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

PubMed

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

2016-01-01

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

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

PubMed Central

Fagan, Matthew E.; Willig, Michael R.

2016-01-01

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

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

PubMed Central

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

2014-01-01

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

The Relation between Thematic Role Computing and Semantic Relatedness Processing during On-Line Sentence Comprehension

PubMed Central

Li, Xiaoqing; Zhao, Haiyan; Lu, Yong

2014-01-01

Sentence comprehension involves timely computing different types of relations between its verbs and noun arguments, such as morphosyntactic, semantic, and thematic relations. Here, we used EEG technique to investigate the potential differences in thematic role computing and lexical-semantic relatedness processing during on-line sentence comprehension, and the interaction between these two types of processes. Mandarin Chinese sentences were used as materials. The basic structure of those sentences is “Noun+Verb+‘le’+a two-character word”, with the Noun being the initial argument. The verb disambiguates the initial argument as an agent or a patient. Meanwhile, the initial argument and the verb are highly or lowly semantically related. The ERPs at the verbs revealed that: relative to the agent condition, the patient condition evoked a larger N400 only when the argument and verb were lowly semantically related; however, relative to the high-relatedness condition, the low-relatedness condition elicited a larger N400 regardless of the thematic relation; although both thematic role variation and semantic relatedness variation elicited N400 effects, the N400 effect elicited by the former was broadly distributed and reached maximum over the frontal electrodes, and the N400 effect elicited by the latter had a posterior distribution. In addition, the brain oscillations results showed that, although thematic role variation (patient vs. agent) induced power decreases around the beta frequency band (15–30 Hz), semantic relatedness variation (low-relatedness vs. high-relatedness) induced power increases in the theta frequency band (4–7 Hz). These results suggested that, in the sentence context, thematic role computing is modulated by the semantic relatedness between the verb and its argument; semantic relatedness processing, however, is in some degree independent from the thematic relations. Moreover, our results indicated that, during on-line sentence comprehension, thematic role computing and semantic relatedness processing are mediated by distinct neural systems. PMID:24755643

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

PubMed

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

2014-10-03

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

Design of a comprehensive biochemistry and molecular biology experiment: phase variation caused by recombinational regulation of bacterial gene expression.

PubMed

Sheng, Xiumei; Xu, Shungao; Lu, Renyun; Isaac, Dadzie; Zhang, Xueyi; Zhang, Haifang; Wang, Huifang; Qiao, Zheng; Huang, Xinxiang

2014-01-01

Scientific experiments are indispensable parts of Biochemistry and Molecular Biology. In this study, a comprehensive Biochemistry and Molecular Biology experiment about Salmonella enterica serovar Typhi Flagellar phase variation has been designed. It consisted of three parts, namely, inducement of bacterial Flagellar phase variation, antibody agglutination test, and PCR analysis. Phase variation was observed by baterial motility assay and identified by antibody agglutination test and PCR analysis. This comprehensive experiment can be performed to help students improve their ability to use the knowledge acquired in Biochemistry and Molecular Biology. Copyright © 2014 by The International Union of Biochemistry and Molecular Biology.

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

PubMed

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

2015-10-01

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

Design of a Comprehensive Biochemistry and Molecular Biology Experiment: Phase Variation Caused by Recombinational Regulation of Bacterial Gene Expression

ERIC Educational Resources Information Center

Sheng, Xiumei; Xu, Shungao; Lu, Renyun; Isaac, Dadzie; Zhang, Xueyi; Zhang, Haifang; Wang, Huifang; Qiao, Zheng; Huang, Xinxiang

2014-01-01

Scientific experiments are indispensable parts of Biochemistry and Molecular Biology. In this study, a comprehensive Biochemistry and Molecular Biology experiment about "Salmonella enterica" serovar Typhi Flagellar phase variation has been designed. It consisted of three parts, namely, inducement of bacterial Flagellar phase variation,…

A global reference for human genetic variation

PubMed Central

2016-01-01

The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies. PMID:26432245

Why Does Working Memory Capacity Predict Variation in Reading Comprehension? On the Influence of Mind Wandering and Executive Attention

ERIC Educational Resources Information Center

McVay, Jennifer C.; Kane, Michael J.

2012-01-01

Some people are better readers than others, and this variation in comprehension ability is predicted by measures of working memory capacity (WMC). The primary goal of this study was to investigate the mediating role of mind-wandering experiences in the association between WMC and normal individual differences in reading comprehension, as predicted…

AgRISTARS. Supporting research: Algorithms for scene modelling

NASA Technical Reports Server (NTRS)

Rassbach, M. E. (Principal Investigator)

1982-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

Robust Nucleus/Cell Detection and Segmentation in Digital Pathology and Microscopy Images: A Comprehensive Review.

PubMed

Xing, Fuyong; Yang, Lin

2016-01-01

Digital pathology and microscopy image analysis is widely used for comprehensive studies of cell morphology or tissue structure. Manual assessment is labor intensive and prone to interobserver variations. Computer-aided methods, which can significantly improve the objectivity and reproducibility, have attracted a great deal of interest in recent literature. Among the pipeline of building a computer-aided diagnosis system, nucleus or cell detection and segmentation play a very important role to describe the molecular morphological information. In the past few decades, many efforts have been devoted to automated nucleus/cell detection and segmentation. In this review, we provide a comprehensive summary of the recent state-of-the-art nucleus/cell segmentation approaches on different types of microscopy images including bright-field, phase-contrast, differential interference contrast, fluorescence, and electron microscopies. In addition, we discuss the challenges for the current methods and the potential future work of nucleus/cell detection and segmentation.

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

PubMed

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

2015-10-14

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

Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs

PubMed Central

Guttman, Mitchell; Garber, Manuel; Levin, Joshua Z.; Donaghey, Julie; Robinson, James; Adiconis, Xian; Fan, Lin; Koziol, Magdalena J.; Gnirke, Andreas; Nusbaum, Chad; Rinn, John L.; Lander, Eric S.; Regev, Aviv

2010-01-01

RNA-Seq provides an unbiased way to study a transcriptome, including both coding and non-coding genes. To date, most RNA-Seq studies have critically depended on existing annotations, and thus focused on expression levels and variation in known transcripts. Here, we present Scripture, a method to reconstruct the transcriptome of a mammalian cell using only RNA-Seq reads and the genome sequence. We apply it to mouse embryonic stem cells, neuronal precursor cells, and lung fibroblasts to accurately reconstruct the full-length gene structures for the vast majority of known expressed genes. We identify substantial variation in protein-coding genes, including thousands of novel 5′-start sites, 3′-ends, and internal coding exons. We then determine the gene structures of over a thousand lincRNA and antisense loci. Our results open the way to direct experimental manipulation of thousands of non-coding RNAs, and demonstrate the power of ab initio reconstruction to render a comprehensive picture of mammalian transcriptomes. PMID:20436462

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

PubMed

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

2015-01-01

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

Image processing for optical mapping.

PubMed

Ravindran, Prabu; Gupta, Aditya

2015-01-01

Optical Mapping is an established single-molecule, whole-genome analysis system, which has been used to gain a comprehensive understanding of genomic structure and to study structural variation of complex genomes. A critical component of Optical Mapping system is the image processing module, which extracts single molecule restriction maps from image datasets of immobilized, restriction digested and fluorescently stained large DNA molecules. In this review, we describe robust and efficient image processing techniques to process these massive datasets and extract accurate restriction maps in the presence of noise, ambiguity and confounding artifacts. We also highlight a few applications of the Optical Mapping system.

Uncertainty, learning, and the optimal management of wildlife

USGS Publications Warehouse

Williams, B.K.

2001-01-01

Wildlife management is limited by uncontrolled and often unrecognized environmental variation, by limited capabilities to observe and control animal populations, and by a lack of understanding about the biological processes driving population dynamics. In this paper I describe a comprehensive framework for management that includes multiple models and likelihood values to account for structural uncertainty, along with stochastic factors to account for environmental variation, random sampling, and partial controllability. Adaptive optimization is developed in terms of the optimal control of incompletely understood populations, with the expected value of perfect information measuring the potential for improving control through learning. The framework for optimal adaptive control is generalized by including partial observability and non-adaptive, sample-based updating of model likelihoods. Passive adaptive management is derived as a special case of constrained adaptive optimization, representing a potentially efficient suboptimal alternative that nonetheless accounts for structural uncertainty.

Assessing land ownership as a driver of change in the distribution, structure, and composition of California's forests.

NASA Astrophysics Data System (ADS)

Easterday, K.; Kelly, M.; McIntyre, P. J.

2015-12-01

Climate change is forecasted to have considerable influence on the distribution, structure, and function of California's forests. However, human interactions with forested landscapes (e.g. fire suppression, resource extraction and etc.) have complicated scientific understanding of the relative contributions of climate change and anthropogenic land management practices as drivers of change. Observed changes in forest structure towards smaller, denser forests across California have been attributed to both climate change (e.g. increased temperatures and declining water availability) and management practices (e.g. fire suppression and logging). Disentangling how these drivers of change act both together and apart is important to developing sustainable policy and land management practices as well as enhancing knowledge of human and natural system interactions. To that end, a comprehensive historical dataset - the Vegetation Type Mapping project (VTM) - and a modern forest inventory dataset (FIA) are used to analyze how spatial variations in vegetation composition and structure over a ~100 year period can be explained by land ownership.Climate change is forecasted to have considerable influence on the distribution, structure, and function of California's forests. However, human interactions with forested landscapes (e.g. fire suppression, resource extraction and etc.) have complicated scientific understanding of the relative contributions of climate change and anthropogenic land management practices as drivers of change. Observed changes in forest structure towards smaller, denser forests across California have been attributed to both climate change (e.g. increased temperatures and declining water availability) and management practices (e.g. fire suppression and logging). Disentangling how these drivers of change act both together and apart is important to developing sustainable policy and land management practices as well as enhancing knowledge of human and natural system interactions. To that end, a comprehensive historical dataset - the Vegetation Type Mapping project (VTM) - and a modern forest inventory dataset (FIA) are used to analyze how spatial variations in vegetation composition and structure over a ~100 year period can be explained by land ownership.

A comprehensive analysis of the Omp85/TpsB protein superfamily structural diversity, taxonomic occurrence, and evolution

PubMed Central

Heinz, Eva; Lithgow, Trevor

2014-01-01

Members of the Omp85/TpsB protein superfamily are ubiquitously distributed in Gram-negative bacteria, and function in protein translocation (e.g., FhaC) or the assembly of outer membrane proteins (e.g., BamA). Several recent findings are suggestive of a further level of variation in the superfamily, including the identification of the novel membrane protein assembly factor TamA and protein translocase PlpD. To investigate the diversity and the causal evolutionary events, we undertook a comprehensive comparative sequence analysis of the Omp85/TpsB proteins. A total of 10 protein subfamilies were apparent, distinguished in their domain structure and sequence signatures. In addition to the proteins FhaC, BamA, and TamA, for which structural and functional information is available, are families of proteins with so far undescribed domain architectures linked to the Omp85 β-barrel domain. This study brings a classification structure to a dynamic protein superfamily of high interest given its essential function for Gram-negative bacteria as well as its diverse domain architecture, and we discuss several scenarios of putative functions of these so far undescribed proteins. PMID:25101071

Effects of landscape change on fish assemblage structure in a rapidly growing metropolitan area in North Carolina, USA

USGS Publications Warehouse

Kennen, J.G.; Chang, M.; Tracy, B.H.

2005-01-01

We evaluated a comprehensive set of natural and land-use attributes that represent the major facets of urban development at fish monitoring sites in the rapidly growing Raleigh-Durham, North Carolina metropolitan area. We used principal component and correlation analysis to obtain a nonredundant subset of variables that extracted most variation in the complete set. With this subset of variables, we assessed the effect of urban growth on fish assemblage structure. We evaluated variation in fish assemblage structure with nonmetric multidimensional scaling (NMDS). We used correlation analysis to identify the most important environmental and landscape variables associated with significant NMDS axes. The second NMDS axis is related to many indices of land-use/land-cover change and habitat. Significant correlations with proportion of largest forest patch to total patch size (r = -0.460, P < 0.01), diversity of patch types (r = 0.554, P < 0.001), and population density (r = 0.385, P < 0.05) helped identify NMDS axis 2 as a disturbance gradient. Positive and negative correlations between the abundance of redbreast sunfish Lepomis auritus and bluehead chub Nocomis leptocephalus, respectively, and NMDS axis 2 also were evident. The North Carolina index of biotic integrity and many of its component metrics were highly correlated with urbanization. These results indicate that aquatic ecosystem integrity would be optimized by a comprehensive integrated management strategy that includes the preservation of landscape function by maximizing the conservation of contiguous tracts of forested lands and vegetative cover in watersheds. ?? 2005 by the American Fisheries Society.

Information-theoretic measures of hydrogen-like ions in weakly coupled Debye plasmas

NASA Astrophysics Data System (ADS)

Zan, Li Rong; Jiao, Li Guang; Ma, Jia; Ho, Yew Kam

2017-12-01

Recent development of information theory provides researchers an alternative and useful tool to quantitatively investigate the variation of the electronic structure when atoms interact with the external environment. In this work, we make systematic studies on the information-theoretic measures for hydrogen-like ions immersed in weakly coupled plasmas modeled by Debye-Hückel potential. Shannon entropy, Fisher information, and Fisher-Shannon complexity in both position and momentum spaces are quantified in high accuracy for the hydrogen atom in a large number of stationary states. The plasma screening effect on embedded atoms can significantly affect the electronic density distributions, in both conjugate spaces, and it is quantified by the variation of information quantities. It is shown that the composite quantities (the Shannon entropy sum and the Fisher information product in combined spaces and Fisher-Shannon complexity in individual space) give a more comprehensive description of the atomic structure information than single ones. The nodes of wave functions play a significant role in the changes of composite information quantities caused by plasmas. With the continuously increasing screening strength, all composite quantities in circular states increase monotonously, while in higher-lying excited states where nodal structures exist, they first decrease to a minimum and then increase rapidly before the bound state approaches the continuum limit. The minimum represents the most reduction of uncertainty properties of the atom in plasmas. The lower bounds for the uncertainty product of the system based on composite information quantities are discussed. Our research presents a comprehensive survey in the investigation of information-theoretic measures for simple atoms embedded in Debye model plasmas.

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

PubMed

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

2009-04-01

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

Comprehensive Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 1. An Advanced Protocol for Molecular Dynamics Simulations and Collision Cross-Section Calculation.

PubMed

Ghassabi Kondalaji, Samaneh; Khakinejad, Mahdiar; Tafreshian, Amirmahdi; J Valentine, Stephen

2017-05-01

Collision cross-section (CCS) measurements with a linear drift tube have been utilized to study the gas-phase conformers of a model peptide (acetyl-PAAAAKAAAAKAAAAKAAAAK). Extensive molecular dynamics (MD) simulations have been conducted to derive an advanced protocol for the generation of a comprehensive pool of in-silico structures; both higher energy and more thermodynamically stable structures are included to provide an unbiased sampling of conformational space. MD simulations at 300 K are applied to the in-silico structures to more accurately describe the gas-phase transport properties of the ion conformers including their dynamics. Different methods used previously for trajectory method (TM) CCS calculation employing the Mobcal software [1] are evaluated. A new method for accurate CCS calculation is proposed based on clustering and data mining techniques. CCS values are calculated for all in-silico structures, and those with matching CCS values are chosen as candidate structures. With this approach, more than 300 candidate structures with significant structural variation are produced; although no final gas-phase structure is proposed here, in a second installment of this work, gas-phase hydrogen deuterium exchange data will be utilized as a second criterion to select among these structures as well as to propose relative populations for these ion conformers. Here the need to increase conformer diversity and accurate CCS calculation is demonstrated and the advanced methods are discussed. Graphical Abstract ᅟ.

Comprehensive Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 1. An Advanced Protocol for Molecular Dynamics Simulations and Collision Cross-Section Calculation

NASA Astrophysics Data System (ADS)

Ghassabi Kondalaji, Samaneh; Khakinejad, Mahdiar; Tafreshian, Amirmahdi; J. Valentine, Stephen

2017-05-01

Collision cross-section (CCS) measurements with a linear drift tube have been utilized to study the gas-phase conformers of a model peptide (acetyl-PAAAAKAAAAKAAAAKAAAAK). Extensive molecular dynamics (MD) simulations have been conducted to derive an advanced protocol for the generation of a comprehensive pool of in-silico structures; both higher energy and more thermodynamically stable structures are included to provide an unbiased sampling of conformational space. MD simulations at 300 K are applied to the in-silico structures to more accurately describe the gas-phase transport properties of the ion conformers including their dynamics. Different methods used previously for trajectory method (TM) CCS calculation employing the Mobcal software [1] are evaluated. A new method for accurate CCS calculation is proposed based on clustering and data mining techniques. CCS values are calculated for all in-silico structures, and those with matching CCS values are chosen as candidate structures. With this approach, more than 300 candidate structures with significant structural variation are produced; although no final gas-phase structure is proposed here, in a second installment of this work, gas-phase hydrogen deuterium exchange data will be utilized as a second criterion to select among these structures as well as to propose relative populations for these ion conformers. Here the need to increase conformer diversity and accurate CCS calculation is demonstrated and the advanced methods are discussed.

Robust Nucleus/Cell Detection and Segmentation in Digital Pathology and Microscopy Images: A Comprehensive Review

PubMed Central

Xing, Fuyong; Yang, Lin

2016-01-01

Digital pathology and microscopy image analysis is widely used for comprehensive studies of cell morphology or tissue structure. Manual assessment is labor intensive and prone to inter-observer variations. Computer-aided methods, which can significantly improve the objectivity and reproducibility, have attracted a great deal of interest in recent literatures. Among the pipeline of building a computer-aided diagnosis system, nucleus or cell detection and segmentation play a very important role to describe the molecular morphological information. In the past few decades, many efforts have been devoted to automated nucleus/cell detection and segmentation. In this review, we provide a comprehensive summary of the recent state-of-the-art nucleus/cell segmentation approaches on different types of microscopy images including bright-field, phase-contrast, differential interference contrast (DIC), fluorescence, and electron microscopies. In addition, we discuss the challenges for the current methods and the potential future work of nucleus/cell detection and segmentation. PMID:26742143

Global assessment of genomic variation in cattle by genome resequencing and high-throughput genotyping

PubMed Central

2011-01-01

Background Integration of genomic variation with phenotypic information is an effective approach for uncovering genotype-phenotype associations. This requires an accurate identification of the different types of variation in individual genomes. Results We report the integration of the whole genome sequence of a single Holstein Friesian bull with data from single nucleotide polymorphism (SNP) and comparative genomic hybridization (CGH) array technologies to determine a comprehensive spectrum of genomic variation. The performance of resequencing SNP detection was assessed by combining SNPs that were identified to be either in identity by descent (IBD) or in copy number variation (CNV) with results from SNP array genotyping. Coding insertions and deletions (indels) were found to be enriched for size in multiples of 3 and were located near the N- and C-termini of proteins. For larger indels, a combination of split-read and read-pair approaches proved to be complementary in finding different signatures. CNVs were identified on the basis of the depth of sequenced reads, and by using SNP and CGH arrays. Conclusions Our results provide high resolution mapping of diverse classes of genomic variation in an individual bovine genome and demonstrate that structural variation surpasses sequence variation as the main component of genomic variability. Better accuracy of SNP detection was achieved with little loss of sensitivity when algorithms that implemented mapping quality were used. IBD regions were found to be instrumental for calculating resequencing SNP accuracy, while SNP detection within CNVs tended to be less reliable. CNV discovery was affected dramatically by platform resolution and coverage biases. The combined data for this study showed that at a moderate level of sequencing coverage, an ensemble of platforms and tools can be applied together to maximize the accurate detection of sequence and structural variants. PMID:22082336

Cognitive Modeling of Individual Variation in Reference Production and Comprehension

PubMed Central

Hendriks, Petra

2016-01-01

A challenge for most theoretical and computational accounts of linguistic reference is the observation that language users vary considerably in their referential choices. Part of the variation observed among and within language users and across tasks may be explained from variation in the cognitive resources available to speakers and listeners. This paper presents a computational model of reference production and comprehension developed within the cognitive architecture ACT-R. Through simulations with this ACT-R model, it is investigated how cognitive constraints interact with linguistic constraints and features of the linguistic discourse in speakers’ production and listeners’ comprehension of referring expressions in specific tasks, and how this interaction may give rise to variation in referential choice. The ACT-R model of reference explains and predicts variation among language users in their referential choices as a result of individual and task-related differences in processing speed and working memory capacity. Because of limitations in their cognitive capacities, speakers sometimes underspecify or overspecify their referring expressions, and listeners sometimes choose incorrect referents or are overly liberal in their interpretation of referring expressions. PMID:27092101

Comprehensive Forced Response Analysis of J2X Turbine Bladed-Discs with 36- Degree Variation in CFD Loading

NASA Technical Reports Server (NTRS)

Elrod, David; Christensen, Eric; Brown, Andrew

2011-01-01

At NASA/MSFC, Structural Dynamics personnel continue to perform advanced analysis for the turbomachinery in the J2X Rocket Engine, which is under consideration for the new Space Launch System. One of the most challenging analyses in the program is predicting turbine blade structural capability. Resonance was predicted by modal analysis, so comprehensive forced response analyses using high fidelity cyclic symmetric finite element models were initiated as required. Analysis methodologies up to this point have assumed the flow field could be fully described by a sector, so the loading on every blade would be identical as it travelled through it. However, in the J2X the CFD flow field varied over the 360 deg of a revolution because of the flow speeds and tortuous axial path. MSFC therefore developed a complex procedure using Nastran Dmap's and Matlab scripts to apply this circumferentially varying loading onto the cyclically symmetric structural models to produce accurate dynamic stresses for every blade on the disk. This procedure is coupled with static, spin, and thermal loading to produce high cycle fatigue safety factors resulting in much more accurate analytical assessments of the blades.

The HART II International Workshop: An Assessment of the State-of-the-Art in Comprehensive Code Prediction

NASA Technical Reports Server (NTRS)

vanderWall, Berend G.; Lim, Joon W.; Smith, Marilyn J.; Jung, Sung N.; Bailly, Joelle; Baeder, James D.; Boyd, D. Douglas, Jr.

2013-01-01

Significant advancements in computational fluid dynamics (CFD) and their coupling with computational structural dynamics (CSD, or comprehensive codes) for rotorcraft applications have been achieved recently. Despite this, CSD codes with their engineering level of modeling the rotor blade dynamics, the unsteady sectional aerodynamics and the vortical wake are still the workhorse for the majority of applications. This is especially true when a large number of parameter variations is to be performed and their impact on performance, structural loads, vibration and noise is to be judged in an approximate yet reliable and as accurate as possible manner. In this article, the capabilities of such codes are evaluated using the HART II International Workshop database, focusing on a typical descent operating condition which includes strong blade-vortex interactions. A companion article addresses the CFD/CSD coupled approach. Three cases are of interest: the baseline case and two cases with 3/rev higher harmonic blade root pitch control (HHC) with different control phases employed. One setting is for minimum blade-vortex interaction noise radiation and the other one for minimum vibration generation. The challenge is to correctly predict the wake physics-especially for the cases with HHC-and all the dynamics, aerodynamics, modifications of the wake structure and the aero-acoustics coming with it. It is observed that the comprehensive codes used today have a surprisingly good predictive capability when they appropriately account for all of the physics involved. The minimum requirements to obtain these results are outlined.

An Assessment of Comprehensive Code Prediction State-of-the-Art Using the HART II International Workshop Data

NASA Technical Reports Server (NTRS)

vanderWall, Berend G.; Lim, Joon W.; Smith, Marilyn J.; Jung, Sung N.; Bailly, Joelle; Baeder, James D.; Boyd, D. Douglas, Jr.

2012-01-01

Despite significant advancements in computational fluid dynamics and their coupling with computational structural dynamics (= CSD, or comprehensive codes) for rotorcraft applications, CSD codes with their engineering level of modeling the rotor blade dynamics, the unsteady sectional aerodynamics and the vortical wake are still the workhorse for the majority of applications. This is especially true when a large number of parameter variations is to be performed and their impact on performance, structural loads, vibration and noise is to be judged in an approximate yet reliable and as accurate as possible manner. In this paper, the capabilities of such codes are evaluated using the HART II Inter- national Workshop data base, focusing on a typical descent operating condition which includes strong blade-vortex interactions. Three cases are of interest: the baseline case and two cases with 3/rev higher harmonic blade root pitch control (HHC) with different control phases employed. One setting is for minimum blade-vortex interaction noise radiation and the other one for minimum vibration generation. The challenge is to correctly predict the wake physics - especially for the cases with HHC - and all the dynamics, aerodynamics, modifications of the wake structure and the aero-acoustics coming with it. It is observed that the comprehensive codes used today have a surprisingly good predictive capability when they appropriately account for all of the physics involved. The minimum requirements to obtain these results are outlined.

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

Wang, Yiyu; Kannan, Rangasayee; Li, Leijun, E-mail

Non-equilibrium microstructure of the heat-affected zone (HAZ) in the as-welded modified 9Cr–1Mo–V–Nb pipe steel (P91) weldment deposited by gas tungsten arc welding (GTAW) and flux core arc welding (FCAW) has been characterized by field-emission scanning electron microscope (FESEM) and electron backscatter diffraction (EBSD). The heterogeneous structures in the sub-layers of the as-welded HAZ are attributable to phase transformations caused by the welding thermal cycles and the local structure variations in the as-received base metal. Coarse-grained heat-affected zone (CGHAZ) has a prior austenite grain (PAG) size of 20 μm. Fine uniformly-distributed precipitates and a higher fraction of MX carbonitrides are observedmore » in the CGHAZ. Fine-grained heat-affected zone (FGHAZ) consists of the finest grains (1.22 μm measured by EBSD, 5 μm PAG size), coarse undissolved M{sub 23}C{sub 6} carbides within the PAG boundaries and fine nucleated M{sub 23}C{sub 6} particles within the martensite laths. Inter-critical heat-affected zone (ICHAZ) consists of partially austenitized grains and over-tempered martensite laths. EBSD kernel average misorientation (KAM) map in the FGHAZ close to the ICHAZ illustrates the greatest local strain variations with a moderate normalized KAM value of 0.92°. The majority (88.1%) of the matrix grains in the CGHAZ are classified as deformed grains by EBSD grain average misorientation (GAM) evaluation. The FGHAZ close to the ICHAZ has the most recrystallized grains with an area fraction of 14.4%. The highest density variation of precipitates within grains in the FGHAZ originates from the inhomogeneous chemistry in the base metal. - Highlights: •A comprehensive characterization of the as-welded HAZ of P91 weldment is conducted. •Structural features in the each layer of the HAZ are quantified by EBSD. •Structural heterogenities in HAZ are due to welding cycle and base metal structure. •FGHAZ contains the finest grain structure and largest precipitate density variation.« less

Comprehensive Schooling: In Need of Definition?

ERIC Educational Resources Information Center

Heath, Natalie

2004-01-01

Comprehensive secondary schooling is currently beset by changes and challenges. The creation of specialist schools and emphasis upon league tables and parental choice appears to be undermining comprehensive schooling. Inequalities within the current system are highlighted by increased variation of perceived quality between schools, the existence…

Comprehensive phase diagram of two-dimensional space charge doped Bi2Sr2CaCu2O8+x.

PubMed

Sterpetti, Edoardo; Biscaras, Johan; Erb, Andreas; Shukla, Abhay

2017-12-12

The phase diagram of hole-doped high critical temperature superconductors as a function of doping and temperature has been intensively studied with chemical variation of doping. Chemical doping can provoke structural changes and disorder, masking intrinsic effects. Alternatively, a field-effect transistor geometry with an electrostatically doped, ultra-thin sample can be used. However, to probe the phase diagram, carrier density modulation beyond 10 14  cm -2 and transport measurements performed over a large temperature range are needed. Here we use the space charge doping method to measure transport characteristics from 330 K to low temperature. We extract parameters and characteristic temperatures over a large doping range and establish a comprehensive phase diagram for one-unit-cell-thick BSCCO-2212 as a function of doping, temperature and disorder.

Numerical modeling of an estuary: A comprehensive skill assessment

USGS Publications Warehouse

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

2005-01-01

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

ShapeRotator: An R tool for standardized rigid rotations of articulated three-dimensional structures with application for geometric morphometrics.

PubMed

Vidal-García, Marta; Bandara, Lashi; Keogh, J Scott

2018-05-01

The quantification of complex morphological patterns typically involves comprehensive shape and size analyses, usually obtained by gathering morphological data from all the structures that capture the phenotypic diversity of an organism or object. Articulated structures are a critical component of overall phenotypic diversity, but data gathered from these structures are difficult to incorporate into modern analyses because of the complexities associated with jointly quantifying 3D shape in multiple structures. While there are existing methods for analyzing shape variation in articulated structures in two-dimensional (2D) space, these methods do not work in 3D, a rapidly growing area of capability and research. Here, we describe a simple geometric rigid rotation approach that removes the effect of random translation and rotation, enabling the morphological analysis of 3D articulated structures. Our method is based on Cartesian coordinates in 3D space, so it can be applied to any morphometric problem that also uses 3D coordinates (e.g., spherical harmonics). We demonstrate the method by applying it to a landmark-based dataset for analyzing shape variation using geometric morphometrics. We have developed an R tool (ShapeRotator) so that the method can be easily implemented in the commonly used R package geomorph and MorphoJ software. This method will be a valuable tool for 3D morphological analyses in articulated structures by allowing an exhaustive examination of shape and size diversity.

Representational Complexity and Memory Retrieval in Language Comprehension

ERIC Educational Resources Information Center

Hofmeister, Philip

2011-01-01

Mental representations formed from words or phrases may vary considerably in their feature-based complexity. Modern theories of retrieval in sentence comprehension do not indicate how this variation and the role of encoding processes should influence memory performance. Here, memory retrieval in language comprehension is shown to be influenced by…

Understanding human DNA sequence variation.

PubMed

Kidd, K K; Pakstis, A J; Speed, W C; Kidd, J R

2004-01-01

Over the past century researchers have identified normal genetic variation and studied that variation in diverse human populations to determine the amounts and distributions of that variation. That information is being used to develop an understanding of the demographic histories of the different populations and the species as a whole, among other studies. With the advent of DNA-based markers in the last quarter century, these studies have accelerated. One of the challenges for the next century is to understand that variation. One component of that understanding will be population genetics. We present here examples of many of the ways these new data can be analyzed from a population perspective using results from our laboratory on multiple individual DNA-based polymorphisms, many clustered in haplotypes, studied in multiple populations representing all major geographic regions of the world. These data support an "out of Africa" hypothesis for human dispersal around the world and begin to refine the understanding of population structures and genetic relationships. We are also developing baseline information against which we can compare findings at different loci to aid in the identification of loci subject, now and in the past, to selection (directional or balancing). We do not yet have a comprehensive understanding of the extensive variation in the human genome, but some of that understanding is coming from population genetics.

Reading comprehension and its underlying components in second-language learners: A meta-analysis of studies comparing first- and second-language learners.

PubMed

Melby-Lervåg, Monica; Lervåg, Arne

2014-03-01

We report a systematic meta-analytic review of studies comparing reading comprehension and its underlying components (language comprehension, decoding, and phonological awareness) in first- and second-language learners. The review included 82 studies, and 576 effect sizes were calculated for reading comprehension and underlying components. Key findings were that, compared to first-language learners, second-language learners display a medium-sized deficit in reading comprehension (pooled effect size d = -0.62), a large deficit in language comprehension (pooled effect size d = -1.12), but only small differences in phonological awareness (pooled effect size d = -0.08) and decoding (pooled effect size d = -0.12). A moderator analysis showed that characteristics related to the type of reading comprehension test reliably explained the variation in the differences in reading comprehension between first- and second-language learners. For language comprehension, studies of samples from low socioeconomic backgrounds and samples where only the first language was used at home generated the largest group differences in favor of first-language learners. Test characteristics and study origin reliably contributed to the variations between the studies of language comprehension. For decoding, Canadian studies showed group differences in favor of second-language learners, whereas the opposite was the case for U.S. studies. Regarding implications, unless specific decoding problems are detected, interventions that aim to ameliorate reading comprehension problems among second-language learners should focus on language comprehension skills.

Sociolinguistic variables and cognition.

PubMed

Thomas, Erik R

2011-11-01

Sociolinguistics has examined mental organization of language only sporadically. Meanwhile, areas of linguistics that deal with cognitive organization seldom delve deeply into language variation. Variation is essential for understanding how language is structured cognitively, however. Three kinds of evidence are discussed to illustrate this point. First, style shifting demonstrates that language users develop detailed associations of when to produce specific linguistic forms, depending on the pragmatic context. Second, variation in fine-grained phonetic cues shows that cognitive organization applies to linguistic forms not otherwise known to be under speakers' control. Finally, experiments on dialect comprehension and identification demonstrate that listeners have detailed cognitive associations of language variants with groups of people, whether or not they can produce the same variants themselves. A model is presented for how sociolinguistic knowledge can be viewed in relation to other parts of language with regard to cognitive and neural representations. WIREs Cogni Sci 2011 2 701-716 DOI: 10.1002/wcs.152 For further resources related to this article, please visit the WIREs website. Copyright © 2011 John Wiley & Sons, Ltd.

An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder.

PubMed

Werling, Donna M; Brand, Harrison; An, Joon-Yong; Stone, Matthew R; Zhu, Lingxue; Glessner, Joseph T; Collins, Ryan L; Dong, Shan; Layer, Ryan M; Markenscoff-Papadimitriou, Eirene; Farrell, Andrew; Schwartz, Grace B; Wang, Harold Z; Currall, Benjamin B; Zhao, Xuefang; Dea, Jeanselle; Duhn, Clif; Erdman, Carolyn A; Gilson, Michael C; Yadav, Rachita; Handsaker, Robert E; Kashin, Seva; Klei, Lambertus; Mandell, Jeffrey D; Nowakowski, Tomasz J; Liu, Yuwen; Pochareddy, Sirisha; Smith, Louw; Walker, Michael F; Waterman, Matthew J; He, Xin; Kriegstein, Arnold R; Rubenstein, John L; Sestan, Nenad; McCarroll, Steven A; Neale, Benjamin M; Coon, Hilary; Willsey, A Jeremy; Buxbaum, Joseph D; Daly, Mark J; State, Matthew W; Quinlan, Aaron R; Marth, Gabor T; Roeder, Kathryn; Devlin, Bernie; Talkowski, Michael E; Sanders, Stephan J

2018-05-01

Genomic association studies of common or rare protein-coding variation have established robust statistical approaches to account for multiple testing. Here we present a comparable framework to evaluate rare and de novo noncoding single-nucleotide variants, insertion/deletions, and all classes of structural variation from whole-genome sequencing (WGS). Integrating genomic annotations at the level of nucleotides, genes, and regulatory regions, we define 51,801 annotation categories. Analyses of 519 autism spectrum disorder families did not identify association with any categories after correction for 4,123 effective tests. Without appropriate correction, biologically plausible associations are observed in both cases and controls. Despite excluding previously identified gene-disrupting mutations, coding regions still exhibited the strongest associations. Thus, in autism, the contribution of de novo noncoding variation is probably modest in comparison to that of de novo coding variants. Robust results from future WGS studies will require large cohorts and comprehensive analytical strategies that consider the substantial multiple-testing burden.

Application of the Probabilistic Dynamic Synthesis Method to the Analysis of a Realistic Structure

NASA Technical Reports Server (NTRS)

Brown, Andrew M.; Ferri, Aldo A.

1998-01-01

The Probabilistic Dynamic Synthesis method is a new technique for obtaining the statistics of a desired response engineering quantity for a structure with non-deterministic parameters. The method uses measured data from modal testing of the structure as the input random variables, rather than more "primitive" quantities like geometry or material variation. This modal information is much more comprehensive and easily measured than the "primitive" information. The probabilistic analysis is carried out using either response surface reliability methods or Monte Carlo simulation. A previous work verified the feasibility of the PDS method on a simple seven degree-of-freedom spring-mass system. In this paper, extensive issues involved with applying the method to a realistic three-substructure system are examined, and free and forced response analyses are performed. The results from using the method are promising, especially when the lack of alternatives for obtaining quantitative output for probabilistic structures is considered.

Survey and analysis of crystal polymorphism in organic structures

PubMed Central

Kaur, Ramanpreet

2018-01-01

With the intention of producing the most comprehensive treatment of the prevalence of crystal polymorphism among structurally characterized materials, all polymorphic compounds flagged as such within the Cambridge Structural Database (CSD) are analysed and a list of crystallographically characterized organic polymorphic compounds is assembled. Classifying these structures into subclasses of anhydrates, salts, hydrates, non-hydrated solvates and cocrystals reveals that there are significant variations in polymorphism prevalence as a function of crystal type, a fact which has not previously been recognized in the literature. It is also shown that, as a percentage, polymorphic entries are decreasing temporally within the CSD, with the notable exception of cocrystals, which continue to rise at a rate that is a constant fraction of the overall entries. Some phenomena identified that require additional scrutiny include the relative prevalence of temperature-induced phase transitions among organic salts and the paucity of polymorphism in crystals with three or more chemical components. PMID:29765601

Application of the Probabilistic Dynamic Synthesis Method to Realistic Structures

NASA Technical Reports Server (NTRS)

Brown, Andrew M.; Ferri, Aldo A.

1998-01-01

The Probabilistic Dynamic Synthesis method is a technique for obtaining the statistics of a desired response engineering quantity for a structure with non-deterministic parameters. The method uses measured data from modal testing of the structure as the input random variables, rather than more "primitive" quantities like geometry or material variation. This modal information is much more comprehensive and easily measured than the "primitive" information. The probabilistic analysis is carried out using either response surface reliability methods or Monte Carlo simulation. In previous work, the feasibility of the PDS method applied to a simple seven degree-of-freedom spring-mass system was verified. In this paper, extensive issues involved with applying the method to a realistic three-substructure system are examined, and free and forced response analyses are performed. The results from using the method are promising, especially when the lack of alternatives for obtaining quantitative output for probabilistic structures is considered.

CROSS-DISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: Simulation of SET Operation in Phase-Change Random Access Memories with Heater Addition and Ring-Type Contactor for Low-Power Consumption by Finite Element Modeling

NASA Astrophysics Data System (ADS)

Gong, Yue-Feng; Song, Zhi-Tang; Ling, Yun; Liu, Yan; Feng, Song-Lin

2009-11-01

A three-dimensional finite element model for phase change random access memory (PCRAM) is established for comprehensive electrical and thermal analysis during SET operation. The SET behaviours of the heater addition structure (HS) and the ring-type contact in bottom electrode (RIB) structure are compared with each other. There are two ways to reduce the RESET current, applying a high resistivity interfacial layer and building a new device structure. The simulation results indicate that the variation of SET current with different power reduction ways is little. This study takes the RESET and SET operation current into consideration, showing that the RIB structure PCRAM cell is suitable for future devices with high heat efficiency and high-density, due to its high heat efficiency in RESET operation.

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

PubMed

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

2014-01-01

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

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

PubMed

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

2012-01-01

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

The average solar wind in the inner heliosphere: Structures and slow variations

NASA Technical Reports Server (NTRS)

Schwenn, R.

1983-01-01

Measurements from the HELIOS solar probes indicated that apart from solar activity related disturbances there exist two states of the solar wind which might result from basic differences in the acceleration process: the fast solar wind (v 600 kms(-)1) emanating from magnetically open regions in the solar corona and the "slow" solar wind (v 400 kms(-)1) correlated with the more active regions and its mainly closed magnetic structures. In a comprehensive study using all HELIOS data taken between 1974 and 1982 the average behavior of the basic plasma parameters were analyzed as functions of the solar wind speed. The long term variations of the solar wind parameters along the solar cycle were also determined and numerical estimates given. These modulations appear to be distinct though only minor. In agreement with earlier studies it was concluded that the major modulations are in the number and size of high speed streams and in the number of interplanetary shock waves caused by coronal transients. The latter ones usually cause huge deviations from the averages of all parameters.

Enhancing Concept Comprehension in a Web-Based Course Using a Framework Integrating the Learning Cycle with Variation Theory

ERIC Educational Resources Information Center

Hsu, Chih-Chao; Wang, Tzone-I

2014-01-01

Concept comprehension is an important foundation for more complex thoughts. To enhance concept comprehension, teachers of traditional classrooms have been using instructional strategies and specific course designs, which have been proven effective. It initiates a hypothesis that integrating instructional strategies in the course designs of an…

How Working Memory Relates to Children's Reading Comprehension: The Importance of Domain-Specificity in Storage and Processing

ERIC Educational Resources Information Center

Nouwens, Suzan; Groen, Margriet A.; Verhoeven, Ludo

2017-01-01

Working memory is considered a well-established predictor of individual variation in reading comprehension in children and adults. However, how storage and processing capacities of working memory in both the phonological and semantic domain relate to reading comprehension is still unclear. In the current study, we investigated the contribution of…

Lexical Profiles of Comprehensible Second Language Speech: The Role of Appropriateness, Fluency, Variation, Sophistication, Abstractness, and Sense Relations

ERIC Educational Resources Information Center

Saito, Kazuya; Webb, Stuart; Trofimovich, Pavel; Isaacs, Talia

2016-01-01

This study examined contributions of lexical factors to native-speaking raters' assessments of comprehensibility (ease of understanding) of second language (L2) speech. Extemporaneous oral narratives elicited from 40 French speakers of L2 English were transcribed and evaluated for comprehensibility by 10 raters. Subsequently, the samples were…

On the Parity of Structural Persistence in Language Production and Comprehension

PubMed Central

Tooley, Kristen M.; Bock, Kathryn

2014-01-01

Structural priming creates structural persistence. That is, differences in experience with syntax can change subsequent language performance, and the changes can be observed in both language production and comprehension. However, the effects in comprehension and production appear to differ. In comprehension, persistence is typically found when the verbs are the same in primes and targets; in production, persistence occurs without verb overlap. The contrast suggests a theoretically important hypothesis: parsing in comprehension is lexically driven while formulation in production is structurally driven. A major weakness in this hypothesis about comprehension-production differences is that its empirical motivation rests on the outcomes of experiments in which the priming manipulations differ, the primed sentence structures differ, and the measures of priming differ. To sharpen the comparison, we examined structural persistence with and without verb overlap in both reading comprehension and spoken production, using the same prime presentation procedure, the same syntactic structures, the same sentences, and the same participants. These methods yielded abstract sructural persistence in comprehension as well as production. A measure of the strength of persistence revealed significant effects of priming and verb overlap without significant comprehension—production differences. This argues for uniformity in the structural mechanisms of language processing. PMID:24803423

Changes of Water Hydrogen Bond Network with Different Externalities

PubMed Central

Zhao, Lin; Ma, Kai; Yang, Zi

2015-01-01

It is crucial to uncover the mystery of water cluster and structural motif to have an insight into the abundant anomalies bound to water. In this context, the analysis of influence factors is an alternative way to shed light on the nature of water clusters. Water structure has been tentatively explained within different frameworks of structural models. Based on comprehensive analysis and summary of the studies on the response of water to four externalities (i.e., temperature, pressure, solutes and external fields), the changing trends of water structure and a deduced intrinsic structural motif are put forward in this work. The variations in physicochemical and biological effects of water induced by each externality are also discussed to emphasize the role of water in our daily life. On this basis, the underlying problems that need to be further studied are formulated by pointing out the limitations attached to current study techniques and to outline prominent studies that have come up recently. PMID:25884333

TARGET Research Goals

Cancer.gov

TARGET researchers use various sequencing and array-based methods to examine the genomes, transcriptomes, and for some diseases epigenomes of select childhood cancers. This “multi-omic” approach generates a comprehensive profile of molecular alterations for each cancer type. Alterations are changes in DNA or RNA, such as rearrangements in chromosome structure or variations in gene expression, respectively. Through computational analyses and assays to validate biological function, TARGET researchers predict which alterations disrupt the function of a gene or pathway and promote cancer growth, progression, and/or survival. Researchers identify candidate therapeutic targets and/or prognostic markers from the cancer-associated alterations.

Extreme ultraviolet quantum efficiency of opaque alkali halide photocathodes on microchannel plates

NASA Technical Reports Server (NTRS)

Siegmund, O. H. W.; Everman, E.; Vallerga, J. V.; Lampton, M.

1988-01-01

Comprehensive measurements are presented for the quantum detection efficiency (QDE) of the microchannel plate materials CsI, KBr, KCl, and MgF2, over the 44-1800 A wavelength range. QDEs in excess of 40 percent are achieved by several materials in specific wavelength regions of the EUV. Structure is noted in the wavelength dependence of the QDE that is directly related to the valence-band/conduction-band gap energy and the onset of atomic-like resonant transitions. A simple photocathode model allows interpretation of these features, together with the QDE efficiency variation, as a function of illumination angle.

A comprehensive profile of DNA copy number variations in a Korean population: identification of copy number invariant regions among Koreans.

PubMed

Jeon, Jae Pil; Shim, Sung Mi; Jung, Jong Sun; Nam, Hye Young; Lee, Hye Jin; Oh, Berm Seok; Kim, Kuchan; Kim, Hyung Lae; Han, Bok Ghee

2009-09-30

To examine copy number variations among the Korean population, we compared individual genomes with the Korean reference genome assembly using the publicly available Korean HapMap SNP 50 k chip data from 90 individuals. Korean individuals exhibited 123 copy number variation regions (CNVRs) covering 27.2 mb, equivalent to 1.0% of the genome in the copy number variation (CNV) analysis using the combined criteria of P value (P<0.01) and standard deviation of copy numbers (SD>or= 0.25) among study subjects. In contrast, when compared to the Affymetrix reference genome assembly from multiple ethnic groups, considerably more CNVRs (n=643) were detected in larger proportions (5.0%) of the genome covering 135.1 mb even by more stringent criteria (P<0.001 and SD>or=0.25), reflecting ethnic diversity of structural variations between Korean and other populations. Some CNVRs were validated by the quantitative multiplex PCR of short fluorescent fragment (QMPSF) method, and then copy number invariant regions were detected among the study subjects. These copy number invariant regions would be used as good internal controls for further CNV studies. Lastly, we demonstrated that the CNV information could stratify even a single ethnic population with a proper reference genome assembly from multiple heterogeneous populations.

The Evolution of Personality Variation in Humans and Other Animals

ERIC Educational Resources Information Center

Nettle, Daniel

2006-01-01

A comprehensive evolutionary framework for understanding the maintenance of heritable behavioral variation in humans is yet to be developed. Some evolutionary psychologists have argued that heritable variation will not be found in important, fitness-relevant characteristics because of the winnowing effect of natural selection. This article…

The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data

PubMed Central

Clarke, Laura; Fairley, Susan; Zheng-Bradley, Xiangqun; Streeter, Ian; Perry, Emily; Lowy, Ernesto; Tassé, Anne-Marie; Flicek, Paul

2017-01-01

The International Genome Sample Resource (IGSR; http://www.internationalgenome.org) expands in data type and population diversity the resources from the 1000 Genomes Project. IGSR represents the largest open collection of human variation data and provides easy access to these resources. IGSR was established in 2015 to maintain and extend the 1000 Genomes Project data, which has been widely used as a reference set of human variation and by researchers developing analysis methods. IGSR has mapped all of the 1000 Genomes sequence to the newest human reference (GRCh38), and will release updated variant calls to ensure maximal usefulness of the existing data. IGSR is collecting new structural variation data on the 1000 Genomes samples from long read sequencing and other technologies, and will collect relevant functional data into a single comprehensive resource. IGSR is extending coverage with new populations sequenced by collaborating groups. Here, we present the new data and analysis that IGSR has made available. We have also introduced a new data portal that increases discoverability of our data—previously only browseable through our FTP site—by focusing on particular samples, populations or data sets of interest. PMID:27638885

Apprehending ganglioside diversity: a comprehensive methodological approach[S

PubMed Central

Masson, Elodie A. Y.; Sibille, Estelle; Martine, Lucy; Chaux-Picquet, Fanny; Bretillon, Lionel; Berdeaux, Olivier

2015-01-01

Gangliosides (GGs) make a wide family of glycosphingolipids ubiquitously expressed in mammalian tissues and particularly abundant in the brain and nervous system. They exhibit a huge diversity due to structural variations in both their oligosaccharidic chain and ceramide moiety, which represent a real analytical challenge. Since their discovery in the 1940s, methods have persistently improved until the emergence of LC/MS, which offers a high level of specificity and sensitivity and is suitable with high-throughput profiling studies. We describe here a comprehensive approach relying on various techniques and aiming at fully characterizing GGs in biological samples. First, total GG content was determined by a biochemical assay. Second, GG class composition was assessed by high-performance thin-layer chromatography followed by colorimetric revelation. Then, ceramide types of GG classes were identified, and their relative quantification was performed thanks to the development of a powerful and reliable LC/MS method. Finally, ceramides were structurally characterized, and minor and less common GG classes were identified using high-resolution MS. These methods were applied to the rat retina to provide an exhaustive description of its GG composition, giving the base for a better understanding of the precise roles of GGs in this tissue. PMID:26142958

Why the Simple View of Reading Is Not Simplistic: Unpacking Component Skills of Reading Using a Direct and Indirect Effect Model of Reading (DIER)

ERIC Educational Resources Information Center

Kim, Young-Suk Grace

2017-01-01

Pathways of relations of language, cognitive, and literacy skills (i.e., working memory, vocabulary, grammatical knowledge, inference, comprehension monitoring, word reading, and listening comprehension) to reading comprehension were examined by comparing four variations of direct and indirect effects model of reading. Results from 350…

Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm.

PubMed

Yu, Isseki; Mori, Takaharu; Ando, Tadashi; Harada, Ryuhei; Jung, Jaewoon; Sugita, Yuji; Feig, Michael

2016-11-01

Biological macromolecules function in highly crowded cellular environments. The structure and dynamics of proteins and nucleic acids are well characterized in vitro, but in vivo crowding effects remain unclear. Using molecular dynamics simulations of a comprehensive atomistic model cytoplasm we found that protein-protein interactions may destabilize native protein structures, whereas metabolite interactions may induce more compact states due to electrostatic screening. Protein-protein interactions also resulted in significant variations in reduced macromolecular diffusion under crowded conditions, while metabolites exhibited significant two-dimensional surface diffusion and altered protein-ligand binding that may reduce the effective concentration of metabolites and ligands in vivo. Metabolic enzymes showed weak non-specific association in cellular environments attributed to solvation and entropic effects. These effects are expected to have broad implications for the in vivo functioning of biomolecules. This work is a first step towards physically realistic in silico whole-cell models that connect molecular with cellular biology.

Copy number variation identification and analysis of the chicken genome using a 60K SNP BeadChip.

PubMed

Rao, Y S; Li, J; Zhang, R; Lin, X R; Xu, J G; Xie, L; Xu, Z Q; Wang, L; Gan, J K; Xie, X J; He, J; Zhang, X Q

2016-08-01

Copy number variation (CNV) is an important source of genetic variation in organisms and a main factor that affects phenotypic variation. A comprehensive study of chicken CNV can provide valuable information on genetic diversity and facilitate future analyses of associations between CNV and economically important traits in chickens. In the present study, an F2 full-sib chicken population (554 individuals), established from a cross between Xinghua and White Recessive Rock chickens, was used to explore CNV in the chicken genome. Genotyping was performed using a chicken 60K SNP BeadChip. A total of 1,875 CNV were detected with the PennCNV algorithm, and the average number of CNV was 3.42 per individual. The CNV were distributed across 383 independent CNV regions (CNVR) and covered 41 megabases (3.97%) of the chicken genome. Seven CNVR in 108 individuals were validated by quantitative real-time PCR, and 81 of these individuals (75%) also were detected with the PennCNV algorithm. In total, 274 CNVR (71.54%) identified in the current study were previously reported. Of these, 147 (38.38%) were reported in at least 2 studies. Additionally, 109 of the CNVR (28.46%) discovered here are novel. A total of 709 genes within or overlapping with the CNVR was retrieved. Out of the 2,742 quantitative trait loci (QTL) collected in the chicken QTL database, 43 QTL had confidence intervals overlapping with the CNVR, and 32 CNVR encompassed one or more functional genes. The functional genes located in the CNVR are likely to be the QTG that are associated with underlying economic traits. This study considerably expands our insight into the structural variation in the genome of chickens and provides an important resource for genomic variation, especially for genomic structural variation related to economic traits in chickens. © 2016 Poultry Science Association Inc.

Intraspecific karyotypic polymorphism is highly concordant with allozyme variation in Lysimachia mauritiana (Primulaceae: Myrsinoideae) in Taiwan: implications for the colonization history and dispersal patterns of coastal plants

PubMed Central

Kono, Yoshiko; Chung, Kuo-Fang; Chen, Chih-Hui; Hoshi, Yoshikazu; Setoguchi, Hiroaki; Chou, Chang-Hung; Oginuma, Kazuo; Peng, Ching-I

2012-01-01

Background and Aims Investigating intraspecific karyotypic and genetic variations jointly can provide unique insights into how historical, ecological and cytogenetic factors influence microevolution. A coastal herb, Lysimachia mauritiana, exhibits extensive karyotypic polymorphism and displays a complex cytogeographic pattern across the Ryukyus. To explore whether a similar degree of chromosomal variation exists south of the Ryukyus, and in an attempt to ascertain the mechanisms that may have generated the patterns, comprehensive sampling was conducted in Taiwan. Methods Karyotypes were analysed at mitotic metaphase for 550 individuals from 42 populations throughout Taiwan Proper and its adjacent islands. In addition, genetic variation was estimated using 12 allozymes (21 loci) of 314 individuals sampled from 12 localities. Key Results Four chromosome numbers and eight cytotypes, including four endemic cytotypes, were detected. Cytotype distributions were highly structured geographically, with single cytotypes present in most populations and four major cytotypes dominating the north, east and south of Taiwan and the Penghu Archipelago. Allozyme variation was very low and F-statistics indicated an extremely high level of population differentiation, implying limited gene flow among populations. Cluster analysis of allozyme variation uncovered four geographic groups, each corresponding perfectly to the four dominant cytotypes. The geographic structure of cytotype distribution and allozyme variation probably resulted from severe genetic drift triggered by genetic bottlenecks, suggesting that Taiwanese populations were likely to be derived from four independent founder events. In the few localities with multiple cytotypes, cytogeographic patterns and inferences of chromosomal evolution revealed a trend of northward dispersal, consistent with the course of the Kuroshio Current that has been influential in shaping the coastal biota of the region. Conclusions The data elucidate the patterns of colonization and the effects of the Kuroshio Current on the distribution of L. mauritiana in Taiwan. These inferences are highly relevant to other coastal plant species in the region and will stimulate further studies. PMID:23022678

Mechanical analysis of non-uniform bi-directional functionally graded intelligent micro-beams using modified couple stress theory

NASA Astrophysics Data System (ADS)

Bakhshi Khaniki, Hossein; Rajasekaran, Sundaramoorthy

2018-05-01

This study develops a comprehensive investigation on mechanical behavior of non-uniform bi-directional functionally graded beam sensors in the framework of modified couple stress theory. Material variation is modelled through both length and thickness directions using power-law, sigmoid and exponential functions. Moreover, beam is assumed with linear, exponential and parabolic cross-section variation through the length using power-law and sigmoid varying functions. Using these assumptions, a general model for microbeams is presented and formulated by employing Hamilton’s principle. Governing equations are solved using a mixed finite element method with Lagrangian interpolation technique, Gaussian quadrature method and Wilson’s Lagrangian multiplier method. It is shown that by using bi-directional functionally graded materials in nonuniform microbeams, mechanical behavior of such structures could be affected noticeably and scale parameter has a significant effect in changing the rigidity of nonuniform bi-directional functionally graded beams.

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

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

Genome-wide association study of Arabidopsis thaliana leaf microbial community.

PubMed

Horton, Matthew W; Bodenhausen, Natacha; Beilsmith, Kathleen; Meng, Dazhe; Muegge, Brian D; Subramanian, Sathish; Vetter, M Madlen; Vilhjálmsson, Bjarni J; Nordborg, Magnus; Gordon, Jeffrey I; Bergelson, Joy

2014-11-10

Identifying the factors that influence the outcome of host-microbial interactions is critical to protecting biodiversity, minimizing agricultural losses and improving human health. A few genes that determine symbiosis or resistance to infectious disease have been identified in model species, but a comprehensive examination of how a host genotype influences the structure of its microbial community is lacking. Here we report the results of a field experiment with the model plant Arabidopsis thaliana to identify the fungi and bacteria that colonize its leaves and the host loci that influence the microbe numbers. The composition of this community differs among accessions of A. thaliana. Genome-wide association studies (GWAS) suggest that plant loci responsible for defense and cell wall integrity affect variation in this community. Furthermore, species richness in the bacterial community is shaped by host genetic variation, notably at loci that also influence the reproduction of viruses, trichome branching and morphogenesis.

Conformation and Stability of Intramolecular Telomeric G-Quadruplexes: Sequence Effects in the Loops

PubMed Central

Sattin, Giovanna; Artese, Anna; Nadai, Matteo; Costa, Giosuè; Parrotta, Lucia; Alcaro, Stefano; Palumbo, Manlio; Richter, Sara N.

2013-01-01

Telomeres are guanine-rich sequences that protect the ends of chromosomes. These regions can fold into G-quadruplex structures and their stabilization by G-quadruplex ligands has been employed as an anticancer strategy. Genetic analysis in human telomeres revealed extensive allelic variation restricted to loop bases, indicating that the variant telomeric sequences maintain the ability to fold into G-quadruplex. To assess the effect of mutations in loop bases on G-quadruplex folding and stability, we performed a comprehensive analysis of mutant telomeric sequences by spectroscopic techniques, molecular dynamics simulations and gel electrophoresis. We found that when the first position in the loop was mutated from T to C or A the resulting structure adopted a less stable antiparallel topology; when the second position was mutated to C or A, lower thermal stability and no evident conformational change were observed; in contrast, substitution of the third position from A to C induced a more stable and original hybrid conformation, while mutation to T did not significantly affect G-quadruplex topology and stability. Our results indicate that allelic variations generate G-quadruplex telomeric structures with variable conformation and stability. This aspect needs to be taken into account when designing new potential anticancer molecules. PMID:24367632

Projected quasiparticle theory for molecular electronic structure

NASA Astrophysics Data System (ADS)

Scuseria, Gustavo E.; Jiménez-Hoyos, Carlos A.; Henderson, Thomas M.; Samanta, Kousik; Ellis, Jason K.

2011-09-01

We derive and implement symmetry-projected Hartree-Fock-Bogoliubov (HFB) equations and apply them to the molecular electronic structure problem. All symmetries (particle number, spin, spatial, and complex conjugation) are deliberately broken and restored in a self-consistent variation-after-projection approach. We show that the resulting method yields a comprehensive black-box treatment of static correlations with effective one-electron (mean-field) computational cost. The ensuing wave function is of multireference character and permeates the entire Hilbert space of the problem. The energy expression is different from regular HFB theory but remains a functional of an independent quasiparticle density matrix. All reduced density matrices are expressible as an integration of transition density matrices over a gauge grid. We present several proof-of-principle examples demonstrating the compelling power of projected quasiparticle theory for quantum chemistry.

The Reading-Writing Connection II: Text Structure and Reading Comprehension.

ERIC Educational Resources Information Center

Schatzberg-Smith, Kathleen

1987-01-01

Distinguishes between macrostructures and microstructures in text, reviews research on the comprehension of text structures, and concludes that both theory and research support the presence of a link between text structure and reading comprehension. (DMM)

Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop.

PubMed

Hazzouri, Khaled M; Flowers, Jonathan M; Visser, Hendrik J; Khierallah, Hussam S M; Rosas, Ulises; Pham, Gina M; Meyer, Rachel S; Johansen, Caryn K; Fresquez, Zoë A; Masmoudi, Khaled; Haider, Nadia; El Kadri, Nabila; Idaghdour, Youssef; Malek, Joel A; Thirkhill, Deborah; Markhand, Ghulam S; Krueger, Robert R; Zaid, Abdelouahhab; Purugganan, Michael D

2015-11-09

Date palms (Phoenix dactylifera) are the most significant perennial crop in arid regions of the Middle East and North Africa. Here, we present a comprehensive catalogue of approximately seven million single nucleotide polymorphisms in date palms based on whole genome re-sequencing of a collection of 62 cultivars. Population structure analysis indicates a major genetic divide between North Africa and the Middle East/South Asian date palms, with evidence of admixture in cultivars from Egypt and Sudan. Genome-wide scans for selection suggest at least 56 genomic regions associated with selective sweeps that may underlie geographic adaptation. We report candidate mutations for trait variation, including nonsense polymorphisms and presence/absence variation in gene content in pathways for key agronomic traits. We also identify a copia-like retrotransposon insertion polymorphism in the R2R3 myb-like orthologue of the oil palm virescens gene associated with fruit colour variation. This analysis documents patterns of post-domestication diversification and provides a genomic resource for this economically important perennial tree crop.

Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop

PubMed Central

Hazzouri, Khaled M.; Flowers, Jonathan M.; Visser, Hendrik J.; Khierallah, Hussam S. M.; Rosas, Ulises; Pham, Gina M.; Meyer, Rachel S.; Johansen, Caryn K.; Fresquez, Zoë A.; Masmoudi, Khaled; Haider, Nadia; El Kadri, Nabila; Idaghdour, Youssef; Malek, Joel A.; Thirkhill, Deborah; Markhand, Ghulam S.; Krueger, Robert R.; Zaid, Abdelouahhab; Purugganan, Michael D.

2015-01-01

Date palms (Phoenix dactylifera) are the most significant perennial crop in arid regions of the Middle East and North Africa. Here, we present a comprehensive catalogue of approximately seven million single nucleotide polymorphisms in date palms based on whole genome re-sequencing of a collection of 62 cultivars. Population structure analysis indicates a major genetic divide between North Africa and the Middle East/South Asian date palms, with evidence of admixture in cultivars from Egypt and Sudan. Genome-wide scans for selection suggest at least 56 genomic regions associated with selective sweeps that may underlie geographic adaptation. We report candidate mutations for trait variation, including nonsense polymorphisms and presence/absence variation in gene content in pathways for key agronomic traits. We also identify a copia-like retrotransposon insertion polymorphism in the R2R3 myb-like orthologue of the oil palm virescens gene associated with fruit colour variation. This analysis documents patterns of post-domestication diversification and provides a genomic resource for this economically important perennial tree crop. PMID:26549859

Geography, Ethnicity or Subsistence-Specific Variations in Human Microbiome Composition and Diversity

PubMed Central

Gupta, Vinod K.; Paul, Sandip; Dutta, Chitra

2017-01-01

One of the fundamental issues in the microbiome research is characterization of the healthy human microbiota. Recent studies have elucidated substantial divergences in the microbiome structure between healthy individuals from different race and ethnicity. This review provides a comprehensive account of such geography, ethnicity or life-style-specific variations in healthy microbiome at five major body habitats—Gut, Oral-cavity, Respiratory Tract, Skin, and Urogenital Tract (UGT). The review focuses on the general trend in the human microbiome evolution—a gradual transition in the gross compositional structure along with a continual decrease in diversity of the microbiome, especially of the gut microbiome, as the human populations passed through three stages of subsistence like foraging, rural farming and industrialized urban western life. In general, gut microbiome of the hunter-gatherer populations is highly abundant with Prevotella, Proteobacteria, Spirochaetes, Clostridiales, Ruminobacter etc., while those of the urban communities are often enriched in Bacteroides, Bifidobacterium, and Firmicutes. The oral and skin microbiome are the next most diverse among different populations, while respiratory tract and UGT microbiome show lesser variations. Higher microbiome diversity is observed for oral-cavity in hunter-gatherer group with higher prevalence of Haemophilus than agricultural group. In case of skin microbiome, rural and urban Chinese populations show variation in abundance of Trabulsiella and Propionibacterium. On the basis of published data, we have characterized the core microbiota—the set of genera commonly found in all populations, irrespective of their geographic locations, ethnicity or mode of subsistence. We have also identified the major factors responsible for geography-based alterations in microbiota; though it is not yet clear which factor plays a dominant role in shaping the microbiome—nature or nurture, host genetics or his environment. Some of the geographical/racial variations in microbiome structure have been attributed to differences in host genetics and innate/adaptive immunity, while in many other cases, cultural/behavioral features like diet, hygiene, parasitic load, environmental exposure etc. overshadow genetics. The ethnicity or population-specific variations in human microbiome composition, as reviewed in this report, question the universality of the microbiome-based therapeutic strategies and recommend for geographically tailored community-scale approaches to microbiome engineering. PMID:28690602

Natural genetic variation of root system architecture from Arabidopsis to Brachypodium: towards adaptive value.

PubMed

Pacheco-Villalobos, David; Hardtke, Christian S

2012-06-05

Root system architecture is a trait that displays considerable plasticity because of its sensitivity to environmental stimuli. Nevertheless, to a significant degree it is genetically constrained as suggested by surveys of its natural genetic variation. A few regulators of root system architecture have been isolated as quantitative trait loci through the natural variation approach in the dicotyledon model, Arabidopsis. This provides proof of principle that allelic variation for root system architecture traits exists, is genetically tractable, and might be exploited for crop breeding. Beyond Arabidopsis, Brachypodium could serve as both a credible and experimentally accessible model for root system architecture variation in monocotyledons, as suggested by first glimpses of the different root morphologies of Brachypodium accessions. Whether a direct knowledge transfer gained from molecular model system studies will work in practice remains unclear however, because of a lack of comprehensive understanding of root system physiology in the native context. For instance, apart from a few notable exceptions, the adaptive value of genetic variation in root system modulators is unknown. Future studies should thus aim at comprehensive characterization of the role of genetic players in root system architecture variation by taking into account the native environmental conditions, in particular soil characteristics.

Measurement and simulation of the relatively competitive advantages and weaknesses between economies based on bipartite graph theory.

PubMed

Guan, Jun; Xu, Xiaoyu; Wu, Shan; Xing, Lizhi

2018-01-01

The input-output table is very comprehensive and detailed in describing the national economic systems with abundant economic relationships, which contain supply and demand information among various industrial sectors. The complex network, a theory, and method for measuring the structure of a complex system can depict the structural characteristics of the internal structure of the researched object by measuring the structural indicators of the social and economic systems, revealing the complex relationships between the inner hierarchies and the external economic functions. In this paper, functions of industrial sectors on the global value chain are to be distinguished with bipartite graph theory, and inter-sector competitive relationships are to be extracted through resource allocation process. Furthermore, quantitative analysis indices will be proposed under the perspective of a complex network, which will be used to bring about simulations on the variation tendencies of economies' status in different situations of commercial intercourses. Finally, a new econophysics analytical framework of international trade is to be established.

Measurement and simulation of the relatively competitive advantages and weaknesses between economies based on bipartite graph theory

PubMed Central

Guan, Jun; Xu, Xiaoyu; Wu, Shan

2018-01-01

The input-output table is very comprehensive and detailed in describing the national economic systems with abundant economic relationships, which contain supply and demand information among various industrial sectors. The complex network, a theory, and method for measuring the structure of a complex system can depict the structural characteristics of the internal structure of the researched object by measuring the structural indicators of the social and economic systems, revealing the complex relationships between the inner hierarchies and the external economic functions. In this paper, functions of industrial sectors on the global value chain are to be distinguished with bipartite graph theory, and inter-sector competitive relationships are to be extracted through resource allocation process. Furthermore, quantitative analysis indices will be proposed under the perspective of a complex network, which will be used to bring about simulations on the variation tendencies of economies’ status in different situations of commercial intercourses. Finally, a new econophysics analytical framework of international trade is to be established. PMID:29813083

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

PubMed

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

2018-01-01

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

Assessment of genetic diversity, population structure, and gene flow of tigers (Panthera tigris tigris) across Nepal's Terai Arc Landscape.

PubMed

Thapa, Kanchan; Manandhar, Sulochana; Bista, Manisha; Shakya, Jivan; Sah, Govind; Dhakal, Maheshwar; Sharma, Netra; Llewellyn, Bronwyn; Wultsch, Claudia; Waits, Lisette P; Kelly, Marcella J; Hero, Jean-Marc; Hughes, Jane; Karmacharya, Dibesh

2018-01-01

With fewer than 200 tigers (Panthera tigris tigris) left in Nepal, that are generally confined to five protected areas across the Terai Arc Landscape, genetic studies are needed to provide crucial information on diversity and connectivity for devising an effective country-wide tiger conservation strategy. As part of the Nepal Tiger Genome Project, we studied landscape change, genetic variation, population structure, and gene flow of tigers across the Terai Arc Landscape by conducting Nepal's first comprehensive and systematic scat-based, non-invasive genetic survey. Of the 770 scat samples collected opportunistically from five protected areas and six presumed corridors, 412 were tiger (57%). Out of ten microsatellite loci, we retain eight markers that were used in identifying 78 individual tigers. We used this dataset to examine population structure, genetic variation, contemporary gene flow, and potential population bottlenecks of tigers in Nepal. We detected three genetic clusters consistent with three demographic sub-populations and found moderate levels of genetic variation (He = 0.61, AR = 3.51) and genetic differentiation (FST = 0.14) across the landscape. We detected 3-7 migrants, confirming the potential for dispersal-mediated gene flow across the landscape. We found evidence of a bottleneck signature likely caused by large-scale land-use change documented in the last two centuries in the Terai forest. Securing tiger habitat including functional forest corridors is essential to enhance gene flow across the landscape and ensure long-term tiger survival. This requires cooperation among multiple stakeholders and careful conservation planning to prevent detrimental effects of anthropogenic activities on tigers.

Assessment of genetic diversity, population structure, and gene flow of tigers (Panthera tigris tigris) across Nepal's Terai Arc Landscape

PubMed Central

Manandhar, Sulochana; Bista, Manisha; Shakya, Jivan; Sah, Govind; Dhakal, Maheshwar; Sharma, Netra; Llewellyn, Bronwyn; Wultsch, Claudia; Waits, Lisette P.; Kelly, Marcella J.; Hero, Jean-Marc; Hughes, Jane

2018-01-01

With fewer than 200 tigers (Panthera tigris tigris) left in Nepal, that are generally confined to five protected areas across the Terai Arc Landscape, genetic studies are needed to provide crucial information on diversity and connectivity for devising an effective country-wide tiger conservation strategy. As part of the Nepal Tiger Genome Project, we studied landscape change, genetic variation, population structure, and gene flow of tigers across the Terai Arc Landscape by conducting Nepal’s first comprehensive and systematic scat-based, non-invasive genetic survey. Of the 770 scat samples collected opportunistically from five protected areas and six presumed corridors, 412 were tiger (57%). Out of ten microsatellite loci, we retain eight markers that were used in identifying 78 individual tigers. We used this dataset to examine population structure, genetic variation, contemporary gene flow, and potential population bottlenecks of tigers in Nepal. We detected three genetic clusters consistent with three demographic sub-populations and found moderate levels of genetic variation (He = 0.61, AR = 3.51) and genetic differentiation (FST = 0.14) across the landscape. We detected 3–7 migrants, confirming the potential for dispersal-mediated gene flow across the landscape. We found evidence of a bottleneck signature likely caused by large-scale land-use change documented in the last two centuries in the Terai forest. Securing tiger habitat including functional forest corridors is essential to enhance gene flow across the landscape and ensure long-term tiger survival. This requires cooperation among multiple stakeholders and careful conservation planning to prevent detrimental effects of anthropogenic activities on tigers. PMID:29561865

A comprehensive dairy valorization model.

PubMed

Banaszewska, A; Cruijssen, F; van der Vorst, J G A J; Claassen, G D H; Kampman, J L

2013-02-01

Dairy processors face numerous challenges resulting from both unsteady dairy markets and some specific characteristics of dairy supply chains. To maintain a competitive position on the market, companies must look beyond standard solutions currently used in practice. This paper presents a comprehensive dairy valorization model that serves as a decision support tool for mid-term allocation of raw milk to end products and production planning. The developed model was used to identify the optimal product portfolio composition. The model allocates raw milk to the most profitable dairy products while accounting for important constraints (i.e., recipes, composition variations, dairy production interdependencies, seasonality, demand, supply, capacities, and transportation flows). The inclusion of all relevant constraints and the ease of understanding dairy production dynamics make the model comprehensive. The developed model was tested at the international dairy processor FrieslandCampina (Amersfoort, the Netherlands). The structure of the model and its output were discussed in multiple sessions with and approved by relevant FrieslandCampina employees. The elements included in the model were considered necessary to optimally valorize raw milk. To illustrate the comprehensiveness and functionality of the model, we analyzed the effect of seasonality on milk valorization. A large difference in profit and a shift in the allocation of milk showed that seasonality has a considerable impact on the valorization of raw milk. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Inter- and intraspecific variation in leaf economic traits in wheat and maize

PubMed Central

Hale, Christine E; Cerabolini, Bruno E L; Cornelissen, Johannes H C; Craine, Joseph; Gough, William A; Kattge, Jens; Tirona, Cairan K F

2018-01-01

Abstract Leaf Economics Spectrum (LES) trait variation underpins multiple agroecological processes and many prominent crop yield models. While there are numerous independent studies assessing trait variation in crops, to date there have been no comprehensive assessments of intraspecific trait variation (ITV) in LES traits for wheat and maize: the world’s most widespread crops. Using trait databases and peer-reviewed literature, we compiled over 700 records of specific leaf area (SLA), maximum photosynthetic rates (Amax) and leaf nitrogen (N) concentrations, for wheat and maize. We evaluated intraspecific LES trait variation, and intraspecific trait–environment relationships. While wheat and maize occupy the upper 90th percentile of LES trait values observed across a global species pool, ITV ranged widely across the LES in wheat and maize. Fertilization treatments had strong impacts on leaf N, while plant developmental stage (here standardized as the number of days since planting) had strong impacts on Amax; days since planting, N fertilization and irrigation all influenced SLA. When controlling for these factors, intraspecific responses to temperature and precipitation explained 39.4 and 43.7 % of the variation in Amax and SLA, respectively, but only 5.4 % of the variation in leaf N. Despite a long history of domestication in these species, ITV in wheat and maize among and within cultivars remains large. Intraspecific trait variation is a critical consideration to refine regional to global models of agroecosystem structure, function and food security. Considerable opportunities and benefits exist for consolidating a crop trait database for a wider range of domesticated plant species. PMID:29484152

Inter- and intraspecific variation in leaf economic traits in wheat and maize.

PubMed

Martin, Adam R; Hale, Christine E; Cerabolini, Bruno E L; Cornelissen, Johannes H C; Craine, Joseph; Gough, William A; Kattge, Jens; Tirona, Cairan K F

2018-02-01

Leaf Economics Spectrum (LES) trait variation underpins multiple agroecological processes and many prominent crop yield models. While there are numerous independent studies assessing trait variation in crops, to date there have been no comprehensive assessments of intraspecific trait variation (ITV) in LES traits for wheat and maize: the world's most widespread crops. Using trait databases and peer-reviewed literature, we compiled over 700 records of specific leaf area (SLA), maximum photosynthetic rates ( A max ) and leaf nitrogen (N) concentrations, for wheat and maize. We evaluated intraspecific LES trait variation, and intraspecific trait-environment relationships. While wheat and maize occupy the upper 90th percentile of LES trait values observed across a global species pool, ITV ranged widely across the LES in wheat and maize. Fertilization treatments had strong impacts on leaf N, while plant developmental stage (here standardized as the number of days since planting) had strong impacts on A max ; days since planting, N fertilization and irrigation all influenced SLA. When controlling for these factors, intraspecific responses to temperature and precipitation explained 39.4 and 43.7 % of the variation in A max and SLA, respectively, but only 5.4 % of the variation in leaf N. Despite a long history of domestication in these species, ITV in wheat and maize among and within cultivars remains large. Intraspecific trait variation is a critical consideration to refine regional to global models of agroecosystem structure, function and food security. Considerable opportunities and benefits exist for consolidating a crop trait database for a wider range of domesticated plant species.

On Teaching about the Coefficient of Variation in Introductory Statistics Courses

ERIC Educational Resources Information Center

Trafimow, David

2014-01-01

The standard deviation is related to the mean by virtue of the coefficient of variation. Teachers of statistics courses can make use of that fact to make the standard deviation more comprehensible for statistics students.

Spatiotemporal Dynamics and Epistatic Interaction Sites in Dengue Virus Type 1: A Comprehensive Sequence-Based Analysis

PubMed Central

Chu, Pei-Yu; Ke, Guan-Ming; Chen, Po-Chih; Liu, Li-Teh; Tsai, Yen-Chun; Tsai, Jih-Jin

2013-01-01

The continuing threat of dengue fever necessitates a comprehensive characterisation of its epidemiological trends. Phylogenetic and recombination events were reconstructed based on 100 worldwide dengue virus (DENV) type 1 genome sequences with an outgroup (prototypes of DENV2-4). The phylodynamic characteristics and site-specific variation were then analysed using data without the outgroup. Five genotypes (GI-GV) and a ladder-like structure with short terminal branch topology were observed in this study. Apparently, the transmission of DENV1 was geographically random before gradual localising with human activity as GI-GIII in South Asia, GIV in the South Pacific, and GV in the Americas. Genotypes IV and V have recently shown higher population densities compared to older genotypes. All codon regions and all tree branches were skewed toward a negative selection, which indicated that their variation was restricted by protein function. Notably, multi-epistatic interaction sites were found in both PrM 221 and NS3 1730. Recombination events accumulated in regions E, NS3-NS4A, and particularly in region NS5. The estimated coevolution pattern also highlights the need for further study of the biological role of protein PrM 221 and NS3 1730. The recent transmission of emergent GV sublineages into Central America and Europe mandates closely monitoring of genotype interaction and succession. PMID:24040199

Comprehensive analysis of line-edge and line-width roughness for EUV lithography

NASA Astrophysics Data System (ADS)

Bonam, Ravi; Liu, Chi-Chun; Breton, Mary; Sieg, Stuart; Seshadri, Indira; Saulnier, Nicole; Shearer, Jeffrey; Muthinti, Raja; Patlolla, Raghuveer; Huang, Huai

2017-03-01

Pattern transfer fidelity is always a major challenge for any lithography process and needs continuous improvement. Lithographic processes in semiconductor industry are primarily driven by optical imaging on photosensitive polymeric material (resists). Quality of pattern transfer can be assessed by quantifying multiple parameters such as, feature size uniformity (CD), placement, roughness, sidewall angles etc. Roughness in features primarily corresponds to variation of line edge or line width and has gained considerable significance, particularly due to shrinking feature sizes and variations of features in the same order. This has caused downstream processes (Etch (RIE), Chemical Mechanical Polish (CMP) etc.) to reconsider respective tolerance levels. A very important aspect of this work is relevance of roughness metrology from pattern formation at resist to subsequent processes, particularly electrical validity. A major drawback of current LER/LWR metric (sigma) is its lack of relevance across multiple downstream processes which effects material selection at various unit processes. In this work we present a comprehensive assessment of Line Edge and Line Width Roughness at multiple lithographic transfer processes. To simulate effect of roughness a pattern was designed with periodic jogs on the edges of lines with varying amplitudes and frequencies. There are numerous methodologies proposed to analyze roughness and in this work we apply them to programmed roughness structures to assess each technique's sensitivity. This work also aims to identify a relevant methodology to quantify roughness with relevance across downstream processes.

A comprehensive data set of lake surface water temperature over the Tibetan Plateau derived from MODIS LST products 2001–2015

PubMed Central

Wan, Wei; Li, Huan; Xie, Hongjie; Hong, Yang; Long, Di; Zhao, Limin; Han, Zhongying; Cui, Yaokui; Liu, Baojian; Wang, Cunguang; Yang, Wenting

2017-01-01

Lake surface water temperature (LSWT) is sensitive to long-term changes in thermal structure of lakes and regional air temperature. In the context of global climate change, recent studies showed a significant warming trend of LSWT based on investigating 291 lakes (71% are large lakes, ≥50 km2 each) globally. However, further efforts are needed to examine variation in LSWT at finer regional spatial and temporal scales. The Tibetan Plateau (TP), known as ‘the Roof of the World’ and ‘Asia’s water towers’, exerts large influences on and is sensitive to regional and even global climates. Aiming to examine detailed changing patterns and potential driven mechanisms for temperature variations of lakes across the TP region, this paper presents the first comprehensive data set of 15-year (2001–2015) nighttime and daytime LSWT for 374 lakes (≥10 km2 each), using MODIS (Moderate Resolution Imaging Spectroradiometer) Land Surface Temperature (LST) products as well as four lake boundary shapefiles (i.e., 2002, 2005, 2009, and 2014) derived from Landsat/CBERS/GaoFen-1 satellite images. The data set itself reveals significant information on LSWT and its changes over the TP and is an indispensable variable for numerous applications related to climate change, water budget analysis (particularly lake evaporation), water storage changes, glacier melting and permafrost degradation, etc. PMID:28742066

A comprehensive data set of lake surface water temperature over the Tibetan Plateau derived from MODIS LST products 2001-2015.

PubMed

Wan, Wei; Li, Huan; Xie, Hongjie; Hong, Yang; Long, Di; Zhao, Limin; Han, Zhongying; Cui, Yaokui; Liu, Baojian; Wang, Cunguang; Yang, Wenting

2017-07-25

Lake surface water temperature (LSWT) is sensitive to long-term changes in thermal structure of lakes and regional air temperature. In the context of global climate change, recent studies showed a significant warming trend of LSWT based on investigating 291 lakes (71% are large lakes, ≥50 km 2 each) globally. However, further efforts are needed to examine variation in LSWT at finer regional spatial and temporal scales. The Tibetan Plateau (TP), known as 'the Roof of the World' and 'Asia's water towers', exerts large influences on and is sensitive to regional and even global climates. Aiming to examine detailed changing patterns and potential driven mechanisms for temperature variations of lakes across the TP region, this paper presents the first comprehensive data set of 15-year (2001-2015) nighttime and daytime LSWT for 374 lakes (≥10 km 2 each), using MODIS (Moderate Resolution Imaging Spectroradiometer) Land Surface Temperature (LST) products as well as four lake boundary shapefiles (i.e., 2002, 2005, 2009, and 2014) derived from Landsat/CBERS/GaoFen-1 satellite images. The data set itself reveals significant information on LSWT and its changes over the TP and is an indispensable variable for numerous applications related to climate change, water budget analysis (particularly lake evaporation), water storage changes, glacier melting and permafrost degradation, etc.

Web-Based Text Structure Strategy Instruction Improves Seventh Graders' Content Area Reading Comprehension

ERIC Educational Resources Information Center

Wijekumar, Kausalai; Meyer, Bonnie J. F.; Lei, Puiwa

2017-01-01

Reading comprehension in the content areas is a challenge for many middle grade students. Text structure-based instruction has yielded positive outcomes in reading comprehension at all grade levels in small and large studies. The text structure strategy delivered via the web, called Intelligent Tutoring System for the Text Structure Strategy…

Comprehension and production of idioms in dysphasia.

PubMed

Bush, P G; Drummond, S S

1985-10-01

The comprehension and production of idioms was investigated in 10 dysphasic adults. Two different tasks, one comprehension and the other production, were developed. The production task required the subject to verbally explain 15 idioms. The comprehension task necessitated the selection of the correct figurative representation of the idiom from four illustrations: a literal, a literal variation, a figurative, and an unrelated picture. Results indicated no significant correlation between overall comprehension and production performances. No significant difference was found between the comprehension or the production of idioms when type or severity of dysphasia was considered. A significant difference was found, however, in the type of incorrect response, in that subjects selected the literal depiction more often than other foil representations for the comprehension.

Spectral analysis of magnetic anomalies in and around the Philippine Sea

NASA Astrophysics Data System (ADS)

Tanaka, A.; Ishihara, T.

2009-12-01

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

VarioML framework for comprehensive variation data representation and exchange.

PubMed

Byrne, Myles; Fokkema, Ivo Fac; Lancaster, Owen; Adamusiak, Tomasz; Ahonen-Bishopp, Anni; Atlan, David; Béroud, Christophe; Cornell, Michael; Dalgleish, Raymond; Devereau, Andrew; Patrinos, George P; Swertz, Morris A; Taschner, Peter Em; Thorisson, Gudmundur A; Vihinen, Mauno; Brookes, Anthony J; Muilu, Juha

2012-10-03

Sharing of data about variation and the associated phenotypes is a critical need, yet variant information can be arbitrarily complex, making a single standard vocabulary elusive and re-formatting difficult. Complex standards have proven too time-consuming to implement. The GEN2PHEN project addressed these difficulties by developing a comprehensive data model for capturing biomedical observations, Observ-OM, and building the VarioML format around it. VarioML pairs a simplified open specification for describing variants, with a toolkit for adapting the specification into one's own research workflow. Straightforward variant data can be captured, federated, and exchanged with no overhead; more complex data can be described, without loss of compatibility. The open specification enables push-button submission to gene variant databases (LSDBs) e.g., the Leiden Open Variation Database, using the Cafe Variome data publishing service, while VarioML bidirectionally transforms data between XML and web-application code formats, opening up new possibilities for open source web applications building on shared data. A Java implementation toolkit makes VarioML easily integrated into biomedical applications. VarioML is designed primarily for LSDB data submission and transfer scenarios, but can also be used as a standard variation data format for JSON and XML document databases and user interface components. VarioML is a set of tools and practices improving the availability, quality, and comprehensibility of human variation information. It enables researchers, diagnostic laboratories, and clinics to share that information with ease, clarity, and without ambiguity.

VarioML framework for comprehensive variation data representation and exchange

PubMed Central

2012-01-01

Background Sharing of data about variation and the associated phenotypes is a critical need, yet variant information can be arbitrarily complex, making a single standard vocabulary elusive and re-formatting difficult. Complex standards have proven too time-consuming to implement. Results The GEN2PHEN project addressed these difficulties by developing a comprehensive data model for capturing biomedical observations, Observ-OM, and building the VarioML format around it. VarioML pairs a simplified open specification for describing variants, with a toolkit for adapting the specification into one's own research workflow. Straightforward variant data can be captured, federated, and exchanged with no overhead; more complex data can be described, without loss of compatibility. The open specification enables push-button submission to gene variant databases (LSDBs) e.g., the Leiden Open Variation Database, using the Cafe Variome data publishing service, while VarioML bidirectionally transforms data between XML and web-application code formats, opening up new possibilities for open source web applications building on shared data. A Java implementation toolkit makes VarioML easily integrated into biomedical applications. VarioML is designed primarily for LSDB data submission and transfer scenarios, but can also be used as a standard variation data format for JSON and XML document databases and user interface components. Conclusions VarioML is a set of tools and practices improving the availability, quality, and comprehensibility of human variation information. It enables researchers, diagnostic laboratories, and clinics to share that information with ease, clarity, and without ambiguity. PMID:23031277

Winged Scapula: A Comprehensive Review of Surgical Treatment

PubMed Central

Charran, Ordessia; Yilmaz, Emre; Edwards, Bryan; Muhleman, Mitchel A; Oskouian, Rod J; Tubbs, R. Shane; Loukas, Marios

2017-01-01

Winged scapula is caused by paralysis of the serratus anterior or trapezius muscles due to damage to the long thoracic or accessory nerves, resulting in loss of strength and range of motion of the shoulder. Because this nerve damage can happen in a variety of ways, initial diagnosis may be overlooked. This paper discusses the anatomical structures involved in several variations of winged scapula, the pathogenesis of winged scapula, and several historical and contemporary surgical procedures used to treat this condition. Additionally, this review builds upon the conclusions of several studies in order to suggest areas for continued research regarding the treatment of winged scapula. PMID:29456903

New comprehensive standard seismic noise models and 3D seismic noise variation for Morocco territory, North Africa, obtained using seismic broadband stations

NASA Astrophysics Data System (ADS)

El Fellah, Younes; El-Aal, Abd El-Aziz Khairy Abd; Harnafi, Mimoun; Villaseñor, Antonio

2017-05-01

In the current work, we constructed new comprehensive standard seismic noise models and 3D temporal-spatial seismic noise level cubes for Morocco in north-west Africa to be used for seismological and engineering purposes. Indeed, the original global standard seismic noise models published by Peterson (1993) and their following updates by Astiz and Creager (1995), Ekström (2001) and Berger et al. (2003) had no contributing seismic stations deployed in North Africa. Consequently, this preliminary study was conducted to shed light on seismic noise levels specific to north-west Africa. For this purpose, 23 broadband seismic stations recently installed in different structural domains throughout Morocco are used to study the nature and characteristics of seismic noise and to create seismic noise models for Morocco. Continuous data recorded during 2009, 2010 and 2011 were processed and analysed to construct these new noise models and 3D noise levels from all stations. We compared the Peterson new high-noise model (NHNM) and low-noise model (NLNM) with the Moroccan high-noise model (MHNM) and low-noise model (MLNM). These new noise models are comparable to the United States Geological Survey (USGS) models in the short period band; however, in the period range 1.2 s to 1000 s for MLNM and 10 s to 1000 s for MHNM display significant variations. This variation is attributed to differences in the nature of seismic noise sources that dominate Morocco in these period bands. The results of this study have a new perception about permanent seismic noise models for this spectacular region and can be considered a significant contribution because it supplements the Peterson models and can also be used to site future permanent seismic stations in Morocco.

Relevance of graph literacy in the development of patient-centered communication tools.

PubMed

Nayak, Jasmir G; Hartzler, Andrea L; Macleod, Liam C; Izard, Jason P; Dalkin, Bruce M; Gore, John L

2016-03-01

To determine the literacy skill sets of patients in the context of graphical interpretation of interactive dashboards. We assessed literacy characteristics of prostate cancer patients and assessed comprehension of quality of life dashboards. Health literacy, numeracy and graph literacy were assessed with validated tools. We divided patients into low vs. high numeracy and graph literacy. We report descriptive statistics on literacy, dashboard comprehension, and relationships between groups. We used correlation and multiple linear regressions to examine factors associated with dashboard comprehension. Despite high health literacy in educated patients (78% college educated), there was variation in numeracy and graph literacy. Numeracy and graph literacy scores were correlated (r=0.37). In those with low literacy, graph literacy scores most strongly correlated with dashboard comprehension (r=0.59-0.90). On multivariate analysis, graph literacy was independently associated with dashboard comprehension, adjusting for age, education, and numeracy level. Even among higher educated patients; variation in the ability to comprehend graphs exists. Clinicians must be aware of these differential proficiencies when counseling patients. Tools for patient-centered communication that employ visual displays need to account for literacy capabilities to ensure that patients can effectively engage these resources. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

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

PubMed Central

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

2017-01-01

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

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

PubMed

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

2017-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-10-01

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

Orthopaedic service lines-revisited.

PubMed

Patterson, Cheryl

2008-01-01

This article revisits the application of orthopaedic service lines from early introduction and growth of this organizational approach in the 1980s, through the 1990s, and into the current decade. The author has experienced and worked in various service-line structures through these three decades, as well as the preservice-line era of 1970s orthopaedics. Past lessons learned during earlier phases and then current trends and analysis by industry experts are summarized briefly, with indication given of the future for service lines. Variation versus consistency of certain elements in service-line definitions and in operational models is discussed. Main components of service-line structures and typical processes are described briefly, along with a more detailed section on the service-line director/manager role. Current knowledge contained here will help guide the reader to more "out-of-the-box" thinking toward comprehensive orthopaedic centers of excellence.

Story Map Instruction: A Road Map for Reading Comprehension.

ERIC Educational Resources Information Center

Davis, Zephaniah, T.; McPherson, Michael D.

1989-01-01

Introduces teachers to the development and use of story maps as a tool for promoting reading comprehension. Presents a definition and review of story map research. Explains how to construct story maps, and offers suggestions for starting story map instruction. Provides variations on the use of story maps. (MG)

Effective Implementation of a Comprehension-Improvement Approach in Secondary Schools.

ERIC Educational Resources Information Center

Levine, Daniel U.; Sherk, John K.

This report describes in depth the implementation and impact of instructional strategies to improve students' comprehension skills at three diverse urban secondary schools. While activities and characteristics varied, educators at all three locations were implementing local variations of a school-improvement approach based on the use of the…

The Cumulative Effect of Hyperactivity and Peer Relationships on Reading Comprehension

ERIC Educational Resources Information Center

Johnson, Kaprea F.

2014-01-01

The impact of hyperactivity and peer relationships on academic achievement has long been highlighted in the professional literature. This study highlights how much variation in reading comprehension scores, an indicator of academic achievement, are accounted for by hyperactivity, conduct problems, and peer problems. The participants included 129…

Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection

USDA-ARS?s Scientific Manuscript database

Current advances in sequencing technologies and bioinformatics allow to determine a nearly complete genomic background of rice, a staple food for the poor people. Consequently, comprehensive databases of variation among thousands of varieties is currently being assembled and released. Proper analysi...

Bending induced electrical response variations in ultra-thin flexible chips and device modeling

NASA Astrophysics Data System (ADS)

Heidari, Hadi; Wacker, Nicoleta; Dahiya, Ravinder

2017-09-01

Electronics that conform to 3D surfaces are attracting wider attention from both academia and industry. The research in the field has, thus far, focused primarily on showcasing the efficacy of various materials and fabrication methods for electronic/sensing devices on flexible substrates. As the device response changes are bound to change with stresses induced by bending, the next step will be to develop the capacity to predict the response of flexible systems under various bending conditions. This paper comprehensively reviews the effects of bending on the response of devices on ultra-thin chips in terms of variations in electrical parameters such as mobility, threshold voltage, and device performance (static and dynamic). The discussion also includes variations in the device response due to crystal orientation, applied mechanics, band structure, and fabrication processes. Further, strategies for compensating or minimizing these bending-induced variations have been presented. Following the in-depth analysis, this paper proposes new mathematical relations to simulate and predict the device response under various bending conditions. These mathematical relations have also been used to develop new compact models that have been verified by comparing simulation results with the experimental values reported in the recent literature. These advances will enable next generation computer-aided-design tools to meet the future design needs in flexible electronics.

The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data.

PubMed

Clarke, Laura; Fairley, Susan; Zheng-Bradley, Xiangqun; Streeter, Ian; Perry, Emily; Lowy, Ernesto; Tassé, Anne-Marie; Flicek, Paul

2017-01-04

The International Genome Sample Resource (IGSR; http://www.internationalgenome.org) expands in data type and population diversity the resources from the 1000 Genomes Project. IGSR represents the largest open collection of human variation data and provides easy access to these resources. IGSR was established in 2015 to maintain and extend the 1000 Genomes Project data, which has been widely used as a reference set of human variation and by researchers developing analysis methods. IGSR has mapped all of the 1000 Genomes sequence to the newest human reference (GRCh38), and will release updated variant calls to ensure maximal usefulness of the existing data. IGSR is collecting new structural variation data on the 1000 Genomes samples from long read sequencing and other technologies, and will collect relevant functional data into a single comprehensive resource. IGSR is extending coverage with new populations sequenced by collaborating groups. Here, we present the new data and analysis that IGSR has made available. We have also introduced a new data portal that increases discoverability of our data-previously only browseable through our FTP site-by focusing on particular samples, populations or data sets of interest. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Evaluating mitochondrial DNA variation in autism spectrum disorders

PubMed Central

HADJIXENOFONTOS, ATHENA; SCHMIDT, MICHAEL A.; WHITEHEAD, PATRICE L.; KONIDARI, IOANNA; HEDGES, DALE J.; WRIGHT, HARRY H.; ABRAMSON, RUTH K.; MENON, RAMKUMAR; WILLIAMS, SCOTT M.; CUCCARO, MICHAEL L.; HAINES, JONATHAN L.; GILBERT, JOHN R.; PERICAK-VANCE, MARGARET A.; MARTIN, EDEN R.; MCCAULEY, JACOB L.

2012-01-01

SUMMARY Despite the increasing speculation that oxidative stress and abnormal energy metabolism may play a role in Autism Spectrum Disorders (ASD), and the observation that patients with mitochondrial defects have symptoms consistent with ASD, there are no comprehensive published studies examining the role of mitochondrial variation in autism. Therefore, we have sought to comprehensively examine the role of mitochondrial DNA (mtDNA) variation with regard to ASD risk, employing a multi-phase approach. In phase 1 of our experiment, we examined 132 mtDNA single-nucleotide polymorphisms (SNPs) genotyped as part of our genome-wide association studies of ASD. In phase 2 we genotyped the major European mitochondrial haplogroup-defining variants within an expanded set of autism probands and controls. Finally in phase 3, we resequenced the entire mtDNA in a subset of our Caucasian samples (~400 proband-father pairs). In each phase we tested whether mitochondrial variation showed evidence of association to ASD. Despite a thorough interrogation of mtDNA variation, we found no evidence to suggest a major role for mtDNA variation in ASD susceptibility. Accordingly, while there may be attractive biological hints suggesting the role of mitochondria in ASD our data indicate that mtDNA variation is not a major contributing factor to the development of ASD. PMID:23130936

EFL Learners' Levels of Comprehension Across Text Structures: A Comparison of Literal and Inferential Comprehension of Descriptive and Enumerative Expository Texts.

PubMed

Saadatnia, Mahmood; Ketabi, Saeed; Tavakoli, Mansoor

2016-12-01

The purpose of this study was to investigate the relationship between text structure and two levels of reading comprehension, namely literal and inferential, in Iranian EFL learners. Studies have generally found that learners perform differently after they have read different text structures (Amiri et al. in Proc Soc Behav Sci 66:402-409, 2012). The text structures in focus were descriptive and enumerative expository texts. One hundred eighty upper-intermediate EFL learners were assigned four reading passages, two including descriptive and the other two enumerative text structure, followed by both literal and inferential multiple-choice items. A number of paired-samples t tests were run to provide answers to the research questions of this study. The results indicated that the participants meaningfully outperformed on the descriptive texts at both levels of literal and inferential comprehension. The findings also revealed that in both text structures of description and enumeration, literal comprehension significantly outweighed inferential comprehension. Implications were made for L2 materials developers, language teachers, and language testers regarding the consideration of text typical features in their practice.

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

PubMed

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

2013-01-15

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

Scanning the human genome at kilobase resolution.

PubMed

Chen, Jun; Kim, Yeong C; Jung, Yong-Chul; Xuan, Zhenyu; Dworkin, Geoff; Zhang, Yanming; Zhang, Michael Q; Wang, San Ming

2008-05-01

Normal genome variation and pathogenic genome alteration frequently affect small regions in the genome. Identifying those genomic changes remains a technical challenge. We report here the development of the DGS (Ditag Genome Scanning) technique for high-resolution analysis of genome structure. The basic features of DGS include (1) use of high-frequent restriction enzymes to fractionate the genome into small fragments; (2) collection of two tags from two ends of a given DNA fragment to form a ditag to represent the fragment; (3) application of the 454 sequencing system to reach a comprehensive ditag sequence collection; (4) determination of the genome origin of ditags by mapping to reference ditags from known genome sequences; (5) use of ditag sequences directly as the sense and antisense PCR primers to amplify the original DNA fragment. To study the relationship between ditags and genome structure, we performed a computational study by using the human genome reference sequences as a model, and analyzed the ditags experimentally collected from the well-characterized normal human DNA GM15510 and the leukemic human DNA of Kasumi-1 cells. Our studies show that DGS provides a kilobase resolution for studying genome structure with high specificity and high genome coverage. DGS can be applied to validate genome assembly, to compare genome similarity and variation in normal populations, and to identify genomic abnormality including insertion, inversion, deletion, translocation, and amplification in pathological genomes such as cancer genomes.

AnatomicalTerms.info: heading for an online solution to the anatomical synonym problem hurdles in data-reuse from the Terminologia Anatomica and the foundational model of anatomy and potentials for future development.

PubMed

Gobée, O Paul; Jansma, Daniël; DeRuiter, Marco C

2011-10-01

The many synonyms for anatomical structures confuse medical students and complicate medical communication. Easily accessible translations would alleviate this problem. None of the presently available resources-Terminologia Anatomica (TA), digital terminologies such as the Foundational Model of Anatomy (FMA), and websites-are fully satisfactory to this aim. Internet technologies offer new possibilities to solve the problem. Several authors have called for an online TA. An online translation resource should be easily accessible, user-friendly, comprehensive, expandable, and its quality determinable. As first step towards this goal, we built a translation website that we named www.AnatomicalTerms.info, based on the database of the FMA. It translates between English, Latin, eponyms, and to a lesser extent other languages, and presently contains over 31,000 terms for 7,250 structures, covering 95% of TA. In addition, it automatically presents searches for images, documents and anatomical variations regarding the sought structure. Several terminological and conceptual issues were encountered in transferring data from TA and FMA into AnatomicalTerms.info, resultant from these resources' different set-ups (paper versus digital) and targets (machine versus human-user). To the best of our knowledge, AnatomicalTerms.info is unique in its combination of user-friendliness and comprehensiveness. As next step, wiki-like expandability will be added to enable open contribution of clinical synonyms and terms in different languages. Specific quality measures will be taken to strike a balance between open contribution and quality assurance. AnatomicalTerms.info's mechanism that "translates" terms to structures furthermore may enhance targeted searching by linking images, descriptions, and other anatomical resources to the structures. Copyright © 2011 Wiley-Liss, Inc.

Interpreting "Personality" Taxonomies: Why Previous Models Cannot Capture Individual-Specific Experiencing, Behaviour, Functioning and Development. Major Taxonomic Tasks Still Lay Ahead.

PubMed

Uher, Jana

2015-12-01

As science seeks to make generalisations, a science of individual peculiarities encounters intricate challenges. This article explores these challenges by applying the Transdisciplinary Philosophy-of-Science Paradigm for Research on Individuals (TPS-Paradigm) and by exploring taxonomic "personality" research as an example. Analyses of researchers' interpretations of the taxonomic "personality" models, constructs and data that have been generated in the field reveal widespread erroneous assumptions about the abilities of previous methodologies to appropriately represent individual-specificity in the targeted phenomena. These assumptions, rooted in everyday thinking, fail to consider that individual-specificity and others' minds cannot be directly perceived, that abstract descriptions cannot serve as causal explanations, that between-individual structures cannot be isomorphic to within-individual structures, and that knowledge of compositional structures cannot explain the process structures of their functioning and development. These erroneous assumptions and serious methodological deficiencies in widely used standardised questionnaires have effectively prevented psychologists from establishing taxonomies that can comprehensively model individual-specificity in most of the kinds of phenomena explored as "personality", especially in experiencing and behaviour and in individuals' functioning and development. Contrary to previous assumptions, it is not universal models but rather different kinds of taxonomic models that are required for each of the different kinds of phenomena, variations and structures that are commonly conceived of as "personality". Consequently, to comprehensively explore individual-specificity, researchers have to apply a portfolio of complementary methodologies and develop different kinds of taxonomies, most of which have yet to be developed. Closing, the article derives some meta-desiderata for future research on individuals' "personality".

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

PubMed

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

2014-12-04

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

Effective Implementation of a Comprehension-Improvement Approach in Secondary Schools. Summary.

ERIC Educational Resources Information Center

Levine, Daniel U.; Sherk, John K.

This document summarizes a report on the implementation and impact of instructional strategies to improve students' comprehension skills at three diverse urban secondary schools. While activities and characteristics varied, educators at all three locations were implementing local variations of a school-improvement approach based on the use of the…

Comprehensive Genome-wide Screen for Genes with Cis-acting Regulatory Elements That Respond to Marek's Disease Virus Infection

USDA-ARS?s Scientific Manuscript database

The comprehensive identification of genes underlying phenotypic variation of complex traits such as disease resistance remains one of the greatest challenges in biology despite having genome sequences and more powerful tools. Most genome-wide screens lack sufficient resolving power as they typically...

Effects of Electronic Reading Environments' Structure on L2 Reading Comprehension

ERIC Educational Resources Information Center

Al-Seghayer, Khalid

2017-01-01

This study examines the effects of an electronic reading environment's structure on second language (L2) reading comprehension. In particular, this study explores whether clarifying the underlying structure of an electronic text, along with the ways in which its units or nodes are organized and interrelated results in better comprehension as well…

The Role of Structured Cooperative Learning Groups for Enhancing Chinese Primary Students' Reading Comprehension

ERIC Educational Resources Information Center

Law, Yin-Kum

2014-01-01

The present study aimed to compare the effectiveness of two types of cooperative learning groups used in reciprocal teaching (RT) classes (i.e. high-structured vs. low-structured groups) for enhancing students' reading comprehension. The participants were 235 Hong Kong Chinese Grade 6 students in nine classes. Reading comprehension tests and…

Preliminary Findings on the Computer-Administered Multiple-Choice Online Causal Comprehension Assessment, a Diagnostic Reading Comprehension Test

ERIC Educational Resources Information Center

Davison, Mark L.; Biancarosa, Gina; Carlson, Sarah E.; Seipel, Ben; Liu, Bowen

2018-01-01

The computer-administered Multiple-Choice Online Causal Comprehension Assessment (MOCCA) for Grades 3 to 5 has an innovative, 40-item multiple-choice structure in which each distractor corresponds to a comprehension process upon which poor comprehenders have been shown to rely. This structure requires revised thinking about measurement issues…

How to achieve optimal organization of primary care service delivery at system level: lessons from Europe.

PubMed

Pelone, Ferruccio; Kringos, Dionne S; Spreeuwenberg, Peter; De Belvis, Antonio G; Groenewegen, Peter P

2013-09-01

To measure the relative efficiency of primary care (PC) in turning their structures into services delivery and turning their services delivery into quality outcomes. Cross-sectional study based on the dataset of the Primary Healthcare Activity Monitor for Europe project. Two Data Envelopment models were run to compare the relative technical efficiency. A sensitivity analysis of the resulting efficiency scores was performed. PC systems in 22 European countries in 2009/2010. Model 1 included data on PC governance, workforce development and economic conditions as inputs and access, coordination, continuity and comprehensiveness of care as outputs. Model 2 included the previous process dimensions as inputs and quality indicators as outputs. There is relatively reasonable efficiency in all countries at delivering as many as possible PC processes at a given level of PC structure. It is particularly important to invest in economic conditions to achieve an efficient structure-process balance. Only five countries have fully efficient PC systems in turning their services delivery into high quality outcomes, using a similar combination of access, continuity and comprehensiveness, although they differ on the adoption of coordination of services. There is a large variation in efficiency levels obtained by countries with inefficient PC in turning their services delivery into quality outcomes. Maximizing the individual functions of PC without taking into account the coherence within the health-care system is not sufficient from a policymaker's point of view when aiming to achieve efficiency.

Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm

PubMed Central

Yu, Isseki; Mori, Takaharu; Ando, Tadashi; Harada, Ryuhei; Jung, Jaewoon; Sugita, Yuji; Feig, Michael

2016-01-01

Biological macromolecules function in highly crowded cellular environments. The structure and dynamics of proteins and nucleic acids are well characterized in vitro, but in vivo crowding effects remain unclear. Using molecular dynamics simulations of a comprehensive atomistic model cytoplasm we found that protein-protein interactions may destabilize native protein structures, whereas metabolite interactions may induce more compact states due to electrostatic screening. Protein-protein interactions also resulted in significant variations in reduced macromolecular diffusion under crowded conditions, while metabolites exhibited significant two-dimensional surface diffusion and altered protein-ligand binding that may reduce the effective concentration of metabolites and ligands in vivo. Metabolic enzymes showed weak non-specific association in cellular environments attributed to solvation and entropic effects. These effects are expected to have broad implications for the in vivo functioning of biomolecules. This work is a first step towards physically realistic in silico whole-cell models that connect molecular with cellular biology. DOI: http://dx.doi.org/10.7554/eLife.19274.001 PMID:27801646

The Spatiotemporal Structure of 20th Century Climate Variations in Observations and Reanalyses. Part 1; Long-term Trend

NASA Technical Reports Server (NTRS)

Chen, Junye; DelGenio, Anthony D.; Carlson, Barbara e.; Bosilovich, Michael G.

2007-01-01

The dominant interannual El Nino-Southern Oscillation phenomenon (ENSO) and the short length of climate observation records make it difficult to study long-term climate variations in the spatiotemporal domain. Based on the fact that the ENS0 signal spreads to remote regions and induces delayed climate variation through atmospheric teleconnections, we develop an ENSO-removal method through which the ENS0 signal can be approximately removed at the grid box level from the spatiotemporal field of a climate parameter. After this signal is removed, long-term climate variations, namely, the global warming trend (GW) and the Pacific pan-decadal variability (PDV), are isolated at middle and low latitudes in the climate parameter fields from observed and reanalyses datasets. Except for known GW characteristics, the warming that occurs in the Pacific basin (approximately 0.4K in the 2oth century) is much weaker than in surrounding regions and the other two ocean basins (approximately 0.8K). The modest warming in the Pacific basin is likely due to its dynamic nature on the interannual and decadal time scales and/or the leakage of upper ocean water through the Indonesian Throughflow. Based on NCEP/NCAR and ERA-40 reanalyses, a comprehensive atmospheric structure associated with GW is given. Significant discrepancies exist between the two datasets, especially in the tightly coupled dynamic and water vapor fields. The dynamic field based on NCEP/NCAR reanalysis, which shows a change in the Walker Circulation, is consistent with the GW change in the surface temperature field. However, intensification in the Hadley Circulation is associated with GW trend in the ERA-40 reanalysis.

Microbial, physical and chemical properties of irrigation water in rice fields of Southern Brazil.

PubMed

Reche, Maria Helena L R; Machado, Vilmar; Saul, Danilo A; Macedo, Vera R M; Marcolin, Elio; Knaak, Neiva; Fiuza, Lidia M

2016-03-01

This paper presents the results of the statistical analysis of microbiological, physical and chemical parameters related to the quality of the water used in rice fields in Southern Brazil. Data were collected during three consecutive crop years, within structure of a comprehensive monitoring program. The indicators used were: potential hydrogen, electrical conductivity, turbidity, nitrogen, phosphorus, potassium, calcium, total and fecal coliforms. Principal Component and Discriminant Analysis showed consistent differences between the water irrigation and drainage, as the temporal variation demonstrated a clear reduction in the concentration of most of the variables analyzed. The pattern of this reduction is not the same in the two regions - that is, the importance of each of the different variables in the observed differentiation is modified in two locations. These results suggested that the variations in the water quality utilized for rice irrigation was influenced by certain specific aspects of each rice region in South Brazilian - such as anthropic action or soil/climate conditions in each hydrographic basin.

Innovative application of optical techniques to comprehensive study of the etiology of osteoarthritis

NASA Astrophysics Data System (ADS)

Ugryumova, Nadya; Matcher, Stephen J.

2006-08-01

Osteoarthritis is a painful condition, causing restricted mobility in the articular joints. In this paper we present a review of different optical techniques that might be used to clarify the etiology of degeneration of connective joint tissues, such as bone and articular cartilage. Significant correlation (R2 = 0.8) between bone mineral density and scattering coefficient of cortical bone tissue are found by using Integrating Sphere Technique. Optical Coherence Tomography and Polarization-Sensitive Optical Coherence Tomography images of cartilage tissue are presented. They were performed as series of angle-dependant measurements for different location along the surface. Method for spatial mapping the birefringence of equine articular cartilage is proposed. Variations in band spacing of birefringence obtained from visually healthy and abnormal cartilage samples are compared. Visible osteoarthritic lesions are characterized by a loss of the regular birefringence bands shown by normal cartilage. We discuss the hypothesis that some of these variations may be due to changes in intrinsic structure of tissue.

An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes

PubMed Central

Cho, Yun Sung; Kim, Hyunho; Kim, Hak-Min; Jho, Sungwoong; Jun, JeHoon; Lee, Yong Joo; Chae, Kyun Shik; Kim, Chang Geun; Kim, Sangsoo; Eriksson, Anders; Edwards, Jeremy S.; Lee, Semin; Kim, Byung Chul; Manica, Andrea; Oh, Tae-Kwang; Church, George M.; Bhak, Jong

2016-01-01

Human genomes are routinely compared against a universal reference. However, this strategy could miss population-specific and personal genomic variations, which may be detected more efficiently using an ethnically relevant or personal reference. Here we report a hybrid assembly of a Korean reference genome (KOREF) for constructing personal and ethnic references by combining sequencing and mapping methods. We also build its consensus variome reference, providing information on millions of variants from 40 additional ethnically homogeneous genomes from the Korean Personal Genome Project. We find that the ethnically relevant consensus reference can be beneficial for efficient variant detection. Systematic comparison of human assemblies shows the importance of assembly quality, suggesting the necessity of new technologies to comprehensively map ethnic and personal genomic structure variations. In the era of large-scale population genome projects, the leveraging of ethnicity-specific genome assemblies as well as the human reference genome will accelerate mapping all human genome diversity. PMID:27882922

Electronic structure of germanium selenide investigated using ultra-violet photo-electron spectroscopy

NASA Astrophysics Data System (ADS)

Mishra, P.; Lohani, H.; Kundu, A. K.; Patel, R.; Solanki, G. K.; Menon, Krishnakumar S. R.; Sekhar, B. R.

2015-07-01

The valence band electronic structure of GeSe single crystals has been investigated using angle resolved photoemission spectroscopy (ARPES) and x-ray photoelectron spectroscopy. The experimentally observed bands from ARPES, match qualitatively with our LDA-based band structure calculations along the Γ-Z, Γ-Y and Γ-T symmetry directions. The valence band maximum occurs nearly midway along the Γ-Z direction, at a binding energy of -0.5 eV, substantiating the indirect band gap of GeSe. Non-dispersive features associated with surface states and indirect transitions have been observed. The difference in hybridization of Se and Ge 4p orbitals leads to the variation of dispersion along the three symmetry directions. The predominance of the Se 4pz orbitals, evidenced from theoretical calculations, may be the cause for highly dispersive bands along the Γ-T direction. Detailed electronic structure analysis reveals the significance of the cation-anion 4p orbitals hybridization in the valence band dispersion of IV-VI semiconductors. This is the first comprehensive report of the electronic structure of a GeSe single crystal using ARPES in conjugation with theoretical band structure analysis.

A Program Based on the Pragmatic Theory to Develop Grammatical Structure Comprehension Skills for Foreign Learners of Arabic

ERIC Educational Resources Information Center

Elsamman, Marwan

2014-01-01

This study aimed at designing a program based on the Pragmatic theory to develop grammatical structure comprehension skills for foreign learners of Arabic and examining its effectiveness. Hence, the problem of the study has been summarized in the weakness of grammatical structure comprehension skills for foreign learners of Arabic and in the need…

The Effect of Phonological Variation on Adult Learner Comprehension.

ERIC Educational Resources Information Center

Eisenstein, Miriam; Berkowitz, Diana

1981-01-01

Reports on a study of the relationship of English phonological variation to intelligibility for adult second language learners of English. Indicates that learners tested on their ability to understand working-class (New Yorkese), educated (Standard English), and Foreign-accented speakers of English found the standard more intelligible than the…

Associations between prenatal, childhood, and adolescent stress and variations in white-matter properties in young men.

PubMed

Jensen, Sarah K G; Pangelinan, Melissa; Björnholm, Lassi; Klasnja, Anja; Leemans, Alexander; Drakesmith, Mark; Evans, C J; Barker, Edward D; Paus, Tomáš

2017-10-21

Previous studies have shown that both pre- and post-natal adversities, the latter including exposures to stress during childhood and adolescence, explain variation in structural properties of white matter (WM) in the brain. While previous studies have examined effects of independent stress exposures within one developmental period, such as childhood, we examine effects of stress across development using data from a prospective longitudinal study. More specifically, we ask how stressful events during prenatal development, childhood, and adolescence relate to variation in WM properties in early adulthood in young men recruited from a birth cohort. Using data from 393 mother-son pairs from a community-based birth cohort from England (Avon Longitudinal Study of Parents and Children), we examined how stressful life events relate to variation in different structural properties of WM in the corpus callosum and across the whole brain in early adulthood in men aged 18-21 years. We distinguish between stress occurring during three developmental periods: a) prenatal maternal stress, b) postnatal stress within the first four years of life, c) stress during adolescence (age 12-16 years). To obtain a comprehensive quantification of variation in WM, we assess structural properties of WM using four different measures, namely fractional anisotropy (FA), mean diffusivity (MD), magnetization transfer ratio (MTR) and myelin water fraction (MWF). The developmental model shows that prenatal stress is associated with lower MTR and MWF in the genu and/or splenium of the corpus callosum, and with lower MTR in global (lobar) WM. Stress during early childhood is associated with higher MTR in the splenium, and stress during adolescence is associated with higher MTR in the genu and lower MD in the splenium. We see no associations between postnatal stress and variation in global (lobar) WM. The current study found evidence for independent effects of stress on WM properties during distinct neurodevelopmental periods. We speculate that these independent effects are due to differences in the developmental processes unfolding at different developmental time points. We suggest that associations between prenatal stress and WM properties may relate to abnormalities in neurogenesis, affecting the number and density of axons, while postnatal stress may interfere with processes related to myelination or radial growth of axons. Potential consequences of prenatal glucocorticoid exposure should be considered in obstetric care. Copyright © 2017 Elsevier Inc. All rights reserved.

Contrasting evolutionary genome dynamics between domesticated and wild yeasts

PubMed Central

Yue, Jia-Xing; Li, Jing; Aigrain, Louise; Hallin, Johan; Persson, Karl; Oliver, Karen; Bergström, Anders; Coupland, Paul; Warringer, Jonas; Lagomarsino, Marco Consentino; Fischer, Gilles; Durbin, Richard; Liti, Gianni

2017-01-01

Structural rearrangements have long been recognized as an important source of genetic variation with implications in phenotypic diversity and disease, yet their detailed evolutionary dynamics remain elusive. Here, we use long-read sequencing to generate end-to-end genome assemblies for 12 strains representing major subpopulations of the partially domesticated yeast Saccharomyces cerevisiae and its wild relative Saccharomyces paradoxus. These population-level high-quality genomes with comprehensive annotation allow for the first time a precise definition of chromosomal boundaries between cores and subtelomeres and a high-resolution view of evolutionary genome dynamics. In chromosomal cores, S. paradoxus exhibits faster accumulation of balanced rearrangements (inversions, reciprocal translocations and transpositions) whereas S. cerevisiae accumulates unbalanced rearrangements (novel insertions, deletions and duplications) more rapidly. In subtelomeres, both species show extensive interchromosomal reshuffling, with a higher tempo in S. cerevisiae. Such striking contrasts between wild and domesticated yeasts likely reflect the influence of human activities on structural genome evolution. PMID:28416820

Restructuring of the Aquatic Bacterial Community by Hydric Dynamics Associated with Superstorm Sandy

PubMed Central

Ulrich, Nikea; Rosenberger, Abigail; Brislawn, Colin; Wright, Justin; Kessler, Collin; Toole, David; Solomon, Caroline; Strutt, Steven; McClure, Erin

2016-01-01

ABSTRACT Bacterial community composition and longitudinal fluctuations were monitored in a riverine system during and after Superstorm Sandy to better characterize inter- and intracommunity responses associated with the disturbance associated with a 100-year storm event. High-throughput sequencing of the 16S rRNA gene was used to assess microbial community structure within water samples from Muddy Creek Run, a second-order stream in Huntingdon, PA, at 12 different time points during the storm event (29 October to 3 November 2012) and under seasonally matched baseline conditions. High-throughput sequencing of the 16S rRNA gene was used to track changes in bacterial community structure and divergence during and after Superstorm Sandy. Bacterial community dynamics were correlated to measured physicochemical parameters and fecal indicator bacteria (FIB) concentrations. Bioinformatics analyses of 2.1 million 16S rRNA gene sequences revealed a significant increase in bacterial diversity in samples taken during peak discharge of the storm. Beta-diversity analyses revealed longitudinal shifts in the bacterial community structure. Successional changes were observed, in which Betaproteobacteria and Gammaproteobacteria decreased in 16S rRNA gene relative abundance, while the relative abundance of members of the Firmicutes increased. Furthermore, 16S rRNA gene sequences matching pathogenic bacteria, including strains of Legionella, Campylobacter, Arcobacter, and Helicobacter, as well as bacteria of fecal origin (e.g., Bacteroides), exhibited an increase in abundance after peak discharge of the storm. This study revealed a significant restructuring of in-stream bacterial community structure associated with hydric dynamics of a storm event. IMPORTANCE In order to better understand the microbial risks associated with freshwater environments during a storm event, a more comprehensive understanding of the variations in aquatic bacterial diversity is warranted. This study investigated the bacterial communities during and after Superstorm Sandy to provide fine time point resolution of dynamic changes in bacterial composition. This study adds to the current literature by revealing the variation in bacterial community structure during the course of a storm. This study employed high-throughput DNA sequencing, which generated a deep analysis of inter- and intracommunity responses during a significant storm event. This study has highlighted the utility of applying high-throughput sequencing for water quality monitoring purposes, as this approach enabled a more comprehensive investigation of the bacterial community structure. Altogether, these data suggest a drastic restructuring of the stream bacterial community during a storm event and highlight the potential of high-throughput sequencing approaches for assessing the microbiological quality of our environment. PMID:27060115

A Fine-Tuned Look at White Space Variation in Desktop Publishing.

ERIC Educational Resources Information Center

Knupfer, Nancy Nelson; McIsaac, Marina Stock

This investigation of the use of white space in print-based, computer-generated text focused on the point at which the white space interferes with reading speed and comprehension. It was hypothesized that reading speed and comprehension would be significantly greater when text was wrapped tightly around the graphic than when it had one-half inch…

The Substrata-Factor Theory of Reading: Differential Development of Subsystems Underlying Reading Comprehension in the First Year of Instruction.

ERIC Educational Resources Information Center

Katz, Ina; Singer, Harry

A study tested the instructional hypothesis that variation in instructional methods in the initial stages of formal reading development will differentially develop subsystems for attaining comprehension. The 91 kindergarten and first grade students in the study received their usual reading instruction plus supplementary instruction in one of four…

Comprehensive Identification Of Specific Genes Controlling Complex Traits Through A Genome-Wide Screen for Cis-Acting Regulatory Elements - An Example Using Marek's Disease

USDA-ARS?s Scientific Manuscript database

The comprehensive identification of genes underlying phenotypic variation of complex traits remains a major challenge. Most genome-wide screens lack sufficient resolving power as they typically depend on linkage. An alternate method is to screen for allele-specific expression (ASE), a simple yet pow...

Differentiation Practices in Grade 2 and 3: Variations in Teacher Behavior in Mathematics and Reading Comprehension Lessons

ERIC Educational Resources Information Center

Ritzema, Evelien S.; Deunk, Marjolein I.; Bosker, Roel J.

2016-01-01

This study focused on the differentiation practices of second- and third-grade teachers in mathematics and reading comprehension lessons. Preconditions for differentiation, classroom organization, and how teachers dealt with students of different ability levels were investigated through observations, using a time-sampling instrument. Data of 43…

Comprehensive Analysis of Non-Synonymous Natural Variants of G Protein-Coupled Receptors.

PubMed

Kim, Hee Ryung; Duc, Nguyen Minh; Chung, Ka Young

2018-03-01

G protein-coupled receptors (GPCRs) are the largest superfamily of transmembrane receptors and have vital signaling functions in various organs. Because of their critical roles in physiology and pathology, GPCRs are the most commonly used therapeutic target. It has been suggested that GPCRs undergo massive genetic variations such as genetic polymorphisms and DNA insertions or deletions. Among these genetic variations, non-synonymous natural variations change the amino acid sequence and could thus alter GPCR functions such as expression, localization, signaling, and ligand binding, which may be involved in disease development and altered responses to GPCR-targeting drugs. Despite the clinical importance of GPCRs, studies on the genotype-phenotype relationship of GPCR natural variants have been limited to a few GPCRs such as β-adrenergic receptors and opioid receptors. Comprehensive understanding of non-synonymous natural variations within GPCRs would help to predict the unknown genotype-phenotype relationship and yet-to-be-discovered natural variants. Here, we analyzed the non-synonymous natural variants of all non-olfactory GPCRs available from a public database, UniProt. The results suggest that non-synonymous natural variations occur extensively within the GPCR superfamily especially in the N-terminus and transmembrane domains. Within the transmembrane domains, natural variations observed more frequently in the conserved residues, which leads to disruption of the receptor function. Our analysis also suggests that only few non-synonymous natural variations have been studied in efforts to link the variations with functional consequences.

Local structure preserving sparse coding for infrared target recognition

PubMed Central

Han, Jing; Yue, Jiang; Zhang, Yi; Bai, Lianfa

2017-01-01

Sparse coding performs well in image classification. However, robust target recognition requires a lot of comprehensive template images and the sparse learning process is complex. We incorporate sparsity into a template matching concept to construct a local sparse structure matching (LSSM) model for general infrared target recognition. A local structure preserving sparse coding (LSPSc) formulation is proposed to simultaneously preserve the local sparse and structural information of objects. By adding a spatial local structure constraint into the classical sparse coding algorithm, LSPSc can improve the stability of sparse representation for targets and inhibit background interference in infrared images. Furthermore, a kernel LSPSc (K-LSPSc) formulation is proposed, which extends LSPSc to the kernel space to weaken the influence of the linear structure constraint in nonlinear natural data. Because of the anti-interference and fault-tolerant capabilities, both LSPSc- and K-LSPSc-based LSSM can implement target identification based on a simple template set, which just needs several images containing enough local sparse structures to learn a sufficient sparse structure dictionary of a target class. Specifically, this LSSM approach has stable performance in the target detection with scene, shape and occlusions variations. High performance is demonstrated on several datasets, indicating robust infrared target recognition in diverse environments and imaging conditions. PMID:28323824

The systematics and population genetics of Opisthorchis viverrini sensu lato: implications in parasite epidemiology and bile duct cancer.

PubMed

Sithithaworn, Paiboon; Andrews, Ross H; Petney, Trevor N; Saijuntha, Weerachai; Laoprom, Nonglak

2012-03-01

Together with host and environmental factors, the systematics and population genetic variation of Opisthorchis viverrini may contribute to recorded local and regional differences in epidemiology and host morbidity in opisthorchiasis and cholangiocarcinoma (CCA). In this review, we address recent findings that O. viverrini comprises a species complex with varying degrees of population genetic variation which are associated with specific river wetland systems within Thailand as well as the Lao PDR. Having an accurate understanding of systematics is a prerequisite for a meaningful assessment of the population structure of each species within the O. viverrini complex in nature, as well as a better understanding of the magnitude of genetic variation that occurs within different species of hosts in its life cycle. Whether specific genotypes are related to habitat type(s) and/or specific intermediate host species are discussed based on current available data. Most importantly, we focus on whether there is a correlation between incidence of CCA and genotype(s) of O. viverrini. This will provide a solid basis for further comprehensive investigations of the role of genetic variation within each species of O. viverrini sensu lato in human epidemiology and genotype related morbidity as well as co-evolution of parasites with primary and secondary intermediate species of host. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Three-dimensional variations of atmospheric CO2: aircraft measurements and multi-transport model simulations

NASA Astrophysics Data System (ADS)

Niwa, Y.; Patra, P. K.; Sawa, Y.; Machida, T.; Matsueda, H.; Belikov, D.; Maki, T.; Ikegami, M.; Imasu, R.; Maksyutov, S.; Oda, T.; Satoh, M.; Takigawa, M.

2011-12-01

Numerical simulation and validation of three-dimensional structure of atmospheric carbon dioxide (CO2) is necessary for quantification of transport model uncertainty and its role on surface flux estimation by inverse modeling. Simulations of atmospheric CO2 were performed using four transport models and two sets of surface fluxes compared with an aircraft measurement dataset of Comprehensive Observation Network for Trace gases by AIrLiner (CONTRAIL), covering various latitudes, longitudes, and heights. Under this transport model intercomparison project, spatiotemporal variations of CO2 concentration for 2006-2007 were analyzed with a three-dimensional perspective. Results show that the models reasonably simulated vertical profiles and seasonal variations not only over northern latitude areas but also over the tropics and southern latitudes. From CONTRAIL measurements and model simulations, intrusion of northern CO2 in to the Southern Hemisphere, through the upper troposphere, was confirmed. Furthermore, models well simulated the vertical propagation of seasonal variation in the northern free troposphere. However, significant model-observation discrepancies were found in Asian regions, which are attributable to uncertainty of the surface CO2 flux data. In summer season, differences in latitudinal gradients by the fluxes are comparable to or greater than model-model differences even in the free troposphere. This result suggests that active summer vertical transport sufficiently ventilates flux signals up to the free troposphere and the models could use those for inferring surface CO2 fluxes.

Three-dimensional variations of atmospheric CO2: aircraft measurements and multi-transport model simulations

NASA Astrophysics Data System (ADS)

Niwa, Y.; Patra, P. K.; Sawa, Y.; Machida, T.; Matsueda, H.; Belikov, D.; Maki, T.; Ikegami, M.; Imasu, R.; Maksyutov, S.; Oda, T.; Satoh, M.; Takigawa, M.

2011-04-01

Numerical simulation and validation of three-dimensional structure of atmospheric carbon dioxide (CO2) is necessary for quantification of transport model uncertainty and its role on surface flux estimation by inverse modeling. Simulations of atmospheric CO2 were performed using four transport models and two sets of surface fluxes compared with an aircraft measurement dataset of Comprehensive Observation Network for Trace gases by AIrLiner (CONTRAIL), covering various latitudes, longitudes, and heights. Under this transport model intercomparison project, spatiotemporal variations of CO2 concentration for 2006-2007 were analyzed with a three-dimensional perspective. Results show that the models reasonably simulated vertical profiles and seasonal variations not only over northern latitude areas but also over the tropics and southern latitudes. From CONTRAIL measurements and model simulations, intrusion of northern CO2 in to the Southern Hemisphere, through the upper troposphere, was confirmed. Furthermore, models well simulated the vertical propagation of seasonal variation in the northern free-troposphere. However, significant model-observation discrepancies were found in Asian regions, which are attributable to uncertainty of the surface CO2 flux data. The models consistently underestimated the north-tropics mean gradient of CO2 both in the free-troposphere and marine boundary layer during boreal summer. This result suggests that the north-tropics contrast of annual mean net non-fossil CO2 flux should be greater than 2.7 Pg C yr-1 for 2007.

Discordant coral-symbiont structuring: factors shaping geographical variation of Symbiodinium communities in a facultative zooxanthellate coral genus, Oculina

NASA Astrophysics Data System (ADS)

Leydet, Karine Posbic; Hellberg, Michael E.

2016-06-01

Understanding the factors that help shape the association between corals and their algal symbionts, zooxanthellae ( Symbiodinium), is necessary to better understand the functional diversity and acclimatization potential of the coral host. However, most studies focus on tropical zooxanthellate corals and their obligate algal symbionts, thus limiting our full comprehension of coral-algal symbiont associations. Here, we examine algal associations in a facultative zooxanthellate coral. We survey the Symbiodinium communities associated with Oculina corals in the western North Atlantic and the Mediterranean using one clade-level marker ( psbA coding region) and three fine-scale markers ( cp23S- rDNA, b7sym15 flanking region, and b2sym17). We ask whether Oculina spp. harbor geographically different Symbiodinium communities across their geographic range and, if so, whether the host's genetics or habitat differences are correlated with this geographical variation. We found that Oculina corals harbor different Symbiodinium communities across their geographical range. Of the habitat differences (including chlorophyll a concentration and depth), sea surface temperature is better correlated with this geographical variation than the host's genetics, a pattern most evident in the Mediterranean. Our results suggest that although facultative zooxanthellate corals may be less dependent on their algal partners compared to obligate zooxanthellate corals, the Symbiodinium communities that they harbor may nevertheless reflect acclimatization to environmental variation among habitats.

Identification of structural variation in mouse genomes.

PubMed

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

2014-01-01

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

Using 3D modeling techniques to enhance teaching of difficult anatomical concepts

PubMed Central

Pujol, Sonia; Baldwin, Michael; Nassiri, Joshua; Kikinis, Ron; Shaffer, Kitt

2016-01-01

Rationale and Objectives Anatomy is an essential component of medical education as it is critical for the accurate diagnosis in organs and human systems. The mental representation of the shape and organization of different anatomical structures is a crucial step in the learning process. The purpose of this pilot study is to demonstrate the feasibility and benefits of developing innovative teaching modules for anatomy education of first-year medical students based on 3D reconstructions from actual patient data. Materials and Methods A total of 196 models of anatomical structures from 16 anonymized CT datasets were generated using the 3D Slicer open-source software platform. The models focused on three anatomical areas: the mediastinum, the upper abdomen and the pelvis. Online optional quizzes were offered to first-year medical students to assess their comprehension in the areas of interest. Specific tasks were designed for students to complete using the 3D models. Results Scores of the quizzes confirmed a lack of understanding of 3D spatial relationships of anatomical structures despite standard instruction including dissection. Written task material and qualitative review by students suggested that interaction with 3D models led to a better understanding of the shape and spatial relationships among structures, and helped illustrate anatomical variations from one body to another. Conclusion The study demonstrates the feasibility of one possible approach to the generation of 3D models of the anatomy from actual patient data. The educational materials developed have the potential to supplement the teaching of complex anatomical regions and help demonstrate the anatomic variation among patients. PMID:26897601

Measuring moisture content in living chaparral: a field user's manual

Treesearch

Clive M. Countryman; William A. Dean

1979-01-01

This manual standardizes procedures for determining the moisture content of living chaparral for use in a proposed statewide system of monitoring living fuel moisture. The manual includes a comprehensive examination of fuel moisture variations in California chaparral, and describes techniques for sampling these variations. Equipment needed to sample and determine...

Genetic variation and biological activity of isolates of lymantria dispar multiple nucleopolyhedrovirus from north america, europe, and asia

USDA-ARS?s Scientific Manuscript database

Little is known about genetic variation of Lymantria dispar multiple nucleopolyhedrovirus (LdMNPV; Baculoviridae: Alphabaculovirus) at the nucleotide sequence level. To obtain a more comprehensive view of genetic diversity among isolates of LdMNPV, partial sequences of the lef-8 gene were generated...

Explaining Variation in Instructional Time: An Application of Quantile Regression

ERIC Educational Resources Information Center

Corey, Douglas Lyman; Phelps, Geoffrey; Ball, Deborah Loewenberg; Demonte, Jenny; Harrison, Delena

2012-01-01

This research is conducted in the context of a large-scale study of three nationally disseminated comprehensive school reform projects (CSRs) and examines how school- and classroom-level factors contribute to variation in instructional time in English language arts and mathematics. When using mean-based OLS regression techniques such as…

Modeling historic variation and its application for understanding future variability (section 3)

Treesearch

Robert E. Keane

2012-01-01

Although some may doubt its usefulness in a future with rapidly changing climates, exotic introductions, and increased human land use, the historical range of variation (HRV) of ecological landscape characteristics provides a relatively useful reference point for evaluating the impacts of landmanagement activities. Unfortunately, comprehensive spatial and temporal data...

A comprehensive analysis of rare genetic variation in amyotrophic lateral sclerosis in the UK.

PubMed

Morgan, Sarah; Shatunov, Aleksey; Sproviero, William; Jones, Ashley R; Shoai, Maryam; Hughes, Deborah; Al Khleifat, Ahmad; Malaspina, Andrea; Morrison, Karen E; Shaw, Pamela J; Shaw, Christopher E; Sidle, Katie; Orrell, Richard W; Fratta, Pietro; Hardy, John; Pittman, Alan; Al-Chalabi, Ammar

2017-06-01

Amyotrophic lateral sclerosis is a progressive neurodegenerative disease of motor neurons. About 25 genes have been verified as relevant to the disease process, with rare and common variation implicated. We used next generation sequencing and repeat sizing to comprehensively assay genetic variation in a panel of known amyotrophic lateral sclerosis genes in 1126 patient samples and 613 controls. About 10% of patients were predicted to carry a pathological expansion of the C9orf72 gene. We found an increased burden of rare variants in patients within the untranslated regions of known disease-causing genes, driven by SOD1, TARDBP, FUS, VCP, OPTN and UBQLN2. We found 11 patients (1%) carried more than one pathogenic variant (P = 0.001) consistent with an oligogenic basis of amyotrophic lateral sclerosis. These findings show that the genetic architecture of amyotrophic lateral sclerosis is complex and that variation in the regulatory regions of associated genes may be important in disease pathogenesis. © The Author (2017). Published by Oxford University Press on behalf of the Guarantors of Brain.

Over forty years of bladder cancer glycobiology: Where do glycans stand facing precision oncology?

PubMed Central

Azevedo, Rita; Peixoto, Andreia; Gaiteiro, Cristiana; Fernandes, Elisabete; Neves, Manuel; Lima, Luís; Santos, Lúcio Lara; Ferreira, José Alexandre

2017-01-01

The high molecular heterogeneity of bladder tumours is responsible for significant variations in disease course, as well as elevated recurrence and progression rates, thereby hampering the introduction of more effective targeted therapeutics. The implementation of precision oncology settings supported by robust molecular models for individualization of patient management is warranted. This effort requires a comprehensive integration of large sets of panomics data that is yet to be fully achieved. Contributing to this goal, over 40 years of bladder cancer glycobiology have disclosed a plethora of cancer-specific glycans and glycoconjugates (glycoproteins, glycolipids, proteoglycans) accompanying disease progressions and dissemination. This review comprehensively addresses the main structural findings in the field and consequent biological and clinical implications. Given the cell surface and secreted nature of these molecules, we further discuss their potential for non-invasive detection and therapeutic development. Moreover, we highlight novel mass-spectrometry-based high-throughput analytical and bioinformatics tools to interrogate the glycome in the postgenomic era. Ultimately, we outline a roadmap to guide future developments in glycomics envisaging clinical implementation. PMID:29207682

Geometric Patterns for Neighboring Bases Near the Stacked State in Nucleic Acid Strands.

PubMed

Sedova, Ada; Banavali, Nilesh K

2017-03-14

Structural variation in base stacking has been analyzed frequently in isolated double helical contexts for nucleic acids, but not as often in nonhelical geometries or in complex biomolecular environments. In this study, conformations of two neighboring bases near their stacked state in any environment are comprehensively characterized for single-strand dinucleotide (SSD) nucleic acid crystal structure conformations. An ensemble clustering method is used to identify a reduced set of representative stacking geometries based on pairwise distances between select atoms in consecutive bases, with multiple separable conformational clusters obtained for categories divided by nucleic acid type (DNA/RNA), SSD sequence, stacking face orientation, and the presence or absence of a protein environment. For both DNA and RNA, SSD conformations are observed that are either close to the A-form, or close to the B-form, or intermediate between the two forms, or further away from either form, illustrating the local structural heterogeneity near the stacked state. Among this large variety of distinct conformations, several common stacking patterns are observed between DNA and RNA, and between nucleic acids in isolation or in complex with proteins, suggesting that these might be stable stacking orientations. Noncanonical face/face orientations of the two bases are also observed for neighboring bases in the same strand, but their frequency is much lower, with multiple SSD sequences across categories showing no occurrences of such unusual stacked conformations. The resulting reduced set of stacking geometries is directly useful for stacking-energy comparisons between empirical force fields, prediction of plausible localized variations in single-strand structures near their canonical states, and identification of analogous stacking patterns in newly solved nucleic acid containing structures.

National Structural Survey of Veterans Affairs Home-Based Primary Care Programs.

PubMed

Karuza, Jurgis; Gillespie, Suzanne M; Olsan, Tobie; Cai, Xeuya; Dang, Stuti; Intrator, Orna; Li, Jiejin; Gao, Shan; Kinosian, Bruce; Edes, Thomas

2017-12-01

To describe the current structural and practice characteristics of the Department of Veterans Affairs (VA) Home-Based Primary Care (HBPC) program. We designed a national survey and surveyed HBPC program directors on-line using REDCap. We received 236 surveys from 394 identified HBPC sites (60% response rate). HBPC site characteristics were quantified using closed-ended formats. HBPC program directors were most often registered nurses, and HBPC programs primarily served veterans with complex chronic illnesses that were at high risk of hospitalization and nursing home care. Primary care was delivered using interdisciplinary teams, with nurses, social workers, and registered dietitians as team members in more than 90% of the sites. Most often, nurse practitioners were the principal primary care providers (PCPs), typically working with nurse case managers. Nearly 60% of the sites reported dual PCPs involving VA and community-based physicians. Nearly all sites provided access to a core set of comprehensive services and programs (e.g., case management, supportive home health care). At the same time, there were variations according to site (e.g., size, location (urban, rural), use of non-VA hospitals, primary care models used). HBPC sites reflected the rationale and mission of HBPC by focusing on complex chronic illness of home-based veterans and providing comprehensive primary care using interdisciplinary teams. Our next series of studies will examine how HBPC site structural characteristics and care models are related to the processes and outcomes of care to determine whether there are best practice standards that define an optimal HBPC structure and care model or whether multiple approaches to HBPC better serve the needs of veterans. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.

The Relation of Morphological Awareness and Syntactic Awareness to Adults' Reading Comprehension: Is Vocabulary Knowledge a Mediating Variable?

ERIC Educational Resources Information Center

Guo, Ying; Roehrig, Alysia D.; Williams, Rihana S.

2011-01-01

The authors' goal was to examine the structural relationships among vocabulary knowledge, morphological awareness, syntactic awareness, and reading comprehension in English-speaking adults. Structural equation analysis of data collected from 151 participants revealed that morphological awareness affected reading comprehension directly. Syntactic…

Systematic Variations of Instructional Variables on Learner Performance: Aircraft Instrument Comprehension Task. Final Report, June 1973-July 1974.

ERIC Educational Resources Information Center

Tenpas, Barbara G.; And Others

Incentive, practice, instruction, and feedback were manipulated in a series of four 2 x 2 factorial studies, with Air Force Reserve Officer Training Corps cadets and graduate students in education, to determine the individual and combined effects of these variables on learner performance (both speed and accuracy) of an aircraft comprehension task.…

Ensembl variation resources

PubMed Central

2010-01-01

Background The maturing field of genomics is rapidly increasing the number of sequenced genomes and producing more information from those previously sequenced. Much of this additional information is variation data derived from sampling multiple individuals of a given species with the goal of discovering new variants and characterising the population frequencies of the variants that are already known. These data have immense value for many studies, including those designed to understand evolution and connect genotype to phenotype. Maximising the utility of the data requires that it be stored in an accessible manner that facilitates the integration of variation data with other genome resources such as gene annotation and comparative genomics. Description The Ensembl project provides comprehensive and integrated variation resources for a wide variety of chordate genomes. This paper provides a detailed description of the sources of data and the methods for creating the Ensembl variation databases. It also explores the utility of the information by explaining the range of query options available, from using interactive web displays, to online data mining tools and connecting directly to the data servers programmatically. It gives a good overview of the variation resources and future plans for expanding the variation data within Ensembl. Conclusions Variation data is an important key to understanding the functional and phenotypic differences between individuals. The development of new sequencing and genotyping technologies is greatly increasing the amount of variation data known for almost all genomes. The Ensembl variation resources are integrated into the Ensembl genome browser and provide a comprehensive way to access this data in the context of a widely used genome bioinformatics system. All Ensembl data is freely available at http://www.ensembl.org and from the public MySQL database server at ensembldb.ensembl.org. PMID:20459805

[Development of an index system for the comprehensive evaluation on public health emergency events surveillance system in China].

PubMed

Hong, Zhiheng; Ni, Daxin; Cao, Yang; Meng, Ling; Tu, Wenxiao; Li, Leilei; Li, Qun; Jin, Lianmei

2015-06-01

To establish a comprehensive evaluation index system for the China Public Health Emergency Events Surveillance System (CPHEESS). A draft index system was built through literature review and under the consideration of the characteristics on CPHEESS. Delphi method was adapted to determine the final index system. The index system was divided into primary, secondary and tertiary levels. There were 4 primary indicators: System structure, Network platform, Surveillance implementation reports with Data analysis and utilization. There were 16 secondary and 70 tertiary indicators being set, with System structure including 14 tertiary indicators (accounted for 20.00%), 21 Network platforms (accounted for 30.00%). Twenty-four Surveillance implementation reports (accounted for 34.29%), 11 Data analysis and utilization (accounted for 15.71%). The average score of importance of each indicators was 4.29 (3.77-4.94), with an average coefficient variation as 0.14 (0.12-0.16). The mean Chronbach's α index was 0.84 (0.81-0.89). The adaptability of each related facilities indicator was specified. The primary indicators were set in accordance with the characteristics and goals of the surveillance systems. Secondary indicators provided key elements in the management and control of the system while the tertiary indicators were available and operative. The agreement rate of experts was high with good validity and reliability. This index system could be used for CPHEESS in future.

Modeling α- and β-diversity in a tropical forest from remotely sensed and spatial data

NASA Astrophysics Data System (ADS)

Hernández-Stefanoni, J. Luis; Gallardo-Cruz, J. Alberto; Meave, Jorge A.; Rocchini, Duccio; Bello-Pineda, Javier; López-Martínez, J. Omar

2012-10-01

Comprehensive information on species distribution and species composition patterns of plant communities is required for effective conservation and management of biodiversity. Remote sensing offers an inexpensive means of attaining complete spatial coverage for large areas, at regular time intervals, and can therefore be extremely useful for estimating both species richness and spatial variation of species composition (α- and β-diversity). An essential step to map such attributes is to identify and understand their main drivers. We used remotely sensed data as a surrogate of plant productivity and habitat structure variables for explaining α- and β-diversity, and evaluated the relative roles of productivity-habitat structure and spatial variables in explaining observed patterns of α- and β-diversity by using a Principal Coordinates of Neighbor Matrices analysis. We also examined the relationship between remotely sensed and field data, in order to map α- and β-diversity at the landscape-level in the Yucatan Peninsula, using a regression kriging procedure. These two procedures integrate the relationship of species richness and spatial species turnover both with remotely sensed data and spatial structure. The empirical models so obtained can be used to predict species richness and variation in species composition, and they can be regarded as valuable tools not only for identifying areas with high local species richness (α-diversity), but also areas with high species turnover (β-diversity). Ultimately, information obtained in this way can help maximize the number of species preserved in a landscape.

Genetic Diversity and Demographic History of Cajanus spp. Illustrated from Genome-Wide SNPs

PubMed Central

Saxena, Rachit K.; von Wettberg, Eric; Upadhyaya, Hari D.; Sanchez, Vanessa; Songok, Serah; Saxena, Kulbhushan; Kimurto, Paul; Varshney, Rajeev K.

2014-01-01

Understanding genetic structure of Cajanus spp. is essential for achieving genetic improvement by quantitative trait loci (QTL) mapping or association studies and use of selected markers through genomic assisted breeding and genomic selection. After developing a comprehensive set of 1,616 single nucleotide polymorphism (SNPs) and their conversion into cost effective KASPar assays for pigeonpea (Cajanus cajan), we studied levels of genetic variability both within and between diverse set of Cajanus lines including 56 breeding lines, 21 landraces and 107 accessions from 18 wild species. These results revealed a high frequency of polymorphic SNPs and relatively high level of cross-species transferability. Indeed, 75.8% of successful SNP assays revealed polymorphism, and more than 95% of these assays could be successfully transferred to related wild species. To show regional patterns of variation, we used STRUCTURE and Analysis of Molecular Variance (AMOVA) to partition variance among hierarchical sets of landraces and wild species at either the continental scale or within India. STRUCTURE separated most of the domesticated germplasm from wild ecotypes, and separates Australian and Asian wild species as has been found previously. Among Indian regions and states within regions, we found 36% of the variation between regions, and 64% within landraces or wilds within states. The highest level of polymorphism in wild relatives and landraces was found in Madhya Pradesh and Andhra Pradesh provinces of India representing the centre of origin and domestication of pigeonpea respectively. PMID:24533111

Anthropogenic disturbance and environmental associations with fish assemblage structure in two nonwadeable rivers

USGS Publications Warehouse

Parks, T. P.; Quist, Michael C.; Pierce, C.L.

2016-01-01

Nonwadeable rivers are unique ecosystems that support high levels of aquatic biodiversity, yet they have been greatly altered by human activities. Although riverine fish assemblages have been studied in the past, we still have an incomplete understanding of how fish assemblages respond to both natural and anthropogenic influences in large rivers. The purpose of this study was to evaluate associations between fish assemblage structure and reach-scale habitat, dam, and watershed land use characteristics. In the summers of 2011 and 2012, comprehensive fish and environmental data were collected from 33 reaches in the Iowa and Cedar rivers of eastern-central Iowa. Canonical correspondence analysis (CCA) was used to evaluate environmental relationships with species relative abundance, functional trait abundance (e.g. catch rate of tolerant species), and functional trait composition (e.g. percentage of tolerant species). On the basis of partial CCAs, reach-scale habitat, dam characteristics, and watershed land use features explained 25.0–81.1%, 6.2–25.1%, and 5.8–47.2% of fish assemblage variation, respectively. Although reach-scale, dam, and land use factors contributed to overall assemblage structure, the majority of fish assemblage variation was constrained by reach-scale habitat factors. Specifically, mean annual discharge was consistently selected in nine of the 11 CCA models and accounted for the majority of explained fish assemblage variance by reach-scale habitat. This study provides important insight on the influence of anthropogenic disturbances across multiple spatial scales on fish assemblages in large river systems.

Linking benthic microbial community dynamics to diel redox variations in a near shore costal environment, Héeia Fishpond

NASA Astrophysics Data System (ADS)

Frank, K. L.; Rogers, K. L.; Wheat, C. G.; Alegado, R.

2016-12-01

Microbes play crucial roles in mediating biogeochemical cycling in coastal marine habitats. In shallow coastal ecosystems, excess primary productivity and respiration of pelagic phototrophic organisms generate striking diel variations in dissolved oxygen concentrations, leading to substantial vertical migration of redox transition zones in the sediment. However, the relationship between microbial community dynamics and the establishment of these geochemical gradients, especially over a diel time frame, remains poorly constrained. Here we examine the biogeochemical drivers of diel redox dynamics by integrating comprehensive geochemical, taxonomic, functional gene abundance, and thermodynamic datasets from Héeia Fishpond (HFP) sediment cores. HFP, an 88-acre tidally-influenced, shallow Hawaiian coastal estuarine system, is analogous to a large mesocosm embedded in a natural coastal environment, making it an ideal site for coastal biogeochemical studies. Taxonomic assessments of bacterial diversity via 16S rRNA genes revealed centimeter- scale variability with depth, with similar taxa present in all samples, but their relative abundances varied substantially among horizons. There were significant correlation between changes in geochemical composition and changes in community structure. Additionally, functional gene abundance was correlated with energy potential and aligned with activity. The taxanomic data and porewater geochemistry from HFP sediments suggest that redox variations observed in iron and sulfur speciation result from depth-related changes in microbial activity and community structure over a diel period. By linking community diversity to metabolic activity in the context of the geochemical environment, this research provides valuable insight into the connectivity of iron and sulfur metabolic modes.

Psychometric Structure of a Comprehensive Objective Structured Clinical Examination: A Factor Analytic Approach

ERIC Educational Resources Information Center

Volkan, Kevin; Simon, Steven R.; Baker, Harley; Todres, I. David

2004-01-01

Problem Statement and Background: While the psychometric properties of Objective Structured Clinical Examinations (OSCEs) have been studied, their latent structures have not been well characterized. This study examines a factor analytic model of a comprehensive OSCE and addresses implications for measurement of clinical performance. Methods: An…

Structure of the Sumatra-Andaman subduction zone

NASA Astrophysics Data System (ADS)

Pesicek, Jeremy Dale

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

The strength of primary care in Europe: an international comparative study.

PubMed

Kringos, Dionne; Boerma, Wienke; Bourgueil, Yann; Cartier, Thomas; Dedeu, Toni; Hasvold, Toralf; Hutchinson, Allen; Lember, Margus; Oleszczyk, Marek; Rotar Pavlic, Danica; Svab, Igor; Tedeschi, Paolo; Wilm, Stefan; Wilson, Andrew; Windak, Adam; Van der Zee, Jouke; Groenewegen, Peter

2013-11-01

A suitable definition of primary care to capture the variety of prevailing international organisation and service-delivery models is lacking. Evaluation of strength of primary care in Europe. International comparative cross-sectional study performed in 2009-2010, involving 27 EU member states, plus Iceland, Norway, Switzerland, and Turkey. Outcome measures covered three dimensions of primary care structure: primary care governance, economic conditions of primary care, and primary care workforce development; and four dimensions of primary care service-delivery process: accessibility, comprehensiveness, continuity, and coordination of primary care. The primary care dimensions were operationalised by a total of 77 indicators for which data were collected in 31 countries. Data sources included national and international literature, governmental publications, statistical databases, and experts' consultations. Countries with relatively strong primary care are Belgium, Denmark, Estonia, Finland, Lithuania, the Netherlands, Portugal, Slovenia, Spain, and the UK. Countries either have many primary care policies and regulations in place, combined with good financial coverage and resources, and adequate primary care workforce conditions, or have consistently only few of these primary care structures in place. There is no correlation between the access, continuity, coordination, and comprehensiveness of primary care of countries. Variation is shown in the strength of primary care across Europe, indicating a discrepancy in the responsibility given to primary care in national and international policy initiatives and the needed investments in primary care to solve, for example, future shortages of workforce. Countries are consistent in their primary care focus on all important structure dimensions. Countries need to improve their primary care information infrastructure to facilitate primary care performance management.

Inferences in the Comprehension of and Memory for Text. Technical Report No. 49.

ERIC Educational Resources Information Center

Goetz, Ernest T.

Two studies investigated whether variations in the importance of inferences and the salience of premises within a text would affect the probability that the inference would be made. Six stories of about 500 words were used, with eight variations of each story. The target inference, and its plausibility, was constant across all versions. Inference…

The Comparability of Scores from Different Digital Devices: A Literature Review and Synthesis with Recommendations for Practice

ERIC Educational Resources Information Center

Dadey, Nathan; Lyons, Susan; DePascale, Charles

2018-01-01

Evidence of comparability is generally needed whenever there are variations in the conditions of an assessment administration, including variations introduced by the administration of an assessment on multiple digital devices (e.g., tablet, laptop, desktop). This article is meant to provide a comprehensive examination of issues relevant to the…

The Effect of Screen Size on Mobile Phone User Comprehension of Health Information and Application Structure: An Experimental Approach.

PubMed

Al Ghamdi, Ebtisam; Yunus, Faisal; Da'ar, Omar; El-Metwally, Ashraf; Khalifa, Mohamed; Aldossari, Bakheet; Househ, Mowafa

2016-01-01

This research analyzes the impact of mobile phone screen size on user comprehension of health information and application structure. Applying experimental approach, we asked randomly selected users to read content and conduct tasks on a commonly used diabetes mobile application using three different mobile phone screen sizes. We timed and tracked a number of parameters, including correctness, effectiveness of completing tasks, content ease of reading, clarity of information organization, and comprehension. The impact of screen size on user comprehension/retention, clarity of information organization, and reading time were mixed. It is assumed on first glance that mobile screen size would affect all qualities of information reading and comprehension, including clarity of displayed information organization, reading time and user comprehension/retention of displayed information, but actually the screen size, in this experimental research, did not have significant impact on user comprehension/retention of the content or on understanding the application structure. However, it did have significant impact on clarity of information organization and reading time. Participants with larger screen size took shorter time reading the content with a significant difference in the ease of reading. While there was no significant difference in the comprehension of information or the application structures, there were a higher task completion rate and a lower number of errors with the bigger screen size. Screen size does not directly affect user comprehension of health information. However, it does affect clarity of information organization, reading time and user's ability to recall information.

The Structure of Oral Language and Reading and Their Relation to Comprehension in Kindergarten through Grade 2

PubMed Central

Foorman, Barbara R.; Herrera, Sarah; Petscher, Yaacov; Mitchell, Alison; Truckenmiller, Adrea

2016-01-01

This study examined the structure of oral language and reading and their relation to comprehension from a latent variable modeling perspective in Kindergarten, Grade 1, and Grade 2. Participants were students in Kindergarten (n = 218), Grade 1 (n = 372), and Grade 2 (n = 273), attending Title 1 schools. Students were administered phonological awareness, syntax, vocabulary, listening comprehension, and decoding fluency measures in mid-year. Outcome measures included a listening comprehension measure in Kindergarten and a reading comprehension test in Grades1 and 2. In Kindergarten, oral language (consisting of listening comprehension, syntax, and vocabulary) shared variance with phonological awareness in predicting a listening comprehension outcome. However, in Grades 1 and 2, phonological awareness was no longer predictive of reading comprehension when decoding fluency and oral language were included in the model. In Grades 1 and 2, oral language and decoding fluency were significant predictors of reading comprehension. PMID:27660395

Comparative cytogenetics of Auchenorrhyncha (Hemiptera, Homoptera): a review

PubMed Central

Kuznetsova, Valentina; Aguin-Pombo, Dora

2015-01-01

Abstract A comprehensive review of cytogenetic features is provided for the large hemipteran suborder Auchenorrhyncha, which currently contains approximately 42,000 valid species. This review is based on the analysis of 819 species, 483 genera, and 31 families representing all presently recognized Auchenorrhyncha superfamilies, e.i. Cicadoidea (cicadas), Cercopoidea (spittle bugs), Membracoidea (leafhoppers and treehoppers), Myerslopioidea (ground-dwelling leafhoppers), and Fulgoroidea (planthoppers). History and present status of chromosome studies are described, as well as the structure of chromosomes, chromosome counts, trends and mechanisms of evolution of karyotypes and sex determining systems, their variation at different taxonomic levels and most characteristic (modal) states, occurrence of parthenogenesis, polyploidy, B-chromosomes and chromosome rearrangements, and methods used for cytogenetic analysis of Auchenorrhyncha. PMID:26807037

Comprehensive benefits analysis of steel structure modular residence based on the entropy evaluation

NASA Astrophysics Data System (ADS)

Zhang, Xiaoxiao; Wang, Li; Jiang, Pengming

2017-04-01

Steel structure modular residence is the outstanding residential industrialization. It has many advantages, such as the low whole cost, high resource recovery, a high degree of industrialization. This paper compares the comprehensive benefits of steel structural in modular buildings with prefabricated reinforced concrete residential from economic benefits, environmental benefits, social benefits and technical benefits by the method of entropy evaluation. Finally, it is concluded that the comprehensive benefits of steel structural in modular buildings is better than that of prefabricated reinforced concrete residential. The conclusion of this study will provide certain reference significance to the development of steel structural in modular buildings in China.

Foundations of reading comprehension in children with intellectual disabilities.

PubMed

van Wingerden, Evelien; Segers, Eliane; van Balkom, Hans; Verhoeven, Ludo

2017-01-01

Knowledge about predictors for reading comprehension in children with intellectual disabilities (ID) is still fragmented. This study compared reading comprehension, word decoding, listening comprehension, and reading related linguistic and cognitive precursor measures in children with mild ID and typically developing controls. Moreover, it was explored how the precursors related to reading achievement. Children with mild ID and typical controls were assessed on reading comprehension, decoding, language comprehension, and linguistic (early literacy skills, vocabulary, grammar) and cognitive (rapid naming, phonological short-term memory, working memory, temporal processing, nonverbal reasoning) precursor measures. It was tested to what extent variations in reading comprehension could be explained from word decoding, listening comprehension and precursor measures. The ID group scored significantly below typical controls on all measures. Word decoding was at or above first grade level in half the ID group. Reading comprehension in the ID group was related to word decoding, listening comprehension, early literacy skills, and temporal processing. The reading comprehension profile of children with mild ID strongly resembles typical early readers. The simple view of reading pertains to children with mild ID, with additional influence of early literacy skills and temporal processing. Copyright © 2016 Elsevier Ltd. All rights reserved.

The Geography of Sexual Orientation: Structural Stigma and Sexual Attraction, Behavior, and Identity Among Men Who Have Sex with Men Across 38 European Countries.

PubMed

Pachankis, John E; Hatzenbuehler, Mark L; Mirandola, Massimo; Weatherburn, Peter; Berg, Rigmor C; Marcus, Ulrich; Schmidt, Axel J

2017-07-01

While the prevalence of sexual identities and behaviors of men who have sex with men (MSM) varies across countries, no study has examined country-level structural stigma toward sexual minorities as a correlate of this variation. Drawing on emerging support for the context-dependent nature of MSM's open sexual self-identification cross-nationally, we examined country-level structural stigma as a key correlate of the geographic variation in MSM's sexual attraction, behavior, and identity, and concordance across these factors. Data come from the European MSM Internet Survey, a multi-national dataset containing a multi-component assessment of sexual orientation administered across 38 European countries (N = 174,209). Country-level stigma was assessed using a combination of national laws and policies affecting sexual minorities and a measure of attitudes toward sexual minorities held by the citizens of each country. Results demonstrate that in more stigmatizing countries, MSM were significantly more likely to report bisexual/heterosexual attractions, behaviors, and identities, and significantly less likely to report concordance across these factors, than in less stigmatizing countries. Settlement size moderated associations between country-level structural stigma and odds of bisexual/heterosexual attraction and behavior, such that MSM living in sparsely populated locales within high-structural stigma countries were the most likely to report bisexual or heterosexual behaviors and attractions. While previous research has demonstrated associations between structural stigma and adverse physical and mental health outcomes among sexual minorities, this study was the first to show that structural stigma was also a key correlate not only of sexual orientation identification, but also of MSM's sexual behavior and even attraction. Findings have implications for understanding the ontology of MSM's sexuality and suggest that a comprehensive picture of MSM's sexuality will come from attending to the local contexts surrounding this important segment of the global population.

SNPnexus: assessing the functional relevance of genetic variation to facilitate the promise of precision medicine.

PubMed

Dayem Ullah, Abu Z; Oscanoa, Jorge; Wang, Jun; Nagano, Ai; Lemoine, Nicholas R; Chelala, Claude

2018-05-11

Broader functional annotation of genetic variation is a valuable means for prioritising phenotypically-important variants in further disease studies and large-scale genotyping projects. We developed SNPnexus to meet this need by assessing the potential significance of known and novel SNPs on the major transcriptome, proteome, regulatory and structural variation models. Since its previous release in 2012, we have made significant improvements to the annotation categories and updated the query and data viewing systems. The most notable changes include broader functional annotation of noncoding variants and expanding annotations to the most recent human genome assembly GRCh38/hg38. SNPnexus has now integrated rich resources from ENCODE and Roadmap Epigenomics Consortium to map and annotate the noncoding variants onto different classes of regulatory regions and noncoding RNAs as well as providing their predicted functional impact from eight popular non-coding variant scoring algorithms and computational methods. A novel functionality offered now is the support for neo-epitope predictions from leading tools to facilitate its use in immunotherapeutic applications. These updates to SNPnexus are in preparation for its future expansion towards a fully comprehensive computational workflow for disease-associated variant prioritization from sequencing data, placing its users at the forefront of translational research. SNPnexus is freely available at http://www.snp-nexus.org.

Mutational landscape of yeast mutator strains.

PubMed

Serero, Alexandre; Jubin, Claire; Loeillet, Sophie; Legoix-Né, Patricia; Nicolas, Alain G

2014-02-04

The acquisition of mutations is relevant to every aspect of genetics, including cancer and evolution of species on Darwinian selection. Genome variations arise from rare stochastic imperfections of cellular metabolism and deficiencies in maintenance genes. Here, we established the genome-wide spectrum of mutations that accumulate in a WT and in nine Saccharomyces cerevisiae mutator strains deficient for distinct genome maintenance processes: pol32Δ and rad27Δ (replication), msh2Δ (mismatch repair), tsa1Δ (oxidative stress), mre11Δ (recombination), mec1Δ tel1Δ (DNA damage/S-phase checkpoints), pif1Δ (maintenance of mitochondrial genome and telomere length), cac1Δ cac3Δ (nucleosome deposition), and clb5Δ (cell cycle progression). This study reveals the diversity, complexity, and ultimate unique nature of each mutational spectrum, composed of punctual mutations, chromosomal structural variations, and/or aneuploidies. The mutations produced in clb5Δ/CCNB1, mec1Δ/ATR, tel1Δ/ATM, and rad27Δ/FEN1 strains extensively reshape the genome, following a trajectory dependent on previous events. It comprises the transmission of unstable genomes that lead to colony mosaicisms. This comprehensive analytical approach of mutator defects provides a model to understand how genome variations might accumulate during clonal evolution of somatic cell populations, including tumor cells.

Multi-Directional Multi-Level Dual-Cross Patterns for Robust Face Recognition.

PubMed

Ding, Changxing; Choi, Jonghyun; Tao, Dacheng; Davis, Larry S

2016-03-01

To perform unconstrained face recognition robust to variations in illumination, pose and expression, this paper presents a new scheme to extract "Multi-Directional Multi-Level Dual-Cross Patterns" (MDML-DCPs) from face images. Specifically, the MDML-DCPs scheme exploits the first derivative of Gaussian operator to reduce the impact of differences in illumination and then computes the DCP feature at both the holistic and component levels. DCP is a novel face image descriptor inspired by the unique textural structure of human faces. It is computationally efficient and only doubles the cost of computing local binary patterns, yet is extremely robust to pose and expression variations. MDML-DCPs comprehensively yet efficiently encodes the invariant characteristics of a face image from multiple levels into patterns that are highly discriminative of inter-personal differences but robust to intra-personal variations. Experimental results on the FERET, CAS-PERL-R1, FRGC 2.0, and LFW databases indicate that DCP outperforms the state-of-the-art local descriptors (e.g., LBP, LTP, LPQ, POEM, tLBP, and LGXP) for both face identification and face verification tasks. More impressively, the best performance is achieved on the challenging LFW and FRGC 2.0 databases by deploying MDML-DCPs in a simple recognition scheme.

Vision Problems and Reduced Reading Outcomes in Queensland Schoolchildren.

PubMed

Hopkins, Shelley; Sampson, Geoff P; Hendicott, Peter L; Wood, Joanne M

2017-03-01

To assess the relationship between vision and reading outcomes in Indigenous and non-Indigenous schoolchildren to determine whether vision problems are associated with lower reading outcomes in these populations. Vision testing and reading assessments were performed on 508 Indigenous and non-Indigenous schoolchildren in Queensland, Australia divided into two age groups: Grades 1 and 2 (6-7 years of age) and Grades 6 and 7 (12-13 years of age). Vision parameters measured included cycloplegic refraction, near point of convergence, heterophoria, fusional vergence range, rapid automatized naming, and visual motor integration. The following vision conditions were then classified based on the vision findings: uncorrected hyperopia, convergence insufficiency, reduced rapid automatized naming, and delayed visual motor integration. Reading accuracy and reading comprehension were measured with the Neale reading test. The effect of uncorrected hyperopia, convergence insufficiency, reduced rapid automatized naming, and delayed visual motor integration on reading accuracy and reading comprehension were investigated with ANCOVAs. The ANCOVAs explained a significant proportion of variance in both reading accuracy and reading comprehension scores in both age groups, with 40% of the variation in reading accuracy and 33% of the variation in reading comprehension explained in the younger age group, and 27% and 10% of the variation in reading accuracy and reading comprehension, respectively, in the older age group. The vision parameters of visual motor integration and rapid automatized naming were significant predictors in all ANCOVAs (P < .01). The direction of the relationship was such that reduced reading results were explained by reduced visual motor integration and rapid automatized naming results. Both reduced rapid automatized naming and visual motor integration were associated with poorer reading outcomes in Indigenous and non-Indigenous children. This is an important finding given the recent emphasis placed on Indigenous children's reading skills and the fact that reduced rapid automatized naming and visual motor integration skills are more common in this group.

Arousal and Cognition: The Stimulation-Seeking Motive and Structural Effects in the Comprehension of Film.

ERIC Educational Resources Information Center

Braverman, Marc T.; Farley, Frank H.

Comprehension of film was studied in an ATI (aptitude x treatment interaction) framework which investigated comprehension as a function of the interaction of the stimulation-seeking motive (arousal) and degree of structure in information presented in film. Three levels of organizational coherence of a short film and two levels of the stimulation…

Long-term impact of hydrological regime on structure and functions of microbial communities in riverine wetland sediments.

PubMed

Foulquier, Arnaud; Volat, Bernadette; Neyra, Marc; Bornette, Gudrun; Montuelle, Bernard

2013-08-01

In a context of global change, alterations in the water cycle may impact the structure and function of terrestrial and aquatic ecosystems. Wetlands are particularly at risk because hydrological regime has a major influence on microbially mediated biogeochemical processes in sediments. While the influence of water availability on wetland biogeochemical processes has been comprehensively studied, the influence of hydrological regime on microbial community structure has been overlooked. We tested for the effect of hydrological regime on the structure and functions of microbial communities by comparing sediments collected at multiple sites in the Ain département (Eastern France). Each site consisted of two plots, one permanently and one seasonally inundated. At the time of sampling, all plots were continuously inundated for more than 6 months but still harboured distinct bacterial communities. This change in community structure was not associated with marked modifications in the rates of microbial activities involved in the C and N cycles. These results suggest that the observed structural change could be related to bacterial taxa responding to the environmental variations associated with different hydrological regimes, but not strongly associated with the biogeochemical processes monitored here. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Determination of Oriented Strandboard properties from a three-dimensional density distribution using the finite element method

NASA Astrophysics Data System (ADS)

Tackie, Alan Derek Nii

Computer modeling of Oriented Strand Board (OSB) properties has gained widespread attention with numerous models created to better understand OBS behavior. Recent models allow researchers to observe multiple variables such as changes in moisture content, density and resin effects on panel performance. Thickness-swell variation influences panel durability and often has adverse effects on a structural panel's bending stiffness. The prediction of out-of-plane swell under changing moisture conditions was, therefore, the essence for developing a model in this research. The finite element model accounted for both vertical and horizontal density variations, the three-dimensional (3D) density variation of the board. The density variation, resulting from manufacturing processes, affects the uniformity of thickness-swell in OSB and is often exacerbated by continuous sorption of moisture that leads to potentially damaging internal stresses in the panel. The overall thickness-swell (the cumulative swell from non-uniform horizontal density profile, panel swell from free water, and spring-back from panel compression) was addressed through the finite element model in this research. The pursued goals in this study were, first and foremost, the development of a robust and comprehensive finite element model which integrated several component studies to investigate the effects of moisture variation on the out-of-plane thickness-swell of OSB panels, and second, the extension of the developed model to predict panel stiffness. It is hoped that this paper will encourage researchers to adopt the 3D density distribution approach as a viable approach to analyzing the physical and mechanical properties of OSB.

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription.

PubMed

Tang, Zhonghui; Luo, Oscar Junhong; Li, Xingwang; Zheng, Meizhen; Zhu, Jacqueline Jufen; Szalaj, Przemyslaw; Trzaskoma, Pawel; Magalska, Adriana; Wlodarczyk, Jakub; Ruszczycki, Blazej; Michalski, Paul; Piecuch, Emaly; Wang, Ping; Wang, Danjuan; Tian, Simon Zhongyuan; Penrad-Mobayed, May; Sachs, Laurent M; Ruan, Xiaoan; Wei, Chia-Lin; Liu, Edison T; Wilczynski, Grzegorz M; Plewczynski, Dariusz; Li, Guoliang; Ruan, Yijun

2015-12-17

Spatial genome organization and its effect on transcription remains a fundamental question. We applied an advanced chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) strategy to comprehensively map higher-order chromosome folding and specific chromatin interactions mediated by CCCTC-binding factor (CTCF) and RNA polymerase II (RNAPII) with haplotype specificity and nucleotide resolution in different human cell lineages. We find that CTCF/cohesin-mediated interaction anchors serve as structural foci for spatial organization of constitutive genes concordant with CTCF-motif orientation, whereas RNAPII interacts within these structures by selectively drawing cell-type-specific genes toward CTCF foci for coordinated transcription. Furthermore, we show that haplotype variants and allelic interactions have differential effects on chromosome configuration, influencing gene expression, and may provide mechanistic insights into functions associated with disease susceptibility. 3D genome simulation suggests a model of chromatin folding around chromosomal axes, where CTCF is involved in defining the interface between condensed and open compartments for structural regulation. Our 3D genome strategy thus provides unique insights in the topological mechanism of human variations and diseases. Copyright © 2015 Elsevier Inc. All rights reserved.

Sampling Strategies for Three-Dimensional Spatial Community Structures in IBD Microbiota Research

PubMed Central

Zhang, Shaocun; Cao, Xiaocang; Huang, He

2017-01-01

Identifying intestinal microbiota is arguably an important task that is performed to determine the pathogenesis of inflammatory bowel diseases (IBD); thus, it is crucial to collect and analyze intestinally-associated microbiota. Analyzing a single niche to categorize individuals does not enable researchers to comprehensively study the spatial variations of the microbiota. Therefore, characterizing the spatial community structures of the inflammatory bowel disease microbiome is critical for advancing our understanding of the inflammatory landscape of IBD. However, at present there is no universally accepted consensus regarding the use of specific sampling strategies in different biogeographic locations. In this review, we discuss the spatial distribution when screening sample collections in IBD microbiota research. Here, we propose a novel model, a three-dimensional spatial community structure, which encompasses the x-, y-, and z-axis distributions; it can be used in some sampling sites, such as feces, colonoscopic biopsy, the mucus gel layer, and oral cavity. On the basis of this spatial model, this article also summarizes various sampling and processing strategies prior to and after DNA extraction and recommends guidelines for practical application in future research. PMID:28286741

Age-structured gametocyte allocation links immunity to epidemiology in malaria parasites.

PubMed

Paul, Richard E; Bonnet, Sarah; Boudin, Christian; Tchuinkam, Timoleon; Robert, Vincent

2007-09-12

Despite a long history of attempts to model malaria epidemiology, the over-riding conclusion is that a detailed understanding of host-parasite interactions leading to immunity is required. It is still not known what governs the duration of an infection and how within-human parasite dynamics relate to malaria epidemiology. Immunity to Plasmodium falciparum develops slowly and requires repeated exposure to the parasite, which thus generates age-structure in the host-parasite interaction. An age-structured degree of immunity would present the parasite with humans of highly variable quality. Evolutionary theory suggests that natural selection will mould adaptive phenotypes that are more precise (less variant) in "high quality" habitats, where lifetime reproductive success is best. Variability in malaria parasite gametocyte density is predicted to be less variable in those age groups who best infect mosquitoes. Thus, the extent to which variation in gametocyte density is a simple parasite phenotype reflecting the complex within-host parasite dynamics is addressed. Gametocyte densities and corresponding infectiousness to mosquitoes from published data sets and studies in both rural and urban Cameroon are analysed. The mean and variation in gametocyte density according to age group are considered and compared with transmission success (proportion of mosquitoes infected). Across a wide range of settings endemic for malaria, the age group that infected most mosquitoes had the least variation in gametocyte density, i.e. there was a significant relationship between the variance rather than the mean gametocyte density and age-specific parasite transmission success. In these settings, the acquisition of immunity over time was evident as a decrease in asexual parasite densities with age. By contrast, in an urban setting, there were no such age-structured relationships either with variation in gametocyte density or asexual parasite density. Gametocyte production is seemingly predicted by evolutionary theory, insofar as a reproductive phenotype (gametocyte density) is most precisely expressed (i.e. is most invariant) in the most infectious human age group. This human age group would thus be expected to be the habitat most suitable for the parasite. Comprehension of the immuno-epidemiology of malaria, a requisite for any vaccine strategies, remains poor. Immunological characterization of the human population stratified by parasite gametocyte allocation would be a step forward in identifying the salient immunological pathways of what makes a human a good habitat.

Performance range of SMA actuator wires and SMA-FRP structure in terms of manufacturing, modeling and actuation

NASA Astrophysics Data System (ADS)

Hübler, M.; Gurka, M.; Schmeer, S.; Breuer, U. P.

2013-09-01

In this contribution we present a comprehensive theoretical and experimental description of an active shape memory alloy (SMA) fiber reinforced composite (FRP) hybrid structure. The major influences on actuation performance arising from variations in the design and manufacturing process are discussed, utilizing a new phenomenological model to describe the actuating SMA material. The different material properties for the activated, respective the unactivated, SMA as well as the influence of different loading conditions or pre-treatment of the material are taken into account in this model. To validate our material model we performed new actuation experiments with an exemplary SMA-FRP structure, which we compared to finite element (FE) simulation results. Our FE-model is based on a material model for the actuating SMA elements derived from experiments and data on the actual microscopic geometry of the hybrid composite. Therefore it is able to predict very precisely the actuation behavior of a typical FRP structure for industrial use cases: a thin walled CFRP sheet with SMA wires attached to the top for performing a bending motion with a maximum deflection of approx. 25% of its length.

Persistent Structural Priming from Language Comprehension to Language Production

ERIC Educational Resources Information Center

Bock, Kathryn; Dell, Gary S.; Chang, Franklin; Onishi, Kristine H.

2007-01-01

To examine the relationship between syntactic processes in language comprehension and language production, we compared structural persistence from sentence primes that speakers heard to persistence from primes that speakers produced. [Bock, J. K., & Griffin, Z. M. (2000). The persistence of structural priming: transient activation or implicit…

Aberrant RNA splicing in cancer; expression changes and driver mutations of splicing factor genes.

PubMed

Sveen, A; Kilpinen, S; Ruusulehto, A; Lothe, R A; Skotheim, R I

2016-05-12

Alternative splicing is a widespread process contributing to structural transcript variation and proteome diversity. In cancer, the splicing process is commonly disrupted, resulting in both functional and non-functional end-products. Cancer-specific splicing events are known to contribute to disease progression; however, the dysregulated splicing patterns found on a genome-wide scale have until recently been less well-studied. In this review, we provide an overview of aberrant RNA splicing and its regulation in cancer. We then focus on the executors of the splicing process. Based on a comprehensive catalog of splicing factor encoding genes and analyses of available gene expression and somatic mutation data, we identify cancer-associated patterns of dysregulation. Splicing factor genes are shown to be significantly differentially expressed between cancer and corresponding normal samples, and to have reduced inter-individual expression variation in cancer. Furthermore, we identify enrichment of predicted cancer-critical genes among the splicing factors. In addition to previously described oncogenic splicing factor genes, we propose 24 novel cancer-critical splicing factors predicted from somatic mutations.

Landscape correlates of breeding bird richness across the United States mid-Atlantic region

USGS Publications Warehouse

Jones, K.B.; Neale, A.C.; Nash, M.S.; Riitters, K.H.; Wickham, J.D.; O'Neill, R. V.; Van Remortel, R. D.

2000-01-01

Using a new set of landscape indicator data generated by the U.S.EPA, and a comprehensive breeding bird database from the National Breeding Bird Survey, we evaluated associations between breeding bird richness and landscape characteristics across the entire mid-Atlantic region of the United States. We evaluated how these relationships varied among different groupings (guilds) of birds based on functional, structural, and compositional aspects of individual species demographics. Forest edge was by far the most important landscape attribute affecting the richness of the lumped specialist and generalist guilds; specialist species richness was negatively associated with forest edge and generalist richness was positively associated with forest edge. Landscape variables (indicators) explained a greater proportion of specialist species richness than the generalist guild (46% and 31%, respectively). The lower value in generalists may reflect freer-scale distributions of open habitat that go undetected by the Landsat satellite, open habitats created by roads (the areas from which breeding bird data are obtained), and the lumping of a wide variety of species into the generalist category. A further breakdown of species into 16 guilds showed considerable variation in the response of breeding birds to landscape conditions; forest obligate species had the strongest association with landscape indicators measured in this study (55% of the total variation explained) and forest generalists and open ground nesters the lowest (17% of the total variation explained). The variable response of guild species richness to landscape pattern suggests that one must consider species' demographics when assessing the consequences of landscape change on breeding birds.Using a new set of landscape indicator data generated by the U.S. EPA, and a comprehensive breeding bird database from the National Breeding Bird Survey, we evaluated associations between breeding bird richness and landscape characteristics across the entire mid-Atlantic region of the United States. We evaluated how these relationships varied among different groupings (guilds) of birds based on functional, structural, and compositional aspects of individual species demographics. Forest edge was by far the most important landscape attribute affecting the richness of the lumped specialist and generalist guilds; specialist species richness was negatively associated with forest edge and generalist richness was positively associated with forest edge. Landscape variables (indicators) explained a greater proportion of specialist species richness than the generalist guild (46% and 31%, respectively). The lower value in generalists may reflect finer-scale distributions of open habitat that go undetected by the Landsat satellite, open habitats created by roads (the areas from which breeding bird data are obtained), and the lumping of a wide variety of species into the generalist category. A further breakdown of species into 16 guilds showed considerable variation in the response of breeding birds to landscape conditions; forest obligate species had the strongest association with landscape indicators measured in this study (55% of the total variation explained) and forest generalists and open ground nesters the lowest (17% of the total variation explained). The variable response of guild species richness to landscape pattern suggests that one must consider species' demographics when assessing the consequences of landscape change on breeding birds.

Spatial Genetic Structure and Mitochondrial DNA Phylogeography of Argentinean Populations of the Grasshopper Dichroplus elongatus

PubMed Central

Rosetti, Natalia; Remis, Maria Isabel

2012-01-01

Many grasshopper species are considered of agronomical importance because they cause damage to pastures and crops. Comprehension of pest population dynamics requires a clear understanding of the genetic diversity and spatial structure of populations. In this study we report on patterns of genetic variation in the South American grasshopper Dichroplus elongatus which is an agricultural pest of crops and forage grasses of great economic significance in Argentina. We use Direct Amplification of Minisatellite Regions (DAMD) and partial sequences of the cytochrome oxydase 1 (COI) mitochondrial gene to investigate intraspecific structure, demographic history and gene flow patterns in twenty Argentinean populations of this species belonging to different geographic and biogeographic regions. DAMD data suggest that, although genetic drift and migration occur within and between populations, measurable relatedness among neighbouring populations declines with distance and dispersal over distances greater than 200 km is not typical, whereas effective gene flow may occur for populations separated by less than 100 km. Landscape analysis was useful to detect genetic discontinuities associated with environmental heterogeneity reflecting the changing agroecosystem. The COI results indicate the existence of strong genetic differentiation between two groups of populations located at both margins of the Paraná River which became separated during climate oscillations of the Middle Pleistocene, suggesting a significant restriction in effective dispersion mediated by females and large scale geographic differentiation. The number of migrants between populations estimated through mitochondrial and DAMD markers suggest that gene flow is low prompting a non-homogeneous spatial structure and justifying the variation through space. Moreover, the genetic analysis of both markers allows us to conclude that males appear to disperse more than females, reducing the chance of the genetic loss associated with recent anthropogenic fragmentation of the D. elongatus studied range. PMID:22859953

Microbial community pattern detection in human body habitats via ensemble clustering framework.

PubMed

Yang, Peng; Su, Xiaoquan; Ou-Yang, Le; Chua, Hon-Nian; Li, Xiao-Li; Ning, Kang

2014-01-01

The human habitat is a host where microbial species evolve, function, and continue to evolve. Elucidating how microbial communities respond to human habitats is a fundamental and critical task, as establishing baselines of human microbiome is essential in understanding its role in human disease and health. Recent studies on healthy human microbiome focus on particular body habitats, assuming that microbiome develop similar structural patterns to perform similar ecosystem function under same environmental conditions. However, current studies usually overlook a complex and interconnected landscape of human microbiome and limit the ability in particular body habitats with learning models of specific criterion. Therefore, these methods could not capture the real-world underlying microbial patterns effectively. To obtain a comprehensive view, we propose a novel ensemble clustering framework to mine the structure of microbial community pattern on large-scale metagenomic data. Particularly, we first build a microbial similarity network via integrating 1920 metagenomic samples from three body habitats of healthy adults. Then a novel symmetric Nonnegative Matrix Factorization (NMF) based ensemble model is proposed and applied onto the network to detect clustering pattern. Extensive experiments are conducted to evaluate the effectiveness of our model on deriving microbial community with respect to body habitat and host gender. From clustering results, we observed that body habitat exhibits a strong bound but non-unique microbial structural pattern. Meanwhile, human microbiome reveals different degree of structural variations over body habitat and host gender. In summary, our ensemble clustering framework could efficiently explore integrated clustering results to accurately identify microbial communities, and provide a comprehensive view for a set of microbial communities. The clustering results indicate that structure of human microbiome is varied systematically across body habitats and host genders. Such trends depict an integrated biography of microbial communities, which offer a new insight towards uncovering pathogenic model of human microbiome.

Microbial community pattern detection in human body habitats via ensemble clustering framework

PubMed Central

2014-01-01

Background The human habitat is a host where microbial species evolve, function, and continue to evolve. Elucidating how microbial communities respond to human habitats is a fundamental and critical task, as establishing baselines of human microbiome is essential in understanding its role in human disease and health. Recent studies on healthy human microbiome focus on particular body habitats, assuming that microbiome develop similar structural patterns to perform similar ecosystem function under same environmental conditions. However, current studies usually overlook a complex and interconnected landscape of human microbiome and limit the ability in particular body habitats with learning models of specific criterion. Therefore, these methods could not capture the real-world underlying microbial patterns effectively. Results To obtain a comprehensive view, we propose a novel ensemble clustering framework to mine the structure of microbial community pattern on large-scale metagenomic data. Particularly, we first build a microbial similarity network via integrating 1920 metagenomic samples from three body habitats of healthy adults. Then a novel symmetric Nonnegative Matrix Factorization (NMF) based ensemble model is proposed and applied onto the network to detect clustering pattern. Extensive experiments are conducted to evaluate the effectiveness of our model on deriving microbial community with respect to body habitat and host gender. From clustering results, we observed that body habitat exhibits a strong bound but non-unique microbial structural pattern. Meanwhile, human microbiome reveals different degree of structural variations over body habitat and host gender. Conclusions In summary, our ensemble clustering framework could efficiently explore integrated clustering results to accurately identify microbial communities, and provide a comprehensive view for a set of microbial communities. The clustering results indicate that structure of human microbiome is varied systematically across body habitats and host genders. Such trends depict an integrated biography of microbial communities, which offer a new insight towards uncovering pathogenic model of human microbiome. PMID:25521415

Ion Temperature Control of the Io Plasma Torus

NASA Technical Reports Server (NTRS)

Delamere, P. A.; Schneider, N. M.; Steffl, A. J.; Robbins, S. J.

2005-01-01

We report on observational and theoretical studies of ion temperature in the Io plasma torus. Ion temperature is a critical factor for two reasons. First, ions are a major supplier of energy to the torus electrons which power the intense EUV emissions. Second, ion temperature determines the vertical extent of plasma along field lines. Higher temperatures spread plasma out, lowers the density and slows reaction rates. The combined effects can play a controlling role in torus energetics and chemistry. An unexpected tool for the study of ion temperature is the longitudinal structure in the plasma torus which often manifests itself as periodic brightness variations. Opposite sides of the torus (especially magnetic longitudes 20 and 200 degrees) have been observed on numerous occasions to have dramatically different brightness, density, composition, ionization state, electron temperature and ion temperature. These asymmetries must ultimately be driven by different energy flows on the opposite sides, presenting an opportunity to observe key torus processes operating under different conditions. The most comprehensive dataset for the study of longitudinal variations was obtained by the Cassini UVIS instrument during its Jupiter flyby. Steffl (Ph.D. thesis, 2005) identified longitudinal variations in all the quantities listed above wit the exception of ion temperature. We extend his work by undertaking the first search for such variation in the UVIS dataset. We also report on a 'square centimeter' model of the torus which extend the traditional 'cubic centimeter' models by including the controlling effects of ion temperature more completely.

How logical reasoning mediates the relation between lexical quality and reading comprehension.

PubMed

Segers, Eliane; Verhoeven, Ludo

The present study aimed to examine the role of logical reasoning in the relation between lexical quality and reading comprehension in 146 fourth grade Dutch children. We assessed their standardized reading comprehension measure, along with their decoding efficiency and vocabulary as measures of lexical quality, syllogistic reasoning as measure of (verbal) logical reasoning, and nonverbal reasoning as a control measure. Syllogistic reasoning was divided into a measure tapping basic, coherence inferencing skill using logical syllogisms, and a measure tapping elaborative inferencing skill using indeterminate syllogisms. Results showed that both types of syllogisms partly mediated the relation between lexical quality and reading comprehension, but also had a unique additional effect on reading comprehension. The indirect effect of lexical quality on reading comprehension via syllogisms was driven by vocabulary knowledge. It is concluded that measures of syllogistic reasoning account for higher-order thinking processes that are needed to make inferences in reading comprehension. The role of lexical quality appears to be pivotal in explaining the variation in reading comprehension both directly and indirectly via syllogistic reasoning.

Text Structure Strategies for Improving Expository Reading Comprehension

ERIC Educational Resources Information Center

Roehling, Julia V.; Hebert, Michael; Nelson, J. Ron; Bohaty, Janet J.

2017-01-01

Comprehending expository reading material is a challenge for many students. Research has shown that students' expository reading comprehension can improve with the help of text structure instruction. The purpose of this article is to present teachers with a framework for effectively implementing text structure instruction in their classrooms.…

Water Structure and Dynamics in Smectites: X-ray Diffraction and 2 H NMR Spectroscopy of Mg–, Ca–, Sr–, Na–, Cs–, and Pb–Hectorite

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

Reddy, U. Venkateswara; Bowers, Geoffrey M.; Loganathan, Narasimhan

2016-04-06

Variable-temperature X-ray diffraction and 2H NMR spectroscopy of the smectite mineral, hectorite, containing interlayer Na +, K +, Cs +, Mg 2+, Ca 2+, Sr 2+, and Pb 2+ equilibrated at 43% relative humidity (RH) and mixed with 2H 2O to form a paste provide a comprehensive picture of the structural environments and dynamics of interlayer 2H 2O and the relationships of these properties to interlayer hydration state, the hydration energy and polarizability of the cation, temperature, and the formation of ice-1h in the interparticle pores. The variation in basal spacing shown by the XRD data correlates well with themore » 2H NMR behavior, and the XRD data show for the first time in hectorites that crystallization of interparticle ice-1h causes a decrease in the interlayer spacing, likely due to removal of interlayer 2H 2O. The variation of the 2H NMR behavior of all the samples with decreasing temperature reflects decreasing frequencies of motion for the rotation of the 2H 2O molecules around their dipoles, reorientation of the 2H 2O molecules, and exchange of the 2H 2O molecules between interlayer sites coordinated to and not coordinated to the cations.« less

Patch reef modeling: a comparison of Devonian and recent examples

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

Precht, W.F.

In reef research, models have been developed to define variations in the lithic and biotic development of facies. Walker and Alberstadt, and Hoffman and Narkiewicz developed models for growth of ancient reef communities. Although these models form a solid foundation by which patch reefs can be classed and zoned, they are neither complete nor accurate for all reef types. A comparison was made of Lower Devonian patch reefs from the Appalachian basin of New York, New Jersey, and Pennsylvania, and Holocene examples from the Bahamas and Florida Keys to identify the structure, orientation, community variability, and succession of the reefmore » biofacies. The complexion and genesis of the carbonate lithofacies were also studied. Results show similarities; these include the size, areal distribution, 3-D geometry, wave-resistance potential, lateral sequences of facies, sedimentary textures and structures, vertical zonation explained by growth from low-energy to high-energy regimes, biotic diversity, growth habit and form, and postmortem alteration. Thus, when used in conjunction with the traditional models, the recent can serve as the basis for a general model which include most patch reef types. However, these models should not be used as explicit analogs for all Phanerozoic reefs. Knowing and understanding the limitations of these comparative studies are essential to a fuller comprehension of the potential for variations which exist within and between the traditional models.« less

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

PubMed

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

2015-01-01

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

Matching consumer feeding behaviours and resource traits: a fourth-corner problem in food-web theory.

PubMed

Monteiro, Angelo Barbosa; Faria, Lucas Del Bianco

2018-06-06

For decades, food web theory has proposed phenomenological models for the underlying structure of ecological networks. Generally, these models rely on latent niche variables that match the feeding behaviour of consumers with their resource traits. In this paper, we used a comprehensive database to evaluate different hypotheses on the best dependency structure of trait-matching patterns between consumers and resource traits. We found that consumer feeding behaviours had complex interactions with resource traits; however, few dimensions (i.e. latent variables) could reproduce the trait-matching patterns. We discuss our findings in the light of three food web models designed to reproduce the multidimensionality of food web data; additionally, we discuss how using species traits clarify food webs beyond species pairwise interactions and enable studies to infer ecological generality at larger scales, despite potential taxonomic differences, variations in ecological conditions and differences in species abundance between communities. © 2018 John Wiley & Sons Ltd/CNRS.

Atomic-scale observation of structural and electronic orders in the layered compound α-RuCl3

NASA Astrophysics Data System (ADS)

Ziatdinov, M.; Banerjee, A.; Maksov, A.; Berlijn, T.; Zhou, W.; Cao, H. B.; Yan, J.-Q.; Bridges, C. A.; Mandrus, D. G.; Nagler, S. E.; Baddorf, A. P.; Kalinin, S. V.

2016-12-01

A pseudospin-1/2 Mott phase on a honeycomb lattice is proposed to host the celebrated two-dimensional Kitaev model which has an elusive quantum spin liquid ground state, and fascinating physics relevant to the development of future templates towards topological quantum bits. Here we report a comprehensive, atomically resolved real-space study by scanning transmission electron and scanning tunnelling microscopies on a novel layered material displaying Kitaev physics, α-RuCl3. Our local crystallography analysis reveals considerable variations in the geometry of the ligand sublattice in thin films of α-RuCl3 that opens a way to realization of a spatially inhomogeneous magnetic ground state at the nanometre length scale. Using scanning tunnelling techniques, we observe the electronic energy gap of ~0.25 eV and intra-unit cell symmetry breaking of charge distribution in individual α-RuCl3 surface layer. The corresponding charge-ordered pattern has a fine structure associated with two different types of charge disproportionation at Cl-terminated surface.

Oil and drug control the release rate from lyotropic liquid crystals.

PubMed

Martiel, Isabelle; Baumann, Nicole; Vallooran, Jijo J; Bergfreund, Jotam; Sagalowicz, Laurent; Mezzenga, Raffaele

2015-04-28

The control of the diffusion coefficient by the dimensionality d of the structure appears as a most promising lever to efficiently tune the release rate from lyotropic liquid crystalline (LLC) phases and dispersed particles towards sustained, controlled and targeted release. By using phosphatidylcholine (PC)- and monolinoleine (MLO)-based mesophases with various apolar structural modifiers and water-soluble drugs, we present a comprehensive study of the dimensional structural control of hydrophilic drug release, including 3-d bicontinuous cubic, 2-d lamellar, 1-d hexagonal and 0-d micellar cubic phases in excess water. We investigate how the surfactant, the oil properties and the drug hydrophilicity mitigate or even cancel the effect of structure variation on the drug release rate. Unexpectedly, the observed behavior cannot be fully explained by the thermodynamic partition of the drug into the lipid matrix, which points out to previously overlooked kinetic effects. We therefore interpret our results by discussing the mechanism of structural control of the diffusion rate in terms of drug permeation through the lipid membrane, which includes exchange kinetics. A wide range of implications follow regarding formulation and future developments, both for dispersed LLC delivery systems and topical applications in bulk phase. Copyright © 2015 Elsevier B.V. All rights reserved.

Simulation of the Indian Summer Monsoon Using Comprehensive Atmosphere-land Interactions, in the Absence of Two-way Air-sea Interactions

NASA Technical Reports Server (NTRS)

Lim, Young-Kwon; Shin, D. W.; Cocke, Steven; Kang, Sung-Dae; Kim, Hae-Dong

2011-01-01

Community Land Model version 2 (CLM2) as a comprehensive land surface model and a simple land surface model (SLM) were coupled to an atmospheric climate model to investigate the role of land surface processes in the development and the persistence of the South Asian summer monsoon. Two-way air-sea interactions were not considered in order to identify the reproducibility of the monsoon evolution by the comprehensive land model, which includes more realistic vertical soil moisture structures, vegetation and 2-way atmosphere-land interactions at hourly intervals. In the monsoon development phase (May and June). comprehensive land-surface treatment improves the representation of atmospheric circulations and the resulting convergence/divergence through the improvements in differential heating patterns and surface energy fluxes. Coupling with CLM2 also improves the timing and spatial distribution of rainfall maxima, reducing the seasonal rainfall overestimation by approx.60 % (1.8 mm/d for SLM, 0.7 mm/dI for CLM2). As for the interannual variation of the simulated rainfall, correlation coefficients of the Indian seasonal rainfall with observation increased from 0.21 (SLM) to 0.45 (CLM2). However, in the mature monsoon phase (July to September), coupling with the CLM2 does not exhibit a clear improvement. In contrast to the development phase, latent heat flux is underestimated and sensible heat flux and surface temperature over India are markedly overestimated. In addition, the moisture fluxes do not correlate well with lower-level atmospheric convergence, yielding correlation coefficients and root mean square errors worse than those produced by coupling with the SLM. A more realistic representation of the surface temperature and energy fluxes is needed to achieve an improved simulation for the mature monsoon period.

The Role of Elaboration in the Comprehension and Retention of Prose: A Critical Review.

ERIC Educational Resources Information Center

Reder, Lynne M.

1980-01-01

Recent research in the area of prose comprehension is reviewed, including factors that affect amount of recall, representations of text structures, and use of world knowledge to aid comprehension. The need for more information processing models of comprehension is emphasized. Elaboration is considered important for comprehension and retention.…

Genetic markers for the identification and characterization of Opisthorchis viverrini, a medically important food borne trematode in Southeast Asia.

PubMed

Saijuntha, Weerachai; Sithithaworn, Paiboon; Wongkham, Sopit; Laha, Thewarach; Pipitgool, Vichit; Petney, Trevor N; Andrews, Ross H

2006-12-01

The liver fluke, Opisthorchis viverrini, is one of the major food borne trematodes in Southeast Asia, where infection causes hepatobiliary disease and subsequent development of cholangiocarcinoma. In Thailand, O. viverrini is most prevalent in the northeast where there is marked regional variation in the rate of infection in humans at provincial, district and village levels. To date, the roles of genetic variation of O. viverrini on this observed variability in infection, transmission and associated disease are not known. We have applied multilocus enzyme electrophoresis (MEE), specifically allozyme electrophoresis, to isolates of O. viverrini from Thailand and Laos to establish genetic markers to examine its systematics and population structure. Forty-six enzymes commonly found useful for genetic characterisation in parasitic helminths were screened, and of these, 33 enzymes gave sufficient staining and resolution to act as potential genetic markers. Sixteen enzymes were monomorphic and 17 enzymes were polymorphic in the pools of worms examined. Whether they are indicative of different enzyme loci, heterozygosity or unique genotypes within the pools of worms examined remains to be determined. Preliminary investigations examining five individual worms at enzyme loci where pools of worms showed multiple bands have confirmed the diagnostic value of the enzyme loci established as well as providing evidence of potential population sub structuring and heterozygosity. For the first time, we have established at least 17 enzymes that provide the basis to undertake comprehensive genetic analyses of the systematics and population structure of O. viverrini, a medically important food borne trematode in Southeast Asia.

Cenozoic intraplate tectonics in Central Patagonia: Record of main Andean phases in a weak upper plate

NASA Astrophysics Data System (ADS)

Gianni, G. M.; Echaurren, A.; Folguera, A.; Likerman, J.; Encinas, A.; García, H. P. A.; Dal Molin, C.; Valencia, V. A.

2017-11-01

Contraction in intraplate areas is still poorly understood relative to similar deformation at plate margins. In order to contribute to its comprehension, we study the Patagonian broken foreland (PBF) in South America whose evolution remains controversial. Time constraints of tectonic events and structural characterization of this belt are limited. Also, major causes of strain location in this orogen far from the plate margin are enigmatic. To unravel tectonic events, we studied the Cenozoic sedimentary record of the central sector of the Patagonian broken foreland (San Bernardo fold and thrust belt, 44°30‧S-46°S) and the Andes (Meseta de Chalia, 46°S) following an approach involving growth-strata detection, U-Pb geochronology and structural modeling. Additionally, we elaborate a high resolution analysis of the effective elastic thickness (Te) to examine the relation between intraplate contraction location and variations in lithospheric strength. The occurrence of Eocene growth-strata ( 44-40 Ma) suggests that contraction in the Andes and the Patagonian broken foreland was linked to the Incaic phase. Detection of synextensional deposits suggests that the broken foreland collapsed partially during Oligocene to early Miocene. During middle Miocene times, the Quechua contractional phase produced folding of Neogene volcanic rocks and olistostrome deposition at 17 Ma. Finally, the presented Te map shows that intraplate contraction related to Andean phases localized preferentially along weak lithospheric zones (Te < 15 km). Hence, the observed strain distribution in the PBF appears to be controlled by lateral variations in the lithospheric strength. Variations in this parameter could be related to thermo-mechanical weakening produced by intraplate rifting in Paleozoic-Mesozoic times.

Comprehensive risk analysis for structure type selection.

DOT National Transportation Integrated Search

2010-04-01

Optimization of bridge selection and design traditionally has been sought in terms of the finished structure. This study presents a : more comprehensive risk-based analysis that includes user costs and accidents during the construction phase. Costs f...

Design and Testing of a Tool for Evaluating the Quality of Diabetes Consumer-Information Web Sites

PubMed Central

Steinwachs, Donald; Rubin, Haya R

2003-01-01

Background Most existing tools for measuring the quality of Internet health information focus almost exclusively on structural criteria or other proxies for quality information rather than evaluating actual accuracy and comprehensiveness. Objective This research sought to develop a new performance-measurement tool for evaluating the quality of Internet health information, test the validity and reliability of the tool, and assess the variability in diabetes Web site quality. Methods An objective, systematic tool was developed to evaluate Internet diabetes information based on a quality-of-care measurement framework. The principal investigator developed an abstraction tool and trained an external reviewer on its use. The tool included 7 structural measures and 34 performance measures created by using evidence-based practice guidelines and experts' judgments of accuracy and comprehensiveness. Results Substantial variation existed in all categories, with overall scores following a normal distribution and ranging from 15% to 95% (mean was 50% and median was 51%). Lin's concordance correlation coefficient to assess agreement between raters produced a rho of 0.761 (Pearson's r of 0.769), suggesting moderate to high agreement. The average agreement between raters for the performance measures was 0.80. Conclusions Diabetes Web site quality varies widely. Alpha testing of this new tool suggests that it could become a reliable and valid method for evaluating the quality of Internet health sites. Such an instrument could help lay people distinguish between beneficial and misleading information. PMID:14713658

Hypertext comprehension of deaf and hard-of-hearing students and students with specific language impairment.

PubMed

Blom, Helen; Segers, Eliane; Hermans, Daan; Knoors, Harry; Verhoeven, Ludo

2017-02-01

This paper provides insight into the reading comprehension of hierarchically structured hypertexts within D/HH students and students with SLI. To our knowledge, it is the first study on hypertext comprehension in D/HH students and students with SLI, and it also considers the role of working memory. We compared hypertext versus linear text comprehension in D/HH students and students with SLI versus younger students without language problems who had a similar level of decoding and vocabulary. The results demonstrated no difference in text comprehension between the hierarchically structured hypertext and the linear text. Text comprehension of D/HH students and students with SLI was comparable to that of the students without language problems. In addition, there was a similar positive predictive value of visuospatial and not verbal working memory on hypertext comprehension for all three groups. The findings implicate that educational settings can make use of hierarchically structured hypertexts as well as linear texts and that children can navigate in the digital world from young age on, even if language or working memory problems are present. Copyright © 2016 Elsevier Ltd. All rights reserved.

Statistics and classification of the microwave zebra patterns associated with solar flares

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

Tan, Baolin; Tan, Chengming; Zhang, Yin

2014-01-10

The microwave zebra pattern (ZP) is the most interesting, intriguing, and complex spectral structure frequently observed in solar flares. A comprehensive statistical study will certainly help us to understand the formation mechanism, which is not exactly clear now. This work presents a comprehensive statistical analysis of a big sample with 202 ZP events collected from observations at the Chinese Solar Broadband Radio Spectrometer at Huairou and the Ondŕejov Radiospectrograph in the Czech Republic at frequencies of 1.00-7.60 GHz from 2000 to 2013. After investigating the parameter properties of ZPs, such as the occurrence in flare phase, frequency range, polarization degree,more » duration, etc., we find that the variation of zebra stripe frequency separation with respect to frequency is the best indicator for a physical classification of ZPs. Microwave ZPs can be classified into three types: equidistant ZPs, variable-distant ZPs, and growing-distant ZPs, possibly corresponding to mechanisms of the Bernstein wave model, whistler wave model, and double plasma resonance model, respectively. This statistical classification may help us to clarify the controversies between the existing various theoretical models and understand the physical processes in the source regions.« less

A Study of the Effects of Variation of Short-Term Memory Load, Reading Response Length, and Processing Hierarchy on TOEFL Listening Comprehension Item Performance. Report 33.

ERIC Educational Resources Information Center

Henning, Grant

Criticisms of the Test of English as a Foreign Language (TOEFL) have included speculation that the listening test places too much burden on short-term memory as compared with comprehension, that a knowledge of reading is required to respond successfully, and that many items appear to require mere recall and matching rather than higher-order…

Background | Office of Cancer Clinical Proteomics Research

Cancer.gov

The term "proteomics" refers to a large-scale comprehensive study of a specific proteome resulting from its genome, including abundances of proteins, their variations and modifications, and interacting partners and networks in order to understand cellular processes involved.  Similarly, “Cancer proteomics” refers to comprehensive analyses of proteins and their derivatives translated from a specific cancer genome using a human biospecimen or a preclinical model (e.g., cultured cell or animal model).

Visualization of terahertz surface waves propagation on metal foils

PubMed Central

Wang, Xinke; Wang, Sen; Sun, Wenfeng; Feng, Shengfei; Han, Peng; Yan, Haitao; Ye, Jiasheng; Zhang, Yan

2016-01-01

Exploitation of surface plasmonic devices (SPDs) in the terahertz (THz) band is always beneficial for broadening the application potential of THz technologies. To clarify features of SPDs, a practical characterization means is essential for accurately observing the complex field distribution of a THz surface wave (TSW). Here, a THz digital holographic imaging system is employed to coherently exhibit temporal variations and spectral properties of TSWs activated by a rectangular or semicircular slit structure on metal foils. Advantages of the imaging system are comprehensively elucidated, including the exclusive measurement of TSWs and fall-off of the time consumption. Numerical simulations of experimental procedures further verify the imaging measurement accuracy. It can be anticipated that this imaging system will provide a versatile tool for analyzing the performance and principle of SPDs. PMID:26729652

Vibrations of single-crystal gold nanorods and nanowires

NASA Astrophysics Data System (ADS)

Saviot, L.

2018-04-01

The vibrations of gold nanowires and nanorods are investigated numerically in the framework of continuum elasticity using the Rayleigh-Ritz variational method. Special attention is paid to identify the vibrations relevant in Raman scattering experiments. A comprehensive description of the vibrations of nanorods is proposed by determining their symmetry, comparing with standing waves in the corresponding nanowires, and estimating their Raman intensity. The role of experimentally relevant parameters such as the anisotropic cubic lattice structure, the presence of faceted lateral surfaces, and the shape of the ends of the nanorods is evaluated. Elastic anisotropy is shown to play a significant role contrarily to the presence of facets. Localized vibrations are found for nanorods with flat ends. Their evolution as the shape of the ends is changed to half-spheres is discussed.

Decomposing variation in male reproductive success: age-specific variances and covariances through extra-pair and within-pair reproduction.

PubMed

Lebigre, Christophe; Arcese, Peter; Reid, Jane M

2013-07-01

Age-specific variances and covariances in reproductive success shape the total variance in lifetime reproductive success (LRS), age-specific opportunities for selection, and population demographic variance and effective size. Age-specific (co)variances in reproductive success achieved through different reproductive routes must therefore be quantified to predict population, phenotypic and evolutionary dynamics in age-structured populations. While numerous studies have quantified age-specific variation in mean reproductive success, age-specific variances and covariances in reproductive success, and the contributions of different reproductive routes to these (co)variances, have not been comprehensively quantified in natural populations. We applied 'additive' and 'independent' methods of variance decomposition to complete data describing apparent (social) and realised (genetic) age-specific reproductive success across 11 cohorts of socially monogamous but genetically polygynandrous song sparrows (Melospiza melodia). We thereby quantified age-specific (co)variances in male within-pair and extra-pair reproductive success (WPRS and EPRS) and the contributions of these (co)variances to the total variances in age-specific reproductive success and LRS. 'Additive' decomposition showed that within-age and among-age (co)variances in WPRS across males aged 2-4 years contributed most to the total variance in LRS. Age-specific (co)variances in EPRS contributed relatively little. However, extra-pair reproduction altered age-specific variances in reproductive success relative to the social mating system, and hence altered the relative contributions of age-specific reproductive success to the total variance in LRS. 'Independent' decomposition showed that the (co)variances in age-specific WPRS, EPRS and total reproductive success, and the resulting opportunities for selection, varied substantially across males that survived to each age. Furthermore, extra-pair reproduction increased the variance in age-specific reproductive success relative to the social mating system to a degree that increased across successive age classes. This comprehensive decomposition of the total variances in age-specific reproductive success and LRS into age-specific (co)variances attributable to two reproductive routes showed that within-age and among-age covariances contributed substantially to the total variance and that extra-pair reproduction can alter the (co)variance structure of age-specific reproductive success. Such covariances and impacts should consequently be integrated into theoretical assessments of demographic and evolutionary processes in age-structured populations. © 2013 The Authors. Journal of Animal Ecology © 2013 British Ecological Society.

Water Quality Assessment for Deep-water Channel area of Guangzhou Port based on the Comprehensive Water Quality Identification Index Method

NASA Astrophysics Data System (ADS)

Chen, Yi

2018-03-01

The comprehensive water quality identification index method is able to assess the general water quality situation comprehensively and represent the water quality classification; water environment functional zone achieves pollution level and standard objectively and systematically. This paper selects 3 representative zones along deep-water channel of Guangzhou port and applies comprehensive water quality identification index method to calculate sea water quality monitoring data for different selected zones from year 2006 to 2014, in order to investigate the temporal variation of water quality along deep-water channel of Guangzhou port. The comprehensive water quality level from north to south presents an increased trend, and the water quality of the three zones in 2014 is much better than in 2006. This paper puts forward environmental protection measurements and suggestions for Pearl River Estuary, provides data support and theoretical basis for studied sea area pollution prevention and control.

[Spatiotemporal dynamic fuzzy evaluation of wetland environmental pollution risk in Dayang estuary of Liaoning Province, Northeast China based on remote sensing].

PubMed

Sun, Yong-Guang; Zhao, Dong-Zhi; Zhang, Feng-Shou; Wei, Bao-Quan; Chu, Jia-Lan; Su, Xiu

2012-11-01

Based on the aerial image data of Dayang estuary in 2008, and by virtue of Analytic Hierarchy Process (AHP) , remote sensing technology, and GIS spatial analysis, a spatiotemporal evaluation was made on the comprehensive level of wetland environmental pollution risk in Dayang estuary, with the impacts of typical human activities on the dynamic variation of this comprehensive level discussed. From 1958 to 2008, the comprehensive level of the environmental pollution risk in study area presented an increasing trend. Spatially, this comprehensive level declined from land to ocean, and showed a zonal distribution. Tourism development activities unlikely led to the increase of the comprehensive level, while human inhabitation, transportation, and aquaculture would exacerbate the risk of environmental pollution. This study could provide reference for the sea area use planning, ecological function planning, and pollutants control of estuary region.

Examining the Effects of Text Genre and Structure on Fourth-and Fifth-Grade Students' High-Level Comprehension as Evidenced in Small-Group Discussions

ERIC Educational Resources Information Center

Li, Mengyi; Murphy, P. Karen; Firetto, Carla M.

2014-01-01

Although there is a rich literature on the role of text genre and structure on students' literal comprehension, more research is needed regarding the role of these text features on students' high-level comprehension as evidenced in their small-group discussions. As such, the present study examined the effects of text genre (i.e., narrative and…

Is It All in the Telling?: A Study of the Role of Text Schemas and Schematic Text Structures in the Recall and Comprehension of Printed News Stories.

ERIC Educational Resources Information Center

Durham, Meenakshi Gigi

This study hypothesized that altering a news story to conform to a more familiar structure might increase comprehension and recall. Subjects, 104 undergraduate students, completed a Media Use Survey, a questionnaire for collecting demographic information, the WIRE test, a strength of text schema measure, and a comprehension questionnaire. Students…

Novel quality indicators for metastatic colorectal cancer management identify significant variations in these measures across treatment centers in Australia.

PubMed

Turner, Natalie Heather; Wong, Hui-Li; Field, Kathryn; Wong, Rachel; Shapiro, Jeremy; Yip, Desmond; Nott, Louise; Tie, Jeanne; Kosmider, Suzanne; Tran, Ben; Desai, Jayesh; McKendrick, Joseph; Zimet, Allan; Richardson, Gary; Iddawela, Mahesh; Gibbs, Peter

2015-09-01

Defining multidisciplinary quality of care indicators (QCIs) for metastatic colorectal cancer (mCRC) could improve understanding of variations in routine practice care. This may identify areas of below-average performance, which could then be addressed by clinicians to improve the quality of care delivered. This study aimed to define a panel of QCIs in mCRC and, based on these QCIs, to evaluate quality of care across multiple Australian sites. A panel of clinicians with expertise in colorectal cancer defined evidence-based or best practice-based QCIs relevant to the routine multidisciplinary management of mCRC patients through structured consensus discussion. Related data were extracted from the Treatment of Recurrent and Advanced Colorectal Cancer (TRACC) registry, a prospectively maintained database recording comprehensive details on consecutive mCRC patients across multiple Australian hospitals. Variations in QCIs across sites were explored. Of 13 QCIs defined, data related to 10 were reliably extracted from TRACC. Analysis of data on 1276 patients across 10 sites demonstrated low rates of screening for hereditary nonpolyposis colorectal cancer in young patients and significant variation in surveillance-detected recurrences, lung resection rates and palliative chemotherapy use. Exploratory analyses suggested correlation between liver resection rates and survival. We have defined a novel set of mCRC QCIs and have demonstrated wide variation in the quality of care of mCRC across multiple Australian sites. With further validation to confirm a direct correlation between QCI and patient outcomes, these QCIs could be applied to improve the quality of care received by all mCRC patients. © 2015 Wiley Publishing Asia Pty Ltd.

Close Analysis of Texts with Structure (CATS): An Intervention to Teach Reading Comprehension to At-Risk Second Graders

ERIC Educational Resources Information Center

Williams, Joanna P.; Kao, Jenny C.; Pao, Lisa S.; Ordynans, Jill G.; Atkins, J. Grant; Cheng, Rong; DeBonis, Daniel

2016-01-01

We developed and evaluated an intervention that teaches reading comprehension via expository text structure training to second graders in urban public schools at risk for academic failure. Fifty lessons on 5 basic text structures (sequence, comparison, causation, description, and problem-solution) were embedded in a social studies curriculum that…

Do You Want to Know What I Learned? Using Informational Trade Books as Models to Teach Text Structure

ERIC Educational Resources Information Center

Read, Sylvia; Reutzel, D. Ray; Fawson, Parker C.

2008-01-01

Informational text is an important resource for classroom teachers that places unique comprehension demands on young students. Research on teaching expository text structure to young children shows that explicit instruction improves student comprehension. This practical article addresses how to use "well-structured" expository trade book titles to…

A common haplotype of the glucokinase gene alters fasting glucose and birth weight: association in six studies and population-genetics analyses.

PubMed

Weedon, Michael N; Clark, Vanessa J; Qian, Yudong; Ben-Shlomo, Yoav; Timpson, Nicholas; Ebrahim, Shah; Lawlor, Debbie A; Pembrey, Marcus E; Ring, Susan; Wilkin, Terry J; Voss, Linda D; Jeffery, Alison N; Metcalf, Brad; Ferrucci, Luigi; Corsi, Anna Maria; Murray, Anna; Melzer, David; Knight, Bridget; Shields, Bev; Smith, George Davey; Hattersley, Andrew T; Di Rienzo, Anna; Frayling, Tim M

2006-12-01

Fasting glucose is associated with future risk of type 2 diabetes and ischemic heart disease and is tightly regulated despite considerable variation in quantity, type, and timing of food intake. In pregnancy, maternal fasting glucose concentration is an important determinant of offspring birth weight. The key determinant of fasting glucose is the enzyme glucokinase (GCK). Rare mutations of GCK cause fasting hyperglycemia and alter birth weight. The extent to which common variation of GCK explains normal variation of fasting glucose and birth weight is not known. We aimed to comprehensively define the role of variation of GCK in determination of fasting glucose and birth weight, using a tagging SNP (tSNP) approach and studying 19,806 subjects from six population-based studies. Using 22 tSNPs, we showed that the variant rs1799884 is associated with fasting glucose at all ages in the normal population and exceeded genomewide levels of significance (P=10-9). rs3757840 was also highly significantly associated with fasting glucose (P=8x10-7), but haplotype analysis revealed that this is explained by linkage disequilibrium (r2=0.2) with rs1799884. A maternal A allele at rs1799884 was associated with a 32-g (95% confidence interval 11-53 g) increase in offspring birth weight (P=.002). Genetic variation influencing birth weight may have conferred a selective advantage in human populations. We performed extensive population-genetics analyses to look for evidence of recent positive natural selection on patterns of GCK variation. However, we found no strong signature of positive selection. In conclusion, a comprehensive analysis of common variation of the glucokinase gene shows that this is the first gene to be reproducibly associated with fasting glucose and fetal growth.

Discovery and characterization of antibody variants using mass spectrometry-based comparative analysis for biosimilar candidates of monoclonal antibody drugs.

PubMed

Li, Wenhua; Yang, Bin; Zhou, Dongmei; Xu, Jun; Ke, Zhi; Suen, Wen-Chen

2016-07-01

Liquid chromatography mass spectrometry (LC-MS) is the most commonly used technique for the characterization of antibody variants. MAb-X and mAb-Y are two approved IgG1 subtype monoclonal antibody drugs recombinantly produced in Chinese hamster ovary (CHO) cells. We report here that two unexpected and rare antibody variants have been discovered during cell culture process development of biosimilars for these two approved drugs through intact mass analysis. We then used comprehensive mass spectrometry-based comparative analysis including reduced light, heavy chains, and domain-specific mass as well as peptide mapping analysis to fully characterize the observed antibody variants. The "middle-up" mass comparative analysis demonstrated that the antibody variant from mAb-X biosimilar candidate was caused by mass variation of antibody crystalline fragment (Fc), whereas a different variant with mass variation in antibody antigen-binding fragment (Fab) from mAb-Y biosimilar candidate was identified. Endoproteinase Lys-C digested peptide mapping and tandem mass spectrometry analysis further revealed that a leucine to glutamine change in N-terminal 402 site of heavy chain was responsible for the generation of mAb-X antibody variant. Lys-C and trypsin coupled non-reduced and reduced peptide mapping comparative analysis showed that the formation of the light-heavy interchain trisulfide bond resulted in the mAb-Y antibody variant. These two cases confirmed that mass spectrometry-based comparative analysis plays a critical role for the characterization of monoclonal antibody variants, and biosimilar developers should start with a comprehensive structural assessment and comparative analysis to decrease the risk of the process development for biosimilars. Copyright © 2016 Elsevier B.V. All rights reserved.

Brown and polar bear Y chromosomes reveal extensive male-biased gene flow within brother lineages.

PubMed

Bidon, Tobias; Janke, Axel; Fain, Steven R; Eiken, Hans Geir; Hagen, Snorre B; Saarma, Urmas; Hallström, Björn M; Lecomte, Nicolas; Hailer, Frank

2014-06-01

Brown and polar bears have become prominent examples in phylogeography, but previous phylogeographic studies relied largely on maternally inherited mitochondrial DNA (mtDNA) or were geographically restricted. The male-specific Y chromosome, a natural counterpart to mtDNA, has remained underexplored. Although this paternally inherited chromosome is indispensable for comprehensive analyses of phylogeographic patterns, technical difficulties and low variability have hampered its application in most mammals. We developed 13 novel Y-chromosomal sequence and microsatellite markers from the polar bear genome and screened these in a broad geographic sample of 130 brown and polar bears. We also analyzed a 390-kb-long Y-chromosomal scaffold using sequencing data from published male ursine genomes. Y chromosome evidence support the emerging understanding that brown and polar bears started to diverge no later than the Middle Pleistocene. Contrary to mtDNA patterns, we found 1) brown and polar bears to be reciprocally monophyletic sister (or rather brother) lineages, without signals of introgression, 2) male-biased gene flow across continents and on phylogeographic time scales, and 3) male dispersal that links the Alaskan ABC islands population to mainland brown bears. Due to female philopatry, mtDNA provides a highly structured estimate of population differentiation, while male-biased gene flow is a homogenizing force for nuclear genetic variation. Our findings highlight the importance of analyzing both maternally and paternally inherited loci for a comprehensive view of phylogeographic history, and that mtDNA-based phylogeographic studies of many mammals should be reevaluated. Recent advances in sequencing technology render the analysis of Y-chromosomal variation feasible, even in nonmodel organisms. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Is It All Relative? Relative Pitch and L2 Lexical Tone Perception/Tone Language Comprehension by Adult Tone and Non-Tone Language Speakers

ERIC Educational Resources Information Center

von Wertz, Sloane Celeste

2017-01-01

Languages generally use musical pitch variation of the voice as part of their sound systems (Maddieson, 2011)--pitch variations that can be somewhat reminiscent of music. Music ability and/or training may influence language processing (e.g., Bidelman et al., 2011; Delogue et al., 2010). In particular, studies have concluded that there may be a…

Effects of Episodic Variations in Web-Based Avian Influenza Education: Influence of Fear and Humor on Perception, Comprehension, Retention and Behavior

ERIC Educational Resources Information Center

Kim, Paul; Sorcar, Piya; Um, Sujung; Chung, Heedoo; Lee, Young Sung

2009-01-01

In order to provide empirical evidence on the role of a web-based avian influenza (AI) education program for mass communication and also ultimately help young children learn and develop healthy behaviors against AI and all types of influenza, an education program with two episodic variations (i.e. fear and humor) has been developed and examined…

Recommendations for genetic variation data capture in developing countries to ensure a comprehensive worldwide data collection.

PubMed

Patrinos, George P; Al Aama, Jumana; Al Aqeel, Aida; Al-Mulla, Fahd; Borg, Joseph; Devereux, Andrew; Felice, Alex E; Macrae, Finlay; Marafie, Makia J; Petersen, Michael B; Qi, Ming; Ramesar, Rajkumar S; Zlotogora, Joel; Cotton, Richard G H

2011-01-01

Developing countries have significantly contributed to the elucidation of the genetic basis of both common and rare disorders, providing an invaluable resource of cases due to large family sizes, consanguinity, and potential founder effects. Moreover, the recognized depth of genomic variation in indigenous African populations, reflecting the ancient origins of humanity on the African continent, and the effect of selection pressures on the genome, will be valuable in understanding the range of both pathological and nonpathological variations. The involvement of these populations in accurately documenting the extant genetic heterogeneity is more than essential. Developing nations are regarded as key contributors to the Human Variome Project (HVP; http://www.humanvariomeproject.org), a major effort to systematically collect mutations that contribute to or cause human disease and create a cyber infrastructure to tie databases together. However, biomedical research has not been the primary focus in these countries even though such activities are likely to produce economic and health benefits for all. Here, we propose several recommendations and guidelines to facilitate participation of developing countries in genetic variation data documentation, ensuring an accurate and comprehensive worldwide data collection. We also summarize a few well-coordinated genetic data collection initiatives that would serve as paradigms for similar projects.

Reducing variation in decomposition odour profiling using comprehensive two-dimensional gas chromatography.

PubMed

Perrault, Katelynn A; Stefanuto, Pierre-Hugues; Stuart, Barbara H; Rai, Tapan; Focant, Jean-François; Forbes, Shari L

2015-01-01

Challenges in decomposition odour profiling have led to variation in the documented odour profile by different research groups worldwide. Background subtraction and use of controls are important considerations given the variation introduced by decomposition studies conducted in different geographical environments. The collection of volatile organic compounds (VOCs) from soil beneath decomposing remains is challenging due to the high levels of inherent soil VOCs, further confounded by the use of highly sensitive instrumentation. This study presents a method that provides suitable chromatographic resolution for profiling decomposition odour in soil by comprehensive two-dimensional gas chromatography coupled with time-of-flight mass spectrometry using appropriate controls and field blanks. Logarithmic transformation and t-testing of compounds permitted the generation of a compound list of decomposition VOCs in soil. Principal component analysis demonstrated the improved discrimination between experimental and control soil, verifying the value of the data handling method. Data handling procedures have not been well documented in this field and standardisation would thereby reduce misidentification of VOCs present in the surrounding environment as decomposition byproducts. Uniformity of data handling and instrumental procedures will reduce analytical variation, increasing confidence in the future when investigating the effect of taphonomic variables on the decomposition VOC profile. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Proof of Concept Study of Function-Based Statistical Analysis of fNIRS Data: Syntax Comprehension in Children with Specific Language Impairment Compared to Typically-Developing Controls.

PubMed

Fu, Guifang; Wan, Nicholas J A; Baker, Joseph M; Montgomery, James W; Evans, Julia L; Gillam, Ronald B

2016-01-01

Functional near infrared spectroscopy (fNIRS) is a neuroimaging technology that enables investigators to indirectly monitor brain activity in vivo through relative changes in the concentration of oxygenated and deoxygenated hemoglobin. One of the key features of fNIRS is its superior temporal resolution, with dense measurements over very short periods of time (100 ms increments). Unfortunately, most statistical analysis approaches in the existing literature have not fully utilized the high temporal resolution of fNIRS. For example, many analysis procedures are based on linearity assumptions that only extract partial information, thereby neglecting the overall dynamic trends in fNIRS trajectories. The main goal of this article is to assess the ability of a functional data analysis (FDA) approach for detecting significant differences in hemodynamic responses recorded by fNIRS. Children with and without SLI wore two, 3 × 5 fNIRS caps situated over the bilateral parasylvian areas as they completed a language comprehension task. FDA was used to decompose the high dimensional hemodynamic curves into the mean function and a few eigenfunctions to represent the overall trend and variation structures over time. Compared to the most popular GLM, we did not assume any parametric structure and let the data speak for itself. This analysis identified significant differences between the case and control groups in the oxygenated hemodynamic mean trends in the bilateral inferior frontal and left inferior posterior parietal brain regions. We also detected significant group differences in the deoxygenated hemodynamic mean trends in the right inferior posterior parietal cortex and left temporal parietal junction. These findings, using dramatically different approaches, experimental designs, data sets, and foci, were consistent with several other reports, confirming group differences in the importance of these two areas for syntax comprehension. The proposed FDA was consistent with the temporal characteristics of fNIRS, thus providing an alternative methodology for fNIRS analyses.

Anomaly of the geomagnetic Sq variation in Japan: effect from 3-D subterranean structure or the ocean effect?

NASA Astrophysics Data System (ADS)

Kuvshinov, Alexei; Utada, Hisashi

2010-12-01

Many years ago Rikitake et al. described the anomalous behaviour of the vertical component Z of the geomagnetic solar quiet (Sq) daily variation field at observatories in central and northern Japan - namely about 2 hr shift of the local noontime peak towards morning hours. They suggested that this anomaly is associated with the anomalous distribution of electrical conductivity in the mantle beneath central Japan. Although a few works have been done to confirm or argue this explanation, no clear answer has been obtained so far. The goal of this work is to understand the nature of this anomaly using our 3-D forward solution. The conductivity model of the Earth includes oceans of laterally variable conductance and conducting mantle either spherically symmetric or 3-D underneath. Data from six Japanese observatories at four seasons for two different years of the solar cycle are analysed. As an inducing ionospheric (Sq) current system, we use those provided by the Comprehensive Model (CM4) of Sabaka et al. Our analysis clearly demonstrates that 3-D induction in the ocean is responsible for the anomalous behaviour of Z daily variations in this region. We also show that the effects from a suite of 3-D mantle models that include mantle wedge and subducting slab are minor compared with the ocean effect.

A survey of tools for variant analysis of next-generation genome sequencing data

PubMed Central

Pabinger, Stephan; Dander, Andreas; Fischer, Maria; Snajder, Rene; Sperk, Michael; Efremova, Mirjana; Krabichler, Birgit; Speicher, Michael R.; Zschocke, Johannes

2014-01-01

Recent advances in genome sequencing technologies provide unprecedented opportunities to characterize individual genomic landscapes and identify mutations relevant for diagnosis and therapy. Specifically, whole-exome sequencing using next-generation sequencing (NGS) technologies is gaining popularity in the human genetics community due to the moderate costs, manageable data amounts and straightforward interpretation of analysis results. While whole-exome and, in the near future, whole-genome sequencing are becoming commodities, data analysis still poses significant challenges and led to the development of a plethora of tools supporting specific parts of the analysis workflow or providing a complete solution. Here, we surveyed 205 tools for whole-genome/whole-exome sequencing data analysis supporting five distinct analytical steps: quality assessment, alignment, variant identification, variant annotation and visualization. We report an overview of the functionality, features and specific requirements of the individual tools. We then selected 32 programs for variant identification, variant annotation and visualization, which were subjected to hands-on evaluation using four data sets: one set of exome data from two patients with a rare disease for testing identification of germline mutations, two cancer data sets for testing variant callers for somatic mutations, copy number variations and structural variations, and one semi-synthetic data set for testing identification of copy number variations. Our comprehensive survey and evaluation of NGS tools provides a valuable guideline for human geneticists working on Mendelian disorders, complex diseases and cancers. PMID:23341494

Seasonal variation in the content of hydrolyzable tannins, flavonoid glycosides, and proanthocyanidins in oak leaves.

PubMed

Salminen, Juha-Pekka; Roslin, Tomas; Karonen, Maarit; Sinkkonen, Jari; Pihlaja, Kalevi; Pulkkinen, Pertti

2004-09-01

Oaks have been one of the classic model systems in elucidating the role of polyphenols in plant-herbivore interactions. This study provides a comprehensive description of seasonal variation in the phenolic content of the English oak (Quercus robur). Seven different trees were followed over the full course of the growing season, and their foliage repeatedly sampled for gallic acid, 9 individual hydrolyzable tannins, and 14 flavonoid glycosides, as well as for total phenolics, total proanthocyanidins, carbon, and nitrogen. A rare dimeric ellagitannin, cocciferin D2, was detected for the first time in leaves of Q. robur, and relationships between the chemical structures of individual tannins were used to propose a biosynthetic pathway for its formation. Overall, hydrolyzable tannins were the dominant phenolic group in leaves of all ages. Nevertheless, young oak leaves were much richer in hydrolyzable tannins and flavonoid glycosides than old leaves, whereas the opposite pattern was observed for proanthocyanidins. However, when quantified as individual compounds, hydrolyzable tannins and flavonoid glycosides showed highly variable seasonal patterns. This large variation in temporal trends among compounds, and a generally weak correlation between the concentration of any individual compound and the total concentration of phenolics, as quantified by the Folin-Ciocalteau method, leads us to caution against the uncritical use of summary quantifications of composite phenolic fractions in ecological studies.

Genome-wide genetic variation and comparison of fruit-associated traits between kumquat (Citrus japonica) and Clementine mandarin (Citrus clementina).

PubMed

Liu, Tian-Jia; Li, Yong-Ping; Zhou, Jing-Jing; Hu, Chun-Gen; Zhang, Jin-Zhi

2018-03-01

The comprehensive genetic variation of two citrus species were analyzed at genome and transcriptome level. A total of 1090 differentially expressed genes were found during fruit development by RNA-sequencing. Fruit size (fruit equatorial diameter) and weight (fresh weight) are the two most important components determining yield and consumer acceptability for many horticultural crops. However, little is known about the genetic control of these traits. Here, we performed whole-genome resequencing to reveal the comprehensive genetic variation of the fruit development between kumquat (Citrus japonica) and Clementine mandarin (Citrus clementina). In total, 5,865,235 single-nucleotide polymorphisms (SNPs) and 414,447 insertions/deletions (InDels) were identified in the two citrus species. Based on integrative analysis of genome and transcriptome of fruit, 640,801 SNPs and 20,733 InDels were identified. The features, genomic distribution, functional effect, and other characteristics of these genetic variations were explored. RNA-sequencing identified 1090 differentially expressed genes (DEGs) during fruit development of kumquat and Clementine mandarin. Gene Ontology revealed that these genes were involved in various molecular functional and biological processes. In addition, the genetic variation of 939 DEGs and 74 multiple fruit development pathway genes from previous reports were also identified. A global survey identified 24,237 specific alternative splicing events in the two citrus species and showed that intron retention is the most prevalent pattern of alternative splicing. These genome variation data provide a foundation for further exploration of citrus diversity and gene-phenotype relationships and for future research on molecular breeding to improve kumquat, Clementine mandarin and related species.

Assessment of oral storytelling abilities of Latino junior high school students with learning handicaps.

PubMed

Goldstein, B C; Harris, K C; Klein, M D

1993-02-01

This study investigated the relationship between reading comprehension and oral storytelling abilities. Thirty-one Latino junior high school students with learning handicaps were selected as subjects based on learning handicapped designation, home language, and language proficiency status. Reading comprehension was measured by the Reading Comprehension subtest of the Peabody Individual Achievement Test. Storytelling was measured by (a) the Oral Production subtest of the Language Assessment Scales using the standard scoring protocol and (b) a story structure analysis. A comparison of the standard scoring protocol and reading comprehension revealed no relationship, while the comparison of the story structure analysis and reading comprehension revealed a significant correlation. The implications of these results for language assessment of bilingual students are discussed.

The Multidimensional Structure of Verbal Comprehension Test Items.

ERIC Educational Resources Information Center

Peled, Zimra

1984-01-01

The multidimensional structure of verbal comprehension test items was investigated. Empirical evidence was provided to support the theory that item tasks are multivariate-multiordered composites of faceted components: language, contextual knowledge, and cognitive operation. Linear and circular properties of cylindrical manifestation were…

Impact of germline and somatic missense variations on drug binding sites.

PubMed

Yan, C; Pattabiraman, N; Goecks, J; Lam, P; Nayak, A; Pan, Y; Torcivia-Rodriguez, J; Voskanian, A; Wan, Q; Mazumder, R

2017-03-01

Advancements in next-generation sequencing (NGS) technologies are generating a vast amount of data. This exacerbates the current challenge of translating NGS data into actionable clinical interpretations. We have comprehensively combined germline and somatic nonsynonymous single-nucleotide variations (nsSNVs) that affect drug binding sites in order to investigate their prevalence. The integrated data thus generated in conjunction with exome or whole-genome sequencing can be used to identify patients who may not respond to a specific drug because of alterations in drug binding efficacy due to nsSNVs in the target protein's gene. To identify the nsSNVs that may affect drug binding, protein-drug complex structures were retrieved from Protein Data Bank (PDB) followed by identification of amino acids in the protein-drug binding sites using an occluded surface method. Then, the germline and somatic mutations were mapped to these amino acids to identify which of these alter protein-drug binding sites. Using this method we identified 12 993 amino acid-drug binding sites across 253 unique proteins bound to 235 unique drugs. The integration of amino acid-drug binding sites data with both germline and somatic nsSNVs data sets revealed 3133 nsSNVs affecting amino acid-drug binding sites. In addition, a comprehensive drug target discovery was conducted based on protein structure similarity and conservation of amino acid-drug binding sites. Using this method, 81 paralogs were identified that could serve as alternative drug targets. In addition, non-human mammalian proteins bound to drugs were used to identify 142 homologs in humans that can potentially bind to drugs. In the current protein-drug pairs that contain somatic mutations within their binding site, we identified 85 proteins with significant differential gene expression changes associated with specific cancer types. Information on protein-drug binding predicted drug target proteins and prevalence of both somatic and germline nsSNVs that disrupt these binding sites can provide valuable knowledge for personalized medicine treatment. A web portal is available where nsSNVs from individual patient can be checked by scanning against DrugVar to determine whether any of the SNVs affect the binding of any drug in the database.

Reading Comprehension Performance of Adolescents with Learning Disabilities.

ERIC Educational Resources Information Center

Snider, Vicki E.

1989-01-01

The study found that instructing 13 learning-disabled junior high students in the necessary prior knowledge (information and vocabulary concepts) led to superior reading comprehension performance. Textually explicit text structure also improved reading comprehension. (DB)

The Effects of Text Structure Instruction on Expository Reading Comprehension: A Meta-Analysis

ERIC Educational Resources Information Center

Hebert, Michael; Bohaty, Janet J.; Nelson, J. Ron; Brown, Jessica

2016-01-01

In this meta-analysis of 45 studies involving students in Grades 2-12, the authors present evidence on the effects of text structure instruction on the expository reading comprehension of students. The meta-analysis was deigned to answer 2 sets of questions. The first set of questions examined the effectiveness of text structure instruction on…

“Whatdunit?” Sentence Comprehension Abilities of Children With SLI: Sensitivity to Word Order in Canonical and Noncanonical Structures

PubMed Central

Gillam, Ronald B.; Evans, Julia L.; Sergeev, Alexander V.

2017-01-01

Purpose With Aim 1, we compared the comprehension of and sensitivity to canonical and noncanonical word order structures in school-age children with specific language impairment (SLI) and same-age typically developing (TD) children. Aim 2 centered on the developmental improvement of sentence comprehension in the groups. With Aim 3, we compared the comprehension error patterns of the groups. Method Using a “Whatdunit” agent selection task, 117 children with SLI and 117 TD children (ages 7:0–11:11, years:months) propensity matched on age, gender, mother's education, and family income pointed to the picture that best represented the agent in semantically implausible canonical structures (subject–verb–object, subject relative) and noncanonical structures (passive, object relative). Results The SLI group performed worse than the TD group across sentence types. TD children demonstrated developmental improvement across each sentence type, but children with SLI showed improvement only for canonical sentences. Both groups chose the object noun as agent significantly more often than the noun appearing in a prepositional phrase. Conclusions In the absence of semantic–pragmatic cues, comprehension of canonical and noncanonical sentences by children with SLI is limited, with noncanonical sentence comprehension being disproportionately limited. The children's ability to make proper semantic role assignments to the noun arguments in sentences, especially noncanonical, is significantly hindered. PMID:28832884

Sequence Polymorphisms and Structural Variations among Four Grapevine (Vitis vinifera L.) Cultivars Representing Sardinian Agriculture

PubMed Central

Mercenaro, Luca; Nieddu, Giovanni; Porceddu, Andrea; Pezzotti, Mario; Camiolo, Salvatore

2017-01-01

The genetic diversity among grapevine (Vitis vinifera L.) cultivars that underlies differences in agronomic performance and wine quality reflects the accumulation of single nucleotide polymorphisms (SNPs) and small indels as well as larger genomic variations. A combination of high throughput sequencing and mapping against the grapevine reference genome allows the creation of comprehensive sequence variation maps. We used next generation sequencing and bioinformatics to generate an inventory of SNPs and small indels in four widely cultivated Sardinian grape cultivars (Bovale sardo, Cannonau, Carignano and Vermentino). More than 3,200,000 SNPs were identified with high statistical confidence. Some of the SNPs caused the appearance of premature stop codons and thus identified putative pseudogenes. The analysis of SNP distribution along chromosomes led to the identification of large genomic regions with uninterrupted series of homozygous SNPs. We used a digital comparative genomic hybridization approach to identify 6526 genomic regions with significant differences in copy number among the four cultivars compared to the reference sequence, including 81 regions shared between all four cultivars and 4953 specific to single cultivars (representing 1.2 and 75.9% of total copy number variation, respectively). Reads mapping at a distance that was not compatible with the insert size were used to identify a dataset of putative large deletions with cultivar Cannonau revealing the highest number. The analysis of genes mapping to these regions provided a list of candidates that may explain some of the phenotypic differences among the Bovale sardo, Cannonau, Carignano and Vermentino cultivars. PMID:28775732

Direct Laser Writing of Single-Material Sheets with Programmable Self-Rolling Capability

NASA Astrophysics Data System (ADS)

Bauhofer, Anton; KröDel, Sebastian; Bilal, Osama; Daraio, Chiara; Constantinescu, Andrei

Direct laser writing, a sub-class of two-photon polymerization, facilitates 3D-printing of single-material microstructures with inherent residual stresses. Here we show that controlled distribution of these stresses allows for fast and cost-effective fabrication of structures with programmable self-rolling capability. We investigate 2D sheets that evolve into versatile 3D structures. Precise control over the shape morphing potential is acquired through variations in geometry and writing parameters. Effects of capillary action and gravity were shown to be relevant for very thin sheets (thickness <1.5um) and have been analytically and experimentally quantified. In contrast to that, the deformations of sheets with larger thickness (>1.5um) are dominated by residual stresses and adhesion forces. The presented structures create local tensions up to 180MPa, causing rolling curvatures of 25E3m-1. A comprehensive analytical model that captures the relevant influence factors was developed based on laminate plate theory. The predicted curvature and directionality correspond well with the experimentally obtained data. Potential applications are found in drug encapsulation and particle traps for emulsions with differing surface energies. This work was supported by the Swiss National Science Foundation.

Structural, energetic, and electronic trends in low-dimensional late-transition-metal systems

NASA Astrophysics Data System (ADS)

Hu, C. H.; Chizallet, C.; Toulhoat, H.; Raybaud, P.

2009-05-01

Using first-principles calculations, we present a comprehensive investigation of the structural trends of low dimensionality late 4d (from Tc to Ag) and 5d (from Re to Au) transition-metal systems including 13-atom clusters. Energetically favorable clusters not being reported previously are discovered by molecular-dynamics simulation based on the simulated annealing method. They allow a better agreement between experiments and theory for their magnetic properties. The structural periodic trend exhibits a nonmonotonic variation of the ratio of square to triangular facets for the two rows, with a maximum for Rh13 and Ir13 . By a comparative analysis of the relevant energetic and electronic properties performed on other metallic systems with reduced dimensionalities such as four-atom planar clusters, one-dimensional (1D) scales, double scales, 1D cylinders, monatomic films, two and seven layer slabs, we highlight that this periodic trend can be generalized. Hence, it appears that 1D-metallic nanocylinders or 1D-double nanoscales (with similar binding energies as TM13 ) also favor square facets for Rh and Ir. We finally propose an interpretation based on the evolution of the width of the valence band and of the Coulombic repulsions of the bonding basins.

Electronic structure of strongly reduced (1 ‾ 1 1) surface of monoclinic HfO2

NASA Astrophysics Data System (ADS)

Cheng, YingXing; Zhu, Linggang; Ying, Yile; Zhou, Jian; Sun, Zhimei

2018-07-01

Material surface is playing an increasingly important role in electronic devices as their size down to nanoscale. Here, by first-principles calculations we studied the surface oxygen-vacancies (Vos) induced electronic-structure variation of HfO2 , in order to explore its potential applications in surface-controlled electronic devices. Firstly, it is found that single Vo tends to segregate onto the surface and attracts each other as they form pairs, making the formation of vacancies-contained functional surface possible. Then extensive Vo-chains whose formation/rupture can represent the high/low conductivity state are constructed. The electronic states induced by the Vos remain localized in the band-gap region for most of the Vo-chains studied here. A transition to a metallic conductance is found in metastable Vo-chain with formation energy increased by 0.25 eV per Vo. Moreover, we highlight the significance of the Hubbard U correction for density functional theory when studying the electronic-structure based conductance in the oxides. By comprehensive calculations, we find a conductivity-stability dilemma of the Vo-chains, providing guideline for understanding and designing the electronic devices based on HfO2 surface.

Characterizing polymorphic inversions in human genomes by single-cell sequencing

PubMed Central

Sanders, Ashley D.; Hills, Mark; Porubský, David; Guryev, Victor; Falconer, Ester; Lansdorp, Peter M.

2016-01-01

Identifying genomic features that differ between individuals and cells can help uncover the functional variants that drive phenotypes and disease susceptibilities. For this, single-cell studies are paramount, as it becomes increasingly clear that the contribution of rare but functional cellular subpopulations is important for disease prognosis, management, and progression. Until now, studying these associations has been challenged by our inability to map structural rearrangements accurately and comprehensively. To overcome this, we coupled single-cell sequencing of DNA template strands (Strand-seq) with custom analysis software to rapidly discover, map, and genotype genomic rearrangements at high resolution. This allowed us to explore the distribution and frequency of inversions in a heterogeneous cell population, identify several polymorphic domains in complex regions of the genome, and locate rare alleles in the reference assembly. We then mapped the entire genomic complement of inversions within two unrelated individuals to characterize their distinct inversion profiles and built a nonredundant global reference of structural rearrangements in the human genome. The work described here provides a powerful new framework to study structural variation and genomic heterogeneity in single-cell samples, whether from individuals for population studies or tissue types for biomarker discovery. PMID:27472961

False belief and language comprehension in Cantonese-speaking children.

PubMed

Cheung, Him

2006-10-01

The current research compared two accounts of the relation between language and false belief in children, namely that (a) language is generally related to false belief because both require secondary representation in a social-interactional context and that (b) specific language structures that explicitly code metarepresentation contribute uniquely to the language-false belief relation. In three studies, attempts were made to correlate Cantonese-speaking children's false belief with their general language comprehension and understanding of certain structures that explicitly express metarepresentational knowledge. Results showed that these structures failed to predict false belief after age, nonverbal intelligence, and general language comprehension were considered. In contrast, general language remained predictive of false belief after controlling for age, nonverbal intelligence, and language structures. The current findings are more consistent with a general language account than a language structure account.

Direct Instruction of Comprehension: Instructional Examples from Intervention Research on Listening and Reading Comprehension

ERIC Educational Resources Information Center

Coyne, Michael D.; Zipoli, Richard P., Jr.; Chard, David J.; Faggella-Luby, Michael; Ruby, Maureen; Santoro, Lana E.; Baker, Scott

2009-01-01

This article examines the role of direct instruction in promoting listening and reading comprehension. Instructional examples from 2 programs of intervention research focused on improving comprehension; the Story Read Aloud Program and the Embedded Story Structure Routine are used to illustrate principles of direct instruction. An analysis of…

Biodiversity and body size are linked across metazoans

PubMed Central

McClain, Craig R.; Boyer, Alison G.

2009-01-01

Body size variation across the Metazoa is immense, encompassing 17 orders of magnitude in biovolume. Factors driving this extreme diversification in size and the consequences of size variation for biological processes remain poorly resolved. Species diversity is invoked as both a predictor and a result of size variation, and theory predicts a strong correlation between the two. However, evidence has been presented both supporting and contradicting such a relationship. Here, we use a new comprehensive dataset for maximum and minimum body sizes across all metazoan phyla to show that species diversity is strongly correlated with minimum size, maximum size and consequently intra-phylum variation. Similar patterns are also observed within birds and mammals. The observations point to several fundamental linkages between species diversification and body size variation through the evolution of animal life. PMID:19324730

Classification of constraints and degrees of freedom for quadratic discrete actions

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

Höhn, Philipp A., E-mail: phoehn@perimeterinstitute.ca

2014-11-15

We provide a comprehensive classification of constraints and degrees of freedom for variational discrete systems governed by quadratic actions. This classification is based on the different types of null vectors of the Lagrangian two-form and employs the canonical formalism developed in Dittrich and Höhn [“Constraint analysis for variational discrete systems,” J. Math. Phys. 54, 093505 (2013); e-print http://arxiv.org/abs/arXiv:1303.4294 [math-ph

Is WD 1437-008 a cataclysmic variable?

NASA Astrophysics Data System (ADS)

Shimansky, V. V.; Nurtdinova, D. N.; Borisov, N. V.; Spiridonova, O. I.

2011-10-01

Comprehensive observations of a close binary candidate WD 1437-008 are performed. The shape and amplitude of the observed brightness variations are shown to be inconsistent with the hypothesis of reflection effects, and the photometric period of the system, P phot = 0. d 2775, is found to differ from the period of spectral variations, P sp = 0. d 272060. As a result, WD 1437-008 has been preliminarily classified as a low-inclination cataclysmic variable.

The Twenty-four Hour Workday: Proceedings of a Symposium on Variations in Work-Sleep Schedules

DTIC Science & Technology

1980-10-01

medical care, transportation facilities, and security); (2) technological (continuous process operations, e.g., steel production, petrochemical refineries...able, has stL-nulated measurement of variations across time series. In the 2 process , it has identified a wide and important range of behavioral and phy...dimensions. However, this is a complex and interdependent process and a comprehensive understanding of work/rest schedules will be ulti- mately dependent

A study of perceptual and verbal skills of disabled readers in grades 4, 5 and 6.

PubMed

Solan, H A; Ficarra, A P

1990-08-01

This investigation addresses the role of the optometrist in diagnosing and treating children in grades 4, 5, and 6 who have been identified as reading disabled. Fifty-one subjects with average intelligence, but whose reading comprehension skills were below the 31st percentile (mean, 20th percentile), were evaluated using verbal and perceptual tests. When the performance of this experimental group was compared with the mean scores from standardized test norms for each of the various tasks, the disabled readers scored significantly lower in seven of the eight perceptual and five of the six verbal tasks. These results lend support to the hypothesis that both perceptual and verbal deficits are related to reading comprehension. Using step-wise multiple correlation analysis, three perceptual factors; eye-movements, Auditory-Visual Integration Test (AVIT), and grooved peg-board, contributed 38 percent of the variance whereas the addition of two verbal factors (digit span and token test) provided just 2 percent. That is, 38 percent of the variations in reading comprehension could be accounted for by variations in perceptual skills in the disabled readers. The results were interpreted in terms of spatial-simultaneous and verbal-successive processing skills.

The Reader Effect (Instruction/Awareness of Text Structure) and Text Effect (Well-Structured vs. Bad-Structured Texts) on First and Second/Foreign Language Reading Comprehension and Recall--What Does Research Teach Us?

ERIC Educational Resources Information Center

Chang, Carrie

This paper first gives a brief chronological overview of reading theory development and a short introduction to schema theory, and then comprehensively reviews, comments, and synthesizes research-based studies, published between 1980 and 2002, that examined the effect of text structure (reader effect and text effect) on L1 and L2 reading…

Language Comprehension as Structure Building

DTIC Science & Technology

1991-10-17

Final Tech Report 89-0258 LANGUAGE COMPREHENSION AS STRUCTURE BUILDING Morton Ann Gemsbacher Psychology De artment Uiversity of regon Eugene, OR 97403...they represent is no longer as necessary. My students and I have investigated the three subprocesses involved in structure building, namely, laying a...memory nodes; once activated, two cognitive mechanisms control memory nodes’ activation levels: suppression and enhancement. My students and I have also

Genome-wide characterization of pectin methyl esterase genes reveals members differentially expressed in tolerant and susceptible wheats in response to Fusarium graminearum.

PubMed

Zega, Alessandra; D'Ovidio, Renato

2016-11-01

Pectin methyl esterase (PME) genes code for enzymes that are involved in structural modifications of the plant cell wall during plant growth and development. They are also involved in plant-pathogen interaction. PME genes belong to a multigene family and in this study we report the first comprehensive analysis of the PME gene family in bread wheat (Triticum aestivum L.). Like in other species, the members of the TaPME family are dispersed throughout the genome and their encoded products retain the typical structural features of PMEs. qRT-PCR analysis showed variation in the expression pattern of TaPME genes in different tissues and revealed that these genes are mainly expressed in flowering spikes. In our attempt to identify putative TaPME genes involved in wheat defense, we revealed a strong variation in the expression of the TaPME following Fusarium graminearum infection, the causal agent of Fusarium head blight (FHB). Particularly interesting was the finding that the expression profile of some PME genes was markedly different between the FHB-resistant wheat cultivar Sumai3 and the FHB-susceptible cultivar Bobwhite, suggesting a possible involvement of these PME genes in FHB resistance. Moreover, the expression analysis of the TaPME genes during F. graminearum progression within the spike revealed those genes that responded more promptly to pathogen invasion. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Using "Mighty Mouse" to understand masticatory plasticity: myostatin-deficient mice and musculoskeletal function.

PubMed

Ravosa, Matthew J; López, Elisabeth K; Menegaz, Rachel A; Stock, Stuart R; Stack, M Sharon; Hamrick, Mark W

2008-09-01

Knockout mice lacking myostatin (Mstn), a negative regulator of the growth of skeletal muscle, develop significant increases in the relative mass of masticatory muscles as well as the ability to generate higher maximal muscle forces. Wild-type and Mstn-deficient mice were compared to investigate the postnatal influence of elevated masticatory loads due to increased jaw-adductor and bite forces on the biomineralization of mandibular articular and cortical bone, the internal structure of the jaw joints, and the composition of temporomandibular joint (TMJ) articular cartilage. To provide an interspecific perspective on the long-term responses of mammalian jaw joints to altered loading conditions, the findings on mice were compared to similar data for growing rabbits subjected to long-term dietary manipulation. Statistically significant differences in joint proportions and bone mineral density between normal and Mstn-deficient mice, which are similar to those observed between rabbit loading cohorts, underscore the need for a comprehensive analysis of masticatory tissue plasticity vis-à-vis altered mechanical loads, one in which variation in external and internal structure are considered. Differences in the expression of proteoglycans and type-II collagen in TMJ articular cartilage between the mouse and rabbit comparisons suggest that the duration and magnitude of the loading stimulus will significantly affect patterns of adaptive and degradative responses. These data on mammals subjected to long-term loading conditions offer novel insights regarding variation in ontogeny, life history, and the ecomorphology of the feeding apparatus.

Analysis of grain characters in temperate grasses reveals distinctive patterns of endosperm organization associated with grain shape

PubMed Central

Drea, Sinéad

2012-01-01

Members of the core pooids represent the most important crops in temperate zones including wheat, barley, and oats. Their importance as crops is largely due to the grain, particularly the storage capabilities of the endosperm. In this study, a comprehensive survey of grain morphology and endosperm organization in representatives of wild and cultivated species throughout the core pooids was performed. As sister to the core pooid tribes Poeae, Aveneae, Triticeae, and Bromeae within the Pooideae subfamily, Brachypodium provides a taxonomically relevant reference point. Using macroscopic, histological, and molecular analyses distinct patterns of grain tissue organization in these species, focusing on the peripheral and modified aleurone, are described. The results indicate that aleurone organization is correlated with conventional grain quality characters such as grain shape and starch content. In addition to morphological and organizational variation, expression patterns of candidate gene markers underpinning this variation were examined. Features commonly associated with grains are largely defined by analyses on lineages within the Triticeae and knowledge of grain structure may be skewed as a result of the focus on wheat and barley. Specifically, the data suggest that the modified aleurone is largely restricted to species in the Triticeae tribe. PMID:23081982

A national appraisal of haemodialysis vascular access provision in Scotland.

PubMed

Oliver, Scott W; Campbell, Jacqueline; Kingsmore, David B; Kasthuri, Ram; Metcalfe, Wendy; Traynor, Jamie P; Fischbacher-Smith, Denis; Jardine, Alan G; Thomson, Peter C

2017-03-21

Published registry data demonstrate longstanding variation in the utilisation of different vascular access (VA) modalities between Scottish renal units; this may reflect different clinical processes between centres. A comprehensive appraisal was undertaken to understand the processes underpinning VA creation and maintenance across Scotland. A mixed methods approach was utilised. Fifty-two semi-structured interviews were conducted with patients and clinicians in all ten, adult and paediatric, Scottish renal units. Interview transcripts were subjected to thematic analysis. Clinical activity data were prospectively collected for six weeks, and correlated with registry data. VA accounts for a large clinical workload. There was significant inter-centre variation in the utilisation of different VA modalities, and patients described frustrating, dissatisfying experiences. VA creation and maintenance pathways functioned best when nephrologists, surgeons and radiologists were co-located on the same campus with close multi-disciplinary working, protected clinical time, and proactive VA maintenance. No unit routinely measured or discussed procedure outcomes or strategic aspects of their service. Varied clinical outcomes reflected varied clinical processes. Optimised clinical pathways, staff education and measurement of clinical outcomes may improve VA service quality and facilitate safer, more effective, patient-centred care.

The spatial architecture of protein function and adaptation

PubMed Central

McLaughlin, Richard N.; Poelwijk, Frank J.; Raman, Arjun; Gosal, Walraj S.; Ranganathan, Rama

2014-01-01

Statistical analysis of protein evolution suggests a design for natural proteins in which sparse networks of coevolving amino acids (termed sectors) comprise the essence of three-dimensional structure and function1, 2, 3, 4, 5. However, proteins are also subject to pressures deriving from the dynamics of the evolutionary process itself—the ability to tolerate mutation and to be adaptive to changing selection pressures6, 7, 8, 9, 10. To understand the relationship of the sector architecture to these properties, we developed a high-throughput quantitative method for a comprehensive single-mutation study in which every position is substituted individually to every other amino acid. Using a PDZ domain (PSD95pdz3) model system, we show that sector positions are functionally sensitive to mutation, whereas non-sector positions are more tolerant to substitution. In addition, we find that adaptation to a new binding specificity initiates exclusively through variation within sector residues. A combination of just two sector mutations located near and away from the ligand-binding site suffices to switch the binding specificity of PSD95pdz3 quantitatively towards a class-switching ligand. The localization of functional constraint and adaptive variation within the sector has important implications for understanding and engineering proteins. PMID:23041932

Molecular screening of the CYP4V2 gene in Bietti crystalline dystrophy that is associated with choroidal neovascularization

PubMed Central

Mamatha, Gandra; Umashankar, Vetrivel; Kasinathan, Nachiappan; Krishnan, Tandava; Sathyabaarathi, Ravichandran; Karthiyayini, Thirumalai; Amali, John; Rao, Chetan

2011-01-01

Purpose Bietti crystalline dystrophy (BCD) is an autosomal recessive disease characterized by intraretinal deposits of multiple small crystals, with or without associated crystal deposits in the cornea. The disease is caused by mutation in the cytochrome p450, family 4, subfamily v, polypeptide 2 (CYP4V2) gene. Choroidal neovascularization (CNV) is a rare event in BCD. We report two cases of BCD associated with CNV. CYP4V2 and exon 5 of tissue inhibitor of metalloproteinase 3 (TIMP3) were screened in both cases. A patient with BCD, but without CNV, was also screened to identify pathogenic variations. Methods Three BCD families of Asian Indian origin were recruited after a comprehensive ophthalmic examination. Genomic DNA was isolated from blood leukocytes, and coding exons and flanking introns of CYP4V2 and exon 5 of TIMP3 were amplified via polymerase chain reaction (PCR) and were sequenced. Family segregation, control screening, and bioinformatics tools were used to assess the pathogenicity of the novel variations. Results Of the three BCD patients, two had parafoveal CNV. The patient with BCD, but without CNV had novel single base-pair duplication (c.1062_1063dupA). This mutation results in a structurally defective and unstable protein with impaired protein function. Four novel benign variations (three in exons and one in an intron) were observed in the cohort. Screening of exon 5 of TIMP3 did not reveal any variation in these families. Conclusions A novel mutation was found in a patient with BCD but without CNV, while patients with BCD and CNV did not show any pathogenic variation. The modifier role of TIMP3 in the pathogenesis of CNV in BCD was partly ruled out, as no variation was observed in exon 5 of the gene. A larger BCD cohort with CNV needs to be studied and screened to understand the genetics of CNV in BCD. PMID:21850171

The spatiotemporal variation analysis of virtual water for agriculture and livestock husbandry: A study for Jilin Province in China.

PubMed

Ma, Xiaolei; Ma, Yanji

2017-05-15

With the rapid development of economic, water crisis is becoming more and more serious and would be an important obstacle to the sustainable development of society. Virtual water theory and its applications in agriculture can provide important strategies for realizing the reasonable utilization and sustainable development of water resources. Using the Penman-Monteith model and Theil index combining the CROPWAT software, this work takes Jilin Province as study area quantifying the virtual water content of agriculture and livestock husbandry and giving a comprehensive evaluation of their spatiotemporal structure evolution. This study aims to help make clear the water consumption of agriculture and livestock husbandry, and offer advice on rational water utilization and agricultural structure adjustment. The results show that the total virtual water (TVW) proportion of agriculture presents a gradual growth trend while that of livestock husbandry reduces during the study period. In space, central Jilin shows the highest virtual water content of agriculture as well as livestock husbandry, the TVW in central Jilin is about 35.8billionm 3 . The TVW of maize is highest among six studied crops, and the cattle shows the highest TVW in the four kinds of animals. The distribution of TVW calculated by us and the distribution of actual water resources have remarkable difference, which leads to the increase of water consumption and cost of agricultural production. Finally, we discuss the driving force of the spatiotemporal variation of the TVW for agriculture and livestock husbandry, and also give some advises for the planting structural adjustment. This work is helpful for the sustainable development of agricultural and livestock husbandry and realizing efficient utilization of water resources. Copyright © 2017 Elsevier B.V. All rights reserved.

Iterative weighting of multiblock data in the orthogonal partial least squares framework.

PubMed

Boccard, Julien; Rutledge, Douglas N

2014-02-27

The integration of multiple data sources has emerged as a pivotal aspect to assess complex systems comprehensively. This new paradigm requires the ability to separate common and redundant from specific and complementary information during the joint analysis of several data blocks. However, inherent problems encountered when analysing single tables are amplified with the generation of multiblock datasets. Finding the relationships between data layers of increasing complexity constitutes therefore a challenging task. In the present work, an algorithm is proposed for the supervised analysis of multiblock data structures. It associates the advantages of interpretability from the orthogonal partial least squares (OPLS) framework and the ability of common component and specific weights analysis (CCSWA) to weight each data table individually in order to grasp its specificities and handle efficiently the different sources of Y-orthogonal variation. Three applications are proposed for illustration purposes. A first example refers to a quantitative structure-activity relationship study aiming to predict the binding affinity of flavonoids toward the P-glycoprotein based on physicochemical properties. A second application concerns the integration of several groups of sensory attributes for overall quality assessment of a series of red wines. A third case study highlights the ability of the method to combine very large heterogeneous data blocks from Omics experiments in systems biology. Results were compared to the reference multiblock partial least squares (MBPLS) method to assess the performance of the proposed algorithm in terms of predictive ability and model interpretability. In all cases, ComDim-OPLS was demonstrated as a relevant data mining strategy for the simultaneous analysis of multiblock structures by accounting for specific variation sources in each dataset and providing a balance between predictive and descriptive purpose. Copyright © 2014 Elsevier B.V. All rights reserved.

Differences in Cellulosic Supramolecular Structure of Compositionally Similar Rice Straw Affect Biomass Metabolism by Paddy Soil Microbiota

PubMed Central

Ogura, Tatsuki; Date, Yasuhiro; Kikuchi, Jun

2013-01-01

Because they are strong and stable, lignocellulosic supramolecular structures in plant cell walls are resistant to decomposition. However, they can be degraded and recycled by soil microbiota. Little is known about the biomass degradation profiles of complex microbiota based on differences in cellulosic supramolecular structures without compositional variations. Here, we characterized and evaluated the cellulosic supramolecular structures and composition of rice straw biomass processed under different milling conditions. We used a range of techniques including solid- and solution-state nuclear magnetic resonance (NMR) and Fourier transform infrared spectroscopy followed by thermodynamic and microbial degradability characterization using thermogravimetric analysis, solution-state NMR, and denaturing gradient gel electrophoresis. These measured data were further analyzed using an “ECOMICS” web-based toolkit. From the results, we found that physical pretreatment of rice straw alters the lignocellulosic supramolecular structure by cleaving significant molecular lignocellulose bonds. The transformation from crystalline to amorphous cellulose shifted the thermal degradation profiles to lower temperatures. In addition, pretreated rice straw samples developed different microbiota profiles with different metabolic dynamics during the biomass degradation process. This is the first report to comprehensively characterize the structure, composition, and thermal degradation and microbiota profiles using the ECOMICS toolkit. By revealing differences between lignocellulosic supramolecular structures of biomass processed under different milling conditions, our analysis revealed how the characteristic compositions of microbiota profiles develop in addition to their metabolic profiles and dynamics during biomass degradation. PMID:23840554

Tribute to Julian Schwinger

NASA Astrophysics Data System (ADS)

Kohn, Walter

It is a melancholy privilege for me to take part in this symposium in honor of my venerated teacher, Julian Schwinger. All of us here know that his brilliant scientific insights and methodologies have l deep imprints across the entire spectrum of theoretical physics, both pure and applied. No doubt his most outstanding work was his monumental relativistically covariant renormalization theory of quantum electrodynamics; other areas which he substantially reshaped include quantum gauge theories, whose significance he was one of the first to realize; nuclear physics — beginning with his first papers written as a teenager and in which he offered perhaps the first comprehensive lecture course; the theory of waveguides, a powerful reformulation during World War II in terms of tensor Green's functions and variational principles; scattering theory; particle accelerators; and, very broadly, the structure of elementary particle theory…

Computer program for analysis of split-Stirling-cycle cryogenic coolers

NASA Technical Reports Server (NTRS)

Brown, M. T.; Russo, S. C.

1983-01-01

A computer program for predicting the detailed thermodynamic performance of split-Stirling-cycle refrigerators has been developed. The mathematical model includes the refrigerator cold head, free-displacer/regenerator, gas transfer line, and provision for modeling a mechanical or thermal compressor. To allow for dynamic processes (such as aerodynamic friction and heat transfer) temperature, pressure, and mass flow rate are varied by sub-dividing the refrigerator into an appropriate number of fluid and structural control volumes. Of special importance to modeling of cryogenic coolers is the inclusion of real gas properties, and allowance for variation of thermo-physical properties such as thermal conductivities, specific heats and viscosities, with temperature and/or pressure. The resulting model, therefore, comprehensively simulates the split-cycle cooler both spatially and temporally by reflecting the effects of dynamic processes and real material properties.

Relative Expression Levels Rather Than Specific Activity Plays the Major Role in Determining In Vivo AKT Isoform Substrate Specificity

PubMed Central

Lee, Rachel S.; House, Colin M.; Cristiano, Briony E.; Hannan, Ross D.; Pearson, Richard B.; Hannan, Katherine M.

2011-01-01

The AKT protooncogene mediates many cellular processes involved in normal development and disease states such as cancer. The three structurally similar isoforms: AKT1, AKT2, and AKT3 exhibit both functional redundancy and isoform-specific functions; however the basis for their differential signalling remains unclear. Here we show that in vitro, purified AKT3 is ∼47-fold more active than AKT1 at phosphorylating peptide and protein substrates. Despite these marked variations in specific activity between the individual isoforms, a comprehensive analysis of phosphorylation of validated AKT substrates indicated only subtle differences in signalling via individual isoforms in vivo. Therefore, we hypothesise, at least in this model system, that relative tissue/cellular abundance, rather than specific activity, plays the dominant role in determining AKT substrate specificity in situ. PMID:21869924

Brain Imaging of Human Sexual Response: Recent Developments and Future Directions.

PubMed

Ruesink, Gerben B; Georgiadis, Janniko R

2017-01-01

The purpose of this study is to provide a comprehensive summary of the latest developments in the experimental brain study of human sexuality, focusing on brain connectivity during the sexual response. Stable patterns of brain activation have been established for different phases of the sexual response, especially with regard to the wanting phase, and changes in these patterns can be linked to sexual response variations, including sexual dysfunctions. From this solid basis, connectivity studies of the human sexual response have begun to add a deeper understanding of the brain network function and structure involved. The study of "sexual" brain connectivity is still very young. Yet, by approaching the brain as a connected organ, the essence of brain function is captured much more accurately, increasing the likelihood of finding useful biomarkers and targets for intervention in sexual dysfunction.

Structural classification of small, disulfide-rich protein domains.

PubMed

Cheek, Sara; Krishna, S Sri; Grishin, Nick V

2006-05-26

Disulfide-rich domains are small protein domains whose global folds are stabilized primarily by the formation of disulfide bonds and, to a much lesser extent, by secondary structure and hydrophobic interactions. Disulfide-rich domains perform a wide variety of roles functioning as growth factors, toxins, enzyme inhibitors, hormones, pheromones, allergens, etc. These domains are commonly found both as independent (single-domain) proteins and as domains within larger polypeptides. Here, we present a comprehensive structural classification of approximately 3000 small, disulfide-rich protein domains. We find that these domains can be arranged into 41 fold groups on the basis of structural similarity. Our fold groups, which describe broader structural relationships than existing groupings of these domains, bring together representatives with previously unacknowledged similarities; 18 of the 41 fold groups include domains from several SCOP folds. Within the fold groups, the domains are assembled into families of homologs. We define 98 families of disulfide-rich domains, some of which include newly detected homologs, particularly among knottin-like domains. On the basis of this classification, we have examined cases of convergent and divergent evolution of functions performed by disulfide-rich proteins. Disulfide bonding patterns in these domains are also evaluated. Reducible disulfide bonding patterns are much less frequent, while symmetric disulfide bonding patterns are more common than expected from random considerations. Examples of variations in disulfide bonding patterns found within families and fold groups are discussed.

Dissecting maize diversity in lowland South America: genetic structure and geographic distribution models.

PubMed

Bracco, Mariana; Cascales, Jimena; Hernández, Julián Cámara; Poggio, Lidia; Gottlieb, Alexandra M; Lia, Verónica V

2016-08-26

Maize landraces from South America have traditionally been assigned to two main categories: Andean and Tropical Lowland germplasm. However, the genetic structure and affiliations of the lowland gene pools have been difficult to assess due to limited sampling and the lack of comparative analysis. Here, we examined SSR and Adh2 sequence variation in a diverse sample of maize landraces from lowland middle South America, and performed a comprehensive integrative analysis of population structure and diversity including already published data of archaeological and extant specimens from the Americas. Geographic distribution models were used to explore the relationship between environmental factors and the observed genetic structure. Bayesian and multivariate analyses of population structure showed the existence of two previously overlooked lowland gene pools associated with Guaraní indigenous communities of middle South America. The singularity of this germplasm was also evidenced by the frequency distribution of microsatellite repeat motifs of the Adh2 locus and the distinct spatial pattern inferred from geographic distribution models. Our results challenge the prevailing view that lowland middle South America is just a contact zone between Andean and Tropical Lowland germplasm and highlight the occurrence of a unique, locally adapted gene pool. This information is relevant for the conservation and utilization of maize genetic resources, as well as for a better understanding of environment-genotype associations.

Memory Interference as a Determinant of Language Comprehension

PubMed Central

Van Dyke, Julie A.; Johns, Clinton L.

2012-01-01

The parameters of the human memory system constrain the operation of language comprehension processes. In the memory literature, both decay and interference have been proposed as causes of forgetting; however, while there is a long history of research establishing the nature of interference effects in memory, the effects of decay are much more poorly supported. Nevertheless, research investigating the limitations of the human sentence processing mechanism typically focus on decay-based explanations, emphasizing the role of capacity, while the role of interference has received comparatively little attention. This paper reviews both accounts of difficulty in language comprehension by drawing direct connections to research in the memory domain. Capacity-based accounts are found to be untenable, diverging substantially from what is known about the operation of the human memory system. In contrast, recent research investigating comprehension difficulty using a retrieval-interference paradigm is shown to be wholly consistent with both behavioral and neuropsychological memory phenomena. The implications of adopting a retrieval-interference approach to investigating individual variation in language comprehension are discussed. PMID:22773927

Cognitive Attributes of Adequate and Inadequate Responders to Reading Intervention in Middle School

PubMed Central

Miciak, Jeremy; Stuebing, Karla K.; Vaughn, Sharon; Roberts, Greg; Barth, Amy Elizabeth; Fletcher, Jack M.

2016-01-01

No studies have investigated the cognitive attributes of middle school students who are adequate and inadequate responders to Tier 2 reading intervention. We compared students in Grades 6 and 7 representing groups of adequate responders (n = 77) and inadequate responders who fell below criteria in (a) comprehension (n = 54); (b) fluency (n = 45); and (c) decoding, fluency, and comprehension (DFC; n = 45). These students received measures of phonological awareness, listening comprehension, rapid naming, processing speed, verbal knowledge, and nonverbal reasoning. Multivariate comparisons showed a significant Group-by-Task interaction: the comprehension-impaired group demonstrated primary difficulties with verbal knowledge and listening comprehension, the DFC group with phonological awareness, and the fluency-impaired group with phonological awareness and rapid naming. A series of regression models investigating whether responder status explained unique variation in cognitive skills yielded largely null results consistent with a continuum of severity associated with level of reading impairment, with no evidence for qualitative differences in the cognitive attributes of adequate and inadequate responders. PMID:28579668

Cross-Study Differences in the Etiology of Reading Comprehension: a Meta-Analytical Review of Twin Studies.

PubMed

Little, Callie W; Haughbrook, Rasheda; Hart, Sara A

2017-01-01

Numerous twin studies have examined the genetic and environmental etiology of reading comprehension, though it is likely that etiological estimates are influenced by unidentified sample conditions (e.g. Tucker-Drob and Bates, Psychol Sci:0956797615612727, 2015). The purpose of this meta-analysis was to average the etiological influences of reading comprehension and to explore the potential moderators influencing these estimates. Results revealed an average heritability estimate of h 2  = 0.59, with significant variation in estimates across studies, suggesting potential moderation. Moderation results indicated publication year, grade level, project, zygosity methods, and response type moderated heritability estimates. The average shared environmental estimate was c 2  = 0.16, with publication year, grade and zygosity methods acting as significant moderators. These findings support the role of genetics on reading comprehension, and a small significant role of shared environmental influences. The results suggest that our interpretation of how genes and environments influence reading comprehension should reflect aspects of study and sample.

Cognitive Attributes of Adequate and Inadequate Responders to Reading Intervention in Middle School.

PubMed

Miciak, Jeremy; Stuebing, Karla K; Vaughn, Sharon; Roberts, Greg; Barth, Amy Elizabeth; Fletcher, Jack M

2014-12-01

No studies have investigated the cognitive attributes of middle school students who are adequate and inadequate responders to Tier 2 reading intervention. We compared students in Grades 6 and 7 representing groups of adequate responders ( n = 77) and inadequate responders who fell below criteria in (a) comprehension ( n = 54); (b) fluency ( n = 45); and (c) decoding, fluency, and comprehension (DFC; n = 45). These students received measures of phonological awareness, listening comprehension, rapid naming, processing speed, verbal knowledge, and nonverbal reasoning. Multivariate comparisons showed a significant Group-by-Task interaction: the comprehension-impaired group demonstrated primary difficulties with verbal knowledge and listening comprehension, the DFC group with phonological awareness, and the fluency-impaired group with phonological awareness and rapid naming. A series of regression models investigating whether responder status explained unique variation in cognitive skills yielded largely null results consistent with a continuum of severity associated with level of reading impairment, with no evidence for qualitative differences in the cognitive attributes of adequate and inadequate responders.

Why reread? Evidence from garden-path and local coherence structures.

PubMed

Christianson, Kiel; Luke, Steven G; Hussey, Erika K; Wochna, Kacey L

2017-07-01

Two eye-tracking experiments were conducted to compare the online reading and offline comprehension of main verb/reduced relative garden-path sentences and local coherence sentences. Rereading of early material in garden-path reduced relatives should be revisionary, aimed at reanalysing an earlier misparse; however, rereading of early material in a local coherence reduced relative need only be confirmatory, as the original parse of the earlier portion of these sentences is ultimately correct. Results of online and offline measures showed that local coherence structures elicited signals of reading disruption that arose earlier and lasted longer, and local coherence comprehension was also better than garden path comprehension. Few rereading measures in either sentence type were predicted by structural features of these sentences, nor was rereading related to comprehension accuracy, which was extremely low overall. Results are discussed with respect to selective reanalysis and good-enough processing.

Death Penalty Decisions: Instruction Comprehension, Attitudes, and Decision Mediators.

PubMed

Patry, Marc W; Penrod, Steven D

2013-01-01

A primary goal of this research was to empirically evaluate a set of assumptions, advanced in the Supreme Court's ruling in Buchanan v. Angelone (1998), about jury comprehension of death penalty instructions. Further, this research examined the use of evidence in capital punishment decision making by exploring underlying mediating factors upon which death penalty decisions may be based. Manipulated variables included the type of instructions and several variations of evidence. Study 1 was a paper and pencil study of 245 undergraduate mock jurors. The experimental design was an incomplete 4×2×2×2×2 factorial model resulting in 56 possible conditions. Manipulations included four different types of instructions, presence of a list of case-specific mitigators to accompany the instructions, and three variations in the case facts: age of the defendant, bad prior record, and defendant history of emotional abuse. Study 2 was a fully-crossed 2×2×2×2×2 experiment with four deliberating mock juries per cell. Manipulations included jury instructions (original or revised), presence of a list of case-specific mitigators, defendant history of emotional abuse, bad prior record, and heinousness of the crime. The sample of 735 jury-eligible participants included 130 individuals who identified themselves as students. Participants watched one of 32 stimulus videotapes based on a replication of a capital sentencing hearing. The present findings support previous research showing low comprehension of capital penalty instructions. Further, we found that higher instruction comprehension was associated with higher likelihood of issuing life sentence decisions. The importance of instruction comprehension is emphasized in a social cognitive model of jury decision making at the sentencing phase of capital cases.

Death Penalty Decisions: Instruction Comprehension, Attitudes, and Decision Mediators

PubMed Central

Patry, Marc W.; Penrod, Steven D.

2013-01-01

A primary goal of this research was to empirically evaluate a set of assumptions, advanced in the Supreme Court’s ruling in Buchanan v. Angelone (1998), about jury comprehension of death penalty instructions. Further, this research examined the use of evidence in capital punishment decision making by exploring underlying mediating factors upon which death penalty decisions may be based. Manipulated variables included the type of instructions and several variations of evidence. Study 1 was a paper and pencil study of 245 undergraduate mock jurors. The experimental design was an incomplete 4×2×2×2×2 factorial model resulting in 56 possible conditions. Manipulations included four different types of instructions, presence of a list of case-specific mitigators to accompany the instructions, and three variations in the case facts: age of the defendant, bad prior record, and defendant history of emotional abuse. Study 2 was a fully-crossed 2×2×2×2×2 experiment with four deliberating mock juries per cell. Manipulations included jury instructions (original or revised), presence of a list of case-specific mitigators, defendant history of emotional abuse, bad prior record, and heinousness of the crime. The sample of 735 jury-eligible participants included 130 individuals who identified themselves as students. Participants watched one of 32 stimulus videotapes based on a replication of a capital sentencing hearing. The present findings support previous research showing low comprehension of capital penalty instructions. Further, we found that higher instruction comprehension was associated with higher likelihood of issuing life sentence decisions. The importance of instruction comprehension is emphasized in a social cognitive model of jury decision making at the sentencing phase of capital cases. PMID:24072981

Practice variation in surgical procedures and IUD-insertions among general practitioners in Norway - a longitudinal study.

PubMed

Pahle, Andreas Saxlund; Sørli, Daniel; Kristiansen, Ivar Sønbø; Deraas, Trygve S; Halvorsen, Peder A

2017-01-21

Studies of Primary Health Care (PHC) reveal considerable practice variations in terms of the range of services provided. In Norway, general practitioners (GPs) are traditionally expected to perform IUD-insertions and several surgical procedures as a part of comprehensive PHC. We aimed to investigate variation in the provision of surgical procedures and IUD-insertions across GPs and over time and explore determinants of such variation. Retrospective registry study of Norwegian GPs. From a comprehensive database of GPs' reimbursement claims, we obtained procedure codes and GP characteristics such as age, gender, list size and municipality characteristics from 2006 through 2013. Multivariable logistic regression models were fitted to explore determinants of practice variation. We extracted data from 4,828 GPs. In 2013, 91.0, 76.1 and 74.8% were reimbursed at least once for minor and major surgical procedures and IUD-insertion, respectively. Female GPs had lower odds for performing major surgical procedures (OR 0.38, 95% CI 0.32-0.45) and higher odds for performing IUD-insertions (OR 6.28, 95% CI 4.47-8.82) than male GPs. Older GPs and GPs with shorter patient lists were less likely to perform surgical procedures. GPs with longer patient lists had higher odds for performing IUD-insertions. The proportion of GPs performing surgical procedures increased over time, while the proportion decreased for IUD-insertions. The number of IUD-insertions in specialist care increased from 12,575 in 2011 to 15 216 (+21.0%) in 2014. We observed a large variation in the provision of surgical procedures and IUD-insertions amongst GPs in Norway. The GPs' age, gender, list size and size of municipality were associated with performing the procedures. Our findings suggest a shift of IUD-insertions from primary to specialist care.

Developing "Personality" Taxonomies: Metatheoretical and Methodological Rationales Underlying Selection Approaches, Methods of Data Generation and Reduction Principles.

PubMed

Uher, Jana

2015-12-01

Taxonomic "personality" models are widely used in research and applied fields. This article applies the Transdisciplinary Philosophy-of-Science Paradigm for Research on Individuals (TPS-Paradigm) to scrutinise the three methodological steps that are required for developing comprehensive "personality" taxonomies: 1) the approaches used to select the phenomena and events to be studied, 2) the methods used to generate data about the selected phenomena and events and 3) the reduction principles used to extract the "most important" individual-specific variations for constructing "personality" taxonomies. Analyses of some currently popular taxonomies reveal frequent mismatches between the researchers' explicit and implicit metatheories about "personality" and the abilities of previous methodologies to capture the particular kinds of phenomena toward which they are targeted. Serious deficiencies that preclude scientific quantifications are identified in standardised questionnaires, psychology's established standard method of investigation. These mismatches and deficiencies derive from the lack of an explicit formulation and critical reflection on the philosophical and metatheoretical assumptions being made by scientists and from the established practice of radically matching the methodological tools to researchers' preconceived ideas and to pre-existing statistical theories rather than to the particular phenomena and individuals under study. These findings raise serious doubts about the ability of previous taxonomies to appropriately and comprehensively reflect the phenomena towards which they are targeted and the structures of individual-specificity occurring in them. The article elaborates and illustrates with empirical examples methodological principles that allow researchers to appropriately meet the metatheoretical requirements and that are suitable for comprehensively exploring individuals' "personality".

Recommendations for Genetic Variation Data Capture in Developing Countries to Ensure a Comprehensive Worldwide Data Collection

PubMed Central

Patrinos, George P; Al Aama, Jumana; Al Aqeel, Aida; Al-Mulla, Fahd; Borg, Joseph; Devereux, Andrew; Felice, Alex E; Macrae, Finlay; Marafie, Makia J; Petersen, Michael B; Qi, Ming; Ramesar, Rajkumar S; Zlotogora, Joel; Cotton, Richard GH

2011-01-01

Developing countries have significantly contributed to the elucidation of the genetic basis of both common and rare disorders, providing an invaluable resource of cases due to large family sizes, consanguinity, and potential founder effects. Moreover, the recognized depth of genomic variation in indigenous African populations, reflecting the ancient origins of humanity on the African continent, and the effect of selection pressures on the genome, will be valuable in understanding the range of both pathological and nonpathological variations. The involvement of these populations in accurately documenting the extant genetic heterogeneity is more than essential. Developing nations are regarded as key contributors to the Human Variome Project (HVP; http://www.humanvariomeproject.org), a major effort to systematically collect mutations that contribute to or cause human disease and create a cyber infrastructure to tie databases together. However, biomedical research has not been the primary focus in these countries even though such activities are likely to produce economic and health benefits for all. Here, we propose several recommendations and guidelines to facilitate participation of developing countries in genetic variation data documentation, ensuring an accurate and comprehensive worldwide data collection. We also summarize a few well-coordinated genetic data collection initiatives that would serve as paradigms for similar projects. Hum Mutat 31:1–8, 2010. © 2010 Wiley-Liss, Inc. PMID:21089065

Comprehensive Evaluation of the Association of APOE Genetic Variation with Plasma Lipoprotein Traits in U.S. Whites and African Blacks

PubMed Central

Radwan, Zaheda H.; Wang, Xingbin; Waqar, Fahad; Pirim, Dilek; Niemsiri, Vipavee; Hokanson, John E.; Hamman, Richard F.; Bunker, Clareann H.; Barmada, M. Michael; Demirci, F. Yesim; Kamboh, M. Ilyas

2014-01-01

Although common APOE genetic variation has a major influence on plasma LDL-cholesterol, its role in affecting HDL-cholesterol and triglycerides is not well established. Recent genome-wide association studies suggest that APOE also affects plasma variation in HDL-cholesterol and triglycerides. It is thus important to resequence the APOE gene to identify both common and uncommon variants that affect plasma lipid profile. Here, we have sequenced the APOE gene in 190 subjects with extreme HDL-cholesterol levels selected from two well-defined epidemiological samples of U.S. non-Hispanic Whites (NHWs) and African Blacks followed by genotyping of identified variants in the entire datasets (623 NHWs, 788 African Blacks) and association analyses with major lipid traits. We identified a total of 40 sequence variants, of which 10 are novel. A total of 32 variants, including common tagSNPs (≥5% frequency) and all uncommon variants (<5% frequency) were successfully genotyped and considered for genotype-phenotype associations. Other than the established associations of APOE*2 and APOE*4 with LDL-cholesterol, we have identified additional independent associations with LDL-cholesterol. We have also identified multiple associations of uncommon and common APOE variants with HDL-cholesterol and triglycerides. Our comprehensive sequencing and genotype-phenotype analyses indicate that APOE genetic variation impacts HDL-cholesterol and triglycerides in addition to affecting LDL-cholesterol. PMID:25502880

Improving Listening Comprehension through a Whole-Schema Approach.

ERIC Educational Resources Information Center

Ellermeyer, Deborah

1993-01-01

Examines the development of the schema, or cognitive structure, theory of reading comprehension. Advances a model for improving listening comprehension within the classroom through a teacher-facilitated approach which leads students to selecting and utilizing existing schema within a whole-language environment. (MDM)

The Comprehension of Idiomatic Expressions in Schizophrenic Patients

ERIC Educational Resources Information Center

Schettino, Antonio; Lauro, Leonor Romero; Crippa, Franca; Anselmetti, Simona; Cavallaro, Roberto; Papagno, Costanza

2010-01-01

Recent fMRI and TMS studies on idiom comprehension have shown that the prefrontal cortex is involved in idiom processing. Since schizophrenic patients exhibit prefrontal "structural" changes and dysexecutive "behavioural" deficits, we hypothesised an impairment in idiom comprehension, correlating with performance on executive…

Test Plan for SSR Antenna Rotation Rate Stabilization

DOT National Transportation Integrated Search

1981-10-01

A comprehensive test plan is presented to evaluate the impact of wind and ice loading on the rotation rate stability of a Secondary Surveillance Radar (SSR) antenna used for air traffic control surveillance. Antenna rotation rate variations may intro...

Fluxes of MeV particles at Earth's orbit and their relationship with the global structure of the solar corona: Observations from SOHO

NASA Technical Reports Server (NTRS)

Posner, A.; Bothmer, V.; Kunow, H.; Heber, B.; Mueller-Mellin, R.; Delaboudiniere, J.-P.; Thompson, B. J.; Brueckner, G. E.; Howard, R. A.; Michels, D. J.

1997-01-01

The SOHO satellite, launched on 2 December 1995, combines a unique set of instruments which allow comparative studies of the interior of the sun, the outer corona and solar to be carried out. In its halo orbit around the L1 Lagrangian point of the sun-earth system, SOHO's comprehensive suprathermal and energetic particle analyzer (COSTEP) measures in situ energetic particles in the energy range of 44 keV/particle to greater than 53 MeV/n. The MeV proton, electron and helium nuclei measurements from the COSTEP electron proton helium instrument (EPHIN) were used to investigate the relationships of intensity increases of these particle species with the large-scale structures of the solar corona and heliosphere, including temporal variations. Coronal observatons are provided by the large angle spectroscopic coronagraph (LASCO) and the extreme ultraviolet imaging telescope (EIT). It was found that during times of minimum solar activity, intensity increases of the particles have two well defined sources: corotating interaction regions (CIRs) in the heliosphere related to coronal holes at the sun and coronal mass ejections.

Atomic-scale observation of structural and electronic orders in the layered compound α-RuCl3

PubMed Central

Ziatdinov, M.; Banerjee, A.; Maksov, A.; Berlijn, T.; Zhou, W.; Cao, H. B.; Yan, J.-Q.; Bridges, C. A.; Mandrus, D. G.; Nagler, S. E.; Baddorf, A. P.; Kalinin, S. V.

2016-01-01

A pseudospin-1/2 Mott phase on a honeycomb lattice is proposed to host the celebrated two-dimensional Kitaev model which has an elusive quantum spin liquid ground state, and fascinating physics relevant to the development of future templates towards topological quantum bits. Here we report a comprehensive, atomically resolved real-space study by scanning transmission electron and scanning tunnelling microscopies on a novel layered material displaying Kitaev physics, α-RuCl3. Our local crystallography analysis reveals considerable variations in the geometry of the ligand sublattice in thin films of α-RuCl3 that opens a way to realization of a spatially inhomogeneous magnetic ground state at the nanometre length scale. Using scanning tunnelling techniques, we observe the electronic energy gap of ≈0.25 eV and intra-unit cell symmetry breaking of charge distribution in individual α-RuCl3 surface layer. The corresponding charge-ordered pattern has a fine structure associated with two different types of charge disproportionation at Cl-terminated surface. PMID:27941761

Atomic-scale observation of structural and electronic orders in the layered compound α-RuCl3.

PubMed

Ziatdinov, M; Banerjee, A; Maksov, A; Berlijn, T; Zhou, W; Cao, H B; Yan, J-Q; Bridges, C A; Mandrus, D G; Nagler, S E; Baddorf, A P; Kalinin, S V

2016-12-12

A pseudospin-1/2 Mott phase on a honeycomb lattice is proposed to host the celebrated two-dimensional Kitaev model which has an elusive quantum spin liquid ground state, and fascinating physics relevant to the development of future templates towards topological quantum bits. Here we report a comprehensive, atomically resolved real-space study by scanning transmission electron and scanning tunnelling microscopies on a novel layered material displaying Kitaev physics, α-RuCl 3 . Our local crystallography analysis reveals considerable variations in the geometry of the ligand sublattice in thin films of α-RuCl 3 that opens a way to realization of a spatially inhomogeneous magnetic ground state at the nanometre length scale. Using scanning tunnelling techniques, we observe the electronic energy gap of ≈0.25 eV and intra-unit cell symmetry breaking of charge distribution in individual α-RuCl 3 surface layer. The corresponding charge-ordered pattern has a fine structure associated with two different types of charge disproportionation at Cl-terminated surface.

Observing Consistency in Online Communication Patterns for User Re-Identification.

PubMed

Adeyemi, Ikuesan Richard; Razak, Shukor Abd; Salleh, Mazleena; Venter, Hein S

2016-01-01

Comprehension of the statistical and structural mechanisms governing human dynamics in online interaction plays a pivotal role in online user identification, online profile development, and recommender systems. However, building a characteristic model of human dynamics on the Internet involves a complete analysis of the variations in human activity patterns, which is a complex process. This complexity is inherent in human dynamics and has not been extensively studied to reveal the structural composition of human behavior. A typical method of anatomizing such a complex system is viewing all independent interconnectivity that constitutes the complexity. An examination of the various dimensions of human communication pattern in online interactions is presented in this paper. The study employed reliable server-side web data from 31 known users to explore characteristics of human-driven communications. Various machine-learning techniques were explored. The results revealed that each individual exhibited a relatively consistent, unique behavioral signature and that the logistic regression model and model tree can be used to accurately distinguish online users. These results are applicable to one-to-one online user identification processes, insider misuse investigation processes, and online profiling in various areas.

Epigenetics and Epigenomics of Plants.

PubMed

Yadav, Chandra Bhan; Pandey, Garima; Muthamilarasan, Mehanathan; Prasad, Manoj

2018-01-23

The genetic material DNA in association with histone proteins forms the complex structure called chromatin, which is prone to undergo modification through certain epigenetic mechanisms including cytosine DNA methylation, histone modifications, and small RNA-mediated methylation. Alterations in chromatin structure lead to inaccessibility of genomic DNA to various regulatory proteins such as transcription factors, which eventually modulates gene expression. Advancements in high-throughput sequencing technologies have provided the opportunity to study the epigenetic mechanisms at genome-wide levels. Epigenomic studies using high-throughput technologies will widen the understanding of mechanisms as well as functions of regulatory pathways in plant genomes, which will further help in manipulating these pathways using genetic and biochemical approaches. This technology could be a potential research tool for displaying the systematic associations of genetic and epigenetic variations, especially in terms of cytosine methylation onto the genomic region in a specific cell or tissue. A comprehensive study of plant populations to correlate genotype to epigenotype and to phenotype, and also the study of methyl quantitative trait loci (QTL) or epiGWAS, is possible by using high-throughput sequencing methods, which will further accelerate molecular breeding programs for crop improvement. Graphical Abstract.

Atomic-scale observation of structural and electronic orders in the layered compound α-RuCl 3

DOE PAGES

Ziatdinov, Maxim A.; Banerjee, Arnab; Maksov, Artem B.; ...

2016-12-12

A pseudospin-1/2 Mott phase on a honeycomb lattice is proposed to host the celebrated two-dimensional Kitaev model which has an elusive quantum spin liquid ground state, and fascinating physics relevant to the development of future templates towards topological quantum bits. Here we report a comprehensive, atomically resolved real-space study by scanning transmission electron and scanning tunnelling microscopies on a novel layered material displaying Kitaev physics, -RuCl3. Our local crystallography analysis reveals considerable variations in the geometry of the ligand sublattice in thin films of -RuCl3 that opens a way to realization of a spatially inhomogeneous magnetic ground state at themore » nanometre length scale. Using scanning tunnelling techniques, we observe the electronic energy gap of 0.25 eV and intra-unit cell symmetry breaking of charge distribution in individual -RuCl3 surface layer. The corresponding charge-ordered pattern has a fine structure associated with two different types of charge disproportionation at Cl-terminated surface.« less

Spreading of Emulsions on Glass Substrates

NASA Astrophysics Data System (ADS)

Mohammad Karim, Alireza; Kavehpour, Pirouz

2012-11-01

The wettability of emulsions is an important factor with explicit influence in an extensive variety of industrial applications ranging from the petroleum to food industries. Surprisingly, there is no comprehensive study of emulsion spreading to date; this is due to the complexity of the structure of the emulsions and non-homogeneity of the dispersed phase bubbles in size as well as distribution through the emulsion. The spreading of water/silicone oil emulsions on glass substrates was investigated. The emulsions were prepared with varying volume fractions of water dispersed in silicone oil, with addition of small amounts of surfactant to stabilize the emulsion structure. The time dependent variation of dynamic contact angle, base diameter, and the spreading rate of the droplets of an emulsion are different from a pure substance. The effect of water/silicone oil weight percentage as well as the droplet size and dispersed phase bubble size were also investigated. The weight percentage of water/silicone oil emulsion and droplet size did not have significant influence on the spreading dynamics; however the dispersed phase drop size affected the spreading dynamics substantially.

Statistical Analysis of Bus Networks in India

PubMed Central

2016-01-01

In this paper, we model the bus networks of six major Indian cities as graphs in L-space, and evaluate their various statistical properties. While airline and railway networks have been extensively studied, a comprehensive study on the structure and growth of bus networks is lacking. In India, where bus transport plays an important role in day-to-day commutation, it is of significant interest to analyze its topological structure and answer basic questions on its evolution, growth, robustness and resiliency. Although the common feature of small-world property is observed, our analysis reveals a wide spectrum of network topologies arising due to significant variation in the degree-distribution patterns in the networks. We also observe that these networks although, robust and resilient to random attacks are particularly degree-sensitive. Unlike real-world networks, such as Internet, WWW and airline, that are virtual, bus networks are physically constrained. Our findings therefore, throw light on the evolution of such geographically and constrained networks that will help us in designing more efficient bus networks in the future. PMID:27992590

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

PubMed Central

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

2013-01-01

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

Total generalized variation-regularized variational model for single image dehazing

NASA Astrophysics Data System (ADS)

Shu, Qiao-Ling; Wu, Chuan-Sheng; Zhong, Qiu-Xiang; Liu, Ryan Wen

2018-04-01

Imaging quality is often significantly degraded under hazy weather condition. The purpose of this paper is to recover the latent sharp image from its hazy version. It is well known that the accurate estimation of depth information could assist in improving dehazing performance. In this paper, a detail-preserving variational model was proposed to simultaneously estimate haze-free image and depth map. In particular, the total variation (TV) and total generalized variation (TGV) regularizers were introduced to restrain haze-free image and depth map, respectively. The resulting nonsmooth optimization problem was efficiently solved using the alternating direction method of multipliers (ADMM). Comprehensive experiments have been conducted on realistic datasets to compare our proposed method with several state-of-the-art dehazing methods. Results have illustrated the superior performance of the proposed method in terms of visual quality evaluation.

Navigation and Comprehension of Digital Expository Texts: Hypertext Structure, Previous Domain Knowledge, and Working Memory Capacity

ERIC Educational Resources Information Center

Burin, Debora I.; Barreyro, Juan P.; Saux, Gastón; Irrazábal, Natalia C.

2015-01-01

Introduction: In contemporary information societies, reading digital text has become pervasive. One of the most distinctive features of digital texts is their internal connections via hyperlinks, resulting in non-linear hypertexts. Hypertext structure and previous knowledge affect navigation and comprehension of digital expository texts. From the…

Structure, Meaning, and Constituency in Visual Narrative Comprehension

ERIC Educational Resources Information Center

Cohn, Neil Thomas

2012-01-01

Narrative has been formally studied for at least two millennia, dating back to the writings of Aristotle. While most theories began by describing the construction of plotlines in theatre, most contemporary research on the structure and comprehension of narratives has examined the discourse of spoken language. However, visual narratives in the form…

The Relationship of Morphological Analysis and Morphological Decoding to Reading Comprehension

ERIC Educational Resources Information Center

Deacon, S. Hélène; Tong, Xiuli; Francis, Kathryn

2017-01-01

The ultimate goal of children's reading development is the full and fluid understanding of texts. Morphological structure awareness, or children's awareness of the minimal units of meaning in language, has been identified as a key skill influencing reading comprehension. Here, we evaluate the roles of morphological structure awareness and two…

Effects of Expository Text Structure Interventions on Comprehension: A Meta-Analysis

ERIC Educational Resources Information Center

Pyle, Nicole; Vasquez, Ariana C.; Lignugaris/Kraft, Benjamin; Gillam, Sandra L.; Reutzel, D. Ray; Olszewski, Abbie; Segura, Hugo; Hartzheim, Daphne; Laing, Woodrow; Pyle, Daniel

2017-01-01

This meta-analysis synthesizes results from expository text structure interventions designed to increase comprehension for students in kindergarten to grade 12 published between 1970 and 2013. Twenty-one studies were identified, 19 of which met criteria for a meta-analysis, including 48 studywise effect sizes that were meta-analyzed to determine…

Structure and variation of the mitochondrial genome of fishes.

PubMed

Satoh, Takashi P; Miya, Masaki; Mabuchi, Kohji; Nishida, Mutsumi

2016-09-07

The mitochondrial (mt) genome has been used as an effective tool for phylogenetic and population genetic analyses in vertebrates. However, the structure and variability of the vertebrate mt genome are not well understood. A potential strategy for improving our understanding is to conduct a comprehensive comparative study of large mt genome data. The aim of this study was to characterize the structure and variability of the fish mt genome through comparative analysis of large datasets. An analysis of the secondary structure of proteins for 250 fish species (248 ray-finned and 2 cartilaginous fishes) illustrated that cytochrome c oxidase subunits (COI, COII, and COIII) and a cytochrome bc1 complex subunit (Cyt b) had substantial amino acid conservation. Among the four proteins, COI was the most conserved, as more than half of all amino acid sites were invariable among the 250 species. Our models identified 43 and 58 stems within 12S rRNA and 16S rRNA, respectively, with larger numbers than proposed previously for vertebrates. The models also identified 149 and 319 invariable sites in 12S rRNA and 16S rRNA, respectively, in all fishes. In particular, the present result verified that a region corresponding to the peptidyl transferase center in prokaryotic 23S rRNA, which is homologous to mt 16S rRNA, is also conserved in fish mt 16S rRNA. Concerning the gene order, we found 35 variations (in 32 families) that deviated from the common gene order in vertebrates. These gene rearrangements were mostly observed in the area spanning the ND5 gene to the control region as well as two tRNA gene cluster regions (IQM and WANCY regions). Although many of such gene rearrangements were unique to a specific taxon, some were shared polyphyletically between distantly related species. Through a large-scale comparative analysis of 250 fish species mt genomes, we elucidated various structural aspects of the fish mt genome and the encoded genes. The present results will be important for understanding functions of the mt genome and developing programs for nucleotide sequence analysis. This study demonstrated the significance of extensive comparisons for understanding the structure of the mt genome.

The application of cluster analysis in the intercomparison of loop structures in RNA.

PubMed

Huang, Hung-Chung; Nagaswamy, Uma; Fox, George E

2005-04-01

We have developed a computational approach for the comparison and classification of RNA loop structures. Hairpin or interior loops identified in atomic resolution RNA structures were intercompared by conformational matching. The root-mean-square deviation (RMSD) values between all pairs of RNA fragments of interest, even if from different molecules, are calculated. Subsequently, cluster analysis is performed on the resulting matrix of RMSD distances using the unweighted pair group method with arithmetic mean (UPGMA). The cluster analysis objectively reveals groups of folds that resemble one another. To demonstrate the utility of the approach, a comprehensive analysis of all the terminal hairpin tetraloops that have been observed in 15 RNA structures that have been determined by X-ray crystallography was undertaken. The method found major clusters corresponding to the well-known GNRA and UNCG types. In addition, two tetraloops with the unusual primary sequence UMAC (M is A or C) were successfully assigned to the GNRA cluster. Larger loop structures were also examined and the clustering results confirmed the occurrence of variations of the GNRA and UNCG tetraloops in these loops and provided a systematic means for locating them. Nineteen examples of larger loops that closely resemble either the GNRA or UNCG tetraloop were found in the large ribosomal RNAs. When the clustering approach was extended to include all structures in the SCOR database, novel relationships were detected including one between the ANYA motif and a less common folding of the GAAA tetraloop sequence.

The application of cluster analysis in the intercomparison of loop structures in RNA

PubMed Central

HUANG, HUNG-CHUNG; NAGASWAMY, UMA; FOX, GEORGE E.

2005-01-01

We have developed a computational approach for the comparison and classification of RNA loop structures. Hairpin or interior loops identified in atomic resolution RNA structures were intercompared by conformational matching. The root-mean-square deviation (RMSD) values between all pairs of RNA fragments of interest, even if from different molecules, are calculated. Subsequently, cluster analysis is performed on the resulting matrix of RMSD distances using the unweighted pair group method with arithmetic mean (UPGMA). The cluster analysis objectively reveals groups of folds that resemble one another. To demonstrate the utility of the approach, a comprehensive analysis of all the terminal hairpin tetraloops that have been observed in 15 RNA structures that have been determined by X-ray crystallography was undertaken. The method found major clusters corresponding to the well-known GNRA and UNCG types. In addition, two tetraloops with the unusual primary sequence UMAC (M is A or C) were successfully assigned to the GNRA cluster. Larger loop structures were also examined and the clustering results confirmed the occurrence of variations of the GNRA and UNCG tetraloops in these loops and provided a systematic means for locating them. Nineteen examples of larger loops that closely resemble either the GNRA or UNCG tetraloop were found in the large ribosomal RNAs. When the clustering approach was extended to include all structures in the SCOR database, novel relationships were detected including one between the ANYA motif and a less common folding of the GAAA tetraloop sequence. PMID:15769871

The interface between spoken and written language: developmental disorders.

PubMed

Hulme, Charles; Snowling, Margaret J

2014-01-01

We review current knowledge about reading development and the origins of difficulties in learning to read. We distinguish between the processes involved in learning to decode print, and the processes involved in reading for meaning (reading comprehension). At a cognitive level, difficulties in learning to read appear to be predominantly caused by deficits in underlying oral language skills. The development of decoding skills appears to depend critically upon phonological language skills, and variations in phoneme awareness, letter-sound knowledge and rapid automatized naming each appear to be causally related to problems in learning to read. Reading comprehension difficulties in contrast appear to be critically dependent on a range of oral language comprehension skills (including vocabulary knowledge and grammatical, morphological and pragmatic skills).

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

PubMed Central

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

2015-01-01

Background Public hospitals deliver over ninety percent of all outpatient and inpatient services in China. Their quality is graded into three levels (A, B, and C) largely based on structural resources, but empirical evidence on the quality of process and outcome of care is extremely scarce. As expectations for quality care rise with higher living standards and cost of care, such evidence is urgently needed and vital to improve care and to inform future health reforms. Methods We compiled and analyzed a multicenter database of over 4 million inpatient discharge summary records to provide a comprehensive assessment of the level and variations in clinical outcomes of hospitalization at 39 tertiary hospitals in Beijing. We assessed six outcome measures of clinical quality: in-hospital mortality rates (RSMR) for AMI, stroke, pneumonia and CABG, post-procedural complication rate (RS-CR), and failure-to-rescue rate (RS-FTR). The measures were adjusted for pre-admission patient case-mix using indirect standardization method with hierarchical linear mixed models. Results We found good overall quality with large variations by hospital and condition (mean/range, in %): RSMR-AMI: 6.23 (2.37–14.48), RSMR-stroke: 4.18 (3.58–4.44), RSMR-pneumonia: 7.78 (7.20–8.59), RSMR-CABG: 1.93 (1.55–2.23), RS-CR: 11.38 (9.9–12.88), and RS-FTR: 6.41 (5.17–7.58). Hospital grade was not significantly associated with any risk-adjusted outcome measures. Conclusions Going to a higher grade public hospital does not always lead to better patient outcome because hospital grade only contains information about hospital structural resources. A hospital report card with some outcome measures of quality would provide valuable information to patients in choosing providers, and for regulators to identify gaps in health care quality. Reducing the variations in clinical practice and patient outcome should be a focus for policy makers in the next round of health sector reforms in China. PMID:26430748

Reconciling Time, Space and Function: A New Dorsal-Ventral Stream Model of Sentence Comprehension

ERIC Educational Resources Information Center

Bornkessel-Schlesewsky, Ina; Schlesewsky, Matthias

2013-01-01

We present a new dorsal-ventral stream framework for language comprehension which unifies basic neurobiological assumptions (Rauschecker & Scott, 2009) with a cross-linguistic neurocognitive sentence comprehension model (eADM; Bornkessel & Schlesewsky, 2006). The dissociation between (time-dependent) syntactic structure-building and…

Some Relationships between Operativity and Reading Comprehension.

ERIC Educational Resources Information Center

Stack, Wesner Brown

Samples of 98 fourth graders and 111 sixth graders participated in a study of the relationships between operational thinking and reading comprehension of texts involving operational structures. Tests of operational thinking, reading comprehension, IQ, and vocabulary were administered in class groups. Results from correlational and factor analyses…

A Comprehensive Theory of Integration.

PubMed

Singer, Sara J; Kerrissey, Michaela; Friedberg, Mark; Phillips, Russell

2018-03-01

Efforts to transform health care delivery to improve care have increasingly focused on care integration. However, variation in how integration is defined has complicated efforts to design, synthesize, and compare studies of integration in health care. Evaluations of integration initiatives would be enhanced by describing them according to clear definitions of integration and specifying which empirical relationships they seek to test-whether among types of integration or between integration and outcomes of care. Drawing on previous work, we present a comprehensive theoretical model of relationships between types of integration and propose how to measure them.

The Redshift Evolution of Rest-UV Spectroscopic Properties in Lyman-break Galaxies at z ∼ 2–4

NASA Astrophysics Data System (ADS)

Du, Xinnan; Shapley, Alice E.; Reddy, Naveen A.; Jones, Tucker; Stark, Daniel P.; Steidel, Charles C.; Strom, Allison L.; Rudie, Gwen C.; Erb, Dawn K.; Ellis, Richard S.; Pettini, Max

2018-06-01

We present the first comprehensive evolutionary analysis of the rest-frame UV spectroscopic properties of star-forming galaxies at z ∼ 2–4. We match samples at different redshifts in UV luminosity and stellar mass, and perform systematic measurements of spectral features and stellar population modeling. By creating composite spectra grouped according to Lyα equivalent width (EW) and various galaxy properties, we study the evolutionary trends among Lyα, low- and high-ionization interstellar (LIS and HIS) absorption features, and integrated galaxy properties. We also examine the redshift evolution of Lyα and LIS absorption kinematics, and fine-structure emission EWs. The connections among the strengths of Lyα, LIS lines, and dust extinction are redshift independent, as is the decoupling of the Lyα and HIS line strengths, and the bulk outflow kinematics as traced by the LIS lines. Stronger Lyα emission is observed at higher redshift at fixed UV luminosity, stellar mass, SFR, and age. Much of this variation in the average Lyα strength with redshift, and the variation in Lyα strength at fixed redshift, can be explained in terms of variations in the neutral gas covering fraction and/or dust content in the ISM and CGM. However, based on the connection between Lyα and C III] emission strengths, we additionally find evidence for variations in the intrinsic production rate of Lyα photons at the highest Lyα EWs. The challenge now is to understand the observed evolution of the neutral gas covering fraction and dust extinction within a coherent model for galaxy formation, and make robust predictions for the escape of ionizing radiation at z > 6.

LPA and PLG sequence variation and kringle IV-2 copy number in two populations.

PubMed

Crawford, Dana C; Peng, Ze; Cheng, Jan-Fang; Boffelli, Dario; Ahearn, Magdalena; Nguyen, Dan; Shaffer, Tristan; Yi, Qian; Livingston, Robert J; Rieder, Mark J; Nickerson, Deborah A

2008-01-01

Lp(a) levels have long been recognized as a potential risk factor for coronary heart disease that is almost completely under genetic control. Much of the genetics impacting Lp(a) levels has been attributed to the highly polymorphic LPA kringle IV-2 copy number variant, and most of the variance in Lp(a) levels in populations of European-descent is inversely correlated with kringle IV copy number. However, less of the variance is explained in African-descent populations for the same structural variation. African-descent populations have, on average, higher levels of Lp(a), suggesting other genetic factors contribute to Lp(a) level variability across populations. To identify potential cis-acting factors, we re-sequenced the gene LPA for single nucleotide polymorphism (SNP) discovery in 23 European-Americans and 24 African-Americans. We also re- sequenced the neighboring gene plasminogen (PLG) and genotyped the kringle IV copy number variant in the same reference samples. These data are the most comprehensive description of sequence variation in LPA and its relationship with the kringle IV copy number variant. With these data, we demonstrate that only a fraction of LPA sequence diversity has been previously documented. Also, we identify several high frequency SNPs present in the African-American sample but absent in the European-American sample. Finally, we show that SNPs within PLG are not in linkage disequilibrium with SNPs in LPA, and we show that kringle IV copy number variation is not in linkage disequilibrium with either LPA or PLG SNPs. Together, these data suggest that LPA SNPs could independently contribute to Lp(a) levels in the general population. Copyright (c) 2008 S. Karger AG, Basel.

Hospital Variation in Perioperative Complications for Laparoscopic Sleeve Gastrectomy in Michigan

PubMed Central

Pradarelli, Jason C.; Varban, Oliver A.; Ghaferi, Amir A.; Weiner, Matthew; Carlin, Arthur M.; Dimick, Justin B.

2015-01-01

Structured Abstract Background Laparoscopic sleeve gastrectomy has recently surpassed gastric bypass and laparoscopic adjustable gastric banding as the most common weight-loss procedure. Previously, substantial concerns existed regarding variation in perioperative safety with bariatric surgery. This study aimed to assess rates of perioperative complications for laparoscopic sleeve gastrectomy across hospitals and in relation to procedure volume. Study Design We analyzed 8,693 patients who underwent laparoscopic sleeve gastrectomy from 2013 through 2014 across 40 hospitals in the Michigan Bariatric Surgery Collaborative. Mixed-effects logistic regression was used to assess hospital variation in risk- and reliability-adjusted rates of overall and serious 30-day complications and their relationship with hospital annual stapling procedure volume (gastric bypass and sleeve gastrectomy). Results Overall, 5.4% of patients experienced perioperative complications. Adjusted rates of overall complications varied three-fold across hospitals, ranging from 3.6% (95% CI, 1.9–6.8%) to 11.0% (95% CI, 7.7–15.5%). Serious complications occurred in just 1.2% of patients and varied minimally. In this analysis, hospital volume was not associated with overall or serious complications. The 1 hospital with significantly lower overall complication rates was high-volume (≥125 procedures/year); however, of the 4 hospitals with significantly higher complication rates, 3 were medium-volume (50–124 procedures/year) and 1 was high-volume. The remaining hospitals were not significantly different than the cohort mean. Conclusions Serious complications among patients undergoing laparoscopic sleeve gastrectomy were relatively infrequent. Rates of overall complications varied widely across Michigan hospitals enrolled in a quality collaborative, although this variation was unrelated to volume standards required for accreditation as a comprehensive bariatric surgery center. PMID:26506567

Molecular Population Genetics of the Northern Elephant Seal Mirounga angustirostris.

PubMed

Abadía-Cardoso, Alicia; Freimer, Nelson B; Deiner, Kristy; Garza, John Carlos

2017-09-01

The northern elephant seal, Mirounga angustirostris, was heavily hunted and declared extinct in the 19th century. However, a colony remained on remote Guadalupe Island, Mexico and the species has since repopulated most of its historical distribution. Here, we present a comprehensive evaluation of genetic variation in the species. First, we assess the effect of the demographic bottleneck on microsatellite variability and compare it with that found in other pinnipeds, demonstrating levels of variation similar to that in species that continue to be threatened with extinction. Next, we use sequence data from these markers to demonstrate that some of the limited polymorphism predates the bottleneck. However, most contemporary variation appears to have arisen recently and persisted due to exponential growth. We also describe how we use the range in allele size of microsatellites to estimate ancestral effective population size before the bottleneck, demonstrating a large reduction in effective size. We then employ a classical method for bacteria to estimate the microsatellite mutation rate in the species, deriving an estimate that is extremely similar to that estimated for a similar set of loci in humans, indicating consistency of microsatellite mutation rates in mammals. Finally, we find slight significant structure between some geographically separated colonies, although its biological significance is unclear. This work demonstrates that genetic analysis can be useful for evaluating the population biology of the northern elephant seal, in spite of the bottleneck that removed most genetic variation from the species. Published by Oxford University Press on behalf of The American Genetic Association 2017. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Eleventh NASTRAN User's Colloquium

NASA Technical Reports Server (NTRS)

1983-01-01

NASTRAN (NASA STRUCTURAL ANALYSIS) is a large, comprehensive, nonproprietary, general purpose finite element computer code for structural analysis which was developed under NASA sponsorship. The Eleventh Colloquium provides some comprehensive general papers on the application of finite element methods in engineering, comparisons with other approaches, unique applications, pre- and post-processing or auxiliary programs, and new methods of analysis with NASTRAN.

The Effects of Distance to Dentists and Dentist Supply on Children's Use of Dental Care.

PubMed

Wehby, George L; Shane, Dan M; Joshi, Adweta; Momany, Elizabeth; Chi, Donald L; Kuthy, Raymond A; Damiano, Peter C

2017-10-01

To examine the effects of distance to dentists and dentist supply on dental services use among children with Medicaid coverage in Iowa. Iowa Medicaid claims for enrolled children between 2000 and 2009. The study sample included 41,554 children (providing 158,942 child-year observations) who were born in Iowa between 2000 and 2006 and enrolled from birth in the Iowa Medicaid program. Children were followed through 2009. We used logistic regression to simultaneously examine the effects of distance (miles to nearest dentist) and county-level dentist supply on a broad range of dental services controlling for key confounders. Additional models only used within-child variation over time to remove unobservable time-invariant confounders. Distance was related to lower utilization of comprehensive dental exams (2 percent lower odds per 1 mile increase in distance), an effect that also held in models using within-child variation only. Dentist supply was positively related to comprehensive exams and other preventive services and negatively related to major dental treatments; however, these associations became smaller and insignificant when examining within-child changes except for other preventive services. Longer distance to dentists is a barrier for use of comprehensive dental exams, conditional on dentist supply. © Health Research and Educational Trust.

Cognitive Processing in Oral and Silent Reading Comprehension.

ERIC Educational Resources Information Center

Salasoo, Aita

1986-01-01

Reading rates and comprehension measures that probed recognition of various levels of text structure were collected for passages read orally and silently by 16 college students. Results showed that memory traces of text microstructure created in oral reading were accessed faster during memory-based comprehension tasks than traces established by…

The evolution of personality variation in humans and other animals.

PubMed

Nettle, Daniel

2006-09-01

A comprehensive evolutionary framework for understanding the maintenance of heritable behavioral variation in humans is yet to be developed. Some evolutionary psychologists have argued that heritable variation will not be found in important, fitness-relevant characteristics because of the winnowing effect of natural selection. This article propounds the opposite view. Heritable variation is ubiquitous in all species, and there are a number of frameworks for understanding its persistence. The author argues that each of the Big Five dimensions of human personality can be seen as the result of a trade-off between different fitness costs and benefits. As there is no unconditionally optimal value of these trade-offs, it is to be expected that genetic diversity will be retained in the population. ((c) 2006 APA, all rights reserved).

Relating Human Genetic Variation to Variation in Drug Responses

PubMed Central

Madian, Ashraf G.; Wheeler, Heather E.; Jones, Richard Baker; Dolan, M. Eileen

2012-01-01

Although sequencing a single human genome was a monumental effort a decade ago, more than one thousand genomes have now been sequenced. The task ahead lies in transforming this information into personalized treatment strategies that are tailored to the unique genetics of each individual. One important aspect of personalized medicine is patient-to-patient variation in drug response. Pharmacogenomics addresses this issue by seeking to identify genetic contributors to human variation in drug efficacy and toxicity. Here, we present a summary of the current status of this field, which has evolved from studies of single candidate genes to comprehensive genome-wide analyses. Additionally, we discuss the major challenges in translating this knowledge into a systems-level understanding of drug physiology with the ultimate goal of developing more effective personalized clinical treatment strategies. PMID:22840197

The catechol-O-methyltransferase gene (COMT) and cognitive function from childhood through adolescence

PubMed Central

Gaysina, Darya; Xu, Man K.; Barnett, Jennifer H.; Croudace, Tim J.; Wong, Andrew; Richards, Marcus; Jones, Peter B.

2013-01-01

Genetic variation in the catechol-O-methyltransferase gene (COMT) can influence cognitive function, and this effect may depend on developmental stage. Using a large representative British birth cohort, we investigated the effect of COMT on cognitive function (verbal and non-verbal) at ages 8 and 15 years taking into account the possible modifying effect of pubertal stage. Five functional COMT polymorphisms, rs6269, rs4818, rs4680, rs737865 and rs165599 were analysed. Associations between COMT polymorphisms and cognition were tested using regression and latent variable structural equation modelling (SEM). Before correction for multiple testing, COMT rs737865 showed association with reading comprehension, verbal ability and global cognition at age 15 years in pubescent boys only. Although there was some evidence for age- and sex-specific effects of the COMT rs737865 none remained significant after correction for multiple testing. Further studies are necessary in order to make firmer conclusions. PMID:23178897

The Signature of Southern Hemisphere Atmospheric Circulation Patterns in Antarctic Precipitation

PubMed Central

Thompson, David W. J.; van den Broeke, Michiel R.

2017-01-01

Abstract We provide the first comprehensive analysis of the relationships between large‐scale patterns of Southern Hemisphere climate variability and the detailed structure of Antarctic precipitation. We examine linkages between the high spatial resolution precipitation from a regional atmospheric model and four patterns of large‐scale Southern Hemisphere climate variability: the southern baroclinic annular mode, the southern annular mode, and the two Pacific‐South American teleconnection patterns. Variations in all four patterns influence the spatial configuration of precipitation over Antarctica, consistent with their signatures in high‐latitude meridional moisture fluxes. They impact not only the mean but also the incidence of extreme precipitation events. Current coupled‐climate models are able to reproduce all four patterns of atmospheric variability but struggle to correctly replicate their regional impacts on Antarctic climate. Thus, linking these patterns directly to Antarctic precipitation variability may allow a better estimate of future changes in precipitation than using model output alone. PMID:29398735

Computational intelligence in bioinformatics: SNP/haplotype data in genetic association study for common diseases.

PubMed

Kelemen, Arpad; Vasilakos, Athanasios V; Liang, Yulan

2009-09-01

Comprehensive evaluation of common genetic variations through association of single-nucleotide polymorphism (SNP) structure with common complex disease in the genome-wide scale is currently a hot area in human genome research due to the recent development of the Human Genome Project and HapMap Project. Computational science, which includes computational intelligence (CI), has recently become the third method of scientific enquiry besides theory and experimentation. There have been fast growing interests in developing and applying CI in disease mapping using SNP and haplotype data. Some of the recent studies have demonstrated the promise and importance of CI for common complex diseases in genomic association study using SNP/haplotype data, especially for tackling challenges, such as gene-gene and gene-environment interactions, and the notorious "curse of dimensionality" problem. This review provides coverage of recent developments of CI approaches for complex diseases in genetic association study with SNP/haplotype data.

Regional fracture patterns around volcanoes: Possible evidence for volcanic spreading on Venus

NASA Astrophysics Data System (ADS)

López, I.; Lillo, J.; Hansen, V. L.

2008-06-01

Magellan data show that the surface of Venus is dominated by volcanic landforms including large flow fields and a wide range of volcanic edifices that occur in different magmatic and tectonic environments. This study presents the results from a comprehensive survey of volcano-rift interaction in the BAT region and its surroundings. We carried out structural mapping of examples where interaction between volcanoes and regional fractures results in a deflection of the fractures around the volcanic features and discuss the nature of the local volcano-related stress fields that might be responsible for the observed variations of the regional fracture systems. We propose that the deflection of the regional fractures around these venusian volcanoes might be related to volcanic spreading, a process recognized as of great importance in the tectonic evolution of volcanoes on Earth and Mars, but not previously described on Venus.

Synchrotron X-ray reciprocal-space mapping, topography and diffraction resolution studies of macromolecular crystal quality.

PubMed

Boggon, T J; Helliwell, J R; Judge, R A; Olczak, A; Siddons, D P; Snell, E H; Stojanoff, V

2000-07-01

A comprehensive study of microgravity and ground-grown chicken egg-white lysozyme crystals is presented using synchrotron X-ray reciprocal-space mapping, topography techniques and diffraction resolution. Microgravity crystals displayed reduced intrinsic mosaicities on average, but no differences in terms of strain over their ground-grown counterparts. Topographic analysis revealed that in the microgravity case the majority of the crystal was contributing to the peak of the reflection at the appropriate Bragg angle. In the ground-control case only a small volume of the crystal contributed to the intensity at the diffraction peak. The techniques prove to be highly complementary, with the reciprocal-space mapping providing a quantitative measure of the crystal mosaicity and strain (or variation in lattice spacing) and the topography providing a qualitative overall assessment of the crystal in terms of its X-ray diffraction properties. Structural data collection was also carried out at the synchrotron.

Complement dysregulation and disease: from genes and proteins to diagnostics and drugs.

PubMed

de Cordoba, Santiago Rodriguez; Tortajada, Agustin; Harris, Claire L; Morgan, B Paul

2012-11-01

During the last decade, numerous studies have associated genetic variations in complement components and regulators with a number of chronic and infectious diseases. The functional characterization of these complement protein variants, in addition to recent structural advances in understanding of the assembly, activation and regulation of the AP C3 convertase, have provided important insights into the pathogenic mechanisms involved in some of these complement related disorders. This knowledge has identified potential targets for complement inhibitory therapies which are demonstrating efficacy and generating considerable expectation in changing the natural history of these diseases. Comprehensive understanding of the genetic and non-genetic risk factors contributing to these disorders will also result in targeting of the right patient groups in a stratified medicine approach through better diagnostics and individually tailored treatments, thereby improving management of patients. Crown Copyright © 2012. Published by Elsevier GmbH. All rights reserved.

Investigating the Pressure-Induced Amorphization of Zeolitic Imidazolate Framework ZIF-8: Mechanical Instability Due to Shear Mode Softening.

PubMed

Ortiz, Aurélie U; Boutin, Anne; Fuchs, Alain H; Coudert, François-Xavier

2013-06-06

We provide the first molecular dynamics study of the mechanical instability that is the cause of pressure-induced amorphization of zeolitic imidazolate framework ZIF-8. By measuring the elastic constants of ZIF-8 up to the amorphization pressure, we show that the crystal-to-amorphous transition is triggered by the mechanical instability of ZIF-8 under compression, due to shear mode softening of the material. No similar softening was observed under temperature increase, explaining the absence of temperature-induced amorphization in ZIF-8. We also demonstrate the large impact of the presence of adsorbate in the pores on the mechanical stability and compressibility of the framework, increasing its shear stability. This first molecular dynamics study of ZIF mechanical properties under variations of pressure, temperature, and pore filling opens the way to a more comprehensive understanding of their mechanical stability, structural transitions, and amorphization.

Achieving Cost Reduction Through Data Analytics.

PubMed

Rocchio, Betty Jo

2016-10-01

The reimbursement structure of the US health care system is shifting from a volume-based system to a value-based system. Adopting a comprehensive data analytics platform has become important to health care facilities, in part to navigate this shift. Hospitals generate plenty of data, but actionable analytics are necessary to help personnel interpret and apply data to improve practice. Perioperative services is an important revenue-generating department for hospitals, and each perioperative service line requires a tailored approach to be successful in managing outcomes and controlling costs. Perioperative leaders need to prepare to use data analytics to reduce variation in supplies, labor, and overhead. Mercy, based in Chesterfield, Missouri, adopted a perioperative dashboard that helped perioperative leaders collaborate with surgeons and perioperative staff members to organize and analyze health care data, which ultimately resulted in significant cost savings. Copyright © 2016 AORN, Inc. Published by Elsevier Inc. All rights reserved.

Synchrotron X-Ray Reciprocal Space Mapping, Topography and Diffraction Resolution Studies of Macromolecular Crystal Quality

NASA Technical Reports Server (NTRS)

Boggon, T. J.; Helliwell, J. R.; Judge, Russell A.; Siddons, D. P.; Snell, Edward H.; Stojanoff, V.

2000-01-01

A comprehensive study of microgravity and ground grown chicken egg white lysozyme crystals is presented using synchrotron X-ray reciprocal space mapping, topography techniques and diffraction resolution. Microgravity crystals displayed, on average, reduced intrinsic mosaicities but no differences in terms of stress over their earth grown counterparts. Topographic analysis revealed that in the microgravity case the majority of the crystal was contributing to the peak of the reflection at the appropriate Bragg angle. In the earth case at the diffraction peak only a small volume of the crystal contributed to the intensity. The techniques prove to be highly complementary with the reciprocal space mapping providing a quantitative measure of the crystal mosaicity and stress (or variation in lattice spacing) and topography providing a qualitative overall assessment of the crystal in terms of its X-ray diffraction properties. Structural data collection was also carried out both at the synchrotron and in the laboratory.

Nanopatterning of swinging substrates by ion-beam sputtering

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

Yoon, Sun Mi; Kim, J.-S., E-mail: jskim@sm.ac.kr

Graphite substrates are azimuthally swung during ion-beam sputtering (IBS) at a polar angle θ = 78° from the surface normal. The swinging of the substrate not only causes quasi-two-dimensional mass transport but also makes various sputter effects from the different incident angles to work together. Through variation of the swing angle, both the transport and sputtering effects synergistically produce a series of salient patterns, such as asymmetric wall-like structures, which can grow to several tens of nanometers and exhibit a re-entrant orientational change with the increased swing angle. Thus, the present work demonstrates that dynamic variables such as the swing angle, whichmore » have been little utilized, offer an additional parameter space that can be exploited to diversify the sputtered patterns, thereby expanding the applicability of an IBS as well as the comprehension of the IBS nano patterning mechanism.« less

Theoretical study of polarization insensitivity of carrier-induced refractive index change of multiple quantum well.

PubMed

Miao, Qingyuan; Zhou, Qunjie; Cui, Jun; He, Ping-An; Huang, Dexiu

2014-12-29

Characteristics of polarization insensitivity of carrier-induced refractive index change of 1.55 μm tensile-strained multiple quantum well (MQW) are theoretically investigated. A comprehensive MQW model is proposed to effectively extend the application range of previous models. The model considers the temperature variation as well as the nonuniform distribution of injected carrier in MQW. Tensile-strained MQW is expected to achieve polarization insensitivity of carrier-induced refractive index change over a wide wavelength range as temperature varies from 0°C to 40°C, while the magnitude of refractive index change keeps a large value (more than 3 × 10^-3). And that the polarization insensitivity of refractive index change can maintain for a wide range of carrier concentration. Multiple quantum well with different material and structure parameters is anticipated to have the similar polarization insensitivity of refractive index change, which shows the design flexibility.

The Description of Shale Reservoir Pore Structure Based on Method of Moments Estimation

PubMed Central

Li, Wenjie; Wang, Changcheng; Shi, Zejin; Wei, Yi; Zhou, Huailai; Deng, Kun

2016-01-01

Shale has been considered as good gas reservoir due to its abundant interior nanoscale pores. Thus, the study of the pore structure of shale is of great significance for the evaluation and development of shale oil and gas. To date, the most widely used approaches for studying the shale pore structure include image analysis, radiation and fluid invasion methods. The detailed pore structures can be studied intuitively by image analysis and radiation methods, but the results obtained are quite sensitive to sample preparation, equipment performance and experimental operation. In contrast, the fluid invasion method can be used to obtain information on pore size distribution and pore structure, but the relative simple parameters derived cannot be used to evaluate the pore structure of shale comprehensively and quantitatively. To characterize the nanoscale pore structure of shale reservoir more effectively and expand the current research techniques, we proposed a new method based on gas adsorption experimental data and the method of moments to describe the pore structure parameters of shale reservoir. Combined with the geological mixture empirical distribution and the method of moments estimation principle, the new method calculates the characteristic parameters of shale, including the mean pore size (x¯), standard deviation (σ), skewness (Sk) and variation coefficient (c). These values are found by reconstructing the grouping intervals of observation values and optimizing algorithms for eigenvalues. This approach assures a more effective description of the characteristics of nanoscale pore structures. Finally, the new method has been applied to analyze the Yanchang shale in the Ordos Basin (China) and Longmaxi shale from the Sichuan Basin (China). The results obtained well reveal the pore characteristics of shale, indicating the feasibility of this new method in the study of the pore structure of shale reservoir. PMID:26992168

The Description of Shale Reservoir Pore Structure Based on Method of Moments Estimation.

PubMed

Li, Wenjie; Wang, Changcheng; Shi, Zejin; Wei, Yi; Zhou, Huailai; Deng, Kun

2016-01-01

Shale has been considered as good gas reservoir due to its abundant interior nanoscale pores. Thus, the study of the pore structure of shale is of great significance for the evaluation and development of shale oil and gas. To date, the most widely used approaches for studying the shale pore structure include image analysis, radiation and fluid invasion methods. The detailed pore structures can be studied intuitively by image analysis and radiation methods, but the results obtained are quite sensitive to sample preparation, equipment performance and experimental operation. In contrast, the fluid invasion method can be used to obtain information on pore size distribution and pore structure, but the relative simple parameters derived cannot be used to evaluate the pore structure of shale comprehensively and quantitatively. To characterize the nanoscale pore structure of shale reservoir more effectively and expand the current research techniques, we proposed a new method based on gas adsorption experimental data and the method of moments to describe the pore structure parameters of shale reservoir. Combined with the geological mixture empirical distribution and the method of moments estimation principle, the new method calculates the characteristic parameters of shale, including the mean pore size (mean), standard deviation (σ), skewness (Sk) and variation coefficient (c). These values are found by reconstructing the grouping intervals of observation values and optimizing algorithms for eigenvalues. This approach assures a more effective description of the characteristics of nanoscale pore structures. Finally, the new method has been applied to analyze the Yanchang shale in the Ordos Basin (China) and Longmaxi shale from the Sichuan Basin (China). The results obtained well reveal the pore characteristics of shale, indicating the feasibility of this new method in the study of the pore structure of shale reservoir.

Genetics of the dentofacial variation in human malocclusion

PubMed Central

Moreno Uribe, L. M.; Miller, S. F.

2015-01-01

Malocclusions affect individuals worldwide, resulting in compromised function and esthetics. Understanding the etiological factors contributing to the variation in dentofacial morphology associated with malocclusions is the key to develop novel treatment approaches. Advances in dentofacial phenotyping, which is the comprehensive characterization of hard and soft tissue variation in the craniofacial complex, together with the acquisition of large-scale genomic data have started to unravel genetic mechanisms underlying facial variation. Knowledge on the genetics of human malocclusion is limited even though results attained thus far are encouraging, with promising opportunities for future research. This review summarizes the most common dentofacial variations associated with malocclusions and reviews the current knowledge of the roles of genes in the development of malocclusions. Lastly, this review will describe ways to advance malocclusion research, following examples from the expanding fields of phenomics and genomic medicine, which aim to better patient outcomes. PMID:25865537

Systematic documentation and analysis of human genetic variation in hemoglobinopathies using the microattribution approach.

PubMed

Giardine, Belinda; Borg, Joseph; Higgs, Douglas R; Peterson, Kenneth R; Philipsen, Sjaak; Maglott, Donna; Singleton, Belinda K; Anstee, David J; Basak, A Nazli; Clark, Barnaby; Costa, Flavia C; Faustino, Paula; Fedosyuk, Halyna; Felice, Alex E; Francina, Alain; Galanello, Renzo; Gallivan, Monica V E; Georgitsi, Marianthi; Gibbons, Richard J; Giordano, Piero C; Harteveld, Cornelis L; Hoyer, James D; Jarvis, Martin; Joly, Philippe; Kanavakis, Emmanuel; Kollia, Panagoula; Menzel, Stephan; Miller, Webb; Moradkhani, Kamran; Old, John; Papachatzopoulou, Adamantia; Papadakis, Manoussos N; Papadopoulos, Petros; Pavlovic, Sonja; Perseu, Lucia; Radmilovic, Milena; Riemer, Cathy; Satta, Stefania; Schrijver, Iris; Stojiljkovic, Maja; Thein, Swee Lay; Traeger-Synodinos, Jan; Tully, Ray; Wada, Takahito; Waye, John S; Wiemann, Claudia; Zukic, Branka; Chui, David H K; Wajcman, Henri; Hardison, Ross C; Patrinos, George P

2011-03-20

We developed a series of interrelated locus-specific databases to store all published and unpublished genetic variation related to hemoglobinopathies and thalassemia and implemented microattribution to encourage submission of unpublished observations of genetic variation to these public repositories. A total of 1,941 unique genetic variants in 37 genes, encoding globins and other erythroid proteins, are currently documented in these databases, with reciprocal attribution of microcitations to data contributors. Our project provides the first example of implementing microattribution to incentivise submission of all known genetic variation in a defined system. It has demonstrably increased the reporting of human variants, leading to a comprehensive online resource for systematically describing human genetic variation in the globin genes and other genes contributing to hemoglobinopathies and thalassemias. The principles established here will serve as a model for other systems and for the analysis of other common and/or complex human genetic diseases.

More than a simple lipophilic contact: a detailed thermodynamic analysis of nonbasic residues in the s1 pocket of thrombin.

PubMed

Baum, Bernhard; Mohamed, Menshawy; Zayed, Mohamed; Gerlach, Christof; Heine, Andreas; Hangauer, David; Klebe, Gerhard

2009-07-03

The field of medicinal chemistry aims to design and optimize small molecule leads into drug candidates that may positively interfere with pathological disease situations in humans or combat the growth of infective pathogens. From the plethora of crystal structures of protein-inhibitor complexes we have learned how molecules recognize each other geometrically, but we still have rather superficial understanding of why they bind to each other. This contribution surveys a series of 26 thrombin inhibitors with small systematic structural differences to elucidate the rationale for their widely deviating binding affinity from 185 microM to 4 nM as recorded by enzyme kinetic measurements. Five well-resolved (resolution 2.30 - 1.47 A) crystal structures of thrombin-inhibitor complexes and an apo-structure of the uncomplexed enzyme (1.50 A) are correlated with thermodynamic data recorded by isothermal titration calorimetry with 12 selected inhibitors from the series. Taking solubility data into account, the variation in physicochemical properties allows conclusions to be reached about the relative importance of the enthalpic binding features as well as to estimate the importance of the parameters more difficult to capture, such as residual ligand entropy and desolvation properties. The collected data reveal a comprehensive picture of the thermodynamic signature that explains the so far poorly understood attractive force experienced by m-chloro-benzylamides to thrombin.

Impact of 3D Canopy Structure on Remote Sensing Vegetation Index and Solar Induced Chlorophyll Fluorescence

NASA Astrophysics Data System (ADS)

Zeng, Y.; Berry, J. A.; Jing, L.; Qinhuo, L.

2017-12-01

Terrestrial ecosystem plays a critical role in removing CO2 from atmosphere by photosynthesis. Remote sensing provides a possible way to monitor the Gross Primary Production (GPP) at the global scale. Vegetation Indices (VI), e.g., NDVI and NIRv, and Solar Induced Fluorescence (SIF) have been widely used as a proxy for GPP, while the impact of 3D canopy structure on VI and SIF has not be comprehensively studied yet. In this research, firstly, a unified radiative transfer model for visible/near-infrared reflectance and solar induced chlorophyll fluorescence has been developed based on recollision probability and directional escape probability. Then, the impact of view angles, solar angles, weather conditions, leaf area index, and multi-layer leaf angle distribution (LAD) on VI and SIF has been studied. Results suggest that canopy structure plays a critical role in distorting pixel-scale remote sensing signal from leaf-scale scattering. In thin canopy, LAD affects both of the remote sensing estimated GPP and real GPP, while in dense canopy, SIF variations are mainly due to canopy structure, instead of just due to physiology. At the microscale, leaf angle reflects the plant strategy to light on the photosynthesis efficiency, and at the macroscale, a priori knowledge of leaf angle distribution for specific species can improve the global GPP estimation by remote sensing.

Structure-Function Correlation Using Confocal Laser Ophthalmoscope in Primary Open-Angle Glaucoma and Pseudoexfoliative Glaucoma.

PubMed

Pappas, Theofanis; Founti, Panayiota; Yin, Xiang Jun; Koskosas, Archimidis; Anastasopoulos, Eleftherios; Salonikiou, Angeliki; Kilintzis, Vasilios; Antoniadis, Antonios; Ziakas, Nikolaos; Topouzis, Fotis

2016-04-01

To compare Heidelberg Retina Tomograph (HRT) optic disc parameters and structure-function correlation between primary open-angle glaucoma (POAG) and pseudoexfoliative glaucoma (PEXG). Prospective, observation case series. A total of 54 POAG and 33 PEXG cases, consecutively recruited from a University Glaucoma Service, underwent a comprehensive ophthalmic examination, including HRT optic disc imaging. Glaucoma definition required the presence of both structural and functional damage. One eye per subject was included in the analysis. T test, Mann-Whitney U test, and analysis of covariance were used to compare HRT parameters between POAG and PEXG, adjusting for age, mean deviation (MD) in the visual field, intraocular pressure, and disc area. The correlation between HRT and MD was assessed in each group. Cup area (P=0.048), height variation contour (P=0.016), and cup/disc area ratio (P=0.023) were higher in POAG, whereas the mean retinal nerve fiber layer thickness (P=0.048), retinal nerve fiber layer cross-section area (P=0.044), and rim area (P=0.048) were lower in POAG, compared with PEXG. The correlation of HRT parameters with MD was significant only in the POAG group. At a similar level of functional damage, POAG subjects presented with more pronounced structural damage than PEXG subjects. The correlation between HRT and visual field parameters was more evident in POAG, compared with PEXG.

Variation in Definitive Therapy for Localized Non-Small Cell Lung Cancer Among National Comprehensive Cancer Network Institutions

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

Valle, Luca F.; Jagsi, Reshma; Bobiak, Sarah N.

Purpose: This study determined practice patterns in the staging and treatment of patients with stage I non-small cell lung cancer (NSCLC) among National Comprehensive Cancer Network (NCCN) member institutions. Secondary aims were to determine trends in the use of definitive therapy, predictors of treatment type, and acute adverse events associated with primary modalities of treatment. Methods and Materials: Data from the National Comprehensive Cancer Network Oncology Outcomes Database from 2007 to 2011 for US patients with stage I NSCLC were used. Main outcome measures included patterns of care, predictors of treatment, acute morbidity, and acute mortality. Results: Seventy-nine percent ofmore » patients received surgery, 16% received definitive radiation therapy (RT), and 3% were not treated. Seventy-four percent of the RT patients received stereotactic body RT (SBRT), and the remainder received nonstereotactic RT (NSRT). Among participating NCCN member institutions, the number of surgeries-to-RT course ratios varied between 1.6 and 34.7 (P<.01), and the SBRT-to-NSRT ratio varied between 0 and 13 (P=.01). Significant variations were also observed in staging practices, with brain imaging 0.33 (0.25-0.43) times as likely and mediastinoscopy 31.26 (21.84-44.76) times more likely for surgical patients than for RT patients. Toxicity rates for surgical and for SBRT patients were similar, although the rates were double for NSRT patients. Conclusions: The variations in treatment observed among NCCN institutions reflects the lack of level I evidence directing the use of surgery or SBRT for stage I NSCLC. In this setting, research of patient and physician preferences may help to guide future decision making.« less

Process quality indicators in family medicine: results of an international comparison.

PubMed

Pavlič, Danica Rotar; Sever, Maja; Klemenc-Ketiš, Zalika; Švab, Igor

2015-12-02

The aim of our study was to describe variability in process quality in family medicine among 31 European countries plus Australia, New Zealand, and Canada. The quality of family medicine was measured in terms of continuity, coordination, community orientation, and comprehensiveness of care. The QUALICOPC study (Quality and Costs of Primary Care in Europe) was carried out among family physicians in 31 European countries (the EU 27 except for France, plus Macedonia, Iceland, Norway, Switzerland, and Turkey) and three non-European countries (Australia, Canada, and New Zealand). We used random sampling when national registers of practitioners were available. Regional registers or lists of facilities were used for some countries. A standardized questionnaire was distributed to the physicians, resulting in a sample of 6734 participants. Data collection took place between October 2011 and December 2013. Based on completed questionnaires, a three-dimensional framework was established to measure continuity, coordination, community orientation, and comprehensiveness of care. Multilevel linear regression analysis was performed to evaluate the variation of quality attributable to the family physician level and the country level. None of the 34 countries in this study consistently scored the best or worst in all categories. Continuity of care was perceived by family physicians as the most important dimension of quality. Some components of comprehensiveness of care, including medical technical procedures, preventive care and health care promotion, varied substantially between countries. Coordination of care was identified as the weakest part of quality. We found that physician-level characteristics contributed to the majority of variation. A comparison of process quality indicators in family medicine revealed similarities and differences within and between countries. The researchers found that the major proportion of variation can be explained by physicians' characteristics.

Structural Priming and Frequency Effects Interact in Chinese Sentence Comprehension

PubMed Central

Wei, Hang; Dong, Yanping; Boland, Julie E.; Yuan, Fang

2016-01-01

Previous research in several European languages has shown that the language processing system is sensitive to both structural frequency and structural priming effects. However, it is currently not clear whether these two types of effects interact during online sentence comprehension, especially for languages that do not have morphological markings. To explore this issue, the present study investigated the possible interplay between structural priming and frequency effects for sentences containing the Chinese ambiguous construction V NP1 de NP2 in a self-paced reading experiment. The sentences were disambiguated to either the more frequent/preferred NP structure or the less frequent VP structure. Each target sentence was preceded by a prime sentence of three possible types: NP primes, VP primes, and neutral primes. When the ambiguous construction V NP1 de NP2 was disambiguated to the dispreferred VP structure, participants experienced more processing difficulty following an NP prime relative to following a VP prime or a neutral baseline. When the ambiguity was resolved to the preferred NP structure, prime type had no effect. These results suggest that structural priming in comprehension is modulated by the baseline frequency of alternative structures, with the less frequent structure being more subject to structural priming effects. These results are discussed in the context of the error-based, implicit learning account of structural priming. PMID:26869954

Cross-study differences in the etiology of reading comprehension: A meta-analytical review of twin studies

PubMed Central

Little, Callie W; Haughbrook, Rasheda; Hart, Sara A

2016-01-01

Numerous twin studies have been published examining the genetic and environmental etiology of reading comprehension, though the etiological estimates may be influenced currently unidentified sample conditions (e.g., Tucker-Drob & Bates, 2015). The purpose of the current meta-analysis was to average the etiological influences of reading comprehension and to explore the potential moderators that may be influencing these estimates. Results revealed an average heritability estimate of h2 = .59, with significant variation in estimates across studies, suggesting potential moderation. Heritability was moderated by publication year, grade level, project, zygosity determination method, and response type. The average shared environmental estimate was c2 = .16, with publication year, grade and zygosity determination method acting as significant moderators. These findings support the large role of genetic influences on reading comprehension, and a small but significant role of shared environmental influences. The significant moderators of etiological influences within the current synthesis suggest our interpretation of how genes and environment influence reading comprehension should reflect aspects of study and sample. PMID:27630039

National evaluation of the benefits and risks of greater structuring and coding of the electronic health record: exploratory qualitative investigation.

PubMed

Morrison, Zoe; Fernando, Bernard; Kalra, Dipak; Cresswell, Kathrin; Sheikh, Aziz

2014-01-01

We aimed to explore stakeholder views, attitudes, needs, and expectations regarding likely benefits and risks resulting from increased structuring and coding of clinical information within electronic health records (EHRs). Qualitative investigation in primary and secondary care and research settings throughout the UK. Data were derived from interviews, expert discussion groups, observations, and relevant documents. Participants (n=70) included patients, healthcare professionals, health service commissioners, policy makers, managers, administrators, systems developers, researchers, and academics. Four main themes arose from our data: variations in documentation practice; patient care benefits; secondary uses of information; and informing and involving patients. We observed a lack of guidelines, co-ordination, and dissemination of best practice relating to the design and use of information structures. While we identified immediate benefits for direct care and secondary analysis, many healthcare professionals did not see the relevance of structured and/or coded data to clinical practice. The potential for structured information to increase patient understanding of their diagnosis and treatment contrasted with concerns regarding the appropriateness of coded information for patients. The design and development of EHRs requires the capture of narrative information to reflect patient/clinician communication and computable data for administration and research purposes. Increased structuring and/or coding of EHRs therefore offers both benefits and risks. Documentation standards within clinical guidelines are likely to encourage comprehensive, accurate processing of data. As data structures may impact upon clinician/patient interactions, new models of documentation may be necessary if EHRs are to be read and authored by patients.

National evaluation of the benefits and risks of greater structuring and coding of the electronic health record: exploratory qualitative investigation

PubMed Central

Morrison, Zoe; Fernando, Bernard; Kalra, Dipak; Cresswell, Kathrin; Sheikh, Aziz

2014-01-01

Objective We aimed to explore stakeholder views, attitudes, needs, and expectations regarding likely benefits and risks resulting from increased structuring and coding of clinical information within electronic health records (EHRs). Materials and methods Qualitative investigation in primary and secondary care and research settings throughout the UK. Data were derived from interviews, expert discussion groups, observations, and relevant documents. Participants (n=70) included patients, healthcare professionals, health service commissioners, policy makers, managers, administrators, systems developers, researchers, and academics. Results Four main themes arose from our data: variations in documentation practice; patient care benefits; secondary uses of information; and informing and involving patients. We observed a lack of guidelines, co-ordination, and dissemination of best practice relating to the design and use of information structures. While we identified immediate benefits for direct care and secondary analysis, many healthcare professionals did not see the relevance of structured and/or coded data to clinical practice. The potential for structured information to increase patient understanding of their diagnosis and treatment contrasted with concerns regarding the appropriateness of coded information for patients. Conclusions The design and development of EHRs requires the capture of narrative information to reflect patient/clinician communication and computable data for administration and research purposes. Increased structuring and/or coding of EHRs therefore offers both benefits and risks. Documentation standards within clinical guidelines are likely to encourage comprehensive, accurate processing of data. As data structures may impact upon clinician/patient interactions, new models of documentation may be necessary if EHRs are to be read and authored by patients. PMID:24186957

Effective communication between ENT and primary care - a survey of outpatient correspondence.

PubMed

Addison, A B; Watts, S; Fleming, J

2015-06-01

To improve the quality of outpatient clinic communication between Otolaryngology and primary care doctors. Three example outpatient letters with identical content were created using different structure styles - full prose, headline subheadings with full prose and full subheadings throughout. Electronic questionnaires were sent out to 30 randomly selected General Practitioners in the area served by Western Sussex NHS Trust. The electronic mail study invite contained the initial GP referral, the three different letter formats and a link to the Sheffield Assessment for Letters (SAIL) questionnaire, which contained a 18-point checklist, 6 rating subheadings with a 10-point rating scale and a free text comment section. Study participants were asked to read the letters in the time usually afforded to outpatient letters in their routine practice, answer questions and then rate the letters. With a response rate of 66.7%, overall comparison of GP preferences demonstrated a significant variation between the three letter formats (Freidman P value = 0.0001). Post hoc multiple comparisons showed statistically significant preference for the headline subheading and prose letter compared to the full subheaded letter (P < 0.05). In assessing the letters for readability, comprehension, usefulness, informativeness and helpfulness, analysis showed significant preference for both fully subheaded and headline subheaded with full prose structures compared to the full prose letter. Although the headline subheadings and prose letter had the highest word count, it scored the highest in almost all the rating categories analysed. This study is the first published work to study primary care physician's preference for the structure of letters from secondary care. Prominent headline subheadings of diagnosis and management improve interpretation of content and comprehension and are helpful to GPs for co-ordinating patient management. Lack of subheadings or conversely an excess of subheadings may be a hindrance to effective communication between healthcare professionals. © 2014 John Wiley & Sons Ltd.

A mobile threat to genome stability: The impact of non-LTR retrotransposons upon the human genome

PubMed Central

Konkel, Miriam K.; Batzer, Mark A.

2010-01-01

It is now commonly agreed that the human genome is not the stable entity originally presumed. Deletions, duplications, inversions, and insertions are common, and contribute significantly to genomic structural variations (SVs). Their collective impact generates much of the inter-individual genomic diversity observed among humans. Not only do these variations change the structure of the genome; they may also have functional implications, e.g. altered gene expression. Some SVs have been identified as the cause of genetic disorders, including cancer predisposition. Cancer cells are notorious for their genomic instability, and often show genomic rearrangements at the microscopic and submicroscopic level to which transposable elements (TEs) contribute. Here, we review the role of TEs in genome instability, with particular focus on non-LTR retrotransposons. Currently, three non-LTR retrotransposon families – long interspersed element 1 (L1), SVA (short interspersed element (SINE-R), variable number of tandem repeats (VNTR), and Alu), and Alu (a SINE) elements – mobilize in the human genome, and cause genomic instability through both insertion- and post-insertion-based mutagenesis. Due to the abundance and high sequence identity of TEs, they frequently mislead the homologous recombination repair pathway into non-allelic homologous recombination, causing deletions, duplications, and inversions. While less comprehensively studied, non-LTR retrotransposon insertions and TE-mediated rearrangements are probably more common in cancer cells than in healthy tissue. This may be at least partially attributed to the commonly seen global hypomethylation as well as general epigenetic dysfunction of cancer cells. Where possible, we provide examples that impact cancer predisposition and/or development. PMID:20307669

Dry Juan de Fuca slab revealed by quantification of water entering Cascadia subduction zone

NASA Astrophysics Data System (ADS)

Canales, J. P.; Carbotte, S. M.; Nedimović, M. R.; Carton, H.

2017-11-01

Water is carried by subducting slabs as a pore fluid and in structurally bound minerals, yet no comprehensive quantification of water content and how it is stored and distributed at depth within incoming plates exists for any segment of the global subduction system. Here we use seismic data to quantify the amount of pore and structurally bound water in the Juan de Fuca plate entering the Cascadia subduction zone. Specifically, we analyse these water reservoirs in the sediments, crust and lithospheric mantle, and their variations along the central Cascadia margin. We find that the Juan de Fuca lower crust and mantle are drier than at any other subducting plate, with most of the water stored in the sediments and upper crust. Variable but limited bend faulting along the margin limits slab access to water, and a warm thermal structure resulting from a thick sediment cover and young plate age prevents significant serpentinization of the mantle. The dryness of the lower crust and mantle indicates that fluids that facilitate episodic tremor and slip must be sourced from the subducted upper crust, and that decompression rather than hydrous melting must dominate arc magmatism in central Cascadia. Additionally, dry subducted lower crust and mantle can explain the low levels of intermediate-depth seismicity in the Juan de Fuca slab.

GlycoWorkbench: a tool for the computer-assisted annotation of mass spectra of glycans.

PubMed

Ceroni, Alessio; Maass, Kai; Geyer, Hildegard; Geyer, Rudolf; Dell, Anne; Haslam, Stuart M

2008-04-01

Mass spectrometry is the main analytical technique currently used to address the challenges of glycomics as it offers unrivalled levels of sensitivity and the ability to handle complex mixtures of different glycan variations. Determination of glycan structures from analysis of MS data is a major bottleneck in high-throughput glycomics projects, and robust solutions to this problem are of critical importance. However, all the approaches currently available have inherent restrictions to the type of glycans they can identify, and none of them have proved to be a definitive tool for glycomics. GlycoWorkbench is a software tool developed by the EUROCarbDB initiative to assist the manual interpretation of MS data. The main task of GlycoWorkbench is to evaluate a set of structures proposed by the user by matching the corresponding theoretical list of fragment masses against the list of peaks derived from the spectrum. The tool provides an easy to use graphical interface, a comprehensive and increasing set of structural constituents, an exhaustive collection of fragmentation types, and a broad list of annotation options. The aim of GlycoWorkbench is to offer complete support for the routine interpretation of MS data. The software is available for download from: http://www.eurocarbdb.org/applications/ms-tools.

Measuring body structures and body functions from the International Classification of Functioning, Disability, and Health perspective: considerations for biomedical parameters in spinal cord injury research.

PubMed

Eriks-Hoogland, Inge E; Brinkhof, Martin W G; Al-Khodairy, Abdul; Baumberger, Michael; Brechbühl, Jörg; Curt, Armin; Mäder, Mark; Stucki, Gerold; Post, Marcel W M

2011-11-01

The aims of this study were to provide a selection of biomedical domains based on the comprehensive International Classification of Functioning, Disability, and Health (ICF) core sets for spinal cord injury (SCI) and to present an overview of the corresponding measurement instruments. Based on the Biomedical Domain Set, the SCI literature, the International Spinal Cord Society international data sets, and the Spinal Cord Injury Rehabilitation Evidence project publications were used to derive category specifications for use in SCI research. Expert opinion was used to derive a priority selection. The same sources were used to determine candidate measurement instruments for the specification of body functions and body structures using an example, and guiding principles were applied to select the most appropriate biomedical measurement instrument(s) for use in an SCI research project. Literature searches were performed for 41 second-level ICF body functions categories and for four second-level ICF body structures categories. For some of these categories, only a few candidate measurement instruments were found with limited variation in the type of measurement instruments. An ICF-based measurement set for biomedical aspects of functioning with SCI was established. For some categories of the ICF core sets for SCI, there is a need to develop measurement instruments.

A reliable ground bounce noise reduction technique for nanoscale CMOS circuits

NASA Astrophysics Data System (ADS)

Sharma, Vijay Kumar; Pattanaik, Manisha

2015-11-01

Power gating is the most effective method to reduce the standby leakage power by adding header/footer high-VTH sleep transistors between actual and virtual power/ground rails. When a power gating circuit transitions from sleep mode to active mode, a large instantaneous charge current flows through the sleep transistors. Ground bounce noise (GBN) is the high voltage fluctuation on real ground rail during sleep mode to active mode transitions of power gating circuits. GBN disturbs the logic states of internal nodes of circuits. A novel and reliable power gating structure is proposed in this article to reduce the problem of GBN. The proposed structure contains low-VTH transistors in place of high-VTH footer. The proposed power gating structure not only reduces the GBN but also improves other performance metrics. A large mitigation of leakage power in both modes eliminates the need of high-VTH transistors. A comprehensive and comparative evaluation of proposed technique is presented in this article for a chain of 5-CMOS inverters. The simulation results are compared to other well-known GBN reduction circuit techniques at 22 nm predictive technology model (PTM) bulk CMOS model using HSPICE tool. Robustness against process, voltage and temperature (PVT) variations is estimated through Monte-Carlo simulations.

Syntactic Priming and the Lexical Boost Effect during Sentence Production and Sentence Comprehension: An fMRI Study

ERIC Educational Resources Information Center

Segaert, Katrien; Kempen, Gerard; Petersson, Karl Magnus; Hagoort, Peter

2013-01-01

Behavioral syntactic priming effects during sentence comprehension are typically observed only if both the syntactic structure and lexical head are repeated. In contrast, during production syntactic priming occurs with structure repetition alone, but the effect is boosted by repetition of the lexical head. We used fMRI to investigate the neuronal…

Impacts of environmental factors on the whole microbial communities in the rhizosphere of a metal-tolerant plant: Elsholtzia haichowensis Sun.

PubMed

Deng, Songqiang; Ke, Tan; Li, Longtai; Cai, Shenwen; Zhou, Yuyue; Liu, Yue; Guo, Limin; Chen, Lanzhou; Zhang, Dayi

2018-06-01

Rhizospheric microbes play important roles in plant growth and heavy metals (HMs) transformation, possessing great potential for the successful phytoremediation of environmental pollutants. In the present study, the rhizosphere of Elsholtzia haichowensis Sun was comprehensively studied to uncover the influence of environmental factors (EFs) on the whole microbial communities including bacteria, fungi and archaea, via quantitative polymerase chain reaction (qPCR) and high-throughput sequencing. By analyzing molecular ecological network and multivariate regression trees (MRT), we evaluated the distinct impacts of 37 EFs on soil microbial community. Of them, soil pH, HMs, soil texture and nitrogen were identified as the most influencing factors, and their roles varied across different domains. Soil pH was the main environmental variable on archaeal and bacterial community but not fungi, explaining 25.7%, 46.5% and 40.7% variation of bacterial taxonomic composition, archaeal taxonomic composition and a-diversity, respectively. HMs showed important roles in driving the whole microbial community and explained the major variation in different domains. Nitrogen (NH 4 -N, NO 3 -N, NO 2 -N and TN) explained 47.3% variation of microbial population composition and 15.9% of archaeal taxonomic composition, demonstrating its influence in structuring the rhizospheric microbiome, particularly archaeal and bacterial community. Soil texture accounted for 10.2% variation of population composition, 28.9% of fungal taxonomic composition, 19.2% of fungal a-diversity and 7.8% of archaeal a-diversity. Rhizosphere only showed strong impacts on fungi and bacteria, accounting for 14.7% and 4.9% variation of fungal taxonomic composition and bacterial a-diversity. Spatial distance had stronger influence on bacteria and archaea than fungi, but not as significant as other EFs. For the first time, our study provides a complete insight into key influential EFs on rhizospheric microbes and how their roles vary across microbial domains, giving a hand for understanding the construction of microbial communities in rhizosphere. Copyright © 2017 Elsevier Ltd. All rights reserved.

A systematic review and meta-analysis of variations in branching patterns of the adult aortic arch.

PubMed

Popieluszko, Patrick; Henry, Brandon Michael; Sanna, Beatrice; Hsieh, Wan Chin; Saganiak, Karolina; Pękala, Przemysław A; Walocha, Jerzy A; Tomaszewski, Krzysztof A

2018-07-01

The aortic arch (AA) is the main conduit of the left side of the heart, providing a blood supply to the head, neck, and upper limbs. As it travels through the thorax, the pattern in which it gives off the branches to supply these structures can vary. Variations of these branching patterns have been studied; however, a study providing a comprehensive incidence of these variations has not yet been conducted. The objective of this study was to perform a meta-analysis of all the studies that report prevalence data on AA variants and to provide incidence data on the most common variants. A systematic search of online databases including PubMed, Embase, Scopus, ScienceDirect, Web of Science, SciELO, BIOSIS, and CNKI was performed for literature describing incidence of AA variations in adults. Studies including prevalence data on adult patients or cadavers were collected and their data analyzed. A total of 51 articles were included (N = 23,882 arches). Seven of the most common variants were analyzed. The most common variants found included the classic branching pattern, defined as a brachiocephalic trunk, a left common carotid, and a left subclavian artery (80.9%); the bovine arch variant (13.6%); and the left vertebral artery variant (2.8%). Compared by geographic data, bovine arch variants were noted to have a prevalence as high as 26.8% in African populations. Although patients who have an AA variant are often asymptomatic, they compose a significant portion of the population of patients and pose a greater risk of hemorrhage and ischemia during surgery in the thorax. Because of the possibility of encountering such variants, it is prudent for surgeons to consider potential variations in planning procedures, especially of an endovascular nature, in the thorax. Copyright © 2017 Society for Vascular Surgery. Published by Elsevier Inc. All rights reserved.

Neocortical malformation as consequence of nonadaptive regulation of neuronogenetic sequence

NASA Technical Reports Server (NTRS)

Caviness, V. S. Jr; Takahashi, T.; Nowakowski, R. S.

2000-01-01

Variations in the structure of the neocortex induced by single gene mutations may be extreme or subtle. They differ from variations in neocortical structure encountered across and within species in that these "normal" structural variations are adaptive (both structurally and behaviorally), whereas those associated with disorders of development are not. Here we propose that they also differ in principle in that they represent disruptions of molecular mechanisms that are not normally regulatory to variations in the histogenetic sequence. We propose an algorithm for the operation of the neuronogenetic sequence in relation to the overall neocortical histogenetic sequence and highlight the restriction point of the G1 phase of the cell cycle as the master regulatory control point for normal coordinate structural variation across species and importantly within species. From considerations based on the anatomic evidence from neocortical malformation in humans, we illustrate in principle how this overall sequence appears to be disrupted by molecular biological linkages operating principally outside the control mechanisms responsible for the normal structural variation of the neocortex. MRDD Research Reviews 6:22-33, 2000. Copyright 2000 Wiley-Liss, Inc.

Temporal variation in bat-fruit interactions: Foraging strategies influence network structure over time

NASA Astrophysics Data System (ADS)

Zapata-Mesa, Natalya; Montoya-Bustamante, Sebastián; Murillo-García, Oscar E.

2017-11-01

Mutualistic interactions, such as seed dispersal, are important for the maintenance of structure and stability of tropical communities. However, there is a lack of information about spatial and temporal variation in plant-animal interaction networks. Thus, our goal was to assess the effect of bat's foraging strategies on temporal variation in the structure and robustness of bat-fruit networks in both a dry and a rain tropical forest. We evaluated monthly variation in bat-fruit networks by using seven structure metrics: network size, average path length, nestedness, modularity, complementary specialization, normalized degree and betweenness centrality. Seed dispersal networks showed variations in size, species composition and modularity; did not present nested structures and their complementary specialization was high compared to other studies. Both networks presented short path lengths, and a constantly high robustness, despite their monthly variations. Sedentary bat species were recorded during all the study periods and occupied more central positions than nomadic species. We conclude that foraging strategies are important structuring factors that affect the dynamic of networks by determining the functional roles of frugivorous bats over time; thus sedentary bats are more important than nomadic species for the maintenance of the network structure, and their conservation is a must.

(Pea)nuts and bolts of visual narrative: Structure and meaning in sequential image comprehension

PubMed Central

Cohn, Neil; Paczynski, Martin; Jackendoff, Ray; Holcomb, Phillip J.; Kuperberg, Gina R.

2012-01-01

Just as syntax differentiates coherent sentences from scrambled word strings, the comprehension of sequential images must also use a cognitive system to distinguish coherent narrative sequences from random strings of images. We conducted experiments analogous to two classic studies of language processing to examine the contributions of narrative structure and semantic relatedness to processing sequential images. We compared four types of comic strips: 1) Normal sequences with both structure and meaning, 2) Semantic Only sequences (in which the panels were related to a common semantic theme, but had no narrative structure), 3) Structural Only sequences (narrative structure but no semantic relatedness), and 4) Scrambled sequences of randomly-ordered panels. In Experiment 1, participants monitored for target panels in sequences presented panel-by-panel. Reaction times were slowest to panels in Scrambled sequences, intermediate in both Structural Only and Semantic Only sequences, and fastest in Normal sequences. This suggests that both semantic relatedness and narrative structure offer advantages to processing. Experiment 2 measured ERPs to all panels across the whole sequence. The N300/N400 was largest to panels in both the Scrambled and Structural Only sequences, intermediate in Semantic Only sequences and smallest in the Normal sequences. This implies that a combination of narrative structure and semantic relatedness can facilitate semantic processing of upcoming panels (as reflected by the N300/N400). Also, panels in the Scrambled sequences evoked a larger left-lateralized anterior negativity than panels in the Structural Only sequences. This localized effect was distinct from the N300/N400, and appeared despite the fact that these two sequence types were matched on local semantic relatedness between individual panels. These findings suggest that sequential image comprehension uses a narrative structure that may be independent of semantic relatedness. Altogether, we argue that the comprehension of visual narrative is guided by an interaction between structure and meaning. PMID:22387723

Nondimensional Parameters and Equations for Nonlinear and Bifurcation Analyses of Thin Anisotropic Quasi-Shallow Shells

NASA Technical Reports Server (NTRS)

Nemeth, Michael P.

2010-01-01

A comprehensive development of nondimensional parameters and equations for nonlinear and bifurcations analyses of quasi-shallow shells, based on the Donnell-Mushtari-Vlasov theory for thin anisotropic shells, is presented. A complete set of field equations for geometrically imperfect shells is presented in terms general of lines-of-curvature coordinates. A systematic nondimensionalization of these equations is developed, several new nondimensional parameters are defined, and a comprehensive stress-function formulation is presented that includes variational principles for equilibrium and compatibility. Bifurcation analysis is applied to the nondimensional nonlinear field equations and a comprehensive set of bifurcation equations are presented. An extensive collection of tables and figures are presented that show the effects of lamina material properties and stacking sequence on the nondimensional parameters.

Instructional Implications of Listening Comprehension Research. Reading Education Report No. 39.

ERIC Educational Resources Information Center

Pearson, P. David; Fielding, Linda

While listening comprehension is perhaps the most ignored area of the language arts, a review of the literature suggests that it is deserving of more classroom instructional time. Involving the simultaneous orchestration of skills in phonology, syntax, semantics, and knowledge of text structure, listening comprehension seems to be controlled by…

Content Validity of the Comprehensive ICF Core Set for Multiple Sclerosis from the Perspective of Speech and Language Therapists

ERIC Educational Resources Information Center

Renom, Marta; Conrad, Andrea; Bascuñana, Helena; Cieza, Alarcos; Galán, Ingrid; Kesselring, Jürg; Coenen, Michaela

2014-01-01

Background: The Comprehensive International Classification of Functioning, Disability and Health (ICF) Core Set for Multiple Sclerosis (MS) is a comprehensive framework to structure the information obtained in multidisciplinary clinical settings according to the biopsychosocial perspective of the International Classification of Functioning,…

Imitated Prosodic Fluency Predicts Reading Comprehension Ability in Good and Poor High School Readers

PubMed Central

Breen, Mara; Kaswer, Lianne; Van Dyke, Julie A.; Krivokapić, Jelena; Landi, Nicole

2016-01-01

Researchers have established a relationship between beginning readers' silent comprehension ability and their prosodic fluency, such that readers who read aloud with appropriate prosody tend to have higher scores on silent reading comprehension assessments. The current study was designed to investigate this relationship in two groups of high school readers: Specifically Poor Comprehenders (SPCs), who have adequate word level and phonological skills but poor reading comprehension ability, and a group of age- and decoding skill-matched controls. We compared the prosodic fluency of the two groups by determining how effectively they produced prosodic cues to syntactic and semantic structure in imitations of a model speaker's production of syntactically and semantically varied sentences. Analyses of pitch and duration patterns revealed that speakers in both groups produced the expected prosodic patterns; however, controls provided stronger durational cues to syntactic structure. These results demonstrate that the relationship between prosodic fluency and reading comprehension continues past the stage of early reading instruction. Moreover, they suggest that prosodically fluent speakers may also generate more fluent implicit prosodic representations during silent reading, leading to more effective comprehension. PMID:27486409

A Winning Combination

ERIC Educational Resources Information Center

Henrichs, Erinn L.; Jackson, Julie K.

2012-01-01

Establishing classroom routines that provide students with the opportunities to learn and successfully apply the language of science is a daunting task. With minor variations, research has shown that effective and comprehensive vocabulary programs share four common elements: they are rich and varied language experiences; they teach well-selected…

Agricultural land use alters the seasonality and magnitude of stream metabolism

EPA Science Inventory

Streams are active processors of organic carbon; however, spatial and temporal variation in the rates and controls on metabolism are not well quantified in streams draining intensively-farmed landscapes. We present a comprehensive dataset of gross primary production (GPP) and ec...

FACTORS AFFECTING THINKING AND COMPREHENSION SKILLS.

ERIC Educational Resources Information Center

ABRAMS, JULES C.

INTELLECTUAL, EDUCATIONAL, NEUROLOGICAL, PHYSIOLOGICAL, PSYCHOLOGICAL, AND SOCIOLOGICAL FACTORS IN VARIOUS PATTERNS OF INTERRELATIONSHIPS INFLUENCE THE THINKING PROCESS. INDIVIDUALS DIFFER IN THE CONCEPTS THEY HOLD AND IN THEIR USE OF THESE CONCEPTS BECAUSE OF VARIATIONS IN INTELLIGENCE AND BACKGROUND OF EXPERIENCE. THE RANGE AND LEVEL OF CONCEPTS…

Potential Nucleosynthetic Sources of the Titanium Isotope Variations in Solar System Materials

NASA Astrophysics Data System (ADS)

Williams, N. H.; Fehr, M. A.; Akram, W. M.; Parkinson, I. J.; Schönbächler, M.

2012-09-01

The Ti isotope ratios of a comprehensive sample suite of solar system material were analyzed by MC-ICPMS. This data was then used to evaluate nucleosynthetic models for the source of isotopic correlations observed in Iron group elements and Zr.

A Model of the Acoustic Interactions Occurring Under Arctic Ice

DTIC Science & Technology

1990-05-22

agreement at angles near ecrit - Finally there is undoubtedly some error in the collected data as any temperature variations were not accounted for...acoustic attenuation in various media will supplement the overall comprehension of reflection and transmission phenomena as well. Continued collection of

The Genetics of Urinary Tract Infections and the Innate Defense of the Kidney and Urinary tract

PubMed Central

Ambite, Ines; Rydstrom, Gustav; Schwaderer, Andrew L.; Hains, David S.

2015-01-01

The urinary tract is a sterile organ system. Urinary tract infections (UTIs) are common and often serious infections. Research has focused on uropathogen, environment, and host factors leading to UTI pathogenesis. A growing body of evidence exists implicating genetic factors that can contribute to UTI risks. In this review, we highlight genetic variations in aspects of the innate immune system critical to the host response to uropathogens. This overview includes genetic variations in pattern recognition receptor molecules, chemokines/cytokines, and neutrophil activation. We also comprehensively cover murine knockout models of UTI, genetic variations involved in renal scarring as a result of ascending UTIs, and asymptomatic bacteriuria. PMID:27617139

Differential Targeting of Unpaired Bases within Duplex DNA by the Natural Compound Clerocidin: A Valuable Tool to Dissect DNA Secondary Structure

PubMed Central

Nadai, Matteo; Palù, Giorgio; Palumbo, Manlio; Richter, Sara N.

2012-01-01

Non-canonical DNA structures have been postulated to mediate protein-nucleic acid interactions and to function as intermediates in the generation of frame-shift mutations when errors in DNA replication occur, which result in a variety of diseases and cancers. Compounds capable of binding to non-canonical DNA conformations may thus have significant diagnostic and therapeutic potential. Clerocidin is a natural diterpenoid which has been shown to selectively react with single-stranded bases without targeting the double helix. Here we performed a comprehensive analysis on several non-canonical DNA secondary structures, namely mismatches, nicks, bulges, hairpins, with sequence variations in both the single-stranded region and the double-stranded flanking segment. By analysis of clerocidin reactivity, we were able to identify the exposed reactive residues which provided information on both the secondary structure and the accessibility of the non-paired sites. Mismatches longer than 1 base were necessary to be reached by clerocidin reactive groups, while 1-base nicks were promptly targeted by clerocidin; in hairpins, clerocidin reactivity increased with the length of the hairpin loop, while, interestingly, reactivity towards bulges reached a maximum in 3-base-long bulges and declined in longer bulges. Electrophoretic mobility shift analysis demonstrated that bulges longer than 3 bases (i.e. 5- and 7-bases) folded or stacked on the duplex region therefore being less accessible by the compound. Clerocidin thus represents a new valuable diagnostic tool to dissect DNA secondary structures. PMID:23285245

Differential targeting of unpaired bases within duplex DNA by the natural compound clerocidin: a valuable tool to dissect DNA secondary structure.

PubMed

Nadai, Matteo; Palù, Giorgio; Palumbo, Manlio; Richter, Sara N

2012-01-01

Non-canonical DNA structures have been postulated to mediate protein-nucleic acid interactions and to function as intermediates in the generation of frame-shift mutations when errors in DNA replication occur, which result in a variety of diseases and cancers. Compounds capable of binding to non-canonical DNA conformations may thus have significant diagnostic and therapeutic potential. Clerocidin is a natural diterpenoid which has been shown to selectively react with single-stranded bases without targeting the double helix. Here we performed a comprehensive analysis on several non-canonical DNA secondary structures, namely mismatches, nicks, bulges, hairpins, with sequence variations in both the single-stranded region and the double-stranded flanking segment. By analysis of clerocidin reactivity, we were able to identify the exposed reactive residues which provided information on both the secondary structure and the accessibility of the non-paired sites. Mismatches longer than 1 base were necessary to be reached by clerocidin reactive groups, while 1-base nicks were promptly targeted by clerocidin; in hairpins, clerocidin reactivity increased with the length of the hairpin loop, while, interestingly, reactivity towards bulges reached a maximum in 3-base-long bulges and declined in longer bulges. Electrophoretic mobility shift analysis demonstrated that bulges longer than 3 bases (i.e. 5- and 7-bases) folded or stacked on the duplex region therefore being less accessible by the compound. Clerocidin thus represents a new valuable diagnostic tool to dissect DNA secondary structures.

Inter-Ethnic/Racial Facial Variations: A Systematic Review and Bayesian Meta-Analysis of Photogrammetric Studies

PubMed Central

Wen, Yi Feng; Wong, Hai Ming; Lin, Ruitao; Yin, Guosheng; McGrath, Colman

2015-01-01

Background Numerous facial photogrammetric studies have been published around the world. We aimed to critically review these studies so as to establish population norms for various angular and linear facial measurements; and to determine inter-ethnic/racial facial variations. Methods and Findings A comprehensive and systematic search of PubMed, ISI Web of Science, Embase, and Scopus was conducted to identify facial photogrammetric studies published before December, 2014. Subjects of eligible studies were either Africans, Asians or Caucasians. A Bayesian hierarchical random effects model was developed to estimate posterior means and 95% credible intervals (CrI) for each measurement by ethnicity/race. Linear contrasts were constructed to explore inter-ethnic/racial facial variations. We identified 38 eligible studies reporting 11 angular and 18 linear facial measurements. Risk of bias of the studies ranged from 0.06 to 0.66. At the significance level of 0.05, African males were found to have smaller nasofrontal angle (posterior mean difference: 8.1°, 95% CrI: 2.2°–13.5°) compared to Caucasian males and larger nasofacial angle (7.4°, 0.1°–13.2°) compared to Asian males. Nasolabial angle was more obtuse in Caucasian females than in African (17.4°, 0.2°–35.3°) and Asian (9.1°, 0.4°–17.3°) females. Additional inter-ethnic/racial variations were revealed when the level of statistical significance was set at 0.10. Conclusions A comprehensive database for angular and linear facial measurements was established from existing studies using the statistical model and inter-ethnic/racial variations of facial features were observed. The results have implications for clinical practice and highlight the need and value for high quality photogrammetric studies. PMID:26247212

Inter-Ethnic/Racial Facial Variations: A Systematic Review and Bayesian Meta-Analysis of Photogrammetric Studies.

PubMed

Wen, Yi Feng; Wong, Hai Ming; Lin, Ruitao; Yin, Guosheng; McGrath, Colman

2015-01-01

Numerous facial photogrammetric studies have been published around the world. We aimed to critically review these studies so as to establish population norms for various angular and linear facial measurements; and to determine inter-ethnic/racial facial variations. A comprehensive and systematic search of PubMed, ISI Web of Science, Embase, and Scopus was conducted to identify facial photogrammetric studies published before December, 2014. Subjects of eligible studies were either Africans, Asians or Caucasians. A Bayesian hierarchical random effects model was developed to estimate posterior means and 95% credible intervals (CrI) for each measurement by ethnicity/race. Linear contrasts were constructed to explore inter-ethnic/racial facial variations. We identified 38 eligible studies reporting 11 angular and 18 linear facial measurements. Risk of bias of the studies ranged from 0.06 to 0.66. At the significance level of 0.05, African males were found to have smaller nasofrontal angle (posterior mean difference: 8.1°, 95% CrI: 2.2°-13.5°) compared to Caucasian males and larger nasofacial angle (7.4°, 0.1°-13.2°) compared to Asian males. Nasolabial angle was more obtuse in Caucasian females than in African (17.4°, 0.2°-35.3°) and Asian (9.1°, 0.4°-17.3°) females. Additional inter-ethnic/racial variations were revealed when the level of statistical significance was set at 0.10. A comprehensive database for angular and linear facial measurements was established from existing studies using the statistical model and inter-ethnic/racial variations of facial features were observed. The results have implications for clinical practice and highlight the need and value for high quality photogrammetric studies.

Systematic pharmacogenomics analysis of a Malay whole genome: proof of concept for personalized medicine.

PubMed

Salleh, Mohd Zaki; Teh, Lay Kek; Lee, Lian Shien; Ismet, Rose Iszati; Patowary, Ashok; Joshi, Kandarp; Pasha, Ayesha; Ahmed, Azni Zain; Janor, Roziah Mohd; Hamzah, Ahmad Sazali; Adam, Aishah; Yusoff, Khalid; Hoh, Boon Peng; Hatta, Fazleen Haslinda Mohd; Ismail, Mohamad Izwan; Scaria, Vinod; Sivasubbu, Sridhar

2013-01-01

With a higher throughput and lower cost in sequencing, second generation sequencing technology has immense potential for translation into clinical practice and in the realization of pharmacogenomics based patient care. The systematic analysis of whole genome sequences to assess patient to patient variability in pharmacokinetics and pharmacodynamics responses towards drugs would be the next step in future medicine in line with the vision of personalizing medicine. Genomic DNA obtained from a 55 years old, self-declared healthy, anonymous male of Malay descent was sequenced. The subject's mother died of lung cancer and the father had a history of schizophrenia and deceased at the age of 65 years old. A systematic, intuitive computational workflow/pipeline integrating custom algorithm in tandem with large datasets of variant annotations and gene functions for genetic variations with pharmacogenomics impact was developed. A comprehensive pathway map of drug transport, metabolism and action was used as a template to map non-synonymous variations with potential functional consequences. Over 3 million known variations and 100,898 novel variations in the Malay genome were identified. Further in-depth pharmacogenetics analysis revealed a total of 607 unique variants in 563 proteins, with the eventual identification of 4 drug transport genes, 2 drug metabolizing enzyme genes and 33 target genes harboring deleterious SNVs involved in pharmacological pathways, which could have a potential role in clinical settings. The current study successfully unravels the potential of personal genome sequencing in understanding the functionally relevant variations with potential influence on drug transport, metabolism and differential therapeutic outcomes. These will be essential for realizing personalized medicine through the use of comprehensive computational pipeline for systematic data mining and analysis.

Modelling inter-supply chain competition with resource limitation and demand disruption

NASA Astrophysics Data System (ADS)

Chen, Zhaobo; Teng, Chunxian; Zhang, Ding; Sun, Jiayi

2016-05-01

This paper proposes a comprehensive model for studying supply chain versus supply chain competition with resource limitation and demand disruption. We assume that there are supply chains with heterogeneous supply network structures that compete at multiple demand markets. Each supply chain is comprised of internal and external firms. The internal firms are coordinated in production and distribution and share some common but limited resources within the supply chain, whereas the external firms are independent and do not share the internal resources. The supply chain managers strive to develop optimal strategies in terms of production level and resource allocation in maximising their profit while facing competition at the end market. The Cournot-Nash equilibrium of this inter-supply chain competition is formulated as a variational inequality problem. We further study the case when there is demand disruption in the plan-execution phase. In such a case, the managers need to revise their planned strategy in order to maximise their profit with the new demand under disruption and minimise the cost of change. We present a bi-criteria decision-making model for supply chain managers and develop the optimal conditions in equilibrium, which again can be formulated by another variational inequality problem. Numerical examples are presented for illustrative purpose.

Magnetic Susceptibility Effects and Lorentz Damping in Diamagnetic Fluids

NASA Technical Reports Server (NTRS)

Ramachandran, Narayanan; Leslie, Fred W.

2000-01-01

A great number of crystals (semi-conductor and protein) grown in space are plagued by convective motions which contribute to structural flaws. The character of these instabilities is not well understood but is associated with density variations in the presence of residual gravity and g-jitter. Both static and dynamic (rotating or travelling wave) magnetic fields can be used to reduce the effects of convection in materials processing. In semi-conductor melts, due to their relatively high electrical conductivity, the induced Lorentz force can be effectively used to curtail convective effects. In melts/solutions with reduced electrical conductivity, such as aqueous solutions used in solution crystal growth, protein crystal growth and/or model fluid experiments for simulating melt growth, however, the variation of the magnetic susceptibility with temperature and/or concentration can be utilized to better damp fluid convection than the Lorentz force method. This paper presents a comprehensive, comparative numerical study of the relative damping effects using static magnetic fields and gradients in a simple geometry subjected to a thermal gradient. The governing equations are formulated in general terms and then simplified for the numerical calculations. Operational regimes, based on the best damping technique for different melts/solutions are identified based on fluid properties. Comparisons are provided between the numerical results and available results from experiments in surveyed literature.

Comprehensive Survey on Improved Focality and Penetration Depth of Transcranial Magnetic Stimulation Employing Multi-Coil Arrays.

PubMed

Wei, Xile; Li, Yao; Lu, Meili; Wang, Jiang; Yi, Guosheng

2017-11-14

Multi-coil arrays applied in transcranial magnetic stimulation (TMS) are proposed to accurately stimulate brain tissues and modulate neural activities by an induced electric field (EF). Composed of numerous independently driven coils, a multi-coil array has alternative energizing strategies to evoke EFs targeting at different cerebral regions. To improve the locating resolution and the stimulating focality, we need to fully understand the variation properties of induced EFs and the quantitative control method of the spatial arrangement of activating coils, both of which unfortunately are still unclear. In this paper, a comprehensive analysis of EF properties was performed based on multi-coil arrays. Four types of planar multi-coil arrays were used to study the relationship between the spatial distribution of EFs and the structure of stimuli coils. By changing coil-driven strategies in a basic 16-coil array, we find that an EF induced by compactly distributed coils decays faster than that induced by dispersedly distributed coils, but the former has an advantage over the latter in terms of the activated brain volume. Simulation results also indicate that the attenuation rate of an EF induced by the 36-coil dense array is 3 times and 1.5 times greater than those induced by the 9-coil array and the 16-coil array, respectively. The EF evoked by the 36-coil dispense array has the slowest decay rate. This result demonstrates that larger multi-coil arrays, compared to smaller ones, activate deeper brain tissues at the expense of decreased focality. A further study on activating a specific field of a prescribed shape and size was conducted based on EF variation. Accurate target location was achieved with a 64-coil array 18 mm in diameter. A comparison between the figure-8 coil, the planar array, and the cap-formed array was made and demonstrates an improvement of multi-coil configurations in the penetration depth and the focality. These findings suggest that there is a tradeoff between attenuation rate and focality in the application of multi-coil arrays. Coil-energizing strategies and array dimensions should be based on an adequate evaluation of these two important demands and the topological structure of target tissues.

Child Development and Structural Variation in the Human Genome

ERIC Educational Resources Information Center

Zhang, Ying; Haraksingh, Rajini; Grubert, Fabian; Abyzov, Alexej; Gerstein, Mark; Weissman, Sherman; Urban, Alexander E.

2013-01-01

Structural variation of the human genome sequence is the insertion, deletion, or rearrangement of stretches of DNA sequence sized from around 1,000 to millions of base pairs. Over the past few years, structural variation has been shown to be far more common in human genomes than previously thought. Very little is currently known about the effects…

Predicting and understanding comprehensive drug-drug interactions via semi-nonnegative matrix factorization.

PubMed

Yu, Hui; Mao, Kui-Tao; Shi, Jian-Yu; Huang, Hua; Chen, Zhi; Dong, Kai; Yiu, Siu-Ming

2018-04-11

Drug-drug interactions (DDIs) always cause unexpected and even adverse drug reactions. It is important to identify DDIs before drugs are used in the market. However, preclinical identification of DDIs requires much money and time. Computational approaches have exhibited their abilities to predict potential DDIs on a large scale by utilizing pre-market drug properties (e.g. chemical structure). Nevertheless, none of them can predict two comprehensive types of DDIs, including enhancive and degressive DDIs, which increases and decreases the behaviors of the interacting drugs respectively. There is a lack of systematic analysis on the structural relationship among known DDIs. Revealing such a relationship is very important, because it is able to help understand how DDIs occur. Both the prediction of comprehensive DDIs and the discovery of structural relationship among them play an important guidance when making a co-prescription. In this work, treating a set of comprehensive DDIs as a signed network, we design a novel model (DDINMF) for the prediction of enhancive and degressive DDIs based on semi-nonnegative matrix factorization. Inspiringly, DDINMF achieves the conventional DDI prediction (AUROC = 0.872 and AUPR = 0.605) and the comprehensive DDI prediction (AUROC = 0.796 and AUPR = 0.579). Compared with two state-of-the-art approaches, DDINMF shows it superiority. Finally, representing DDIs as a binary network and a signed network respectively, an analysis based on NMF reveals crucial knowledge hidden among DDIs. Our approach is able to predict not only conventional binary DDIs but also comprehensive DDIs. More importantly, it reveals several key points about the DDI network: (1) both binary and signed networks show fairly clear clusters, in which both drug degree and the difference between positive degree and negative degree show significant distribution; (2) the drugs having large degrees tend to have a larger difference between positive degree and negative degree; (3) though the binary DDI network contains no information about enhancive and degressive DDIs at all, it implies some of their relationship in the comprehensive DDI matrix; (4) the occurrence of signs indicating enhancive and degressive DDIs is not random because the comprehensive DDI network is equipped with a structural balance.

A comprehensive review of the prevalence of beta globin gene variations and the co-inheritance of related gene variants in Saudi Arabians with beta-thalassemia

PubMed Central

Alaithan, Mousa A.; AbdulAzeez, Sayed; Borgio, J. Francis

2018-01-01

Beta-thalassemia is a genetic disorder that is caused by variations in the beta-hemoglobin (HBB) gene. Saudi Arabia is among the countries most affected by beta-thalassemia, and this is particularly problematic in the Eastern regions. This review article is an attempt to compile all the reported mutations to facilitate further national-level studies to prepare a Saudi repository of HBB gene variations. In Saudi Arabians, IVSI-5 (G>C) and Cd 39 (C>T) are the most prevalent HBB gene variations out of 42 variations. The coinheritance of HBB gene variations with ATRX, HBA1, HBA2, HBA12, AHSP, and KLF1 gene variations were observed to be common in the Saudi population. National surveys on the molecular nature of hemoglobinopathies should be set up through collaborations between research centers from various regions to create a well-documented molecular data bank. This data bank can be used to develop a premarital screening program and lead to the best treatment and prevention strategies for beta-thalassemia. PMID:29619482

How Problems of Reading Fluency and Comprehension Are Related to Difficulties in Syntactic Awareness Skills among Fifth Graders

ERIC Educational Resources Information Center

Mokhtari, Kouider; Thompson, H. Brian

2006-01-01

In this study, we assessed and analyzed 5th grade students' levels of syntactic awareness in relation to their reading fluency and comprehension. The aim was to examine the role of syntactic awareness (children's awareness of the syntactic structure of sentences and their ability to reflect on and manipulate that structure) as a potential source…

The Structure of Oral Language and Reading and Their Relation to Comprehension in Kindergarten through Grade 2

ERIC Educational Resources Information Center

Foorman, Barbara R.; Herrera, Sarah; Petscher, Yaacov; Mitchell, Alison; Truckenmiller, Adrea

2015-01-01

This study examined the structure of oral language and reading and their relation to comprehension from a latent variable modeling perspective in Kindergarten, Grade 1, and Grade 2. Participants were students in Kindergarten (n = 218), Grade 1 (n = 372), and Grade 2 (n = 273), attending Title 1 schools. Students were administered phonological…

Genecology of Thurber’s needlegrass (Achnatherum thurberianum (Piper) Barkworth) in the Western U.S.

USDA-ARS?s Scientific Manuscript database

Thurber’s needlegrass (Achnatherum thurberianum (Piper) Barkworth) is a key restoration species in the Great Basin and surrounding areas, yet comprehensive studies of how climate relates to genetic variation and seed zones for restoration projects are lacking. Potentially adaptive phenotypic traits...

Relations among Personal Initiative and the Development of Reading Strategy Knowledge and Reading Comprehension

ERIC Educational Resources Information Center

Warner, Greta J.; Fay, Doris; Spörer, Nadine

2017-01-01

Reading comprehension is a self-regulated activity that depends on the proactive effort of the reader. Therefore, the authors studied the effects of personal initiative (PI) on the development of reading comprehension, mediated by reading strategy knowledge. Structural equation modelling was applied to a longitudinal study with two data waves…

Determinants of Success in Native and Non-Native Listening Comprehension: An Individual Differences Approach

ERIC Educational Resources Information Center

Andringa, Sible; Olsthoorn, Nomi; van Beuningen, Catherine; Schoonen, Rob; Hulstijn, Jan

2012-01-01

The goal of this study was to explain individual differences in both native and non-native listening comprehension; 121 native and 113 non-native speakers of Dutch were tested on various linguistic and nonlinguistic cognitive skills thought to underlie listening comprehension. Structural equation modeling was used to identify the predictors of…

Molecular Modeling of the Structural and Dynamical Changes in Calcium Channel TRPV5 Induced by the African-Specific A563T Variation.

PubMed

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

2016-03-01

Transient receptor potential cation channels, vanilloid subfamily, member 5 (TRPV5) plays a key role in active Ca(2+) reabsorption in the kidney. Variations in TRPV5 occur at high frequency in African populations and may contribute to their higher efficiency of Ca(2+) reabsorption. One of the African specific variations, A563T, exhibits increased Ca(2+) transport ability. However, it is unclear how this variation influences the channel pore. On the basis of the structure of TRPV1, a TRPV5 model was generated to simulate the structural and dynamical changes induced by the A563T variation. On the basis of this model, amino acid residue 563 interacts with V540, which is one residue away from the key residue, D542, involved in Ca(2+) selectivity and Mg(2+) blockade. The A563T variation increases secondary structure stability and reduces dynamical motion of D542. In addition, the A563T variation alters the electrostatic potential of the outer surface of the pore. Differences in contact between selective filter residues and residue 563 and in electrostatic potential between the two TRPV5 variants were also observed in another model derived from an alternative alignment in the selective filters between TRPV5 and TRPV1. These findings indicate that the A563T variation induces structural, dynamical, and electrostatic changes in the TRPV5 pore, providing structural insight into the functional alterations associated with the A563T variation.

Towards Structural Analysis of Audio Recordings in the Presence of Musical Variations

NASA Astrophysics Data System (ADS)

Müller, Meinard; Kurth, Frank

2006-12-01

One major goal of structural analysis of an audio recording is to automatically extract the repetitive structure or, more generally, the musical form of the underlying piece of music. Recent approaches to this problem work well for music, where the repetitions largely agree with respect to instrumentation and tempo, as is typically the case for popular music. For other classes of music such as Western classical music, however, musically similar audio segments may exhibit significant variations in parameters such as dynamics, timbre, execution of note groups, modulation, articulation, and tempo progression. In this paper, we propose a robust and efficient algorithm for audio structure analysis, which allows to identify musically similar segments even in the presence of large variations in these parameters. To account for such variations, our main idea is to incorporate invariance at various levels simultaneously: we design a new type of statistical features to absorb microvariations, introduce an enhanced local distance measure to account for local variations, and describe a new strategy for structure extraction that can cope with the global variations. Our experimental results with classical and popular music show that our algorithm performs successfully even in the presence of significant musical variations.

The architecture of visual narrative comprehension: the interaction of narrative structure and page layout in understanding comics.

PubMed

Cohn, Neil

2014-01-01

How do people make sense of the sequential images in visual narratives like comics? A growing literature of recent research has suggested that this comprehension involves the interaction of multiple systems: The creation of meaning across sequential images relies on a "narrative grammar" that packages conceptual information into categorical roles organized in hierarchic constituents. These images are encapsulated into panels arranged in the layout of a physical page. Finally, how panels frame information can impact both the narrative structure and page layout. Altogether, these systems operate in parallel to construct the Gestalt whole of comprehension of this visual language found in comics.

ENGINES: exploring single nucleotide variation in entire human genomes.

PubMed

Amigo, Jorge; Salas, Antonio; Phillips, Christopher

2011-04-19

Next generation ultra-sequencing technologies are starting to produce extensive quantities of data from entire human genome or exome sequences, and therefore new software is needed to present and analyse this vast amount of information. The 1000 Genomes project has recently released raw data for 629 complete genomes representing several human populations through their Phase I interim analysis and, although there are certain public tools available that allow exploration of these genomes, to date there is no tool that permits comprehensive population analysis of the variation catalogued by such data. We have developed a genetic variant site explorer able to retrieve data for Single Nucleotide Variation (SNVs), population by population, from entire genomes without compromising future scalability and agility. ENGINES (ENtire Genome INterface for Exploring SNVs) uses data from the 1000 Genomes Phase I to demonstrate its capacity to handle large amounts of genetic variation (>7.3 billion genotypes and 28 million SNVs), as well as deriving summary statistics of interest for medical and population genetics applications. The whole dataset is pre-processed and summarized into a data mart accessible through a web interface. The query system allows the combination and comparison of each available population sample, while searching by rs-number list, chromosome region, or genes of interest. Frequency and FST filters are available to further refine queries, while results can be visually compared with other large-scale Single Nucleotide Polymorphism (SNP) repositories such as HapMap or Perlegen. ENGINES is capable of accessing large-scale variation data repositories in a fast and comprehensive manner. It allows quick browsing of whole genome variation, while providing statistical information for each variant site such as allele frequency, heterozygosity or FST values for genetic differentiation. Access to the data mart generating scripts and to the web interface is granted from http://spsmart.cesga.es/engines.php. © 2011 Amigo et al; licensee BioMed Central Ltd.

Cost-effective use of minicomputers to solve structural problems

NASA Technical Reports Server (NTRS)

Storaasli, O. O.; Foster, E. P.

1978-01-01

Minicomputers are receiving increased use throughout the aerospace industry. Until recently, their use focused primarily on process control and numerically controlled tooling applications, while their exposure to and the opportunity for structural calculations has been limited. With the increased availability of this computer hardware, the question arises as to the feasibility and practicality of carrying out comprehensive structural analysis on a minicomputer. This paper presents results on the potential for using minicomputers for structural analysis by (1) selecting a comprehensive, finite-element structural analysis system in use on large mainframe computers; (2) implementing the system on a minicomputer; and (3) comparing the performance of the minicomputers with that of a large mainframe computer for the solution to a wide range of finite element structural analysis problems.

Microbes as engines of ecosystem function: When does community structure enhance predictions of ecosystem processes?

DOE PAGES

Graham, Emily B.; Knelman, Joseph E.; Schindlbacher, Andreas; ...

2016-02-24

In this study, microorganisms are vital in mediating the earth’s biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: ‘When do we need to understand microbial community structure to accurately predict function?’ We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of processmore » rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.« less

Microbes as engines of ecosystem function: When does community structure enhance predictions of ecosystem processes?

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

Graham, Emily B.; Knelman, Joseph E.; Schindlbacher, Andreas

In this study, microorganisms are vital in mediating the earth’s biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: ‘When do we need to understand microbial community structure to accurately predict function?’ We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of processmore » rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.« less

Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?

PubMed Central

Graham, Emily B.; Knelman, Joseph E.; Schindlbacher, Andreas; Siciliano, Steven; Breulmann, Marc; Yannarell, Anthony; Beman, J. M.; Abell, Guy; Philippot, Laurent; Prosser, James; Foulquier, Arnaud; Yuste, Jorge C.; Glanville, Helen C.; Jones, Davey L.; Angel, Roey; Salminen, Janne; Newton, Ryan J.; Bürgmann, Helmut; Ingram, Lachlan J.; Hamer, Ute; Siljanen, Henri M. P.; Peltoniemi, Krista; Potthast, Karin; Bañeras, Lluís; Hartmann, Martin; Banerjee, Samiran; Yu, Ri-Qing; Nogaro, Geraldine; Richter, Andreas; Koranda, Marianne; Castle, Sarah C.; Goberna, Marta; Song, Bongkeun; Chatterjee, Amitava; Nunes, Olga C.; Lopes, Ana R.; Cao, Yiping; Kaisermann, Aurore; Hallin, Sara; Strickland, Michael S.; Garcia-Pausas, Jordi; Barba, Josep; Kang, Hojeong; Isobe, Kazuo; Papaspyrou, Sokratis; Pastorelli, Roberta; Lagomarsino, Alessandra; Lindström, Eva S.; Basiliko, Nathan; Nemergut, Diana R.

2016-01-01

Microorganisms are vital in mediating the earth’s biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: ‘When do we need to understand microbial community structure to accurately predict function?’ We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology. PMID:26941732

Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?

PubMed

Graham, Emily B; Knelman, Joseph E; Schindlbacher, Andreas; Siciliano, Steven; Breulmann, Marc; Yannarell, Anthony; Beman, J M; Abell, Guy; Philippot, Laurent; Prosser, James; Foulquier, Arnaud; Yuste, Jorge C; Glanville, Helen C; Jones, Davey L; Angel, Roey; Salminen, Janne; Newton, Ryan J; Bürgmann, Helmut; Ingram, Lachlan J; Hamer, Ute; Siljanen, Henri M P; Peltoniemi, Krista; Potthast, Karin; Bañeras, Lluís; Hartmann, Martin; Banerjee, Samiran; Yu, Ri-Qing; Nogaro, Geraldine; Richter, Andreas; Koranda, Marianne; Castle, Sarah C; Goberna, Marta; Song, Bongkeun; Chatterjee, Amitava; Nunes, Olga C; Lopes, Ana R; Cao, Yiping; Kaisermann, Aurore; Hallin, Sara; Strickland, Michael S; Garcia-Pausas, Jordi; Barba, Josep; Kang, Hojeong; Isobe, Kazuo; Papaspyrou, Sokratis; Pastorelli, Roberta; Lagomarsino, Alessandra; Lindström, Eva S; Basiliko, Nathan; Nemergut, Diana R

2016-01-01

Microorganisms are vital in mediating the earth's biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: 'When do we need to understand microbial community structure to accurately predict function?' We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.

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

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

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

2014-02-14

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

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

PubMed

Steenbergen, K G; Gaston, N

2014-02-14

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

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

PubMed

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

2009-07-01

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

ERP Evidence for the Activation of Syntactic Structure During Comprehension of Lexical Idiom.

PubMed

Zhang, Meichao; Lu, Aitao; Song, Pingfang

2017-10-01

The present study used event-related potentials to investigate whether the syntactic structure was activated in the comprehension of lexical idioms, and if so, whether it varied as a function of familiarity and semantic transparency. Participants were asked to passively read the "1+2" structural Chinese lexical idioms with each being presented following 3-5 contextual "1+2" (congruent-structure condition) or "2+1" structural Chinese phrases (incongruent-structure condition). The N400 ERP responses showed more positivity in congruent-structure condition relative to incongruent-structure condition in idioms with high familiarity and high semantic transparency, but less positivity in congruent-structure condition in idioms with high familiarity but low semantic transparency, idioms with low familiarity but high semantic transparency, and idioms with low familiarity and low semantic transparency. Our results suggest that syntactic structure, as the unnecessarity of lexical idiomatic words, was nevertheless activated, independent of familiarity and semantic transparency.

Novel origins of copy number variation in the dog genome

PubMed Central

2012-01-01

Background Copy number variants (CNVs) account for substantial variation between genomes and are a major source of normal and pathogenic phenotypic differences. The dog is an ideal model to investigate mutational mechanisms that generate CNVs as its genome lacks a functional ortholog of the PRDM9 gene implicated in recombination and CNV formation in humans. Here we comprehensively assay CNVs using high-density array comparative genomic hybridization in 50 dogs from 17 dog breeds and 3 gray wolves. Results We use a stringent new method to identify a total of 430 high-confidence CNV loci, which range in size from 9 kb to 1.6 Mb and span 26.4 Mb, or 1.08%, of the assayed dog genome, overlapping 413 annotated genes. Of CNVs observed in each breed, 98% are also observed in multiple breeds. CNVs predicted to disrupt gene function are significantly less common than expected by chance. We identify a significant overrepresentation of peaks of GC content, previously shown to be enriched in dog recombination hotspots, in the vicinity of CNV breakpoints. Conclusions A number of the CNVs identified by this study are candidates for generating breed-specific phenotypes. Purifying selection seems to be a major factor shaping structural variation in the dog genome, suggesting that many CNVs are deleterious. Localized peaks of GC content appear to be novel sites of CNV formation in the dog genome by non-allelic homologous recombination, potentially activated by the loss of PRDM9. These sequence features may have driven genome instability and chromosomal rearrangements throughout canid evolution. PMID:22916802

Culture History and Population Heterogeneity as Determinants of Bacterial Adaptation: the Adaptomics of a Single Environmental Transition

PubMed Central

Ryall, Ben; Eydallin, Gustavo

2012-01-01

Summary: Diversity in adaptive responses is common within species and populations, especially when the heterogeneity of the frequently large populations found in environments is considered. By focusing on events in a single clonal population undergoing a single transition, we discuss how environmental cues and changes in growth rate initiate a multiplicity of adaptive pathways. Adaptation is a comprehensive process, and stochastic, regulatory, epigenetic, and mutational changes can contribute to fitness and overlap in timing and frequency. We identify culture history as a major determinant of both regulatory adaptations and microevolutionary change. Population history before a transition determines heterogeneities due to errors in translation, stochastic differences in regulation, the presence of aged, damaged, cheating, or dormant cells, and variations in intracellular metabolite or regulator concentrations. It matters whether bacteria come from dense, slow-growing, stressed, or structured states. Genotypic adaptations are history dependent due to variations in mutation supply, contingency gene changes, phase variation, lateral gene transfer, and genome amplifications. Phenotypic adaptations underpin genotypic changes in situations such as stress-induced mutagenesis or prophage induction or in biofilms to give a continuum of adaptive possibilities. Evolutionary selection additionally provides diverse adaptive outcomes in a single transition and generally does not result in single fitter types. The totality of heterogeneities in an adapting population increases the chance that at least some individuals meet immediate or future challenges. However, heterogeneity complicates the adaptomics of single transitions, and we propose that subpopulations will need to be integrated into future population biology and systems biology predictions of bacterial behavior. PMID:22933562

The Many Facets and Applications of Text Structure in Supporting Educational Trajectories of Elementary and Middle Grade Children in Content Area Reading Comprehension and Writing

ERIC Educational Resources Information Center

Albro, Elizabeth; Williams, Joanna P.; Wijekumar, Kausalai; Meyer, Bonnie J. F.; Harris, Karen R.

2015-01-01

Content area reading comprehension and writing have been a challenge for children in the U.S. schools for many years as evidenced by state and national assessments. One promising solution to the problem is text structure based instruction that promotes strategic selection, encoding, retrieval, and use of information for myriads of activities…

Odor and odorous chemical emissions from animal buildings: Part 2. Odor emissions

USDA-ARS?s Scientific Manuscript database

This study was an add-on project to the National Air Emissions Monitoring Study (NAEMS) and focused on comprehensive measurement of odor emissions considering variations in seasons, animal types and olfactometry laboratories. Odor emissions from four of 14 NEAMS sites with nine barns/rooms (two dair...

Assessing the Quality of Expertise Differences in the Comprehension of Medical Visualizations

ERIC Educational Resources Information Center

Gegenfurtner, Andreas; Siewiorek, Anna; Lehtinen, Erno; Saljo, Roger

2013-01-01

Understanding how best to assess expertise, the situational variations of expertise, and distinctive qualities of expertise that arises from particular workplace experiences, presents an important challenge. Certainly, at this time, there is much interest in identifying standard occupational measures and competences, which are not well aligned…

Measure the color distribution of a cotton sample using image analysis

USDA-ARS?s Scientific Manuscript database

The most commonly used measurement of cotton color is by the colorimeter principal that reports the sample’s color grade. However, the color distribution and variation within the sample are not reported. Obtaining color distributions of cotton samples will enable a more comprehensive evaluation of...

Factors that Contribute to Child Maltreatment Severity: A Multi-Method and Multidimensional Investigation

ERIC Educational Resources Information Center

Sprang, G.; Clark, J.J.; Bass, S.

2005-01-01

Objectives:: This study used data gathered during evaluations conducted by the Comprehensive Assessment and Training Services (CATS) Project to determine the relative contribution of four primary domains (demographic, adult characteristics, child characteristics, relational characteristics) to variation in the severity of child maltreatment, and…

The Qualifications of Teachers in American High Schools.

ERIC Educational Resources Information Center

Pascal, Anthony

This monograph describes the formal qualifications of the teachers currently teaching in public high schools and notes the variations of qualifications among schools with different characteristics. A survey of an average of 30 randomly selected teachers in each of 340 comprehensive high schools obtained information on: (1) the number of college…

The Present Perfect in World Englishes

ERIC Educational Resources Information Center

Yao, Xinyue; Collins, Peter

2012-01-01

This paper reports on a comprehensive corpus-based study of regional and stylistic variation in the distribution of the English present perfect. The data represents ten English varieties of both the Inner Circle and Outer Circle, covering four major text types: conversation, news reportage, academic and fictional writing. The results are discussed…

Identification, quantitation, and comprehensive assessment of green, white, and pu-erh teas using UPLC/UV/MS

USDA-ARS?s Scientific Manuscript database

Tea (Camellia sinensis L.), an important drink and a traditional medicine for thousands of years, contains many compounds of potential benefit to health. Growing season, geographic region, and fermentation method create many variations in tea composition, which contributes to the unique characteris...

Teaching English Metaphors Using Cross-Linguistic Awareness-Raising Activities.

ERIC Educational Resources Information Center

Deignan, A.; Gabrys, D.; Solska, A.

1997-01-01

Reports on a translation exercise undertaken by Polish learners of English which revealed how metaphorical expressions vary between the two languages and how this variation confuses learners. Suggests that group discussion and comparison of metaphors in both languages will increase students' comprehension and use of metaphors. (nine references)…

High-throughput genotyping of hop (Humulus lupulus L.) utilising diversity arrays technology (DArT)

USDA-ARS?s Scientific Manuscript database

Implementation of molecular methods in hop breeding is dependent on the availability of sizeable numbers of polymorphic markers and a comprehensive understanding of genetic variation. Diversity Arrays Technology (DArT) is a high-throughput cost-effective method for the discovery of large numbers of...

Comprehensive lake dynamics mapping at continental scales using Landsat 8

USDA-ARS?s Scientific Manuscript database

Inland lakes, important water resources, play a crucial role in the global water cycle and are sensitive to global warming and human activities. There clearly is a pressing need to understand temporal and spatial variations of lakes at global and continental scales. The recent operation of Landsat...

On the Treatment of Authors, Outliers, and Purchasing Power Parity Exchange Rates.

ERIC Educational Resources Information Center

Jaeger, Richard M.

1993-01-01

Ruth Stott violates canons of scholarly debate by attacking author's October 1992 "Kappan" article on world-class academic standards. Average class size predicted only 10% of variation in 13 year-olds' mean mathematics scores in 14 nations supplying reasonable comprehensive sampling frames for International Assessment of Academic…

Observing Consistency in Online Communication Patterns for User Re-Identification

PubMed Central

Venter, Hein S.

2016-01-01

Comprehension of the statistical and structural mechanisms governing human dynamics in online interaction plays a pivotal role in online user identification, online profile development, and recommender systems. However, building a characteristic model of human dynamics on the Internet involves a complete analysis of the variations in human activity patterns, which is a complex process. This complexity is inherent in human dynamics and has not been extensively studied to reveal the structural composition of human behavior. A typical method of anatomizing such a complex system is viewing all independent interconnectivity that constitutes the complexity. An examination of the various dimensions of human communication pattern in online interactions is presented in this paper. The study employed reliable server-side web data from 31 known users to explore characteristics of human-driven communications. Various machine-learning techniques were explored. The results revealed that each individual exhibited a relatively consistent, unique behavioral signature and that the logistic regression model and model tree can be used to accurately distinguish online users. These results are applicable to one-to-one online user identification processes, insider misuse investigation processes, and online profiling in various areas. PMID:27918593

Chromosome Nomenclature and Cytological Characterization of Sacred Lotus.

PubMed

Meng, Zhuang; Hu, Xiaoxu; Zhang, Zhiliang; Li, Zhanjie; Lin, Qingfang; Yang, Mei; Yang, Pingfang; Ming, Ray; Yu, Qingyi; Wang, Kai

2017-01-01

Sacred lotus is a basal eudicot plant that has been cultivated in Asia for over 7,000 years for its agricultural, ornamental, religious, and medicinal importance. A notable characteristic of lotus is the seed longevity. Extensive endeavors have been devoted to dissect its genome assembly, including the variety China Antique, which germinated from a 1,300-year-old seed. Here, cytogenetic markers representing the 10 largest megascaffolds, which constitute approximately 70% of the lotus genome assembly, were developed. These 10 megascaffolds were then anchored to the corresponding lotus chromosomes by fluorescence in situ hybridization using these cytogenetic markers, and a set of chromosome-specific cytogenetic markers that could unambiguously identify each of the 8 chromosomes was generated. Karyotyping was conducted, and a nomenclature based on chromosomal length was established for the 8 chromosomes of China Antique. Comparative karyotyping revealed relatively conserved chromosomal structures between China Antique and 3 modern cultivars. Interestingly, significant variations in the copy number of 45S rDNA were detected between China Antique and modern cultivars. Our results provide a comprehensive view on the chromosomal structure of sacred lotus and will facilitate further studies and the genome assembly of lotus. © 2018 S. Karger AG, Basel.

Phytoplankton variability and community structure in relation to hydrographic features in the NE Aegean frontal area (NE Mediterranean Sea)

NASA Astrophysics Data System (ADS)

Lagaria, A.; Mandalakis, M.; Mara, P.; Frangoulis, C.; Karatsolis, B.-Th.; Pitta, P.; Triantaphyllou, M.; Tsiola, A.; Psarra, S.

2017-10-01

The structure of phytoplankton community in the salinity-stratified Northeastern Aegean frontal area adjacent to the Dardanelles Straits was investigated on a seasonal basis (autumn, spring and summer) and in relation to circulating water masses: the modified Black Sea Water (BSW) and the Levantine Water (LW). By employing High Performance Liquid Chromatography (HPLC) for the analysis of phytoplankton pigments in conjunction with conventional cell counting methodologies (i.e. inverted light microscopy, flow cytometry) and primary production measurements, a comprehensive qualitative and quantitative characterization of phytoplankton community composition and its activity was conducted. Chlorophyll-a normalized production and estimated growth rates presented the highest values within the 'fresh' BSW mass during summer, though generally growth rates were low (<0.4 d-1) at all seasons. The spatiotemporal variation of BSW outflow was found to greatly affect the relative contribution of pico-, nano- and micro-phytoplankton to total phytoplankton biomass and production. Large cell organisms, and in particular diatoms, were closely associated with the surface BSW masses outflowing from the Straits. Our results showed that all phytoplankton size components were significant over time and space suggesting a rather multivorous food web functioning of the system.

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

USDA-ARS?s Scientific Manuscript database

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

Host-associated differences in morphometric traits of parasitic larvae Hirsutiella zachvatkini (Actinotrichida: Trombiculidae).

PubMed

Moniuszko, Hanna; Zaleśny, Grzegorz; Mąkol, Joanna

2015-09-01

Examination of host-associated variation in the chigger mite Hirsutiella zachvatkini (Schluger) revealed morphological differences among larvae infesting sympatric hosts: Apodemus agrarius, Apodemus flavicollis and Myodes glareolus. The analysis included 61 variables of larvae obtained from their gnathosoma, idiosoma and legs (measurements and counts). Statistically significant differences were observed for metric characters of the legs as opposed to the scutum. In view of the conspecificity of the mites, supported by comparison of COI gene products obtained from larvae and laboratory-reared deutonymphs, the observed variation is attributed to phenotypic plasticity. The knowledge of larval morphology, including intraspecific variation of metric characters, supported by molecular and host range data, places H. zachvatkini among the most comprehensively defined members of Trombiculidae.

Variational data assimilation for tropospheric chemistry modeling

NASA Astrophysics Data System (ADS)

Elbern, Hendrik; Schmidt, Hauke; Ebel, Adolf

1997-07-01

The method of variational adjoint data assimilation has been applied to assimilate chemistry observations into a comprehensive tropospheric gas phase model. The rationale of this method is to find the correct initial values for a subsequent atmospheric chemistry model run when observations scattered in time are available. The variational adjoint technique is esteemed to be a promising tool for future advanced meteorological forecasting. The stimulating experience gained with the application of four-dimensional variational data assimilation in this research area has motivated the attempt to apply the technique to air quality modeling and analysis of the chemical state of the atmosphere. The present study describes the development and application of the adjoint of the second-generation regional acid deposition model gas phase mechanism, which is used in the European air pollution dispersion model system. Performance results of the assimilation scheme using both model-generated data and real observations are presented for tropospheric conditions. In the former case it is demonstrated that time series of only few or even one measured key species convey sufficient information to improve considerably the analysis of unobserved species which are directly coupled with the observed species. In the latter case a Lagrangian approach is adopted where trajectory calculations between two comprehensively furnished measurement sites are carried out. The method allows us to analyze initial data for air pollution modeling even when only sparse observations are available. Besides remarkable improvements of the model performance by properly analyzed initial concentrations, it is shown that the adjoint algorithm offers the feasibility to estimate the sensitivity of ozone concentrations relative to its precursors.

Disparity in Dental Coverage Among Older Adult Populations: A Comparative Analysis Across Selected European Countries and the United States

PubMed Central

Manski, Richard; Moeller, John; Chen, Haiyan; Widström, Eeva; Lee, Jinkook; Listl, Stefan

2014-01-01

Background Insurance against the cost risks associated with prevention and treatment of oral diseases can reduce inequalities in dental care use and oral health. The purpose of this study was to examine the extent of variation in dental insurance coverage for older adult populations within and between the United States and various European countries. Method The analyses relied on 2006/2007 data from the Survey of Health, Ageing, and Retirement in Europe (SHARE) and 2004-2006 data from of the Health and Retirement Study (HRS) in the United States for respondents aged 51 years and older. A series of logistic regression models was estimated to identify disparities in dental coverage. Results The highest extent of significant insurance differences between various population subgroups was found for the United States. In comparison with countries belonging to the Eastern and Southern welfare state regimes, a lower number of significant coverage differences occurred for Scandinavian countries. Countries categorized as having comprehensive public insurance coverage showed a tendency towards less insurance variation within their populations than countries categorized as not having comprehensive public coverage, exceptions being Poland and Switzerland. Conclusions The findings of the present study suggest that significant variations in dental coverage exist within all elderly populations examined and the extent of inequalities also differs between countries. By and large, the observed variations corroborate the perception that population dental coverage is more equally distributed under public subsidy. This could be relevant information for decision makers who seek to improve policies towards more equitable dental coverage. PMID:25363376

Sex-biased survival predicts adult sex ratio variation in wild birds

PubMed Central

Székely, Tamás; Liker, András; Freckleton, Robert P.; Fichtel, Claudia; Kappeler, Peter M.

2014-01-01

Adult sex ratio (ASR) is a central concept in population demography and breeding system evolution, and has implications for population viability and biodiversity conservation. ASR exhibits immense interspecific variation in wild populations, although the causes of this variation have remained elusive. Using phylogenetic analyses of 187 avian species from 59 families, we show that neither hatching sex ratios nor fledging sex ratios correlate with ASR. However, sex-biased adult mortality is a significant predictor of ASR, and this relationship is robust to 100 alternative phylogenetic hypotheses, and potential ecological and life-history confounds. A significant component of adult mortality bias is sexual selection acting on males, whereas increased reproductive output predicts higher mortality in females. These results provide the most comprehensive insights into ASR variation to date, and suggest that ASR is an outcome of selective processes operating differentially on adult males and females. Therefore, revealing the causes of ASR variation in wild populations is essential for understanding breeding systems and population dynamics. PMID:24966308

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

PubMed

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

2016-03-01

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

Effect of basement structure and salt tectonics on deformation styles along strike: An example from the Kuqa fold-thrust belt, West China

NASA Astrophysics Data System (ADS)

Neng, Yuan; Xie, Huiwen; Yin, Hongwei; Li, Yong; Wang, Wei

2018-04-01

The Kuqa fold-thrust belt (KFTB) has a complex thrust-system geometry and comprises basement-involved thrusts, décollement thrusts, triangle zones, strike-slip faults, transpressional faults, and pop-up structures. These structures, combined with the effects of Paleogene salt tectonics and Paleozoic basement uplift form a complex structural zone trending E-W. Interpretation and comprehensive analysis of recent high-quality seismic data, field observations, boreholes, and gravity data covering the KFTB has been performed to understand the characteristics and mechanisms of the deformation styles along strike. Regional sections, fold-thrust system maps of the surface and the sub-salt layer, salt and basement structure distribution maps have been created, and a comprehensive analysis of thrust systems performed. The results indicate that the thrust-fold system in Paleogene salt range can be divided into five segments from east to west: the Kela-3, Keshen, Dabei, Bozi, and Awate segments. In the easternmost and westernmost parts of the Paleogene salt range, strike-slip faulting and basement-involved thrusting are the dominant deformation styles, as basement uplift and the limits of the Cenozoic evaporite deposit are the main controls on deformation. Salt-core detachment fold-thrust systems coincide with areas of salt tectonics, and pop-up, imbricate, and duplex structures are associated with the main thrust faults in the sub-salt layer. Distribution maps of thrust systems, basement structures, and salt tectonics show that Paleozoic basement uplift controlled the Paleozoic foreland basin morphology and the distribution of Cenozoic salt in the KFTB, and thus had a strong influence on the segmented structural deformation and evolution of the fold-thrust belt. Three types of transfer zone are identified, based on the characteristics of the salt layer and basement uplift, and the effects of these zones on the fault systems are evaluated. Basement uplift and the boundary of the salt deposit generated strike-slip faults in the sub-salt layer and supra-salt layers at the basin boundary (Model A). When changes in the basement occurred within the salt basin, strike-slip faults controlled the deformation styles in the sub-salt layer and shear-zone dominated in the supra-salt layer (Model B). A homogeneous basement and discontinues salt layer formed different accommodation zones in the sub- and supra-salt layers (Model C). In the sub-salt layer the thrusts form imbricate structures on the basal décollement, whereas the supra-salt layer shows overlapping, discontinuous faults and folds with kinds of salt tectonics, and has greater structural variation than the sub-salt layer.

DOMMINO 2.0: integrating structurally resolved protein-, RNA-, and DNA-mediated macromolecular interactions

PubMed Central

Kuang, Xingyan; Dhroso, Andi; Han, Jing Ginger; Shyu, Chi-Ren; Korkin, Dmitry

2016-01-01

Macromolecular interactions are formed between proteins, DNA and RNA molecules. Being a principle building block in macromolecular assemblies and pathways, the interactions underlie most of cellular functions. Malfunctioning of macromolecular interactions is also linked to a number of diseases. Structural knowledge of the macromolecular interaction allows one to understand the interaction’s mechanism, determine its functional implications and characterize the effects of genetic variations, such as single nucleotide polymorphisms, on the interaction. Unfortunately, until now the interactions mediated by different types of macromolecules, e.g. protein–protein interactions or protein–DNA interactions, are collected into individual and unrelated structural databases. This presents a significant obstacle in the analysis of macromolecular interactions. For instance, the homogeneous structural interaction databases prevent scientists from studying structural interactions of different types but occurring in the same macromolecular complex. Here, we introduce DOMMINO 2.0, a structural Database Of Macro-Molecular INteractiOns. Compared to DOMMINO 1.0, a comprehensive database on protein-protein interactions, DOMMINO 2.0 includes the interactions between all three basic types of macromolecules extracted from PDB files. DOMMINO 2.0 is automatically updated on a weekly basis. It currently includes ∼1 040 000 interactions between two polypeptide subunits (e.g. domains, peptides, termini and interdomain linkers), ∼43 000 RNA-mediated interactions, and ∼12 000 DNA-mediated interactions. All protein structures in the database are annotated using SCOP and SUPERFAMILY family annotation. As a result, protein-mediated interactions involving protein domains, interdomain linkers, C- and N- termini, and peptides are identified. Our database provides an intuitive web interface, allowing one to investigate interactions at three different resolution levels: whole subunit network, binary interaction and interaction interface. Database URL: http://dommino.org PMID:26827237

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

NASA Astrophysics Data System (ADS)

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

2018-06-01

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

The architecture of visual narrative comprehension: the interaction of narrative structure and page layout in understanding comics

PubMed Central

Cohn, Neil

2014-01-01

How do people make sense of the sequential images in visual narratives like comics? A growing literature of recent research has suggested that this comprehension involves the interaction of multiple systems: The creation of meaning across sequential images relies on a “narrative grammar” that packages conceptual information into categorical roles organized in hierarchic constituents. These images are encapsulated into panels arranged in the layout of a physical page. Finally, how panels frame information can impact both the narrative structure and page layout. Altogether, these systems operate in parallel to construct the Gestalt whole of comprehension of this visual language found in comics. PMID:25071651

A genomic perspective on the generation and maintenance of genetic diversity in herbivorous insects

PubMed Central

Gloss, Andrew D.; Groen, Simon C.; Whiteman, Noah K.

2017-01-01

Understanding the processes that generate and maintain genetic variation within populations is a central goal in evolutionary biology. Theory predicts that some of this variation is maintained as a consequence of adapting to variable habitats. Studies in herbivorous insects have played a key role in confirming this prediction. Here, we highlight theoretical and conceptual models for the maintenance of genetic diversity in herbivorous insects, empirical genomic studies testing these models, and pressing questions within the realm of evolutionary and functional genomic studies. To address key gaps, we propose an integrative approach combining population genomic scans for adaptation, genome-wide characterization of targets of selection through experimental manipulations, mapping the genetic architecture of traits influencing fitness, and functional studies. We also stress the importance of studying the maintenance of genetic variation across biological scales—from variation within populations to divergence among populations—to form a comprehensive view of adaptation in herbivorous insects. PMID:28736510

Selection and phenotypic characterization of a core collection of Brachypodium distachyon inbred lines.

PubMed

Tyler, Ludmila; Fangel, Jonatan U; Fagerström, Alexandra Dotson; Steinwand, Michael A; Raab, Theodore K; Willats, William Gt; Vogel, John P

2014-01-14

The model grass Brachypodium distachyon is increasingly used to study various aspects of grass biology. A large and genotypically diverse collection of B. distachyon germplasm has been assembled by the research community. The natural variation in this collection can serve as a powerful experimental tool for many areas of inquiry, including investigating biomass traits. We surveyed the phenotypic diversity in a large collection of inbred lines and then selected a core collection of lines for more detailed analysis with an emphasis on traits relevant to the use of grasses as biofuel and grain crops. Phenotypic characters examined included plant height, growth habit, stem density, flowering time, and seed weight. We also surveyed differences in cell wall composition using near infrared spectroscopy (NIR) and comprehensive microarray polymer profiling (CoMPP). In all cases, we observed extensive natural variation including a two-fold variation in stem density, four-fold variation in ferulic acid bound to hemicellulose, and 1.7-fold variation in seed mass. These characterizations can provide the criteria for selecting diverse lines for future investigations of the genetic basis of the observed phenotypic variation.

The structural conversion from α-AgVO3 to β-AgVO3: Ag nanoparticle decorated nanowires with application as cathode materials for Li-ion batteries.

PubMed

McNulty, David; Ramasse, Quentin; O'Dwyer, Colm

2016-09-15

The majority of electrode materials in batteries and related electrochemical energy storage devices are fashioned into slurries via the addition of a conductive additive and a binder. However, aggregation of smaller diameter nanoparticles in current generation electrode compositions can result in non-homogeneous active materials. Inconsistent slurry formulation may lead to inconsistent electrical conductivity throughout the material, local variations in electrochemical response, and the overall cell performance. Here we demonstrate the hydrothermal preparation of Ag nanoparticle (NP) decorated α-AgVO 3 nanowires (NWs) and their conversion to tunnel structured β-AgVO 3 NWs by annealing to form a uniform blend of intercalation materials that are well connected electrically. The synthesis of nanostructures with chemically bound conductive nanoparticles is an elegant means to overcome the intrinsic issues associated with electrode slurry production, as wire-to-wire conductive pathways are formed within the overall electrode active mass of NWs. The conversion from α-AgVO 3 to β-AgVO 3 is explained in detail through a comprehensive structural characterization. Meticulous EELS analysis of β-AgVO 3 NWs offers insight into the true β-AgVO 3 structure and how the annealing process facilitates a higher surface coverage of Ag NPs directly from ionic Ag content within the α-AgVO 3 NWs. Variations in vanadium oxidation state across the surface of the nanowires indicate that the β-AgVO 3 NWs have a core-shell oxidation state structure, and that the vanadium oxidation state under the Ag NP confirms a chemically bound NP from reduction of diffused ionic silver from the α-AgVO 3 NWs core material. Electrochemical comparison of α-AgVO 3 and β-AgVO 3 NWs confirms that β-AgVO 3 offers improved electrochemical performance. An ex situ structural characterization of β-AgVO 3 NWs after the first galvanostatic discharge and charge offers new insight into the Li + reaction mechanism for β-AgVO 3 . Ag + between the van der Waals layers of the vanadium oxide is reduced during discharge and deposited as metallic Ag, the vacant sites are then occupied by Li + .

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

Measurement invariance across Genders on the Childhood Illness Attitude Scales (CIAS).

PubMed

Thorisdottir, Audur S; Villadsen, Anna; LeBouthillier, Daniel M; Rask, Charlotte Ulrikka; Wright, Kristi D; Walker, John R; Feldgaier, Steven; Asmundson, Gordon J G

2017-07-01

The Childhood Illness Attitude Scales (CIAS) were created as a developmentally appropriate measure for symptoms of health anxiety (HA) in school-aged children. Despite overall sound psychometric properties reported in previous studies, more comprehensive examination of the latent structure and potential response bias in the CIAS is needed. The purpose of the present study was to cross-validate the latent structure of the CIAS across genders and to examine gender-specific variations in CIAS scores. The sample comprised data from 602 Canadian and Danish school-aged children (M age =10.54, SD=0.99; 52.5% girls). Confirmatory factor analyses were conducted to test 3-, modified 3-, and 4-factor models in both samples. Multigroup confirmatory factor analysis was performed to test factor structure invariance across boys and girls in a combined sample. Differential Item Functioning (DIF) was assessed using test characteristic curves. A modified 3-factor solution (i.e., fears=11 items, help-seeking=6 items, and symptom effects=4 items) provided the best fit to the data (χ 2 (364, N=602)=681.7, p<0.001; χ 2 /df=1.803; RMSEA=0.037; CFI=0.926). The factor structure was stable, well-fitting, and indicated measurement invariance across groups. DIF analyses revealed no gender-based response bias at the scale level. Results support a revised 3-factor version of the CIAS that can be used with confidence to assess symptoms of HA in school-aged boys and girls. Copyright © 2017 Elsevier Inc. All rights reserved.

Mesoscale Eddies in the Northwestern Pacific Ocean: Three-Dimensional Eddy Structures and Heat/Salt Transports

NASA Astrophysics Data System (ADS)

Dong, Di; Brandt, Peter; Chang, Ping; Schütte, Florian; Yang, Xiaofeng; Yan, Jinhui; Zeng, Jisheng

2017-12-01

The region encompassing the Kuroshio Extension (KE) in the Northwestern Pacific Ocean (25°N-45°N and 130°E-180°E) is one of the most eddy-energetic regions of the global ocean. The three-dimensional structures and transports of mesoscale eddies in this region are comprehensively investigated by combined use of satellite data and Argo profiles. With the allocation of Argo profiles inside detected eddies, the spatial variations of structures of eddy temperature and salinity anomalies are analyzed. The results show that eddies predominantly have subsurface (near-surface) intensified temperature and salinity anomalies south (north) of the KE jet, which is related to different background stratifications between these regions. A new method based on eddy trajectories and the inferred three-dimensional eddy structures is proposed to estimate heat and salt transports by eddy movements in a Lagrangian framework. Spatial distributions of eddy transports are presented over the vicinity of the KE for the first time. The magnitude of eddy-induced meridional heat (freshwater volume) transport is on the order of 0.01 PW (103 m3/s). The eddy heat transport divergence results in an oceanic heat loss south and heat gain north of the KE, thereby reinforcing and counteracting the oceanic heat loss from air-sea fluxes south and north of the KE jet, respectively. It also suggests a poleward heat transport across the KE jet due to eddy propagation.

Reading, Comprehension, and Memory Processes: Abstracts of Doctoral Dissertations Published in "Dissertation Abstracts International," July through September 1977 (Vol. 38 Nos. 1 through 3).

ERIC Educational Resources Information Center

ERIC Clearinghouse on Reading and Communication Skills, Urbana, IL.

This collection of abstracts is part of a continuing series providing information on recent doctoral dissertations. The 14 titles deal with the following topics: children's ability to read their own dictated oral language; adjunct structure and reading comprehension; learning and comprehension of simultaneously presented stimuli in children of…

Transposon Insertions, Structural Variations, and SNPs Contribute to the Evolution of the Melon Genome.

PubMed

Sanseverino, Walter; Hénaff, Elizabeth; Vives, Cristina; Pinosio, Sara; Burgos-Paz, William; Morgante, Michele; Ramos-Onsins, Sebastián E; Garcia-Mas, Jordi; Casacuberta, Josep Maria

2015-10-01

The availability of extensive databases of crop genome sequences should allow analysis of crop variability at an unprecedented scale, which should have an important impact in plant breeding. However, up to now the analysis of genetic variability at the whole-genome scale has been mainly restricted to single nucleotide polymorphisms (SNPs). This is a strong limitation as structural variation (SV) and transposon insertion polymorphisms are frequent in plant species and have had an important mutational role in crop domestication and breeding. Here, we present the first comprehensive analysis of melon genetic diversity, which includes a detailed analysis of SNPs, SV, and transposon insertion polymorphisms. The variability found among seven melon varieties representing the species diversity and including wild accessions and highly breed lines, is relatively high due in part to the marked divergence of some lineages. The diversity is distributed nonuniformly across the genome, being lower at the extremes of the chromosomes and higher in the pericentromeric regions, which is compatible with the effect of purifying selection and recombination forces over functional regions. Additionally, this variability is greatly reduced among elite varieties, probably due to selection during breeding. We have found some chromosomal regions showing a high differentiation of the elite varieties versus the rest, which could be considered as strongly selected candidate regions. Our data also suggest that transposons and SV may be at the origin of an important fraction of the variability in melon, which highlights the importance of analyzing all types of genetic variability to understand crop genome evolution. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

A mobile threat to genome stability: The impact of non-LTR retrotransposons upon the human genome.

PubMed

Konkel, Miriam K; Batzer, Mark A

2010-08-01

It is now commonly agreed that the human genome is not the stable entity originally presumed. Deletions, duplications, inversions, and insertions are common, and contribute significantly to genomic structural variations (SVs). Their collective impact generates much of the inter-individual genomic diversity observed among humans. Not only do these variations change the structure of the genome; they may also have functional implications, e.g. altered gene expression. Some SVs have been identified as the cause of genetic disorders, including cancer predisposition. Cancer cells are notorious for their genomic instability, and often show genomic rearrangements at the microscopic and submicroscopic level to which transposable elements (TEs) contribute. Here, we review the role of TEs in genome instability, with particular focus on non-LTR retrotransposons. Currently, three non-LTR retrotransposon families - long interspersed element 1 (L1), SVA (short interspersed element (SINE-R), variable number of tandem repeats (VNTR), and Alu), and Alu (a SINE) elements - mobilize in the human genome, and cause genomic instability through both insertion- and post-insertion-based mutagenesis. Due to the abundance and high sequence identity of TEs, they frequently mislead the homologous recombination repair pathway into non-allelic homologous recombination, causing deletions, duplications, and inversions. While less comprehensively studied, non-LTR retrotransposon insertions and TE-mediated rearrangements are probably more common in cancer cells than in healthy tissue. This may be at least partially attributed to the commonly seen global hypomethylation as well as general epigenetic dysfunction of cancer cells. Where possible, we provide examples that impact cancer predisposition and/or development. Copyright © 2010 Elsevier Ltd. All rights reserved.

The spatial coherence structure of infrasonic waves: analysis of data from International Monitoring System arrays

NASA Astrophysics Data System (ADS)

Green, David N.

2015-04-01

The spatial coherence structure of 30 infrasound array detections, with source-to-receiver ranges of 25-6500 km, has been measured within the 0.25-1 Hz passband. The data were recorded at International Monitoring System (IMS) microbarograph arrays with apertures of between 1 and 4 km. Such array detections are of interest for Comprehensive Nuclear-Test-Ban Treaty monitoring. The majority of array detections (e.g. 80 per cent of recordings in the third-octave passband centred on 0.63 Hz) exhibit spatial coherence loss anisotropy that is consistent with previous lower frequency atmospheric acoustic studies; coherence loss is more rapid perpendicular to the acoustic propagation direction than parallel to it. The thirty array detections display significant interdetection variation in the magnitude of spatial coherence loss. The measurements can be explained by the simultaneous arrival of wave fronts at the recording array with angular beamwidths of between 0.4 and 7° and velocity bandwidths of between 2 and 40 m s-1. There is a statistically significant positive correlation between source-to-receiver range and the magnitude of coherence loss. Acoustic multipathing generated by interactions with fine-scale wind and temperature gradients along stratospheric propagation paths is qualitatively consistent with the observations. In addition, the study indicates that to isolate coherence loss generated by propagation effects, analysis of signals exhibiting high signal-to-noise ratios (SNR) is required (SNR2 > 11 in this study). The rapid temporal variations in infrasonic noise observed in recordings at IMS arrays indicates that correcting measured coherence values for the effect of noise, using pre-signal estimates of noise power, is ineffective.

Wide-ranging phylogeographic structure of invasive red lionfish in the Western Atlantic and Greater Caribbean

USGS Publications Warehouse

Butterfield, John S.; Díaz-Ferguson, Edgardo; Silliman, Brian R.; Saunders, Jonathan W.; Buddo, Dayne; Mignucci-Giannoni, Antonio A.; Searle, Linda; Allen, Aarin Conrad; Hunter, Margaret E.

2015-01-01

The red lionfish (Pterois volitans) is an invasive predatory marine fish that has rapidly expanded its presence in the Western Hemisphere. We collected 214 invasive red lionfish samples from nine countries and territories, including seven unpublished locations. To more comprehensively evaluate connectivity, we compiled our d-loop sequence data with 846 published sequences, resulting in 1,060 samples from 14 locations. We found low nucleotide diversity (π = 0.003) and moderate haplotype diversity (h = 0.59). Using haplotype population pairwise ΦST tests, we analyzed possible phylogeographic breaks that were previously proposed based on other reef organisms. We found support for the Bahamas/Turks/Caicos versus Caribbean break (ΦST = 0.12) but not for the Northwestern Caribbean, Eastern Caribbean, or US East Coast versus Bahamas breaks. The Northern Region had higher variation and more haplotypes, supporting introductions of at least five haplotypes to the region. Our wide-ranging samples showed that a lower-frequency haplotype in the Northern Region dominated the Southern Region and suggested multiple introductions, possibly to the south. We tested multiple scenarios of phylogeographic structure with analyses of molecular variance and found support for a Northern and Southern Region split at the Bahamas/Turks/Caicos versus Caribbean break (percentage of variation among regions = 8.49 %). We found that Puerto Rico clustered with the Southern Region more strongly than with the Northern Region, as opposed to previous reports. We also found the rare haplotype H03 for the first time in the southern Caribbean (Panama), indicating that either secondary releases occurred or that the low-frequency haplotypes have had time to disperse to extreme southern Caribbean locations.

Unravelling the architecture of functional variability in wild populations of Polygonum viviparum L

PubMed Central

Boucher, Florian C.; Thuiller, Wilfried; Arnoldi, Cindy; Albert, Cécile H.; Lavergne, Sébastien

2014-01-01

SUMMARY Functional variability (FV) of populations can be decomposed into three main features: the individual variability of multiple traits, the strength of correlations between those traits and the main direction of these correlations, the latter two being known as ‘phenotypic integration’. Evolutionary biology has long recognized that FV in natural populations is key to determining potential evolutionary responses, but this topic has been little studied in functional ecology. Here we focus on the arctico-alpine perennial plant species Polygonum viviparum L.. We used a comprehensive sampling of seven functional traits in 29 wild populations covering the whole environmental niche of the species. The niche of the species was captured by a temperature gradient, which separated alpine stressful habitats from species-rich, competitive sub-alpine ones. We seeked to assess the relative roles of abiotic stress and biotic interactions in shaping different aspects of functional variation within and among populations, that is, the multi-trait variability, the strength of correlations between traits, and the main directions of functional trade-offs. Populations with the highest extent of functional variability were found in the warm end of the gradient whereas populations exhibiting the strongest degree of phenotypic integration were located in sites with intermediate temperatures. This could reveal both the importance of environmental filtering and population demography in structuring FV. Interestingly, we found that the main axes of multivariate functional variation were radically different within and across population. Although the proximate causes of FV structure remain uncertain, our study presents a robust methodology for the quantitative study of functional variability in connection with species’ niches. It also opens up new perspectives for the conceptual merging of intraspecific functional patterns with community ecology. PMID:24790285

Studies on cattle genomic structural variation provide insights into ruminant speciation and adaptation

USDA-ARS?s Scientific Manuscript database

Genomic structural variations, including segmental duplications (SD) and copy number variations (CNV), contribute significantly to individual health and disease in primates and rodents. As a part of the bovine genome annotation effort, we performed the first genome-wide analysis of SD in cattle usin...

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

EPA Science Inventory

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

The history of the CATH structural classification of protein domains.

PubMed

Sillitoe, Ian; Dawson, Natalie; Thornton, Janet; Orengo, Christine

2015-12-01

This article presents a historical review of the protein structure classification database CATH. Together with the SCOP database, CATH remains comprehensive and reasonably up-to-date with the now more than 100,000 protein structures in the PDB. We review the expansion of the CATH and SCOP resources to capture predicted domain structures in the genome sequence data and to provide information on the likely functions of proteins mediated by their constituent domains. The establishment of comprehensive function annotation resources has also meant that domain families can be functionally annotated allowing insights into functional divergence and evolution within protein families. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Utilization of Optimization for Design of Morphing Wing Structures for Enhanced Flight

NASA Astrophysics Data System (ADS)

Detrick, Matthew Scott

Conventional aircraft control surfaces constrain maneuverability. This work is a comprehensive study that looks at both smart material and conventional actuation methods to achieve wing twist to potentially improve flight capability using minimal actuation energy while allowing minimal wing deformation under aerodynamic loading. A continuous wing is used in order to reduce drag while allowing the aircraft to more closely approximate the wing deformation used by birds while loitering. The morphing wing for this work consists of a skin supported by an underlying truss structure whose goal is to achieve a given roll moment using less actuation energy than conventional control surfaces. A structural optimization code has been written in order to achieve minimal wing deformation under aerodynamic loading while allowing wing twist under actuation. The multi-objective cost function for the optimization consists of terms that ensure small deformation under aerodynamic loading, small change in airfoil shape during wing twist, a linear variation of wing twist along the length of the wing, small deviation from the desired wing twist, minimal number of truss members, minimal wing weight, and minimal actuation energy. Hydraulic cylinders and a two member linkage driven by a DC motor are tested separately to provide actuation. Since the goal of the current work is simply to provide a roll moment, only one actuator is implemented along the wing span. Optimization is also used to find the best location within the truss structure for the actuator. The active structure produced by optimization is then compared to simulated and experimental results from other researchers as well as characteristics of conventional aircraft.

Two Decades of Structure Building

PubMed Central

Gernsbacher, Morton Ann

2014-01-01

During the past decade I have been developing a very simple framework for describing the cognitive processes and mechanisms involved in discourse comprehension. I call this framework the Structure Building Framework, and it is based on evidence provided during the first decade of discourse processing research. According to the Structure Building Framework, the goal of comprehension is to build coherent mental representations or structures. Comprehenders build each structure by first laying a foundation. Comprehenders develop mental structures by mapping on new information when that information coheres or relates to previous information. However, when the incoming information is less related, comprehenders shift and attach a new substructure. The building blocks of mental structures are memory nodes, which are activated by incoming stimuli and controlled by two cognitive mechanisms: suppression and enhancement. In this article, first I review the seminal work on which the Structure Building Framework is based (the first decade of structure building research); then I recount the research I have conducted to test the Structure Building Framework (the second decade of structure building research). PMID:25484476

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

Herman, Michael F.; Currier, Robert Patrick; Clegg, Samuel M.

The impact of isotopic variation on the electronic energy and intermolecular potentials is often suppressed when calculating isotopologue thermodynamics. Intramolecular potential energy surfaces for distinct isotopologues are in fact equivalent under the Born–Oppenheimer approximation, which is sometimes used to imply that the intermolecular interactions are independent of isotopic mass. In this paper, the intermolecular dipole–dipole interaction between hetero-nuclear diatomic molecules is considered. It is shown that the intermolecular potential contains mass-dependent terms even though each nucleus moves on a Born–Oppenheimer surface. Finally, the analysis suggests that mass dependent variations in intermolecular potentials should be included in comprehensive descriptions of isotopologuemore » thermodynamics.« less

A Variational Assimilation Method for Satellite and Conventional Data: Development of Basic Model for Diagnosis of Cyclone Systems

NASA Technical Reports Server (NTRS)

Achtemeier, Gary L.; Scott, Robert W.; Chen, J.

1991-01-01

A summary is presented of the progress toward the completion of a comprehensive diagnostic objective analysis system based upon the calculus of variations. The approach was to first develop the objective analysis subject to the constraints that the final product satisfies the five basic primitive equations for a dry inviscid atmosphere: the two nonlinear horizontal momentum equations, the continuity equation, the hydrostatic equation, and the thermodynamic equation. Then, having derived the basic model, there would be added to it the equations for moist atmospheric processes and the radiative transfer equation.

EcoTurf - a case study: genetic variation and agronomic potential of bermudagrass (Cynodon spp.) germplasm collected from Australian biodiversity

USDA-ARS?s Scientific Manuscript database

Australian Cynodon germplasm has not been comprehensively exploited for bermudagrass improvement. In this paper we will describe ‘EcoTurf’ a four year (2007-2011) project to develop water and nutrient use efficient bermudagrasses from Australian biodiversity. We describe the sampling strategies of A...

Higher-Order Activity beyond the Word Level: Cortical Dynamics of Simple Transitive Sentence Comprehension

ERIC Educational Resources Information Center

Martin-Loeches, M.; Casado, P.; Hinojosa, J.A.; Carretie, L.; Munoz, F.; Pozo, M.A.

2005-01-01

Slow electrophysiological effects, which fluctuate throughout the course of a sentence, independent of transient responses to individual words, have been reported. However, this type of activity has scarcely been studied, and with only limited use of electrophysiological information, so that the brain areas in which these variations originate have…

How the Size of Our Social Network Influences Our Semantic Skills

ERIC Educational Resources Information Center

Lev-Ari, Shiri

2016-01-01

People differ in the size of their social network, and thus in the properties of the linguistic input they receive. This article examines whether differences in social network size influence individuals' linguistic skills in their native language, focusing on global comprehension of evaluative language. Study 1 exploits the natural variation in…

Reading Rate, Readability and Variations in Task-Induced Processing.

ERIC Educational Resources Information Center

Coke, Esther U.

This study examined the adaptability of reading rate to passage difficulty under different conditions of task-induced processing. Sixteen experimental passages varying in subject matter and ranging from 85 to 171 words were selected from a set of 32 texts rated for comprehensibility. The eight easiest and eight hardest texts were selected. Another…

Are Patient-Administered Attention Deficit Hyperactivity Disorder Scales Suitable for Adults?

ERIC Educational Resources Information Center

Rogers, Edwin S.; Spalding, Steven L.; Eckard, Alexis A.; Wallace, Lorraine S.

2009-01-01

Objective: This primary purpose of this study was to examine cognitive complexity and readability of patient-administered ADHD scales. The secondary purpose was to estimate variation in readability of individual ADHD scale items. Method: Using comprehensive search strategies, we identified eight English-language ADHD scales for inclusion in our…

Rapid Automatized Naming and Reading Performance: A Meta-Analysis

ERIC Educational Resources Information Center

Araújo, Susana; Reis, Alexandra; Petersson, Karl Magnus; Faísca, Luís

2015-01-01

Evidence that rapid naming skill is associated with reading ability has become increasingly prevalent in recent years. However, there is considerable variation in the literature concerning the magnitude of this relationship. The objective of the present study was to provide a comprehensive analysis of the evidence on the relationship between rapid…

Rurality/Urbanism and Extended Familism Among Working- and Lower-Class Blacks.

ERIC Educational Resources Information Center

Dietrich, Katheryn Thomas

A comprehensive look is taken at the rural-urban variation in extended familism among a segment of the population for which extended familism purportedly is especially salient: lower and working class black Americans. The study is guided by the general hypothesis that rurality/urbanism affects extended familism when nonecological variables are…

The Neural Mechanisms of Word Order Processing Revisited: Electrophysiological Evidence from Japanese

ERIC Educational Resources Information Center

Wolff, Susann; Schlesewsky, Matthias; Hirotani, Masako; Bornkessel-Schlesewsky, Ina

2008-01-01

We present two ERP studies on the processing of word order variations in Japanese, a language that is suited to shedding further light on the implications of word order freedom for neurocognitive approaches to sentence comprehension. Experiment 1 used auditory presentation and revealed that initial accusative objects elicit increased processing…

Climate-related genetic variation in drought-resistance of Douglas-fir ( Pseudotsuga menziesii )

Treesearch

Sheel Bansal; Constance A. Harrington; Peter J. Gould; J. Bradley St.Clair

2014-01-01

There is a general assumption that intraspecific populations originating from relatively arid climates will be better adapted to cope with the expected increase in drought from climate change. For ecologically and economically important species, more comprehensive, genecological studies that utilize large distributions of populations and direct measures of traits...

Geographic Variations in Public Schools' Costs. Working Paper Series.

ERIC Educational Resources Information Center

Chambers, Jay G.

This report addresses the following question: How much more or less does it cost to provide the same levels of educational resources across different geographic locations in the United States? To answer this question, the report develops a comprehensive geographic cost-of-education index (GCEI) that focuses on the prices of inputs (personnel and…

Think Globally: Cross-Linguistic Variation in Electrophysiological Activity during Sentence Comprehension

ERIC Educational Resources Information Center

Bornkessel-Schlesewsky, Ina; Kretzschmar, Franziska; Tune, Sarah; Wang, Luming; Genc, Safiye; Philipp, Markus; Roehm, Dietmar; Schlesewsky, Matthias

2011-01-01

This paper demonstrates systematic cross-linguistic differences in the electrophysiological correlates of conflicts between form and meaning ("semantic reversal anomalies"). These engender P600 effects in English and Dutch (e.g. [Kolk et al., 2003] and [Kuperberg et al., 2003]), but a biphasic N400--late positivity pattern in German (Schlesewsky…

Mentally Simulating Narrative Perspective Is Not Universal or Necessary for Language Comprehension

ERIC Educational Resources Information Center

Brunyé, Tad T.; Ditman, Tali; Giles, Grace E.; Holmes, Amanda; Taylor, Holly A.

2016-01-01

Readers differentially adopt an agent's perspective as a function of pronouns encountered during reading. The present study assessed the reliability of this effect across narrative contexts and self-reported variation in levels of engagement during reading. Experiment 1 used an extended sample (N = 263) and replicated an interactive influence of…

Genome re-sequencing reveals the history of apple and supports a two-stage model for fruit enlargement

USDA-ARS?s Scientific Manuscript database

Human selection has reshaped crop genomes. Here we report an apple genome variation map generated through genome sequencing of 117 diverse accessions. A comprehensive model of apple speciation and domestication along the Silk Road was proposed based on evidence from diverse genomic analyses. Cultiva...

The New Institutional Governance of Italian State Universities: What Role for the New Governing Bodies?

ERIC Educational Resources Information Center

Donina, Davide; Meoli, Michele; Paleari, Stefano

2015-01-01

In 2010, a comprehensive reform required Italian state universities to restructure their institutional governance by revising their statutes. This interpretative paper aims to evaluate whether the Italian reform is congruent with its declarations, examine the variations in the implementation within the same country of a unitary national regulation…

QTL meta-analysis provides a comprehensive view of loci controlling partial resistance to Aphanomyces euteiches in four sources of resistance in pea

USDA-ARS?s Scientific Manuscript database

More knowledge about diversity of Quantitative Trait Loci (QTL) controlling polygenic disease resistance in natural genetic variation of crop species is required for durably improving plant genetic resistances to pathogens. Polygenic partial resistance to Aphanomyces root rot, due to Aphanomcyces eu...

Using Meta-Analysis to Explain Variation in Head Start Research Results: The Role of Research Design

ERIC Educational Resources Information Center

Shager, Hilary M.; Schindler, Holly S.; Hart, Cassandra M.D.; Duncan, Greg J.; Magnuson, Katherine A.; Yoshikawa, Hirokazu

2010-01-01

Head Start was designed as a holistic intervention to improve economically disadvantaged, preschool-aged children's cognitive and social development by providing a comprehensive set of educational, health, nutritional, and social services, as well as opportunities for parent involvement (Zigler & Valentine, 1979). Given the current interest in ECE…

Neuroanatomically Separable Effects of Imageability and Grammatical Class during Single-Word Comprehension

ERIC Educational Resources Information Center

Bedny, Marina; Thompson-Schill, Sharon L.

2006-01-01

The present study characterizes the neural correlates of noun and verb imageability and addresses the question of whether components of the neural network supporting word recognition can be separately modified by variations in grammatical class and imageability. We examined the effect of imageability on BOLD signal during single-word comprehension…

Competition, Anxiety, and Depression in the College Classroom: Variations by Student Identity and Field of Study

ERIC Educational Resources Information Center

Posselt, Julie R.; Lipson, Sarah Ketchen

2016-01-01

In light of rising academic stress and an increase in diagnosed mental illnesses among adolescents and young adults, this article offers the first comprehensive analysis of relationships between perceived competition and depression/anxiety among college students. Analyses were conducted by using clinically validated instruments for depression and…

Variations in the Recruitment of Syntactic Knowledge Contribute to SES Differences in Syntactic Development

ERIC Educational Resources Information Center

Leech, Kathryn A.; Rowe, Meredith L.; Huang, Yi Ting

2017-01-01

Average differences in children's language abilities by socioeconomic status (SES) emerge early in development and predict academic achievement. Previous research has focused on coarse-grained outcome measures such as vocabulary size, but less is known about the extent to which SES differences exist in children's strategies for comprehension and…

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

NASA Astrophysics Data System (ADS)

Sharapov, A. A.

2015-09-01

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

Apical root resorption in patients treated with comprehensive orthodontics.

PubMed

Harris, E F; Boggan, B W; Wheeler, D A

2001-01-01

External apical root resorption (EARR) is a common--but seldom extreme--consequence of orthodontic treatment. Incisors are most at risk, perhaps because of their single roots and because they typically are moved farther than other teeth. We followed a cohort of patients (n = 153) treated with comprehensive orthodontics. EARR was scored on the upper incisors with a qualitative five-grade ordinal scale. There was no EARR at the start of treatment, but most (> 80%) exhibited slight-to-moderate EARR by the end of treatment (i.e., a loss of 1-2 mm). Cases treated with premolar extractions experienced more EARR because their incisors were retracted farther; however, the sum of the effects of patients' sex and age, and severity of the malocclusion, and the kind of mechanics used accounts for little of the overall variation in EARR. Instead, it appears that genetically-based inter-individual variation in susceptibility to EARR is the most influential factor. Research should be directed at understanding the biochemical nature of susceptibility so prospective patients can be screened to identify those at particular risk.

Structural crossover from nonmodulated to long-period modulated tetragonal phase and anomalous change in ferroelectric properties in the lead-free piezoelectric N a1 /2B i1 /2Ti O3-BaTi O3

NASA Astrophysics Data System (ADS)

Rao, Badari Narayana; Khatua, Dipak Kumar; Garg, Rohini; Senyshyn, Anatoliy; Ranjan, Rajeev

2015-06-01

The highly complex structure-property interrelationship in the lead-free piezoelectric (x )N a1 /2B i1 /2Ti O3- (1 -x ) BaTi O3 is a subject of considerable contemporary debate. Using comprehensive x-ray, neutron diffraction, dielectric, and ferroelectric studies, we have shown the existence of a new criticality in this system at x =0.80 , i.e., well within the conventional tetragonal phase field. This criticality manifests as a nonmonotonic variation of the tetragonality and coercivity and is shown to be associated with a crossover from a nonmodulated tetragonal phase (for x <0.8 ) to a long-period modulated tetragonal phase (for x >0.80 ). It is shown that the stabilization of long-period modulation introduces a characteristic depolarization temperature in the system. While differing qualitatively from the two-phase model often suggested for the critical compositions of this system, our results support the view with regard to the tendency in perovskites to stabilize long-period modulated structures as a result of complex interplay of antiferrodistortive modes [Bellaiche and Iniguez, Phys. Rev. B 88, 014104 (2013), 10.1103/PhysRevB.88.014104; Prosandeev, Wang, Ren, Iniguez, ands Bellaiche, Adv. Funct. Mater. 23, 234 (2013), 10.1002/adfm.201201467].

High Throughput Biodegradation-Screening Test To Prioritize and Evaluate Chemical Biodegradability.

PubMed

Martin, Timothy J; Goodhead, Andrew K; Acharya, Kishor; Head, Ian M; Snape, Jason R; Davenport, Russell J

2017-06-20

Comprehensive assessment of environmental biodegradability of pollutants is limited by the use of low throughput systems. These are epitomized by the Organisation for Economic Cooperation and Development (OECD) Ready Biodegradability Tests (RBTs), where one sample from an environment may be used to assess a chemical's ability to readily biodegrade or persist universally in that environment. This neglects the considerable spatial and temporal microbial variation inherent in any environment. Inaccurate designations of biodegradability or persistence can occur as a result. RBTs are central in assessing the biodegradation fate of chemicals and inferring exposure concentrations in environmental risk assessments. We developed a colorimetric assay for the reliable quantification of suitable aromatic compounds in a high throughput biodegradation screening test (HT-BST). The HT-BST accurately differentiated and prioritized a range of structurally diverse aromatic compounds on the basis of their assigned relative biodegradabilities and quantitative structure-activity relationship (QSAR) model outputs. Approximately 20 000 individual biodegradation tests were performed, returning analogous results to conventional RBTs. The effect of substituent group structure and position on biodegradation potential demonstrated a significant correlation (P < 0.05) with Hammett's constant for substituents on position 3 of the phenol ring. The HT-BST may facilitate the rapid screening of 100 000 chemicals reportedly manufactured in Europe and reduce the need for higher-tier fate and effects tests.

Novel serine-based gemini surfactants as chemical permeation enhancers of local anesthetics: A comprehensive study on structure-activity relationships, molecular dynamics and dermal delivery.

PubMed

Teixeira, Raquel S; Cova, Tânia F G G; Silva, Sérgio M C; Oliveira, Rita; do Vale, M Luísa C; Marques, Eduardo F; Pais, Alberto A C C; Veiga, Francisco J B

2015-06-01

This work aims at studying the efficacy of a series of novel biocompatible, serine-based surfactants as chemical permeation enhancers for two different local anesthetics, tetracaine and ropivacaine, combining an experimental and computational approach. The surfactants consist of gemini molecules structurally related, but with variations in headgroup charge (nonionic vs. cationic) and in the hydrocarbon chain lengths (main and spacer chains). In vitro permeation and molecular dynamics studies combined with cytotoxicity profiles were performed to investigate the permeation of both drugs, probe skin integrity, and rationalize the interactions at molecular level. Results show that these enhancers do not have significant deleterious effects on the skin structure and do not cause relevant changes on cell viability. Permeation across the skin is clearly improved using some of the selected serine-based gemini surfactants, namely the cationic ones with long alkyl chains and shorter spacer. This is noteworthy in the case of ropivacaine hydrochloride, which is not easily administered through the stratum corneum. Molecular dynamics results provide a mechanistic view of the surfactant action on lipid membranes that essentially corroborate the experimental observations. Overall, this study suggests the viability of these serine-based surfactants as suitable and promising delivery agents in pharmaceutical formulations. Copyright © 2015. Published by Elsevier B.V.

Premaxillary crest variation within the Wukongopteridae (Reptilia, Pterosauria) and comments on cranial structures in pterosaurs.

PubMed

Cheng, Xin; Jiang, Shunxing; Wang, Xiaolin; Kellner, Alexander W A

2017-01-01

Cranial crests show considerable variation within the Pterosauria, a group of flying reptiles that developed powered flight. This includes the Wukongopteridae, a clade of non-pterodactyloids, where the presence or absence of such head structures, allied with variation in the pelvic canal, have been regarded as evidence for sexual dimorphism. Here we discuss the cranial crest variation within wukongopterids and briefly report on a new specimen (IVPP V 17957). We also show that there is no significant variation in the anatomy of the pelvis of crested and crestless specimens. We further revisit the discussion regarding the function of cranial structures in pterosaurs and argue that they cannot be dismissed a priori as a valuable tool for species recognition.

ComprehensiveBench: a Benchmark for the Extensive Evaluation of Global Scheduling Algorithms

NASA Astrophysics Data System (ADS)

Pilla, Laércio L.; Bozzetti, Tiago C.; Castro, Márcio; Navaux, Philippe O. A.; Méhaut, Jean-François

2015-10-01

Parallel applications that present tasks with imbalanced loads or complex communication behavior usually do not exploit the underlying resources of parallel platforms to their full potential. In order to mitigate this issue, global scheduling algorithms are employed. As finding the optimal task distribution is an NP-Hard problem, identifying the most suitable algorithm for a specific scenario and comparing algorithms are not trivial tasks. In this context, this paper presents ComprehensiveBench, a benchmark for global scheduling algorithms that enables the variation of a vast range of parameters that affect performance. ComprehensiveBench can be used to assist in the development and evaluation of new scheduling algorithms, to help choose a specific algorithm for an arbitrary application, to emulate other applications, and to enable statistical tests. We illustrate its use in this paper with an evaluation of Charm++ periodic load balancers that stresses their characteristics.

Direct and mediated effects of language and cognitive skills on comprehension of oral narrative texts (listening comprehension) for children.

PubMed

Kim, Young-Suk Grace

2016-01-01

We investigated component language and cognitive skills of oral language comprehension of narrative texts (i.e., listening comprehension). Using the construction-integration model of text comprehension as an overarching theoretical framework, we examined direct and mediated relations of foundational cognitive skills (working memory and attention), foundational language skills (vocabulary and grammatical knowledge), and higher-order cognitive skills (inference, theory of mind, and comprehension monitoring) to listening comprehension. A total of 201 first grade children in South Korea participated in the study. Structural equation modeling results showed that listening comprehension is directly predicted by working memory, grammatical knowledge, inference, and theory of mind and is indirectly predicted by attention, vocabulary, and comprehension monitoring. The total effects were .46 for working memory, .07 for attention, .30 for vocabulary, .49 for grammatical knowledge, .31 for inference, .52 for theory of mind, and .18 for comprehension monitoring. These results suggest that multiple language and cognitive skills make contributions to listening comprehension, and their contributions are both direct and indirect. Copyright © 2015 Elsevier Inc. All rights reserved.

Comprehensive design of omnidirectional high-performance perovskite solar cells

PubMed Central

Zhang, Yutao; Xuan, Yimin

2016-01-01

The comprehensive design approach is established with coupled optical-electrical simulation for perovskite-based solar cell, which emerged as one of the most promising competitors to silicon solar cell for its low-cost fabrication and high PCE. The selection of structured surface, effect of geometry parameters, incident angle-dependence and polarization-sensitivity are considered in the simulation. The optical modeling is performed via the finite-difference time-domain method whilst the electrical properties are obtained by solving the coupled nonlinear equations of Poisson, continuity, and drift-diffusion equations. The optical and electrical performances of five different structured surfaces are compared to select a best structured surface for perovskite solar cell. The effects of the geometry parameters on the optical and electrical properties of the perovskite cell are analyzed. The results indicate that the light harvesting is obviously enhanced by the structured surface. The electrical performance can be remarkably improved due to the enhanced light harvesting of the designed best structured surface. The angle-dependence for s- and p-polarizations is investigated. The structured surface exhibits omnidirectional behavior and favorable polarization-insensitive feature within a wide incident angle range. Such a comprehensive design approach can highlight the potential of perovskite cell for power conversion in the full daylight. PMID:27405419

Comprehensive design of omnidirectional high-performance perovskite solar cells.

PubMed

Zhang, Yutao; Xuan, Yimin

2016-07-13

The comprehensive design approach is established with coupled optical-electrical simulation for perovskite-based solar cell, which emerged as one of the most promising competitors to silicon solar cell for its low-cost fabrication and high PCE. The selection of structured surface, effect of geometry parameters, incident angle-dependence and polarization-sensitivity are considered in the simulation. The optical modeling is performed via the finite-difference time-domain method whilst the electrical properties are obtained by solving the coupled nonlinear equations of Poisson, continuity, and drift-diffusion equations. The optical and electrical performances of five different structured surfaces are compared to select a best structured surface for perovskite solar cell. The effects of the geometry parameters on the optical and electrical properties of the perovskite cell are analyzed. The results indicate that the light harvesting is obviously enhanced by the structured surface. The electrical performance can be remarkably improved due to the enhanced light harvesting of the designed best structured surface. The angle-dependence for s- and p-polarizations is investigated. The structured surface exhibits omnidirectional behavior and favorable polarization-insensitive feature within a wide incident angle range. Such a comprehensive design approach can highlight the potential of perovskite cell for power conversion in the full daylight.

[Comprehensive weighted recognition method for hydrological abrupt change: With the runoff series of Jiajiu hydrological station in Lancang River as an example].

PubMed

Gu, Hai Ting; Xie, Ping; Sang, Yan Fang; Wu, Zi Yi

2018-04-01

Abrupt change is an important manifestation of hydrological process with dramatic variation in the context of global climate change, the accurate recognition of which has great significance to understand hydrological process changes and carry out the actual hydrological and water resources works. The traditional method is not reliable at both ends of the samples. The results of the methods are often inconsistent. In order to solve the problem, we proposed a comprehensive weighted recognition method for hydrological abrupt change based on weighting by comparing of 12 commonly used methods for testing change points. The reliability of the method was verified by Monte Carlo statistical test. The results showed that the efficiency of the 12 methods was influenced by the factors including coefficient of variation (Cv), deviation coefficient (Cs) before the change point, mean value difference coefficient, Cv difference coefficient and Cs difference coefficient, but with no significant relationship with the mean value of the sequence. Based on the performance of each method, the weight of each test method was given following the results from statistical test. The sliding rank sum test method and the sliding run test method had the highest weight, whereas the RS test method had the lowest weight. By this means, the change points with the largest comprehensive weight could be selected as the final result when the results of the different methods were inconsistent. This method was used to analyze the daily maximum sequence of Jiajiu station in the lower reaches of the Lancang River (1-day, 3-day, 5-day, 7-day and 1-month). The results showed that each sequence had obvious jump variation in 2004, which was in agreement with the physical causes of hydrological process change and water conservancy construction. The rationality and reliability of the proposed method was verified.

Comprehensive Characterization a Tidal Energy Site (Invited)

NASA Astrophysics Data System (ADS)

Polagye, B. L.; Thomson, J. M.; Bassett, C. S.; Epler, J.; Northwest National Marine Renewable Energy Center

2010-12-01

Northern Admiralty Inlet, Puget Sound, Washington is the proposed location of a pilot tidal energy project. Site-specific characterization of the physical and biological environment is required for device engineering and environmental analysis. However, the deep water and strong currents which make the site attractive for tidal energy development also pose unique challenges to collecting comprehensive information. This talk focuses on efforts to optimally site hydrokinetic turbines and estimate their acoustic impact, based on 18 months of field data collected to date. Additional characterization efforts being undertaken by the University of Washington branch of the Northwest National Marine Renewable Energy Center and its partners include marine mammal presence and behavior, water quality, seabed geology, and biofouling potential. Because kinetic power density varies with the cube of horizontal current velocity, an accurate map of spatial current variations is required to optimally site hydrokinetic turbines. Acoustic Doppler profilers deployed on the seabed show operationally meaningful variations in flow characteristics (e.g., power density, directionality, vertical shear) and tidal harmonic constituents over length scales of less than 100m. This is, in part, attributed to the proximity of this site to a headland. Because of these variations, interpolation between stationary measurement locations introduces potentially high uncertainty. The use of shipboard acoustic Doppler profilers is shown to be an effective tool for mapping peak currents and, combined with information from seabed profilers, may be able to resolve power density variations in the project area. Because noise levels from operating turbines are expected to exceed regulatory thresholds for incidental harassment of marine mammals known to be present in the project area, an estimate of the acoustic footprint is required to permit the pilot project. This requires site-specific descriptions of pre-existing ambient noise levels and the transmission loss (or practical spreading) at frequencies of interest. Recording hydrophones deployed on the seabed are used to quantify ambient noise, but are contaminated by self-noise during periods of strong currents. An empirical estimate of transmission loss is obtained from a source of opportunity - a passenger ferry which operates for more than twelve hours each day. By comparing recorded sound pressure levels against the location of the passenger ferry and other vessels (logged by an AIS receiver), the empirical transmission loss and source level for the ferry are obtained. Measurements of current velocity and underwater noise can apply routine oceanographic instruments and techniques. More unique measurements will be more challenging, such as high resolution sampling of current structure upstream and downstream of an operating device tens of meters off the seabed. Innovative approaches are required for cost effective characterization of tidal energy sites and monitoring of operating projects.

Structural Priming: A Critical Review

PubMed Central

Pickering, Martin J.; Ferreira, Victor S.

2009-01-01

Repetition is a central phenomenon of behavior, and researchers make extensive use of it to illuminate psychological functioning. In the language sciences, a ubiquitous form of such repetition is structural priming, a tendency to repeat or better process a current sentence because of its structural similarity to a previously experienced (“prime”) sentence (Bock, 1986). The recent explosion of research in structural priming has made it the dominant means of investigating the processes involved in the production (and increasingly, comprehension) of complex expressions such as sentences. This review considers its implications for the representation of syntax and the mechanisms of production, comprehension, and their relationship. It then addresses the potential functions of structural priming, before turning to its implications for first language acquisition, bilingualism, and aphasia We close with theoretical and empirical recommendations for future investigations. PMID:18444704

Subtelomeric Rearrangements and Copy Number Variations in People with Intellectual Disabilities

ERIC Educational Resources Information Center

Christofolini, D. M.; De Paula Ramos, M. A.; Kulikowski, L. D.; Da Silva Bellucco, F. T.; Belangero, S. I. N.; Brunoni, D.; Melaragno, M. I.

2010-01-01

Background: The most prevalent type of structural variation in the human genome is represented by copy number variations that can affect transcription levels, sequence, structure and function of genes. Method: In the present study, we used the multiplex ligation-dependent probe amplification (MLPA) technique and quantitative PCR for the detection…

The Effects of Environmental Characteristics on the Structure of Hospital Clusters.

ERIC Educational Resources Information Center

Fennell, Mary L.

1980-01-01

The population ecology view that variation in sets or clusters of organizations should be isomorphic with variation in cluster environment was used to explain structural variation among hospital clusters. Cluster differentiation seems to be casually affected by range of services, average hospital size, and the periodic closing of hospitals.…

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

PubMed

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

2015-03-01

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

Microbial community functional structures in wastewater treatment plants as characterized by GeoChip.

PubMed

Wang, Xiaohui; Xia, Yu; Wen, Xianghua; Yang, Yunfeng; Zhou, Jizhong

2014-01-01

Biological WWTPs must be functionally stable to continuously and steadily remove contaminants which rely upon the activity of complex microbial communities. However, knowledge is still lacking in regard to microbial community functional structures and their linkages to environmental variables. To investigate microbial community functional structures of activated sludge in wastewater treatment plants (WWTPs) and to understand the effects of environmental factors on their structure. 12 activated sludge samples were collected from four WWTPs in Beijing. A comprehensive functional gene array named GeoChip 4.2 was used to determine the microbial functional genes involved in a variety of biogeochemical processes such as carbon, nitrogen, phosphorous and sulfur cycles, metal resistance, antibiotic resistance and organic contaminant degradation. High similarities of the microbial community functional structures were found among activated sludge samples from the four WWTPs, as shown by both diversity indices and the overlapped genes. For individual gene category, such as egl, amyA, lip, nirS, nirK, nosZ, ureC, ppx, ppk, aprA, dsrA, sox and benAB, there were a number of microorganisms shared by all 12 samples. Canonical correspondence analysis (CCA) showed that the microbial functional patterns were highly correlated with water temperature, dissolved oxygen (DO), ammonia concentrations and loading rate of chemical oxygen demand (COD). Based on the variance partitioning analyses (VPA), a total of 53% of microbial community variation from GeoChip data can be explained by wastewater characteristics (25%) and operational parameters (23%), respectively. This study provided an overall picture of microbial community functional structures of activated sludge in WWTPs and discerned the linkages between microbial communities and environmental variables in WWTPs.

Promote quantitative ischemia imaging via myocardial perfusion CT iterative reconstruction with tensor total generalized variation regularization

NASA Astrophysics Data System (ADS)

Gu, Chengwei; Zeng, Dong; Lin, Jiahui; Li, Sui; He, Ji; Zhang, Hao; Bian, Zhaoying; Niu, Shanzhou; Zhang, Zhang; Huang, Jing; Chen, Bo; Zhao, Dazhe; Chen, Wufan; Ma, Jianhua

2018-06-01

Myocardial perfusion computed tomography (MPCT) imaging is commonly used to detect myocardial ischemia quantitatively. A limitation in MPCT is that an additional radiation dose is required compared to unenhanced CT due to its repeated dynamic data acquisition. Meanwhile, noise and streak artifacts in low-dose cases are the main factors that degrade the accuracy of quantifying myocardial ischemia and hamper the diagnostic utility of the filtered backprojection reconstructed MPCT images. Moreover, it is noted that the MPCT images are composed of a series of 2/3D images, which can be naturally regarded as a 3/4-order tensor, and the MPCT images are globally correlated along time and are sparse across space. To obtain higher fidelity ischemia from low-dose MPCT acquisitions quantitatively, we propose a robust statistical iterative MPCT image reconstruction algorithm by incorporating tensor total generalized variation (TTGV) regularization into a penalized weighted least-squares framework. Specifically, the TTGV regularization fuses the spatial correlation of the myocardial structure and the temporal continuation of the contrast agent intake during the perfusion. Then, an efficient iterative strategy is developed for the objective function optimization. Comprehensive evaluations have been conducted on a digital XCAT phantom and a preclinical porcine dataset regarding the accuracy of the reconstructed MPCT images, the quantitative differentiation of ischemia and the algorithm’s robustness and efficiency.

Whole genome sequences in pulse crops: a global community resource to expedite translational genomics and knowledge-based crop improvement.

PubMed

Bohra, Abhishek; Singh, Narendra P

2015-08-01

Unprecedented developments in legume genomics over the last decade have resulted in the acquisition of a wide range of modern genomic resources to underpin genetic improvement of grain legumes. The genome enabled insights direct investigators in various ways that primarily include unearthing novel structural variations, retrieving the lost genetic diversity, introducing novel/exotic alleles from wider gene pools, finely resolving the complex quantitative traits and so forth. To this end, ready availability of cost-efficient and high-density genotyping assays allows genome wide prediction to be increasingly recognized as the key selection criterion in crop breeding. Further, the high-dimensional measurements of agronomically significant phenotypes obtained by using new-generation screening techniques will empower reference based resequencing as well as allele mining and trait mapping methods to comprehensively associate genome diversity with the phenome scale variation. Besides stimulating the forward genetic systems, accessibility to precisely delineated genomic segments reveals novel candidates for reverse genetic techniques like targeted genome editing. The shifting paradigm in plant genomics in turn necessitates optimization of crop breeding strategies to enable the most efficient integration of advanced omics knowledge and tools. We anticipate that the crop improvement schemes will be bolstered remarkably with rational deployment of these genome-guided approaches, ultimately resulting in expanded plant breeding capacities and improved crop performance.

Interspecific variation in mitochondrial serine transfer RNA (UCN) in Euptychiina butterflies (Lepidoptera: Satyrinae): structure and alignment.

PubMed

Marín, Mario Alejandro; López, Andrés; Uribe, Sandra Inés

2012-06-01

The nucleotide variation and structural patterns of mitochondrial RNA molecule have been proposed as useful tools in molecular systematics; however, their usefulness is always subject to a proper assessment of homology in the sequence alignment. The present study describes the secondary structure of mitochondrial tRNA for the amino acid serine (UCN) on 13 Euptychiina species and the evaluation of its potential use for evolutionary studies in this group of butterflies. The secondary structure of tRNAs showed variation among the included species except between Hermeuptychia sp1 and sp2. Variation was concentrated in the ribotimidina-pseudouridine-cystosine (TψC), dihydrouridine (DHU) and variable loops and in the DHU and TψC arms. These results suggest this region as a potential marker useful for taxonomic differentiation of species in this group and also confirm the importance of including information from the secondary structure of tRNA to optimize the alignments.

Emergence of intercolonial variation in termite shelter tube patterns and prediction of its underlying mechanism

PubMed Central

2015-01-01

Building behaviours occur in various organisms from bacteria to humans. Social insects build various structures such as large nests and underground galleries, achieved by self-organization. Structures built by social insects have recently been demonstrated to vary widely in size and shape within a species, even under the same environmental conditions. However, little is known about how intraspecific variation in structures emerges from collective behaviours. Here we show that the colony variation of structures can be generated by simply changing two behavioural parameters of group members, even with the same building algorithm. Our laboratory experiment of termite shelter tube construction demonstrated clear intercolonial variation, and a two-dimensional lattice model showed that it can be attributed to the extent of positive feedback and the number of individuals engaged in building. This study contributes to explaining the great diversity of structures emerging from collective building in social insects. PMID:26715997

Advanced in-line metrology strategy for self-aligned quadruple patterning

NASA Astrophysics Data System (ADS)

Chao, Robin; Breton, Mary; L'herron, Benoit; Mendoza, Brock; Muthinti, Raja; Nelson, Florence; De La Pena, Abraham; Le, Fee li; Miller, Eric; Sieg, Stuart; Demarest, James; Gin, Peter; Wormington, Matthew; Cepler, Aron; Bozdog, Cornel; Sendelbach, Matthew; Wolfling, Shay; Cardinal, Tom; Kanakasabapathy, Sivananda; Gaudiello, John; Felix, Nelson

2016-03-01

Self-Aligned Quadruple Patterning (SAQP) is a promising technique extending the 193-nm lithography to manufacture structures that are 20nm half pitch or smaller. This process adopts multiple sidewall spacer image transfers to split a rather relaxed design into a quarter of its original pitch. Due to the number of multiple process steps required for the pitch splitting in SAQP, the process error propagates through each deposition and etch, and accumulates at the final step into structure variations, such as pitch walk and poor critical dimension uniformity (CDU). They can further affect the downstream processes and lower the yield. The impact of this error propagation becomes significant for advanced technology nodes when the process specifications of device design CD requirements are at nanometer scale. Therefore, semiconductor manufacturing demands strict in-line process control to ensure a high process yield and improved performance, which must rely on precise measurements to enable corrective actions and quick decision making for process development. This work aims to provide a comprehensive metrology solution for SAQP. During SAQP process development, the challenges in conventional in-line metrology techniques start to surface. For instance, critical-dimension scanning electron microscopy (CDSEM) is commonly the first choice for CD and pitch variation control. However, it is found that the high aspect ratio at mandrel level processes and the trench variations after etch prevent the tool from extracting the true bottom edges of the structure in order to report the position shift. On the other hand, while the complex shape and variations can be captured with scatterometry, or optical CD (OCD), the asymmetric features, such as pitch walk, show low sensitivity with strong correlations in scatterometry. X-ray diffraction (XRD) is known to provide useful direct measurements of the pitch walk in crystalline arrays, yet the data analysis is influenced by the incoming geometry and must be used carefully. A successful implementation of SAQP process control for yield improvement requires the metrology issues to be addressed. By optimizing the measurement parameters and beam configurations, CDSEM measurements distinguish each of the spaces corresponding to the upstream mandrel processes and report their CDs separately to feed back to the process team for the next development cycle. We also utilize the unique capability in scatterometry to measure the structure details in-line and implement a "predictive" process control, which shows a good correlation between the "predictive" measurement and the cross-sections from our design of experiments (DOE). The ability to measure the pitch walk in scatterometry was also demonstrated. This work also explored the frontier of in-line XRD capability by enabling an automatic RSM fitting on tool to output pitch walk values. With these advances in metrology development, we are able to demonstrate the impacts of in-line monitoring in the SAQP process, to shorten the patterning development learning cycle to improve the yield.

Polarized light imaging of birefringence and diattenuation at high resolution and high sensitivity

PubMed Central

Mehta, Shalin B.; Shribak, Michael; Oldenbourg, Rudolf

2013-01-01

Polarized light microscopy provides unique opportunities for analyzing the molecular order in man-made and natural materials, including biological structures inside living cells, tissues, and whole organisms. 20 years ago, the LC-PolScope was introduced as a modern version of the traditional polarizing microscope enhanced by liquid crystal devices for the control of polarization, and by electronic imaging and digital image processing for fast and comprehensive image acquisition and analysis. The LCPolScope is commonly used for birefringence imaging, analyzing the spatial and temporal variations of the differential phase delay in ordered and transparent materials. Here we describe an alternative use of the LC-PolScope for imaging the polarization dependent transmittance of dichroic materials. We explain the minor changes needed to convert the instrument between the two imaging modes, discuss the relationship between the quantities measured with either instrument, and touch on the physical connection between refractive index, birefringence, transmittance, diattenuation, and dichroism. PMID:24273640

Gender and risk of depression in Saudi Arabia, a systematic review and meta-analysis

PubMed Central

Alibrahim, Osama A.; Al-Sadat, Nabilla; Elawad, Nagi A. M.

2010-01-01

Depression is one of the leading causes of mortality and morbidity worldwide. In the year 2000 depression accounted for 4.4% of the global disability adjusted life years (DALYs). The Kingdom of Saudi Arabia (KSA) has a population of 28 million people and is one of the countries experiencing demographic transition in its population structure. Improvements in socioeconomic status have been shown to be associated with increased chronic diseases including chronic mental diseases like depression, but still there is no comprehensive review summarizing the various reports currently existing in the literature. Although individual studies within Saudi Arabia have reported prevalence rates and risks, the quality of such studies need to be subjected to rigorous assessment and their findings pooled to give combined weighted evidence that will provide basis for targeted intervention. Pooled risks have the advantage of adjusting inherent variations within sampled populations and therefore providing more reliable estimates even though there are concerns about possible magnification of smaller individual risks. PMID:28299041

Managing Complex IT Security Processes with Value Based Measures

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

Abercrombie, Robert K; Sheldon, Frederick T; Mili, Ali

2009-01-01

Current trends indicate that IT security measures will need to greatly expand to counter the ever increasingly sophisticated, well-funded and/or economically motivated threat space. Traditional risk management approaches provide an effective method for guiding courses of action for assessment, and mitigation investments. However, such approaches no matter how popular demand very detailed knowledge about the IT security domain and the enterprise/cyber architectural context. Typically, the critical nature and/or high stakes require careful consideration and adaptation of a balanced approach that provides reliable and consistent methods for rating vulnerabilities. As reported in earlier works, the Cyberspace Security Econometrics System provides amore » comprehensive measure of reliability, security and safety of a system that accounts for the criticality of each requirement as a function of one or more stakeholders interests in that requirement. This paper advocates a dependability measure that acknowledges the aggregate structure of complex system specifications, and accounts for variations by stakeholder, by specification components, and by verification and validation impact.« less

Overview of Boundary Layer Clouds Using Satellite and Ground-Based Measurements

NASA Astrophysics Data System (ADS)

Xi, B.; Dong, X.; Wu, P.; Qiu, S.

2017-12-01

A comprehensive summary of boundary layer clouds properties based on our few recently studies will be presented. The analyses include the global cloud fractions and cloud macro/micro- physical properties based on satellite measurements using both CERES-MODIS and CloudSat/Caliposo data products,; the annual/seasonal/diurnal variations of stratocumulus clouds over different climate regions (mid-latitude land, mid-latitude ocean, and Arctic region) using DOE ARM ground-based measurements over Southern great plain (SGP), Azores (GRW), and North slope of Alaska (NSA) sites; the impact of environmental conditions to the formation and dissipation process of marine boundary layer clouds over Azores site; characterizing Arctice mixed-phase cloud structure and favorable environmental conditions for the formation/maintainess of mixed-phase clouds over NSA site. Though the presentation has widely spread topics, we will focus on the representation of the ground-based measurements over different climate regions; evaluation of satellite retrieved cloud properties using these ground-based measurements, and understanding the uncertainties of both satellite and ground-based retrievals and measurements.

Mapping cis- and trans-regulatory effects across multiple tissues in twins

PubMed Central

Grundberg, Elin; Small, Kerrin S.; Hedman, Åsa K.; Nica, Alexandra C.; Buil, Alfonso; Keildson, Sarah; Bell, Jordana T.; Yang, Tsun-Po; Meduri, Eshwar; Barrett, Amy; Nisbett, James; Sekowska, Magdalena; Wilk, Alicja; Shin, So-Youn; Glass, Daniel; Travers, Mary; Min, Josine L.; Ring, Sue; Ho, Karen; Thorleifsson, Gudmar; Kong, Augustine; Thorsteindottir, Unnur; Ainali, Chrysanthi; Dimas, Antigone S.; Hassanali, Neelam; Ingle, Catherine; Knowles, David; Krestyaninova, Maria; Lowe, Christopher E.; Di Meglio, Paola; Montgomery, Stephen B.; Parts, Leopold; Potter, Simon; Surdulescu, Gabriela; Tsaprouni, Loukia; Tsoka, Sophia; Bataille, Veronique; Durbin, Richard; Nestle, Frank O.; O’Rahilly, Stephen; Soranzo, Nicole; Lindgren, Cecilia M.; Zondervan, Krina T.; Ahmadi, Kourosh R.; Schadt, Eric E.; Stefansson, Kari; Smith, George Davey; McCarthy, Mark I.; Deloukas, Panos; Dermitzakis, Emmanouil T.; Spector, Tim D.

2013-01-01

Sequence-based variation in gene expression is a key driver of disease risk. Common variants regulating expression in cis have been mapped in many eQTL studies typically in single tissues from unrelated individuals. Here, we present a comprehensive analysis of gene expression across multiple tissues conducted in a large set of mono- and dizygotic twins that allows systematic dissection of genetic (cis and trans) and non-genetic effects on gene expression. Using identity-by-descent estimates, we show that at least 40% of the total heritable cis-effect on expression cannot be accounted for by common cis-variants, a finding which exposes the contribution of low frequency and rare regulatory variants with respect to both transcriptional regulation and complex trait susceptibility. We show that a substantial proportion of gene expression heritability is trans to the structural gene and identify several replicating trans-variants which act predominantly in a tissue-restricted manner and may regulate the transcription of many genes. PMID:22941192

Development of an integrated CAD-FEA system for patient-specific design of spinal cages.

PubMed

Zhang, Mingzheng; Pu, Fang; Xu, Liqiang; Zhang, Linlin; Liang, Hang; Li, Deyu; Wang, Yu; Fan, Yubo

2017-03-01

Spinal cages are used to create a suitable mechanical environment for interbody fusion in cases of degenerative spinal instability. Due to individual variations in bone structures and pathological conditions, patient-specific cages can provide optimal biomechanical conditions for fusion, strengthening patient recovery. Finite element analysis (FEA) is a valuable tool in the biomechanical evaluation of patient-specific cage designs, but the time- and labor-intensive process of modeling limits its clinical application. In an effort to facilitate the design and analysis of patient-specific spinal cages, an integrated CAD-FEA system (CASCaDeS, comprehensive analytical spinal cage design system) was developed. This system produces a biomechanical-based patient-specific design of spinal cages and is capable of rapid implementation of finite element modeling. By comparison with commercial software, this system was validated and proven to be both accurate and efficient. CASCaDeS can be used to design patient-specific cages with a superior biomechanical performance to commercial spinal cages.

Island phytophagy: explaining the remarkable diversity of plant-feeding insects

PubMed Central

Joy, Jeffrey B.; Crespi, Bernard J.

2012-01-01

Plant-feeding insects have undergone unparalleled diversification among different plant taxa, yet explanations for variation in their diversity lack a quantitative, predictive framework. Island biogeographic theory has been applied to spatially discrete habitats but not to habitats, such as host plants, separated by genetic distance. We show that relationships between the diversity of gall-inducing flies and their host plants meet several fundamental predictions from island biogeographic theory. First, plant-taxon genetic distinctiveness, an integrator for long-term evolutionary history of plant lineages, is a significant predictor of variance in the diversity of gall-inducing flies among host-plant taxa. Second, range size and structural complexity also explain significant proportions of the variance in diversity of gall-inducing flies among different host-plant taxa. Third, as with other island systems, plant-lineage age does not predict species diversity. Island biogeographic theory, applied to habitats defined by genetic distance, provides a novel, comprehensive framework for analysing and explaining the diversity of plant-feeding insects and other host-specific taxa. PMID:22553094

Striking changes in tea metabolites due to elevational effects.

PubMed

Kfoury, Nicole; Morimoto, Joshua; Kern, Amanda; Scott, Eric R; Orians, Colin M; Ahmed, Selena; Griffin, Timothy; Cash, Sean B; Stepp, John Richard; Xue, Dayuan; Long, Chunlin; Robbat, Albert

2018-10-30

Climate effects on crop quality at the molecular level are not well-understood. Gas and liquid chromatography-mass spectrometry were used to measure changes of hundreds of compounds in tea at different elevations in Yunnan Province, China. Some increased in concentration while others decreased by 100's of percent. Orthogonal projection to latent structures-discriminant analysis revealed compounds exhibiting analgesic, antianxiety, antibacterial, anticancer, antidepressant, antifungal, anti-inflammatory, antioxidant, anti-stress, and cardioprotective properties statistically (p = 0.003) differentiated high from low elevation tea. Also, sweet, floral, honey-like notes were higher in concentration in the former while the latter displayed grassy, hay-like aroma. In addition, multivariate analysis of variance showed low elevation tea had statistically (p = 0.0062) higher concentrations of caffeine, epicatechin gallate, gallocatechin, and catechin; all bitter compounds. Although volatiles represent a small fraction of the total mass, this is the first comprehensive report illustrating how normal variations in temperature, 5 °C, due to elevational effects impact tea quality. Copyright © 2018 Elsevier Ltd. All rights reserved.

Disability Benefit Generosity and Labor Force Withdrawal*

PubMed Central

Mullen, Kathleen J.; Staubli, Stefan

2016-01-01

A key component for estimating the optimal size and structure of disability insurance (DI) programs is the elasticity of DI claiming with respect to benefit generosity. Yet, in many countries, including the United States, all workers face identical benefit schedules, which are a function of one’s labor market history, making it difficult to separate the effect of the benefit level from the effect of unobserved preferences for work on individuals’ claiming decisions. To circumvent this problem, we exploit exogenous variation in DI benefits in Austria arising from several reforms to its DI and old age pension system in the 1990s and 2000s. We use comprehensive administrative social security records data on the universe of Austrian workers to compute benefit levels under six different regimes, allowing us to identify and precisely estimate the elasticity of DI claiming with respect to benefit generosity. We find that, over this time period, a one percent increase in potential DI benefits was associated with a 1.2 percent increase in DI claiming. PMID:28216797

Island phytophagy: explaining the remarkable diversity of plant-feeding insects.

PubMed

Joy, Jeffrey B; Crespi, Bernard J

2012-08-22

Plant-feeding insects have undergone unparalleled diversification among different plant taxa, yet explanations for variation in their diversity lack a quantitative, predictive framework. Island biogeographic theory has been applied to spatially discrete habitats but not to habitats, such as host plants, separated by genetic distance. We show that relationships between the diversity of gall-inducing flies and their host plants meet several fundamental predictions from island biogeographic theory. First, plant-taxon genetic distinctiveness, an integrator for long-term evolutionary history of plant lineages, is a significant predictor of variance in the diversity of gall-inducing flies among host-plant taxa. Second, range size and structural complexity also explain significant proportions of the variance in diversity of gall-inducing flies among different host-plant taxa. Third, as with other island systems, plant-lineage age does not predict species diversity. Island biogeographic theory, applied to habitats defined by genetic distance, provides a novel, comprehensive framework for analysing and explaining the diversity of plant-feeding insects and other host-specific taxa.

Experimental evaluation of shape memory alloy actuation technique in adaptive antenna design concepts

NASA Astrophysics Data System (ADS)

Kefauver, W. Neill; Carpenter, Bernie F.

1994-09-01

Creation of an antenna system that could autonomously adapt contours of reflecting surfaces to compensate for structural loads induced by a variable environment would maximize performance of space-based communication systems. Design of such a system requires the comprehensive development and integration of advanced actuator, sensor, and control technologies. As an initial step in this process, a test has been performed to assess the use of a shape memory alloy as a potential actuation technique. For this test, an existing, offset, cassegrain antenna system was retrofit with a subreflector equipped with shape memory alloy actuators for surface contour control. The impacts that the actuators had on both the subreflector contour and the antenna system patterns were measured. The results of this study indicate the potential for using shape memory alloy actuation techniques to adaptively control antenna performance; both variations in gain and beam steering capabilities were demonstrated. Future development effort is required to evolve this potential into a useful technology for satellite applications.

Relationship of Powder Feedstock Variability to Microstructure and Defects in Selective Laser Melted Alloy 718

NASA Technical Reports Server (NTRS)

Smith, T. M.; Kloesel, M. F.; Sudbrack, C. K.

2017-01-01

Powder-bed additive manufacturing processes use fine powders to build parts layer by layer. For selective laser melted (SLM) Alloy 718, the powders that are available off-the-shelf are in the 10-45 or 15-45 micron size range. A comprehensive investigation of sixteen powders from these typical ranges and two off-nominal-sized powders is underway to gain insight into the impact of feedstock on processing, durability and performance of 718 SLM space-flight hardware. This talk emphasizes an aspect of this work: the impact of powder variability on the microstructure and defects observed in the as-fabricated and full heated material, where lab-scale components were built using vendor recommended parameters. These typical powders exhibit variation in composition, percentage of fines, roughness, morphology and particle size distribution. How these differences relate to the melt-pool size, porosity, grain structure, precipitate distributions, and inclusion content will be presented and discussed in context of build quality and powder acceptance.

Experimental evaluation of shape memory alloy actuation technique in adaptive antenna design concepts

NASA Technical Reports Server (NTRS)

Kefauver, W. Neill; Carpenter, Bernie F.

1994-01-01

Creation of an antenna system that could autonomously adapt contours of reflecting surfaces to compensate for structural loads induced by a variable environment would maximize performance of space-based communication systems. Design of such a system requires the comprehensive development and integration of advanced actuator, sensor, and control technologies. As an initial step in this process, a test has been performed to assess the use of a shape memory alloy as a potential actuation technique. For this test, an existing, offset, cassegrain antenna system was retrofit with a subreflector equipped with shape memory alloy actuators for surface contour control. The impacts that the actuators had on both the subreflector contour and the antenna system patterns were measured. The results of this study indicate the potential for using shape memory alloy actuation techniques to adaptively control antenna performance; both variations in gain and beam steering capabilities were demonstrated. Future development effort is required to evolve this potential into a useful technology for satellite applications.