with pairwise genetic distances. Clustering and hierarchical analyses of molecular variance indicated that the largest genetic differentiation occurred between populations from distinct lakes or subdrainages. Within one population-rich lake, however, Mantel tests suggested a greater role of spawn timing than geographic distance on population divergence when each variable was correlated with pairwise genetic distances. Variable spawn timing among populations was linked to specific spawning habitats as revealed by principal coordinate analyses. We additionally identified two outlier SNPs located in the major histocompatibility complex (MHC) class II that appeared robust to violations of demographic assumptions from an initial pool of eight candidates for selection. Conclusions First, our results suggest that geography and ecology have influenced genetic divergence between Alaskan sockeye salmon populations in a hierarchical manner depending on the spatial scale. Second, we found consistent evidence for diversifying selection in two loci located in the MHC class II by means of outlier detection methods; yet, alternative scenarios for the evolution of these loci were also evaluated. Both conclusions argue that historical contingency and contemporary adaptation have likely driven differentiation between Kvichak River sockeye salmon populations, as revealed by a suite of SNPs. Our findings highlight the need for conservation of complex population structure, because it provides resilience in the face of environmental change, both natural and anthropogenic. PMID:21332997

Prospects for inferring pairwise relationships with single nucleotide polymorphisms

Treesearch

Jeffery C. Glaubitz; O. Eugene, Jr. Rhodes; J. Andrew DeWoody

2003-01-01

An extraordinarily large number of single nucleotide polymorphisms (SNPs) are now available in humans as well as in other model organisms. Technological advancements may soon make it feasible to assay hundreds of SNPs in virtually any organism of interest. One potential application of SNPs is the determination of pairwise genetic relationships in populations without...

The Bicycle Assembly Line Game

ERIC Educational Resources Information Center

Klotz, Dorothy

2011-01-01

"The Bicycle Assembly Line Game" is a team-based, in-class activity that helps students develop a basic understanding of continuously operating processes. Each team of 7-10 students selects one of seven prefigured bicycle assembly lines to operate. The lines are run in real-time, and the team that operates the line that yields the…

Adhesives for assembly of lightweight wood containers

Treesearch

R. S. Kurtenacker

1964-01-01

This report discusses the screening of various adhesive and mastic systems for possible use in assembling lightweight wood containers. Results showed that dynamic tests of simulated box corners correlated reasonably well with rough handling evaluations of eight selected systems when used to assemble lightweight wood boxes made from a Group I container wood....

EXTENSION ADMINISTRATION AND STATE LEGISLATIVE PROCESS--A CASE STUDY OF THE 71ST MISSOURI GENERAL ASSEMBLY.

ERIC Educational Resources Information Center

KYD, STIRLING

TO GAIN UNDERSTANDING OF MISSOURI'S LEGISLATIVE PROCESS AND AID ADMINISTRATORS OF THE EXTENSION DIVISION, THE AUTHOR INVESTIGATED THE 71ST GENERAL ASSEMBLY. HE READ PUBLICATIONS, INTERVIEWED LOBBYISTS, AND CONDUCTED OPEN ENDED DEPTH INTERVIEWS WITH LEGISLATORS SELECTED TO COMPRISE THE LEADERSHIP OF THE ASSEMBLY. HIS DISSERTATION PRESENTS THE…

First fluorescent sensor for fluoride based on 2-ureido-4[1H]-pyrimidinone quadruple hydrogen-bonded AADD supramolecular assembly.

PubMed

Zhao, Yao-Peng; Zhao, Chun-Chang; Wu, Li-Zhu; Zhang, Li-Ping; Tung, Chen-Ho; Pan, Yuan-Jiang

2006-03-03

A simple, highly selective, neutral, fluorescent sensor for fluoride anions is reported. It is based on 2-ureido-4[1H]-pyrimidinone quadruple hydrogen-bonded AADD supramolecular assembly, and its assembling and disassembling processes are also able to respond to external stimuli reversibly.

Hierarchical semi-numeric method for pairwise fuzzy group decision making.

PubMed

Marimin, M; Umano, M; Hatono, I; Tamura, H

2002-01-01

Gradual improvements to a single-level semi-numeric method, i.e., linguistic labels preference representation by fuzzy sets computation for pairwise fuzzy group decision making are summarized. The method is extended to solve multiple criteria hierarchical structure pairwise fuzzy group decision-making problems. The problems are hierarchically structured into focus, criteria, and alternatives. Decision makers express their evaluations of criteria and alternatives based on each criterion by using linguistic labels. The labels are converted into and processed in triangular fuzzy numbers (TFNs). Evaluations of criteria yield relative criteria weights. Evaluations of the alternatives, based on each criterion, yield a degree of preference for each alternative or a degree of satisfaction for each preference value. By using a neat ordered weighted average (OWA) or a fuzzy weighted average operator, solutions obtained based on each criterion are aggregated into final solutions. The hierarchical semi-numeric method is suitable for solving a larger and more complex pairwise fuzzy group decision-making problem. The proposed method has been verified and applied to solve some real cases and is compared to Saaty's (1996) analytic hierarchy process (AHP) method.

A new method of content based medical image retrieval and its applications to CT imaging sign retrieval.

PubMed

Ma, Ling; Liu, Xiabi; Gao, Yan; Zhao, Yanfeng; Zhao, Xinming; Zhou, Chunwu

2017-02-01

This paper proposes a new method of content based medical image retrieval through considering fused, context-sensitive similarity. Firstly, we fuse the semantic and visual similarities between the query image and each image in the database as their pairwise similarities. Then, we construct a weighted graph whose nodes represent the images and edges measure their pairwise similarities. By using the shortest path algorithm over the weighted graph, we obtain a new similarity measure, context-sensitive similarity measure, between the query image and each database image to complete the retrieval process. Actually, we use the fused pairwise similarity to narrow down the semantic gap for obtaining a more accurate pairwise similarity measure, and spread it on the intrinsic data manifold to achieve the context-sensitive similarity for a better retrieval performance. The proposed method has been evaluated on the retrieval of the Common CT Imaging Signs of Lung Diseases (CISLs) and achieved not only better retrieval results but also the satisfactory computation efficiency. Copyright © 2017 Elsevier Inc. All rights reserved.

SVM-dependent pairwise HMM: an application to protein pairwise alignments.

PubMed

Orlando, Gabriele; Raimondi, Daniele; Khan, Taushif; Lenaerts, Tom; Vranken, Wim F

2017-12-15

Methods able to provide reliable protein alignments are crucial for many bioinformatics applications. In the last years many different algorithms have been developed and various kinds of information, from sequence conservation to secondary structure, have been used to improve the alignment performances. This is especially relevant for proteins with highly divergent sequences. However, recent works suggest that different features may have different importance in diverse protein classes and it would be an advantage to have more customizable approaches, capable to deal with different alignment definitions. Here we present Rigapollo, a highly flexible pairwise alignment method based on a pairwise HMM-SVM that can use any type of information to build alignments. Rigapollo lets the user decide the optimal features to align their protein class of interest. It outperforms current state of the art methods on two well-known benchmark datasets when aligning highly divergent sequences. A Python implementation of the algorithm is available at http://ibsquare.be/rigapollo. wim.vranken@vub.be. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Consistency-based rectification of nonrigid registrations

PubMed Central

Gass, Tobias; Székely, Gábor; Goksel, Orcun

2015-01-01

Abstract. We present a technique to rectify nonrigid registrations by improving their group-wise consistency, which is a widely used unsupervised measure to assess pair-wise registration quality. While pair-wise registration methods cannot guarantee any group-wise consistency, group-wise approaches typically enforce perfect consistency by registering all images to a common reference. However, errors in individual registrations to the reference then propagate, distorting the mean and accumulating in the pair-wise registrations inferred via the reference. Furthermore, the assumption that perfect correspondences exist is not always true, e.g., for interpatient registration. The proposed consistency-based registration rectification (CBRR) method addresses these issues by minimizing the group-wise inconsistency of all pair-wise registrations using a regularized least-squares algorithm. The regularization controls the adherence to the original registration, which is additionally weighted by the local postregistration similarity. This allows CBRR to adaptively improve consistency while locally preserving accurate pair-wise registrations. We show that the resulting registrations are not only more consistent, but also have lower average transformation error when compared to known transformations in simulated data. On clinical data, we show improvements of up to 50% target registration error in breathing motion estimation from four-dimensional MRI and improvements in atlas-based segmentation quality of up to 65% in terms of mean surface distance in three-dimensional (3-D) CT. Such improvement was observed consistently using different registration algorithms, dimensionality (two-dimensional/3-D), and modalities (MRI/CT). PMID:26158083

Structure and energetics of pairwise interactions between proteasome subunits RPN2, RPN13, and ubiquitin clarify a substrate recruitment mechanism

DOE PAGES

VanderLinden, Ryan T.; Hemmis, Casey W.; Yao, Tingting; ...

2017-04-25

This work presents that the 26S proteasome is a large cellular assembly that mediates the selective degradation of proteins in the nucleus and cytosol and is an established target for anticancer therapeutics. Protein substrates are typically targeted to the proteasome through modification with a polyubiquitin chain, which can be recognized by several proteasome-associated ubiquitin receptors. One of these receptors, RPN13/ADRM1, is recruited to the proteasome through direct interaction with the large scaffolding protein RPN2 within the 19S regulatory particle. To better understand the interactions between RPN13, RPN2, and ubiquitin, we used human proteins to map the RPN13-binding epitope to themore » C-terminal 14 residues of RPN2, which, like ubiquitin, binds the N-terminal pleckstrin-like receptor of ubiquitin (PRU) domain of RPN13. We also report the crystal structures of the RPN13 PRU domain in complex with peptides corresponding to the RPN2 C terminus and ubiquitin. Through mutational analysis, we validated the RPN2-binding interface revealed by our structures and quantified binding interactions with surface plasmon resonance and fluorescence polarization. In contrast to a previous report, we find that RPN13 binds ubiquitin with an affinity similar to that of other proteasome-associated ubiquitin receptors and that RPN2, ubiquitin, and the deubiquitylase UCH37 bind to RPN13 with independent energetics. In conclusion, these findings provide a detailed characterization of interactions that are important for proteasome function, indicate ubiquitin affinities that are consistent with the role of RPN13 as a proteasomal ubiquitin receptor, and have major implications for the development of novel anticancer therapeutics.« less

Characterization of transcriptome in the Indian meal moth Plodia interpunctella (Lepidoptera: Pyralidae) and gene expression analysis during developmental stages.

PubMed

Tang, Pei-An; Wu, Hai-Jing; Xue, Hao; Ju, Xing-Rong; Song, Wei; Zhang, Qi-Lin; Yuan, Ming-Long

2017-07-30

The Indian meal moth Plodia interpunctella (Lepidoptera: Pyralidae) is a worldwide pest that causes serious damage to stored foods. Although many efforts have been conducted on this species due to its economic importance, the study of genetic basis of development, behavior and insecticide resistance has been greatly hampered due to lack of genomic information. In this study, we used high throughput sequencing platform to perform a de novo transcriptome assembly and tag-based digital gene expression profiling (DGE) analyses across four different developmental stages of P. interpunctella (egg, third-instar larvae, pupae and adult). We obtained approximate 9gigabyte (GB) of clean data and recovered 84,938 unigenes, including 37,602 clusters and 47,336 singletons. These unigenes were annotated using BLAST against the non-redundant protein databases and then functionally classified based on Gene Ontology (GO), Clusters of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genomes databases (KEGG). A large number of differentially expressed genes were identified by pairwise comparisons among different developmental stages. Gene expression profiles dramatically changed between developmental stage transitions. Some of these differentially expressed genes were related to digestion and cuticularization. Quantitative real-time PCR results of six randomly selected genes conformed the findings in the DGEs. Furthermore, we identified over 8000 microsatellite markers and 97,648 single nucleotide polymorphisms which will be useful for population genetics studies of P. interpunctella. This transcriptomic information provided insight into the developmental basis of P. interpunctella and will be helpful for establishing integrated management strategies and developing new targets of insecticides for this serious pest. Copyright © 2017 Elsevier B.V. All rights reserved.

Structure and energetics of pairwise interactions between proteasome subunits RPN2, RPN13, and ubiquitin clarify a substrate recruitment mechanism.

PubMed

VanderLinden, Ryan T; Hemmis, Casey W; Yao, Tingting; Robinson, Howard; Hill, Christopher P

2017-06-09

The 26S proteasome is a large cellular assembly that mediates the selective degradation of proteins in the nucleus and cytosol and is an established target for anticancer therapeutics. Protein substrates are typically targeted to the proteasome through modification with a polyubiquitin chain, which can be recognized by several proteasome-associated ubiquitin receptors. One of these receptors, RPN13/ADRM1, is recruited to the proteasome through direct interaction with the large scaffolding protein RPN2 within the 19S regulatory particle. To better understand the interactions between RPN13, RPN2, and ubiquitin, we used human proteins to map the RPN13-binding epitope to the C-terminal 14 residues of RPN2, which, like ubiquitin, binds the N-terminal pleckstrin-like receptor of ubiquitin (PRU) domain of RPN13. We also report the crystal structures of the RPN13 PRU domain in complex with peptides corresponding to the RPN2 C terminus and ubiquitin. Through mutational analysis, we validated the RPN2-binding interface revealed by our structures and quantified binding interactions with surface plasmon resonance and fluorescence polarization. In contrast to a previous report, we find that RPN13 binds ubiquitin with an affinity similar to that of other proteasome-associated ubiquitin receptors and that RPN2, ubiquitin, and the deubiquitylase UCH37 bind to RPN13 with independent energetics. These findings provide a detailed characterization of interactions that are important for proteasome function, indicate ubiquitin affinities that are consistent with the role of RPN13 as a proteasomal ubiquitin receptor, and have major implications for the development of novel anticancer therapeutics. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Query-seeded iterative sequence similarity searching improves selectivity 5–20-fold

PubMed Central

Li, Weizhong; Lopez, Rodrigo

2017-01-01

Abstract Iterative similarity search programs, like psiblast, jackhmmer, and psisearch, are much more sensitive than pairwise similarity search methods like blast and ssearch because they build a position specific scoring model (a PSSM or HMM) that captures the pattern of sequence conservation characteristic to a protein family. But models are subject to contamination; once an unrelated sequence has been added to the model, homologs of the unrelated sequence will also produce high scores, and the model can diverge from the original protein family. Examination of alignment errors during psiblast PSSM contamination suggested a simple strategy for dramatically reducing PSSM contamination. psiblast PSSMs are built from the query-based multiple sequence alignment (MSA) implied by the pairwise alignments between the query model (PSSM, HMM) and the subject sequences in the library. When the original query sequence residues are inserted into gapped positions in the aligned subject sequence, the resulting PSSM rarely produces alignment over-extensions or alignments to unrelated sequences. This simple step, which tends to anchor the PSSM to the original query sequence and slightly increase target percent identity, can reduce the frequency of false-positive alignments more than 20-fold compared with psiblast and jackhmmer, with little loss in search sensitivity. PMID:27923999

Development of a Multimetric Indicator of Pelagic Zooplankton ...

EPA Pesticide Factsheets

We used zooplankton data collected for the 2012 National Lakes Assessment (NLA) to develop multimetric indices (MMIs) for five aggregated ecoregions of the conterminous USA (Coastal Plains, Eastern Highlands, Plains, Upper Midwest, and Western Mountains and Xeric [“West’]). We classified candidate metrics into six categories: We evaluated the performance of candidate metrics, and used metrics that had passed these screens to calculate all possible candidate MMIs that included at least one metric from each category. We selected the candidate MMI that had high responsiveness, a reasonable value for repeatability, low mean pairwise correlation among component metrics, and, when possible, a maximum pairwise correlation among component metrics that was <0.7. We were able to develop MMIs that were sufficiently responsive and repeatable to assess ecological condition for the NLA without the need to reduce the effects of natural variation using models. We did not observe effects of either lake size, lake origin, or site depth on the MMIs. The MMIs appear to respond more strongly to increased nutrient concentrations than to shoreline habitat conditions. Improving our understanding of how zooplankton assemblages respond to increased human disturbance, and obtaining more complete autecological information for zooplankton taxa would likely improve MMIs developed for future assessments. Using zooplankton assemblage data from the 2012 National Lakes Assessment (NLA),

Modeling protein conformational changes by iterative fitting of distance constraints using reoriented normal modes.

PubMed

Zheng, Wenjun; Brooks, Bernard R

2006-06-15

Recently we have developed a normal-modes-based algorithm that predicts the direction of protein conformational changes given the initial state crystal structure together with a small number of pairwise distance constraints for the end state. Here we significantly extend this method to accurately model both the direction and amplitude of protein conformational changes. The new protocol implements a multisteps search in the conformational space that is driven by iteratively minimizing the error of fitting the given distance constraints and simultaneously enforcing the restraint of low elastic energy. At each step, an incremental structural displacement is computed as a linear combination of the lowest 10 normal modes derived from an elastic network model, whose eigenvectors are reorientated to correct for the distortions caused by the structural displacements in the previous steps. We test this method on a list of 16 pairs of protein structures for which relatively large conformational changes are observed (root mean square deviation >3 angstroms), using up to 10 pairwise distance constraints selected by a fluctuation analysis of the initial state structures. This method has achieved a near-optimal performance in almost all cases, and in many cases the final structural models lie within root mean square deviation of 1 approximately 2 angstroms from the native end state structures.

Kernel Machine SNP-set Testing under Multiple Candidate Kernels

PubMed Central

Wu, Michael C.; Maity, Arnab; Lee, Seunggeun; Simmons, Elizabeth M.; Harmon, Quaker E.; Lin, Xinyi; Engel, Stephanie M.; Molldrem, Jeffrey J.; Armistead, Paul M.

2013-01-01

Joint testing for the cumulative effect of multiple single nucleotide polymorphisms grouped on the basis of prior biological knowledge has become a popular and powerful strategy for the analysis of large scale genetic association studies. The kernel machine (KM) testing framework is a useful approach that has been proposed for testing associations between multiple genetic variants and many different types of complex traits by comparing pairwise similarity in phenotype between subjects to pairwise similarity in genotype, with similarity in genotype defined via a kernel function. An advantage of the KM framework is its flexibility: choosing different kernel functions allows for different assumptions concerning the underlying model and can allow for improved power. In practice, it is difficult to know which kernel to use a priori since this depends on the unknown underlying trait architecture and selecting the kernel which gives the lowest p-value can lead to inflated type I error. Therefore, we propose practical strategies for KM testing when multiple candidate kernels are present based on constructing composite kernels and based on efficient perturbation procedures. We demonstrate through simulations and real data applications that the procedures protect the type I error rate and can lead to substantially improved power over poor choices of kernels and only modest differences in power versus using the best candidate kernel. PMID:23471868

MIDAS: software for analysis and visualisation of interallelic disequilibrium between multiallelic markers

PubMed Central

Gaunt, Tom R; Rodriguez, Santiago; Zapata, Carlos; Day, Ian NM

2006-01-01

Background Various software tools are available for the display of pairwise linkage disequilibrium across multiple single nucleotide polymorphisms. The HapMap project also presents these graphics within their website. However, these approaches are limited in their use of data from multiallelic markers and provide limited information in a graphical form. Results We have developed a software package (MIDAS – Multiallelic Interallelic Disequilibrium Analysis Software) for the estimation and graphical display of interallelic linkage disequilibrium. Linkage disequilibrium is analysed for each allelic combination (of one allele from each of two loci), between all pairwise combinations of any type of multiallelic loci in a contig (or any set) of many loci (including single nucleotide polymorphisms, microsatellites, minisatellites and haplotypes). Data are presented graphically in a novel and informative way, and can also be exported in tabular form for other analyses. This approach facilitates visualisation of patterns of linkage disequilibrium across genomic regions, analysis of the relationships between different alleles of multiallelic markers and inferences about patterns of evolution and selection. Conclusion MIDAS is a linkage disequilibrium analysis program with a comprehensive graphical user interface providing novel views of patterns of linkage disequilibrium between all types of multiallelic and biallelic markers. Availability Available from and PMID:16643648

Weak Higher-Order Interactions in Macroscopic Functional Networks of the Resting Brain.

PubMed

Huang, Xuhui; Xu, Kaibin; Chu, Congying; Jiang, Tianzi; Yu, Shan

2017-10-25

Interactions among different brain regions are usually examined through functional connectivity (FC) analysis, which is exclusively based on measuring pairwise correlations in activities. However, interactions beyond the pairwise level, that is, higher-order interactions (HOIs), are vital in understanding the behavior of many complex systems. So far, whether HOIs exist among brain regions and how they can affect the brain's activities remains largely elusive. To address these issues, here, we analyzed blood oxygenation level-dependent (BOLD) signals recorded from six typical macroscopic functional networks of the brain in 100 human subjects (46 males and 54 females) during the resting state. Through examining the binarized BOLD signals, we found that HOIs within and across individual networks were both very weak regardless of the network size, topology, degree of spatial proximity, spatial scales, and whether the global signal was regressed. To investigate the potential mechanisms underlying the weak HOIs, we analyzed the dynamics of a network model and also found that HOIs were generally weak within a wide range of key parameters provided that the overall dynamic feature of the model was similar to the empirical data and it was operating close to a linear fluctuation regime. Our results suggest that weak HOI may be a general property of brain's macroscopic functional networks, which implies the dominance of pairwise interactions in shaping brain activities at such a scale and warrants the validity of widely used pairwise-based FC approaches. SIGNIFICANCE STATEMENT To explain how activities of different brain areas are coordinated through interactions is essential to revealing the mechanisms underlying various brain functions. Traditionally, such an interaction structure is commonly studied using pairwise-based functional network analyses. It is unclear whether the interactions beyond the pairwise level (higher-order interactions or HOIs) play any role in this process. Here, we show that HOIs are generally weak in macroscopic brain networks. We also suggest a possible dynamical mechanism that may underlie this phenomenon. These results provide plausible explanation for the effectiveness of widely used pairwise-based approaches in analyzing brain networks. More importantly, it reveals a previously unknown, simple organization of the brain's macroscopic functional systems. Copyright © 2017 the authors 0270-6474/17/3710481-17$15.00/0.

Does technique matter; a pilot study exploring weighting techniques for a multi-criteria decision support framework.

PubMed

van Til, Janine; Groothuis-Oudshoorn, Catharina; Lieferink, Marijke; Dolan, James; Goetghebeur, Mireille

2014-01-01

There is an increased interest in the use of multi-criteria decision analysis (MCDA) to support regulatory and reimbursement decision making. The EVIDEM framework was developed to provide pragmatic multi-criteria decision support in health care, to estimate the value of healthcare interventions, and to aid in priority-setting. The objectives of this study were to test 1) the influence of different weighting techniques on the overall outcome of an MCDA exercise, 2) the discriminative power in weighting different criteria of such techniques, and 3) whether different techniques result in similar weights in weighting the criteria set proposed by the EVIDEM framework. A sample of 60 Dutch and Canadian students participated in the study. Each student used an online survey to provide weights for 14 criteria with two different techniques: a five-point rating scale and one of the following techniques selected randomly: ranking, point allocation, pairwise comparison and best worst scaling. The results of this study indicate that there is no effect of differences in weights on value estimates at the group level. On an individual level, considerable differences in criteria weights and rank order occur as a result of the weight elicitation method used, and the ability of different techniques to discriminate in criteria importance. Of the five techniques tested, the pair-wise comparison of criteria has the highest ability to discriminate in weights when fourteen criteria are compared. When weights are intended to support group decisions, the choice of elicitation technique has negligible impact on criteria weights and the overall value of an innovation. However, when weights are used to support individual decisions, the choice of elicitation technique influences outcome and studies that use dissimilar techniques cannot be easily compared. Weight elicitation through pairwise comparison of criteria is preferred when taking into account its superior ability to discriminate between criteria and respondents' preferences.

Environmental cell assembly for use in for use in spectroscopy and microscopy applications

DOEpatents

Stowe, Ashley Clinton; Smyrl, Norman; Hallman, Jr., Russell L.

2014-09-02

An environmental cell assembly for use in microscopy and spectroscopy applications, including: an environmentally sealed body assembly configured to selectively hold and contain a sample; a plurality of ports manufactured into one or more surfaces of the body assembly for one or more of evacuating the body assembly and injecting a gas into or removing a gas from the body assembly; a port manufactured into a surface of the body assembly for receiving a translating stage configured to move the sample within the body assembly; and a port manufactured into a surface of the body assembly for receiving one or more lenses utilized in a microscopy or spectroscopy application; wherein the one or more lenses are disposed adjacent the sample without intervening structures disposed there between. The cell assembly also includes a port manufactured into a surface of the body assembly for retaining a window and providing visualization of the sample.

Geometry directed self-selection in the coordination-driven self-assembly of irregular supramolecular polygons.

PubMed

Zheng, Yao-Rong; Northrop, Brian H; Yang, Hai-Bo; Zhao, Liang; Stang, Peter J

2009-05-01

The self-assembly of irregular metallo-supramolecular hexagons and parallelograms has been achieved in a self-selective manner upon mixing 120 degrees unsymmetrical dipyridyl ligands with 60 degrees or 120 degrees organoplatinum acceptors in a 1:1 ratio. The polygons have been characterized using (31)P and (1)H multinuclear NMR spectroscopy and electrospray ionization mass spectrometry (ESI-MS) as well as X-ray crystallography. Geometric features of the molecular subunits direct the self-selection process, which is supported by molecular force field computations.

Geometry Directed Self-Selection in the Coordination-Driven Self-Assembly of Irregular Supramolecular Polygons

PubMed Central

Zheng, Yao-Rong; Northrop, Brian H; Yang, Hai-Bo; Zhao, Liang; Stang, Peter J.

2009-01-01

The self-assembly of irregular metallo-supramolecular hexagons and parallelograms has been achieved in a self-selective manner upon mixing 120° unsymmetrical dipyridyl ligands with 60° or 120° organoplatinum acceptors in a 1:1 ratio. The polygons have been characterized using 31P and 1H multinuclear NMR spectroscopy and electrospray ionization mass spectrometry (ESI-MS), as well as X-ray crystallography. Geometric features of the molecular subunits direct the self-selection process, which is supported by molecular force field computations. PMID:19348444

Hierarchical assembly of viral nanotemplates with encoded microparticles via nucleic acid hybridization.

PubMed

Tan, Wui Siew; Lewis, Christina L; Horelik, Nicholas E; Pregibon, Daniel C; Doyle, Patrick S; Yi, Hyunmin

2008-11-04

We demonstrate hierarchical assembly of tobacco mosaic virus (TMV)-based nanotemplates with hydrogel-based encoded microparticles via nucleic acid hybridization. TMV nanotemplates possess a highly defined structure and a genetically engineered high density thiol functionality. The encoded microparticles are produced in a high throughput microfluidic device via stop-flow lithography (SFL) and consist of spatially discrete regions containing encoded identity information, an internal control, and capture DNAs. For the hybridization-based assembly, partially disassembled TMVs were programmed with linker DNAs that contain sequences complementary to both the virus 5' end and a selected capture DNA. Fluorescence microscopy, atomic force microscopy (AFM), and confocal microscopy results clearly indicate facile assembly of TMV nanotemplates onto microparticles with high spatial and sequence selectivity. We anticipate that our hybridization-based assembly strategy could be employed to create multifunctional viral-synthetic hybrid materials in a rapid and high-throughput manner. Additionally, we believe that these viral-synthetic hybrid microparticles may find broad applications in high capacity, multiplexed target sensing.

Ion Thruster Support and Positioning System

NASA Technical Reports Server (NTRS)

Haag, Thomas W. (Inventor)

1996-01-01

A system for supporting and selectively positioning an ion thruster relative to a surface of a spacecraft includes three angularly spaced thruster support assemblies. Each thruster support assembly includes a frame which has a rotary actuator mounted thereon. The rotary actuator is connected to an actuator member which is rotatably connected to a thruster attachment member connected to a body of the thruster. A stabilizer member is rotatably mounted to the frame and to the thruster attachment member. The thruster is selectively movable in the pitch and yaw directions responsive to movement of the actuator members by the actuators on the thruster support assemblies. A failure of any one actuator on a thruster support assembly will generally still enable limited thruster positioning capability in two directions. In a retracted position the thruster attachment members are held in nested relation in saddles supported on the frames of the thruster support assemblies. The thruster is securely held in the retracted position during periods of high loading such as during launch of the spacecraft.

Ion Thruster Support and Positioning System

NASA Technical Reports Server (NTRS)

Haag, Thomas W. (Inventor)

1998-01-01

A system for supporting and selectively positioning an ion thruster relative to a surface of a spacecraft includes three angularly spaced thruster support assemblies. Each thruster support assembly includes a frame which has a rotary actuator mounted thereon. The rotary actuator is connected to an actuator member which is rotatably connected to a thruster attachment member connected to a body of the thruster. A stabilizer member is rotatably mounted to the frame and to the thruster attachment member. The thruster is selectively movable in the pitch and yaw directions responsive to movement of the actuator members by the actuators on the thruster support assemblies. A failure of any one actuator on a thruster support assembly will generally still enable limited thruster positioning capability in two directions. In a retracted position the thruster attachment members are held in nested relation in saddles supported on the frames of the thruster support assemblies. The thruster is securely held in the retracted position during periods of high loading such as during launch of the spacecraft.

Sequence-selective encapsulation and protection of long peptides by a self-assembled FeII8L6 cubic cage

NASA Astrophysics Data System (ADS)

Mosquera, Jesús; Szyszko, Bartosz; Ho, Sarah K. Y.; Nitschke, Jonathan R.

2017-03-01

Self-assembly offers a general strategy for the preparation of large, hollow high-symmetry structures. Although biological capsules, such as virus capsids, are capable of selectively recognizing complex cargoes, synthetic encapsulants have lacked the capability to specifically bind large and complex biomolecules. Here we describe a cubic host obtained from the self-assembly of FeII and a zinc-porphyrin-containing ligand. This cubic cage is flexible and compatible with aqueous media. Its selectivity of encapsulation is driven by the coordination of guest functional groups to the zinc porphyrins. This new host thus specifically encapsulates guests incorporating imidazole and thiazole moieties, including drugs and peptides. Once encapsulated, the reactivity of a peptide is dramatically altered: encapsulated peptides are protected from trypsin hydrolysis, whereas physicochemically similar peptides that do not bind are cleaved.

Method for selective immobilization of macromolecules on self assembled monolayer surfaces

DOEpatents

Laskin, Julia [Richland, WA; Wang, Peng [Billerica, MA

2011-11-29

Disclosed is a method for selective chemical binding and immobilization of macromolecules on solid supports in conjunction with self-assembled monolayer (SAM) surfaces. Immobilization involves selective binding of peptides and other macromolecules to SAM surfaces using reactive landing (RL) of mass-selected, gas phase ions. SAM surfaces provide a simple and convenient platform for tailoring chemical properties of a variety of substrates. The invention finds applications in biochemistry ranging from characterization of molecular recognition events at the amino acid level and identification of biologically active motifs in proteins, to development of novel biosensors and substrates for stimulated protein and cell adhesion.

A guide to phylogenetic metrics for conservation, community ecology and macroecology.

PubMed

Tucker, Caroline M; Cadotte, Marc W; Carvalho, Silvia B; Davies, T Jonathan; Ferrier, Simon; Fritz, Susanne A; Grenyer, Rich; Helmus, Matthew R; Jin, Lanna S; Mooers, Arne O; Pavoine, Sandrine; Purschke, Oliver; Redding, David W; Rosauer, Dan F; Winter, Marten; Mazel, Florent

2017-05-01

The use of phylogenies in ecology is increasingly common and has broadened our understanding of biological diversity. Ecological sub-disciplines, particularly conservation, community ecology and macroecology, all recognize the value of evolutionary relationships but the resulting development of phylogenetic approaches has led to a proliferation of phylogenetic diversity metrics. The use of many metrics across the sub-disciplines hampers potential meta-analyses, syntheses, and generalizations of existing results. Further, there is no guide for selecting the appropriate metric for a given question, and different metrics are frequently used to address similar questions. To improve the choice, application, and interpretation of phylo-diversity metrics, we organize existing metrics by expanding on a unifying framework for phylogenetic information. Generally, questions about phylogenetic relationships within or between assemblages tend to ask three types of question: how much; how different; or how regular? We show that these questions reflect three dimensions of a phylogenetic tree: richness, divergence, and regularity. We classify 70 existing phylo-diversity metrics based on their mathematical form within these three dimensions and identify 'anchor' representatives: for α-diversity metrics these are PD (Faith's phylogenetic diversity), MPD (mean pairwise distance), and VPD (variation of pairwise distances). By analysing mathematical formulae and using simulations, we use this framework to identify metrics that mix dimensions, and we provide a guide to choosing and using the most appropriate metrics. We show that metric choice requires connecting the research question with the correct dimension of the framework and that there are logical approaches to selecting and interpreting metrics. The guide outlined herein will help researchers navigate the current jungle of indices. © 2016 The Authors. Biological Reviews published by John Wiley © Sons Ltd on behalf of Cambridge Philosophical Society.

A guide to phylogenetic metrics for conservation, community ecology and macroecology

PubMed Central

Cadotte, Marc W.; Carvalho, Silvia B.; Davies, T. Jonathan; Ferrier, Simon; Fritz, Susanne A.; Grenyer, Rich; Helmus, Matthew R.; Jin, Lanna S.; Mooers, Arne O.; Pavoine, Sandrine; Purschke, Oliver; Redding, David W.; Rosauer, Dan F.; Winter, Marten; Mazel, Florent

2016-01-01

ABSTRACT The use of phylogenies in ecology is increasingly common and has broadened our understanding of biological diversity. Ecological sub‐disciplines, particularly conservation, community ecology and macroecology, all recognize the value of evolutionary relationships but the resulting development of phylogenetic approaches has led to a proliferation of phylogenetic diversity metrics. The use of many metrics across the sub‐disciplines hampers potential meta‐analyses, syntheses, and generalizations of existing results. Further, there is no guide for selecting the appropriate metric for a given question, and different metrics are frequently used to address similar questions. To improve the choice, application, and interpretation of phylo‐diversity metrics, we organize existing metrics by expanding on a unifying framework for phylogenetic information. Generally, questions about phylogenetic relationships within or between assemblages tend to ask three types of question: how much; how different; or how regular? We show that these questions reflect three dimensions of a phylogenetic tree: richness, divergence, and regularity. We classify 70 existing phylo‐diversity metrics based on their mathematical form within these three dimensions and identify ‘anchor’ representatives: for α‐diversity metrics these are PD (Faith's phylogenetic diversity), MPD (mean pairwise distance), and VPD (variation of pairwise distances). By analysing mathematical formulae and using simulations, we use this framework to identify metrics that mix dimensions, and we provide a guide to choosing and using the most appropriate metrics. We show that metric choice requires connecting the research question with the correct dimension of the framework and that there are logical approaches to selecting and interpreting metrics. The guide outlined herein will help researchers navigate the current jungle of indices. PMID:26785932

Dynamics of social behaviour at parturition in a gregarious ungulate.

PubMed

Pérez-Barbería, F J; Walker, D M

2018-05-01

Group living is the behavioural response that results when individuals assess the costs vs benefits of sociality, and these trade-offs vary across an animal's life. Here we quantitatively assess how periparturient condition (mother/non-mother) and births affect the dynamics of social interactions of a gregarious ungulate, and how such can help to explain evolutionary hypotheses of the mother-offspring bond. To achieve this we used data of the individual movement of a group of Scottish blackface sheep (Ovis aries) marked with GPS collars and properties of mathematical graphs (networks). Euclidean pair-wise distance between sheep were threshold at different percentiles to determine network links, and these thresholds have a profound effect on the connectivity of the resulting network. Births increased the average pair-wise distance between mothers, and between mothers and non-mothers, with less effect on the distance between non-mothers. Mothers occupied peripheral positions within the flock, more evident following births. Associations between individuals (i.e. network community change) were highly dynamic, though mothers were less likely to change community than non-mothers, especially after births. Births hampered individual communication within the flock (assessed via network closeness centrality), especially in mothers. Overall leadership (lead positioning relative to flock movement) was not associated to reproductive condition, and individual leadership rank was not affected by births. A ten minute GPS acquisition time was adequate to capture complex social dynamics in sheep movement. The results on mother's isolation behaviour support the hypotheses of selection for maternal imprint facilitation, reducing risks to nursing alien offspring, and group/multilevel selection on group formation. Copyright © 2018 Elsevier B.V. All rights reserved.

Landscape characteristics influencing the genetic structure of greater sage-grouse within the stronghold of their range: a holistic modeling approach

USGS Publications Warehouse

Row, Jeff R; Oyler-McCance, Sara J.; Fike, Jennifer; O'Donnell, Michael; Doherty, Kevin E.; Aldridge, Cameron L.; Bowen, Zachary H.; Fedy, Brad C.

2015-01-01

Given the significance of animal dispersal to population dynamics and geographic variability, understanding how dispersal is impacted by landscape patterns has major ecological and conservation importance. Speaking to the importance of dispersal, the use of linear mixed models to compare genetic differentiation with pairwise resistance derived from landscape resistance surfaces has presented new opportunities to disentangle the menagerie of factors behind effective dispersal across a given landscape. Here, we combine these approaches with novel resistance surface parameterization to determine how the distribution of high- and low-quality seasonal habitat and individual landscape components shape patterns of gene flow for the greater sage-grouse (Centrocercus urophasianus) across Wyoming. We found that pairwise resistance derived from the distribution of low-quality nesting and winter, but not summer, seasonal habitat had the strongest correlation with genetic differentiation. Although the patterns were not as strong as with habitat distribution, multivariate models with sagebrush cover and landscape ruggedness or forest cover and ruggedness similarly had a much stronger fit with genetic differentiation than an undifferentiated landscape. In most cases, landscape resistance surfaces transformed with 17.33-km-diameter moving windows were preferred, suggesting small-scale differences in habitat were unimportant at this large spatial extent. Despite the emergence of these overall patterns, there were differences in the selection of top models depending on the model selection criteria, suggesting research into the most appropriate criteria for landscape genetics is required. Overall, our results highlight the importance of differences in seasonal habitat preferences to patterns of gene flow and suggest the combination of habitat suitability modeling and linear mixed models with our resistance parameterization is a powerful approach to discerning the effects of landscape on gene flow.

Supramolecular fabrication of multilevel graphene-based gas sensors with high NO2 sensibility.

PubMed

Chen, Zhuo; Umar, Ahmad; Wang, Shiwei; Wang, Yao; Tian, Tong; Shang, Ying; Fan, Yuzun; Qi, Qi; Xu, Dongmei; Jiang, Lei

2015-06-14

This study reports the supramolecular assembly of a silver nanoparticle-naphthalene-1-sulphonic acid-reduced graphene oxide composite (Ag-NA-rGO) and its utilization to fabricate a highly sensitive and selective gas sensor. The prepared supramolecular assembly acted not only as a non-covalent functionalization platform (π-π interaction) but was also an excellent scaffold to fabricate a highly sensitive and selective low concentration NO2 gas sensor. The prepared composites were characterized using several techniques, which revealed that the graphene sheets were dispersed as ultrathin monolayers with a uniform distribution of silver nanoparticles. The fabricated multilevel structure exhibited an excellent sensing performance, i.e. 2.8 times better, towards 10 ppm NO2 compared to the NA-rGO and rGO based sensors. Apart from its high sensitivity, superior reversibility and selectivity, the prepared supramolecular assembly exhibited an outstanding linear response over the large concentration range from 1 ppm to 10 ppm. The obtained results demonstrate that the prepared supramolecular assembly holds great potential in the fabrication of efficient and effective low-concentration NO2 gas sensors for practical applications.

Automated characterization and assembly of individual nanowires for device fabrication.

PubMed

Yu, Kaiyan; Yi, Jingang; Shan, Jerry W

2018-05-15

The automated sorting and positioning of nanowires and nanotubes is essential to enabling the scalable manufacturing of nanodevices for a variety of applications. However, two fundamental challenges still remain: (i) automated placement of individual nanostructures in precise locations, and (ii) the characterization and sorting of highly variable nanomaterials to construct well-controlled nanodevices. Here, we propose and demonstrate an integrated, electric-field based method for the simultaneous automated characterization, manipulation, and assembly of nanowires (ACMAN) with selectable electrical conductivities into nanodevices. We combine contactless and solution-based electro-orientation spectroscopy and electrophoresis-based motion-control, planning and manipulation strategies to simultaneously characterize and manipulate multiple individual nanowires. These nanowires can be selected according to their electrical characteristics and precisely positioned at different locations in a low-conductivity liquid to form functional nanodevices with desired electrical properties. We validate the ACMAN design by assembling field-effect transistors (FETs) with silicon nanowires of selected electrical conductivities. The design scheme provides a key enabling technology for the scalable, automated sorting and assembly of nanowires and nanotubes to build functional nanodevices.

Combining native MS approaches to decipher archaeal box H/ACA ribonucleoprotein particle structure and activity.

PubMed

Saliou, Jean-Michel; Manival, Xavier; Tillault, Anne-Sophie; Atmanene, Cédric; Bobo, Claude; Branlant, Christiane; Van Dorsselaer, Alain; Charpentier, Bruno; Cianférani, Sarah

2015-08-01

Site-specific isomerization of uridines into pseudouridines in RNAs is catalyzed either by stand-alone enzymes or by box H/ACA ribonucleoprotein particles (sno/sRNPs). The archaeal box H/ACA sRNPs are five-component complexes that consist of a guide RNA and the aCBF5, aNOP10, L7Ae, and aGAR1 proteins. In this study, we performed pairwise incubations of individual constituents of archaeal box H/ACA sRNPs and analyzed their interactions by native MS to build a 2D-connectivity map of direct binders. We describe the use of native MS in combination with ion mobility-MS to monitor the in vitro assembly of the active H/ACA sRNP particle. Real-time native MS was used to monitor how box H/ACA particle functions in multiple-turnover conditions. Native MS also unambiguously revealed that a substrate RNA containing 5-fluorouridine (f(5) U) was hydrolyzed into 5-fluoro-6-hydroxy-pseudouridine (f(5) ho(6) Ψ). In terms of enzymatic mechanism, box H/ACA sRNP was shown to catalyze the pseudouridylation of a first RNA substrate, then to release the RNA product (S22 f(5) ho(6) ψ) from the RNP enzyme and reload a new substrate RNA molecule. Altogether, our native MS-based approaches provide relevant new information about the potential assembly process and catalytic mechanism of box H/ACA RNPs. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Document Level Assessment of Document Retrieval Systems in a Pairwise System Evaluation

ERIC Educational Resources Information Center

Rajagopal, Prabha; Ravana, Sri Devi

2017-01-01

Introduction: The use of averaged topic-level scores can result in the loss of valuable data and can cause misinterpretation of the effectiveness of system performance. This study aims to use the scores of each document to evaluate document retrieval systems in a pairwise system evaluation. Method: The chosen evaluation metrics are document-level…

Pairwise Multiple Comparisons in Single Group Repeated Measures Analysis.

ERIC Educational Resources Information Center

Barcikowski, Robert S.; Elliott, Ronald S.

Research was conducted to provide educational researchers with a choice of pairwise multiple comparison procedures (P-MCPs) to use with single group repeated measures designs. The following were studied through two Monte Carlo (MC) simulations: (1) The T procedure of J. W. Tukey (1953); (2) a modification of Tukey's T (G. Keppel, 1973); (3) the…

Impaired Discrimination Learning in Mice Lacking the NMDA Receptor NR2A Subunit

ERIC Educational Resources Information Center

Brigman, Jonathan L.; Feyder, Michael; Saksida, Lisa M.; Bussey, Timothy J.; Mishina, Masayoshi; Holmes, Andrew

2008-01-01

N-Methyl-D-aspartate receptors (NMDARs) mediate certain forms of synaptic plasticity and learning. We used a touchscreen system to assess NR2A subunit knockout mice (KO) for (1) pairwise visual discrimination and reversal learning and (2) acquisition and extinction of an instrumental response requiring no pairwise discrimination. NR2A KO mice…

Pairwise-additive hydrophobic effect for alkanes in water

PubMed Central

Wu, Jianzhong; Prausnitz, John M.

2008-01-01

Pairwise additivity of the hydrophobic effect is indicated by reliable experimental Henry's constants for a large number of linear and branched low-molecular-weight alkanes in water. Pairwise additivity suggests that the hydrophobic effect is primarily a local phenomenon and that the hydrophobic interaction may be represented by a semiempirical force field. By representing the hydrophobic potential between two methane molecules as a linear function of the overlap volume of the hydration layers, we find that the contact value of the hydrophobic potential (−0.72 kcal/mol) is smaller than that from quantum mechanics simulations (−2.8 kcal/mol) but is close to that from classical molecular dynamics (−0.5∼−0.9 kcal/mol). PMID:18599448

Triggered and catalyzed self-assembly of hyperbranched DNA structures for logic operations and homogeneous CRET biosensing of microRNA.

PubMed

Bi, Sai; Yue, Shuzhen; Wu, Qiang; Ye, Jiayan

2016-04-07

Toehold-mediated strand displacement-based nanocircuits are developed by integrating catalytic hairpin assembly (CHA) with hybridization chain reaction (HCR), which achieves self-assembly of hyperbranched DNA structures and is readily utilized as an enzyme-free amplifier for homogeneous CRET detection of microRNA with high sensitivity and selectivity.

The structured ancestral selection graph and the many-demes limit.

PubMed

Slade, Paul F; Wakeley, John

2005-02-01

We show that the unstructured ancestral selection graph applies to part of the history of a sample from a population structured by restricted migration among subpopulations, or demes. The result holds in the limit as the number of demes tends to infinity with proportionately weak selection, and we have also made the assumptions of island-type migration and that demes are equivalent in size. After an instantaneous sample-size adjustment, this structured ancestral selection graph converges to an unstructured ancestral selection graph with a mutation parameter that depends inversely on the migration rate. In contrast, the selection parameter for the population is independent of the migration rate and is identical to the selection parameter in an unstructured population. We show analytically that estimators of the migration rate, based on pairwise sequence differences, derived under the assumption of neutrality should perform equally well in the presence of weak selection. We also modify an algorithm for simulating genealogies conditional on the frequencies of two selected alleles in a sample. This permits efficient simulation of stronger selection than was previously possible. Using this new algorithm, we simulate gene genealogies under the many-demes ancestral selection graph and identify some situations in which migration has a strong effect on the time to the most recent common ancestor of the sample. We find that a similar effect also increases the sensitivity of the genealogy to selection.

Self assembled materials: design strategies and drug delivery perspectives.

PubMed

Verma, Gunjan; Hassan, P A

2013-10-28

Self assembly of small molecules in complex supramolecular structures provides a new avenue in the development of materials for drug delivery applications. Owing to the low aqueous solubility of various drugs, an effective delivery system is often required to reach sufficient drug bioavailability and/or to facilitate clinical use. Micelles, amphiphilic gels, vesicles (liposomes), nanodisks, cubosomes, colloidosomes, tubules, microemulsions, lipid particles, polyelectrolyte capsules etc. are some of the intriguing structures formed via self assembly. As well as enabling improved solubilization, such materials can be tuned to offer a range of other advantages, including controlled or stimuli sensitive drug release, protection from drug hydrolysis and chemical or enzymatic degradation, a reduction in toxicity, improvement of drug availability, prevention of RES uptake or selective targeting to organelles etc. Such multiple functionalities can be brought together by self assembly of different functional molecules. This route offers a cost effective means of developing drug delivery carriers tailored to specific needs. Our current understanding of the microstructure evolution of self assembled materials will go a long way towards designing/selecting molecules to create well defined structures. We believe that most of the potential resources mentioned above are untapped and that there is a need to further strengthen research in this area to fully exploit their potential. Selective cross linking of core or shell, stimuli sensitive amphiphiles, prodrug amphiphiles, antibody coupled amphiphiles etc. are only some of the new approaches for the development of effective drug delivery systems via self assembly.

Transcriptomic resources for the medicinal legume Mucuna pruriens: de novo transcriptome assembly, annotation, identification and validation of EST-SSR markers.

PubMed

Sathyanarayana, N; Pittala, Ranjith Kumar; Tripathi, Pankaj Kumar; Chopra, Ratan; Singh, Heikham Russiachand; Belamkar, Vikas; Bhardwaj, Pardeep Kumar; Doyle, Jeff J; Egan, Ashley N

2017-05-25

The medicinal legume Mucuna pruriens (L.) DC. has attracted attention worldwide as a source of the anti-Parkinson's drug L-Dopa. It is also a popular green manure cover crop that offers many agronomic benefits including high protein content, nitrogen fixation and soil nutrients. The plant currently lacks genomic resources and there is limited knowledge on gene expression, metabolic pathways, and genetics of secondary metabolite production. Here, we present transcriptomic resources for M. pruriens, including a de novo transcriptome assembly and annotation, as well as differential transcript expression analyses between root, leaf, and pod tissues. We also develop microsatellite markers and analyze genetic diversity and population structure within a set of Indian germplasm accessions. One-hundred ninety-one million two hundred thirty-three thousand two hundred forty-two bp cleaned reads were assembled into 67,561 transcripts with mean length of 626 bp and N50 of 987 bp. Assembled sequences were annotated using BLASTX against public databases with over 80% of transcripts annotated. We identified 7,493 simple sequence repeat (SSR) motifs, including 787 polymorphic repeats between the parents of a mapping population. 134 SSRs from expressed sequenced tags (ESTs) were screened against 23 M. pruriens accessions from India, with 52 EST-SSRs retained after quality control. Population structure analysis using a Bayesian framework implemented in fastSTRUCTURE showed nearly similar groupings as with distance-based (neighbor-joining) and principal component analyses, with most of the accessions clustering per geographical origins. Pair-wise comparison of transcript expression in leaves, roots and pods identified 4,387 differentially expressed transcripts with the highest number occurring between roots and leaves. Differentially expressed transcripts were enriched with transcription factors and transcripts annotated as belonging to secondary metabolite pathways. The M. pruriens transcriptomic resources generated in this study provide foundational resources for gene discovery and development of molecular markers. Polymorphic SSRs identified can be used for genetic diversity, marker-trait analyses, and development of functional markers for crop improvement. The results of differential expression studies can be used to investigate genes involved in L-Dopa synthesis and other key metabolic pathways in M. pruriens.

A model for the sustainable selection of building envelope assemblies

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

Huedo, Patricia, E-mail: huedo@uji.es; Mulet, Elena, E-mail: emulet@uji.es; López-Mesa, Belinda, E-mail: belinda@unizar.es

2016-02-15

The aim of this article is to define an evaluation model for the environmental impacts of building envelopes to support planners in the early phases of materials selection. The model is intended to estimate environmental impacts for different combinations of building envelope assemblies based on scientifically recognised sustainability indicators. These indicators will increase the amount of information that existing catalogues show to support planners in the selection of building assemblies. To define the model, first the environmental indicators were selected based on the specific aims of the intended sustainability assessment. Then, a simplified LCA methodology was developed to estimate themore » impacts applicable to three types of dwellings considering different envelope assemblies, building orientations and climate zones. This methodology takes into account the manufacturing, installation, maintenance and use phases of the building. Finally, the model was validated and a matrix in Excel was created as implementation of the model. - Highlights: • Method to assess the envelope impacts based on a simplified LCA • To be used at an earlier phase than the existing methods in a simple way. • It assigns a score by means of known sustainability indicators. • It estimates data about the embodied and operating environmental impacts. • It compares the investment costs with the costs of the consumed energy.« less

RSV glycoprotein and genomic RNA dynamics reveal filament assembly prior to the plasma membrane.

PubMed

Vanover, Daryll; Smith, Daisy V; Blanchard, Emmeline L; Alonas, Eric; Kirschman, Jonathan L; Lifland, Aaron W; Zurla, Chiara; Santangelo, Philip J

2017-09-22

The human respiratory syncytial virus G protein plays an important role in the entry and assembly of filamentous virions. Here, we report the use of fluorescently labeled soybean agglutinin to selectively label the respiratory syncytial virus G protein in living cells without disrupting respiratory syncytial virus infectivity or filament formation and allowing for interrogations of respiratory syncytial virus virion assembly. Using this approach, we discovered that plasma membrane-bound respiratory syncytial virus G rapidly recycles from the membrane via clathrin-mediated endocytosis. This event is then followed by the dynamic formation of filamentous and branched respiratory syncytial virus particles, and assembly with genomic ribonucleoproteins and caveolae-associated vesicles prior to re-insertion into the plasma membrane. We demonstrate that these processes are halted by the disruption of microtubules and inhibition of molecular motors. Collectively, our results show that for respiratory syncytial virus assembly, viral filaments are produced and loaded with genomic RNA prior to insertion into the plasma membrane.Assembly of filamentous RSV particles is incompletely understood due to a lack of techniques suitable for live-cell imaging. Here Vanover et al. use labeled soybean agglutinin to selectively label RSV G protein and show how filamentous RSV assembly, initiated in the cytoplasm, uses G protein recycled from the plasma membrane.

A method for the dynamic management of genetic variability in dairy cattle

PubMed Central

Colleau, Jean-Jacques; Moureaux, Sophie; Briend, Michèle; Bechu, Jérôme

2004-01-01

According to the general approach developed in this paper, dynamic management of genetic variability in selected populations of dairy cattle is carried out for three simultaneous purposes: procreation of young bulls to be further progeny-tested, use of service bulls already selected and approval of recently progeny-tested bulls for use. At each step, the objective is to minimize the average pairwise relationship coefficient in the future population born from programmed matings and the existing population. As a common constraint, the average estimated breeding value of the new population, for a selection goal including many important traits, is set to a desired value. For the procreation of young bulls, breeding costs are additionally constrained. Optimization is fully analytical and directly considers matings. Corresponding algorithms are presented in detail. The efficiency of these procedures was tested on the current Norman population. Comparisons between optimized and real matings, clearly showed that optimization would have saved substantial genetic variability without reducing short-term genetic gains. PMID:15231230

Autogrid-based clustering of kinases: selection of representative conformations for docking purposes.

PubMed

Marzaro, Giovanni; Ferrarese, Alessandro; Chilin, Adriana

2014-08-01

The selection of the most appropriate protein conformation is a crucial aspect in molecular docking experiments. In order to reduce the errors arising from the use of a single protein conformation, several authors suggest the use of several tridimensional structures for the target. However, the selection of the most appropriate protein conformations still remains a challenging goal. The protein 3D-structures selection is mainly performed based on pairwise root-mean-square-deviation (RMSD) values computation, followed by hierarchical clustering. Herein we report an alternative strategy, based on the computation of only two atom affinity map for each protein conformation, followed by multivariate analysis and hierarchical clustering. This methodology was applied on seven different kinases of pharmaceutical interest. The comparison with the classical RMSD-based strategy was based on cross-docking of co-crystallized ligands. In the case of epidermal growth factor receptor kinase, also the docking performance on 220 known ligands were evaluated, followed by 3D-QSAR studies. In all the cases, the herein proposed methodology outperformed the RMSD-based one.

A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities.

PubMed

Bastien, Olivier; Ortet, Philippe; Roy, Sylvaine; Maréchal, Eric

2005-03-10

Popular methods to reconstruct molecular phylogenies are based on multiple sequence alignments, in which addition or removal of data may change the resulting tree topology. We have sought a representation of homologous proteins that would conserve the information of pair-wise sequence alignments, respect probabilistic properties of Z-scores (Monte Carlo methods applied to pair-wise comparisons) and be the basis for a novel method of consistent and stable phylogenetic reconstruction. We have built up a spatial representation of protein sequences using concepts from particle physics (configuration space) and respecting a frame of constraints deduced from pair-wise alignment score properties in information theory. The obtained configuration space of homologous proteins (CSHP) allows the representation of real and shuffled sequences, and thereupon an expression of the TULIP theorem for Z-score probabilities. Based on the CSHP, we propose a phylogeny reconstruction using Z-scores. Deduced trees, called TULIP trees, are consistent with multiple-alignment based trees. Furthermore, the TULIP tree reconstruction method provides a solution for some previously reported incongruent results, such as the apicomplexan enolase phylogeny. The CSHP is a unified model that conserves mutual information between proteins in the way physical models conserve energy. Applications include the reconstruction of evolutionary consistent and robust trees, the topology of which is based on a spatial representation that is not reordered after addition or removal of sequences. The CSHP and its assigned phylogenetic topology, provide a powerful and easily updated representation for massive pair-wise genome comparisons based on Z-score computations.

Simulations of the pairwise kinematic Sunyaev-Zel'dovich signal

DOE PAGES

Flender, Samuel; Bleem, Lindsey; Finkel, Hal; ...

2016-05-26

The pairwise kinematic Sunyaev–Zel'dovich (kSZ) signal from galaxy clusters is a probe of their line of sight momenta, and thus a potentially valuable source of cosmological information. In addition to the momenta, the amplitude of the measured signal depends on the properties of the intracluster gas and observational limitations such as errors in determining cluster centers and redshifts. In this work, we simulate the pairwise kSZ signal of clusters atmore » $$z\\lt 1$$, using the output from a cosmological N-body simulation and including the properties of the intracluster gas via a model that can be varied in post-processing. We find that modifications to the gas profile due to star formation and feedback reduce the pairwise kSZ amplitude of clusters by $$\\sim 50\\%$$, relative to the naive "gas traces mass" assumption. We demonstrate that miscentering can reduce the overall amplitude of the pairwise kSZ signal by up to 10%, while redshift errors can lead to an almost complete suppression of the signal at small separations. We confirm that a high-significance detection is expected from the combination of data from current generation, high-resolution cosmic microwave background experiments, such as the South Pole Telescope, and cluster samples from optical photometric surveys, such as the Dark Energy Survey. As a result, we forecast that future experiments such as Advanced ACTPol in conjunction with data from the Dark Energy Spectroscopic Instrument will yield detection significances of at least $$20\\sigma $$, and up to $$57\\sigma $$ in an optimistic scenario.« less

On-Chip Chemical Self-Assembly of Semiconducting Single-Walled Carbon Nanotubes (SWNTs): Toward Robust and Scale Invariant SWNTs Transistors.

PubMed

Derenskyi, Vladimir; Gomulya, Widianta; Talsma, Wytse; Salazar-Rios, Jorge Mario; Fritsch, Martin; Nirmalraj, Peter; Riel, Heike; Allard, Sybille; Scherf, Ullrich; Loi, Maria A

2017-06-01

In this paper, the fabrication of carbon nanotubes field effect transistors by chemical self-assembly of semiconducting single walled carbon nanotubes (s-SWNTs) on prepatterned substrates is demonstrated. Polyfluorenes derivatives have been demonstrated to be effective in selecting s-SWNTs from raw mixtures. In this work the authors functionalized the polymer with side chains containing thiols, to obtain chemical self-assembly of the selected s-SWNTs on substrates with prepatterned gold electrodes. The authors show that the full side functionalization of the conjugated polymer with thiol groups partially disrupts the s-SWNTs selection, with the presence of metallic tubes in the dispersion. However, the authors determine that the selectivity can be recovered either by tuning the number of thiol groups in the polymer, or by modulating the polymer/SWNTs proportions. As demonstrated by optical and electrical measurements, the polymer containing 2.5% of thiol groups gives the best s-SWNT purity. Field-effect transistors with various channel lengths, using networks of SWNTs and individual tubes, are fabricated by direct chemical self-assembly of the SWNTs/thiolated-polyfluorenes on substrates with lithographically defined electrodes. The network devices show superior performance (mobility up to 24 cm 2 V -1 s -1 ), while SWNTs devices based on individual tubes show an unprecedented (100%) yield for working devices. Importantly, the SWNTs assembled by mean of the thiol groups are stably anchored to the substrate and are resistant to external perturbation as sonication in organic solvents. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Classification of forest-based ecotourism areas in Pocahontas County of West Virginia using GIS and pairwise comparison method

Treesearch

Ishwar Dhami; Jinyang. Deng

2012-01-01

Many previous studies have examined ecotourism primarily from the perspective of tourists while largely ignoring ecotourism destinations. This study used geographical information system (GIS) and pairwise comparison to identify forest-based ecotourism areas in Pocahontas County, West Virginia. The study adopted the criteria and scores developed by Boyd and Butler (1994...

Learning Factors Transfer Analysis: Using Learning Curve Analysis to Automatically Generate Domain Models

ERIC Educational Resources Information Center

Pavlik, Philip I. Jr.; Cen, Hao; Koedinger, Kenneth R.

2009-01-01

This paper describes a novel method to create a quantitative model of an educational content domain of related practice item-types using learning curves. By using a pairwise test to search for the relationships between learning curves for these item-types, we show how the test results in a set of pairwise transfer relationships that can be…

Macrobenthic assemblages of the Changjiang River estuary (Yangtze River, China) and adjacent continental shelf relative to mild summer hypoxia

NASA Astrophysics Data System (ADS)

Liao, Yibo; Shou, Lu; Tang, Yanbin; Zeng, Jiangning; Gao, Aigen; Chen, Quanzhen; Yan, Xiaojun

2017-05-01

To assess the effects of hypoxia, macrobenthic communities along an estuarine gradient of the Changjiang estuary and adjacent continental shelf were analyzed. This revealed spatial variations in the communities and relationships with environmental variables during periods of reduced dissolved oxygen (DO) concentration in summer. Statistical analyses revealed significant differences in macrobenthic community composition among the three zones: estuarine zone (EZ), mildly hypoxic zone (MHZ) in the continental shelf, and normoxic zone (NZ) in the continental shelf (Global R =0.206, P =0.002). Pairwise tests showed that the macrobenthic community composition of the EZ was significantly different from the MHZ (pairwise test R =0.305, P =0.001) and the NZ (pairwise test R =0.259, P =0.001). There was no significant difference in macrobenthic communities between the MHZ and the NZ (pairwise test R =0.062, P =0.114). The taxa included small and typically opportunistic polychaetes, which made the greatest contribution to the dissimilarity between the zones. The effects of mild hypoxia on the macrobenthic communities are a result not only of reduced DO concentration but also of differences in environmental variables such as temperature, salinity, and nutrient concentrations caused by stratification.

From pairwise to group interactions in games of cyclic dominance.

PubMed

Szolnoki, Attila; Vukov, Jeromos; Perc, Matjaž

2014-06-01

We study the rock-paper-scissors game in structured populations, where the invasion rates determine individual payoffs that govern the process of strategy change. The traditional version of the game is recovered if the payoffs for each potential invasion stem from a single pairwise interaction. However, the transformation of invasion rates to payoffs also allows the usage of larger interaction ranges. In addition to the traditional pairwise interaction, we therefore consider simultaneous interactions with all nearest neighbors, as well as with all nearest and next-nearest neighbors, thus effectively going from single pair to group interactions in games of cyclic dominance. We show that differences in the interaction range affect not only the stationary fractions of strategies but also their relations of dominance. The transition from pairwise to group interactions can thus decelerate and even revert the direction of the invasion between the competing strategies. Like in evolutionary social dilemmas, in games of cyclic dominance, too, the indirect multipoint interactions that are due to group interactions hence play a pivotal role. Our results indicate that, in addition to the invasion rates, the interaction range is at least as important for the maintenance of biodiversity among cyclically competing strategies.

Detection of the kinematic Sunyaev–Zel'dovich effect with DES Year 1 and SPT

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

Soergel, B.; Flender, S.; Story, K. T.

Here, we detect the kinematic Sunyaev-Zel'dovich (kSZ) effect with a statistical significance ofmore » $$4.2 \\sigma$$ by combining a cluster catalogue derived from the first year data of the Dark Energy Survey (DES) with CMB temperature maps from the South Pole Telescope Sunyaev-Zel'dovich (SPT-SZ) Survey. This measurement is performed with a differential statistic that isolates the pairwise kSZ signal, providing the first detection of the large-scale, pairwise motion of clusters using redshifts derived from photometric data. By fitting the pairwise kSZ signal to a theoretical template we measure the average central optical depth of the cluster sample, $$\\bar{\\tau}_e = (3.75 \\pm 0.89)\\cdot 10^{-3}$$. We compare the extracted signal to realistic simulations and find good agreement with respect to the signal-to-noise, the constraint on $$\\bar{\\tau}_e$$, and the corresponding gas fraction. High-precision measurements of the pairwise kSZ signal with future data will be able to place constraints on the baryonic physics of galaxy clusters, and could be used to probe gravity on scales $$ \\gtrsim 100$$ Mpc.« less

Detection of the kinematic Sunyaev–Zel'dovich effect with DES Year 1 and SPT

DOE PAGES

Soergel, B.; Flender, S.; Story, K. T.; ...

2016-06-17

Here, we detect the kinematic Sunyaev-Zel'dovich (kSZ) effect with a statistical significance ofmore » $$4.2 \\sigma$$ by combining a cluster catalogue derived from the first year data of the Dark Energy Survey (DES) with CMB temperature maps from the South Pole Telescope Sunyaev-Zel'dovich (SPT-SZ) Survey. This measurement is performed with a differential statistic that isolates the pairwise kSZ signal, providing the first detection of the large-scale, pairwise motion of clusters using redshifts derived from photometric data. By fitting the pairwise kSZ signal to a theoretical template we measure the average central optical depth of the cluster sample, $$\\bar{\\tau}_e = (3.75 \\pm 0.89)\\cdot 10^{-3}$$. We compare the extracted signal to realistic simulations and find good agreement with respect to the signal-to-noise, the constraint on $$\\bar{\\tau}_e$$, and the corresponding gas fraction. High-precision measurements of the pairwise kSZ signal with future data will be able to place constraints on the baryonic physics of galaxy clusters, and could be used to probe gravity on scales $$ \\gtrsim 100$$ Mpc.« less

Chemical Demilitarization Assembled Chemical Weapons Alternatives (Chem Demil-ACWA)

DTIC Science & Technology

2015-12-01

Weapons Alternatives (Chem Demil-ACWA) is performing a portion of the chemical warfare materiel elimination mission. In 1996, Congress and the...Selected Acquisition Report (SAR) RCS: DD-A&T(Q&A)823-243 Chemical Demilitarization-Assembled Chemical Weapons Alternatives (Chem Demil-ACWA) As...Date Assigned: December 19, 2010 Program Information Program Name Chemical Demilitarization-Assembled Chemical Weapons Alternatives (Chem Demil

Strategies of marine dinoflagellate survival and some rules of assembly

NASA Astrophysics Data System (ADS)

Smayda, Theodore J.; Reynolds, Colin S.

2003-03-01

Dinoflagellate ecology is based on multiple adaptive strategies and species having diverse habitat preferences. Nine types of mixing-irradiance-nutrient habitats selecting for specific marine dinoflagellate life-form types are recognised, with five rules of assembly proposed to govern bloom-species selection and community organisation within these habitats. Assembly is moulded around an abiotic template of light energy, nutrient supply and physical mixing in permutative combinations. Species selected will have one of three basic ( C-, S-, R-) strategies: colonist species ( C-) which predominate in chemically disturbed habitats; nutrient stress tolerant species ( S-), and species ( R-) tolerant of shear/stress forces in physically disturbed water masses. This organisational plan of three major habitat variables and three major adaptive strategies is termed the 3-3 plan. The bloom behaviour and habitat specialisation of dinoflagellates and diatoms are compared. Dinoflagellates behave as annual species, bloom soloists, are ecophysiologically diverse, and habitat specialists whose blooms tend to be monospecific. Diatoms behave as perennial species, guild members, are habitat cosmopolites, have a relatively uniform bloom strategy based on species-rich pools and exhibit limited habitat specialisation. Dinoflagellate bloom-species selection follows a taxonomic hierarchical pathway which progresses from phylogenetic to generic to species selection, and in that sequence. Each hierarchical taxonomic level has its own adaptive requirements subject to rules of assembly. Dinoflagellates would appear to be well suited to exploit marine habitats and to be competitive with other phylogenetic groups, yet fail to do so.

Highly selective and sensitive method for Cu2 + detection based on chiroptical activity of L-Cysteine mediated Au nanorod assemblies

NASA Astrophysics Data System (ADS)

Abbasi, Shahryar; Khani, Hamzeh

2017-11-01

Herein, we demonstrated a simple and efficient method to detect Cu2 + based on amplified optical activity in the chiral nanoassemblies of gold nanorods (Au NRs). L-Cysteine can induce side-by-side or end-to-end assembly of Au NRs with an evident plasmonic circular dichroism (PCD) response due to coupling between surface plasmon resonances (SPR) of Au NRs and the chiral signal of L-Cys. Because of the obvious stronger plasmonic circular dichrosim (CD) response of the side-by-side assembly compared with the end-to-end assemblies, SS assembled Au NRs was selected as a sensitive platform and used for Cu2 + detection. In the presence of Cu2 +, Cu2 + can catalyze O2 oxidation of cysteine to cystine. With an increase in Cu2 + concentration, the L-Cysteine-mediated assembly of Au NRs decreased because of decrease in the free cysteine thiol groups, and the PCD signal decreased. Taking advantage of this method, Cu2 + could be detected in the concentration range of 20 pM-5 nM. Under optimal conditions, the calculated detection limit was found to be 7 pM.

Self-assembled bionanostructures: proteins following the lead of DNA nanostructures

PubMed Central

2014-01-01

Natural polymers are able to self-assemble into versatile nanostructures based on the information encoded into their primary structure. The structural richness of biopolymer-based nanostructures depends on the information content of building blocks and the available biological machinery to assemble and decode polymers with a defined sequence. Natural polypeptides comprise 20 amino acids with very different properties in comparison to only 4 structurally similar nucleotides, building elements of nucleic acids. Nevertheless the ease of synthesizing polynucleotides with selected sequence and the ability to encode the nanostructural assembly based on the two specific nucleotide pairs underlay the development of techniques to self-assemble almost any selected three-dimensional nanostructure from polynucleotides. Despite more complex design rules, peptides were successfully used to assemble symmetric nanostructures, such as fibrils and spheres. While earlier designed protein-based nanostructures used linked natural oligomerizing domains, recent design of new oligomerizing interaction surfaces and introduction of the platform for topologically designed protein fold may enable polypeptide-based design to follow the track of DNA nanostructures. The advantages of protein-based nanostructures, such as the functional versatility and cost effective and sustainable production methods provide strong incentive for further development in this direction. PMID:24491139

Low Energy Consumption Hydraulic Techniques

DTIC Science & Technology

1988-08-30

usually at welds . 1-15 SECTION II PHASE I - ADVANCED AIRCRAFT HYDRAULIC SYSTEM SELECTION Phase I included Task 1 selection of the aircraft and definition...face was bronze plated. The bearings were 52100 tool steel and the pistons were M50 tool steel. The shoe faces were 4140 with bronze plate and the back...o Magnet assembly o Coil assembly DDV Force Motor - -- ,..._(First Stage) oeMain Control Valve __(Second Sae Main Control Valve LVDT Figure 282 Direct

High surface area graphene-supported metal chalcogenide assembly

DOEpatents

Worsley, Marcus A.; Kuntz, Joshua D.; Orme, Christine A.

2017-04-25

Disclosed here is a method for hydrocarbon conversion, comprising contacting at least one graphene-supported assembly with at least one hydrocarbon feedstock, wherein the graphene-supported assembly comprises (i) a three-dimensional network of graphene sheets crosslinked by covalent carbon bonds and (ii) at least one metal chalcogenide compound disposed on the graphene sheets, wherein the chalcogen of the metal chalcogenide compound is selected from S, Se and Te, and wherein the metal chalcogenide compound accounts for at least 20 wt. % of the graphene-supported assembly.

Ball Screw Actuator Including an Axial Soft Stop

NASA Technical Reports Server (NTRS)

Forrest, Steven Talbert (Inventor); Woessner, George (Inventor); Abel, Steve (Inventor); Wingett, Paul T. (Inventor); Hanlon, Casey (Inventor)

2016-01-01

An actuator includes an actuator housing, a ball screw, and an axial soft stop assembly. The ball screw extends through the actuator housing and has a first end and a second end. The ball screw is coupled to receive a drive force and is configured, upon receipt of the drive force, to selectively move in a retract direction and an extend direction. The axial soft stop assembly is disposed within the actuator housing. The axial soft stop assembly is configured to be selectively engaged by the ball screw and, upon being engaged thereby, to translate, with compliance, a predetermined distance in the extend direction, and to prevent further movement of the ball screw upon translating the predetermined distance.

Ball Screw Actuator Including a Stop with an Integral Guide

NASA Technical Reports Server (NTRS)

Wingett, Paul T. (Inventor); Perek, John (Inventor); Geck, Kellan (Inventor)

2015-01-01

An actuator includes a housing assembly, a ball nut, a ball screw, and a ball screw stop. The ball nut is rotationally mounted in the housing assembly, is adapted to receive an input torque, and is configured, upon receipt thereof, to rotate and supply a drive force. The ball screw is mounted within the housing assembly and extends through the ball nut. The ball screw has a first end and a second end, and is coupled to receive the drive force from the ball nut. The ball screw is configured, upon receipt of the drive force, to selectively translate between a stow position and a deploy position. The ball screw stop is mounted on the ball screw to translate therewith and is configured to at selectively engage the housing assembly while the ball screw is translating, and engage the ball nut when the ball screw is in the deploy position.

Electrostatically Directed Self-Assembly of Ultrathin Supramolecular Polymer Microcapsules

PubMed Central

Parker, Richard M; Zhang, Jing; Zheng, Yu; Coulston, Roger J; Smith, Clive A; Salmon, Andrew R; Yu, Ziyi; Scherman, Oren A; Abell, Chris

2015-01-01

Supramolecular self-assembly offers routes to challenging architectures on the molecular and macroscopic scale. Coupled with microfluidics it has been used to make microcapsules—where a 2D sheet is shaped in 3D, encapsulating the volume within. In this paper, a versatile methodology to direct the accumulation of capsule-forming components to the droplet interface using electrostatic interactions is described. In this approach, charged copolymers are selectively partitioned to the microdroplet interface by a complementary charged surfactant for subsequent supramolecular cross-linking via cucurbit[8]uril. This dynamic assembly process is employed to selectively form both hollow, ultrathin microcapsules and solid microparticles from a single solution. The ability to dictate the distribution of a mixture of charged copolymers within the microdroplet, as demonstrated by the single-step fabrication of distinct core–shell microcapsules, gives access to a new generation of innovative self-assembled constructs. PMID:26213532

Multiparameter vision testing apparatus

NASA Technical Reports Server (NTRS)

Hunt, S. R., Jr.; Homkes, R. J.; Poteate, W. B.; Sturgis, A. C. (Inventor)

1975-01-01

Compact vision testing apparatus is described for testing a large number of physiological characteristics of the eyes and visual system of a human subject. The head of the subject is inserted into a viewing port at one end of a light-tight housing containing various optical assemblies. Visual acuity and other refractive characteristics and ocular muscle balance characteristics of the eyes of the subject are tested by means of a retractable phoroptor assembly carried near the viewing port and a film cassette unit carried in the rearward portion of the housing (the latter selectively providing a variety of different visual targets which are viewed through the optical system of the phoroptor assembly). The visual dark adaptation characteristics and absolute brightness threshold of the subject are tested by means of a projector assembly which selectively projects one or both of a variable intensity fixation target and a variable intensity adaptation test field onto a viewing screen located near the top of the housing.

Multicriteria analysis of product operational effectiveness at design stages

NASA Astrophysics Data System (ADS)

Irzaev, G. Kh

2018-03-01

The multicriteria rapid assessment method of techno-economic parameters of new products is developed. It avoids expensive engineering changes during the operational stages through the analysis of external and internal factors at an early stage in the design that affect the maintainability and manufacturability of the product. The expert selection of the initial multitude of indicators from the five enlarged criteria groups and their subsequent pairwise comparison allow one to distinguish the complex compliance criteria of product design with the average and optimum values of the operational effectiveness. The values comparison provides an opportunity to decide on the continuation of the process for designing and preparation of the product manufacture.

Multi-criteria analysis of potential recovery facilities in a reverse supply chain

NASA Astrophysics Data System (ADS)

Nukala, Satish; Gupta, Surendra M.

2005-11-01

Analytic Hierarchy Process (AHP) has been employed by researchers for solving multi-criteria analysis problems. However, AHP is often criticized for its unbalanced scale of judgments and failure to precisely handle the inherent uncertainty and vagueness in carrying out the pair-wise comparisons. With an objective to address these drawbacks, in this paper, we employ a fuzzy approach in selecting potential recovery facilities in the strategic planning of a reverse supply chain network that addresses the decision maker's level of confidence in the fuzzy assessments and his/her attitude towards risk. A numerical example is considered to illustrate the methodology.

Evidence-Based Reptile Housing and Nutrition.

PubMed

Oonincx, Dennis; van Leeuwen, Jeroen

2017-09-01

The provision of a good light source is important for reptiles. For instance, ultraviolet light is used in social interactions and used for vitamin D synthesis. With respect to housing, most reptilians are best kept pairwise or individually. Environmental enrichment can be effective but depends on the form and the species to which it is applied. Temperature gradients around preferred body temperatures allow accurate thermoregulation, which is essential for reptiles. Natural distributions indicate suitable ambient temperatures, but microclimatic conditions are at least as important. Because the nutrient requirements of reptiles are largely unknown, facilitating self-selection from various dietary items is preferable. Copyright © 2017 Elsevier Inc. All rights reserved.

Learning to rank atlases for multiple-atlas segmentation.

PubMed

Sanroma, Gerard; Wu, Guorong; Gao, Yaozong; Shen, Dinggang

2014-10-01

Recently, multiple-atlas segmentation (MAS) has achieved a great success in the medical imaging area. The key assumption is that multiple atlases have greater chances of correctly labeling a target image than a single atlas. However, the problem of atlas selection still remains unexplored. Traditionally, image similarity is used to select a set of atlases. Unfortunately, this heuristic criterion is not necessarily related to the final segmentation performance. To solve this seemingly simple but critical problem, we propose a learning-based atlas selection method to pick up the best atlases that would lead to a more accurate segmentation. Our main idea is to learn the relationship between the pairwise appearance of observed instances (i.e., a pair of atlas and target images) and their final labeling performance (e.g., using the Dice ratio). In this way, we select the best atlases based on their expected labeling accuracy. Our atlas selection method is general enough to be integrated with any existing MAS method. We show the advantages of our atlas selection method in an extensive experimental evaluation in the ADNI, SATA, IXI, and LONI LPBA40 datasets. As shown in the experiments, our method can boost the performance of three widely used MAS methods, outperforming other learning-based and image-similarity-based atlas selection methods.

A Framework for the Development of Automatic DFA Method to Minimize the Number of Components and Assembly Reorientations

NASA Astrophysics Data System (ADS)

Alfadhlani; Samadhi, T. M. A. Ari; Ma’ruf, Anas; Setiasyah Toha, Isa

2018-03-01

Assembly is a part of manufacturing processes that must be considered at the product design stage. Design for Assembly (DFA) is a method to evaluate product design in order to make it simpler, easier and quicker to assemble, so that assembly cost is reduced. This article discusses a framework for developing a computer-based DFA method. The method is expected to aid product designer to extract data, evaluate assembly process, and provide recommendation for the product design improvement. These three things are desirable to be performed without interactive process or user intervention, so product design evaluation process could be done automatically. Input for the proposed framework is a 3D solid engineering drawing. Product design evaluation is performed by: minimizing the number of components; generating assembly sequence alternatives; selecting the best assembly sequence based on the minimum number of assembly reorientations; and providing suggestion for design improvement.

Evidence That Masking of Synapsis Imperfections Counterbalances Quality Control to Promote Efficient Meiosis

PubMed Central

Mlynarczyk-Evans, Susanna; Roelens, Baptiste; Villeneuve, Anne M.

2013-01-01

Reduction in ploidy to generate haploid gametes during sexual reproduction is accomplished by the specialized cell division program of meiosis. Pairing between homologous chromosomes and assembly of the synaptonemal complex at their interface (synapsis) represent intermediate steps in the meiotic program that are essential to form crossover recombination-based linkages between homologs, which in turn enable segregation of the homologs to opposite poles at the meiosis I division. Here, we challenge the mechanisms of pairing and synapsis during C. elegans meiosis by disrupting the normal 1∶1 correspondence between homologs through karyotype manipulation. Using a combination of cytological tools, including S-phase labeling to specifically identify X chromosome territories in highly synchronous cohorts of nuclei and 3D rendering to visualize meiotic chromosome structures and organization, our analysis of trisomic (triplo-X) and polyploid meiosis provides insight into the principles governing pairing and synapsis and how the meiotic program is “wired” to maximize successful sexual reproduction. We show that chromosomes sort into homologous groups regardless of chromosome number, then preferentially achieve pairwise synapsis during a period of active chromosome mobilization. Further, comparisons of synapsis configurations in triplo-X germ cells that are proficient or defective for initiating recombination suggest a role for recombination in restricting chromosomal interactions to a pairwise state. Increased numbers of homologs prolong markers of the chromosome mobilization phase and/or boost germline apoptosis, consistent with triggering quality control mechanisms that promote resolution of synapsis problems and/or cull meiocytes containing synapsis defects. However, we also uncover evidence for the existence of mechanisms that “mask” defects, thus allowing resumption of prophase progression and survival of germ cells despite some asynapsis. We propose that coupling of saturable masking mechanisms with stringent quality controls maximizes meiotic success by making progression and survival dependent on achieving a level of synapsis sufficient for crossover formation without requiring perfect synapsis. PMID:24339786

Temperate rain forest species partition fine-scale gradients in light availability based on their leaf mass per area (LMA)

PubMed Central

Fajardo, Alex; Siefert, Andrew

2016-01-01

Background and Aims Ecologists are increasingly using plant functional traits to predict community assembly, but few studies have linked functional traits to species’ responses to fine-scale resource gradients. In this study, it was tested whether saplings of woody species partition fine-scale gradients in light availability based on their leaf mass per area (LMA) in three temperate rain forests and one Mediterranean forest in southern Chile. Methods LMA was measured under field conditions of all woody species contained in approx. 60 plots of 2 m2 in each site, and light availability, computed as the gap light index (GLI), was determined. For each site, species’ pairwise differences in mean LMA (Δ LMA) and abundance-weighted mean GLI (Δ light response) of 2 m2 plots were calculated and it was tested whether they were positively related using Mantel tests, i.e. if species with different LMA values differed in their response to light availability. Additionally linear models were fitted to the relationship between plot-level mean LMA and GLI across plots for each site. Key Results A positive and significant relationship was found between species’ pairwise differences in mean LMA and differences in light response across species for all temperate rain forests, but not for the Mediterranean forest. The results also indicated a significant positive interspecific link between LMA and light availability for all forests. This is in contrast to what is traditionally reported and to expectations from the leaf economics spectrum. Conclusions In environments subjected to light limitation, interspecific differences in a leaf trait (LMA) can explain the fine-scale partitioning of light availability gradients by woody plant species. This niche partitioning potentially facilitates species coexistence at the within-community level. The high frequency of evergreen shade-intolerant species in these forests may explain the positive correlation between light availability and LMA. PMID:27604280

Assembly of barcode-like nucleic acid nanostructures.

PubMed

Wang, Pengfei; Tian, Cheng; Li, Xiang; Mao, Chengde

2014-10-15

Barcode-like (BC) nanopatterns from programmed self-assembly of nucleic acids (DNA and RNA) are reported. BC nanostructures are generated by the introduction of open spaces at selected sites to an otherwise closely packed, plain, rectangle nucleic acid nanostructure. This strategy is applied to nanostructures assembled from both origami approach and single stranded tile approach. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Extrapolating Weak Selection in Evolutionary Games

PubMed Central

Wu, Bin; García, Julián; Hauert, Christoph; Traulsen, Arne

2013-01-01

In evolutionary games, reproductive success is determined by payoffs. Weak selection means that even large differences in game outcomes translate into small fitness differences. Many results have been derived using weak selection approximations, in which perturbation analysis facilitates the derivation of analytical results. Here, we ask whether results derived under weak selection are also qualitatively valid for intermediate and strong selection. By “qualitatively valid” we mean that the ranking of strategies induced by an evolutionary process does not change when the intensity of selection increases. For two-strategy games, we show that the ranking obtained under weak selection cannot be carried over to higher selection intensity if the number of players exceeds two. For games with three (or more) strategies, previous examples for multiplayer games have shown that the ranking of strategies can change with the intensity of selection. In particular, rank changes imply that the most abundant strategy at one intensity of selection can become the least abundant for another. We show that this applies already to pairwise interactions for a broad class of evolutionary processes. Even when both weak and strong selection limits lead to consistent predictions, rank changes can occur for intermediate intensities of selection. To analyze how common such games are, we show numerically that for randomly drawn two-player games with three or more strategies, rank changes frequently occur and their likelihood increases rapidly with the number of strategies . In particular, rank changes are almost certain for , which jeopardizes the predictive power of results derived for weak selection. PMID:24339769

Selection of features within and without objects: effects of gestalt appearance and object-based instruction on behavior and event-related brain potentials.

PubMed

Verleger, Rolf; Groen, Margriet; Heide, Wolfgang; Sobieralska, Kinga; Jaśkowski, Piotr

2008-05-01

We studied how physical and instructed embedding of features in gestalts affects perceptual selection. Four ovals on the horizontal midline were either unconnected or pairwise connected by circles, forming ears of left and right heads (gestalts). Relevant to responding was the position of one colored oval, either within its pair or relative to fixation ("object-based" or "fixation-based" instruction). Responses were faster under fixation- than object-based instruction, less so with gestalts. Previously reported increases of N1 when evoked by features within objects were replicated for fixation-based instruction only. There was no effect of instruction on N2pc. However P1 increased under the adequate instruction, object-based for gestalts, fixation-based for unconnected items, which presumably indicated how foci of attention were set by expecting specific stimuli under instructions that specified how to bind these stimuli to objects.

A generalization of Hamilton's rule--love others how much?

PubMed

Alger, Ingela; Weibull, Jörgen W

2012-04-21

According to Hamilton's (1964a, b) rule, a costly action will be undertaken if its fitness cost to the actor falls short of the discounted benefit to the recipient, where the discount factor is Wright's index of relatedness between the two. We propose a generalization of this rule, and show that if evolution operates at the level of behavior rules, rather than directly at the level of actions, evolution will select behavior rules that induce a degree of cooperation that may differ from that predicted by Hamilton's rule as applied to actions. In social dilemmas there will be less (more) cooperation than under Hamilton's rule if the actions are strategic substitutes (complements). Our approach is based on natural selection, defined in terms of personal (direct) fitness, and applies to a wide range of pairwise interactions. Copyright © 2011 Elsevier Ltd. All rights reserved.

Iterative non-sequential protein structural alignment.

PubMed

Salem, Saeed; Zaki, Mohammed J; Bystroff, Christopher

2009-06-01

Structural similarity between proteins gives us insights into their evolutionary relationships when there is low sequence similarity. In this paper, we present a novel approach called SNAP for non-sequential pair-wise structural alignment. Starting from an initial alignment, our approach iterates over a two-step process consisting of a superposition step and an alignment step, until convergence. We propose a novel greedy algorithm to construct both sequential and non-sequential alignments. The quality of SNAP alignments were assessed by comparing against the manually curated reference alignments in the challenging SISY and RIPC datasets. Moreover, when applied to a dataset of 4410 protein pairs selected from the CATH database, SNAP produced longer alignments with lower rmsd than several state-of-the-art alignment methods. Classification of folds using SNAP alignments was both highly sensitive and highly selective. The SNAP software along with the datasets are available online at http://www.cs.rpi.edu/~zaki/software/SNAP.

Decoding grating orientation from microelectrode array recordings in monkey cortical area V4.

PubMed

Manyakov, Nikolay V; Van Hulle, Marc M

2010-04-01

We propose an invasive brain-machine interface (BMI) that decodes the orientation of a visual grating from spike train recordings made with a 96 microelectrodes array chronically implanted into the prelunate gyrus (area V4) of a rhesus monkey. The orientation is decoded irrespective of the grating's spatial frequency. Since pyramidal cells are less prominent in visual areas, compared to (pre)motor areas, the recordings contain spikes with smaller amplitudes, compared to the noise level. Hence, rather than performing spike decoding, feature selection algorithms are applied to extract the required information for the decoder. Two types of feature selection procedures are compared, filter and wrapper. The wrapper is combined with a linear discriminant analysis classifier, and the filter is followed by a radial-basis function support vector machine classifier. In addition, since we have a multiclass classification problen, different methods for combining pairwise classifiers are compared.

Fuzzy sets, rough sets, and modeling evidence: Theory and Application. A Dempster-Shafer based approach to compromise decision making with multiattributes applied to product selection

NASA Technical Reports Server (NTRS)

Dekorvin, Andre

1992-01-01

The Dempster-Shafer theory of evidence is applied to a multiattribute decision making problem whereby the decision maker (DM) must compromise with available alternatives, none of which exactly satisfies his ideal. The decision mechanism is constrained by the uncertainty inherent in the determination of the relative importance of each attribute element and the classification of existing alternatives. The classification of alternatives is addressed through expert evaluation of the degree to which each element is contained in each available alternative. The relative importance of each attribute element is determined through pairwise comparisons of the elements by the decision maker and implementation of a ratio scale quantification method. Then the 'belief' and 'plausibility' that an alternative will satisfy the decision maker's ideal are calculated and combined to rank order the available alternatives. Application to the problem of selecting computer software is given.

CombAlign: a code for generating a one-to-many sequence alignment from a set of pairwise structure-based sequence alignments.

PubMed

Zhou, Carol L Ecale

2015-01-01

In order to better define regions of similarity among related protein structures, it is useful to identify the residue-residue correspondences among proteins. Few codes exist for constructing a one-to-many multiple sequence alignment derived from a set of structure or sequence alignments, and a need was evident for creating such a tool for combining pairwise structure alignments that would allow for insertion of gaps in the reference structure. This report describes a new Python code, CombAlign, which takes as input a set of pairwise sequence alignments (which may be structure based) and generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA). The use and utility of CombAlign was demonstrated by generating gapped MSSAs using sets of pairwise structure-based sequence alignments between structure models of the matrix protein (VP40) and pre-small/secreted glycoprotein (sGP) of Reston Ebolavirus and the corresponding proteins of several other filoviruses. The gapped MSSAs revealed structure-based residue-residue correspondences, which enabled identification of structurally similar versus differing regions in the Reston proteins compared to each of the other corresponding proteins. CombAlign is a new Python code that generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA) given a set of pairwise sequence alignments (which may be structure based). CombAlign has utility in assisting the user in distinguishing structurally conserved versus divergent regions on a reference protein structure relative to other closely related proteins. CombAlign was developed in Python 2.6, and the source code is available for download from the GitHub code repository.

Improving prediction of heterodimeric protein complexes using combination with pairwise kernel.

PubMed

Ruan, Peiying; Hayashida, Morihiro; Akutsu, Tatsuya; Vert, Jean-Philippe

2018-02-19

Since many proteins become functional only after they interact with their partner proteins and form protein complexes, it is essential to identify the sets of proteins that form complexes. Therefore, several computational methods have been proposed to predict complexes from the topology and structure of experimental protein-protein interaction (PPI) network. These methods work well to predict complexes involving at least three proteins, but generally fail at identifying complexes involving only two different proteins, called heterodimeric complexes or heterodimers. There is however an urgent need for efficient methods to predict heterodimers, since the majority of known protein complexes are precisely heterodimers. In this paper, we use three promising kernel functions, Min kernel and two pairwise kernels, which are Metric Learning Pairwise Kernel (MLPK) and Tensor Product Pairwise Kernel (TPPK). We also consider the normalization forms of Min kernel. Then, we combine Min kernel or its normalization form and one of the pairwise kernels by plugging. We applied kernels based on PPI, domain, phylogenetic profile, and subcellular localization properties to predicting heterodimers. Then, we evaluate our method by employing C-Support Vector Classification (C-SVC), carrying out 10-fold cross-validation, and calculating the average F-measures. The results suggest that the combination of normalized-Min-kernel and MLPK leads to the best F-measure and improved the performance of our previous work, which had been the best existing method so far. We propose new methods to predict heterodimers, using a machine learning-based approach. We train a support vector machine (SVM) to discriminate interacting vs non-interacting protein pairs, based on informations extracted from PPI, domain, phylogenetic profiles and subcellular localization. We evaluate in detail new kernel functions to encode these data, and report prediction performance that outperforms the state-of-the-art.

Conformational Changes in the Hepatitis B Virus Core Protein Are Consistent with a Role for Allostery in Virus Assembly

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

Packianathan, Charles; Katen, Sarah P.; Dann, III, Charles E.

2010-01-12

In infected cells, virus components must be organized at the right place and time to ensure assembly of infectious virions. From a different perspective, assembly must be prevented until all components are available. Hypothetically, this can be achieved by allosterically controlling assembly. Consistent with this hypothesis, here we show that the structure of the hepatitis B virus (HBV) core protein dimer, which can spontaneously self-assemble, is incompatible with capsid assembly. Systematic differences between core protein dimer and capsid conformations demonstrate linkage between the intradimer interface and interdimer contact surface. These structures also provide explanations for the capsid-dimer selectivity of somemore » antibodies and the activities of assembly effectors. Solution studies suggest that the assembly-inactive state is more accurately an ensemble of conformations. Simulations show that allostery supports controlled assembly and results in capsids that are resistant to dissociation. We propose that allostery, as demonstrated in HBV, is common to most self-assembling viruses.« less

Force-Based Reasoning for Assembly Planning and Subassembly Stability Analysis

NASA Technical Reports Server (NTRS)

Lee, S.; Yi, C.; Wang, F-C.

1993-01-01

In this paper, we show that force-based reasoning, for identifying a cluster of parts that can be decomposed naturally by the applied force, plays an important role in selecting feasible subassemblies and analyzing subassembly stability in assembly planning.

Crystal-Structure-Guided Design of Self-Assembling RNA Nanotriangles.

PubMed

Boerneke, Mark A; Dibrov, Sergey M; Hermann, Thomas

2016-03-14

RNA nanotechnology uses RNA structural motifs to build nanosized architectures that assemble through selective base-pair interactions. Herein, we report the crystal-structure-guided design of highly stable RNA nanotriangles that self-assemble cooperatively from short oligonucleotides. The crystal structure of an 81 nucleotide nanotriangle determined at 2.6 Å resolution reveals the so-far smallest circularly closed nanoobject made entirely of double-stranded RNA. The assembly of the nanotriangle architecture involved RNA corner motifs that were derived from ligand-responsive RNA switches, which offer the opportunity to control self-assembly and dissociation. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Shuttle APS propellant thermal conditioner study

NASA Technical Reports Server (NTRS)

Pearson, W. E.

1971-01-01

A study program was performed to allow selection of thermal conditioner assemblies for superheating O2 and H2 at supercritical pressures. The application was the auxiliary propulsion system (APS) for the space shuttle vehicle. The O2/H2 APS propellant feed system included propellant conditioners, of which the thermal conditioner assemblies were a part. Cryogens, pumped to pressures above critical, were directed to the thermal conditioner assembly included: (1) a gas generator assembly with ignition system and bipropellant valves, which burned superheated O2 and H2 at rich conditions; (2) a heat exchanger assembly for thermal conditioning of the cryogenic propellant; and (3) a dump nozzle for heat exchanger exhaust.

APOLLO: a quality assessment service for single and multiple protein models.

PubMed

Wang, Zheng; Eickholt, Jesse; Cheng, Jianlin

2011-06-15

We built a web server named APOLLO, which can evaluate the absolute global and local qualities of a single protein model using machine learning methods or the global and local qualities of a pool of models using a pair-wise comparison approach. Based on our evaluations on 107 CASP9 (Critical Assessment of Techniques for Protein Structure Prediction) targets, the predicted quality scores generated from our machine learning and pair-wise methods have an average per-target correlation of 0.671 and 0.917, respectively, with the true model quality scores. Based on our test on 92 CASP9 targets, our predicted absolute local qualities have an average difference of 2.60 Å with the actual distances to native structure. http://sysbio.rnet.missouri.edu/apollo/. Single and pair-wise global quality assessment software is also available at the site.

Genetic parameters for different growth scales in GIFT strain of Nile tilapia (Oreochromis niloticus).

PubMed

He, J; Gao, H; Xu, P; Yang, R

2015-12-01

Body weight, length, width and depth at two growth stages were observed for a total of 5015 individuals of GIFT strain, along with a pedigree including 5588 individuals from 104 sires and 162 dams was collected. Multivariate animal models and a random regression model were used to genetically analyse absolute and relative growth scales of these growth traits. In absolute growth scale, the observed growth traits had moderate heritabilities ranging from 0.321 to 0.576, while pairwise ratios between body length, width and depth were lowly inherited and maximum heritability was only 0.146 for length/depth. All genetic correlations were above 0.5 between pairwise growth traits and genetic correlation between length/width and length/depth varied between both growth stages. Based on those estimates, selection index of multiple traits of interest can be formulated in future breeding program to improve genetically body weight and morphology of the GIFT strain. In relative growth scale, heritabilities in relative growths of body length, width and depth to body weight were 0.257, 0.412 and 0.066, respectively, while genetic correlations among these allometry scalings were above 0.8. Genetic analysis for joint allometries of body weight to body length, width and depth will contribute to genetically regulate the growth rate between body shape and body weight. © 2015 Blackwell Verlag GmbH.

Random regression analysis for body weights and main morphological traits in genetically improved farmed tilapia (Oreochromis niloticus).

PubMed

He, Jie; Zhao, Yunfeng; Zhao, Jingli; Gao, Jin; Xu, Pao; Yang, Runqing

2018-02-01

To genetically analyse growth traits in genetically improved farmed tilapia (GIFT), the body weight (BWE) and main morphological traits, including body length (BL), body depth (BD), body width (BWI), head length (HL) and length of the caudal peduncle (CPL), were measured six times in growth duration on 1451 fish from 45 mixed families of full and half sibs. A random regression model (RRM) was used to model genetic changes of the growth traits with days of age and estimate the heritability for any growth point and genetic correlations between pairwise growth points. Using the covariance function based on optimal RRMs, the heritabilities were estimated to be from 0.102 to 0.662 for BWE, 0.157 to 0.591 for BL, 0.047 to 0.621 for BD, 0.018 to 0.577 for BWI, 0.075 to 0.597 for HL and 0.032 to 0.610 for CPL between 60 and 140 days of age. All genetic correlations exceeded 0.5 between pairwise growth points. Moreover, the traits at initial days of age showed less correlation with those at later days of age. With phenotypes observed repeatedly, the model choice showed that the optimal RRMs could more precisely predict breeding values at a specific growth time than repeatability models or multiple trait animal models, which enhanced the efficiency of selection for the BWE and main morphological traits.

Development and Characterization of 18 Novel EST-SSRs from the Western Flower Thrips, Frankliniella occidentalis (Pergande)

PubMed Central

Yang, Xian-Ming; Sun, Jing-Tao; Xue, Xiao-Feng; Zhu, Wen-Chao; Hong, Xiao-Yue

2012-01-01

The western flower thrips, Frankliniella occidentalis (Pergande), is an invasive species and the most economically important pest within the insect order Thysanoptera. For a better understanding of the genetic makeup and migration patterns of F. occidentalis throughout the world, we characterized 18 novel polymorphic EST-derived microsatellites. The mutational mechanism of these EST-SSRs was also investigated to facilitate the selection of appropriate combinations of markers for population genetic studies. Genetic diversity of these novel markers was assessed in 96 individuals from three populations in China (Harbin, Dali, and Guiyang). The results showed that all these 18 loci were highly polymorphic; the number of alleles ranged from 2 to 15, with an average of 5.50 alleles per locus. The observed (HO) and expected (HE) heterozygosities ranged from 0.072 to 0.707 and 0.089 to 0.851, respectively. Furthermore, only two locus/population combinations (WFT144 in Dali and WFT50 in Guiyang) significantly deviated from Hardy–Weinberg equilibrium (HWE). Pairwise FST analysis showed a low but significant differentiation (0.026 < FST < 0.032) among all three pairwise population comparisons. Sequence analysis of alleles per locus revealed a complex mutational pattern of these EST-SSRs. Thus, these EST-SSRs are useful markers but greater attention should be paid to the mutational characteristics of these microsatellites when they are used in population genetic studies. PMID:22489130

Development and characterization of 18 novel EST-SSRs from the western flower Thrips, Frankliniella occidentalis (Pergande).

PubMed

Yang, Xian-Ming; Sun, Jing-Tao; Xue, Xiao-Feng; Zhu, Wen-Chao; Hong, Xiao-Yue

2012-01-01

The western flower thrips, Frankliniella occidentalis (Pergande), is an invasive species and the most economically important pest within the insect order Thysanoptera. For a better understanding of the genetic makeup and migration patterns of F. occidentalis throughout the world, we characterized 18 novel polymorphic EST-derived microsatellites. The mutational mechanism of these EST-SSRs was also investigated to facilitate the selection of appropriate combinations of markers for population genetic studies. Genetic diversity of these novel markers was assessed in 96 individuals from three populations in China (Harbin, Dali, and Guiyang). The results showed that all these 18 loci were highly polymorphic; the number of alleles ranged from 2 to 15, with an average of 5.50 alleles per locus. The observed (H(O)) and expected (H(E)) heterozygosities ranged from 0.072 to 0.707 and 0.089 to 0.851, respectively. Furthermore, only two locus/population combinations (WFT144 in Dali and WFT50 in Guiyang) significantly deviated from Hardy-Weinberg equilibrium (HWE). Pairwise F(ST) analysis showed a low but significant differentiation (0.026 < F(ST) < 0.032) among all three pairwise population comparisons. Sequence analysis of alleles per locus revealed a complex mutational pattern of these EST-SSRs. Thus, these EST-SSRs are useful markers but greater attention should be paid to the mutational characteristics of these microsatellites when they are used in population genetic studies.

Computer-Based Readability Testing of Information Booklets for German Cancer Patients.

PubMed

Keinki, Christian; Zowalla, Richard; Pobiruchin, Monika; Huebner, Jutta; Wiesner, Martin

2018-04-12

Understandable health information is essential for treatment adherence and improved health outcomes. For readability testing, several instruments analyze the complexity of sentence structures, e.g., Flesch-Reading Ease (FRE) or Vienna-Formula (WSTF). Moreover, the vocabulary is of high relevance for readers. The aim of this study is to investigate the agreement of sentence structure and vocabulary-based (SVM) instruments. A total of 52 freely available German patient information booklets on cancer were collected from the Internet. The mean understandability level L was computed for 51 booklets. The resulting values of FRE, WSTF, and SVM were assessed pairwise for agreement with Bland-Altman plots and two-sided, paired t tests. For the pairwise comparison, the mean L values are L FRE  = 6.81, L WSTF  = 7.39, L SVM  = 5.09. The sentence structure-based metrics gave significantly different scores (P < 0.001) for all assessed booklets, confirmed by the Bland-Altman analysis. The study findings suggest that vocabulary-based instruments cannot be interchanged with FRE/WSTF. However, both analytical aspects should be considered and checked by authors to linguistically refine texts with respect to the individual target group. Authors of health information can be supported by automated readability analysis. Health professionals can benefit by direct booklet comparisons allowing for time-effective selection of suitable booklets for patients.

Pilot Overmyer looks over food selections and experiments with beverage

NASA Image and Video Library

1982-11-16

STS005-07-255 (19 Nov. 1982) --- Astronaut Robert F. Overmyer, STS-5 pilot, using beverage container and drinking straw secured in meal tray assembly (ASSY), experiments with microgravity characteristics of liquid on middeck in front of forward lockers. Overmyer also looks over packages of food attached to middeck lockers in meal tray assemblies. Carry-on food warmer appears overhead and other meal tray assemblies, personal hygiene mirror assembly, personal hygiene kit, and portrait of G.W.S. Abbey, Johnson Space Center's (JSC) Director of Flight Operations, appear on lockers. Photo credit: NASA

Design of a mercury Propellant Storage and Distribution assembly

NASA Technical Reports Server (NTRS)

Holcomb, L. B.; Womack, J. R.

1973-01-01

A study has been conducted of a Propellant Storage and Distribution (PSD) assembly for a solar electric propulsion (SEP) thrust subsystem. As a result of the trade-off study an elastomeric diaphragm propellant tank with nitrogen blowdown pressurization was the method selected for propellant expulsion. This study included the following propellant management devices: surface tension, metallic bellows, and metallic and elastomeric diaphragms. Pressurant supply concepts investigated were blowdown, externally pressure regulated, vaporizing Freon 113, and heated CO2/Zeolite. The configuration selected consists of a single propellant tank, a single main propellant latching-solenoid valve, and individual thruster latching-solenoid valves. Stainless steel was the selected tankage material and AF-E-332 was the selected diaphragm material. The PSD design characteristics and interfaces are summarized.

System and method for heating ferrite magnet motors for low temperatures

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

Reddy, Patel Bhageerath; El-Refaie, Ayman Mohamed Fawzi; Huh, Kum-Kang

A system and method for heating ferrite permanent magnets in an electrical machine is disclosed. The permanent magnet machine includes a stator assembly and a rotor assembly, with a plurality of ferrite permanent magnets disposed within the stator assembly or the rotor assembly to generate a magnetic field that interacts with a stator magnetic field to produce a torque. A controller of the electrical machine is programmed to cause a primary field current to be applied to the stator windings to generate the stator magnetic field, so as to cause the rotor assembly to rotate relative to the stator assembly.more » The controller is further programmed to cause a secondary current to be applied to the stator windings to selectively generate a secondary magnetic field, the secondary magnetic field inducing eddy currents in at least one of the stator assembly and the rotor assembly to heat the ferrite permanent magnets.« less

System and method for heating ferrite magnet motors for low temperatures

DOEpatents

Reddy, Patel Bhageerath; El-Refaie, Ayman Mohamed Fawzi; Huh, Kum-Kang

2017-07-04

A system and method for heating ferrite permanent magnets in an electrical machine is disclosed. The permanent magnet machine includes a stator assembly and a rotor assembly, with a plurality of ferrite permanent magnets disposed within the stator assembly or the rotor assembly to generate a magnetic field that interacts with a stator magnetic field to produce a torque. A controller of the electrical machine is programmed to cause a primary field current to be applied to the stator windings to generate the stator magnetic field, so as to cause the rotor assembly to rotate relative to the stator assembly. The controller is further programmed to cause a secondary current to be applied to the stator windings to selectively generate a secondary magnetic field, the secondary magnetic field inducing eddy currents in at least one of the stator assembly and the rotor assembly to heat the ferrite permanent magnets.

Evaluating factors that predict the structure of a commensalistic epiphyte–phorophyte network

PubMed Central

Sáyago, Roberto; Lopezaraiza-Mikel, Martha; Quesada, Mauricio; Álvarez-Añorve, Mariana Yolotl; Cascante-Marín, Alfredo; Bastida, Jesus Ma.

2013-01-01

A central issue in ecology is the understanding of the establishment of biotic interactions. We studied the factors that affect the assembly of the commensalistic interactions between vascular epiphytes and their host plants. We used an analytical approach that considers all individuals and species of epiphytic bromeliads and woody hosts and non-hosts at study plots. We built models of interaction probabilities among species to assess if host traits and abundance and spatial overlap of species predict the quantitative epiphyte–host network. Species abundance, species spatial overlap and host size largely predicted pairwise interactions and several network metrics. Wood density and bark texture of hosts also contributed to explain network structure. Epiphytes were more common on large hosts, on abundant woody species, with denser wood and/or rougher bark. The network had a low level of specialization, although several interactions were more frequent than expected by the models. We did not detect a phylogenetic signal on the network structure. The effect of host size on the establishment of epiphytes indicates that mature forests are necessary to preserve diverse bromeliad communities. PMID:23407832

A Synthetic Coiled-Coil Interactome Provides Heterospecific Modules for Molecular Engineering

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

Reinke, Aaron W.; Grant, Robert A.; Keating, Amy E.

2010-06-21

The versatile coiled-coil protein motif is widely used to induce and control macromolecular interactions in biology and materials science. Yet the types of interaction patterns that can be constructed using known coiled coils are limited. Here we greatly expand the coiled-coil toolkit by measuring the complete pairwise interactions of 48 synthetic coiled coils and 7 human bZIP coiled coils using peptide microarrays. The resulting 55-member protein 'interactome' includes 27 pairs of interacting peptides that preferentially heteroassociate. The 27 pairs can be used in combinations to assemble sets of 3 to 6 proteins that compose networks of varying topologies. Of specialmore » interest are heterospecific peptide pairs that participate in mutually orthogonal interactions. Such pairs provide the opportunity to dimerize two separate molecular systems without undesired crosstalk. Solution and structural characterization of two such sets of orthogonal heterodimers provide details of their interaction geometries. The orthogonal pair, along with the many other network motifs discovered in our screen, provide new capabilities for synthetic biology and other applications.« less

Twisted ribbon structure of paired helical filaments revealed by atomic force microscopy.

PubMed Central

Pollanen, M. S.; Markiewicz, P.; Bergeron, C.; Goh, M. C.

1994-01-01

Progressive deposition of phosphorylated tau into the paired helical filaments (PHF) that compose neurofibrillary tangles, dystrophic neurites, and neuropil threads is an obligate feature of Alzheimer's disease. The standard model of PHF structure, derived from electron microscopic studies, suggests that two 8- to 10-nm filaments each composed of three to four protofilaments are wound into a helix with a maximal diameter of -20 nm and a half period of 65 to 80 nm. However, recent vertical platinum-carbon replicas of PHF more closely resemble a thin helical ribbon without constitutive protofilaments. Here we report that native PHF imaged with an atomic force microscope appear as twisted ribbons rather than the generally accepted structure derived from electron microscopic studies. These data imply that the assembly of PHF is not due to the twisting of pair-wise filaments but rather the helical winding of self-associated tau molecules arranged into a flattened structure. Future structural models of PHF should be based on quantitative data obtained from imaging techniques, such as scanning probe microscopy, which do not require harsh specimen preparation procedures. Images Figure 1 PMID:8178938

Twisted ribbon structure of paired helical filaments revealed by atomic force microscopy.

PubMed

Pollanen, M S; Markiewicz, P; Bergeron, C; Goh, M C

1994-05-01

Progressive deposition of phosphorylated tau into the paired helical filaments (PHF) that compose neurofibrillary tangles, dystrophic neurites, and neuropil threads is an obligate feature of Alzheimer's disease. The standard model of PHF structure, derived from electron microscopic studies, suggests that two 8- to 10-nm filaments each composed of three to four protofilaments are wound into a helix with a maximal diameter of -20 nm and a half period of 65 to 80 nm. However, recent vertical platinum-carbon replicas of PHF more closely resemble a thin helical ribbon without constitutive protofilaments. Here we report that native PHF imaged with an atomic force microscope appear as twisted ribbons rather than the generally accepted structure derived from electron microscopic studies. These data imply that the assembly of PHF is not due to the twisting of pair-wise filaments but rather the helical winding of self-associated tau molecules arranged into a flattened structure. Future structural models of PHF should be based on quantitative data obtained from imaging techniques, such as scanning probe microscopy, which do not require harsh specimen preparation procedures.

Alphasatellitidae: a new family with two subfamilies for the classification of geminivirus- and nanovirus-associated alphasatellites.

PubMed

Briddon, Rob W; Martin, Darren P; Roumagnac, Philippe; Navas-Castillo, Jesús; Fiallo-Olivé, Elvira; Moriones, Enrique; Lett, Jean-Michel; Zerbini, F Murilo; Varsani, Arvind

2018-05-09

Nanoviruses and geminiviruses are circular, single stranded DNA viruses that infect many plant species around the world. Nanoviruses and certain geminiviruses that belong to the Begomovirus and Mastrevirus genera are associated with additional circular, single stranded DNA molecules (~ 1-1.4 kb) that encode a replication-associated protein (Rep). These Rep-encoding satellite molecules are commonly referred to as alphasatellites and here we communicate the establishment of the family Alphasatellitidae to which these have been assigned. Within the Alphasatellitidae family two subfamilies, Geminialphasatellitinae and Nanoalphasatellitinae, have been established to respectively accommodate the geminivirus- and nanovirus-associated alphasatellites. Whereas the pairwise nucleotide sequence identity distribution of all the known geminialphasatellites (n = 628) displayed a troughs at ~ 70% and 88% pairwise identity, that of the known nanoalphasatellites (n = 54) had a troughs at ~ 67% and ~ 80% pairwise identity. We use these pairwise identity values as thresholds together with phylogenetic analyses to establish four genera and 43 species of geminialphasatellites and seven genera and 19 species of nanoalphasatellites. Furthermore, a divergent alphasatellite associated with coconut foliar decay disease is assigned to a species but not a subfamily as it likely represents a new alphasatellite subfamily that could be established once other closely related molecules are discovered.

Estimating Seven Coefficients of Pairwise Relatedness Using Population-Genomic Data

PubMed Central

Ackerman, Matthew S.; Johri, Parul; Spitze, Ken; Xu, Sen; Doak, Thomas G.; Young, Kimberly; Lynch, Michael

2017-01-01

Population structure can be described by genotypic-correlation coefficients between groups of individuals, the most basic of which are the pairwise relatedness coefficients between any two individuals. There are nine pairwise relatedness coefficients in the most general model, and we show that these can be reduced to seven coefficients for biallelic loci. Although all nine coefficients can be estimated from pedigrees, six coefficients have been beyond empirical reach. We provide a numerical optimization procedure that estimates all seven reduced coefficients from population-genomic data. Simulations show that the procedure is nearly unbiased, even at 3× coverage, and errors in five of the seven coefficients are statistically uncorrelated. The remaining two coefficients have a negative correlation of errors, but their sum provides an unbiased assessment of the overall correlation of heterozygosity between two individuals. Application of these new methods to four populations of the freshwater crustacean Daphnia pulex reveal the occurrence of half siblings in our samples, as well as a number of identical individuals that are likely obligately asexual clone mates. Statistically significant negative estimates of these pairwise relatedness coefficients, including inbreeding coefficients that were typically negative, underscore the difficulties that arise when interpreting genotypic correlations as estimations of the probability that alleles are identical by descent. PMID:28341647

Ensemble survival tree models to reveal pairwise interactions of variables with time-to-events outcomes in low-dimensional setting

PubMed Central

Dazard, Jean-Eudes; Ishwaran, Hemant; Mehlotra, Rajeev; Weinberg, Aaron; Zimmerman, Peter

2018-01-01

Unraveling interactions among variables such as genetic, clinical, demographic and environmental factors is essential to understand the development of common and complex diseases. To increase the power to detect such variables interactions associated with clinical time-to-events outcomes, we borrowed established concepts from random survival forest (RSF) models. We introduce a novel RSF-based pairwise interaction estimator and derive a randomization method with bootstrap confidence intervals for inferring interaction significance. Using various linear and nonlinear time-to-events survival models in simulation studies, we first show the efficiency of our approach: true pairwise interaction-effects between variables are uncovered, while they may not be accompanied with their corresponding main-effects, and may not be detected by standard semi-parametric regression modeling and test statistics used in survival analysis. Moreover, using a RSF-based cross-validation scheme for generating prediction estimators, we show that informative predictors may be inferred. We applied our approach to an HIV cohort study recording key host gene polymorphisms and their association with HIV change of tropism or AIDS progression. Altogether, this shows how linear or nonlinear pairwise statistical interactions of variables may be efficiently detected with a predictive value in observational studies with time-to-event outcomes. PMID:29453930

Detection of the pairwise kinematic Sunyaev-Zel'dovich effect with BOSS DR11 and the Atacama Cosmology Telescope

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

Bernardis, F. De; Aiola, S.; Vavagiakis, E. M.

Here, we present a new measurement of the kinematic Sunyaev-Zel'dovich effect using data from the Atacama Cosmology Telescope (ACT) and the Baryon Oscillation Spectroscopic Survey (BOSS). Using 600 square degrees of overlapping sky area, we evaluate the mean pairwise baryon momentum associated with the positions of 50,000 bright galaxies in the BOSS DR11 Large Scale Structure catalog. A non-zero signal arises from the large-scale motions of halos containing the sample galaxies. The data fits an analytical signal model well, with the optical depth to microwave photon scattering as a free parameter determining the overall signal amplitude. We estimate the covariancemore » matrix of the mean pairwise momentum as a function of galaxy separation, using microwave sky simulations, jackknife evaluation, and bootstrap estimates. The most conservative simulation-based errors give signal-to-noise estimates between 3.6 and 4.1 for varying galaxy luminosity cuts. We discuss how the other error determinations can lead to higher signal-to-noise values, and consider the impact of several possible systematic errors. Estimates of the optical depth from the average thermal Sunyaev-Zel'dovich signal at the sample galaxy positions are broadly consistent with those obtained from the mean pairwise momentum signal.« less

Detection of the pairwise kinematic Sunyaev-Zel'dovich effect with BOSS DR11 and the Atacama Cosmology Telescope

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

Bernardis, F. De; Vavagiakis, E.M.; Niemack, M.D.

We present a new measurement of the kinematic Sunyaev-Zel'dovich effect using data from the Atacama Cosmology Telescope (ACT) and the Baryon Oscillation Spectroscopic Survey (BOSS). Using 600 square degrees of overlapping sky area, we evaluate the mean pairwise baryon momentum associated with the positions of 50,000 bright galaxies in the BOSS DR11 Large Scale Structure catalog. A non-zero signal arises from the large-scale motions of halos containing the sample galaxies. The data fits an analytical signal model well, with the optical depth to microwave photon scattering as a free parameter determining the overall signal amplitude. We estimate the covariance matrixmore » of the mean pairwise momentum as a function of galaxy separation, using microwave sky simulations, jackknife evaluation, and bootstrap estimates. The most conservative simulation-based errors give signal-to-noise estimates between 3.6 and 4.1 for varying galaxy luminosity cuts. We discuss how the other error determinations can lead to higher signal-to-noise values, and consider the impact of several possible systematic errors. Estimates of the optical depth from the average thermal Sunyaev-Zel'dovich signal at the sample galaxy positions are broadly consistent with those obtained from the mean pairwise momentum signal.« less

Detection of the Pairwise Kinematic Sunyaev-Zel'dovich Effect with BOSS DR11 and the Atacama Cosmology Telescope

NASA Technical Reports Server (NTRS)

De Bernardis, F.; Aiola, S.; Vavagiakis, E. M.; Battaglia, N.; Niemack, M. D.; Beall, J.; Becker, D. T.; Bond, J. R.; Calabrese, E.; Cho, H.;

Detection of the pairwise kinematic Sunyaev-Zel'dovich effect with BOSS DR11 and the Atacama Cosmology Telescope

NASA Astrophysics Data System (ADS)

De Bernardis, F.; Aiola, S.; Vavagiakis, E. M.; Battaglia, N.; Niemack, M. D.; Beall, J.; Becker, D. T.; Bond, J. R.; Calabrese, E.; Cho, H.; Coughlin, K.; Datta, R.; Devlin, M.; Dunkley, J.; Dunner, R.; Ferraro, S.; Fox, A.; Gallardo, P. A.; Halpern, M.; Hand, N.; Hasselfield, M.; Henderson, S. W.; Hill, J. C.; Hilton, G. C.; Hilton, M.; Hincks, A. D.; Hlozek, R.; Hubmayr, J.; Huffenberger, K.; Hughes, J. P.; Irwin, K. D.; Koopman, B. J.; Kosowsky, A.; Li, D.; Louis, T.; Lungu, M.; Madhavacheril, M. S.; Maurin, L.; McMahon, J.; Moodley, K.; Naess, S.; Nati, F.; Newburgh, L.; Nibarger, J. P.; Page, L. A.; Partridge, B.; Schaan, E.; Schmitt, B. L.; Sehgal, N.; Sievers, J.; Simon, S. M.; Spergel, D. N.; Staggs, S. T.; Stevens, J. R.; Thornton, R. J.; van Engelen, A.; Van Lanen, J.; Wollack, E. J.

2017-03-01

We present a new measurement of the kinematic Sunyaev-Zel'dovich effect using data from the Atacama Cosmology Telescope (ACT) and the Baryon Oscillation Spectroscopic Survey (BOSS). Using 600 square degrees of overlapping sky area, we evaluate the mean pairwise baryon momentum associated with the positions of 50,000 bright galaxies in the BOSS DR11 Large Scale Structure catalog. A non-zero signal arises from the large-scale motions of halos containing the sample galaxies. The data fits an analytical signal model well, with the optical depth to microwave photon scattering as a free parameter determining the overall signal amplitude. We estimate the covariance matrix of the mean pairwise momentum as a function of galaxy separation, using microwave sky simulations, jackknife evaluation, and bootstrap estimates. The most conservative simulation-based errors give signal-to-noise estimates between 3.6 and 4.1 for varying galaxy luminosity cuts. We discuss how the other error determinations can lead to higher signal-to-noise values, and consider the impact of several possible systematic errors. Estimates of the optical depth from the average thermal Sunyaev-Zel'dovich signal at the sample galaxy positions are broadly consistent with those obtained from the mean pairwise momentum signal.

Ensemble survival tree models to reveal pairwise interactions of variables with time-to-events outcomes in low-dimensional setting.

PubMed

Dazard, Jean-Eudes; Ishwaran, Hemant; Mehlotra, Rajeev; Weinberg, Aaron; Zimmerman, Peter

2018-02-17

Unraveling interactions among variables such as genetic, clinical, demographic and environmental factors is essential to understand the development of common and complex diseases. To increase the power to detect such variables interactions associated with clinical time-to-events outcomes, we borrowed established concepts from random survival forest (RSF) models. We introduce a novel RSF-based pairwise interaction estimator and derive a randomization method with bootstrap confidence intervals for inferring interaction significance. Using various linear and nonlinear time-to-events survival models in simulation studies, we first show the efficiency of our approach: true pairwise interaction-effects between variables are uncovered, while they may not be accompanied with their corresponding main-effects, and may not be detected by standard semi-parametric regression modeling and test statistics used in survival analysis. Moreover, using a RSF-based cross-validation scheme for generating prediction estimators, we show that informative predictors may be inferred. We applied our approach to an HIV cohort study recording key host gene polymorphisms and their association with HIV change of tropism or AIDS progression. Altogether, this shows how linear or nonlinear pairwise statistical interactions of variables may be efficiently detected with a predictive value in observational studies with time-to-event outcomes.

Detection of the pairwise kinematic Sunyaev-Zel'dovich effect with BOSS DR11 and the Atacama Cosmology Telescope

DOE PAGES

Bernardis, F. De; Aiola, S.; Vavagiakis, E. M.; ...

2017-03-07

Here, we present a new measurement of the kinematic Sunyaev-Zel'dovich effect using data from the Atacama Cosmology Telescope (ACT) and the Baryon Oscillation Spectroscopic Survey (BOSS). Using 600 square degrees of overlapping sky area, we evaluate the mean pairwise baryon momentum associated with the positions of 50,000 bright galaxies in the BOSS DR11 Large Scale Structure catalog. A non-zero signal arises from the large-scale motions of halos containing the sample galaxies. The data fits an analytical signal model well, with the optical depth to microwave photon scattering as a free parameter determining the overall signal amplitude. We estimate the covariancemore » matrix of the mean pairwise momentum as a function of galaxy separation, using microwave sky simulations, jackknife evaluation, and bootstrap estimates. The most conservative simulation-based errors give signal-to-noise estimates between 3.6 and 4.1 for varying galaxy luminosity cuts. We discuss how the other error determinations can lead to higher signal-to-noise values, and consider the impact of several possible systematic errors. Estimates of the optical depth from the average thermal Sunyaev-Zel'dovich signal at the sample galaxy positions are broadly consistent with those obtained from the mean pairwise momentum signal.« less

Highly selective and sensitive method for Cu2+ detection based on chiroptical activity of L-Cysteine mediated Au nanorod assemblies.

PubMed

Abbasi, Shahryar; Khani, Hamzeh

2017-11-05

Herein, we demonstrated a simple and efficient method to detect Cu 2+ based on amplified optical activity in the chiral nanoassemblies of gold nanorods (Au NRs). L-Cysteine can induce side-by-side or end-to-end assembly of Au NRs with an evident plasmonic circular dichroism (PCD) response due to coupling between surface plasmon resonances (SPR) of Au NRs and the chiral signal of L-Cys. Because of the obvious stronger plasmonic circular dichrosim (CD) response of the side-by-side assembly compared with the end-to-end assemblies, SS assembled Au NRs was selected as a sensitive platform and used for Cu 2+ detection. In the presence of Cu 2+ , Cu 2+ can catalyze O 2 oxidation of cysteine to cystine. With an increase in Cu 2+ concentration, the L-Cysteine-mediated assembly of Au NRs decreased because of decrease in the free cysteine thiol groups, and the PCD signal decreased. Taking advantage of this method, Cu 2+ could be detected in the concentration range of 20pM-5nM. Under optimal conditions, the calculated detection limit was found to be 7pM. Copyright © 2017 Elsevier B.V. All rights reserved.

Material selection and assembly method of battery pack for compact electric vehicle

NASA Astrophysics Data System (ADS)

Lewchalermwong, N.; Masomtob, M.; Lailuck, V.; Charoenphonphanich, C.

2018-01-01

Battery packs become the key component in electric vehicles (EVs). The main costs of which are battery cells and assembling processes. The battery cell is indeed priced from battery manufacturers while the assembling cost is dependent on battery pack designs. Battery pack designers need overall cost as cheap as possible, but it still requires high performance and more safety. Material selection and assembly method as well as component design are very important to determine the cost-effectiveness of battery modules and battery packs. Therefore, this work presents Decision Matrix, which can aid in the decision-making process of component materials and assembly methods for a battery module design and a battery pack design. The aim of this study is to take the advantage of incorporating Architecture Analysis method into decision matrix methods by capturing best practices for conducting design architecture analysis in full account of key design components critical to ensure efficient and effective development of the designs. The methodology also considers the impacts of choice-alternatives along multiple dimensions. Various alternatives for materials and assembly techniques of battery pack are evaluated, and some sample costs are presented. Due to many components in the battery pack, only seven components which are positive busbar and Z busbar are represented in this paper for using decision matrix methods.

Pushrod assembly

DOEpatents

Potter, J.D.

1984-03-30

A pushrod assembly including a carriage mounted on a shaft for movement therealong and carrying a pushrod engageable with a load to be moved is described. A magnet is mounted on a supporting bracket for movement along such shaft. Means are provided for adjustably spacing magnet away from the carriage to obtain a selected magnetic attractive or coupling force therebetween. Movement of the supporting bracket and the magnet carried thereby pulls the carriage along with it until the selected magnetic force is exceeded by a resistance load acting on the carriage.

Pushrod assembly

DOEpatents

Potter, Jerry D.

1987-01-01

A pushrod assembly including a carriage mounted on a shaft for movement therealong and carrying a pushrod engageable with a load to be moved. A magnet is mounted on a supporting bracket for movement along such shaft. Means are provided for adjustably spacing said magnet away from said carriage to obtain a selected magnetic attractive or coupling force therebetween. Movement of the supporting bracket and the magnet carried thereby pulls the carriage along with it until the selected magnetic force is exceeded by a resistance load acting on the carriage.

Hash Bit Selection for Nearest Neighbor Search.

PubMed

Xianglong Liu; Junfeng He; Shih-Fu Chang

2017-11-01

To overcome the barrier of storage and computation when dealing with gigantic-scale data sets, compact hashing has been studied extensively to approximate the nearest neighbor search. Despite the recent advances, critical design issues remain open in how to select the right features, hashing algorithms, and/or parameter settings. In this paper, we address these by posing an optimal hash bit selection problem, in which an optimal subset of hash bits are selected from a pool of candidate bits generated by different features, algorithms, or parameters. Inspired by the optimization criteria used in existing hashing algorithms, we adopt the bit reliability and their complementarity as the selection criteria that can be carefully tailored for hashing performance in different tasks. Then, the bit selection solution is discovered by finding the best tradeoff between search accuracy and time using a modified dynamic programming method. To further reduce the computational complexity, we employ the pairwise relationship among hash bits to approximate the high-order independence property, and formulate it as an efficient quadratic programming method that is theoretically equivalent to the normalized dominant set problem in a vertex- and edge-weighted graph. Extensive large-scale experiments have been conducted under several important application scenarios of hash techniques, where our bit selection framework can achieve superior performance over both the naive selection methods and the state-of-the-art hashing algorithms, with significant accuracy gains ranging from 10% to 50%, relatively.

Evolution of resistance to a multiple-herbivore community: genetic correlations, diffuse coevolution, and constraints on the plant's response to selection.

PubMed

Wise, Michael J; Rausher, Mark D

2013-06-01

Although plants are generally attacked by a community of several species of herbivores, relatively little is known about the strength of natural selection for resistance in multiple-herbivore communities-particularly how the strength of selection differs among herbivores that feed on different plant organs or how strongly genetic correlations in resistance affect the evolutionary responses of the plant. Here, we report on a field study measuring natural selection for resistance in a diverse community of herbivores of Solanum carolinense. Using linear phenotypic-selection analyses, we found that directional selection acted to increase resistance to seven species. Selection was strongest to increase resistance to fruit feeders, followed by flower feeders, then leaf feeders. Selection favored a decrease in resistance to a stem borer. Bootstrapping analyses showed that the plant population contained significant genetic variation for each of 14 measured resistance traits and significant covariances in one-third of the pairwise combinations of resistance traits. These genetic covariances reduced the plant's overall predicted evolutionary response for resistance against the herbivore community by about 60%. Diffuse (co)evolution was widespread in this community, and the diffuse interactions had an overwhelmingly constraining (rather than facilitative) effect on the plant's evolution of resistance. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

STRATEGIES OF MARINE DINOFLAGELLATE SURVIVAL AND SOME RULES OF ASSEMBLY. (R829368)

EPA Science Inventory

Dinoflagellate ecology is based on multiple adaptive strategies and species having diverse habitat preferences. Nine types of mixing-irradiance-nutrient habitats selecting for specific marine dinoflagellate life-form types are recognised, with five rules of assembly proposed t...

Fuel assembly design for APR1400 with low CBC

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

Hah, Chang Joo, E-mail: changhah@kings.ac.kr

2015-04-29

APR 1400 is a PWR (Pressurized Water Reactor) with rated power of 3983 MWth and 241 assemblies. Recently, demand for extremely longer cycle up to 24 months is increasing with challenge of higher critical boron concentration (CBC). In this paper, assembly design method of selecting Gd-rods is introduced to reduce CBC. The purpose of the method is to lower the critical boron concentration of the preliminary core loading pattern (PLP), and consequently to achieve more negative or less positive moderator temperature coefficient (MTC). In this method, both the ratio of the number of low-Gd rod to the number of high-Gdmore » rod (r) and assembly average Gd wt% (w) are the decision variables. The target function is the amount of soluble boron concentration reduction, which can be converted to Δk{sub TARGET}. A set of new designed fuel assembly satisfies an objective function, min [f=∑{sub i}(Δk{sub FA}−Δk{sub i})], and enables a final loading pattern to reach a target CBC. The constraints required to determine a set of Δk are physically realizable pair, (r,w), and the sum of Δk of new designed assemblies as close to Δk{sub TARGET} as possible. New Gd-bearing assemblies selected based on valid pairs of (r,w) are replaced with existing assemblies in a PLP. This design methodology is applied to Shin-Kori Unit 3 Cycle 1 used as a reference model. CASMO-3/MASTER code is used for depletion calculation. CASMO-3/MASTER calculations with new designed assemblies produce lower CBC than the expected CBC, proving that the proposed method works successful.« less

Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes

PubMed Central

2011-01-01

Background BAC-based physical maps provide for sequencing across an entire genome or a selected sub-genomic region of biological interest. Such a region can be approached with next-generation whole-genome sequencing and assembly as if it were an independent small genome. Using the minimum tiling path as a guide, specific BAC clones representing the prioritized genomic interval are selected, pooled, and used to prepare a sequencing library. Results This pooled BAC approach was taken to sequence and assemble a QTL-rich region, of ~3 Mbp and represented by twenty-seven BACs, on linkage group 5 of the Theobroma cacao cv. Matina 1-6 genome. Using various mixtures of read coverages from paired-end and linear 454 libraries, multiple assemblies of varied quality were generated. Quality was assessed by comparing the assembly of 454 reads with a subset of ten BACs individually sequenced and assembled using Sanger reads. A mixture of reads optimal for assembly was identified. We found, furthermore, that a quality assembly suitable for serving as a reference genome template could be obtained even with a reduced depth of sequencing coverage. Annotation of the resulting assembly revealed several genes potentially responsible for three T. cacao traits: black pod disease resistance, bean shape index, and pod weight. Conclusions Our results, as with other pooled BAC sequencing reports, suggest that pooling portions of a minimum tiling path derived from a BAC-based physical map is an effective method to target sub-genomic regions for sequencing. While we focused on a single QTL region, other QTL regions of importance could be similarly sequenced allowing for biological discovery to take place before a high quality whole-genome assembly is completed. PMID:21794110

Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes.

PubMed

Feltus, Frank A; Saski, Christopher A; Mockaitis, Keithanne; Haiminen, Niina; Parida, Laxmi; Smith, Zachary; Ford, James; Staton, Margaret E; Ficklin, Stephen P; Blackmon, Barbara P; Cheng, Chun-Huai; Schnell, Raymond J; Kuhn, David N; Motamayor, Juan-Carlos

2011-07-27

BAC-based physical maps provide for sequencing across an entire genome or a selected sub-genomic region of biological interest. Such a region can be approached with next-generation whole-genome sequencing and assembly as if it were an independent small genome. Using the minimum tiling path as a guide, specific BAC clones representing the prioritized genomic interval are selected, pooled, and used to prepare a sequencing library. This pooled BAC approach was taken to sequence and assemble a QTL-rich region, of ~3 Mbp and represented by twenty-seven BACs, on linkage group 5 of the Theobroma cacao cv. Matina 1-6 genome. Using various mixtures of read coverages from paired-end and linear 454 libraries, multiple assemblies of varied quality were generated. Quality was assessed by comparing the assembly of 454 reads with a subset of ten BACs individually sequenced and assembled using Sanger reads. A mixture of reads optimal for assembly was identified. We found, furthermore, that a quality assembly suitable for serving as a reference genome template could be obtained even with a reduced depth of sequencing coverage. Annotation of the resulting assembly revealed several genes potentially responsible for three T. cacao traits: black pod disease resistance, bean shape index, and pod weight. Our results, as with other pooled BAC sequencing reports, suggest that pooling portions of a minimum tiling path derived from a BAC-based physical map is an effective method to target sub-genomic regions for sequencing. While we focused on a single QTL region, other QTL regions of importance could be similarly sequenced allowing for biological discovery to take place before a high quality whole-genome assembly is completed.

Design criteria monograph for valve assemblies

NASA Technical Reports Server (NTRS)

1974-01-01

Monograph is limited to valve selection factors for trade-off studies, configuration analyses, actuator selection, and integration of components. Material is organized along lines of valve design sequence.

Hepatitis C Virus-Induced Rab32 Aggregation and Its Implications for Virion Assembly.

PubMed

Pham, Tu M; Tran, Si C; Lim, Yun-Sook; Hwang, Soon B

2017-02-01

Hepatitis C virus (HCV) is highly dependent on cellular factors for viral propagation. Using high-throughput next-generation sequencing, we analyzed the host transcriptomic changes and identified 30 candidate genes which were upregulated in cell culture-grown HCV (HCVcc)-infected cells. Of these candidates, we selected Rab32 for further investigation. Rab32 is a small GTPase that regulates a variety of intracellular membrane-trafficking events in various cell types. In this study, we demonstrated that both mRNA and protein levels of Rab32 were increased in HCV-infected cells. Furthermore, we showed that HCV infection converted the predominantly expressed GTP-bound Rab32 to GDP-bound Rab32, contributing to the aggregation of Rab32 and thus making it less sensitive to cellular degradation machinery. In addition, GDP-bound Rab32 selectively interacted with HCV core protein and deposited core protein into the endoplasmic reticulum (ER)-associated Rab32-derived aggregated structures in the perinuclear region, which were likely to be viral assembly sites. Using RNA interference technology, we demonstrated that Rab32 was required for the assembly step but not for other stages of the HCV life cycle. Taken together, these data suggest that HCV may modulate Rab32 activity to facilitate virion assembly. Rab32, a member of the Ras superfamily of small GTPases, regulates various intracellular membrane-trafficking events in many cell types. In this study, we showed that HCV infection concomitantly increased Rab32 expression at the transcriptional level and altered the balance between GDP- and GTP-bound Rab32 toward production of Rab32-GDP. GDP-bound Rab32 selectively interacted with HCV core protein and enriched core in the ER-associated Rab32-derived aggregated structures that were probably necessary for viral assembly. Indeed, we showed that Rab32 was specifically required for the assembly of HCV. Collectively, our study identifies that Rab32 is a novel host factor essential for HCV particle assembly. Copyright © 2017 American Society for Microbiology.

Cohesiveness tunes assembly and morphology of FG nucleoporin domain meshworks – Implications for nuclear pore permeability

PubMed Central

Eisele, Nico B.; Labokha, Aksana A.; Frey, Steffen; Görlich, Dirk; Richter, Ralf P.

2013-01-01

Nuclear pore complexes control the exchange of macromolecules between the cytoplasm and the nucleus. A selective permeability barrier that arises from a supramolecular assembly of intrinsically unfolded nucleoporin domains rich in phenylalanine-glycine dipeptides (FG domains) fills the nuclear pore. There is increasing evidence that selective transport requires cohesive FG domain interactions. To understand the functional roles of cohesive interactions, we studied monolayers of end-grafted FG domains as a bottom-up nanoscale model system of the permeability barrier. Based on detailed physicochemical analysis of the model films and comparison of the data with polymer theory, we propose that cohesiveness is tuned to promote rapid assembly of the permeability barrier and to generate a stable and compact pore-filling meshwork with a small mesh size. Our results highlight the functional importance of weak interactions, typically a few kBT per chain, and contribute important information to understand the mechanism of size-selective transport. PMID:24138862

Development of formula varsity race car chassis

NASA Astrophysics Data System (ADS)

Abdullah, M. A.; Mansur, M. R.; Tamaldin, N.; Thanaraj, K.

2013-12-01

Three chassis designs have been developed using commercial computer aided design (CAD) software. The design is based on the specifications of UTeM Formula VarsityTM 2012 (FV2012). The selection of the design is derived from weighted matrix which consists of reliability, cost, time consumption and weight. The score of the matrix is formulated based on relative weighted factor among the selections. All three designs are then fabricated using selected materials available. The actual cost, time consumption and weight of the chassis's are compared with the theoretical weighted scores. Standard processes of cuttings, fittings and welding are performed in chassis mock up and fabrication. The chassis is later assembled together with suspension systems, steering linkages, brake systems, engine system, and drive shaft systems. Once the chassis is assembled, the studies of driver's ergonomic and part accessibility are performed. The completion in final fittings and assembly of the race car and its reliability demonstrate an outstanding design for manufacturing (DFM) practices of the chassis.

Assembly of Colloidal Materials Using Bioadhesive Interactions

NASA Technical Reports Server (NTRS)

Hammer, Daniel A.; Hiddessen, Amy L.; Tohver, Valeria; Crocker, John C.; Weitz, David A.

2002-01-01

We have pursued the use of biological crosslinking molecules of several types to make colloidal materials at relatively low volume fraction of colloidal particles. The objective is to make binary alloys of colloidal particles, made of two different colloidal particles coated with complementary biological lock-and-key binding molecules, which assemble due to the biological specificity. The long-term goal is to use low affinity lock-and-key biological interactions, so that the can anneal to form crystalline states. We have used a variety of different surface chemistries in order to make colloidal materials. Our first system involved using selectin-carbohydrate (sialyl-Lewis) interactions; this chemistry is derived from immune system. This chemical interaction is of relatively low affinity, with timescales for dissociation of several seconds. Furthermore, the adhesion mediated by these molecules can be reversed by the chelation of calcium atoms; thus assembled structures can be disassembled reversibly. Our second system employed avidin-biotin chemistry. This well-studied system is of high affinity, and is generally irreversible on a laboratory time-scale. Thus, we would expect selectin-carbohydrate interactions at high molecular density and avidin-biotin interactions to give kinetically-trapped structures; however, at low densities, we would expect significant differences in the structure and dynamics of the two materials, owing to their very different release rates. We have also begun to use a third chemistry - DNA hybridization. By attaching single stranded DNA oligonucleotide chains to beads, we can drive the assembly of colloidal materials by hybridization of complementary DNA chains. It is well known that DNA adenosine-thymine (A-T) and guanine-cytosine (G-C) bases hybridize pairwise with a Gibbs free energy change of 1.7 kcal/mol per base; thus, the energy of the assembly can be modulated by altering the number of complementary bases in the DNA chains. Using these different crosslinking molecules, we have assembled colloidal materials from different-sized colloidal particles, A and B. In the first sets of experiment, we used high densities of adhesion molecules, and 0.96 micron (A) and 5.5 micron (B) diameter particles. The high density of adhesion molecules means that the structures are kinetically trapped in nonequilibrium configurations. The structure of the suspension can be varied by changing the number ratio of the two types of colloidal particles, NA and NB, where A is the smaller particle. With carbohydrate-selectin or avidin-biotin interactions, large NA/NB leads to the formation of colloidal micelles, with the large center B particle surrounded by many smaller A particles. As the ratio NA/NB decreases, the structures become more extended, approaching the formation of macro-Rouse polymers - extended linear chains where A beads are connected with intervening small B linkers.

40 CFR 86.603-88 - Test orders.

Code of Federal Regulations, 2010 CFR

2010-07-01

...) CONTROL OF EMISSIONS FROM NEW AND IN-USE HIGHWAY VEHICLES AND ENGINES (CONTINUED) Selective Enforcement..., adjustments, or repairs. (d) A manufacturer may indicate preferred assembly plants for the various engine... accomplished by submitting a list of engine families and the corresponding assembly plants from which the...

40 CFR 86.603-88 - Test orders.

Code of Federal Regulations, 2013 CFR

2013-07-01

...) CONTROL OF EMISSIONS FROM NEW AND IN-USE HIGHWAY VEHICLES AND ENGINES (CONTINUED) Selective Enforcement..., adjustments, or repairs. (d) A manufacturer may indicate preferred assembly plants for the various engine... accomplished by submitting a list of engine families and the corresponding assembly plants from which the...

40 CFR 86.603-88 - Test orders.

Code of Federal Regulations, 2011 CFR

2011-07-01

...) CONTROL OF EMISSIONS FROM NEW AND IN-USE HIGHWAY VEHICLES AND ENGINES (CONTINUED) Selective Enforcement..., adjustments, or repairs. (d) A manufacturer may indicate preferred assembly plants for the various engine... accomplished by submitting a list of engine families and the corresponding assembly plants from which the...

Layer-by-layer assembly of patchy particles as a route to nontrivial structures

NASA Astrophysics Data System (ADS)

Patra, Niladri; Tkachenko, Alexei V.

2017-08-01

We propose a strategy for robust high-quality self-assembly of nontrivial periodic structures out of patchy particles and investigate it with Brownian dynamics simulations. Its first element is the use of specific patch-patch and shell-shell interactions between the particles, which can be implemented through differential functionalization of patched and shell regions with specific DNA strands. The other key element of our approach is the use of a layer-by-layer protocol that allows one to avoid the formation of undesired random aggregates. As an example, we design and self-assemble in silico a version of a double diamond lattice in which four particle types are arranged into bcc crystal made of four fcc sublattices. The lattice can be further converted to cubic diamond by selective removal of the particles of certain types. Our results demonstrate that by combining the directionality, selectivity of interactions, and the layer-by-layer protocol, a high-quality robust self-assembly can be achieved.

Temperature-dependent self-assembly and rheological behavior of a thermoreversible pmma-P n BA-PMMA triblock copolymer gel

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

Zabet, Mahla; Mishra, Satish; Boy, Ramiz

Self-assembly and mechanical properties of triblock copolymers in a mid-block selective solvent are of interest in many applications. Herein, we report physical assembly of an ABA triblock copolymer, [PMMA–PnBA–PMMA] in two different mid-block selective solvents, n-butanol and 2-ethyl-1-hexanol. Gel formation resulting from end-block associations and the corresponding changes in mechanical properties have been investigated over a temperature range of -80 °C to 60 °C, from near the solvent melting points to above the gelation temperature. Shear-rheometry, thermal analysis, and small-angle neutron scattering data reveal formation and transition of structure in these systems from a liquid state to a gel statemore » to a percolated cluster network with decrease in temperature. The aggregated PMMA end-blocks display a glass transition temperature. Our results provide new understanding into the structural changes of a self-assembled triblock copolymer gel over a large length scale and wide temperature range.« less

Layer-by-layer assembly of patchy particles as a route to nontrivial structures

DOE PAGES

Patra, Niladri; Tkachenko, Alexei V.

2017-08-02

Here, we propose a strategy for robust high-quality self-assembly of nontrivial periodic structures out of patchy particles and investigate it with Brownian dynamics simulations. Its first element is the use of specific patch-patch and shell-shell interactions between the particles, which can be implemented through differential functionalization of patched and shell regions with specific DNA strands. The other key element of our approach is the use of a layer-by-layer protocol that allows one to avoid the formation of undesired random aggregates. As an example, we design and self-assemble in silico a version of a double diamond lattice in which four particlemore » types are arranged into bcc crystal made of four fcc sublattices. The lattice can be further converted to cubic diamond by selective removal of the particles of certain types. These results demonstrate that by combining the directionality, selectivity of interactions, and the layer-by-layer protocol, a high-quality robust self-assembly can be achieved.« less

Distinct Mechanisms for Synchronization and Temporal Patterning of Odor-Encoding Neural Assemblies

NASA Astrophysics Data System (ADS)

MacLeod, Katrina; Laurent, Gilles

1996-11-01

Stimulus-evoked oscillatory synchronization of neural assemblies and temporal patterns of neuronal activity have been observed in many sensory systems, such as the visual and auditory cortices of mammals or the olfactory system of insects. In the locust olfactory system, single odor puffs cause the immediate formation of odor-specific neural assemblies, defined both by their transient synchronized firing and their progressive transformation over the course of a response. The application of an antagonist of ionotropic γ-aminobutyric acid (GABA) receptors to the first olfactory relay neuropil selectively blocked the fast inhibitory synapse between local and projection neurons. This manipulation abolished the synchronization of the odor-coding neural ensembles but did not affect each neuron's temporal response patterns to odors, even when these patterns contained periods of inhibition. Fast GABA-mediated inhibition, therefore, appears to underlie neuronal synchronization but not response tuning in this olfactory system. The selective desynchronization of stimulus-evoked oscillating neural assemblies in vivo is now possible, enabling direct functional tests of their significance for sensation and perception.

Taxonomical and functional microbial community selection in soybean rhizosphere

PubMed Central

Mendes, Lucas W; Kuramae, Eiko E; Navarrete, Acácio A; van Veen, Johannes A; Tsai, Siu M

2014-01-01

This study addressed the selection of the rhizospheric microbial community from the bulk soil reservoir under agricultural management of soybean in Amazon forest soils. We used a shotgun metagenomics approach to investigate the taxonomic and functional diversities of microbial communities in the bulk soil and in the rhizosphere of soybean plants and tested the validity of neutral and niche theories to explain the rhizosphere community assembly processes. Our results showed a clear selection at both taxonomic and functional levels operating in the assembly of the soybean rhizosphere community. The taxonomic analysis revealed that the rhizosphere community is a subset of the bulk soil community. Species abundance in rhizosphere fits the log-normal distribution model, which is an indicator of the occurrence of niche-based processes. In addition, the data indicate that the rhizosphere community is selected based on functional cores related to the metabolisms of nitrogen, iron, phosphorus and potassium, which are related to benefits to the plant, such as growth promotion and nutrition. The network analysis including bacterial groups and functions was less complex in rhizosphere, suggesting the specialization of some specific metabolic pathways. We conclude that the assembly of the microbial community in the rhizosphere is based on niche-based processes as a result of the selection power of the plant and other environmental factors. PMID:24553468

Pair-Wise and Many-Body Dispersive Interactions Coupled to an Optimally Tuned Range-Separated Hybrid Functional.

PubMed

Agrawal, Piyush; Tkatchenko, Alexandre; Kronik, Leeor

2013-08-13

We propose a nonempirical, pair-wise or many-body dispersion-corrected, optimally tuned range-separated hybrid functional. This functional retains the advantages of the optimal-tuning approach in the prediction of the electronic structure. At the same time, it gains accuracy in the prediction of binding energies for dispersively bound systems, as demonstrated on the S22 and S66 benchmark sets of weakly bound dimers.

Pairwise Classifier Ensemble with Adaptive Sub-Classifiers for fMRI Pattern Analysis.

PubMed

Kim, Eunwoo; Park, HyunWook

2017-02-01

The multi-voxel pattern analysis technique is applied to fMRI data for classification of high-level brain functions using pattern information distributed over multiple voxels. In this paper, we propose a classifier ensemble for multiclass classification in fMRI analysis, exploiting the fact that specific neighboring voxels can contain spatial pattern information. The proposed method converts the multiclass classification to a pairwise classifier ensemble, and each pairwise classifier consists of multiple sub-classifiers using an adaptive feature set for each class-pair. Simulated and real fMRI data were used to verify the proposed method. Intra- and inter-subject analyses were performed to compare the proposed method with several well-known classifiers, including single and ensemble classifiers. The comparison results showed that the proposed method can be generally applied to multiclass classification in both simulations and real fMRI analyses.

A composite likelihood approach for spatially correlated survival data

PubMed Central

Paik, Jane; Ying, Zhiliang

2013-01-01

The aim of this paper is to provide a composite likelihood approach to handle spatially correlated survival data using pairwise joint distributions. With e-commerce data, a recent question of interest in marketing research has been to describe spatially clustered purchasing behavior and to assess whether geographic distance is the appropriate metric to describe purchasing dependence. We present a model for the dependence structure of time-to-event data subject to spatial dependence to characterize purchasing behavior from the motivating example from e-commerce data. We assume the Farlie-Gumbel-Morgenstern (FGM) distribution and then model the dependence parameter as a function of geographic and demographic pairwise distances. For estimation of the dependence parameters, we present pairwise composite likelihood equations. We prove that the resulting estimators exhibit key properties of consistency and asymptotic normality under certain regularity conditions in the increasing-domain framework of spatial asymptotic theory. PMID:24223450

Pairwise adaptive thermostats for improved accuracy and stability in dissipative particle dynamics

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

Leimkuhler, Benedict, E-mail: b.leimkuhler@ed.ac.uk; Shang, Xiaocheng, E-mail: x.shang@brown.edu

2016-11-01

We examine the formulation and numerical treatment of dissipative particle dynamics (DPD) and momentum-conserving molecular dynamics. We show that it is possible to improve both the accuracy and the stability of DPD by employing a pairwise adaptive Langevin thermostat that precisely matches the dynamical characteristics of DPD simulations (e.g., autocorrelation functions) while automatically correcting thermodynamic averages using a negative feedback loop. In the low friction regime, it is possible to replace DPD by a simpler momentum-conserving variant of the Nosé–Hoover–Langevin method based on thermostatting only pairwise interactions; we show that this method has an extra order of accuracy for anmore » important class of observables (a superconvergence result), while also allowing larger timesteps than alternatives. All the methods mentioned in the article are easily implemented. Numerical experiments are performed in both equilibrium and nonequilibrium settings; using Lees–Edwards boundary conditions to induce shear flow.« less

Pairwise Interaction Extended Point-Particle (PIEP) model for multiphase jets and sedimenting particles

NASA Astrophysics Data System (ADS)

Liu, Kai; Balachandar, S.

2017-11-01

We perform a series of Euler-Lagrange direct numerical simulations (DNS) for multiphase jets and sedimenting particles. The forces the flow exerts on the particles in these two-way coupled simulations are computed using the Basset-Bousinesq-Oseen (BBO) equations. These forces do not explicitly account for particle-particle interactions, even though such pairwise interactions induced by the perturbations from neighboring particles may be important especially when the particle volume fraction is high. Such effects have been largely unaddressed in the literature. Here, we implement the Pairwise Interaction Extended Point-Particle (PIEP) model to simulate the effect of neighboring particle pairs. A simple collision model is also applied to avoid unphysical overlapping of solid spherical particles. The simulation results indicate that the PIEP model provides a more elaborative and complicated movement of the dispersed phase (droplets and particles). Office of Naval Research (ONR) Multidisciplinary University Research Initiative (MURI) project N00014-16-1-2617.

Single-atom gold catalysis in the context of developments in parahydrogen-induced polarization.

PubMed

Corma, Avelino; Salnikov, Oleg G; Barskiy, Danila A; Kovtunov, Kirill V; Koptyug, Igor V

2015-05-04

A highly isolated monoatomic gold catalyst, with single gold atoms dispersed on multiwalled carbon nanotubes (MWCNTs), has been synthesized, characterized, and tested in heterogeneous hydrogenation of 1,3-butadiene and 1-butyne with parahydrogen to maximize the polarization level and the contribution of the pairwise hydrogen addition route. The Au/MWCNTs catalyst was found to be active and efficient in pairwise hydrogen addition and the estimated contributions from the pairwise hydrogen addition route are at least an order of magnitude higher than those for supported metal nanoparticle catalysts. Therefore, the use of the highly isolated monoatomic catalysts is very promising for production of hyperpolarized fluids that can be used for the significant enhancement of NMR signals. A mechanism of 1,3-butadiene hydrogenation with parahydrogen over the highly isolated monoatomic Au/MWCNTs catalyst is also proposed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Genetic interactions contribute less than additive effects to quantitative trait variation in yeast

PubMed Central

Bloom, Joshua S.; Kotenko, Iulia; Sadhu, Meru J.; Treusch, Sebastian; Albert, Frank W.; Kruglyak, Leonid

2015-01-01

Genetic mapping studies of quantitative traits typically focus on detecting loci that contribute additively to trait variation. Genetic interactions are often proposed as a contributing factor to trait variation, but the relative contribution of interactions to trait variation is a subject of debate. Here we use a very large cross between two yeast strains to accurately estimate the fraction of phenotypic variance due to pairwise QTL–QTL interactions for 20 quantitative traits. We find that this fraction is 9% on average, substantially less than the contribution of additive QTL (43%). Statistically significant QTL–QTL pairs typically have small individual effect sizes, but collectively explain 40% of the pairwise interaction variance. We show that pairwise interaction variance is largely explained by pairs of loci at least one of which has a significant additive effect. These results refine our understanding of the genetic architecture of quantitative traits and help guide future mapping studies. PMID:26537231

GetReal in network meta-analysis: a review of the methodology.

PubMed

Efthimiou, Orestis; Debray, Thomas P A; van Valkenhoef, Gert; Trelle, Sven; Panayidou, Klea; Moons, Karel G M; Reitsma, Johannes B; Shang, Aijing; Salanti, Georgia

2016-09-01

Pairwise meta-analysis is an established statistical tool for synthesizing evidence from multiple trials, but it is informative only about the relative efficacy of two specific interventions. The usefulness of pairwise meta-analysis is thus limited in real-life medical practice, where many competing interventions may be available for a certain condition and studies informing some of the pairwise comparisons may be lacking. This commonly encountered scenario has led to the development of network meta-analysis (NMA). In the last decade, several applications, methodological developments, and empirical studies in NMA have been published, and the area is thriving as its relevance to public health is increasingly recognized. This article presents a review of the relevant literature on NMA methodology aiming to pinpoint the developments that have appeared in the field. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

A composite likelihood approach for spatially correlated survival data.

PubMed

Paik, Jane; Ying, Zhiliang

2013-01-01

The aim of this paper is to provide a composite likelihood approach to handle spatially correlated survival data using pairwise joint distributions. With e-commerce data, a recent question of interest in marketing research has been to describe spatially clustered purchasing behavior and to assess whether geographic distance is the appropriate metric to describe purchasing dependence. We present a model for the dependence structure of time-to-event data subject to spatial dependence to characterize purchasing behavior from the motivating example from e-commerce data. We assume the Farlie-Gumbel-Morgenstern (FGM) distribution and then model the dependence parameter as a function of geographic and demographic pairwise distances. For estimation of the dependence parameters, we present pairwise composite likelihood equations. We prove that the resulting estimators exhibit key properties of consistency and asymptotic normality under certain regularity conditions in the increasing-domain framework of spatial asymptotic theory.

α-SNAP regulates dynamic, on-site assembly and calcium selectivity of Orai1 channels

PubMed Central

Li, Peiyao; Miao, Yong; Dani, Adish; Vig, Monika

2016-01-01

Orai1 forms a highly calcium-selective pore of the calcium release activated channel, and α-SNAP is necessary for its function. Here we show that α-SNAP regulates on-site assembly of Orai1 dimers into calcium-selective multimers. We find that Orai1 is a dimer in resting primary mouse embryonic fibroblasts but displays variable stoichiometry in the plasma membrane of store-depleted cells. Remarkably, α-SNAP depletion induces formation of higher-order Orai1 oligomers, which permeate significant levels of sodium via Orai1 channels. Sodium permeation in α-SNAP–deficient cells cannot be corrected by tethering multiple Stim1 domains to Orai1 C-terminal tail, demonstrating that α-SNAP regulates functional assembly and calcium selectivity of Orai1 multimers independently of Stim1 levels. Fluorescence nanoscopy reveals sustained coassociation of α-SNAP with Stim1 and Orai1, and α-SNAP–depleted cells show faster and less constrained mobility of Orai1 within ER-PM junctions, suggesting Orai1 and Stim1 coentrapment without stable contacts. Furthermore, α-SNAP depletion significantly reduces fluorescence resonance energy transfer between Stim1 and Orai1 N-terminus but not C-terminus. Taken together, these data reveal a unique role of α-SNAP in the on-site functional assembly of Orai1 subunits and suggest that this process may, in part, involve enabling crucial low-affinity interactions between Orai1 N-terminus and Stim1. PMID:27335124

Bacterium Escherichia coli- and phage P22-templated synthesis of semiconductor nanostructures

NASA Astrophysics Data System (ADS)

Shen, Liming

The properties of inorganic materials in the nanoscale are found to be size- and shape-dependent due to quantum confinement effects, and thereby nanomaterials possess properties very different from those of single molecules as well as those of bulk materials. Assembling monodispersed nanoparticles into highly ordered hierarchical architectures is expected to generate novel collective properties for potential applications in catalysis, energy, biomedicine, etc. The major challenge in the assembly of nanoparticles lies in the development of controllable synthetic strategies that enable the growth and assembly of nanoparticles with high selectivity and good controllability. Biological matter possesses robust and precisely ordered structures that exist in a large variety of shapes and sizes, providing an ideal platform for synthesizing high-performance nanostructures. The primary goal of this thesis work has been to develop rational synthetic strategies for high-performance nanostructured materials using biological templates, which are difficult to achieve through traditional chemical synthetic methods. These approaches can serve as general bio-inspired approaches for synthesizing nanoparticle assemblies with desired components and architectures. CdS- and TiO2-binding peptides have been identified using phage display biopanning technique and the mechanism behind the specific affinity between the selected peptides and inorganic substrates are analyzed. The ZnS- and CdS-binding peptides, identified by the phage display biopanning, are utilized for the selective nucleation and growth of sulfides over self-assembled genetically engineered P22 coat proteins, resulting in ordered nanostructures of sulfide nanocrystal assemblies. The synthetic strategy can be extended to the fabrication of a variety of other nanostructures. A simple sonochemical route for the synthesis and assembly of CdS nanostructures with high yield under ambient conditions has been developed by exploiting the chemical characteristics and structure of permeabilized E. coli bacteria. The crystal phase, morphology, micro/nanostructure, optical absorption, and photocatalytic properties of the CdS nanostructures are tailored over a wide range by merely changing the synthetic conditions. Photoanodes fabricated using the nanoporous hollow CdS microrods exhibit excellent performance for the photocatalytic hydrogen production. This facile approach has been extended to the synthesis and assembly of other semiconducting sulfides, including PbS, ZnS, and HgS.

Viral genome structures, charge, and sequences are optimal for capsid assembly

NASA Astrophysics Data System (ADS)

Hagan, Michael

2014-03-01

For many viruses, the spontaneous assembly of a capsid shell around the nu-cleic acid (NA) genome is an essential step in the viral life cycle. Capsid formation is a multicomponent, out-of-equilibrium assembly process for which kinetic effects and thermodynamic constraints compete to determine the outcome. Understand-ing how viral components drive highly efficient assembly under these constraints could promote biomedical efforts to block viral propagation, and would elucidate the factors controlling assembly in a wide range of systems containing proteins and polyelectrolytes. This talk will describe coarse-grained models of capsid proteins and NAs with which we investigate the dynamics and thermodynamics of virus assembly. In con-trast to recent theoretical models, we find that capsids spontaneously `overcharge' that is, the NA length which is kinetically and thermodynamically optimal possess-es a negative charge greater than the positive charge of the capsid. When applied to specific virus capsids, the calculated optimal NA lengths closely correspond to the natural viral genome lengths. These results suggest that the features included in this model (i.e. electrostatics, excluded volume, and NA tertiary structure) play key roles in determining assembly thermodynamics and consequently exert selec-tive pressure on viral evolution. I will then discuss mechanisms by which se-quence-specific interactions between NAs and capsid proteins promote selective encapsidation of the viral genome. This work was supported by NIH R01GM108021 and the Brandeis MRSEC NSF-MRSEC-0820492.

The icosahedral RNA virus as a grotto: organizing the genome into stalagmites and stalactites.

PubMed

Harvey, Stephen C; Zeng, Yingying; Heitsch, Christine E

2013-03-01

There are two important problems in the assembly of small, icosahedral RNA viruses. First, how does the capsid protein select the viral RNA for packaging, when there are so many other candidate RNA molecules available? Second, what is the mechanism of assembly? With regard to the first question, there are a number of cases where a particular RNA sequence or structure--often one or more stem-loops--either promotes assembly or is required for assembly, but there are others where specific packaging signals are apparently not required. With regard to the assembly pathway, in those cases where stem-loops are involved, the first step is generally believed to be binding of the capsid proteins to these "fingers" of the RNA secondary structure. In the mature virus, the core of the RNA would then occupy the center of the viral particle, and the stem-loops would reach outward, towards the capsid, like stalagmites reaching up from the floor of a grotto towards the ceiling. Those viruses whose assembly does not depend on protein binding to stem-loops could have a different structure, with the core of the RNA lying just under the capsid, and the fingers reaching down into the interior of the virus, like stalactites. We review the literature on these alternative structures, focusing on RNA selectivity and the assembly mechanism, and we propose experiments aimed at determining, in a given virus, which of the two structures actually occurs.

Comparison of potential method in analytic hierarchy process for multi-attribute of catering service companies

NASA Astrophysics Data System (ADS)

Mamat, Siti Salwana; Ahmad, Tahir; Awang, Siti Rahmah

2017-08-01

Analytic Hierarchy Process (AHP) is a method used in structuring, measuring and synthesizing criteria, in particular ranking of multiple criteria in decision making problems. On the other hand, Potential Method is a ranking procedure in which utilizes preference graph ς (V, A). Two nodes are adjacent if they are compared in a pairwise comparison whereby the assigned arc is oriented towards the more preferred node. In this paper Potential Method is used to solve problem on a catering service selection. The comparison of result by using Potential method is made with Extent Analysis. The Potential Method is found to produce the same rank as Extent Analysis in AHP.

SCHIP: Statistics for Chromosome Interphase Positioning Based on Interchange Data

NASA Technical Reports Server (NTRS)

Vives, Sergi; Loucas, Bradford; Vazquez, Mariel; Brenner, David J.; Sachs, Rainer K.; Hlatky, Lynn; Cornforth, Michael; Arsuaga, Javier

2005-01-01

he position of chromosomes in the interphase nucleus is believed to be associated with a number of biological processes. Here, we present a web-based application that helps analyze the relative position of chromosomes during interphase in human cells, based on observed radiogenic chromosome aberrations. The inputs of the program are a table of yields of pairwise chromosome interchanges and a proposed chromosome geometric cluster. Each can either be uploaded or selected from provided datasets. The main outputs are P-values for the proposed chromosome clusters. SCHIP is designed to be used by a number of scientific communities interested in nuclear architecture, including cancer and cell biologists, radiation biologists and mathematical/computational biologists.

Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes.

PubMed

Papudeshi, Bhavya; Haggerty, J Matthew; Doane, Michael; Morris, Megan M; Walsh, Kevin; Beattie, Douglas T; Pande, Dnyanada; Zaeri, Parisa; Silva, Genivaldo G Z; Thompson, Fabiano; Edwards, Robert A; Dinsdale, Elizabeth A

2017-11-28

Microbiome/host interactions describe characteristics that affect the host's health. Shotgun metagenomics includes sequencing a random subset of the microbiome to analyze its taxonomic and metabolic potential. Reconstruction of DNA fragments into genomes from metagenomes (called metagenome-assembled genomes) assigns unknown fragments to taxa/function and facilitates discovery of novel organisms. Genome reconstruction incorporates sequence assembly and sorting of assembled sequences into bins, characteristic of a genome. However, the microbial community composition, including taxonomic and phylogenetic diversity may influence genome reconstruction. We determine the optimal reconstruction method for four microbiome projects that had variable sequencing platforms (IonTorrent and Illumina), diversity (high or low), and environment (coral reefs and kelp forests), using a set of parameters to select for optimal assembly and binning tools. We tested the effects of the assembly and binning processes on population genome reconstruction using 105 marine metagenomes from 4 projects. Reconstructed genomes were obtained from each project using 3 assemblers (IDBA, MetaVelvet, and SPAdes) and 2 binning tools (GroopM and MetaBat). We assessed the efficiency of assemblers using statistics that including contig continuity and contig chimerism and the effectiveness of binning tools using genome completeness and taxonomic identification. We concluded that SPAdes, assembled more contigs (143,718 ± 124 contigs) of longer length (N50 = 1632 ± 108 bp), and incorporated the most sequences (sequences-assembled = 19.65%). The microbial richness and evenness were maintained across the assembly, suggesting low contig chimeras. SPAdes assembly was responsive to the biological and technological variations within the project, compared with other assemblers. Among binning tools, we conclude that MetaBat produced bins with less variation in GC content (average standard deviation: 1.49), low species richness (4.91 ± 0.66), and higher genome completeness (40.92 ± 1.75) across all projects. MetaBat extracted 115 bins from the 4 projects of which 66 bins were identified as reconstructed metagenome-assembled genomes with sequences belonging to a specific genus. We identified 13 novel genomes, some of which were 100% complete, but show low similarity to genomes within databases. In conclusion, we present a set of biologically relevant parameters for evaluation to select for optimal assembly and binning tools. For the tools we tested, SPAdes assembler and MetaBat binning tools reconstructed quality metagenome-assembled genomes for the four projects. We also conclude that metagenomes from microbial communities that have high coverage of phylogenetically distinct, and low taxonomic diversity results in highest quality metagenome-assembled genomes.

Should We Stop Developing Heuristics and Only Rely on Mixed Integer Programming Solvers in Automated Test Assembly? A Rejoinder to van der Linden and Li (2016).

PubMed

Chen, Pei-Hua

2017-05-01

This rejoinder responds to the commentary by van der Linden and Li entiled "Comment on Three-Element Item Selection Procedures for Multiple Forms Assembly: An Item Matching Approach" on the article "Three-Element Item Selection Procedures for Multiple Forms Assembly: An Item Matching Approach" by Chen. Van der Linden and Li made a strong statement calling for the cessation of test assembly heuristics development, and instead encouraged embracing mixed integer programming (MIP). This article points out the nondeterministic polynomial (NP)-hard nature of MIP problems and how solutions found using heuristics could be useful in an MIP context. Although van der Linden and Li provided several practical examples of test assembly supporting their view, the examples ignore the cases in which a slight change of constraints or item pool data might mean it would not be possible to obtain solutions as quickly as before. The article illustrates the use of heuristic solutions to improve both the performance of MIP solvers and the quality of solutions. Additional responses to the commentary by van der Linden and Li are included.

Towards automatic planning for manufacturing generative processes

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

CALTON,TERRI L.

2000-05-24

Generative process planning describes methods process engineers use to modify manufacturing/process plans after designs are complete. A completed design may be the result from the introduction of a new product based on an old design, an assembly upgrade, or modified product designs used for a family of similar products. An engineer designs an assembly and then creates plans capturing manufacturing processes, including assembly sequences, component joining methods, part costs, labor costs, etc. When new products originate as a result of an upgrade, component geometry may change, and/or additional components and subassemblies may be added to or are omitted from themore » original design. As a result process engineers are forced to create new plans. This is further complicated by the fact that the process engineer is forced to manually generate these plans for each product upgrade. To generate new assembly plans for product upgrades, engineers must manually re-specify the manufacturing plan selection criteria and re-run the planners. To remedy this problem, special-purpose assembly planning algorithms have been developed to automatically recognize design modifications and automatically apply previously defined manufacturing plan selection criteria and constraints.« less

Two-component gelator isomers with different combination of amine and acid: Helical/non-helical morphology and selective adsorption of dyes.

PubMed

Han, Xiaoyu; Liu, Jiahui; Zhao, Chaoyue; Zhang, Bao; Xu, Xiufang; Song, Jian

2018-09-01

Hydrogels induced by two-component gelator isomers based on the different amine/acid interactions were investigated. Scanning electron microscopy and atomic force microscopy images of the xerogel obtained from the two hydrogels revealed different assembly morphologies. While left-handed helical fibers were observed for the amine-acid based xerogel, acid-amine underwent self-assembly to afford smooth fibers. Fourier transform infrared spectroscopy, fluorescence, and X-ray diffraction measurements combined with density functional theory calculations suggested that the different self-assembly patterns of gelators resulted in opposite electric charges on the xerogel surfaces, in line with Zeta potential measurements. Based on these opposite charges resulting from their different self-assemblies, both xerogels demonstrated efficient dye adsorption abilities with different selectivities. Interestingly, the adsorption performance was not influenced by the salt in the dye solution. Furthermore, the xerogels still showed high dye adsorption efficiency after four cycles. These results provide a two-component hydrogel method for the purification of dye-polluted water systems, while also paving the way for future design of functionalized supramolecular self-assembly systems. Copyright © 2018 Elsevier Inc. All rights reserved.

Extended Linkage Disequilibrium Surrounding the Hemoglobin E Variant Due to Malarial Selection

PubMed Central

Ohashi, Jun ; Naka, Izumi ; Patarapotikul, Jintana ; Hananantachai, Hathairad ; Brittenham, Gary ; Looareesuwan, Sornchai ; Clark, Andrew G. ; Tokunaga, Katsushi 

2004-01-01

The hemoglobin E variant (HbE; β26Glu→Lys) is concentrated in parts of Southeast Asia where malaria is endemic, and HbE carrier status has been shown to confer some protection against Plasmodium falciparum malaria. To examine the effect of natural selection on the pattern of linkage disequilibrium (LD) and to infer the evolutionary history of the HbE variant, we analyzed biallelic markers surrounding the HbE variant in a Thai population. Pairwise LD analysis of HbE and 43 surrounding biallelic markers revealed LD of HbE extending beyond 100 kb, whereas no LD was observed between non-HbE variants and the same markers. The inferred haplotype network suggests a single origin of the HbE variant in the Thai population. Forward-in-time computer simulations under a variety of selection models indicate that the HbE variant arose 1,240–4,440 years ago. These results support the conjecture that the HbE mutation occurred recently, and the allele frequency has increased rapidly. Our study provides another clear demonstration that a high-resolution LD map across the human genome can detect recent variants that have been subjected to positive selection. PMID:15114532

Extended linkage disequilibrium surrounding the hemoglobin E variant due to malarial selection.

PubMed

Ohashi, Jun; Naka, Izumi; Patarapotikul, Jintana; Hananantachai, Hathairad; Brittenham, Gary; Looareesuwan, Sornchai; Clark, Andrew G; Tokunaga, Katsushi

2004-06-01

The hemoglobin E variant (HbE; ( beta )26Glu-->Lys) is concentrated in parts of Southeast Asia where malaria is endemic, and HbE carrier status has been shown to confer some protection against Plasmodium falciparum malaria. To examine the effect of natural selection on the pattern of linkage disequilibrium (LD) and to infer the evolutionary history of the HbE variant, we analyzed biallelic markers surrounding the HbE variant in a Thai population. Pairwise LD analysis of HbE and 43 surrounding biallelic markers revealed LD of HbE extending beyond 100 kb, whereas no LD was observed between non-HbE variants and the same markers. The inferred haplotype network suggests a single origin of the HbE variant in the Thai population. Forward-in-time computer simulations under a variety of selection models indicate that the HbE variant arose 1,240-4,440 years ago. These results support the conjecture that the HbE mutation occurred recently, and the allele frequency has increased rapidly. Our study provides another clear demonstration that a high-resolution LD map across the human genome can detect recent variants that have been subjected to positive selection.

An Integrated model for Product Quality Development—A case study on Quality functions deployment and AHP based approach

NASA Astrophysics Data System (ADS)

Maitra, Subrata; Banerjee, Debamalya

2010-10-01

Present article is based on application of the product quality and improvement of design related with the nature of failure of machineries and plant operational problems of an industrial blower fan Company. The project aims at developing the product on the basis of standardized production parameters for selling its products in the market. Special attention is also being paid to the blower fans which have been ordered directly by the customer on the basis of installed capacity of air to be provided by the fan. Application of quality function deployment is primarily a customer oriented approach. Proposed model of QFD integrated with AHP to select and rank the decision criterions on the commercial and technical factors and the measurement of the decision parameters for selection of best product in the compettitive environment. The present AHP-QFD model justifies the selection of a blower fan with the help of the group of experts' opinion by pairwise comparison of the customer's and ergonomy based technical design requirements. The steps invoved in implementation of the QFD—AHP and selection of weighted criterion may be helpful for all similar purpose industries maintaining cost and utility for competitive product.

Selective sweep at the Drosophila melanogaster Suppressor of Hairless locus and its association with the In(2L)t inversion polymorphism.

PubMed Central

Depaulis, F; Brazier, L; Veuille, M

1999-01-01

The hitchhiking model of population genetics predicts that an allele favored by Darwinian selection can replace haplotypes from the same locus previously established at a neutral mutation-drift equilibrium. This process, known as "selective sweep," was studied by comparing molecular variation between the polymorphic In(2L)t inversion and the standard chromosome. Sequence variation was recorded at the Suppressor of Hairless (Su[H]) gene in an African population of Drosophila melanogaster. We found 47 nucleotide polymorphisms among 20 sequences of 1.2 kb. Neutrality tests were nonsignificant at the nucleotide level. However, these sites were strongly associated, because 290 out of 741 observed pairwise combinations between them were in significant linkage disequilibrium. We found only seven haplotypes, two occurring in the 9 In(2L)t chromosomes, and five in the 11 standard chromosomes, with no shared haplotype. Two haplotypes, one in each chromosome arrangement, made up two-thirds of the sample. This low haplotype diversity departed from neutrality in a haplotype test. This pattern supports a selective sweep hypothesis for the Su(H) chromosome region. PMID:10388820

Self-assembling multidomain peptide fibers with aromatic cores

USDA-ARS?s Scientific Manuscript database

Self-assembling multidomain peptides have been shown to have desirable properties, such as the ability to form hydrogels that rapidly recover following shear-thinning and the potential to be tailored by amino acid selection to vary their elasticity and encapsulate and deliver proteins and cells. Her...

Ultrathin self-assembled anionic polymer membranes for superfast size-selective separation

NASA Astrophysics Data System (ADS)

Deng, Chao; Zhang, Qiu Gen; Han, Guang Lu; Gong, Yi; Zhu, Ai Mei; Liu, Qing Lin

2013-10-01

Nanoporous membranes with superior separation performance have become more crucial with increasing concerns in functional nanomaterials. Here novel ultrahigh permeable nanoporous membranes have been fabricated on macroporous supports by self-assembly of anionic polymer on copper hydroxide nanostrand templates in organic solution. This facile approach has a great potential for the fabrication of ultrathin anionic polymer membranes as a general method. The as-fabricated self-assembled membranes have a mean pore size of 5-12 nm and an adjustable thickness as low as 85 nm. They allow superfast permeation of water, and exhibit excellent size-selective separation properties and good fouling resistance for negatively-charged solutes during filtration. The 85 nm thick membrane has an ultrahigh water flux (3306 l m-2 h-1 bar-1) that is an order of magnitude larger than commercial membranes, and can highly efficiently separate 5 and 15 nm gold nanoparticles from their mixtures. The newly developed nanoporous membranes have a wide application in separation and purification of biomacromolecules and nanoparticles.Nanoporous membranes with superior separation performance have become more crucial with increasing concerns in functional nanomaterials. Here novel ultrahigh permeable nanoporous membranes have been fabricated on macroporous supports by self-assembly of anionic polymer on copper hydroxide nanostrand templates in organic solution. This facile approach has a great potential for the fabrication of ultrathin anionic polymer membranes as a general method. The as-fabricated self-assembled membranes have a mean pore size of 5-12 nm and an adjustable thickness as low as 85 nm. They allow superfast permeation of water, and exhibit excellent size-selective separation properties and good fouling resistance for negatively-charged solutes during filtration. The 85 nm thick membrane has an ultrahigh water flux (3306 l m-2 h-1 bar-1) that is an order of magnitude larger than commercial membranes, and can highly efficiently separate 5 and 15 nm gold nanoparticles from their mixtures. The newly developed nanoporous membranes have a wide application in separation and purification of biomacromolecules and nanoparticles. Electronic supplementary information (ESI) available: Synthesis and characterization of SPEK-C; effect of the sulfonation degree on membrane formation; structure and properties of the self-assembled membranes; separation of cyt.c by the self-assembled membranes; size-selective separation of gold nanoparticles by the self-assembled membranes; comparison with commercial flat sheet ultrafiltration membranes. See DOI: 10.1039/c3nr03362g

Three-dimensional analysis of the uniqueness of the anterior dentition in orthodontically treated patients and twins.

PubMed

Franco, A; Willems, G; Souza, P H C; Tanaka, O M; Coucke, W; Thevissen, P

2017-04-01

Dental uniqueness can be proven if no perfect match in pair-wise morphological comparisons of human dentitions is detected. Establishing these comparisons in a worldwide random population is practically unfeasible due to the need for a large and representative sample size. Sample stratification is an option to reduce sample size. The present study investigated the uniqueness of the human dentition in randomly selected subjects (Group 1), orthodontically treated patients (Group 2), twins (Group 3), and orthodontically treated twins (Group 4) in comparison with a threshold control sample of identical dentitions (Group 5). The samples consisted of digital cast files (DCF) obtained through extraoral 3D scanning. A total of 2.013 pair-wise morphological comparisons were performed (Group 1 n=110, Group 2 n=1.711, Group 3 n=172, Group 4 n=10, Group 5 n=10) with Geomagic Studio ® (3D Systems ® , Rock Hill, SC, USA) software package. Comparisons within groups were performed quantifying the morphological differences between DCF in Euclidean distances. Comparisons between groups were established applying One-way ANOVA. To ensure fair comparisons a post-hoc Power Analysis was performed. ROC analysis was applied to distinguish unique from non-unique dentures. Identical DCF were not detected within the experimental groups (from 1 to 4). The most similar DCF had Euclidian distance of 5.19mm in Group 1, 2.06mm in Group 2, 2.03mm in Group 3, and 1.88mm in Group 4. Groups 2 and 3 were statistically different from Group 5 (p<0.05). Statistically significant difference between Group 4 and 5 revealed to be possible including more pair-wise comparisons in both groups. The ROC analysis revealed sensitivity rate of 80% and specificity between 66.7% and 81.6%. Evidence to sustain the uniqueness of the human dentition in random and stratified populations was observed in the present study. Further studies testing the influence of the quantity of tooth material on morphological difference between dentitions and its impact on uniqueness remain necessary. Copyright © 2017 Elsevier B.V. All rights reserved.

A conditional Granger causality model approach for group analysis in functional MRI

PubMed Central

Zhou, Zhenyu; Wang, Xunheng; Klahr, Nelson J.; Liu, Wei; Arias, Diana; Liu, Hongzhi; von Deneen, Karen M.; Wen, Ying; Lu, Zuhong; Xu, Dongrong; Liu, Yijun

2011-01-01

Granger causality model (GCM) derived from multivariate vector autoregressive models of data has been employed for identifying effective connectivity in the human brain with functional MR imaging (fMRI) and to reveal complex temporal and spatial dynamics underlying a variety of cognitive processes. In the most recent fMRI effective connectivity measures, pairwise GCM has commonly been applied based on single voxel values or average values from special brain areas at the group level. Although a few novel conditional GCM methods have been proposed to quantify the connections between brain areas, our study is the first to propose a viable standardized approach for group analysis of an fMRI data with GCM. To compare the effectiveness of our approach with traditional pairwise GCM models, we applied a well-established conditional GCM to pre-selected time series of brain regions resulting from general linear model (GLM) and group spatial kernel independent component analysis (ICA) of an fMRI dataset in the temporal domain. Datasets consisting of one task-related and one resting-state fMRI were used to investigate connections among brain areas with the conditional GCM method. With the GLM detected brain activation regions in the emotion related cortex during the block design paradigm, the conditional GCM method was proposed to study the causality of the habituation between the left amygdala and pregenual cingulate cortex during emotion processing. For the resting-state dataset, it is possible to calculate not only the effective connectivity between networks but also the heterogeneity within a single network. Our results have further shown a particular interacting pattern of default mode network (DMN) that can be characterized as both afferent and efferent influences on the medial prefrontal cortex (mPFC) and posterior cingulate cortex (PCC). These results suggest that the conditional GCM approach based on a linear multivariate vector autoregressive (MVAR) model can achieve greater accuracy in detecting network connectivity than the widely used pairwise GCM, and this group analysis methodology can be quite useful to extend the information obtainable in fMRI. PMID:21232892

Proton-Fueled, Reversible DNA Hybridization Chain Assembly for pH Sensing and Imaging.

PubMed

Liu, Lan; Liu, Jin-Wen; Huang, Zhi-Mei; Wu, Han; Li, Na; Tang, Li-Juan; Jiang, Jian-Hui

2017-07-05

Design of DNA self-assembly with reversible responsiveness to external stimuli is of great interest for diverse applications. We for the first time develop a pH-responsive, fully reversible hybridization chain reaction (HCR) assembly that allows sensitive sensing and imaging of pH in living cells. Our design relies on the triplex forming sequences that form DNA triplex with toehold regions under acidic conditions and then induce a cascade of strand displacement and DNA assembly. The HCR assembly has shown dynamic responses in physiological pH ranges with excellent reversibility and demonstrated the potential for in vitro detection and live-cell imaging of pH. Moreover, this method affords HCR assemblies with highly localized fluorescence responses, offering advantages of improving sensitivity and better selectivity. The proton-fueled, reversible HCR assembly may provide a useful approach for pH-related cell biology study and disease diagnostics.

Pyridoxamine driven selective turn-off detection of picric acid using glutathione stabilized fluorescent copper nanoclusters and its applications with chemically modified cellulose strips.

PubMed

Patel, Ravi; Bothra, Shilpa; Kumar, Rajender; Crisponi, Guido; Sahoo, Suban K

2018-04-15

The present work reports the interaction of various vitamin B 6 cofactors with the red emitting glutathione stabilized copper nanoclusters (GSH-CuNCs). Addition of pyridoxamine (PM) resulted a new turn-on band at 410nm due to the possible adsorption over the surface of GSH-CuNCs. The nano-assembly PM-GSH-CuNCs was applied for the selective detection of nitro-aromatic compounds. Upon addition of picric acid (PA), the fluorescence of PM-GSH-CuNCs was selectively quenched at 410nm and ~ 625nm among the other tested nitro-aromatic compounds. With a linearity range from 9.9μM to 43μM, the concentration of PA can be detected down to 2.74μM. The high selectivity exhibited by the nano-assembly allows to detect PA in real samples like tap water, river water and matchstick. Advantageously, the nano-assembly PM-GSH-CuNCs was chemically adsorbed over the cellulosic strips and applied for the naked-eye detection of PA down to 1μM. Copyright © 2017 Elsevier B.V. All rights reserved.

Spitzer Imaging of Planck-Herschel Dusty Proto-Clusters at z=2-3

NASA Astrophysics Data System (ADS)

Cooray, Asantha; Ma, Jingzhe; Greenslade, Joshua; Kubo, Mariko; Nayyeri, Hooshang; Clements, David; Cheng, Tai-An

2018-05-01

We have recently introduced a new proto-cluster selection technique by combing Herschel/SPIRE imaging data and Planck/HFIk all-sky survey point source catalog. These sources are identified as Planck point sources with clumps of Herschel source over-densities with far-IR colors comparable to z=0 ULIRGS redshifted to z=2 to 3. The selection is sensitive to dusty starbursts and obscured QSOs and we have recovered couple of the known proto-clusters and close to 30 new proto-clusters. The candidate proto-clusters selected from this technique have far-IR flux densities several times higher than those that are optically selected, such as using LBG selection, implying that the member galaxies are in a special phase of heightened dusty starburst and dusty QSO activity. This far-IR luminous phase may be short but likely to be necessary piece to understand the whole stellar mass assembly history of clusters. Moreover, our photo-clusters are missed in optical selections, suggesting that optically selected proto-clusters alone do not provide adequate statistics and a comparison of the far-IR and optical selected clusters may reveal the importance of the dusty stellar mass assembly. Here, we propose IRAC observations of six of the highest priority new proto-clusters, to establish the validity of the technique and to determine the total stellar mass through SED models. For a modest observing time the science program will have a substantial impact on an upcoming science topic in cosmology with implications for observations with JWST and WFIRST to understand the mass assembly in the universe.

One-dimensional poly(L-lysine)-block-poly(L-threonine) assemblies exhibit potent anticancer activity by enhancing membranolysis.

PubMed

Chen, Yu-Fon; Shiau, Ai-Li; Chang, Sue-Joan; Fan, Nai-Shin; Wang, Chung-Teng; Wu, Chao-Liang; Jan, Jeng-Shiung

2017-06-01

Herein, we report the oncolytic activity of cationic, one-dimensional (1D) fibril assemblies formed from coil-sheet poly(L-lysine)-block-poly(L-threonine) (PLL-b-PLT) block copolypeptides for cancer therapy. The 1D fibril assemblies can efficiently interact with negatively charged cellular and mitochondrial membranes via electrostatic interactions, leading to necrosis via membrane lysis and apoptosis via the mitochondria-lytic effect. The concept is analogous to that of 1D drug carriers that exhibit enhanced cell penetration. In comparison to free PLL chains, PLL-b-PLT fibril assemblies exhibit selective cytotoxicity toward cancer cells, low hemolysis activity, enhanced membranolytic activity, and a different apoptosis pathway, which may be due to differences in the peptide-membrane interactions. Antitumor studies using a metastatic LL2 lung carcinoma model indicate that the fibril assemblies significantly inhibited tumor growth, improved survival in tumor-bearing mice and suppressed lung metastasis without obvious body weight loss. An additive efficacy was also observed for treatment with both PLL-b-PLT and cisplatin. These results support the feasibility of using 1D fibril assemblies as potential apoptotic anticancer therapeutics. We report that cationic, one-dimensional (1D) fibril assemblies formed by coil-sheet poly(L-lysine)-block-poly(L-threonine) (PLL-b-PLT) block copolypeptides exhibited potent anticancer activity by enhancing membranolysis. The 1D fibril assemblies can efficiently interact with negatively charged cellular and mitochondrial membranes via electrostatic interactions, leading to necrosis via membrane lysis and apoptosis via mitochondria-lytic effect. Moreover, the fibril assemblies exhibited low hemolytic activity and selective cytotoxicity toward cancer cell, which is advantageous as compared to PLL and most antimicrobial/anticancerous peptides. This study provides a new concept of using cationic, 1D fibril assemblies for cancer therapy. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Quantum Spin Dynamics with Pairwise-Tunable, Long-Range Interactions

DTIC Science & Technology

2016-08-05

rection of the arrows. Dashed (dotted) lines mark the NNN hopping terms (coefficients ±t2). NNNN long -range hopping along curved lines are included to...Quantum spin dynamics with pairwise-tunable, long -range interactions C.-L. Hunga,b,1,2, Alejandro González-Tudelac,1,2, J. Ignacio Ciracc, and H. J...atoms) that interact by way of a variety of processes, such as atomic collisions. Such pro- cesses typically lead to short -range, nearest-neighbor

Exploring the roles of cannot-link constraint in community detection via Multi-variance Mixed Gaussian Generative Model.

PubMed

Yang, Liang; Ge, Meng; Jin, Di; He, Dongxiao; Fu, Huazhu; Wang, Jing; Cao, Xiaochun

2017-01-01

Due to the demand for performance improvement and the existence of prior information, semi-supervised community detection with pairwise constraints becomes a hot topic. Most existing methods have been successfully encoding the must-link constraints, but neglect the opposite ones, i.e., the cannot-link constraints, which can force the exclusion between nodes. In this paper, we are interested in understanding the role of cannot-link constraints and effectively encoding pairwise constraints. Towards these goals, we define an integral generative process jointly considering the network topology, must-link and cannot-link constraints. We propose to characterize this process as a Multi-variance Mixed Gaussian Generative (MMGG) Model to address diverse degrees of confidences that exist in network topology and pairwise constraints and formulate it as a weighted nonnegative matrix factorization problem. The experiments on artificial and real-world networks not only illustrate the superiority of our proposed MMGG, but also, most importantly, reveal the roles of pairwise constraints. That is, though the must-link is more important than cannot-link when either of them is available, both must-link and cannot-link are equally important when both of them are available. To the best of our knowledge, this is the first work on discovering and exploring the importance of cannot-link constraints in semi-supervised community detection.

Exploring the roles of cannot-link constraint in community detection via Multi-variance Mixed Gaussian Generative Model

PubMed Central

Ge, Meng; Jin, Di; He, Dongxiao; Fu, Huazhu; Wang, Jing; Cao, Xiaochun

2017-01-01

Due to the demand for performance improvement and the existence of prior information, semi-supervised community detection with pairwise constraints becomes a hot topic. Most existing methods have been successfully encoding the must-link constraints, but neglect the opposite ones, i.e., the cannot-link constraints, which can force the exclusion between nodes. In this paper, we are interested in understanding the role of cannot-link constraints and effectively encoding pairwise constraints. Towards these goals, we define an integral generative process jointly considering the network topology, must-link and cannot-link constraints. We propose to characterize this process as a Multi-variance Mixed Gaussian Generative (MMGG) Model to address diverse degrees of confidences that exist in network topology and pairwise constraints and formulate it as a weighted nonnegative matrix factorization problem. The experiments on artificial and real-world networks not only illustrate the superiority of our proposed MMGG, but also, most importantly, reveal the roles of pairwise constraints. That is, though the must-link is more important than cannot-link when either of them is available, both must-link and cannot-link are equally important when both of them are available. To the best of our knowledge, this is the first work on discovering and exploring the importance of cannot-link constraints in semi-supervised community detection. PMID:28678864

POEM: Identifying Joint Additive Effects on Regulatory Circuits.

PubMed

Botzman, Maya; Nachshon, Aharon; Brodt, Avital; Gat-Viks, Irit

2016-01-01

Expression Quantitative Trait Locus (eQTL) mapping tackles the problem of identifying variation in DNA sequence that have an effect on the transcriptional regulatory network. Major computational efforts are aimed at characterizing the joint effects of several eQTLs acting in concert to govern the expression of the same genes. Yet, progress toward a comprehensive prediction of such joint effects is limited. For example, existing eQTL methods commonly discover interacting loci affecting the expression levels of a module of co-regulated genes. Such "modularization" approaches, however, are focused on epistatic relations and thus have limited utility for the case of additive (non-epistatic) effects. Here we present POEM (Pairwise effect On Expression Modules), a methodology for identifying pairwise eQTL effects on gene modules. POEM is specifically designed to achieve high performance in the case of additive joint effects. We applied POEM to transcription profiles measured in bone marrow-derived dendritic cells across a population of genotyped mice. Our study reveals widespread additive, trans-acting pairwise effects on gene modules, characterizes their organizational principles, and highlights high-order interconnections between modules within the immune signaling network. These analyses elucidate the central role of additive pairwise effect in regulatory circuits, and provide computational tools for future investigations into the interplay between eQTLs. The software described in this article is available at csgi.tau.ac.il/POEM/.

POEM: Identifying Joint Additive Effects on Regulatory Circuits

PubMed Central

Botzman, Maya; Nachshon, Aharon; Brodt, Avital; Gat-Viks, Irit

2016-01-01

Motivation: Expression Quantitative Trait Locus (eQTL) mapping tackles the problem of identifying variation in DNA sequence that have an effect on the transcriptional regulatory network. Major computational efforts are aimed at characterizing the joint effects of several eQTLs acting in concert to govern the expression of the same genes. Yet, progress toward a comprehensive prediction of such joint effects is limited. For example, existing eQTL methods commonly discover interacting loci affecting the expression levels of a module of co-regulated genes. Such “modularization” approaches, however, are focused on epistatic relations and thus have limited utility for the case of additive (non-epistatic) effects. Results: Here we present POEM (Pairwise effect On Expression Modules), a methodology for identifying pairwise eQTL effects on gene modules. POEM is specifically designed to achieve high performance in the case of additive joint effects. We applied POEM to transcription profiles measured in bone marrow-derived dendritic cells across a population of genotyped mice. Our study reveals widespread additive, trans-acting pairwise effects on gene modules, characterizes their organizational principles, and highlights high-order interconnections between modules within the immune signaling network. These analyses elucidate the central role of additive pairwise effect in regulatory circuits, and provide computational tools for future investigations into the interplay between eQTLs. Availability: The software described in this article is available at csgi.tau.ac.il/POEM/. PMID:27148351

Pilot Overmyer looks over food selections and experiments with beverage

NASA Technical Reports Server (NTRS)

1982-01-01

Pilot Overmyer, using beverage container and drinking straw secured in meal tray assembly (ASSY), experiments with microgravity chararcteristics of liquid on middeck in front of forward lockers. Overmyer also looks over packages of food attached to middeck lockers in meal tray assemblies. Carry-on food warmer appears overhead and other meal tray assemblies, personal hygiene mirror assy, personal hygiene kit, and portrait of G.W.S. Abbey, JSC's Director of Flight Operations, appear on lockers.

CAPRRESI: Chimera Assembly by Plasmid Recovery and Restriction Enzyme Site Insertion.

PubMed

Santillán, Orlando; Ramírez-Romero, Miguel A; Dávila, Guillermo

2017-06-25

Here, we present chimera assembly by plasmid recovery and restriction enzyme site insertion (CAPRRESI). CAPRRESI benefits from many strengths of the original plasmid recovery method and introduces restriction enzyme digestion to ease DNA ligation reactions (required for chimera assembly). For this protocol, users clone wildtype genes into the same plasmid (pUC18 or pUC19). After the in silico selection of amino acid sequence regions where chimeras should be assembled, users obtain all the synonym DNA sequences that encode them. Ad hoc Perl scripts enable users to determine all synonym DNA sequences. After this step, another Perl script searches for restriction enzyme sites on all synonym DNA sequences. This in silico analysis is also performed using the ampicillin resistance gene (ampR) found on pUC18/19 plasmids. Users design oligonucleotides inside synonym regions to disrupt wildtype and ampR genes by PCR. After obtaining and purifying complementary DNA fragments, restriction enzyme digestion is accomplished. Chimera assembly is achieved by ligating appropriate complementary DNA fragments. pUC18/19 vectors are selected for CAPRRESI because they offer technical advantages, such as small size (2,686 base pairs), high copy number, advantageous sequencing reaction features, and commercial availability. The usage of restriction enzymes for chimera assembly eliminates the need for DNA polymerases yielding blunt-ended products. CAPRRESI is a fast and low-cost method for fusing protein-coding genes.

Medium Effects are as Important as Catalyst Design for Selectivity in Electrocatalytic Oxygen Reduction by Iron-porphyrin Complexes

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

Rigsby, Matthew L.; Wasylenko, Derek J.; Pegis, Michael L.

2015-04-08

Several substituted iron porphyrin com-plexes were evaluated for oxygen reduction reaction (ORR) electrocatalysis in different homogeneous and heterogeneous media. The selectivity for 4-electron re-duction to H2O vs. 2-electron reduction to H2O2 varies substantially from one medium to another for a given catalyst. In many cases, the influence of the medium in which the catalyst is evaluated has a larger effect on the observed selectivity than the factors attributable to chemical modification of the catalyst. For instance, introduction of potential proton relays has variable effects depending on the catalyst medium. Thus, comparisons of ORR selectivity results need to be interpreted withmore » caution, as the catalysis is a property not just of the catalyst, but also of the larger mesoscale environment be-yond the catalyst. Still, in all the direct pairwise comparisons in the same medium, the catalysts with potential proton relays have similar or better selectivity for the preferred 4e– path. This work was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences.« less

Putting Parameters in Their Proper Place

ERIC Educational Resources Information Center

Montrul, Silvina; Yoon, James

2009-01-01

Seeing the logical problem of second language acquisition as that of primarily selecting and re-assembling bundles of features anew, Lardiere proposes to dispense with the deductive learning approach and its broad range of consequences subsumed under the concept of parameters. While we agree that feature assembly captures more precisely the…

Educational Opportunities for Adults in California

ERIC Educational Resources Information Center

de Cos, Patricia L.

2004-01-01

Assembly member Carol Liu, Chair of the Assembly Select Committee on Adult Education, requested that the California Research Bureau prepare a report on adult education. The legislative request specified that the following topics be covered: (1) a definition of adult education; (2) recent information on student enrollment, funding sources and…

Patterns and Processes of Microbial Community Assembly

PubMed Central

Schmidt, Steven K.; Fukami, Tadashi; O'Neill, Sean P.; Bilinski, Teresa M.; Stanish, Lee F.; Knelman, Joseph E.; Darcy, John L.; Lynch, Ryan C.; Wickey, Phillip; Ferrenberg, Scott

2013-01-01

SUMMARY Recent research has expanded our understanding of microbial community assembly. However, the field of community ecology is inaccessible to many microbial ecologists because of inconsistent and often confusing terminology as well as unnecessarily polarizing debates. Thus, we review recent literature on microbial community assembly, using the framework of Vellend (Q. Rev. Biol. 85:183–206, 2010) in an effort to synthesize and unify these contributions. We begin by discussing patterns in microbial biogeography and then describe four basic processes (diversification, dispersal, selection, and drift) that contribute to community assembly. We also discuss different combinations of these processes and where and when they may be most important for shaping microbial communities. The spatial and temporal scales of microbial community assembly are also discussed in relation to assembly processes. Throughout this review paper, we highlight differences between microbes and macroorganisms and generate hypotheses describing how these differences may be important for community assembly. We end by discussing the implications of microbial assembly processes for ecosystem function and biodiversity. PMID:24006468

Modeling of block copolymer dry etching for directed self-assembly lithography

NASA Astrophysics Data System (ADS)

Belete, Zelalem; Baer, Eberhard; Erdmann, Andreas

2018-03-01

Directed self-assembly (DSA) of block copolymers (BCP) is a promising alternative technology to overcome the limits of patterning for the semiconductor industry. DSA exploits the self-assembling property of BCPs for nano-scale manufacturing and to repair defects in patterns created during photolithography. After self-assembly of BCPs, to transfer the created pattern to the underlying substrate, selective etching of PMMA (poly (methyl methacrylate)) to PS (polystyrene) is required. However, the etch process to transfer the self-assemble "fingerprint" DSA patterns to the underlying layer is still a challenge. Using combined experimental and modelling studies increases understanding of plasma interaction with BCP materials during the etch process and supports the development of selective process that form well-defined patterns. In this paper, a simple model based on a generic surface model has been developed and an investigation to understand the etch behavior of PS-b-PMMA for Ar, and Ar/O2 plasma chemistries has been conducted. The implemented model is calibrated for etch rates and etch profiles with literature data to extract parameters and conduct simulations. In order to understand the effect of the plasma on the block copolymers, first the etch model was calibrated for polystyrene (PS) and poly (methyl methacrylate) (PMMA) homopolymers. After calibration of the model with the homopolymers etch rate, a full Monte-Carlo simulation was conducted and simulation results are compared with the critical-dimension (CD) and selectivity of etch profile measurement. In addition, etch simulations for lamellae pattern have been demonstrated, using the implemented model.

Identification of highly selective and potent histone deacetylase 3 inhibitors using click chemistry-based combinatorial fragment assembly.

PubMed

Suzuki, Takayoshi; Kasuya, Yuki; Itoh, Yukihiro; Ota, Yosuke; Zhan, Peng; Asamitsu, Kaori; Nakagawa, Hidehiko; Okamoto, Takashi; Miyata, Naoki

2013-01-01

To find histone deacetylase 3 (HDAC3)-selective inhibitors, a series of 504 candidates was assembled using "click chemistry", by reacting nine alkynes bearing a zinc-binding group with 56 azide building blocks in the presence of Cu(I) catalyst. Screening of the 504-member triazole library against HDAC3 and other HDAC isozymes led to the identification of potent and selective HDAC3 inhibitors T247 and T326. These compounds showed potent HDAC3 inhibition with submicromolar IC50s, whereas they did not strongly inhibit other isozymes. Compounds T247 and T326 also induced a dose-dependent selective increase of NF-κB acetylation in human colon cancer HCT116 cells, indicating selective inhibition of HDAC3 in the cells. In addition, these HDAC3-selective inhibitors induced growth inhibition of cancer cells, and activated HIV gene expression in latent HIV-infected cells. These findings indicate that HDAC3-selective inhibitors are promising candidates for anticancer drugs and antiviral agents. This work also suggests the usefulness of the click chemistry approach to find isozyme-selective HDAC inhibitors.

Technology resource document for the assembled chemical weapons assessment environmental impact statement. Vol. 2 : assembled systems for weapons destruction at Anniston Army Depot.

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

Kimmell, T.; Folga, S., Frey, G.; Molberg, J.

2001-05-04

This volume of the Technical Resource Document (TRD) for the ''Environmental Impact Statement (EIS) for the Design, Construction and Operation of One or More Pilot Test Facilities for Assembled Chemical Weapons Destruction Technologies at One or More Sites'' (PMACWA 2001g) pertains to the destruction of assembled chemical weapons (ACW) stored at Anniston Army Depot (ANAD), located outside Anniston, Alabama. This volume presents technical and process information on each of the destruction technologies applicable to treatment of the specific ACW stored at ANAD. The destruction technologies described are those that have been demonstrated as part of the Assembled Chemical Weapons Assessmentmore » (ACWA) selection process (see Volume 1).« less

Measurements of the pairwise kinematic Sunyaev-Zel'dovich effect with the Atacama Cosmology Telescope and future surveys

NASA Astrophysics Data System (ADS)

Vavagiakis, Eve Marie; De Bernardis, Francesco; Aiola, Simone; Battaglia, Nicholas; Niemack, Michael D.; ACTPol Collaboration

2017-06-01

We have made improved measurements of the kinematic Sunyaev-Zel’dovich (kSZ) effect using data from the Atacama Cosmology Telescope (ACT) and the Baryon Oscillation Spectroscopic Survey (BOSS). We used a map of the Cosmic Microwave Background (CMB) from two seasons of observations each by ACT and the Atacama Cosmology Telescope Polarimeter (ACTPol) receiver. We evaluated the mean pairwise baryon momentum associated with the positions of 50,000 bright galaxies in the BOSS DR11 Large Scale Structure catalog via 600 square degrees of overlapping sky area. The measurement of the kSZ signal arising from the large-scale motions of clusters was made by fitting data to an analytical model. The free parameter of the fit determined the optical depth to microwave photon scattering for the cluster sample. We estimated the covariance matrix of the mean pairwise momentum as a function of galaxy separation using CMB simulations, jackknife evaluation, and bootstrap estimates. The most conservative simulation-based uncertainties gave signal-to-noise estimates between 3.6 and 4.1 for various luminosity cuts. Additionally, we explored a novel approach to estimating cluster optical depths from the average thermal Sunyaev-Zel’dovich (tSZ) signal at the BOSS DR11 catalog positions. Our results were broadly consistent with those obtained from the kSZ signal. In the future, the tSZ signal may provide a valuable probe of cluster optical depths, enabling the extraction of velocities from the kSZ sourced mean pairwise momenta. New CMB maps from three seasons of ACTPol observations with multi-frequency coverage overlap with nearly four times as many DR11 sources and promise to improve statistics and systematics for SZ measurements. With these and other upcoming data, the pairwise kSZ signal is poised to become a powerful new cosmological tool, able to probe large physical scales to inform neutrino physics and test models of modified gravity and dark energy.

Comorbidities in the diseasome are more apparent than real: What Bayesian filtering reveals about the comorbidities of depression

PubMed Central

Bolgar, Bence; Deakin, Bill

2017-01-01

Comorbidity patterns have become a major source of information to explore shared mechanisms of pathogenesis between disorders. In hypothesis-free exploration of comorbid conditions, disease-disease networks are usually identified by pairwise methods. However, interpretation of the results is hindered by several confounders. In particular a very large number of pairwise associations can arise indirectly through other comorbidity associations and they increase exponentially with the increasing breadth of the investigated diseases. To investigate and filter this effect, we computed and compared pairwise approaches with a systems-based method, which constructs a sparse Bayesian direct multimorbidity map (BDMM) by systematically eliminating disease-mediated comorbidity relations. Additionally, focusing on depression-related parts of the BDMM, we evaluated correspondence with results from logistic regression, text-mining and molecular-level measures for comorbidities such as genetic overlap and the interactome-based association score. We used a subset of the UK Biobank Resource, a cross-sectional dataset including 247 diseases and 117,392 participants who filled out a detailed questionnaire about mental health. The sparse comorbidity map confirmed that depressed patients frequently suffer from both psychiatric and somatic comorbid disorders. Notably, anxiety and obesity show strong and direct relationships with depression. The BDMM identified further directly co-morbid somatic disorders, e.g. irritable bowel syndrome, fibromyalgia, or migraine. Using the subnetwork of depression and metabolic disorders for functional analysis, the interactome-based system-level score showed the best agreement with the sparse disease network. This indicates that these epidemiologically strong disease-disease relations have improved correspondence with expected molecular-level mechanisms. The substantially fewer number of comorbidity relations in the BDMM compared to pairwise methods implies that biologically meaningful comorbid relations may be less frequent than earlier pairwise methods suggested. The computed interactive comprehensive multimorbidity views over the diseasome are available on the web at Co=MorNet: bioinformatics.mit.bme.hu/UKBNetworks. PMID:28644851

CUFID-query: accurate network querying through random walk based network flow estimation.

PubMed

Jeong, Hyundoo; Qian, Xiaoning; Yoon, Byung-Jun

2017-12-28

Functional modules in biological networks consist of numerous biomolecules and their complicated interactions. Recent studies have shown that biomolecules in a functional module tend to have similar interaction patterns and that such modules are often conserved across biological networks of different species. As a result, such conserved functional modules can be identified through comparative analysis of biological networks. In this work, we propose a novel network querying algorithm based on the CUFID (Comparative network analysis Using the steady-state network Flow to IDentify orthologous proteins) framework combined with an efficient seed-and-extension approach. The proposed algorithm, CUFID-query, can accurately detect conserved functional modules as small subnetworks in the target network that are expected to perform similar functions to the given query functional module. The CUFID framework was recently developed for probabilistic pairwise global comparison of biological networks, and it has been applied to pairwise global network alignment, where the framework was shown to yield accurate network alignment results. In the proposed CUFID-query algorithm, we adopt the CUFID framework and extend it for local network alignment, specifically to solve network querying problems. First, in the seed selection phase, the proposed method utilizes the CUFID framework to compare the query and the target networks and to predict the probabilistic node-to-node correspondence between the networks. Next, the algorithm selects and greedily extends the seed in the target network by iteratively adding nodes that have frequent interactions with other nodes in the seed network, in a way that the conductance of the extended network is maximally reduced. Finally, CUFID-query removes irrelevant nodes from the querying results based on the personalized PageRank vector for the induced network that includes the fully extended network and its neighboring nodes. Through extensive performance evaluation based on biological networks with known functional modules, we show that CUFID-query outperforms the existing state-of-the-art algorithms in terms of prediction accuracy and biological significance of the predictions.

On the feasibility of automatically selecting similar patients in highly individualized radiotherapy dose reconstruction for historic data of pediatric cancer survivors.

PubMed

Virgolin, Marco; van Dijk, Irma W E M; Wiersma, Jan; Ronckers, Cécile M; Witteveen, Cees; Bel, Arjan; Alderliesten, Tanja; Bosman, Peter A N

2018-04-01

The aim of this study is to establish the first step toward a novel and highly individualized three-dimensional (3D) dose distribution reconstruction method, based on CT scans and organ delineations of recently treated patients. Specifically, the feasibility of automatically selecting the CT scan of a recently treated childhood cancer patient who is similar to a given historically treated child who suffered from Wilms' tumor is assessed. A cohort of 37 recently treated children between 2- and 6-yr old are considered. Five potential notions of ground-truth similarity are proposed, each focusing on different anatomical aspects. These notions are automatically computed from CT scans of the abdomen and 3D organ delineations (liver, spleen, spinal cord, external body contour). The first is based on deformable image registration, the second on the Dice similarity coefficient, the third on the Hausdorff distance, the fourth on pairwise organ distances, and the last is computed by means of the overlap volume histogram. The relationship between typically available features of historically treated patients and the proposed ground-truth notions of similarity is studied by adopting state-of-the-art machine learning techniques, including random forest. Also, the feasibility of automatically selecting the most similar patient is assessed by comparing ground-truth rankings of similarity with predicted rankings. Similarities (mainly) based on the external abdomen shape and on the pairwise organ distances are highly correlated (Pearson r p ≥ 0.70) and are successfully modeled with random forests based on historically recorded features (pseudo-R 2 ≥ 0.69). In contrast, similarities based on the shape of internal organs cannot be modeled. For the similarities that random forest can reliably model, an estimation of feature relevance indicates that abdominal diameters and weight are the most important. Experiments on automatically selecting similar patients lead to coarse, yet quite robust results: the most similar patient is retrieved only 22% of the times, however, the error in worst-case scenarios is limited, with the fourth most similar patient being retrieved. Results demonstrate that automatically selecting similar patients is feasible when focusing on the shape of the external abdomen and on the position of internal organs. Moreover, whereas the common practice in phantom-based dose reconstruction is to select a representative phantom using age, height, and weight as discriminant factors for any treatment scenario, our analysis on abdominal tumor treatment for children shows that the most relevant features are weight and the anterior-posterior and left-right abdominal diameters. © 2018 American Association of Physicists in Medicine.

A comparative evaluation of genome assembly reconciliation tools.

PubMed

Alhakami, Hind; Mirebrahim, Hamid; Lonardi, Stefano

2017-05-18

The majority of eukaryotic genomes are unfinished due to the algorithmic challenges of assembling them. A variety of assembly and scaffolding tools are available, but it is not always obvious which tool or parameters to use for a specific genome size and complexity. It is, therefore, common practice to produce multiple assemblies using different assemblers and parameters, then select the best one for public release. A more compelling approach would allow one to merge multiple assemblies with the intent of producing a higher quality consensus assembly, which is the objective of assembly reconciliation. Several assembly reconciliation tools have been proposed in the literature, but their strengths and weaknesses have never been compared on a common dataset. We fill this need with this work, in which we report on an extensive comparative evaluation of several tools. Specifically, we evaluate contiguity, correctness, coverage, and the duplication ratio of the merged assembly compared to the individual assemblies provided as input. None of the tools we tested consistently improved the quality of the input GAGE and synthetic assemblies. Our experiments show an increase in contiguity in the consensus assembly when the original assemblies already have high quality. In terms of correctness, the quality of the results depends on the specific tool, as well as on the quality and the ranking of the input assemblies. In general, the number of misassemblies ranges from being comparable to the best of the input assembly to being comparable to the worst of the input assembly.

Asymmetry of intronic pre-miRNA structures in functional RISC assembly

PubMed Central

Lin, Shi-Lung; Chang, Donald; Ying, Shao-Yao

2006-01-01

The two oligonucleotide strands of a siRNA duplex are functionally asymmetric in assembling the RNAi effector, RNA-induced gene silencing complex (RISC). Based on this asymmetric RISC assembly model in vitro, formation of a microRNA (miRNA) and complementary miRNA (miRNA*) duplex was proposed to be an essential step for the assembly of miRNA-associated RISC (miRISC). We observed here that a strong structural bias exists in the selection of a mature miRNA strand for RISC assembly in zebrafish using an intronic miRNA-like vector to target EGFP mRNA for regulation. The position of the stemloop in a precursor miRNA (pre-miRNA) was involved in the determination of miRNA–miRNA* asymmetry of the pre-miRNA stemarm, leading to different miRNA maturation during miRISC assembly. These findings suggest that the miRISC assembly is likely different from the RISC assembly model of siRNA in zebrafish, providing the first in vivo evidence for asymmetric miRISC assembly. PMID:16005165

Ball mounting fixture for a roundness gage

DOEpatents

Gauler, Allen L.; Pasieka, Donald F.

1983-01-01

A ball mounting fixture for a roundness gage is disclosed. The fixture includes a pair of chuck assemblies oriented substantially transversely with respect to one another and mounted on a common base. Each chuck assembly preferably includes a rotary stage and a wobble plate affixed thereto. A ball chuck affixed to each wobble plate is operable to selectively support a ball to be measured for roundness, with the wobble plate permitting the ball chuck to be tilted to center the ball on the axis of rotation of the rotary stage. In a preferred embodiment, each chuck assembly includes a vacuum chuck operable to selectively support the ball to be measured for roundness. The mounting fixture enables a series of roundness measurements to be taken with a conventional rotating gagehead roundness instrument, which measurements can be utilized to determine the sphericity of the ball.

Self-Diffusion of Drops in a Dilute Sheared Emulsion

NASA Technical Reports Server (NTRS)

Loewenberg, Michael; Hinch, E. J.

1996-01-01

Self-diffusion coefficients that describe cross-flow migration of non-Brownian drops in a dilute sheared emulsion were obtained by trajectory calculations. A boundary integral formulation was used to describe pairwise interactions between deformable drops; interactions between undeformed drops were described with mobility functions for spherical drops. The results indicate that drops have large anisotropic self-diffusivities which depend strongly on the drop viscosity and modestly on the shear-rate. Pairwise interactions between drops in shear-flow do not appreciably promote drop breakup.

PTM Along Track Algorithm to Maintain Spacing During Same Direction Pair-Wise Trajectory Management Operations

NASA Technical Reports Server (NTRS)

Carreno, Victor A.

2015-01-01

Pair-wise Trajectory Management (PTM) is a cockpit based delegated responsibility separation standard. When an air traffic service provider gives a PTM clearance to an aircraft and the flight crew accepts the clearance, the flight crew will maintain spacing and separation from a designated aircraft. A PTM along track algorithm will receive state information from the designated aircraft and from the own ship to produce speed guidance for the flight crew to maintain spacing and separation

Unified Pairwise Spatial Relations: An Application to Graphical Symbol Retrieval

NASA Astrophysics Data System (ADS)

Santosh, K. C.; Wendling, Laurent; Lamiroy, Bart

In this paper, we present a novel unifying concept of pairwise spatial relations. We develop two way directional relations with respect to a unique point set, based on topology of the studied objects and thus avoids problems related to erroneous choices of reference objects while preserving symmetry. The method is robust to any type of image configuration since the directional relations are topologically guided. An automatic prototype graphical symbol retrieval is presented in order to establish its expressiveness.

Hilbert-Schmidt Measure of Pairwise Quantum Discord for Three-Qubit X States

NASA Astrophysics Data System (ADS)

Daoud, M.; Laamara, R. Ahl; Seddik, S.

2015-10-01

The Hilbert-Schmidt distance between a mixed three-qubit state and its closest state is used to quantify the amount of pairwise quantum correlations in a tripartite system. Analytical expressions of geometric quantum discord are derived. A particular attention is devoted to two special classes of three-qubit X states. They include three-qubit states of W, GHZ and Bell type. We also discuss the monogamy property of geometric quantum discord in some mixed three-qubit systems.

Study of Damped Set-Back Pins for S and A Mechanisms.

DTIC Science & Technology

1976-11-01

arm device for artillery munitions. This damped set-back pin assembly is one of two safety features on a S and A device used in the M739 PD/XM587 ET...The damped set-back pin study program was for the design, testing, fabrication, and delivery and damped set-back pin assemblies for use in a safe and...fuzes for a rotating projectile. A pin, porous disc, return spring, floating O-ring, and sleeve comprise the selected damped set-back pin assembly

Chapter 8: Selective Stoichiometric and Catalytic Reactivity in the Confines of a Chiral Supramolecular Assembly

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

University of California, Berkeley; Lawrence Berkeley National Laboratory; Raymond, Kenneth

2007-09-27

Nature uses enzymes to activate otherwise unreactive compounds in remarkable ways. For example, DNases are capable of hydrolyzing phosphate diester bonds in DNA within seconds,[1-3]--a reaction with an estimated half-life of 200 million years without an enzyme.[4] The fundamental features of enzyme catalysis have been much discussed over the last sixty years in an effort to explain the dramatic rate increases and high selectivities of enzymes. As early as 1946, Linus Pauling suggested that enzymes must preferentially recognize and stabilize the transition state over the ground state of a substrate.[5] Despite the intense study of enzymatic selectivity and ability tomore » catalyze chemical reactions, the entire nature of enzyme-based catalysis is still poorly understood. For example, Houk and co-workers recently reported a survey of binding affinities in a wide variety of enzyme-ligand, enzyme-transition-state, and synthetic host-guest complexes and found that the average binding affinities were insufficient to generate many of the rate accelerations observed in biological systems.[6] Therefore, transition-state stabilization cannot be the sole contributor to the high reactivity and selectivity of enzymes, but rather, other forces must contribute to the activation of substrate molecules. Inspired by the efficiency and selectivity of Nature, synthetic chemists have admired the ability of enzymes to activate otherwise unreactive molecules in the confines of an active site. Although much less complex than the evolved active sites of enzymes, synthetic host molecules have been developed that can carry out complex reactions with their cavities. While progress has been made toward highly efficient and selective reactivity inside of synthetic hosts, the lofty goal of duplicating enzymes specificity remains.[7-9] Pioneered by Lehn, Cram, Pedersen, and Breslow, supramolecular chemistry has evolved well beyond the crown ethers and cryptands originally studied.[10-12] Despite the increased complexity of synthetic host molecules, most assembly conditions utilize self-assembly to form complex highly-symmetric structures from relatively simple subunits. For supramolecular assemblies able to encapsulate guest molecules, the chemical environment in each assembly--defined by the size, shape, charge, and functional group availability--greatly influences the guest-binding characteristics.[6, 13-17]« less

Neutron and gamma-ray measurements on the LANL Little Boy Comet Assembly

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

Hankins, D.E.

1983-09-01

We measured the neutron and gamma-ray dose rates at various distances from the Little Boy Comet Assembly at Los Alamos National Laboratory (LANL), Los Alamos, New Mexico on April 28 and 29, 1983. The distances selected varied from 350 ft to 1860 ft from the assembly, with the latter point being located at the edge of the mesa overlooking Pajarito Canyon. We varied the power levels for the various runs but we have normalized all of them to a single power-level. We also made corrections for the variations in the power-level indicators of the assembly using data provided by LANL.

Controlling self-assembly of diphenylalanine peptides at high pH using heterocyclic capping groups.

PubMed

Martin, Adam D; Wojciechowski, Jonathan P; Robinson, Andrew B; Heu, Celine; Garvey, Christopher J; Ratcliffe, Julian; Waddington, Lynne J; Gardiner, James; Thordarson, Pall

2017-03-08

Using small angle neutron scattering (SANS), it is shown that the existence of pre-assembled structures at high pH for a capped diphenylalanine hydrogel is controlled by the selection of N-terminal heterocyclic capping group, namely indole or carbazole. At high pH, changing from a somewhat hydrophilic indole capping group to a more hydrophobic carbazole capping group results in a shift from a high proportion of monomers to self-assembled fibers or wormlike micelles. The presence of these different self-assembled structures at high pH is confirmed through NMR and circular dichroism spectroscopy, scanning probe microscopy and cryogenic transmission electron microscopy.

Detecting signatures of selection in nine distinct lines of broiler chickens.

PubMed

Stainton, John J; Haley, Chris S; Charlesworth, Brain; Kranis, Andreas; Watson, Kellie; Wiener, Pamela

2015-02-01

Modern commercial chickens have been bred for one of two specific purposes: meat production (broilers) or egg production (layers). This has led to large phenotypic changes, so that the genomic signatures of selection may be detectable using statistical techniques. Genetic differentiation between nine distinct broiler lines was calculated using Weir and Cockerham's pairwise FST estimator for 11 003 genome-wide markers to identify regions showing evidence of differential selection across lines. Differentiation measures were averaged into overlapping sliding windows for each line, and a permutation approach was used to determine the significance of each window. A total of 51 regions were found to show significant differentiation between the lines. Several lines were consistently found to share significant regions, suggesting that the pattern of line divergence is related to selection for broiler traits. The majority of the 51 regions contain QTL relating to broiler traits, but only five of them were found to be significantly enriched for broiler QTL, including a region on chromosome 27 containing 39 broiler QTL and 114 genes. Additionally, a number of these regions have been identified by other selection mapping studies. This study has identified a large number of potential selection signatures, and further tests with higher-density marker data may narrow these regions down to individual genes. © 2014 Stichting International Foundation for Animal Genetics.

Volatiles in Inter-Specific Bacterial Interactions

PubMed Central

Tyc, Olaf; Zweers, Hans; de Boer, Wietse; Garbeva, Paolina

2015-01-01

The importance of volatile organic compounds for functioning of microbes is receiving increased research attention. However, to date very little is known on how inter-specific bacterial interactions effect volatiles production as most studies have been focused on volatiles produced by monocultures of well-described bacterial genera. In this study we aimed to understand how inter-specific bacterial interactions affect the composition, production and activity of volatiles. Four phylogenetically different bacterial species namely: Chryseobacterium, Dyella, Janthinobacterium, and Tsukamurella were selected. Earlier results had shown that pairwise combinations of these bacteria induced antimicrobial activity in agar media whereas this was not the case for monocultures. In the current study, we examined if these observations were also reflected by the production of antimicrobial volatiles. Thus, the identity and antimicrobial activity of volatiles produced by the bacteria were determined in monoculture as well in pairwise combinations. Antimicrobial activity of the volatiles was assessed against fungal, oomycetal, and bacterial model organisms. Our results revealed that inter-specific bacterial interactions affected volatiles blend composition. Fungi and oomycetes showed high sensitivity to bacterial volatiles whereas the effect of volatiles on bacteria varied between no effects, growth inhibition to growth promotion depending on the volatile blend composition. In total 35 volatile compounds were detected most of which were sulfur-containing compounds. Two commonly produced sulfur-containing volatile compounds (dimethyl disulfide and dimethyl trisulfide) were tested for their effect on three target bacteria. Here, we display the importance of inter-specific interactions on bacterial volatiles production and their antimicrobial activities. PMID:26733959

Age-Related Changes in Pharyngeal Lumen Size: A Retrospective MRI Analysis.

PubMed

Molfenter, Sonja M; Amin, M R; Branski, R C; Brumm, J D; Hagiwara, M; Roof, S A; Lazarus, C L

2015-06-01

Age-related loss of muscle bulk and strength (sarcopenia) is often cited as a potential mechanism underlying age-related changes in swallowing. Our goal was to explore this phenomenon in the pharynx, specifically, by measuring pharyngeal wall thickness and pharyngeal lumen area in a sample of young versus older women. MRI scans of the neck were retrospectively reviewed from 60 women equally stratified into three age groups (20s, 60s, 70+). Four de-identified slices were extracted per scan for randomized, blinded analysis: one mid-sagittal and three axial slices were selected at the anterior inferior border of C2 and C3, and at the pit of the vallecula. Pixel-based measures of pharyngeal wall thickness and pharyngeal lumen area were completed using ImageJ and then converted to metric units. Measures of pharyngeal wall thickness and pharyngeal lumen area were compared between age groups with one-way ANOVAs using Sidak adjustments for post-hoc pairwise comparisons. A significant main effect for age was observed across all variables whereby pharyngeal wall thickness decreased and pharyngeal lumen area increased with advancing age. Pairwise comparisons revealed significant differences between 20s versus 70+ for all variables and 20s versus 60s for all variables except those measured at C2. Effect sizes ranged from 0.54 to 1.34. Consistent with existing sacropenia literature, the pharyngeal muscles appear to atrophy with age and consequently, the size of the pharyngeal lumen increases.

Pleiotropic Models of Polygenic Variation, Stabilizing Selection, and Epistasis

PubMed Central

Gavrilets, S.; de-Jong, G.

1993-01-01

We show that in polymorphic populations many polygenic traits pleiotropically related to fitness are expected to be under apparent ``stabilizing selection'' independently of the real selection acting on the population. This occurs, for example, if the genetic system is at a stable polymorphic equilibrium determined by selection and the nonadditive contributions of the loci to the trait value either are absent, or are random and independent of those to fitness. Stabilizing selection is also observed if the polygenic system is at an equilibrium determined by a balance between selection and mutation (or migration) when both additive and nonadditive contributions of the loci to the trait value are random and independent of those to fitness. We also compare different viability models that can maintain genetic variability at many loci with respect to their ability to account for the strong stabilizing selection on an additive trait. Let V(m) be the genetic variance supplied by mutation (or migration) each generation, V(g) be the genotypic variance maintained in the population, and n be the number of the loci influencing fitness. We demonstrate that in mutation (migration)-selection balance models the strength of apparent stabilizing selection is order V(m)/V(g). In the overdominant model and in the symmetric viability model the strength of apparent stabilizing selection is approximately 1/(2n) that of total selection on the whole phenotype. We show that a selection system that involves pairwise additive by additive epistasis in maintaining variability can lead to a lower genetic load and genetic variance in fitness (approximately 1/(2n) times) than an equivalent selection system that involves overdominance. We show that, in the epistatic model, the apparent stabilizing selection on an additive trait can be as strong as the total selection on the whole phenotype. PMID:8325491

De novo assembly of mitochondrial genomes provides insights into genetic diversity and molecular evolution in wild boars and domestic pigs.

PubMed

Ni, Pan; Bhuiyan, Ali Akbar; Chen, Jian-Hai; Li, Jingjin; Zhang, Cheng; Zhao, Shuhong; Du, Xiaoyong; Li, Hua; Yu, Hui; Liu, Xiangdong; Li, Kui

2018-06-01

Up to date, the scarcity of publicly available complete mitochondrial sequences for European wild pigs hampers deeper understanding about the genetic changes following domestication. Here, we have assembled 26 de novo mtDNA sequences of European wild boars from next generation sequencing (NGS) data and downloaded 174 complete mtDNA sequences to assess the genetic relationship, nucleotide diversity, and selection. The Bayesian consensus tree reveals the clear divergence between the European and Asian clade and a very small portion (10 out of 200 samples) of maternal introgression. The overall nucleotides diversities of the mtDNA sequences have been reduced following domestication. Interestingly, the selection efficiencies in both European and Asian domestic pigs are reduced, probably caused by changes in both selection constraints and maternal population size following domestication. This study suggests that de novo assembled mitogenomes can be a great boon to uncover the genetic turnover following domestication. Further investigation is warranted to include more samples from the ever-increasing amounts of NGS data to help us to better understand the process of domestication.

Hot hollow cathode gun assembly

DOEpatents

Zeren, J.D.

1983-11-22

A hot hollow cathode deposition gun assembly includes a hollow body having a cylindrical outer surface and an end plate for holding an adjustable heat sink, the hot hollow cathode gun, two magnets for steering the plasma from the gun into a crucible on the heat sink, and a shutter for selectively covering and uncovering the crucible.

Vacuum vapor deposition gun assembly

DOEpatents

Zeren, Joseph D.

1985-01-01

A vapor deposition gun assembly includes a hollow body having a cylindrical outer surface and an end plate for holding an adjustable heat sink, a hot hollow cathode gun, two magnets for steering the plasma from the gun into a crucible on the heat sink, and a shutter for selectively covering and uncovering the crucible.

Letter Proposing Candidates for the First UN Assembly. Teaching with Documents.

ERIC Educational Resources Information Center

Haverkamp, Beth; Schamel, Wynell

1994-01-01

Presents a secondary school lesson plan on the selection of delegates to the first United Nations Assembly meeting. Discusses the esteem of Eleanor Roosevelt at that time and how President Truman requested that she be one of five U.S. representatives. Includes two primary source letters and instructional procedures. (CFR)

Optimizing DNA assembly based on statistical language modelling.

PubMed

Fang, Gang; Zhang, Shemin; Dong, Yafei

2017-12-15

By successively assembling genetic parts such as BioBrick according to grammatical models, complex genetic constructs composed of dozens of functional blocks can be built. However, usually every category of genetic parts includes a few or many parts. With increasing quantity of genetic parts, the process of assembling more than a few sets of these parts can be expensive, time consuming and error prone. At the last step of assembling it is somewhat difficult to decide which part should be selected. Based on statistical language model, which is a probability distribution P(s) over strings S that attempts to reflect how frequently a string S occurs as a sentence, the most commonly used parts will be selected. Then, a dynamic programming algorithm was designed to figure out the solution of maximum probability. The algorithm optimizes the results of a genetic design based on a grammatical model and finds an optimal solution. In this way, redundant operations can be reduced and the time and cost required for conducting biological experiments can be minimized. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Temperature-dependent self-assembly and rheological behavior of a thermoreversible pmma-P n BA-PMMA triblock copolymer gel

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

Zabet, Mahla; Mishra, Satish; Boy, Ramiz

We present that self-assembly and mechanical properties of triblock copolymers in a mid-block selective solvent are of interest in many applications. Herein, we report physical assembly of an ABA triblock copolymer, [PMMA–PnBA–PMMA] in two different mid-block selective solvents, n-butanol and 2-ethyl-1-hexanol. Gel formation resulting from end-block associations and the corresponding changes in mechanical properties have been investigated over a temperature range of -80 °C to 60 °C, from near the solvent melting points to above the gelation temperature. Shear-rheometry, thermal analysis, and small-angle neutron scattering data reveal formation and transition of structure in these systems from a liquid state tomore » a gel state to a percolated cluster network with decrease in temperature. The aggregated PMMA end-blocks display a glass transition temperature. Finally, our results provide new understanding into the structural changes of a self-assembled triblock copolymer gel over a large length scale and wide temperature range.« less

Temperature-dependent self-assembly and rheological behavior of a thermoreversible pmma-P n BA-PMMA triblock copolymer gel

DOE PAGES

Zabet, Mahla; Mishra, Satish; Boy, Ramiz; ...

2017-03-25

We present that self-assembly and mechanical properties of triblock copolymers in a mid-block selective solvent are of interest in many applications. Herein, we report physical assembly of an ABA triblock copolymer, [PMMA–PnBA–PMMA] in two different mid-block selective solvents, n-butanol and 2-ethyl-1-hexanol. Gel formation resulting from end-block associations and the corresponding changes in mechanical properties have been investigated over a temperature range of -80 °C to 60 °C, from near the solvent melting points to above the gelation temperature. Shear-rheometry, thermal analysis, and small-angle neutron scattering data reveal formation and transition of structure in these systems from a liquid state tomore » a gel state to a percolated cluster network with decrease in temperature. The aggregated PMMA end-blocks display a glass transition temperature. Finally, our results provide new understanding into the structural changes of a self-assembled triblock copolymer gel over a large length scale and wide temperature range.« less

Microelectromechanical (MEMS) manipulators for control of nanoparticle coupling interactions

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

Lopez, Daniel; Wiederrecht, Gary; Gosztola, David J.

A nanopositioning system for producing a coupling interaction between a first nanoparticle and a second nanoparticle. A first MEMS positioning assembly includes an electrostatic comb drive actuator configured to selectively displace a first nanoparticle in a first dimension and an electrode configured to selectively displace the first nanoparticle in a second dimensions. Accordingly, the first nanoparticle may be selectively positioned in two dimensions to modulate the distance between the first nanoparticle and a second nanoparticle that may be coupled to a second MEMS positioning assembly. Modulating the distance between the first and second nanoparticles obtains a coupling interaction between themore » nanoparticles that alters at least one material property of the nanoparticles applicable to a variety of sensing and control applications.« less

Lockout device for high voltage circuit breaker

DOEpatents

Kozlowski, Lawrence J.; Shirey, Lawrence A.

1993-01-01

An improved lockout assembly is provided for a circuit breaker to lock the switch handle into a selected switch position. The lockout assembly includes two main elements, each having a respective foot for engaging a portion of the upper housing wall of the circuit breaker. The first foot is inserted into a groove in the upper housing wall, and the second foot is inserted into an adjacent aperture (e.g., a slot) in the upper housing wall. The first foot is slid under and into engagement with a first portion, and the second foot is slid under and into engagement with a second portion of the upper housing wall. At the same time the repsective two feet are placed in engagement with the respective portions of the upper housing wall, two holes, one on each of the respective two main elements of the assembly, are placed in registration; and a locking device, such as a special scissors equipped with a padlock, is installed through the registered holes to secure the lockout assembly on the circuit breaker. When the lockout assembly of the invention is secured on the circuit breaker, the switch handle of the circuit breaker is locked into the selected switch position and prevented from being switched to another switch position.

Lockout device for high voltage circuit breaker

DOEpatents

Kozlowski, L.J.; Shirey, L.A.

1993-01-26

An improved lockout assembly is provided for a circuit breaker to lock the switch handle into a selected switch position. The lockout assembly includes two main elements, each having a respective foot for engaging a portion of the upper housing wall of the circuit breaker. The first foot is inserted into a groove in the upper housing wall, and the second foot is inserted into an adjacent aperture (e.g., a slot) in the upper housing wall. The first foot is slid under and into engagement with a first portion, and the second foot is slid under and into engagement with a second portion of the upper housing wall. At the same time the respective two feet are placed in engagement with the respective portions of the upper housing wall, two holes, one on each of the respective two main elements of the assembly, are placed in registration; and a locking device, such as a special scissors equipped with a padlock, is installed through the registered holes to secure the lockout assembly on the circuit breaker. When the lockout assembly of the invention is secured on the circuit breaker, the switch handle of the circuit breaker is locked into the selected switch position and prevented from being switched to another switch position.

Species sorting during biofilm assembly by artificial substrates deployed in a cold seep system

PubMed Central

Zhang, Wei Peng; Wang, Yong; Tian, Ren Mao; Bougouffa, Salim; Yang, Bo; Cao, Hui Luo; Zhang, Gen; Wong, Yue Him; Xu, Wei; Batang, Zenon; Al-Suwailem, Abdulaziz; Zhang, Xi Xiang; Qian, Pei-Yuan

2014-01-01

Studies focusing on biofilm assembly in deep-sea environments are rarely conducted. To examine the effects of substrate type on microbial community assembly, biofilms were developed on different substrates for different durations at two locations in the Red Sea: in a brine pool and in nearby bottom water (NBW) adjacent to the Thuwal cold seep II. The composition of the microbial communities in 51 biofilms and water samples were revealed by classification of pyrosequenced 16S rRNA gene amplicons. Together with the microscopic characteristics of the biofilms, the results indicate a stronger selection effect by the substrates on the microbial assembly in the brine pool compared with the NBW. Moreover, the selection effect by substrate type was stronger in the early stages compared with the later stages of the biofilm development. These results are consistent with the hypotheses proposed in the framework of species sorting theory, which states that the power of species sorting during microbial community assembly is dictated by habitat conditions, duration and the structure of the source community. Therefore, the results of this study shed light on the control strategy underlying biofilm-associated marine fouling and provide supporting evidence for ecological theories important for understanding the formation of deep-sea biofilms. PMID:25323200

Hybrid pairwise likelihood analysis of animal behavior experiments.

PubMed

Cattelan, Manuela; Varin, Cristiano

2013-12-01

The study of the determinants of fights between animals is an important issue in understanding animal behavior. For this purpose, tournament experiments among a set of animals are often used by zoologists. The results of these tournament experiments are naturally analyzed by paired comparison models. Proper statistical analysis of these models is complicated by the presence of dependence between the outcomes of fights because the same animal is involved in different contests. This paper discusses two different model specifications to account for between-fights dependence. Models are fitted through the hybrid pairwise likelihood method that iterates between optimal estimating equations for the regression parameters and pairwise likelihood inference for the association parameters. This approach requires the specification of means and covariances only. For this reason, the method can be applied also when the computation of the joint distribution is difficult or inconvenient. The proposed methodology is investigated by simulation studies and applied to real data about adult male Cape Dwarf Chameleons. © 2013, The International Biometric Society.

Scale dependence in species turnover reflects variance in species occupancy.

PubMed

McGlinn, Daniel J; Hurlbert, Allen H

2012-02-01

Patterns of species turnover may reflect the processes driving community dynamics across scales. While the majority of studies on species turnover have examined pairwise comparison metrics (e.g., the average Jaccard dissimilarity), it has been proposed that the species-area relationship (SAR) also offers insight into patterns of species turnover because these two patterns may be analytically linked. However, these previous links only apply in a special case where turnover is scale invariant, and we demonstrate across three different plant communities that over 90% of the pairwise turnover values are larger than expected based on scale-invariant predictions from the SAR. Furthermore, the degree of scale dependence in turnover was negatively related to the degree of variance in the occupancy frequency distribution (OFD). These findings suggest that species turnover diverges from scale invariance, and as such pairwise turnover and the slope of the SAR are not redundant. Furthermore, models developed to explain the OFD should be linked with those developed to explain species turnover to achieve a more unified understanding of community structure.

Pairwise velocities in the "Running FLRW" cosmological model

NASA Astrophysics Data System (ADS)

Bibiano, Antonio; Croton, Darren J.

2017-05-01

We present an analysis of the pairwise velocity statistics from a suite of cosmological N-body simulations describing the 'Running Friedmann-Lemaître-Robertson-Walker' (R-FLRW) cosmological model. This model is based on quantum field theory in a curved space-time and extends Λ cold dark matter (CDM) with a time-evolving vacuum energy density, ρ _Λ. To enforce local conservation of matter, a time-evolving gravitational coupling is also included. Our results constitute the first study of velocities in the R-FLRW cosmology, and we also compare with other dark energy simulations suites, repeating the same analysis. We find a strong degeneracy between the pairwise velocity and σ8 at z = 0 for almost all scenarios considered, which remains even when we look back to epochs as early as z = 2. We also investigate various coupled dark energy models, some of which show minimal degeneracy, and reveal interesting deviations from ΛCDM that could be readily exploited by future cosmological observations to test and further constrain our understanding of dark energy.

Clear and Measurable Signature of Modified Gravity in the Galaxy Velocity Field

NASA Astrophysics Data System (ADS)

Hellwing, Wojciech A.; Barreira, Alexandre; Frenk, Carlos S.; Li, Baojiu; Cole, Shaun

2014-06-01

The velocity field of dark matter and galaxies reflects the continued action of gravity throughout cosmic history. We show that the low-order moments of the pairwise velocity distribution v12 are a powerful diagnostic of the laws of gravity on cosmological scales. In particular, the projected line-of-sight galaxy pairwise velocity dispersion σ12(r) is very sensitive to the presence of modified gravity. Using a set of high-resolution N-body simulations, we compute the pairwise velocity distribution and its projected line-of-sight dispersion for a class of modified gravity theories: the chameleon f(R) gravity and Galileon gravity (cubic and quartic). The velocities of dark matter halos with a wide range of masses would exhibit deviations from general relativity at the (5-10)σ level. We examine strategies for detecting these deviations in galaxy redshift and peculiar velocity surveys. If detected, this signature would be a "smoking gun" for modified gravity.

Emergent behaviors of the Schrödinger-Lohe model on cooperative-competitive networks

NASA Astrophysics Data System (ADS)

Huh, Hyungjin; Ha, Seung-Yeal; Kim, Dohyun

2017-12-01

We present several sufficient frameworks leading to the emergent behaviors of the coupled Schrödinger-Lohe (S-L) model under the same one-body external potential on cooperative-competitive networks. The S-L model was first introduced as a possible phenomenological model exhibiting quantum synchronization and its emergent dynamics on all-to-all cooperative networks has been treated via two distinct approaches, Lyapunov functional approach and the finite-dimensional reduction based on pairwise correlations. In this paper, we further generalize the finite-dimensional dynamical systems approach for pairwise correlation functions on cooperative-competitive networks and provide several sufficient frameworks leading to the collective exponential synchronization. For small systems consisting of three and four quantum subsystem, we also show that the system for pairwise correlations can be reduced to the Lotka-Volterra model with cooperative and competitive interactions, in which lots of interesting dynamical patterns appear, e.g., existence of closed orbits and limit-cycles.

Micro spectrometer for parallel light and method of use

NASA Technical Reports Server (NTRS)

Park, Yeonjoon (Inventor); Choi, Sang H. (Inventor); King, Glen C. (Inventor); Elliott, James R. (Inventor)

2011-01-01

A spectrometer system includes an optical assembly for collimating light, a micro-ring grating assembly having a plurality of coaxially-aligned ring gratings, an aperture device defining an aperture circumscribing a target focal point, and a photon detector. An electro-optical layer of the grating assembly may be electrically connected to an energy supply to change the refractive index of the electro-optical layer. Alternately, the gratings may be electrically connected to the energy supply and energized, e.g., with alternating voltages, to change the refractive index. A data recorder may record the predetermined spectral characteristic. A method of detecting a spectral characteristic of a predetermined wavelength of source light includes generating collimated light using an optical assembly, directing the collimated light onto the micro-ring grating assembly, and selectively energizing the micro-ring grating assembly to diffract the predetermined wavelength onto the target focal point, and detecting the spectral characteristic using a photon detector.

Superconductive radiofrequency window assembly

DOEpatents

Phillips, Harry Lawrence; Elliott, Thomas S.

1998-01-01

The present invention is a superconducting radiofrequency window assembly for use in an electron beam accelerator. The srf window assembly (20) has a superconducting metal-ceramic design. The srf window assembly (20) comprises a superconducting frame (30), a ceramic plate (40) having a superconducting metallized area, and a superconducting eyelet (50) for sealing plate (40) into frame (30). The plate (40) is brazed to eyelet (50) which is then electron beam welded to frame (30). A method for providing a ceramic object mounted in a metal member to withstand cryogenic temperatures is also provided. The method involves a new metallization process for coating a selected area of a ceramic object with a thin film of a superconducting material. Finally, a method for assembling an electron beam accelerator cavity utilizing the srf window assembly is provided. The procedure is carried out within an ultra clean room to minimize exposure to particulates which adversely affect the performance of the cavity within the electron beam accelerator.

Superconductive radiofrequency window assembly

DOEpatents

Phillips, H.L.; Elliott, T.S.

1998-05-19

The present invention is a superconducting radiofrequency window assembly for use in an electron beam accelerator. The SRF window assembly has a superconducting metal-ceramic design. The SRF window assembly comprises a superconducting frame, a ceramic plate having a superconducting metallized area, and a superconducting eyelet for sealing plate into frame. The plate is brazed to eyelet which is then electron beam welded to frame. A method for providing a ceramic object mounted in a metal member to withstand cryogenic temperatures is also provided. The method involves a new metallization process for coating a selected area of a ceramic object with a thin film of a superconducting material. Finally, a method for assembling an electron beam accelerator cavity utilizing the SRF window assembly is provided. The procedure is carried out within an ultra clean room to minimize exposure to particulates which adversely affect the performance of the cavity within the electron beam accelerator. 11 figs.

Superconducting radiofrequency window assembly

DOEpatents

Phillips, Harry L.; Elliott, Thomas S.

1997-01-01

The present invention is a superconducting radiofrequency window assembly for use in an electron beam accelerator. The srf window assembly (20) has a superconducting metal-ceramic design. The srf window assembly (20) comprises a superconducting frame (30), a ceramic plate (40) having a superconducting metallized area, and a superconducting eyelet (50) for sealing plate (40) into frame (30). The plate (40) is brazed to eyelet (50) which is then electron beam welded to frame (30). A method for providing a ceramic object mounted in a metal member to withstand cryogenic temperatures is also provided. The method involves a new metallization process for coating a selected area of a ceramic object with a thin film of a superconducting material. Finally, a method for assembling an electron beam accelerator cavity utilizing the srf window assembly is provided. The procedure is carried out within an ultra clean room to minimize exposure to particulates which adversely affect the performance of the cavity within the electron beam accelerator.

Superconducting radiofrequency window assembly

DOEpatents

Phillips, H.L.; Elliott, T.S.

1997-03-11

The present invention is a superconducting radiofrequency window assembly for use in an electron beam accelerator. The srf window assembly has a superconducting metal-ceramic design. The srf window assembly comprises a superconducting frame, a ceramic plate having a superconducting metallized area, and a superconducting eyelet for sealing plate into frame. The plate is brazed to eyelet which is then electron beam welded to frame. A method for providing a ceramic object mounted in a metal member to withstand cryogenic temperatures is also provided. The method involves a new metallization process for coating a selected area of a ceramic object with a thin film of a superconducting material. Finally, a method for assembling an electron beam accelerator cavity utilizing the srf window assembly is provided. The procedure is carried out within an ultra clean room to minimize exposure to particulates which adversely affect the performance of the cavity within the electron beam accelerator. 11 figs.

Development of assembly and joint concepts for erectable space structures

NASA Technical Reports Server (NTRS)

Jacquemin, G. G.; Bluck, R. M.; Grotbeck, G. H.; Johnson, R. R.

1980-01-01

The technology associated with the on-orbit assembly of tetrahedral truss platforms erected of graphite epoxy tapered columns is examined. Associated with the assembly process is the design and fabrication of nine member node joints. Two such joints demonstrating somewhat different technology were designed and fabricated. Two methods of automatic assembly using the node designs were investigated, and the time of assembly of tetrahedral truss structures up to 1 square km in size was estimated. The effect of column and node joint packaging on the Space Shuttle cargo bay is examined. A brief discussion is included of operating cost considerations and the selection of energy sources. Consideration was given to the design assembly machines from 5 m to 20 m. The smaller machines, mounted on the Space Shuttle, are deployable and restowable. They provide a means of demonstrating the capabilities of the concept and of erecting small specialized platforms on relatively short notice.

Application of the Modular Automated Reconfigurable Assembly System (MARAS) concept to adaptable vision gauging and parts feeding

NASA Technical Reports Server (NTRS)

By, Andre Bernard; Caron, Ken; Rothenberg, Michael; Sales, Vic

1994-01-01

This paper presents the first phase results of a collaborative effort between university researchers and a flexible assembly systems integrator to implement a comprehensive modular approach to flexible assembly automation. This approach, named MARAS (Modular Automated Reconfigurable Assembly System), has been structured to support multiple levels of modularity in terms of both physical components and system control functions. The initial focus of the MARAS development has been on parts gauging and feeding operations for cylinder lock assembly. This phase is nearing completion and has resulted in the development of a highly configurable system for vision gauging functions on a wide range of small components (2 mm to 100 mm in size). The reconfigurable concepts implemented in this adaptive Vision Gauging Module (VGM) are now being extended to applicable aspects of the singulating, selecting, and orienting functions required for the flexible feeding of similar mechanical components and assemblies.

Structure of a designed protein cage that self-assembles into a highly porous cube

DOE PAGES

Lai, Yen-Ting; Reading, Eamonn; Hura, Greg L.; ...

2014-11-10

Natural proteins can be versatile building blocks for multimeric, self-assembling structures. Yet, creating protein-based assemblies with specific geometries and chemical properties remains challenging. Highly porous materials represent particularly interesting targets for designed assembly. Here we utilize a strategy of fusing two natural protein oligomers using a continuous alpha-helical linker to design a novel protein that self assembles into a 750 kDa, 225 Å diameter, cube-shaped cage with large openings into a 130 Å diameter inner cavity. A crystal structure of the cage showed atomic level agreement with the designed model, while electron microscopy, native mass spectrometry, and small angle x-raymore » scattering revealed alternate assembly forms in solution. These studies show that accurate design of large porous assemblies with specific shapes is feasible, while further specificity improvements will likely require limiting flexibility to select against alternative forms. Finally, these results provide a foundation for the design of advanced materials with applications in bionanotechnology, nanomedicine and material sciences.« less

Inverse Problem in Self-assembly

NASA Astrophysics Data System (ADS)

Tkachenko, Alexei

2012-02-01

By decorating colloids and nanoparticles with DNA, one can introduce highly selective key-lock interactions between them. This leads to a new class of systems and problems in soft condensed matter physics. In particular, this opens a possibility to solve inverse problem in self-assembly: how to build an arbitrary desired structure with the bottom-up approach? I will present a theoretical and computational analysis of the hierarchical strategy in attacking this problem. It involves self-assembly of particular building blocks (``octopus particles''), that in turn would assemble into the target structure. On a conceptual level, our approach combines elements of three different brands of programmable self assembly: DNA nanotechnology, nanoparticle-DNA assemblies and patchy colloids. I will discuss the general design principles, theoretical and practical limitations of this approach, and illustrate them with our simulation results. Our crucial result is that not only it is possible to design a system that has a given nanostructure as a ground state, but one can also program and optimize the kinetic pathway for its self-assembly.

Deployment, release and recovery of ocean riser pipes

DOEpatents

Person, Abraham; Wetmore, Sherman B.; McNary, James F.

1980-11-18

An ocean thermal energy conversion facility includes a long pipe assembly which is supported at its upper end by the hull of the floating facility. Cold water flows to the facility from deep in the ocean. The pipe assembly comprises an elongate pipe construction and a weight connected to the lower end of the construction by a line of selected length. A floatation collar is connected to the construction at its upper end to cause the construction to have positive buoyancy and a center of buoyancy closer to the upper end of the construction than its center of mass. The weight renders the entire pipe assembly negatively buoyant. In the event that support of the pipe assembly should be lost, as by release of the assembly from the facility hull in an emergency, the assembly sinks to the ocean floor where it is moored by the weight. The pipe construction floats submerged above the ocean floor in a substantially vertical attitude which facilitates recovery of the assembly.

Visualization of Bacterial Microcompartment Facet Assembly Using High-Speed Atomic Force Microscopy

DOE PAGES

Sutter, Markus; Faulkner, Matthew; Aussignargues, Clément; ...

2015-11-30

Bacterial microcompartments (BMCs) are proteinaceous organelles widespread among bacterial phyla. They compartmentalize enzymes within a selectively permeable shell and play important roles in CO 2 fixation, pathogenesis, and microbial ecology. Here, we combine X-ray crystallography and high-speed atomic force microscopy to characterize, at molecular resolution, the structure and dynamics of BMC shell facet assembly. Our results show that preformed hexamers assemble into uniformly oriented shell layers, a single hexamer thick. We also observe the dynamic process of shell facet assembly. Shell hexamers can dissociate from and incorporate into assembled sheets, indicating a flexible intermolecular interaction. Furthermore, we demonstrate that themore » self-assembly and dynamics of shell proteins are governed by specific contacts at the interfaces of shell proteins. Our study provides novel insights into the formation, interactions, and dynamics of BMC shell facets, which are essential for the design and engineering of self-assembled biological nanoreactors and scaffolds based on BMC architectures.« less

Improving Photocatalytic Activity through Electrostatic Self-Assembly: Polyelectrolytes as Tool for Solar Energy Conversion?

NASA Astrophysics Data System (ADS)

Groehn, Franziska

2015-03-01

With regard to the world's decreasing energy resources, developing strategies to exploit solar energy become more and more important. One approach is to take advantage of photocatalysis. Inspired by natural systems such as assemblies performing photosynthesis, it is highly promising to self-assemble synthetic functional species to form more effective or tailored supramolecular units. In this contribution, a new type of photocatalytically active self-assembled nanostructures in aqueous solution will be presented: supramolecular nano-objects obtained through self-assembly of macroions and multivalent organic or inorganic counterions. Polyelectrolyte-porphyrin nanoscale assemblies exhibit up to 10-fold higher photocatalytic activity than the corresponding porphyrins without polymeric template. Other self-assembled catalysts based on polyelectrolytes can exhibit expressed selectivity in a photocatalytic model reaction or even allow catalytic reactions in solution that are not possible with the building blocks only. Further, current results on combining different functional units at the polyelectrolyte template represent a next step towards more complex supramolecular structures for solar energy conversion.

Caveats for the spatial arrangement method: Comment on Hout, Goldinger, and Ferguson (2013).

PubMed

Verheyen, Steven; Voorspoels, Wouter; Vanpaemel, Wolf; Storms, Gert

2016-03-01

The gold standard among proximity data collection methods for multidimensional scaling is the (dis)similarity rating of pairwise presented stimuli. A drawback of the pairwise method is its lengthy duration, which may cause participants to change their strategy over time, become fatigued, or disengage altogether. Hout, Goldinger, and Ferguson (2013) recently made a case for the Spatial Arrangement Method (SpAM) as an alternative to the pairwise method, arguing that it is faster and more engaging. SpAM invites participants to directly arrange stimuli on a computer screen such that the interstimuli distances are proportional to psychological proximity. Based on a reanalysis of the Hout et al. (2013), data we identify three caveats for SpAM. An investigation of the distributional characteristics of the SpAM proximity data reveals that the spatial nature of SpAM imposes structure on the data, invoking a bias against featural representations. Individual-differences scaling of the SpAM proximity data reveals that the two-dimensional nature of SpAM allows individuals to only communicate two dimensions of variation among stimuli properly, invoking a bias against high-dimensional scaling representations. Monte Carlo simulations indicate that in order to obtain reliable estimates of the group average, SpAM requires more individuals to be tested. We conclude with an overview of considerations that can inform the choice between SpAM and the pairwise method and offer suggestions on how to overcome their respective limitations. (c) 2016 APA, all rights reserved).

Onymity promotes cooperation in social dilemma experiments

PubMed Central

Wang, Zhen; Jusup, Marko; Wang, Rui-Wu; Shi, Lei; Iwasa, Yoh; Moreno, Yamir; Kurths, Jürgen

2017-01-01

One of the most elusive scientific challenges for over 150 years has been to explain why cooperation survives despite being a seemingly inferior strategy from an evolutionary point of view. Over the years, various theoretical scenarios aimed at solving the evolutionary puzzle of cooperation have been proposed, eventually identifying several cooperation-promoting mechanisms: kin selection, direct reciprocity, indirect reciprocity, network reciprocity, and group selection. We report the results of repeated Prisoner’s Dilemma experiments with anonymous and onymous pairwise interactions among individuals. We find that onymity significantly increases the frequency of cooperation and the median payoff per round relative to anonymity. Furthermore, we also show that the correlation between players’ ranks and the usage of strategies (cooperation, defection, or punishment) underwent a fundamental shift, whereby more prosocial actions are rewarded with a better ranking under onymity. Our findings prove that reducing anonymity is a valid promoter of cooperation, leading to higher payoffs for cooperators and thus suppressing an incentive—anonymity—that would ultimately favor defection. PMID:28435860

Selection of Malaysia School Youth Cadet Corps leader by using analytical hierarchy process: A case study at SMK Ahmad Boestamam

NASA Astrophysics Data System (ADS)

Mohamed, Nurul Huda; Ahmat, Norhayati; Mohamed, Nurul Akmal; Razmi, Syazwani Che; Mohamed, Nurul Farihan

2017-05-01

This research is a case study to identify the best criteria that a person should have as the leader of Malaysia School Youth Cadet Corps (Kadet Remaja Sekolah (KRS)) at SMK Ahmad Boestamam, Sitiawan in order to select the most appropriate person to hold the position. The approach used in this study is Analytical Hierarchy Process (AHP) which include pairwise comparison to compare the criteria and also the candidates. There are four criteria namely charisma, interpersonal communication, personality and physical. Four candidates (1, 2, 3 and 4) are being considered in this study. Purposive sampling and questionnaires are used as instruments to obtain the data which are then analyzed by using the AHP method. The final output indicates that Candidate 1 has the highest score, followed by Candidate 2, Candidate 4 and Candidate 3. It shows that this method is very helpful in the multi-criteria decision making when there are several options available.

Preemptive spatial competition under a reproduction-mortality constraint.

PubMed

Allstadt, Andrew; Caraco, Thomas; Korniss, G

2009-06-21

Spatially structured ecological interactions can shape selection pressures experienced by a population's different phenotypes. We study spatial competition between phenotypes subject to antagonistic pleiotropy between reproductive effort and mortality rate. The constraint we invoke reflects a previous life-history analysis; the implied dependence indicates that although propagation and mortality rates both vary, their ratio is fixed. We develop a stochastic invasion approximation predicting that phenotypes with higher propagation rates will invade an empty environment (no biotic resistance) faster, despite their higher mortality rate. However, once population density approaches demographic equilibrium, phenotypes with lower mortality are favored, despite their lower propagation rate. We conducted a set of pairwise invasion analyses by simulating an individual-based model of preemptive competition. In each case, the phenotype with the lowest mortality rate and (via antagonistic pleiotropy) the lowest propagation rate qualified as evolutionarily stable among strategies simulated. This result, for a fixed propagation to mortality ratio, suggests that a selective response to spatial competition can extend the time scale of the population's dynamics, which in turn decelerates phenotypic evolution.

Polymorphisms of genes coding for ghrelin and its receptor in relation to colorectal cancer risk: a two-step gene-wide case-control study

PubMed Central

2010-01-01

Background Ghrelin, an endogenous ligand for the growth hormone secretagogue receptor (GHSR), has two major functions: the stimulation of the growth hormone production and the stimulation of food intake. Accumulating evidence also indicates a role of ghrelin in cancer development. Methods We conducted a case-control study to examine the association of common genetic variants in the genes coding for ghrelin (GHRL) and its receptor (GHSR) with colorectal cancer risk. Pairwise tagging was used to select the 11 polymorphisms included in the study. The selected polymorphisms were genotyped in 680 cases and 593 controls from the Czech Republic. Results We found two SNPs associated with lower risk of colorectal cancer, namely SNPs rs27647 and rs35683. We replicated the two hits, in additional 569 cases and 726 controls from Germany. Conclusion A joint analysis of the two populations indicated that the T allele of rs27647 SNP exerted a protective borderline effect (Ptrend = 0.004). PMID:20920174

Polymorphisms of genes coding for ghrelin and its receptor in relation to colorectal cancer risk: a two-step gene-wide case-control study.

PubMed

Campa, Daniele; Pardini, Barbara; Naccarati, Alessio; Vodickova, Ludmila; Novotny, Jan; Steinke, Verena; Rahner, Nils; Holinski-Feder, Elke; Morak, Monika; Schackert, Hans K; Görgens, Heike; Kötting, Judith; Betz, Beate; Kloor, Matthias; Engel, Christoph; Büttner, Reinhard; Propping, Peter; Försti, Asta; Hemminki, Kari; Barale, Roberto; Vodicka, Pavel; Canzian, Federico

2010-09-28

Ghrelin, an endogenous ligand for the growth hormone secretagogue receptor (GHSR), has two major functions: the stimulation of the growth hormone production and the stimulation of food intake. Accumulating evidence also indicates a role of ghrelin in cancer development. We conducted a case-control study to examine the association of common genetic variants in the genes coding for ghrelin (GHRL) and its receptor (GHSR) with colorectal cancer risk. Pairwise tagging was used to select the 11 polymorphisms included in the study. The selected polymorphisms were genotyped in 680 cases and 593 controls from the Czech Republic. We found two SNPs associated with lower risk of colorectal cancer, namely SNPs rs27647 and rs35683. We replicated the two hits, in additional 569 cases and 726 controls from Germany. A joint analysis of the two populations indicated that the T allele of rs27647 SNP exerted a protective borderline effect (Ptrend = 0.004).

Inherent health and environmental risk assessment of nanostructured metal oxide production processes.

PubMed

Torabifard, Mina; Arjmandi, Reza; Rashidi, Alimorad; Nouri, Jafar; Mohammadfam, Iraj

2018-01-10

The health and environmental effects of chemical processes can be assessed during the initial stage of their production. In this paper, the Chemical Screening Tool for Exposure and Environmental Release (ChemSTEER) software was used to compare the health and environmental risks of spray pyrolysis and wet chemical techniques for the fabrication of nanostructured metal oxide on a semi-industrial scale with a capacity of 300 kg/day in Iran. The pollution sources identified in each production process were pairwise compared in Expert Choice software using indicators including respiratory damage, skin damage, and environmental damages including air, water, and soil pollution. The synthesis of nanostructured zinc oxide using the wet chemical technique (with 0.523 wt%) leads to lower health and environmental risks compared to when spray pyrolysis is used (with 0.477 wt%). The health and environmental risk assessment of nanomaterial production processes can help select safer processes, modify the operation conditions, and select or modify raw materials that can help eliminate the risks.

NEDDylation promotes stress granule assembly.

PubMed

Jayabalan, Aravinth Kumar; Sanchez, Anthony; Park, Ra Young; Yoon, Sang Pil; Kang, Gum-Yong; Baek, Je-Hyun; Anderson, Paul; Kee, Younghoon; Ohn, Takbum

2016-07-06

Stress granules (SGs) harbour translationally stalled messenger ribonucleoproteins and play important roles in regulating gene expression and cell fate. Here we show that neddylation promotes SG assembly in response to arsenite-induced oxidative stress. Inhibition or depletion of key components of the neddylation machinery concomitantly inhibits stress-induced polysome disassembly and SG assembly. Affinity purification and subsequent mass-spectrometric analysis of Nedd8-conjugated proteins from translationally stalled ribosomal fractions identified ribosomal proteins, translation factors and RNA-binding proteins (RBPs), including SRSF3, a previously known SG regulator. We show that SRSF3 is selectively neddylated at Lys85 in response to arsenite. A non-neddylatable SRSF3 (K85R) mutant do not prevent arsenite-induced polysome disassembly, but fails to support the SG assembly, suggesting that the neddylation pathway plays an important role in SG assembly.

Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly.

PubMed

Rando, Halie M; Farré, Marta; Robson, Michael P; Won, Naomi B; Johnson, Jennifer L; Buch, Ronak; Bastounes, Estelle R; Xiang, Xueyan; Feng, Shaohong; Liu, Shiping; Xiong, Zijun; Kim, Jaebum; Zhang, Guojie; Trut, Lyudmila N; Larkin, Denis M; Kukekova, Anna V

2018-06-20

The genome of a red fox ( Vulpes vulpes ) was recently sequenced and assembled using next-generation sequencing (NGS). The assembly is of high quality, with 94X coverage and a scaffold N50 of 11.8 Mbp, but is split into 676,878 scaffolds, some of which are likely to contain assembly errors. Fragmentation and misassembly hinder accurate gene prediction and downstream analysis such as the identification of loci under selection. Therefore, assembly of the genome into chromosome-scale fragments was an important step towards developing this genomic model. Scaffolds from the assembly were aligned to the dog reference genome and compared to the alignment of an outgroup genome (cat) against the dog to identify syntenic sequences among species. The program Reference-Assisted Chromosome Assembly (RACA) then integrated the comparative alignment with the mapping of the raw sequencing reads generated during assembly against the fox scaffolds. The 128 sequence fragments RACA assembled were compared to the fox meiotic linkage map to guide the construction of 40 chromosomal fragments. This computational approach to assembly was facilitated by prior research in comparative mammalian genomics, and the continued improvement of the red fox genome can in turn offer insight into canid and carnivore chromosome evolution. This assembly is also necessary for advancing genetic research in foxes and other canids.

NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation.

PubMed

Levy, Roie; Carr, Rogan; Kreimer, Anat; Freilich, Shiri; Borenstein, Elhanan

2015-05-17

Host-microbe and microbe-microbe interactions are often governed by the complex exchange of metabolites. Such interactions play a key role in determining the way pathogenic and commensal species impact their host and in the assembly of complex microbial communities. Recently, several studies have demonstrated how such interactions are reflected in the organization of the metabolic networks of the interacting species, and introduced various graph theory-based methods to predict host-microbe and microbe-microbe interactions directly from network topology. Using these methods, such studies have revealed evolutionary and ecological processes that shape species interactions and community assembly, highlighting the potential of this reverse-ecology research paradigm. NetCooperate is a web-based tool and a software package for determining host-microbe and microbe-microbe cooperative potential. It specifically calculates two previously developed and validated metrics for species interaction: the Biosynthetic Support Score which quantifies the ability of a host species to supply the nutritional requirements of a parasitic or a commensal species, and the Metabolic Complementarity Index which quantifies the complementarity of a pair of microbial organisms' niches. NetCooperate takes as input a pair of metabolic networks, and returns the pairwise metrics as well as a list of potential syntrophic metabolic compounds. The Biosynthetic Support Score and Metabolic Complementarity Index provide insight into host-microbe and microbe-microbe metabolic interactions. NetCooperate determines these interaction indices from metabolic network topology, and can be used for small- or large-scale analyses. NetCooperate is provided as both a web-based tool and an open-source Python module; both are freely available online at http://elbo.gs.washington.edu/software_netcooperate.html.

Do bird assemblages predict susceptibility by e-waste pollution? A comparative study based on species- and guild-dependent responses in China agroecosystems.

PubMed

Zhang, Qiang; Wu, Jiangping; Sun, Yuxin; Zhang, Min; Mai, Bixian; Mo, Ling; Lee, Tien Ming; Zou, Fasheng

2015-01-01

Indirect effects of electronic waste (e-waste) have been proposed as a causal factor in the decline of bird populations, but analyses of the severity impacts on community assembly are currently lacking. To explore how population abundance/species diversity are influenced, and which functional traits are important in determining e-waste susceptibility, here we surveyed breeding and overwintering birds with a hierarchically nested sampling design, and used linear mixed models to analyze changes in bird assemblages along an exposure gradient in South China. Total bird abundance and species diversity decreased with e-waste severity (exposed < surrounding < reference), reflecting the decreasing discharge and consequent side effects. Twenty-five breeding species exclusively used natural farmland, and nine species decreased significantly in relative abundance at e-waste polluted sites. A high pairwise similarity between exposed and surrounding sites indicates a diffuse effect of pollutants on the species assembly at local scale. We show that sensitivity to e-waste severity varies substantially across functional guild, with the prevalence of woodland insectivorous and grassland specialists declining, while some open farmland generalists such as arboreal frugivores, and terrestrial granivores were also rare. By contrast, the response of waterbirds, omnivorous and non-breeding visitors seem to be tolerable to a wide range of pollution so far. These findings underscore that improper e-waste dismantling results in a severe decline of bird diversity, and the different bird assemblages on polluted and natural farmlands imply species- and guild-dependent susceptibility with functional traits. Moreover, a better understanding of the impact of e-waste with different pollution levels, combined multiple pollutants, and in a food-web context on bird is required in future.

Do Bird Assemblages Predict Susceptibility by E-Waste Pollution? A Comparative Study Based on Species- and Guild-Dependent Responses in China Agroecosystems

PubMed Central

Zhang, Qiang; Wu, Jiangping; Sun, Yuxin; Zhang, Min; Mai, Bixian; Mo, Ling; Lee, Tien Ming; Zou, Fasheng

2015-01-01

Indirect effects of electronic waste (e-waste) have been proposed as a causal factor in the decline of bird populations, but analyses of the severity impacts on community assembly are currently lacking. To explore how population abundance/species diversity are influenced, and which functional traits are important in determining e-waste susceptibility, here we surveyed breeding and overwintering birds with a hierarchically nested sampling design, and used linear mixed models to analyze changes in bird assemblages along an exposure gradient in South China. Total bird abundance and species diversity decreased with e-waste severity (exposed < surrounding < reference), reflecting the decreasing discharge and consequent side effects. Twenty-five breeding species exclusively used natural farmland, and nine species decreased significantly in relative abundance at e-waste polluted sites. A high pairwise similarity between exposed and surrounding sites indicates a diffuse effect of pollutants on the species assembly at local scale. We show that sensitivity to e-waste severity varies substantially across functional guild, with the prevalence of woodland insectivorous and grassland specialists declining, while some open farmland generalists such as arboreal frugivores, and terrestrial granivores were also rare. By contrast, the response of waterbirds, omnivorous and non-breeding visitors seem to be tolerable to a wide range of pollution so far. These findings underscore that improper e-waste dismantling results in a severe decline of bird diversity, and the different bird assemblages on polluted and natural farmlands imply species- and guild-dependent susceptibility with functional traits. Moreover, a better understanding of the impact of e-waste with different pollution levels, combined multiple pollutants, and in a food-web context on bird is required in future. PMID:25811881

Synthetic CO2-fixation enzyme cascades immobilized on self-assembled nanostructures that enhance CO2/O2 selectivity of RubisCO.

PubMed

Satagopan, Sriram; Sun, Yuan; Parquette, Jon R; Tabita, F Robert

2017-01-01

With increasing concerns over global warming and depletion of fossil-fuel reserves, it is attractive to develop innovative strategies to assimilate CO 2 , a greenhouse gas, into usable organic carbon. Cell-free systems can be designed to operate as catalytic platforms with enzymes that offer exceptional selectivity and efficiency, without the need to support ancillary reactions of metabolic pathways operating in intact cells. Such systems are yet to be exploited for applications involving CO 2 utilization and subsequent conversion to valuable products, including biofuels. The Calvin-Benson-Bassham (CBB) cycle and the enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) play a pivotal role in global CO 2 fixation. We hereby demonstrate the co-assembly of two RubisCO-associated multienzyme cascades with self-assembled synthetic amphiphilic peptide nanostructures. The immobilized enzyme cascades sequentially convert either ribose-5-phosphate (R-5-P) or glucose, a simpler substrate, to ribulose 1,5-bisphosphate (RuBP), the acceptor for incoming CO 2 in the carboxylation reaction catalyzed by RubisCO. Protection from proteolytic degradation was observed in nanostructures associated with the small dimeric form of RubisCO and ancillary enzymes. Furthermore, nanostructures associated with a larger variant of RubisCO resulted in a significant enhancement of the enzyme's selectivity towards CO 2 , without adversely affecting the catalytic activity. The ability to assemble a cascade of enzymes for CO 2 capture using self-assembling nanostructure scaffolds with functional enhancements show promise for potentially engineering entire pathways (with RubisCO or other CO 2 -fixing enzymes) to redirect carbon from industrial effluents into useful bioproducts.

Ball mounting fixture for a roundness gage

DOEpatents

Gauler, A.L.; Pasieka, D.F.

1983-11-15

A ball mounting fixture for a roundness gage is disclosed. The fixture includes a pair of chuck assemblies oriented substantially transversely with respect to one another and mounted on a common base. Each chuck assembly preferably includes a rotary stage and a wobble plate affixed thereto. A ball chuck affixed to each wobble plate is operable to selectively support a ball to be measured for roundness, with the wobble plate permitting the ball chuck to be tilted to center the ball on the axis of rotation of the rotary stage. In a preferred embodiment, each chuck assembly includes a vacuum chuck operable to selectively support the ball to be measured for roundness. The mounting fixture enables a series of roundness measurements to be taken with a conventional rotating gagehead roundness instrument, which measurements can be utilized to determine the sphericity of the ball. 6 figs.

Large-area fluidic assembly of single-walled carbon nanotubes through dip-coating and directional evaporation

NASA Astrophysics Data System (ADS)

Kim, Pilnam; Kang, Tae June

2017-12-01

We present a simple and scalable fluidic-assembly approach, in which bundles of single-walled carbon nanotubes (SWCNTs) are selectively aligned and deposited by directionally controlled dip-coating and solvent evaporation processes. The patterned surface with alternating regions of hydrophobic polydimethyl siloxane (PDMS) (height 100 nm) strips and hydrophilic SiO2 substrate was withdrawn vertically at a constant speed ( 3 mm/min) from a solution bath containing SWCNTs ( 0.1 mg/ml), allowing for directional evaporation and subsequent selective deposition of nanotube bundles along the edges of horizontally aligned PDMS strips. In addition, the fluidic assembly was applied to fabricate a field effect transistor (FET) with highly oriented SWCNTs, which demonstrate significantly higher current density as well as high turn-off ratio (T/O ratio 100) as compared to that with randomly distributed carbon nanotube bundles (T/O ratio <10).

Asymmetric organic-inorganic hybrid membrane formation via block copolymer-nanoparticle co-assembly.

PubMed

Gu, Yibei; Dorin, Rachel M; Wiesner, Ulrich

2013-01-01

A facile method for forming asymmetric organic-inorganic hybrid membranes for selective separation applications is developed. This approach combines co-assembly of block copolymer (BCP) and inorganic nanoparticles (NPs) with non-solvent induced phase separation. The method is successfully applied to two distinct molar mass BCPs with different fractions of titanium dioxide (TiO2) NPs. The resulting hybrid membranes exhibit structural asymmetry with a thin nanoporous surface layer on top of a macroporous fingerlike support layer. Key parameters that dictate membrane surface morphology include the fraction of inorganics used and the length of time allowed for surface layer development. The resulting membranes exhibit both good selectivity and high permeability (3200 ± 500 Lm(-2) h(-1) bar(-1)). This fast and straightforward synthesis method for asymmetric hybrid membranes provides a new self-assembly platform upon which multifunctional and high-performance organic-inorganic hybrid membranes can be formed.

Self-assembly of nitrogen-doped carbon nanoparticles: a new ratiometric UV-vis optical sensor for the highly sensitive and selective detection of Hg(2+) in aqueous solution.

PubMed

Ruan, Yudi; Wu, Lie; Jiang, Xiue

2016-05-23

Water-soluble nitrogen-doped carbon nanoparticles (N-CNPs) prepared by the one-step hydrothermal treatment of uric acid were found to show ratiometric changes in their UV-vis spectra due to Hg(2+)-mediated self-assembly. For the first time, such a property was developed into a UV-vis optical sensor for detecting Hg(2+) in aqueous solutions with high sensitively and selectively (detection limit = 1.4 nM). More importantly, this novel sensor exhibits a higher linear sensitivity over a wider concentration range compared with the fluorescence sensor based on the same N-CNPs. This work opens an exciting new avenue to explore the use of carbon nanoparticles in constructing UV-vis optical sensors for the detection of metal ions and the use of carbon nanoparticles as a new building block to self-assemble into superlattices.

Cytogenetic Analysis of Populus trichocarpa - Ribosomal DNA, Telomere Repeat Sequence, and Marker-selected BACs

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

Tuskan, Gerald A; Gunter, Lee E; DiFazio, Stephen P

The 18S-28S rDNA and 5S rDNA loci in Populus trichocarpa were localized using fluorescent in situ hybridization (FISH). Two 18S-28S rDNA sites and one 5S rDNA site were identified and located at the ends of 3 different chromosomes. FISH signals from the Arabidopsis -type telomere repeat sequence were observed at the distal ends of each chromosome. Six BAC clones selected from 2 linkage groups based on genome sequence assembly (LG-I and LG-VI) were localized on 2 chromosomes, as expected. BACs from LG-I hybridized to the longest chromosome in the complement. All BAC positions were found to be concordant with sequencemore » assembly positions. BAC-FISH will be useful for delineating each of the Populus trichocarpa chromosomes and improving the sequence assembly of this model angiosperm tree species.« less

AVC: Selecting discriminative features on basis of AUC by maximizing variable complementarity.

PubMed

Sun, Lei; Wang, Jun; Wei, Jinmao

2017-03-14

The Receiver Operator Characteristic (ROC) curve is well-known in evaluating classification performance in biomedical field. Owing to its superiority in dealing with imbalanced and cost-sensitive data, the ROC curve has been exploited as a popular metric to evaluate and find out disease-related genes (features). The existing ROC-based feature selection approaches are simple and effective in evaluating individual features. However, these approaches may fail to find real target feature subset due to their lack of effective means to reduce the redundancy between features, which is essential in machine learning. In this paper, we propose to assess feature complementarity by a trick of measuring the distances between the misclassified instances and their nearest misses on the dimensions of pairwise features. If a misclassified instance and its nearest miss on one feature dimension are far apart on another feature dimension, the two features are regarded as complementary to each other. Subsequently, we propose a novel filter feature selection approach on the basis of the ROC analysis. The new approach employs an efficient heuristic search strategy to select optimal features with highest complementarities. The experimental results on a broad range of microarray data sets validate that the classifiers built on the feature subset selected by our approach can get the minimal balanced error rate with a small amount of significant features. Compared with other ROC-based feature selection approaches, our new approach can select fewer features and effectively improve the classification performance.

Integrating Test-Form Formatting into Automated Test Assembly

ERIC Educational Resources Information Center

Diao, Qi; van der Linden, Wim J.

2013-01-01

Automated test assembly uses the methodology of mixed integer programming to select an optimal set of items from an item bank. Automated test-form generation uses the same methodology to optimally order the items and format the test form. From an optimization point of view, production of fully formatted test forms directly from the item pool using…

A Comparison of Learning Styles between Asian and American Seminary Students. Research Methodology.

ERIC Educational Resources Information Center

Algee, Alan; Bowers, Winefred

This study examined learning style differences between Asian and American seminary students at two post-baccalaureate, Assembly of God seminaries. The study randomly selected 100 students from the Asia Pacific Theological Seminary (APTS) in Baguio, Philippines and the Assembly of God Theological Seminary (AGTS) in the United States of whom 24 from…

Forward Modeling of Large-scale Structure: An Open-source Approach with Halotools

DOE PAGES

Hearin, Andrew P.; Campbell, Duncan; Tollerud, Erik; ...

2017-10-20

Here, we present the first stable release of Halotools (v0.2), a community-driven Python package designed to build and test models of the galaxy-halo connection. Halotools provides a modular platform for creating mock universes of galaxies starting from a catalog of dark matter halos obtained from a cosmological simulation. The package supports many of the common forms used to describe galaxy-halo models: the halo occupation distribution (HOD), the conditional luminosity function (CLF), abundance matching, and alternatives to these models that include effects such as environmental quenching or variable galaxy assembly bias. Satellite galaxies can be modeled to live in subhalos, ormore » to follow custom number density profiles within their halos, including spatial and/or velocity bias with respect to the dark matter profile. Here, the package has an optimized toolkit to make mock observations on a synthetic galaxy population, including galaxy clustering, galaxy-galaxy lensing, galaxy group identification, RSD multipoles, void statistics, pairwise velocities and others, allowing direct comparison to observations. Halotools is object-oriented, enabling complex models to be built from a set of simple, interchangeable components, including those of your own creation.« less

Minimap2: pairwise alignment for nucleotide sequences.

PubMed

Li, Heng

2018-05-10

Recent advances in sequencing technologies promise ultra-long reads of ∼100 kilo bases (kb) in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 mega bases (Mb) in length. Existing alignment programs are unable or inefficient to process such data at scale, which presses for the development of new alignment algorithms. Minimap2 is a general-purpose alignment program to map DNA or long mRNA sequences against a large reference database. It works with accurate short reads of ≥ 100bp in length, ≥1kb genomic reads at error rate ∼15%, full-length noisy Direct RNA or cDNA reads, and assembly contigs or closely related full chromosomes of hundreds of megabases in length. Minimap2 does split-read alignment, employs concave gap cost for long insertions and deletions (INDELs) and introduces new heuristics to reduce spurious alignments. It is 3-4 times as fast as mainstream short-read mappers at comparable accuracy, and is ≥30 times faster than long-read genomic or cDNA mappers at higher accuracy, surpassing most aligners specialized in one type of alignment. https://github.com/lh3/minimap2. hengli@broadinstitute.org.

CAFE: aCcelerated Alignment-FrEe sequence analysis

PubMed Central

Lu, Yang Young; Tang, Kujin; Ren, Jie; Fuhrman, Jed A.; Waterman, Michael S.

2017-01-01

Abstract Alignment-free genome and metagenome comparisons are increasingly important with the development of next generation sequencing (NGS) technologies. Recently developed state-of-the-art k-mer based alignment-free dissimilarity measures including CVTree, \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}$d_2^*$\\end{document} and \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}$d_2^S$\\end{document} are more computationally expensive than measures based solely on the k-mer frequencies. Here, we report a standalone software, aCcelerated Alignment-FrEe sequence analysis (CAFE), for efficient calculation of 28 alignment-free dissimilarity measures. CAFE allows for both assembled genome sequences and unassembled NGS shotgun reads as input, and wraps the output in a standard PHYLIP format. In downstream analyses, CAFE can also be used to visualize the pairwise dissimilarity measures, including dendrograms, heatmap, principal coordinate analysis and network display. CAFE serves as a general k-mer based alignment-free analysis platform for studying the relationships among genomes and metagenomes, and is freely available at https://github.com/younglululu/CAFE. PMID:28472388

Dynamics of prebiotic RNA reproduction illuminated by chemical game theory

PubMed Central

Yeates, Jessica A. M.; Hilbe, Christian; Zwick, Martin; Nowak, Martin A.; Lehman, Niles

2016-01-01

Many origins-of-life scenarios depict a situation in which there are common and potentially scarce resources needed by molecules that compete for survival and reproduction. The dynamics of RNA assembly in a complex mixture of sequences is a frequency-dependent process and mimics such scenarios. By synthesizing Azoarcus ribozyme genotypes that differ in their single-nucleotide interactions with other genotypes, we can create molecules that interact among each other to reproduce. Pairwise interplays between RNAs involve both cooperation and selfishness, quantifiable in a 2 × 2 payoff matrix. We show that a simple model of differential equations based on chemical kinetics accurately predicts the outcomes of these molecular competitions using simple rate inputs into these matrices. In some cases, we find that mixtures of different RNAs reproduce much better than each RNA type alone, reflecting a molecular form of reciprocal cooperation. We also demonstrate that three RNA genotypes can stably coexist in a rock–paper–scissors analog. Our experiments suggest a new type of evolutionary game dynamics, called prelife game dynamics or chemical game dynamics. These operate without template-directed replication, illustrating how small networks of RNAs could have developed and evolved in an RNA world. PMID:27091972

Developing a Multiplexed Quantitative Cross-Linking Mass Spectrometry Platform for Comparative Structural Analysis of Protein Complexes.

PubMed

Yu, Clinton; Huszagh, Alexander; Viner, Rosa; Novitsky, Eric J; Rychnovsky, Scott D; Huang, Lan

2016-10-18

Cross-linking mass spectrometry (XL-MS) represents a recently popularized hybrid methodology for defining protein-protein interactions (PPIs) and analyzing structures of large protein assemblies. In particular, XL-MS strategies have been demonstrated to be effective in elucidating molecular details of PPIs at the peptide resolution, providing a complementary set of structural data that can be utilized to refine existing complex structures or direct de novo modeling of unknown protein structures. To study structural and interaction dynamics of protein complexes, quantitative cross-linking mass spectrometry (QXL-MS) strategies based on isotope-labeled cross-linkers have been developed. Although successful, these approaches are mostly limited to pairwise comparisons. In order to establish a robust workflow enabling comparative analysis of multiple cross-linked samples simultaneously, we have developed a multiplexed QXL-MS strategy, namely, QMIX (Quantitation of Multiplexed, Isobaric-labeled cross (X)-linked peptides) by integrating MS-cleavable cross-linkers with isobaric labeling reagents. This study has established a new analytical platform for quantitative analysis of cross-linked peptides, which can be directly applied for multiplexed comparisons of the conformational dynamics of protein complexes and PPIs at the proteome scale in future studies.

Dynamics of prebiotic RNA reproduction illuminated by chemical game theory.

PubMed

Yeates, Jessica A M; Hilbe, Christian; Zwick, Martin; Nowak, Martin A; Lehman, Niles

2016-05-03

Many origins-of-life scenarios depict a situation in which there are common and potentially scarce resources needed by molecules that compete for survival and reproduction. The dynamics of RNA assembly in a complex mixture of sequences is a frequency-dependent process and mimics such scenarios. By synthesizing Azoarcus ribozyme genotypes that differ in their single-nucleotide interactions with other genotypes, we can create molecules that interact among each other to reproduce. Pairwise interplays between RNAs involve both cooperation and selfishness, quantifiable in a 2 × 2 payoff matrix. We show that a simple model of differential equations based on chemical kinetics accurately predicts the outcomes of these molecular competitions using simple rate inputs into these matrices. In some cases, we find that mixtures of different RNAs reproduce much better than each RNA type alone, reflecting a molecular form of reciprocal cooperation. We also demonstrate that three RNA genotypes can stably coexist in a rock-paper-scissors analog. Our experiments suggest a new type of evolutionary game dynamics, called prelife game dynamics or chemical game dynamics. These operate without template-directed replication, illustrating how small networks of RNAs could have developed and evolved in an RNA world.

Forward Modeling of Large-scale Structure: An Open-source Approach with Halotools

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

Hearin, Andrew P.; Campbell, Duncan; Tollerud, Erik

Here, we present the first stable release of Halotools (v0.2), a community-driven Python package designed to build and test models of the galaxy-halo connection. Halotools provides a modular platform for creating mock universes of galaxies starting from a catalog of dark matter halos obtained from a cosmological simulation. The package supports many of the common forms used to describe galaxy-halo models: the halo occupation distribution (HOD), the conditional luminosity function (CLF), abundance matching, and alternatives to these models that include effects such as environmental quenching or variable galaxy assembly bias. Satellite galaxies can be modeled to live in subhalos, ormore » to follow custom number density profiles within their halos, including spatial and/or velocity bias with respect to the dark matter profile. Here, the package has an optimized toolkit to make mock observations on a synthetic galaxy population, including galaxy clustering, galaxy-galaxy lensing, galaxy group identification, RSD multipoles, void statistics, pairwise velocities and others, allowing direct comparison to observations. Halotools is object-oriented, enabling complex models to be built from a set of simple, interchangeable components, including those of your own creation.« less

Deciphering microbial interactions in synthetic human gut microbiome communities.

PubMed

Venturelli, Ophelia S; Carr, Alex C; Fisher, Garth; Hsu, Ryan H; Lau, Rebecca; Bowen, Benjamin P; Hromada, Susan; Northen, Trent; Arkin, Adam P

2018-06-21

The ecological forces that govern the assembly and stability of the human gut microbiota remain unresolved. We developed a generalizable model-guided framework to predict higher-dimensional consortia from time-resolved measurements of lower-order assemblages. This method was employed to decipher microbial interactions in a diverse human gut microbiome synthetic community. We show that pairwise interactions are major drivers of multi-species community dynamics, as opposed to higher-order interactions. The inferred ecological network exhibits a high proportion of negative and frequent positive interactions. Ecological drivers and responsive recipient species were discovered in the network. Our model demonstrated that a prevalent positive and negative interaction topology enables robust coexistence by implementing a negative feedback loop that balances disparities in monospecies fitness levels. We show that negative interactions could generate history-dependent responses of initial species proportions that frequently do not originate from bistability. Measurements of extracellular metabolites illuminated the metabolic capabilities of monospecies and potential molecular basis of microbial interactions. In sum, these methods defined the ecological roles of major human-associated intestinal species and illuminated design principles of microbial communities. © 2018 The Authors. Published under the terms of the CC BY 4.0 license.

Evaluation of beryllium for space shuttle components

NASA Technical Reports Server (NTRS)

Trapp, A. E.

1972-01-01

Application of beryllium to specific full-scale space shuttle structural components and assemblies was studied. Material evaluations were conducted to check the mechanical properties of as-received material to gain design information on characteristics needed for the material in the space shuttle environment, and to obtain data needed for evaluating component and panel tests. Four beryllium structural assemblies were analyzed and designed. Selected components of these assemblies, representing areas of critical loading or design/process uncertainty, were designed and tested, and two panel assemblies were fabricated. Trends in cost and weight factors were determined by progressive estimation at key points of preliminary design, final design, and fabrication to aid in a cost/weight evaluation of the use of beryllium.

Adjustable permanent magnet assembly for NMR and MRI

DOEpatents

Pines, Alexander; Paulsen, Jeffrey; Bouchard, Louis S; Blumich, Bernhard

2013-10-29

System and methods for designing and using single-sided magnet assemblies for magnetic resonance imaging (MRI) are disclosed. The single-sided magnet assemblies can include an array of permanent magnets disposed at selected positions. At least one of the permanent magnets can be configured to rotate about an axis of rotation in the range of at least +/-10 degrees and can include a magnetization having a vector component perpendicular to the axis of rotation. The single-sided magnet assemblies can further include a magnet frame that is configured to hold the permanent magnets in place while allowing the at least one of the permanent magnets to rotate about the axis of rotation.

Controlling self-assembly of diphenylalanine peptides at high pH using heterocyclic capping groups

PubMed Central

Martin, Adam D.; Wojciechowski, Jonathan P.; Robinson, Andrew B.; Heu, Celine; Garvey, Christopher J.; Ratcliffe, Julian; Waddington, Lynne J.; Gardiner, James; Thordarson, Pall

2017-01-01

Using small angle neutron scattering (SANS), it is shown that the existence of pre-assembled structures at high pH for a capped diphenylalanine hydrogel is controlled by the selection of N-terminal heterocyclic capping group, namely indole or carbazole. At high pH, changing from a somewhat hydrophilic indole capping group to a more hydrophobic carbazole capping group results in a shift from a high proportion of monomers to self-assembled fibers or wormlike micelles. The presence of these different self-assembled structures at high pH is confirmed through NMR and circular dichroism spectroscopy, scanning probe microscopy and cryogenic transmission electron microscopy. PMID:28272523

Synthesis, structural characterization and selectively catalytic properties of metal-organic frameworks with nano-sized channels: A modular design strategy

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

Qiu Lingguang; Gu Lina; Hu Gang

2009-03-15

Modular design method for designing and synthesizing microporous metal-organic frameworks (MOFs) with selective catalytical activity was described. MOFs with both nano-sized channels and potential catalytic activities could be obtained through self-assembly of a framework unit and a catalyst unit. By selecting hexaaquo metal complexes and the ligand BTC (BTC=1,3,5-benzenetricarboxylate) as framework-building blocks and using the metal complex [M(phen){sub 2}(H{sub 2}O){sub 2}]{sup 2+} (phen=1,10-phenanthroline) as a catalyst unit, a series of supramolecular MOFs 1-7 with three-dimensional nano-sized channels, i.e. [M{sup 1}(H{sub 2}O){sub 6}].[M{sup 2}(phen){sub 2}(H{sub 2}O){sub 2}]{sub 2}.2(BTC).xH{sub 2}O (M{sup 1}, M{sup 2}=Co(II), Ni(II), Cu(II), Zn(II), or Mn(II), phen=1,10-phenanthroline, BTC=1,3,5-benzenetricarboxylate, x=22-24),more » were synthesized through self-assembly, and their structures were characterized by IR, elemental analysis, and single-crystal X-ray diffraction. These supramolecular microporous MOFs showed significant size and shape selectivity in the catalyzed oxidation of phenols, which is due to catalytic reactions taking place in the channels of the framework. Design strategy, synthesis, and self-assembly mechanism for the construction of these porous MOFs were discussed. - Grapical abstract: A modular design strategy has been developed to synthesize microporous metal-organic frameworks with potential catalytic activity by self-assembly of the framework-building blocks and the catalyst unit.« less

α-SNAP regulates dynamic, on-site assembly and calcium selectivity of Orai1 channels.

PubMed

Li, Peiyao; Miao, Yong; Dani, Adish; Vig, Monika

2016-08-15

Orai1 forms a highly calcium-selective pore of the calcium release activated channel, and α-SNAP is necessary for its function. Here we show that α-SNAP regulates on-site assembly of Orai1 dimers into calcium-selective multimers. We find that Orai1 is a dimer in resting primary mouse embryonic fibroblasts but displays variable stoichiometry in the plasma membrane of store-depleted cells. Remarkably, α-SNAP depletion induces formation of higher-order Orai1 oligomers, which permeate significant levels of sodium via Orai1 channels. Sodium permeation in α-SNAP-deficient cells cannot be corrected by tethering multiple Stim1 domains to Orai1 C-terminal tail, demonstrating that α-SNAP regulates functional assembly and calcium selectivity of Orai1 multimers independently of Stim1 levels. Fluorescence nanoscopy reveals sustained coassociation of α-SNAP with Stim1 and Orai1, and α-SNAP-depleted cells show faster and less constrained mobility of Orai1 within ER-PM junctions, suggesting Orai1 and Stim1 coentrapment without stable contacts. Furthermore, α-SNAP depletion significantly reduces fluorescence resonance energy transfer between Stim1 and Orai1 N-terminus but not C-terminus. Taken together, these data reveal a unique role of α-SNAP in the on-site functional assembly of Orai1 subunits and suggest that this process may, in part, involve enabling crucial low-affinity interactions between Orai1 N-terminus and Stim1. © 2016 Li, Miao, et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Dunkl operator, integrability, and pairwise scattering in rational Calogero model

NASA Astrophysics Data System (ADS)

Karakhanyan, David

2017-05-01

The integrability of the Calogero model can be expressed as zero curvature condition using Dunkl operators. The corresponding flat connections are non-local gauge transformations, which map the Calogero wave functions to symmetrized wave functions of the set of N free particles, i.e. it relates the corresponding scattering matrices to each other. The integrability of the Calogero model implies that any k-particle scattering is reduced to successive pairwise scatterings. The consistency condition of this requirement is expressed by the analog of the Yang-Baxter relation.

Causal analysis of ordinal treatments and binary outcomes under truncation by death.

PubMed

Wang, Linbo; Richardson, Thomas S; Zhou, Xiao-Hua

2017-06-01

It is common that in multi-arm randomized trials, the outcome of interest is "truncated by death," meaning that it is only observed or well-defined conditioning on an intermediate outcome. In this case, in addition to pairwise contrasts, the joint inference for all treatment arms is also of interest. Under a monotonicity assumption we present methods for both pairwise and joint causal analyses of ordinal treatments and binary outcomes in presence of truncation by death. We illustrate via examples the appropriateness of our assumptions in different scientific contexts.

The effective colloid interaction in the Asakura-Oosawa model. Assessment of non-pairwise terms from the virial expansion.

PubMed

Santos, Andrés; López de Haro, Mariano; Fiumara, Giacomo; Saija, Franz

2015-06-14

The relevance of neglecting three- and four-body interactions in the coarse-grained version of the Asakura-Oosawa model is examined. A mapping between the first few virial coefficients of the binary nonadditive hard-sphere mixture representative of this model and those arising from the coarse-grained (pairwise) depletion potential approximation allows for a quantitative evaluation of the effect of such interactions. This turns out to be especially important for large size ratios and large reservoir polymer packing fractions.

Condenser assembly system for an appliance

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

Litch, Andrew David

2017-10-17

An appliance includes a compact condenser assembly formed with at least two separately and independently produced wire on tube condensers. Each of the at least two wire on tube condensers has a condenser inlet and a condenser outlet. The at least two wire on tube condensers are at least substantially locked and positioned in a matingly engaged configuration forming a compact condenser assembly. The at least two wire on tube condensers are configured to be operationally connected in at least one of a parallel configuration, a series configuration, a selectable configuration, and a bypass configuration.

Development of assembly techniques for fire resistant aircraft interior panels

NASA Technical Reports Server (NTRS)

Lee, S. C. S.

1978-01-01

Ten NASA Type A fire resistant aircraft interior panels were fabricated and tested to develop assembly techniques. These techiques were used in the construction of a full scale lavatory test structure for flame propagation testing. The Type A panel is of sandwich construction consisting of Nomex honeycomb filled with quinone dioxime foam, and bismaleimide/glass face sheets bonded to the core with polyimide film adhesive. The materials selected and the assembly techniques developed for the lavatory test structure were designed for obtaining maximum fire containment with minimum smoke and toxic emission.

B61 Mod 12 Life Extension Program Tailkit Assembly (B61 Mod 12 LEP TKA)

DTIC Science & Technology

2013-12-01

Selected Acquisition Report (SAR) RCS: DD-A&T(Q&A)823-468 B61 Mod 12 Life Extension Program Tailkit Assembly ( B61 Mod 12 LEP TKA...REPORT TYPE 3. DATES COVERED 00-00-2013 to 00-00-2013 4. TITLE AND SUBTITLE B61 Mod 12 Life Extension Program Tailkit Assembly ( B61 Mod 12 LEP...REPORT unclassified b. ABSTRACT unclassified c. THIS PAGE unclassified Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39-18 B61 Mod 12

Isoform-selective chemical inhibition of mDia-mediated actin assembly

PubMed Central

Gauvin, Timothy J.; Fukui, Jami; Peterson, Jeffrey R.; Higgs, Henry N.

2009-01-01

Formins are potent actin assembly factors. Diaphanous formins, including mDia1, mDia2, and mDia3 in mammals, are implicated in mitosis and cytokinesis but no chemical interactors have been reported. We developed an in vitro screen for inhibitors of actin assembly by mDia1, and identified an inhibitor of mDia1 and mDia2 that does not inhibit mDia3 at the concentrations tested. These results establish the druggability of mDia formins and introduce a first generation inhibitor. PMID:19764708

Disulfide exchange in hydrogen-bonded cyclic assemblies: stereochemical self-selection by double dynamic chemistry.

PubMed

ten Cate, A Tessa; Dankers, Patricia Y W; Sijbesma, Rint P; Meijer, E W

2005-07-22

Stereoselective cyclization of cystine-based bifunctional 2-ureido-4[1H]-pyrimidinone derivatives in CDCl(3) solutions was demonstrated by (1)H NMR spectroscopy. Thiolate-catalyzed disulfide exchange in solution led to the equilibration of different diastereomers of 1. At low concentrations, where formation of cyclic assemblies is the dominant mode of association, the molecules act as their own template. At these concentrations the meso diastereomer is formed preferentially, indicating a higher stability of its cyclic assemblies under the applied conditions, in comparison to the other diastereomers.

Nonsaturable microdryer

DOEpatents

Hirschfeld, Tomas B.

1985-01-01

A nonsaturable microdryer is provided for electrolytically removing moisture from sealed containers, particularly electronic equipment. An electrode/electrolyte assembly is disposed within a channel between the interior and exterior of a sealed container. A catalytic barrier disposed between the interior of the sealed container and the electrode/electrolyte assembly prevents the build-up of explosive concentrations of hydrogen by converting back-diffusing hydrogen and oxygen back into water, which is then recycled. A semipermeable membrane disposed between the exterior of the sealed container and the electrode/electrolyte assembly allows selective removal of hydrogen and prevents intake of water.

Nonsaturable microdryer

DOEpatents

Hirschfeld, T.B.

1984-05-23

A nonsaturable microdryer is provided for electrolytically removing moisture from sealed containers, particularly electronic equipment. An electrode/electrolyte assembly is disposed within a channel between the interior and exterior of a sealed container. A catalytic barrier disposed between the interior of the sealed container and the electrode/electrolyte assembly prevents the build-up of explosive concentrations of hydrogen by converting back-diffusing hydrogen and oxygen back into water, which is then recycled. A semipermeable membrane disposed between the exterior of the sealed container and the electrode/electrolyte assembly allows selective removal of hydrogen and prevents intake of water.

High surface area graphene-supported metal chalcogenide assembly

DOEpatents

Worsley, Marcus A.; Kuntz, Joshua; Orme, Christine A.

2016-04-19

A composition comprising at least one graphene-supported assembly, which comprises a three-dimensional network of graphene sheets crosslinked by covalent carbon bonds, and at least one metal chalcogenide compound disposed on said graphene sheets, wherein the chalcogen of said metal chalcogenide compound is selected from S, Se and Te. Also disclosed are methods for making and using the graphene-supported assembly, including graphene-supported MoS.sub.2. Monoliths with high surface area and conductivity can be achieved. Lower operating temperatures in some applications can be achieved. Pore size and volume can be tuned.