MicroRNAs show a wide diversity of expression profiles in the developing and mature central nervous system

PubMed Central

Kapsimali, Marika; Kloosterman, Wigard P; de Bruijn, Ewart; Rosa, Frederic; Plasterk, Ronald HA; Wilson, Stephen W

2007-01-01

Background MicroRNA (miRNA) encoding genes are abundant in vertebrate genomes but very few have been studied in any detail. Bioinformatic tools allow prediction of miRNA targets and this information coupled with knowledge of miRNA expression profiles facilitates formulation of hypotheses of miRNA function. Although the central nervous system (CNS) is a prominent site of miRNA expression, virtually nothing is known about the spatial and temporal expression profiles of miRNAs in the brain. To provide an overview of the breadth of miRNA expression in the CNS, we performed a comprehensive analysis of the neuroanatomical expression profiles of 38 abundant conserved miRNAs in developing and adult zebrafish brain. Results Our results show miRNAs have a wide variety of different expression profiles in neural cells, including: expression in neuronal precursors and stem cells (for example, miR-92b); expression associated with transition from proliferation to differentiation (for example, miR-124); constitutive expression in mature neurons (miR-124 again); expression in both proliferative cells and their differentiated progeny (for example, miR-9); regionally restricted expression (for example, miR-222 in telencephalon); and cell-type specific expression (for example, miR-218a in motor neurons). Conclusion The data we present facilitate prediction of likely modes of miRNA function in the CNS and many miRNA expression profiles are consistent with the mutual exclusion mode of function in which there is spatial or temporal exclusion of miRNAs and their targets. However, some miRNAs, such as those with cell-type specific expression, are more likely to be co-expressed with their targets. Our data provide an important resource for future functional studies of miRNAs in the CNS. PMID:17711588

Wide Swath Stereo Mapping from Gaofen-1 Wide-Field-View (WFV) Images Using Calibration

PubMed Central

Chen, Shoubin; Liu, Jingbin; Huang, Wenchao

2018-01-01

The development of Earth observation systems has changed the nature of survey and mapping products, as well as the methods for updating maps. Among optical satellite mapping methods, the multiline array stereo and agile stereo modes are the most common methods for acquiring stereo images. However, differences in temporal resolution and spatial coverage limit their application. In terms of this issue, our study takes advantage of the wide spatial coverage and high revisit frequencies of wide swath images and aims at verifying the feasibility of stereo mapping with the wide swath stereo mode and reaching a reliable stereo accuracy level using calibration. In contrast with classic stereo modes, the wide swath stereo mode is characterized by both a wide spatial coverage and high-temporal resolution and is capable of obtaining a wide range of stereo images over a short period. In this study, Gaofen-1 (GF-1) wide-field-view (WFV) images, with total imaging widths of 800 km, multispectral resolutions of 16 m and revisit periods of four days, are used for wide swath stereo mapping. To acquire a high-accuracy digital surface model (DSM), the nonlinear system distortion in the GF-1 WFV images is detected and compensated for in advance. The elevation accuracy of the wide swath stereo mode of the GF-1 WFV images can be improved from 103 m to 30 m for a DSM with proper calibration, meeting the demands for 1:250,000 scale mapping and rapid topographic map updates and showing improved efficacy for satellite imaging. PMID:29494540

Modes of gene duplication contribute differently to genetic novelty and redundancy, but show parallels across divergent angiosperms.

PubMed

Wang, Yupeng; Wang, Xiyin; Tang, Haibao; Tan, Xu; Ficklin, Stephen P; Feltus, F Alex; Paterson, Andrew H

2011-01-01

Both single gene and whole genome duplications (WGD) have recurred in angiosperm evolution. However, the evolutionary effects of different modes of gene duplication, especially regarding their contributions to genetic novelty or redundancy, have been inadequately explored. In Arabidopsis thaliana and Oryza sativa (rice), species that deeply sample botanical diversity and for which expression data are available from a wide range of tissues and physiological conditions, we have compared expression divergence between genes duplicated by six different mechanisms (WGD, tandem, proximal, DNA based transposed, retrotransposed and dispersed), and between positional orthologs. Both neo-functionalization and genetic redundancy appear to contribute to retention of duplicate genes. Genes resulting from WGD and tandem duplications diverge slowest in both coding sequences and gene expression, and contribute most to genetic redundancy, while other duplication modes contribute more to evolutionary novelty. WGD duplicates may more frequently be retained due to dosage amplification, while inferred transposon mediated gene duplications tend to reduce gene expression levels. The extent of expression divergence between duplicates is discernibly related to duplication modes, different WGD events, amino acid divergence, and putatively neutral divergence (time), but the contribution of each factor is heterogeneous among duplication modes. Gene loss may retard inter-species expression divergence. Members of different gene families may have non-random patterns of origin that are similar in Arabidopsis and rice, suggesting the action of pan-taxon principles of molecular evolution. Gene duplication modes differ in contribution to genetic novelty and redundancy, but show some parallels in taxa separated by hundreds of millions of years of evolution.

Modes of Gene Duplication Contribute Differently to Genetic Novelty and Redundancy, but Show Parallels across Divergent Angiosperms

PubMed Central

Wang, Yupeng; Wang, Xiyin; Tang, Haibao; Tan, Xu; Ficklin, Stephen P.; Feltus, F. Alex; Paterson, Andrew H.

2011-01-01

Background Both single gene and whole genome duplications (WGD) have recurred in angiosperm evolution. However, the evolutionary effects of different modes of gene duplication, especially regarding their contributions to genetic novelty or redundancy, have been inadequately explored. Results In Arabidopsis thaliana and Oryza sativa (rice), species that deeply sample botanical diversity and for which expression data are available from a wide range of tissues and physiological conditions, we have compared expression divergence between genes duplicated by six different mechanisms (WGD, tandem, proximal, DNA based transposed, retrotransposed and dispersed), and between positional orthologs. Both neo-functionalization and genetic redundancy appear to contribute to retention of duplicate genes. Genes resulting from WGD and tandem duplications diverge slowest in both coding sequences and gene expression, and contribute most to genetic redundancy, while other duplication modes contribute more to evolutionary novelty. WGD duplicates may more frequently be retained due to dosage amplification, while inferred transposon mediated gene duplications tend to reduce gene expression levels. The extent of expression divergence between duplicates is discernibly related to duplication modes, different WGD events, amino acid divergence, and putatively neutral divergence (time), but the contribution of each factor is heterogeneous among duplication modes. Gene loss may retard inter-species expression divergence. Members of different gene families may have non-random patterns of origin that are similar in Arabidopsis and rice, suggesting the action of pan-taxon principles of molecular evolution. Conclusion Gene duplication modes differ in contribution to genetic novelty and redundancy, but show some parallels in taxa separated by hundreds of millions of years of evolution. PMID:22164235

Differences in Trait Impulsivity Indicate Diversification of Dog Breeds into Working and Show Lines.

PubMed

Fadel, Fernanda Ruiz; Driscoll, Patricia; Pilot, Malgorzata; Wright, Hannah; Zulch, Helen; Mills, Daniel

2016-03-10

Impulsiveness describes the inability to inhibit behaviour in the presence of salient cues. Trait-level impulsivity exists on a continuum and individual differences can be adaptive in different contexts. While breed related differences in behavioural tendency in the domestic dog (Canis familiaris) are well established, the phenomenon within lines of a breed which have been selected more recently is not well studied, although it may challenge the popular notion of breed-typical behaviour. We describe differences in impulsivity between and within two dog breeds with working and show lines selected for different levels of impulsivity: Border Collies (herding work) and Labrador Retrievers (gun work). Recent show line selection might have lessened differences in impulsivity between breeds. We tested this hypothesis on a dataset of 1161 individuals assessed using a validated psychometric tool (Dog Impulsivity Assessment Scale--DIAS). Collies were more impulsive on average, consistent with the original purpose of breed selection. Regarding line, working Collies differed from working Labradors, but show lines from the two breeds were not significantly different. Altered or relaxed artificial selection for behavioural traits when appearance rather than behaviour become the primary focus for breeders may reduce average differences in impulsivity between breeds in show lines.

A Case of Uveal Colobomas Showing Marked Left-Right Difference in Diabetic Retinopathy.

PubMed

Moriya, Takeshi; Ochi, Ryosuke; Imagawa, Yukihiro; Sato, Bumpei; Morishita, Seita; Tonari, Masahiro; Fukumoto, Masanori; Suzuki, Hiroyuki; Kobayashi, Takatoshi; Kida, Teruyo; Ikeda, Tsunehiko

2016-01-01

Congenital uveal colobomas, including inferior iris and choroidal colobomas, are associated with microcornea and microphthalmia and often show left-right differences (laterality). The purpose of this study was to report a case of choroidal coloboma associated with left-right differences in diabetic retinopathy (DR). This study reports a 59-year-old male with bilateral iris and choroidal colobomas. The colobomatous area in the patient's right eye extended to the macula, and his right eye had been amblyopic since birth. The colobomatous area in his left eye was less extensive and did not involve the macula. Examination of the patient's left eye revealed multiple hemorrhages and hard exudates in the macula due to DR, but examination of his right eye showed almost no changes in DR, thus revealing a marked left-right difference. Optical coherence tomography showed more extensive retinal thinning in the patient's right eye than in his left eye. Fluorescein fundus angiography revealed a retinal nonperfusion area only in the left eye, and panretinal photocoagulation was subsequently performed. Our findings show that the reason for the left-right difference in DR was attributed to the more severe choroidal coloboma and retinal thinning in the patient's right eye compared to his left eye, thus reducing oxygen demand, as is also seen in eyes with severe myopia.

Green Writing Curriculum: Showing Your Students How to Make A Difference

ERIC Educational Resources Information Center

Munger, Roger

2010-01-01

A growing group of green writers are persuading people to change their thinking and their behaviors for the benefit of our planet and its inhabitants. Adding a green writing assignment, unit, or course to your curriculum, the author argues, is an excellent strategy for showing students how their writing can make a difference in their community.…

Novel ratio difference at coabsorptive point spectrophotometric method for determination of components with wide variation in their absorptivities.

PubMed

Saad, Ahmed S; Abo-Talib, Nisreen F; El-Ghobashy, Mohamed R

2016-01-05

Different methods have been introduced to enhance selectivity of UV-spectrophotometry thus enabling accurate determination of co-formulated components, however mixtures whose components exhibit wide variation in absorptivities has been an obstacle against application of UV-spectrophotometry. The developed ratio difference at coabsorptive point method (RDC) represents a simple effective solution for the mentioned problem, where the additive property of light absorbance enabled the consideration of the two components as multiples of the lower absorptivity component at certain wavelength (coabsorptive point), at which their total concentration multiples could be determined, whereas the other component was selectively determined by applying the ratio difference method in a single step. Mixture of perindopril arginine (PA) and amlodipine besylate (AM) figures that problem, where the low absorptivity of PA relative to AM hinders selective spectrophotometric determination of PA. The developed method successfully determined both components in the overlapped region of their spectra with accuracy 99.39±1.60 and 100.51±1.21, for PA and AM, respectively. The method was validated as per the USP guidelines and showed no significant difference upon statistical comparison with reported chromatographic method. Copyright © 2015 Elsevier B.V. All rights reserved.

A Holographic Road Show.

ERIC Educational Resources Information Center

Kirkpatrick, Larry D.; Rugheimer, Mac

1979-01-01

Describes the viewing sessions and the holograms of a holographic road show. The traveling exhibits, believed to stimulate interest in physics, include a wide variety of holograms and demonstrate several physical principles. (GA)

Genome-wide CpG island methylation and intergenic demethylation propensities vary among different tumor sites.

PubMed

Lee, Seung-Tae; Wiemels, Joseph L

2016-02-18

The epigenetic landscape of cancer includes both focal hypermethylation and broader hypomethylation in a genome-wide manner. By means of a comprehensive genomic analysis on 6637 tissues of 21 tumor types, we here show that the degrees of overall methylation in CpG island (CGI) and demethylation in intergenic regions, defined as 'backbone', largely vary among different tumors. Depending on tumor type, both CGI methylation and backbone demethylation are often associated with clinical, epidemiological and biological features such as age, sex, smoking history, anatomic location, histological type and grade, stage, molecular subtype and biological pathways. We found connections between CGI methylation and hypermutability, microsatellite instability, IDH1 mutation, 19p gain and polycomb features, and backbone demethylation with chromosomal instability, NSD1 and TP53 mutations, 5q and 19p loss and long repressive domains. These broad epigenetic patterns add a new dimension to our understanding of tumor biology and its clinical implications. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Coagulation tests show significant differences in patients with breast cancer.

PubMed

Tas, Faruk; Kilic, Leyla; Duranyildiz, Derya

2014-06-01

Activated coagulation and fibrinolytic system in cancer patients is associated with tumor stroma formation and metastasis in different cancer types. The aim of this study is to explore the correlation of blood coagulation assays for various clinicopathologic factors in breast cancer patients. A total of 123 female breast cancer patients were enrolled into the study. All the patients were treatment naïve. Pretreatment blood coagulation tests including PT, APTT, PTA, INR, D-dimer, fibrinogen levels, and platelet counts were evaluated. Median age of diagnosis was 51 years old (range 26-82). Twenty-two percent of the group consisted of metastatic breast cancer patients. The plasma level of all coagulation tests revealed statistically significant difference between patient and control group except for PT (p<0.001 for all variables except for PT; p=0.08). Elderly age (>50 years) was associated with higher D-dimer levels (p=0.003). Metastatic patients exhibited significantly higher D-dimer values when compared with early breast cancer patients (p=0.049). Advanced tumor stage (T3 and T4) was associated with higher INR (p=0.05) and lower PTA (p=0.025). In conclusion, coagulation tests show significant differences in patients with breast cancer.

Methylamphetamine synthesized from cold medication as precursor source via two different routes show significantly different stable isotope signatures

NASA Astrophysics Data System (ADS)

Jayaram, S.; Daeid, N. Nic; Kerr, W. J.; Kemp, H. F.; Meier-Augenstein, W.

2012-04-01

This work exposes the variation in light element stable isotopic abundance values of 13C, 2H and 15N) derived from the analysis of methylamphetamine synthesized via 2 different synthetic routes popular with clandestine laboraties, the Hypophosphorous and the Moscow route. We repeatedly prepared the final product using known clandestine synthetic methods where the precursors, catalysts and reducing agents have themselves been derived from house hold products and commonly available cold medications. Methylamphetamine was prepared from both lab grade pseudoephedrine and pseudoephedrine extracted (using three different solvent systems) from Sudafed®, an over-the-counter cold medication widely available in the United Kingdom. Six repetitive batches of the final product were produced in each case to provide within and between batch variations thus yielding a total of 48 samples (24 for each route). We have demonstrated that stable isotope analysis by Isotope Ratio Mass Spectrometry (IRMS) is potentially useful in the comparison and discrimination of batches of methylamphetamine produced for each route and for each precursor depending on the solvent used for extracting the pseudoephedrine starting material. To our knowledge this is the first time multivariate stable isotope analysis has been applied to methylamphetamine samples synthesized from pseudoephedrine extracted from over-the-counter cold medications.

Genome-wide analysis of coordinated transcript abundance during seed development in different Brassica rapa morphotypes.

PubMed

Basnet, Ram Kumar; Moreno-Pachon, Natalia; Lin, Ke; Bucher, Johan; Visser, Richard G F; Maliepaard, Chris; Bonnema, Guusje

2013-12-01

Brassica seeds are important as basic units of plant growth and sources of vegetable oil. Seed development is regulated by many dynamic metabolic processes controlled by complex networks of spatially and temporally expressed genes. We conducted a global microarray gene co-expression analysis by measuring transcript abundance of developing seeds from two diverse B. rapa morphotypes: a pak choi (leafy-type) and a yellow sarson (oil-type), and two of their doubled haploid (DH) progenies, (1) to study the timing of metabolic processes in developing seeds, (2) to explore the major transcriptional differences in developing seeds of the two morphotypes, and (3) to identify the optimum stage for a genetical genomics study in B. rapa seed. Seed developmental stages were similar in developing seeds of pak choi and yellow sarson of B. rapa; however, the colour of embryo and seed coat differed among these two morphotypes. In this study, most transcriptional changes occurred between 25 and 35 DAP, which shows that the timing of seed developmental processes in B. rapa is at later developmental stages than in the related species B. napus. Using a Weighted Gene Co-expression Network Analysis (WGCNA), we identified 47 "gene modules", of which 27 showed a significant association with temporal and/or genotypic variation. An additional hierarchical cluster analysis identified broad spectra of gene expression patterns during seed development. The predominant variation in gene expression was according to developmental stages rather than morphotype differences. Since lipids are the major storage compounds of Brassica seeds, we investigated in more detail the regulation of lipid metabolism. Four co-regulated gene clusters were identified with 17 putative cis-regulatory elements predicted in their 1000 bp upstream region, either specific or common to different lipid metabolic pathways. This is the first study of genome-wide profiling of transcript abundance during seed development in B

Register based monitoring shows decreasing socioeconomic differences in Finnish perinatal health

PubMed Central

Gissler, M; Merilainen, J; Vuori, E; Hemminki, E

2003-01-01

Study objective: Several studies on differences in infant outcome by socioeconomic position have been done, but these have usually been based on ad hoc data linkages. The aim of this paper was to investigate whether socioeconomic differences in perinatal health in Finland could be regularly monitored using routinely collected data from one single register. Design and setting: Since October 1990, the Finnish Medical Birth Register (MBR) has included data on maternal occupation. A special computer program that converted the occupation name into an occupational code and into a socioeconomic position was prepared. Perinatal health was measured with five different indicators. The Finnish MBR data for years 1991 to 1999 (n=565 863 newborns) were used in the study. The study period was divided into three, three year periods to study time trends. Results: An occupational code was derived for 95% of women, but it was not possible to define a socioeconomic position for 22% of women, including, for example, students and housewives (the group "Others"). For the rest, the data showed socioeconomic differences in all perinatal health indicators. Maternal smoking explained up to half of the excess risk for adverse perinatal outcome in the lowest socioeconomic group. The socioeconomic differences narrowed during the 1990s: infant outcome improved in the lowest socioeconomic group, but remained at the same level or even deteriorated in other groups. When comparing the lowest group with the highest group, the odds ratios (OR) adjusted for maternal background characteristics at least halved for prematurity (from 1.32 (95% confidence intervals 1.24 to 1.43) in 1991–1993 to 1.16 (1.08 to 1.25) in 1997–1999), for low birth weight (from 1.49 (1.36 to 1.63) to 1.25 (1.17 to 1.40)), and for perinatal mortality (from 1.79 (1.44 to 2.21) to 1.33 (1.07 to 1.66)). Conclusions: Social inequality in perinatal health outcomes exists in Finland, but seems to have diminished in the 1990s. These

Genome-wide analyses for personality traits identify six genomic loci and show correlations with psychiatric disorders

PubMed Central

Lo, Min-Tzu; Hinds, David A.; Tung, Joyce Y.; Franz, Carol; Fan, Chun-Chieh; Wang, Yunpeng; Smeland, Olav B.; Schork, Andrew; Holland, Dominic; Kauppi, Karolina; Sanyal, Nilotpal; Escott-Price, Valentina; Smith, Daniel J.; O'Donovan, Michael; Stefansson, Hreinn; Bjornsdottir, Gyda; Thorgeirsson, Thorgeir E.; Stefansson, Kari; McEvoy, Linda K.; Dale, Anders M.; Andreassen, Ole A.; Chen, Chi-Hua

2017-01-01

Summary Personality is influenced by genetic and environmental factors1, and associated with mental health. However, the underlying genetic determinants are largely unknown. We identified six genetic loci, including five novel loci2,3, significantly associated with personality traits in a meta-analysis of genome-wide association studies (N=123,132–260,861). Of these genome-wide significant loci, extraversion was associated with variants in WSCD2 and near PCDH15, and neuroticism with variants on chromosome 8p23.1 and in L3MBTL2. We performed a principal component analysis to extract major dimensions underlying genetic variations among five personality traits and six psychiatric disorders (N=5,422–18,759). The first genetic dimension separated personality traits and psychiatric disorders, except that neuroticism and openness to experience were clustered with the disorders. High genetic correlations were found between extraversion and attention-deficit/hyperactivity disorder (ADHD), and between openness and schizophrenia/bipolar disorder. The second genetic dimension was closely aligned with extraversion-introversion and grouped neuroticism with internalizing psychopathology (e.g., depression/anxiety). PMID:27918536

Genome-wide analyses for personality traits identify six genomic loci and show correlations with psychiatric disorders.

PubMed

Lo, Min-Tzu; Hinds, David A; Tung, Joyce Y; Franz, Carol; Fan, Chun-Chieh; Wang, Yunpeng; Smeland, Olav B; Schork, Andrew; Holland, Dominic; Kauppi, Karolina; Sanyal, Nilotpal; Escott-Price, Valentina; Smith, Daniel J; O'Donovan, Michael; Stefansson, Hreinn; Bjornsdottir, Gyda; Thorgeirsson, Thorgeir E; Stefansson, Kari; McEvoy, Linda K; Dale, Anders M; Andreassen, Ole A; Chen, Chi-Hua

2017-01-01

Personality is influenced by genetic and environmental factors and associated with mental health. However, the underlying genetic determinants are largely unknown. We identified six genetic loci, including five novel loci, significantly associated with personality traits in a meta-analysis of genome-wide association studies (N = 123,132-260,861). Of these genome-wide significant loci, extraversion was associated with variants in WSCD2 and near PCDH15, and neuroticism with variants on chromosome 8p23.1 and in L3MBTL2. We performed a principal component analysis to extract major dimensions underlying genetic variations among five personality traits and six psychiatric disorders (N = 5,422-18,759). The first genetic dimension separated personality traits and psychiatric disorders, except that neuroticism and openness to experience were clustered with the disorders. High genetic correlations were found between extraversion and attention-deficit-hyperactivity disorder (ADHD) and between openness and schizophrenia and bipolar disorder. The second genetic dimension was closely aligned with extraversion-introversion and grouped neuroticism with internalizing psychopathology (e.g., depression or anxiety).

Low gene copy number shows that arbuscular mycorrhizal fungi inherit genetically different nuclei.

PubMed

Hijri, Mohamed; Sanders, Ian R

2005-01-13

Arbuscular mycorrhizal fungi (AMF) are ancient asexually reproducing organisms that form symbioses with the majority of plant species, improving plant nutrition and promoting plant diversity. Little is known about the evolution or organization of the genomes of any eukaryotic symbiont or ancient asexual organism. Direct evidence shows that one AMF species is heterokaryotic; that is, containing populations of genetically different nuclei. It has been suggested, however, that the genetic variation passed from generation to generation in AMF is simply due to multiple chromosome sets (that is, high ploidy). Here we show that previously documented genetic variation in Pol-like sequences, which are passed from generation to generation, cannot be due to either high ploidy or repeated gene duplications. Our results provide the clearest evidence so far for substantial genetic differences among nuclei in AMF. We also show that even AMF with a very large nuclear DNA content are haploid. An underlying principle of evolutionary theory is that an individual passes on one or half of its genome to each of its progeny. The coexistence of a population of many genomes in AMF and their transfer to subsequent generations, therefore, has far-reaching consequences for understanding genome evolution.

Difference structures from time-resolved small-angle and wide-angle x-ray scattering

NASA Astrophysics Data System (ADS)

Nepal, Prakash; Saldin, D. K.

2018-05-01

Time-resolved small-angle x-ray scattering/wide-angle x-ray scattering (SAXS/WAXS) is capable of recovering difference structures directly from difference SAXS/WAXS curves. It does so by means of the theory described here because the structural changes in pump-probe detection in a typical time-resolved experiment are generally small enough to be confined to a single residue or group in close proximity which is identified by a method akin to the difference Fourier method of time-resolved crystallography. If it is assumed, as is usual with time-resolved structures, that the moved atoms lie within the residue, the 100-fold reduction in the search space (assuming a typical protein has about 100 residues) allows the exaction of the structure by a simulated annealing algorithm with a huge reduction in computing time and leads to a greater resolution by varying the positions of atoms only within that residue. This reduction in the number of potential moved atoms allows us to identify the actual motions of the individual atoms. In the case of a crystal, time-resolved calculations are normally performed using the difference Fourier method, which is, of course, not directly applicable to SAXS/WAXS. The method developed in this paper may be thought of as a substitute for that method which allows SAXS/WAXS (and hence disordered molecules) to also be used for time-resolved structural work.

Comparative analysis of the application of different Low Power Wide Area Network technologies in power grid

NASA Astrophysics Data System (ADS)

Wang, Hao; Sui, Hong; Liao, Xing; Li, Junhao

2018-03-01

Low Power Wide Area Network (LPWAN) technologies developed rapidly in recent years, but the application principle of different LPWAN technologies in power grid is still not clear. This paper gives a comparative analysis of two mainstream LPWAN technologies including NB-IoT and LoRa, and gives an application suggestion of these two LPWAN technologies, which can guide the planning and construction of LPWAN in power grid.

Laboratory study of fungal bioreceptivity of different fractions of composite flooring tiles showing efflorescence.

PubMed

Masaphy, Segula; Lavi, Ido; Sultz, Stephan; Zabari, Limor

2014-06-01

Fungi can grow in extreme habitats, such as natural stone and mineral building materials, sometimes causing deterioration. Efflorescence-concentrated salt deposits-results from water movement through building material; it can damage masonry materials and other bricks. Fungal isolate KUR1, capable of growth on, and dissolution of stone chips composing terrazzo-type floor tiles, was isolated from such tiles showing fiber-like crystalline efflorescence. The isolate's ribosomal DNA sequences were 100 % identical to those of Nigrospora sphaerica. The ability of KUR1 to colonize and degrade the different stone chips composing the tiles was studied in axenic culture experiments. When exposed to each of the different mineral chip types composed of dolomite, calcite, or calcite-apatite mineral in low-nutrition medium, the fungus showed selective nutrient consumption, and different growth and stone mineral dissolution rates. Micromorphological examination of the fungus-colonized chips by electron microscopy showed the production of a fungal biofilm with thin films around the hyphae on the surface of the examined chips and disintegration of the calcite-apatite fraction. More than 70 % dissolution of the introduced powdered (<1 mm particle size) mineral was obtained within 10 days of incubation for the soft calcite-apatite fraction.

NSAID loxoprofen inhibits high threshold or wide dynamic range neuronal responses in the rat at different time-courses.

PubMed

Tsuruoka, Masayoshi; Maeda, Masako; Hayashi, Bunsho; Liu, Limin; Inoue, Tomio

2008-01-01

The onset of the antinociceptive effect with loxoprofen sodium (LOX), a non-steroidal anti-inflammatory drug, was examined electrophysiologically during carrageenan-induced hindpaw inflammation in the rat. Extracellular recordings were made from either wide dynamic range (WDR) or high threshold (HT) neurons in the dorsal horn. Recordings from the same neuron were continued for at least 3 h after the injection of carrageenan. Three hours after the induction of inflammation, either a fresh solution of LOX (1 mg/kg) or distilled water was directly administered into the stomach through PE 50 tubing. LOX significantly reduced inflammation-increased background activity and noxious heat-evoked responses in both HT and WDR neurons, whereas distilled water did not produce any change. Asignificant difference in the onset of the inhibitory effect of LOX was observed between HT and WDR neurons. The results show that WDR neurons precede HT neurons regarding inhibition of nociceptive processing in the dorsal horn after administration of LOX.

Evaluating a complex system-wide intervention using the difference in differences method: the Delivering Choice Programme

PubMed Central

Round, Jeff; Drake, Robyn; Kendall, Edward; Addicott, Rachael; Agelopoulos, Nicky; Jones, Louise

2015-01-01

Objectives We report the use of difference in differences (DiD) methodology to evaluate a complex, system-wide healthcare intervention. We use the worked example of evaluating the Marie Curie Delivering Choice Programme (DCP) for advanced illness in a large urban healthcare economy. Methods DiD was selected because a randomised controlled trial was not feasible. The method allows for before and after comparison of changes that occur in an intervention site with a matched control site. This enables analysts to control for the effect of the intervention in the absence of a local control. Any policy, seasonal or other confounding effects over the test period are assumed to have occurred in a balanced way at both sites. Data were obtained from primary care trusts. Outcomes were place of death, inpatient admissions, length of stay and costs. Results Small changes were identified between pre- and post-DCP outputs in the intervention site. The proportion of home deaths and median cost increased slightly, while the number of admissions per patient and the average length of stay per admission decreased slightly. None of these changes was statistically significant. Conclusions Effects estimates were limited by small numbers accessing new services and selection bias in sample population and comparator site. In evaluating the effect of a complex healthcare intervention, the choice of analysis method and output measures is crucial. Alternatives to randomised controlled trials may be required for evaluating large scale complex interventions and the DiD approach is suitable, subject to careful selection of measured outputs and control population. PMID:24644163

Ternary bulk heterojunction for wide spectral range organic photodetectors

NASA Astrophysics Data System (ADS)

Shin, Hojung; Kim, Jaehoon; Lee, Changhee

2017-08-01

Ternary bulk heterojunction (BHJ) system, dual electron donors and an acceptor, was studied for developing wide spectral range organic photodetectors (OPDs). With two electron donor polymers with different bandgaps and an efficient electron acceptor of [6,6]-Phenyl-C71-butyric acid methyl ester (PC70BM), different blend ratios for ternary BHJ OPD were examined to achieve high photoresponsivity over a wide spectral range. OPDs based on ternary BHJ showed improved photovoltage response compared to binary BHJ. Current-voltage (J-V) characteristics as a function of external bias and light illumination were measured to reveal the underlying charge recombination mechanism which is found to be dominantly ruled by space charge limit (SCL) effect. Additional in-depth analyses including absorbance, cross-section scanning electron microscope (SEM), incident photon-to-electron conversion efficiency (IPCE) were performed.

Pseudoscorpion mitochondria show rearranged genes and genome-wide reductions of RNA gene sizes and inferred structures, yet typical nucleotide composition bias

PubMed Central

2012-01-01

Background Pseudoscorpions are chelicerates and have historically been viewed as being most closely related to solifuges, harvestmen, and scorpions. No mitochondrial genomes of pseudoscorpions have been published, but the mitochondrial genomes of some lineages of Chelicerata possess unusual features, including short rRNA genes and tRNA genes that lack sequence to encode arms of the canonical cloverleaf-shaped tRNA. Additionally, some chelicerates possess an atypical guanine-thymine nucleotide bias on the major coding strand of their mitochondrial genomes. Results We sequenced the mitochondrial genomes of two divergent taxa from the chelicerate order Pseudoscorpiones. We find that these genomes possess unusually short tRNA genes that do not encode cloverleaf-shaped tRNA structures. Indeed, in one genome, all 22 tRNA genes lack sequence to encode canonical cloverleaf structures. We also find that the large ribosomal RNA genes are substantially shorter than those of most arthropods. We inferred secondary structures of the LSU rRNAs from both pseudoscorpions, and find that they have lost multiple helices. Based on comparisons with the crystal structure of the bacterial ribosome, two of these helices were likely contact points with tRNA T-arms or D-arms as they pass through the ribosome during protein synthesis. The mitochondrial gene arrangements of both pseudoscorpions differ from the ancestral chelicerate gene arrangement. One genome is rearranged with respect to the location of protein-coding genes, the small rRNA gene, and at least 8 tRNA genes. The other genome contains 6 tRNA genes in novel locations. Most chelicerates with rearranged mitochondrial genes show a genome-wide reversal of the CA nucleotide bias typical for arthropods on their major coding strand, and instead possess a GT bias. Yet despite their extensive rearrangement, these pseudoscorpion mitochondrial genomes possess a CA bias on the major coding strand. Phylogenetic analyses of all 13

Hybrid pig versus Gottingen minipig-derived cartilage and chondrocytes show pig line-dependent differences.

PubMed

Müller, Claudia; Marzahn, Ulrike; Kohl, Benjamin; El Sayed, Karym; Lohan, Anke; Meier, Carola; Ertel, Wolfgang; Schulze-Tanzil, Gundula

2013-11-01

Minipigs are widely used as a large animal model for cartilage repair. However, many in vitro studies are based on porcine chondrocytes derived from abundantly available premature hybrid pigs. It remains unclear whether pig line-dependent differences exist which could limit the comparability between in vitro and in vivo results using either hybrid or miniature pig articular chondrocytes. Porcine knee joint femoral cartilage was isolated from 3- to 5-month-old hybrid pigs and Göttingen minipigs. Cartilage from both pig lines was analysed for thickness, zonality, cell content, size and proteoglycan deposition. Cultured articular chondrocytes from both pig lines were investigated for gene and/or protein expression of cartilage-specific proteins such as type II collagen, aggrecan, the chondrogenic transcription factor Sox9, non-specific type I collagen and the cell-matrix receptor β1-integrin. Cartilage was significantly thinner in the miniature pig compared to the hybrid pig, but the differences between the medial and lateral femur condyles did not reach a significant level. Knee joint cartilage zone formation started only in the minipig, whereas cellularity and cell diameters were comparable in both pig lines. Blood vessels could be detected in the hybrid pig but not the minipig cartilage. Sulphated proteoglycan deposition was more pronounced in cartilage zones II-IV of both pig lines. Minipig chondrocytes expressed type II and I collagen, Sox9 and β1-integrin at a higher level than hybrid pig chondrocytes. These distinct line-dependent differences should be considered when using hybrid pig-derived chondrocytes for tissue engineering and Göttingen minipigs as a large animal model.

Intraspecific Arabidopsis hybrids show different patterns of heterosis despite the close relatedness of the parental genomes.

PubMed

Groszmann, Michael; Gonzalez-Bayon, Rebeca; Greaves, Ian K; Wang, Li; Huen, Amanda K; Peacock, W James; Dennis, Elizabeth S

2014-09-01

Heterosis is important for agriculture; however, little is known about the mechanisms driving hybrid vigor. Ultimately, heterosis depends on the interactions of specific alleles and epialleles provided by the parents, which is why hybrids can exhibit different levels of heterosis, even within the same species. We characterize the development of several intraspecific Arabidopsis (Arabidopsis thaliana) F1 hybrids that show different levels of heterosis at maturity. We identify several phases of heterosis beginning during embryogenesis and culminating in a final phase of vegetative maturity and seed production. During each phase, the hybrids show different levels and patterns of growth, despite the close relatedness of the parents. For instance, during the vegetative phases, the hybrids develop larger leaves than the parents to varied extents, and they do so by exploiting increases in cell size and cell numbers in different ratios. Consistent with this finding, we observed changes in the expression of genes known to regulate leaf size in developing rosettes of the hybrids, with the patterns of altered expression differing between combinations. The data show that heterosis is dependent on changes in development throughout the growth cycle of the hybrid, with the traits of mature vegetative biomass and reproductive yield as cumulative outcomes of heterosis at different levels, tissues, and times of development. © 2014 American Society of Plant Biologists. All Rights Reserved.

Using different growth references to measure thinness and overweight among Swedish primary school children showed considerable variations.

PubMed

Nilsen, Bente B; Yngve, Agneta; Sjöberg, Agneta; Moraeus, Lotta; Lissner, Lauren; Werner, Bo

2016-10-01

The study compared how four different growth references determined the prevalence of thinness and overweight, based on height and weight measurements from a nationally representative sample of Swedish children from seven to nine years of age. The height and weight measurements of 4518 Swedish schoolchildren aged seven to nine years were carried out in 2008 using a standardised protocol. The prevalence of different degrees of thinness and overweight was calculated using international growth references from the World Health Organization, the International Obesity Task Force and two Swedish growth references from Werner and Karlberg. Depending on which growth reference we used, the prevalence of different degrees of thinness varied from 7.5% to 16.9% for the boys and 6.9% to 13.7% for the girls, while the prevalence of overweight, including obesity and severe obesity, varied from 16.5% to 25.7% for the boys and 18.2 to 25.2% for the girls. There were also significant gender differences depending on the growth reference we used. Using four different growth references, two international and two Swedish, produced wide variations in the prevalence of thinness and overweight, together with significant gender differences. In the absence of a global definition, we need both national and international growth references. ©2016 Foundation Acta Paediatrica. Published by John Wiley & Sons Ltd.

Evaluating a complex system-wide intervention using the difference in differences method: the Delivering Choice Programme.

PubMed

Round, Jeff; Drake, Robyn; Kendall, Edward; Addicott, Rachael; Agelopoulos, Nicky; Jones, Louise

2015-03-01

We report the use of difference in differences (DiD) methodology to evaluate a complex, system-wide healthcare intervention. We use the worked example of evaluating the Marie Curie Delivering Choice Programme (DCP) for advanced illness in a large urban healthcare economy. DiD was selected because a randomised controlled trial was not feasible. The method allows for before and after comparison of changes that occur in an intervention site with a matched control site. This enables analysts to control for the effect of the intervention in the absence of a local control. Any policy, seasonal or other confounding effects over the test period are assumed to have occurred in a balanced way at both sites. Data were obtained from primary care trusts. Outcomes were place of death, inpatient admissions, length of stay and costs. Small changes were identified between pre- and post-DCP outputs in the intervention site. The proportion of home deaths and median cost increased slightly, while the number of admissions per patient and the average length of stay per admission decreased slightly. None of these changes was statistically significant. Effects estimates were limited by small numbers accessing new services and selection bias in sample population and comparator site. In evaluating the effect of a complex healthcare intervention, the choice of analysis method and output measures is crucial. Alternatives to randomised controlled trials may be required for evaluating large scale complex interventions and the DiD approach is suitable, subject to careful selection of measured outputs and control population. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Neighbouring chimpanzee communities show different preferences in social grooming behaviour.

PubMed

van Leeuwen, Edwin J C; Cronin, Katherine A; Haun, Daniel B M; Mundry, Roger; Bodamer, Mark D

2012-11-07

Grooming handclasp (GHC) behaviour was originally advocated as the first evidence of social culture in chimpanzees owing to the finding that some populations engaged in the behaviour and others do not. To date, however, the validity of this claim and the extent to which this social behaviour varies between groups is unclear. Here, we measured (i) variation, (ii) durability and (iii) expansion of the GHC behaviour in four chimpanzee communities that do not systematically differ in their genetic backgrounds and live in similar ecological environments. Ninety chimpanzees were studied for a total of 1029 h; 1394 GHC bouts were observed between 2010 and 2012. Critically, GHC style (defined by points of bodily contact) could be systematically linked to the chimpanzee's group identity, showed temporal consistency both within and between groups, and could not be accounted for by the arm-length differential between partners. GHC has been part of the behavioural repertoire of the chimpanzees under study for more than 9 years (surpassing durability criterion) and spread across generations (surpassing expansion criterion). These results strongly indicate that chimpanzees' social behaviour is not only motivated by innate predispositions and individual inclinations, but may also be partly cultural in nature.

Adolescents with current major depressive disorder show dissimilar patterns of age-related differences in ACC and thalamus

PubMed Central

Hagan, Cindy C.; Graham, Julia M.E.; Tait, Roger; Widmer, Barry; van Nieuwenhuizen, Adrienne O.; Ooi, Cinly; Whitaker, Kirstie J.; Simas, Tiago; Bullmore, Edward T.; Lennox, Belinda R.; Sahakian, Barbara J.; Goodyer, Ian M.; Suckling, John

2015-01-01

Objective There is little understanding of the neural system abnormalities subserving adolescent major depressive disorder (MDD). In a cross-sectional study we compare currently unipolar depressed with healthy adolescents to determine if group differences in grey matter volume (GMV) were influenced by age and illness severity. Method Structural neuroimaging was performed on 109 adolescents with current MDD and 36 healthy controls, matched for age, gender, and handedness. GMV differences were examined within the anterior cingulate cortex (ACC) and across the whole-brain. The effects of age and self-reported depressive symptoms were also examined in regions showing significant main or interaction effects. Results Whole-brain voxel based morphometry revealed no significant group differences. At the whole-brain level, both groups showed a main effect of age on GMV, although this effect was more pronounced in controls. Significant group-by-age interactions were noted: A significant regional group-by-age interaction was observed in the ACC. GMV in the ACC showed patterns of age-related differences that were dissimilar between adolescents with MDD and healthy controls. GMV in the thalamus showed an opposite pattern of age-related differences in adolescent patients compared to healthy controls. In patients, GMV in the thalamus, but not the ACC, was inversely related with self-reported depressive symptoms. Conclusions The depressed adolescent brain shows dissimilar age-related and symptom-sensitive patterns of GMV differences compared with controls. The thalamus and ACC may comprise neural markers for detecting these effects in youth. Further investigations therefore need to take both age and level of current symptoms into account when disaggregating antecedent neural vulnerabilities for MDD from the effects of MDD on the developing brain. PMID:25685707

Adolescents with current major depressive disorder show dissimilar patterns of age-related differences in ACC and thalamus.

PubMed

Hagan, Cindy C; Graham, Julia M E; Tait, Roger; Widmer, Barry; van Nieuwenhuizen, Adrienne O; Ooi, Cinly; Whitaker, Kirstie J; Simas, Tiago; Bullmore, Edward T; Lennox, Belinda R; Sahakian, Barbara J; Goodyer, Ian M; Suckling, John

2015-01-01

There is little understanding of the neural system abnormalities subserving adolescent major depressive disorder (MDD). In a cross-sectional study we compare currently unipolar depressed with healthy adolescents to determine if group differences in grey matter volume (GMV) were influenced by age and illness severity. Structural neuroimaging was performed on 109 adolescents with current MDD and 36 healthy controls, matched for age, gender, and handedness. GMV differences were examined within the anterior cingulate cortex (ACC) and across the whole-brain. The effects of age and self-reported depressive symptoms were also examined in regions showing significant main or interaction effects. Whole-brain voxel based morphometry revealed no significant group differences. At the whole-brain level, both groups showed a main effect of age on GMV, although this effect was more pronounced in controls. Significant group-by-age interactions were noted: A significant regional group-by-age interaction was observed in the ACC. GMV in the ACC showed patterns of age-related differences that were dissimilar between adolescents with MDD and healthy controls. GMV in the thalamus showed an opposite pattern of age-related differences in adolescent patients compared to healthy controls. In patients, GMV in the thalamus, but not the ACC, was inversely related with self-reported depressive symptoms. The depressed adolescent brain shows dissimilar age-related and symptom-sensitive patterns of GMV differences compared with controls. The thalamus and ACC may comprise neural markers for detecting these effects in youth. Further investigations therefore need to take both age and level of current symptoms into account when disaggregating antecedent neural vulnerabilities for MDD from the effects of MDD on the developing brain.

Identified motor terminals in Drosophila larvae show distinct differences in morphology and physiology

NASA Technical Reports Server (NTRS)

Lnenicka, G. A.; Keshishian, H.

2000-01-01

In Drosophila, the type I motor terminals innervating the larval ventral longitudinal muscle fibers 6 and 7 have been the most popular preparation for combining synaptic studies with genetics. We have further characterized the normal morphological and physiological properties of these motor terminals and the influence of muscle size on terminal morphology. Using dye-injection and physiological techniques, we show that the two axons supplying these terminals have different innervation patterns: axon 1 innervates only muscle fibers 6 and 7, whereas axon 2 innervates all of the ventral longitudinal muscle fibers. This difference in innervation pattern allows the two axons to be reliably identified. The terminals formed by axons 1 and 2 on muscle fibers 6 and 7 have the same number of branches; however, axon 2 terminals are approximately 30% longer than axon 1 terminals, resulting in a corresponding greater number of boutons for axon 2. The axon 1 boutons are approximately 30% wider than the axon 2 boutons. The excitatory postsynaptic potential (EPSP) produced by axon 1 is generally smaller than that produced by axon 2, although the size distributions show considerable overlap. Consistent with vertebrate studies, there is a correlation between muscle fiber size and terminal size. For a single axon, terminal area and length, the number of terminal branches, and the number of boutons are all correlated with muscle fiber size, but bouton size is not. During prolonged repetitive stimulation, axon 2 motor terminals show synaptic depression, whereas axon 1 EPSPs facilitate. The response to repetitive stimulation appears to be similar at all motor terminals of an axon. Copyright 2000 John Wiley & Sons, Inc.

Genome-wide investigation and expression profiling of APX gene family in Gossypium hirsutum provide new insights in redox homeostasis maintenance during different fiber development stages.

PubMed

Tao, Chengcheng; Jin, Xiang; Zhu, Liping; Xie, Quanliang; Wang, Xuchu; Li, Hongbin

2018-06-01

Ascorbate peroxidase (APX) is a member of heme-containing peroxidases which catalyze the H 2 O 2 -dependent oxidation of a wide range of substrates in plants and animals. As is known, H 2 O 2 acts as a signaling molecule in the regulation of fiber development. Our previous work reported that ascorbate peroxidase 1 (GhAPX1) was important for cotton fiber elongation. However, knowledge about APX gene family members and their evolutionary and functional characteristics in cotton is limited. Here, we report 26 GhAPX genes by genome-wide investigation of tetraploid cotton Gossypium hirsutum. Phylogenetic and gene structure analyses classified these APX members into five clades and syntenic analysis suggested two duplication events. Expression profiling of the 26 APXs revealed that ten members are expressed in cotton fibers. Notably, GhAPX10A, GhAPX10D, GhAPX12A, and GhAPX12D showed high expression levels in 30-day fiber, while GhAPX1A/D, GhAPX3A/D, and GhAPX6A/D showed very low expression levels. The enzyme activity and H 2 O 2 content assays revealed that cotton fiber kept high enzyme activity and the lowest H 2 O 2 level in 30-day fibers, indicating that other than GhAPX1, the newly reported APX members are responsible for the reactive oxygen species homeostasis in the cotton fiber maturation stages. Expression profiling of ten fiber-expressed APXs after phytohormone treatments revealed their regulation patterns by different stimuli, suggesting that GhAPX1, GhAPX12A, and GhAPX12D are responsible to most phytohormone treatments. Our data provided evolutionary and functional information of GhAPX gene family members and revealed that different members are responsible to redox homeostasis during different cotton fiber development stages.

Evaluation of different sources of DNA for use in genome wide studies and forensic application.

PubMed

Al Safar, Habiba S; Abidi, Fatima H; Khazanehdari, Kamal A; Dadour, Ian R; Tay, Guan K

2011-02-01

In the field of epidemiology, Genome-Wide Association Studies (GWAS) are commonly used to identify genetic predispositions of many human diseases. Large repositories housing biological specimens for clinical and genetic investigations have been established to store material and data for these studies. The logistics of specimen collection and sample storage can be onerous, and new strategies have to be explored. This study examines three different DNA sources (namely, degraded genomic DNA, amplified degraded genomic DNA and amplified extracted DNA from FTA card) for GWAS using the Illumina platform. No significant difference in call rate was detected between amplified degraded genomic DNA extracted from whole blood and amplified DNA retrieved from FTA™ cards. However, using unamplified-degraded genomic DNA reduced the call rate to a mean of 42.6% compared to amplified DNA extracted from FTA card (mean of 96.6%). This study establishes the utility of FTA™ cards as a viable storage matrix for cells from which DNA can be extracted to perform GWAS analysis.

Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA.

PubMed

Skvortsova, Ksenia; Zotenko, Elena; Luu, Phuc-Loi; Gould, Cathryn M; Nair, Shalima S; Clark, Susan J; Stirzaker, Clare

2017-01-01

The discovery that 5-methylcytosine (5mC) can be oxidized to 5-hydroxymethylcytosine (5hmC) by the ten-eleven translocation (TET) proteins has prompted wide interest in the potential role of 5hmC in reshaping the mammalian DNA methylation landscape. The gold-standard bisulphite conversion technologies to study DNA methylation do not distinguish between 5mC and 5hmC. However, new approaches to mapping 5hmC genome-wide have advanced rapidly, although it is unclear how the different methods compare in accurately calling 5hmC. In this study, we provide a comparative analysis on brain DNA using three 5hmC genome-wide approaches, namely whole-genome bisulphite/oxidative bisulphite sequencing (WG Bis/OxBis-seq), Infinium HumanMethylation450 BeadChip arrays coupled with oxidative bisulphite (HM450K Bis/OxBis) and antibody-based immunoprecipitation and sequencing of hydroxymethylated DNA (hMeDIP-seq). We also perform loci-specific TET-assisted bisulphite sequencing (TAB-seq) for validation of candidate regions. We show that whole-genome single-base resolution approaches are advantaged in providing precise 5hmC values but require high sequencing depth to accurately measure 5hmC, as this modification is commonly in low abundance in mammalian cells. HM450K arrays coupled with oxidative bisulphite provide a cost-effective representation of 5hmC distribution, at CpG sites with 5hmC levels >~10%. However, 5hmC analysis is restricted to the genomic location of the probes, which is an important consideration as 5hmC modification is commonly enriched at enhancer elements. Finally, we show that the widely used hMeDIP-seq method provides an efficient genome-wide profile of 5hmC and shows high correlation with WG Bis/OxBis-seq 5hmC distribution in brain DNA. However, in cell line DNA with low levels of 5hmC, hMeDIP-seq-enriched regions are not detected by WG Bis/OxBis or HM450K, either suggesting misinterpretation of 5hmC calls by hMeDIP or lack of sensitivity of the latter methods. We

Genome-wide methylation patterns provide insight into differences in breast tumor biology between American women of African and European ancestry

PubMed Central

Ambrosone, Christine B.; Young, Allyson C.; Sucheston, Lara E.; Wang, Dan; Li, Yan; Liu, Song; Tang, Li; Hu, Quang; Freudenheim, Jo L.; Shields, Peter G.; Morrison, Carl D.; Demissie, Kitaw; Higgins, Michael J.

2014-01-01

American women of African ancestry (AA) are more likely than European-Americans (EA) to be diagnosed with aggressive, estrogen receptor (ER) negative breast tumors; mechanisms underlying these disparities are poorly understood. We conducted a genome wide (450K loci) methylation analysis to determine if there were differences in DNA methylation patterns between tumors from AA and EA women and if these differences were similar for both ER positive and ER negative breast cancer. Methylation levels at CpG loci within CpG islands (CGI)s and CGI-shores were significantly higher in tumors (n=138) than in reduction mammoplasty samples (n=124). In hierarchical cluster analysis, there was separation between tumor and normal samples, and in tumors, there was delineation by ER status, but not by ancestry. However, differential methylation analysis identified 157 CpG loci with a mean β value difference of at least 0.17 between races, with almost twice as many differences in ER-negative tumors compared to ER-positive cancers. This first genome-wide methylation study to address disparities indicates that there are likely differing etiologic pathways for the development of ER negative breast cancer between AA and EA women. Further investigation of the genes most differentially methylated by race in ER negative tumors can guide new approaches for cancer prevention and targeted therapies, and elucidate the biologic basis of breast cancer disparities. PMID:24368439

The Zeldovich approximation and wide-angle redshift-space distortions

NASA Astrophysics Data System (ADS)

Castorina, Emanuele; White, Martin

2018-06-01

The contribution of line-of-sight peculiar velocities to the observed redshift of objects breaks the translational symmetry of the underlying theory, modifying the predicted 2-point functions. These `wide angle effects' have mostly been studied using linear perturbation theory in the context of the multipoles of the correlation function and power spectrum . In this work we present the first calculation of wide angle terms in the Zeldovich approximation, which is known to be more accurate than linear theory on scales probed by the next generation of galaxy surveys. We present the exact result for dark matter and perturbatively biased tracers as well as the small angle expansion of the configuration- and Fourier-space two-point functions and the connection to the multi-frequency angular power spectrum. We compare different definitions of the line-of-sight direction and discuss how to translate between them. We show that wide angle terms can reach tens of percent of the total signal in a measurement at low redshift in some approximations, and that a generic feature of wide angle effects is to slightly shift the Baryon Acoustic Oscillation scale.

Evolution of plant cell wall: Arabinogalactan-proteins from three moss genera show structural differences compared to seed plants.

PubMed

Bartels, Desirée; Baumann, Alexander; Maeder, Malte; Geske, Thomas; Heise, Esther Marie; von Schwartzenberg, Klaus; Classen, Birgit

2017-05-01

Arabinogalactan-proteins (AGPs) are important proteoglycans of plant cell walls. They seem to be present in most, if not all seed plants, but their occurrence and structure in bryophytes is widely unknown and actually the focus of AGP research. With regard to evolution of plant cell wall, we isolated AGPs from the three mosses Sphagnum sp., Physcomitrella patens and Polytrichastrum formosum. The moss AGPs show structural characteristics common for AGPs of seed plants, but also unique features, especially 3-O-methyl-rhamnose (trivial name acofriose) as terminal monosaccharide not found in arabinogalactan-proteins of angiosperms and 1,2,3-linked galactose as branching point never found in arabinogalactan-proteins before. Copyright © 2017 Elsevier Ltd. All rights reserved.

Millennial-scale isotope records from a wide-ranging predator show evidence of recent human impact to oceanic food webs

PubMed Central

Wiley, Anne E.; Ostrom, Peggy H.; Welch, Andreanna J.; Fleischer, Robert C.; Gandhi, Hasand; Southon, John R.; Stafford, Thomas W.; Penniman, Jay F.; Hu, Darcy; Duvall, Fern P.; James, Helen F.

2013-01-01

Human exploitation of marine ecosystems is more recent in oceanic than near shore regions, yet our understanding of human impacts on oceanic food webs is comparatively poor. Few records of species that live beyond the continental shelves date back more than 60 y, and the sheer size of oceanic regions makes their food webs difficult to study, even in modern times. Here, we use stable carbon and nitrogen isotopes to study the foraging history of a generalist, oceanic predator, the Hawaiian petrel (Pterodroma sandwichensis), which ranges broadly in the Pacific from the equator to near the Aleutian Islands. Our isotope records from modern and ancient, radiocarbon-dated bones provide evidence of over 3,000 y of dietary stasis followed by a decline of ca. 1.8‰ in δ15N over the past 100 y. Fishery-induced trophic decline is the most likely explanation for this sudden shift, which occurs in genetically distinct populations with disparate foraging locations. Our isotope records also show that coincident with the apparent decline in trophic level, foraging segregation among petrel populations decreased markedly. Because variation in the diet of generalist predators can reflect changing availability of their prey, a foraging shift in wide-ranging Hawaiian petrel populations suggests a relatively rapid change in the composition of oceanic food webs in the Northeast Pacific. Understanding and mitigating widespread shifts in prey availability may be a critical step in the conservation of endangered marine predators such as the Hawaiian petrel. PMID:23671094

Millennial-scale isotope records from a wide-ranging predator show evidence of recent human impact to oceanic food webs.

PubMed

Wiley, Anne E; Ostrom, Peggy H; Welch, Andreanna J; Fleischer, Robert C; Gandhi, Hasand; Southon, John R; Stafford, Thomas W; Penniman, Jay F; Hu, Darcy; Duvall, Fern P; James, Helen F

2013-05-28

Human exploitation of marine ecosystems is more recent in oceanic than near shore regions, yet our understanding of human impacts on oceanic food webs is comparatively poor. Few records of species that live beyond the continental shelves date back more than 60 y, and the sheer size of oceanic regions makes their food webs difficult to study, even in modern times. Here, we use stable carbon and nitrogen isotopes to study the foraging history of a generalist, oceanic predator, the Hawaiian petrel (Pterodroma sandwichensis), which ranges broadly in the Pacific from the equator to near the Aleutian Islands. Our isotope records from modern and ancient, radiocarbon-dated bones provide evidence of over 3,000 y of dietary stasis followed by a decline of ca. 1.8‰ in δ(15)N over the past 100 y. Fishery-induced trophic decline is the most likely explanation for this sudden shift, which occurs in genetically distinct populations with disparate foraging locations. Our isotope records also show that coincident with the apparent decline in trophic level, foraging segregation among petrel populations decreased markedly. Because variation in the diet of generalist predators can reflect changing availability of their prey, a foraging shift in wide-ranging Hawaiian petrel populations suggests a relatively rapid change in the composition of oceanic food webs in the Northeast Pacific. Understanding and mitigating widespread shifts in prey availability may be a critical step in the conservation of endangered marine predators such as the Hawaiian petrel.

Candidate genes for obesity-susceptibility show enriched association within a large genome-wide association study for BMI.

PubMed

Vimaleswaran, Karani S; Tachmazidou, Ioanna; Zhao, Jing Hua; Hirschhorn, Joel N; Dudbridge, Frank; Loos, Ruth J F

2012-10-15

Before the advent of genome-wide association studies (GWASs), hundreds of candidate genes for obesity-susceptibility had been identified through a variety of approaches. We examined whether those obesity candidate genes are enriched for associations with body mass index (BMI) compared with non-candidate genes by using data from a large-scale GWAS. A thorough literature search identified 547 candidate genes for obesity-susceptibility based on evidence from animal studies, Mendelian syndromes, linkage studies, genetic association studies and expression studies. Genomic regions were defined to include the genes ±10 kb of flanking sequence around candidate and non-candidate genes. We used summary statistics publicly available from the discovery stage of the genome-wide meta-analysis for BMI performed by the genetic investigation of anthropometric traits consortium in 123 564 individuals. Hypergeometric, rank tail-strength and gene-set enrichment analysis tests were used to test for the enrichment of association in candidate compared with non-candidate genes. The hypergeometric test of enrichment was not significant at the 5% P-value quantile (P = 0.35), but was nominally significant at the 25% quantile (P = 0.015). The rank tail-strength and gene-set enrichment tests were nominally significant for the full set of genes and borderline significant for the subset without SNPs at P < 10(-7). Taken together, the observed evidence for enrichment suggests that the candidate gene approach retains some value. However, the degree of enrichment is small despite the extensive number of candidate genes and the large sample size. Studies that focus on candidate genes have only slightly increased chances of detecting associations, and are likely to miss many true effects in non-candidate genes, at least for obesity-related traits.

Comprehensive analysis of genome-wide DNA methylation across human polycystic ovary syndrome ovary granulosa cell.

PubMed

Xu, Jiawei; Bao, Xiao; Peng, Zhaofeng; Wang, Linlin; Du, Linqing; Niu, Wenbin; Sun, Yingpu

2016-05-10

Polycystic ovary syndrome (PCOS) affects approximately 7% of the reproductive-age women. A growing body of evidence indicated that epigenetic mechanisms contributed to the development of PCOS. The role of DNA modification in human PCOS ovary granulosa cell is still unknown in PCOS progression. Global DNA methylation and hydroxymethylation were detected between PCOS' and controls' granulosa cell. Genome-wide DNA methylation was profiled to investigate the putative function of DNA methylaiton. Selected genes expressions were analyzed between PCOS' and controls' granulosa cell. Our results showed that the granulosa cell global DNA methylation of PCOS patients was significant higher than the controls'. The global DNA hydroxymethylation showed low level and no statistical difference between PCOS and control. 6936 differentially methylated CpG sites were identified between control and PCOS-obesity. 12245 differential methylated CpG sites were detected between control and PCOS-nonobesity group. 5202 methylated CpG sites were significantly differential between PCOS-obesity and PCOS-nonobesity group. Our results showed that DNA methylation not hydroxymethylation altered genome-wide in PCOS granulosa cell. The different methylation genes were enriched in development protein, transcription factor activity, alternative splicing, sequence-specific DNA binding and embryonic morphogenesis. YWHAQ, NCF2, DHRS9 and SCNA were up-regulation in PCOS-obesity patients with no significance different between control and PCOS-nonobesity patients, which may be activated by lower DNA methylaiton. Global and genome-wide DNA methylation alteration may contribute to different genes expression and PCOS clinical pathology.

Genome-wide analysis of alternative splicing during human heart development

NASA Astrophysics Data System (ADS)

Wang, He; Chen, Yanmei; Li, Xinzhong; Chen, Guojun; Zhong, Lintao; Chen, Gangbing; Liao, Yulin; Liao, Wangjun; Bin, Jianping

2016-10-01

Alternative splicing (AS) drives determinative changes during mouse heart development. Recent high-throughput technological advancements have facilitated genome-wide AS, while its analysis in human foetal heart transition to the adult stage has not been reported. Here, we present a high-resolution global analysis of AS transitions between human foetal and adult hearts. RNA-sequencing data showed extensive AS transitions occurred between human foetal and adult hearts, and AS events occurred more frequently in protein-coding genes than in long non-coding RNA (lncRNA). A significant difference of AS patterns was found between foetal and adult hearts. The predicted difference in AS events was further confirmed using quantitative reverse transcription-polymerase chain reaction analysis of human heart samples. Functional foetal-specific AS event analysis showed enrichment associated with cell proliferation-related pathways including cell cycle, whereas adult-specific AS events were associated with protein synthesis. Furthermore, 42.6% of foetal-specific AS events showed significant changes in gene expression levels between foetal and adult hearts. Genes exhibiting both foetal-specific AS and differential expression were highly enriched in cell cycle-associated functions. In conclusion, we provided a genome-wide profiling of AS transitions between foetal and adult hearts and proposed that AS transitions and deferential gene expression may play determinative roles in human heart development.

Genome-wide analysis of selection on the malaria parasite Plasmodium falciparum in West African populations of differing infection endemicity.

PubMed

Mobegi, Victor A; Duffy, Craig W; Amambua-Ngwa, Alfred; Loua, Kovana M; Laman, Eugene; Nwakanma, Davis C; MacInnis, Bronwyn; Aspeling-Jones, Harvey; Murray, Lee; Clark, Taane G; Kwiatkowski, Dominic P; Conway, David J

2014-06-01

Locally varying selection on pathogens may be due to differences in drug pressure, host immunity, transmission opportunities between hosts, or the intensity of between-genotype competition within hosts. Highly recombining populations of the human malaria parasite Plasmodium falciparum throughout West Africa are closely related, as gene flow is relatively unrestricted in this endemic region, but markedly varying ecology and transmission intensity should cause distinct local selective pressures. Genome-wide analysis of sequence variation was undertaken on a sample of 100 P. falciparum clinical isolates from a highly endemic region of the Republic of Guinea where transmission occurs for most of each year and compared with data from 52 clinical isolates from a previously sampled population from The Gambia, where there is relatively limited seasonal malaria transmission. Paired-end short-read sequences were mapped against the 3D7 P. falciparum reference genome sequence, and data on 136,144 single nucleotide polymorphisms (SNPs) were obtained. Within-population analyses identifying loci showing evidence of recent positive directional selection and balancing selection confirm that antimalarial drugs and host immunity have been major selective agents. Many of the signatures of recent directional selection reflected by standardized integrated haplotype scores were population specific, including differences at drug resistance loci due to historically different antimalarial use between the countries. In contrast, both populations showed a similar set of loci likely to be under balancing selection as indicated by very high Tajima's D values, including a significant overrepresentation of genes expressed at the merozoite stage that invades erythrocytes and several previously validated targets of acquired immunity. Between-population FST analysis identified exceptional differentiation of allele frequencies at a small number of loci, most markedly for five SNPs covering a 15-kb

Genome-Wide Landscapes of Human Local Adaptation in Asia

PubMed Central

Lu, Dongsheng; Xu, Shuhua

2013-01-01

Genetic studies of human local adaptation have been facilitated greatly by recent advances in high-throughput genotyping and sequencing technologies. However, few studies have investigated local adaptation in Asian populations on a genome-wide scale and with a high geographic resolution. In this study, taking advantage of the dense population coverage in Southeast Asia, which is the part of the world least studied in term of natural selection, we depicted genome-wide landscapes of local adaptations in 63 Asian populations representing the majority of linguistic and ethnic groups in Asia. Using genome-wide data analysis, we discovered many genes showing signs of local adaptation or natural selection. Notable examples, such as FOXQ1, MAST2, and CDH4, were found to play a role in hair follicle development and human cancer, signal transduction, and tumor repression, respectively. These showed strong indications of natural selection in Philippine Negritos, a group of aboriginal hunter-gatherers living in the Philippines. MTTP, which has associations with metabolic syndrome, body mass index, and insulin regulation, showed a strong signature of selection in Southeast Asians, including Indonesians. Functional annotation analysis revealed that genes and genetic variants underlying natural selections were generally enriched in the functional category of alternative splicing. Specifically, many genes showing significant difference with respect to allele frequency between northern and southern Asian populations were found to be associated with human height and growth and various immune pathways. In summary, this study contributes to the overall understanding of human local adaptation in Asia and has identified both known and novel signatures of natural selection in the human genome. PMID:23349834

Adaptive and neutral markers both show continent-wide population structure of mountain pine beetle (Dendroctonus ponderosae).

PubMed

Batista, Philip D; Janes, Jasmine K; Boone, Celia K; Murray, Brent W; Sperling, Felix A H

2016-09-01

Assessments of population genetic structure and demographic history have traditionally been based on neutral markers while explicitly excluding adaptive markers. In this study, we compared the utility of putatively adaptive and neutral single-nucleotide polymorphisms (SNPs) for inferring mountain pine beetle population structure across its geographic range. Both adaptive and neutral SNPs, and their combination, allowed range-wide structure to be distinguished and delimited a population that has recently undergone range expansion across northern British Columbia and Alberta. Using an equal number of both adaptive and neutral SNPs revealed that adaptive SNPs resulted in a stronger correlation between sampled populations and inferred clustering. Our results suggest that adaptive SNPs should not be excluded prior to analysis from neutral SNPs as a combination of both marker sets resulted in better resolution of genetic differentiation between populations than either marker set alone. These results demonstrate the utility of adaptive loci for resolving population genetic structure in a nonmodel organism.

Revealing phenotype-associated functional differences by genome-wide scan of ancient haplotype blocks

PubMed Central

Onuki, Ritsuko; Yamaguchi, Rui; Shibuya, Tetsuo; Kanehisa, Minoru; Goto, Susumu

2017-01-01

Genome-wide scans for positive selection have become important for genomic medicine, and many studies aim to find genomic regions affected by positive selection that are associated with risk allele variations among populations. Most such studies are designed to detect recent positive selection. However, we hypothesize that ancient positive selection is also important for adaptation to pathogens, and has affected current immune-mediated common diseases. Based on this hypothesis, we developed a novel linkage disequilibrium-based pipeline, which aims to detect regions associated with ancient positive selection across populations from single nucleotide polymorphism (SNP) data. By applying this pipeline to the genotypes in the International HapMap project database, we show that genes in the detected regions are enriched in pathways related to the immune system and infectious diseases. The detected regions also contain SNPs reported to be associated with cancers and metabolic diseases, obesity-related traits, type 2 diabetes, and allergic sensitization. These SNPs were further mapped to biological pathways to determine the associations between phenotypes and molecular functions. Assessments of candidate regions to identify functions associated with variations in incidence rates of these diseases are needed in the future. PMID:28445522

Distance running as an ideal domain for showing a sex difference in competitiveness.

PubMed

Deaner, Robert O

2013-04-01

Men are over-represented in the arts, sciences, and sports. This has been hypothesized to reflect an evolved male predisposition for enduring competitiveness or long-term motivation to improve one's performance and "show-off." Evidence for this hypothesis is equivocal, however, because there are viable alternative explanations for men's dominance in most cultural display domains. Here, I argue that distance running is an ideal domain for addressing this issue. Distance running is ideal because it indicates enduring competitiveness, allows objective comparisons, and is accessible, acceptable, and popular for both men and women. I review recent studies and present new data showing that substantially more men than women run relatively fast in the U.S., that this sex difference in relative performance can be attributed, at least in part, to men's greater training motivation, and that this pattern has been stable for several decades. Distance running thus provides compelling evidence for an evolved male predisposition for enduring competitiveness. I conclude with suggestions regarding how variation in achievement motivation can be informed by considering how evolved predispositions interact with environmental and social conditions.

Adult monozygotic twins discordant for intra-uterine growth have indistinguishable genome-wide DNA methylation profiles.

PubMed

Souren, Nicole Y P; Lutsik, Pavlo; Gasparoni, Gilles; Tierling, Sascha; Gries, Jasmin; Riemenschneider, Matthias; Fryns, Jean-Pierre; Derom, Catherine; Zeegers, Maurice P; Walter, Jörn

2013-05-26

Low birth weight is associated with an increased adult metabolic disease risk. It is widely discussed that poor intra-uterine conditions could induce long-lasting epigenetic modifications, leading to systemic changes in regulation of metabolic genes. To address this, we acquire genome-wide DNA methylation profiles from saliva DNA in a unique cohort of 17 monozygotic monochorionic female twins very discordant for birth weight. We examine if adverse prenatal growth conditions experienced by the smaller co-twins lead to long-lasting DNA methylation changes. Overall, co-twins show very similar genome-wide DNA methylation profiles. Since observed differences are almost exclusively caused by variable cellular composition, an original marker-based adjustment strategy was developed to eliminate such variation at affected CpGs. Among adjusted and unchanged CpGs 3,153 are differentially methylated between the heavy and light co-twins at nominal significance, of which 45 show sensible absolute mean β-value differences. Deep bisulfite sequencing of eight such loci reveals that differences remain in the range of technical variation, arguing against a reproducible biological effect. Analysis of methylation in repetitive elements using methylation-dependent primer extension assays also indicates no significant intra-pair differences. Severe intra-uterine growth differences observed within these monozygotic twins are not associated with long-lasting DNA methylation differences in cells composing saliva, detectable with up-to-date technologies. Additionally, our results indicate that uneven cell type composition can lead to spurious results and should be addressed in epigenomic studies.

Talk Show Viewing Motives: Does Gender Make a Difference?

ERIC Educational Resources Information Center

Cress, Stacy L.; Rapert, Kevin D.

A study explored the relationship between gender and talk show viewing motives. Students (109) from 6 randomly selected introductory communication classes in a midwestern university, 30 people belonging to a non-traditional student organization called "Oasis," and 8 residents of a retirement home were given Rubin's instrument to assess…

NordicDB: a Nordic pool and portal for genome-wide control data.

PubMed

Leu, Monica; Humphreys, Keith; Surakka, Ida; Rehnberg, Emil; Muilu, Juha; Rosenström, Päivi; Almgren, Peter; Jääskeläinen, Juha; Lifton, Richard P; Kyvik, Kirsten Ohm; Kaprio, Jaakko; Pedersen, Nancy L; Palotie, Aarno; Hall, Per; Grönberg, Henrik; Groop, Leif; Peltonen, Leena; Palmgren, Juni; Ripatti, Samuli

2010-12-01

A cost-efficient way to increase power in a genetic association study is to pool controls from different sources. The genotyping effort can then be directed to large case series. The Nordic Control database, NordicDB, has been set up as a unique resource in the Nordic area and the data are available for authorized users through the web portal (http://www.nordicdb.org). The current version of NordicDB pools together high-density genome-wide SNP information from ∼5000 controls originating from Finnish, Swedish and Danish studies and shows country-specific allele frequencies for SNP markers. The genetic homogeneity of the samples was investigated using multidimensional scaling (MDS) analysis and pairwise allele frequency differences between the studies. The plot of the first two MDS components showed excellent resemblance to the geographical placement of the samples, with a clear NW-SE gradient. We advise researchers to assess the impact of population structure when incorporating NordicDB controls in association studies. This harmonized Nordic database presents a unique genome-wide resource for future genetic association studies in the Nordic countries.

NordicDB: a Nordic pool and portal for genome-wide control data

PubMed Central

Leu, Monica; Humphreys, Keith; Surakka, Ida; Rehnberg, Emil; Muilu, Juha; Rosenström, Päivi; Almgren, Peter; Jääskeläinen, Juha; Lifton, Richard P; Kyvik, Kirsten Ohm; Kaprio, Jaakko; Pedersen, Nancy L; Palotie, Aarno; Hall, Per; Grönberg, Henrik; Groop, Leif; Peltonen, Leena; Palmgren, Juni; Ripatti, Samuli

2010-01-01

A cost-efficient way to increase power in a genetic association study is to pool controls from different sources. The genotyping effort can then be directed to large case series. The Nordic Control database, NordicDB, has been set up as a unique resource in the Nordic area and the data are available for authorized users through the web portal (http://www.nordicdb.org). The current version of NordicDB pools together high-density genome-wide SNP information from ∼5000 controls originating from Finnish, Swedish and Danish studies and shows country-specific allele frequencies for SNP markers. The genetic homogeneity of the samples was investigated using multidimensional scaling (MDS) analysis and pairwise allele frequency differences between the studies. The plot of the first two MDS components showed excellent resemblance to the geographical placement of the samples, with a clear NW–SE gradient. We advise researchers to assess the impact of population structure when incorporating NordicDB controls in association studies. This harmonized Nordic database presents a unique genome-wide resource for future genetic association studies in the Nordic countries. PMID:20664631

Genome-wide association studies on HIV susceptibility, pathogenesis and pharmacogenomics

PubMed Central

2012-01-01

Susceptibility to HIV-1 and the clinical course after infection show a substantial heterogeneity between individuals. Part of this variability can be attributed to host genetic variation. Initial candidate gene studies have revealed interesting host factors that influence HIV infection, replication and pathogenesis. Recently, genome-wide association studies (GWAS) were utilized for unbiased searches at a genome-wide level to discover novel genetic factors and pathways involved in HIV-1 infection. This review gives an overview of findings from the GWAS performed on HIV infection, within different cohorts, with variable patient and phenotype selection. Furthermore, novel techniques and strategies in research that might contribute to the complete understanding of virus-host interactions and its role on the pathogenesis of HIV infection are discussed. PMID:22920050

Map showing how the potentiometric surface of the Magothy Aquifer of August 1980 differed from the potentiometric surface of September 1977, in southern Maryland

USGS Publications Warehouse

Mack, Frederick K.; Wheeler, J.C.; Curtin, Stephen E.

1982-01-01

The map is based on the differences between two sets of water-level measurements made in 65 observation wells. One set was made in 1977, a relatively dry year, and the other set was made in 1980, another relatively dry year. The map shows that the potentiometric surface was higher in 1980, by as much as 9 feet, than it was in 1977, in a band a few miles wide near the outcrop and subcrop areas of the aquifer in northern Prince Georges County and central Anne Arundel County. In the remainder of the map area, the 1980 potentiometric surface was lower than it had been in 1977, with declines as great as 20 feet measured in well fields at Waldorf and Chalk Point. The network of observation wells was developed and is operated and maintained as part of the cooperative program between the U.S. Geological Survey and agencies of the Maryland Department of Natural Resources. (USGS)

Genome-Wide Association Analysis Reveals Different Genetic Control in Panicle Architecture Between and Rice.

PubMed

Bai, Xufeng; Zhao, Hu; Huang, Yong; Xie, Weibo; Han, Zhongmin; Zhang, Bo; Guo, Zilong; Yang, Lin; Dong, Haijiao; Xue, Weiya; Li, Guangwei; Hu, Gang; Hu, Yong; Xing, Yongzhong

2016-07-01

Panicle architecture determines the number of spikelets per panicle (SPP) and is highly associated with grain yield in rice ( L.). Understanding the genetic basis of panicle architecture is important for improving the yield of rice grain. In this study, we dissected panicle architecture traits into eight components, which were phenotyped from a germplasm collection of 529 cultivars. Multiple regression analysis revealed that the number of secondary branch (NSB) was the major factor that contributed to SPP. Genome-wide association analysis was performed independently for the eight particle architecture traits observed in the and rice subpopulations compared with the whole rice population. In total, 30 loci were associated with these traits. Of these, 13 loci were closely linked to known panicle architecture genes, and 17 novel loci were repeatedly identified in different environments. An association signal cluster was identified for NSB and number of spikelets per secondary branch (NSSB) in the region of 31.6 to 31.7 Mb on chromosome 4. In addition to the common associations detected in both and subpopulations, many associated loci were unique to one subpopulation. For example, and were specifically associated with panicle length (PL) in and rice, respectively. Moreover, the -mediated flowering genes and were associated with the formation of panicle architecture in rice. These results suggest that different gene networks regulate panicle architecture in and rice. Copyright © 2016 Crop Science Society of America.

Research on filling scheme and deformation properties of wide subgrade of foamed lightweight soil on soft ground

NASA Astrophysics Data System (ADS)

Zhang, Faru; Yang, Deguang; Zhang, Liujun

2018-01-01

The wide subgrade on soft soil ground has the significantly different transverse settlement curve characteristics and the lacation of the maximum asymmetrical transverse settlement compared with ordinary subgrade. Especially when the subgrade filled with materials of different densities, the synergism deformation of ground-subgrade-pavement and the pavement structure stress become more complex. Combining with the engineering example, the settlement deformation characteristics of wide subgrade adopting the different filling scheme and the stress distribution of pavement structure are analyzed. Results show that the settlement curve of wide subgrade has a shape of flat middle with steep sides, and the maximum transverse asymmetrical settlement locates in close to the shoulder position. The maximum stress within the pavement structure is also in close to the shoulder position. Regarding the wide subgrade composed of main road and relief road, the post-construction settlement can be greatly reduced when both roads are filled with foamed lightweight soil.

Genome-wide analysis reveals signatures of selection for important traits in domestic sheep from different ecoregions.

PubMed

Liu, Zhaohua; Ji, Zhibin; Wang, Guizhi; Chao, Tianle; Hou, Lei; Wang, Jianmin

2016-11-03

Throughout a long period of adaptation and selection, sheep have thrived in a diverse range of ecological environments. Mongolian sheep is the common ancestor of the Chinese short fat-tailed sheep. Migration to different ecoregions leads to changes in selection pressures and results in microevolution. Mongolian sheep and its subspecies differ in a number of important traits, especially reproductive traits. Genome-wide intraspecific variation is required to dissect the genetic basis of these traits. This research resequenced 3 short fat-tailed sheep breeds with a 43.2-fold coverage of the sheep genome. We report more than 17 million single nucleotide polymorphisms and 2.9 million indels and identify 143 genomic regions with reduced pooled heterozygosity or increased genetic distance to each other breed that represent likely targets for selection during the migration. These regions harbor genes related to developmental processes, cellular processes, multicellular organismal processes, biological regulation, metabolic processes, reproduction, localization, growth and various components of the stress responses. Furthermore, we examined the haplotype diversity of 3 genomic regions involved in reproduction and found significant differences in TSHR and PRL gene regions among 8 sheep breeds. Our results provide useful genomic information for identifying genes or causal mutations associated with important economic traits in sheep and for understanding the genetic basis of adaptation to different ecological environments.

Adult monozygotic twins discordant for intra-uterine growth have indistinguishable genome-wide DNA methylation profiles

PubMed Central

2013-01-01

Background Low birth weight is associated with an increased adult metabolic disease risk. It is widely discussed that poor intra-uterine conditions could induce long-lasting epigenetic modifications, leading to systemic changes in regulation of metabolic genes. To address this, we acquire genome-wide DNA methylation profiles from saliva DNA in a unique cohort of 17 monozygotic monochorionic female twins very discordant for birth weight. We examine if adverse prenatal growth conditions experienced by the smaller co-twins lead to long-lasting DNA methylation changes. Results Overall, co-twins show very similar genome-wide DNA methylation profiles. Since observed differences are almost exclusively caused by variable cellular composition, an original marker-based adjustment strategy was developed to eliminate such variation at affected CpGs. Among adjusted and unchanged CpGs 3,153 are differentially methylated between the heavy and light co-twins at nominal significance, of which 45 show sensible absolute mean β-value differences. Deep bisulfite sequencing of eight such loci reveals that differences remain in the range of technical variation, arguing against a reproducible biological effect. Analysis of methylation in repetitive elements using methylation-dependent primer extension assays also indicates no significant intra-pair differences. Conclusions Severe intra-uterine growth differences observed within these monozygotic twins are not associated with long-lasting DNA methylation differences in cells composing saliva, detectable with up-to-date technologies. Additionally, our results indicate that uneven cell type composition can lead to spurious results and should be addressed in epigenomic studies. PMID:23706164

Experimental aspects in acquisition of wide bandwidth solid-state MAS NMR spectra of low-γ nuclei with different opportunities on two commercial NMR spectrometers

NASA Astrophysics Data System (ADS)

Jakobsen, Hans J.; Bildsøe, Henrik; Gan, Zhehong; Brey, William W.

2011-08-01

The acquisition and different appearances observed for wide bandwidth solid-state MAS NMR spectra of low-γ nuclei, using 14N as an illustrative nucleus and employing two different commercial spectrometers (Varian, 14.1 T and Bruker, 19.6 T), have been compared/evaluated and optimized from an experimental NMR and an electronic engineering point of view, to account for the huge differences in these spectra. The large differences in their spectral appearances, employing the recommended/standard experimental set-up for the two different spectrometers, are shown to be associated with quite large differences in the electronic design of the two types of preamplifiers, which are connected to their respective probes through a 50 Ω cable, and are here completely accounted for. This has led to different opportunities for optimum performances in the acquisition of nearly ideal wide bandwidth spectra for low-γ nuclei on the two spectrometers by careful evaluation of the length for the 50 Ω probe-to-preamp cable for the Varian system and appropriate changes to the bandwidth ( Q) of the NMR probe used on the Bruker spectrometer. Earlier, we reported quite distorted spectra obtained with Varian Unity INOVA spectrometers (at 11.4 and 14.1 T) in several exploratory wide bandwidth 14N MAS NMR studies of inorganic nitrates and amino acids. These spectra have now been compared/evaluated with fully analyzed 14N MAS spectra correspondingly acquired at 19.6 T on a Bruker spectrometer. It is shown that our upgraded version of the STARS simulation/iterative-fitting software is capable of providing identical sets for the molecular spectral parameters and corresponding fits to the experimental spectra, which fully agree with the electronic measurements, despite the highly different appearances for the MAS NMR spectra acquired on the Varian and Bruker spectrometers.

Multipotent human stromal cells isolated from cord blood, term placenta and adult bone marrow show distinct differences in gene expression pattern

PubMed Central

Matigian, Nicholas; Brooke, Gary; Zaibak, Faten; Rossetti, Tony; Kollar, Katarina; Pelekanos, Rebecca; Heazlewood, Celena; Mackay-Sim, Alan; Wells, Christine A.; Atkinson, Kerry

2014-01-01

Multipotent mesenchymal stromal cells derived from human placenta (pMSCs), and unrestricted somatic stem cells (USSCs) derived from cord blood share many properties with human bone marrow-derived mesenchymal stromal cells (bmMSCs) and are currently in clinical trials for a wide range of clinical settings. Here we present gene expression profiles of human cord blood-derived unrestricted somatic stem cells (USSCs), human placental-derived mesenchymal stem cells (hpMSCs), and human bone marrow-derived mesenchymal stromal cells (bmMSCs), all derived from four different donors. The microarray data are available on the ArrayExpress database (www.ebi.ac.uk/arrayexpress) under accession number E-TABM-880. Additionally, the data has been integrated into a public portal, www.stemformatics.org. Our data provide a resource for understanding the differences in MSCs derived from different tissues. PMID:26484151

Genome-Wide Analysis of Host Responses to Four Different Types of Microorganisms in Bombyx Mori (Lepidoptera: Bombycidae).

PubMed

Cheng, Tingcai; Lin, Ping; Huang, Lulin; Wu, Yuqian; Jin, Shengkai; Liu, Chun; Xia, Qingyou

2016-01-01

Several pathogenic microorganisms have been used to investigate the genome-wide transcriptional responses of Bombyx mori to infection. However, studies have so far each focused on one microorganism, and systematic genome-wide comparison of transcriptional responses to different pathogenic microorganisms has not been undertaken. Here, we surveyed transcriptional responses of B. mori to its natural bacterial, viral, and fungal pathogens, Bacillus bombyseptieus, B. mori nucleopolyhedrovirus (BmNPV), and Beauveria bassiana, respectively, and to nonpathogenic Escherichia coli, by microarray analysis. In total, the expression of 2,436, 1,804, 1,743, and 912 B. mori genes was modulated by infection with B. bombyseptieus, BmNPV, B. bassiana, and E. coli, respectively. Notably, the expression of 620, 400, 177, or 165 of these genes was only modulated by infection with B. bombyseptieus, BmNPV, B. bassiana, or E. coli, respectively. In contrast to the expression of genes related to juvenile hormone synthesis and metabolism, that of genes encoding juvenile hormone binding proteins was microorganism-specific. Three basal metabolic pathways were modulated by infection with any of the four microorganisms, and 3, 14, 5, and 2 metabolic pathways were specifically modulated by infection with B. bombyseptieus, BmNPV, B. bassiana, and E. coli, respectively. Interestingly, BmNPV infection modulated the JAK/STAT signaling pathway, whereas both the Imd and Toll signaling pathways were modulated by infection with B. bombyseptieus, B. bassiana, or E. coli These results elucidate potential molecular mechanisms of the host response to different microorganisms, and provide a foundation for further work on host-pathogen interaction. © The Author 2016. Published by Oxford University Press on behalf of the Entomological Society of America.

Short-focus and ultra-wide-angle lens design in wavefront coding

NASA Astrophysics Data System (ADS)

Zhang, Jiyan; Huang, Yuanqing; Xiong, Feibing

2016-10-01

Wavefront coding (WFC) is a hybrid technology designed to increase depth of field of conventional optics. The goal of our research is to apply this technology to the short-focus and ultra-wide-angle lens which suffers from the aberration related with large field of view (FOV) such as coma and astigmatism. WFC can also be used to compensate for other aberration which is sensitive to the FOV. Ultra-wide-angle lens has a little depth of focus because it has small F number and short-focus. We design a hybrid lens combing WFC with the ultra-wide-angle lens. The full FOV and relative aperture of the final design are up to170° and 1/1.8 respectively. The focal length is 2 mm. We adopt the cubic phase mask (CPM) in the design. The conventional design will have a wide variation of the point spread function (PSF) across the FOV and it is very sensitive with the variation of the FOV. The new design we obtain the PSF is nearly invariant over the whole FOV. But the result of the design also shows the little difference between the horizontal and vertical length of the PSF. We analyze that the CPM is non-symmetric phase mask and the FOV is so large, which will generate variation in the final image quality. For that reason, we apply a new method to avoid that happened. We try to make the rays incident on the CPM with small angle and decrease the deformation of the PSF. The experimental result shows the new method to optimize the CPM is fit for the ultra-wide-angle lens. The research above will be a helpful instruction to design the ultra-wide-angle lens with WFC.

Novel methodology for wide-ranged multistage morphing waverider based on conical theory

NASA Astrophysics Data System (ADS)

Liu, Zhen; Liu, Jun; Ding, Feng; Xia, Zhixun

2017-11-01

This study proposes the wide-ranged multistage morphing waverider design method. The flow field structure and aerodynamic characteristics of multistage waveriders are also analyzed. In this method, the multistage waverider is generated in the same conical flowfield, which contains a free-stream surface and different compression-stream surfaces. The obtained results show that the introduction of the multistage waverider design method can solve the problem of aerodynamic performance deterioration in the off-design state and allow the vehicle to always maintain the optimal flight state. The multistage waverider design method, combined with transfiguration flight strategy, can lead to greater design flexibility and the optimization of hypersonic wide-ranged waverider vehicles.

A framework to analyze hospital-wide patient flow logistics: evidence from an Italian comparative study.

PubMed

Villa, Stefano; Prenestini, Anna; Giusepi, Isabella

2014-04-01

Through a comparative study of six Italian hospitals, the paper develops and tests a framework to analyze hospital-wide patient flow performance. The framework adopts a system-wide approach to patient flow management and is structured around three different levels: (1) the hospital, (2) the pipelines (possible patient journeys within the hospital) and (3) the production units (physical spaces, such as operating rooms, where service delivery takes places). The focus groups and the data analysis conducted within the study support that the model is a useful tool to investigate hospital-wide implications of patient flows. The paper provides also evidence about the causes of hospital patient flow problems. Particularly, while shortage of capacity does not seem to be a relevant driver, our data shows that patient flow variability caused by inadequate allocation of capacity does represent a key problem. Results also show that the lack of coordination between different pipelines and production units is critical. Finally, the problem of overlapping between elective and unscheduled cases can be solved by setting aside a certain level of capacity for unexpected peaks. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Genome-wide Association Analysis of Psoriatic Arthritis and Cutaneous Psoriasis Reveals Differences in Their Genetic Architecture.

PubMed

Stuart, Philip E; Nair, Rajan P; Tsoi, Lam C; Tejasvi, Trilokraj; Das, Sayantan; Kang, Hyun Min; Ellinghaus, Eva; Chandran, Vinod; Callis-Duffin, Kristina; Ike, Robert; Li, Yanming; Wen, Xiaoquan; Enerbäck, Charlotta; Gudjonsson, Johann E; Kõks, Sulev; Kingo, Külli; Esko, Tõnu; Mrowietz, Ulrich; Reis, Andre; Wichmann, H Erich; Gieger, Christian; Hoffmann, Per; Nöthen, Markus M; Winkelmann, Juliane; Kunz, Manfred; Moreta, Elvia G; Mease, Philip J; Ritchlin, Christopher T; Bowcock, Anne M; Krueger, Gerald G; Lim, Henry W; Weidinger, Stephan; Weichenthal, Michael; Voorhees, John J; Rahman, Proton; Gregersen, Peter K; Franke, Andre; Gladman, Dafna D; Abecasis, Gonçalo R; Elder, James T

2015-12-03

Psoriasis vulgaris (PsV) is a common inflammatory and hyperproliferative skin disease. Up to 30% of people with PsV eventually develop psoriatic arthritis (PsA), an inflammatory musculoskeletal condition. To discern differences in genetic risk factors for PsA and cutaneous-only psoriasis (PsC), we carried out a genome-wide association study (GWAS) of 1,430 PsA case subjects and 1,417 unaffected control subjects. Meta-analysis of this study with three other GWASs and two targeted genotyping studies, encompassing a total of 9,293 PsV case subjects, 3,061 PsA case subjects, 3,110 PsC case subjects, and 13,670 unaffected control subjects of European descent, detected 10 regions associated with PsA and 11 with PsC at genome-wide (GW) significance. Several of these association signals (IFNLR1, IFIH1, NFKBIA for PsA; TNFRSF9, LCE3C/B, TRAF3IP2, IL23A, NFKBIA for PsC) have not previously achieved GW significance. After replication, we also identified a PsV-associated SNP near CDKAL1 (rs4712528, odds ratio [OR] = 1.16, p = 8.4 × 10(-11)). Among identified psoriasis risk variants, three were more strongly associated with PsC than PsA (rs12189871 near HLA-C, p = 5.0 × 10(-19); rs4908742 near TNFRSF9, p = 0.00020; rs10888503 near LCE3A, p = 0.0014), and two were more strongly associated with PsA than PsC (rs12044149 near IL23R, p = 0.00018; rs9321623 near TNFAIP3, p = 0.00022). The PsA-specific variants were independent of previously identified psoriasis variants near IL23R and TNFAIP3. We also found multiple independent susceptibility variants in the IL12B, NOS2, and IFIH1 regions. These results provide insights into the pathogenetic similarities and differences between PsC and PsA. Copyright © 2015 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Sample Reproducibility of Genetic Association Using Different Multimarker TDTs in Genome-Wide Association Studies: Characterization and a New Approach

PubMed Central

Abad-Grau, Mara M.; Medina-Medina, Nuria; Montes-Soldado, Rosana; Matesanz, Fuencisla; Bafna, Vineet

2012-01-01

Multimarker Transmission/Disequilibrium Tests (TDTs) are very robust association tests to population admixture and structure which may be used to identify susceptibility loci in genome-wide association studies. Multimarker TDTs using several markers may increase power by capturing high-degree associations. However, there is also a risk of spurious associations and power reduction due to the increase in degrees of freedom. In this study we show that associations found by tests built on simple null hypotheses are highly reproducible in a second independent data set regardless the number of markers. As a test exhibiting this feature to its maximum, we introduce the multimarker -Groups TDT ( ), a test which under the hypothesis of no linkage, asymptotically follows a distribution with degree of freedom regardless the number of markers. The statistic requires the division of parental haplotypes into two groups: disease susceptibility and disease protective haplotype groups. We assessed the test behavior by performing an extensive simulation study as well as a real-data study using several data sets of two complex diseases. We show that test is highly efficient and it achieves the highest power among all the tests used, even when the null hypothesis is tested in a second independent data set. Therefore, turns out to be a very promising multimarker TDT to perform genome-wide searches for disease susceptibility loci that may be used as a preprocessing step in the construction of more accurate genetic models to predict individual susceptibility to complex diseases. PMID:22363405

Steep Decrease of Gender Difference in DSM-IV Alcohol Use Disorder: A Comparison of Two Nation-wide Surveys Conducted 10 Years Apart in Korea

PubMed Central

Seong, Su Jeong; Hong, Jin Pyo; Hahm, Bong-Jin; Jeon, Hong Jin; Sohn, Jee Hoon; Lee, Jun Young

2015-01-01

While decreasing trend in gender differences in alcohol use disorders was reported in Western countries, the change in Asian countries is unknown. This study aims to explore the shifts in gender difference in alcohol abuse (AA) and dependence (AD) in Korea. We compared the data from two nation-wide community surveys to evaluate gender differences in lifetime AA and AD by Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV). Face-to-face interviews using the Composite International Diagnostic Interview (CIDI) were applied to all subjects in 2001 (n=6,220) and 2011 (n=6,022). Male-to-female ratio of odds was decreased from 6.41 (95% CI, 4.81-8.54) to 4.37 (95% CI, 3.35-5.71) for AA and from 3.75 (95% CI, 2.96-4.75) to 2.40 (95% CI, 1.80-3.19) for AD. Among those aged 18-29, gender gap even became statistically insignificant for AA (OR, 1.59; 95% CI, 0.97-2.63) and AD (OR, 1.18; 95% CI, 0.80-2.41) in 2011. Men generally showed decreased odds for AD (0.55; 95% CI, 0.45-0.67) and women aged 30-39 showed increased odds for AA (2.13; 95% CI 1.18-3.84) in 2011 compared to 2001. Decreased AD in men and increased AA in women seem to contribute to the decrease of gender gap. Increased risk for AA in young women suggests needs for interventions. PMID:26539014

Distributed fiber sensing system with wide frequency response and accurate location

NASA Astrophysics Data System (ADS)

Shi, Yi; Feng, Hao; Zeng, Zhoumo

2016-02-01

A distributed fiber sensing system merging Mach-Zehnder interferometer and phase-sensitive optical time domain reflectometer (Φ-OTDR) is demonstrated for vibration measurement, which requires wide frequency response and accurate location. Two narrow line-width lasers with delicately different wavelengths are used to constitute the interferometer and reflectometer respectively. A narrow band Fiber Bragg Grating is responsible for separating the two wavelengths. In addition, heterodyne detection is applied to maintain the signal to noise rate of the locating signal. Experiment results show that the novel system has a wide frequency from 1 Hz to 50 MHz, limited by the sample frequency of data acquisition card, and a spatial resolution of 20 m, according to 200 ns pulse width, along 2.5 km fiber link.

Identification and validation of seven new loci showing differential DNA methylation related to serum lipid profile: an epigenome-wide approach. The REGICOR study.

PubMed

Sayols-Baixeras, S; Subirana, I; Lluis-Ganella, C; Civeira, F; Roquer, J; Do, A N; Absher, D; Cenarro, A; Muñoz, D; Soriano-Tárraga, C; Jiménez-Conde, J; Ordovas, J M; Senti, M; Aslibekyan, S; Marrugat, J; Arnett, D K; Elosua, R

2016-10-15

Lipid traits (total, low-density and high-density lipoprotein cholesterol, and triglycerides) are risk factors for cardiovascular disease. DNA methylation is not only an inherited but also modifiable epigenetic mark that has been related to cardiovascular risk factors. Our aim was to identify loci showing differential DNA methylation related to serum lipid levels. Blood DNA methylation was assessed using the Illumina Human Methylation 450 BeadChip. A two-stage epigenome-wide association study was performed, with a discovery sample in the REGICOR study (n = 645) and validation in the Framingham Offspring Study (n = 2,542). Fourteen CpG sites located in nine genes (SREBF1, SREBF2, PHOSPHO1, SYNGAP1, ABCG1, CPT1A, MYLIP, TXNIP and SLC7A11) and 2 intergenic regions showed differential methylation in association with lipid traits. Six of these genes and 1 intergenic region were new discoveries showing differential methylation related to total cholesterol (SREBF2), HDL-cholesterol (PHOSPHO1, SYNGAP1 and an intergenic region in chromosome 2) and triglycerides (MYLIP, TXNIP and SLC7A11). These CpGs explained 0.7%, 9.5% and 18.9% of the variability of total cholesterol, HDL cholesterol and triglycerides in the Framingham Offspring Study, respectively. The expression of the genes SREBF2 and SREBF1 was inversely associated with methylation of their corresponding CpGs (P-value = 0.0042 and 0.0045, respectively) in participants of the GOLDN study (n = 98). In turn, SREBF1 expression was directly associated with HDL cholesterol (P-value = 0.0429). Genetic variants in SREBF1, PHOSPHO1, ABCG1 and CPT1A were also associated with lipid profile. Further research is warranted to functionally validate these new loci and assess the causality of new and established associations between these differentially methylated loci and lipid metabolism.

Rubber particle proteins, HbREF and HbSRPP, show different interactions with model membranes.

PubMed

Berthelot, Karine; Lecomte, Sophie; Estevez, Yannick; Zhendre, Vanessa; Henry, Sarah; Thévenot, Julie; Dufourc, Erick J; Alves, Isabel D; Peruch, Frédéric

2014-01-01

The biomembrane surrounding rubber particles from the hevea latex is well known for its content of numerous allergen proteins. HbREF (Hevb1) and HbSRPP (Hevb3) are major components, linked on rubber particles, and they have been shown to be involved in rubber synthesis or quality (mass regulation), but their exact function is still to be determined. In this study we highlighted the different modes of interactions of both recombinant proteins with various membrane models (lipid monolayers, liposomes or supported bilayers, and multilamellar vesicles) to mimic the latex particle membrane. We combined various biophysical methods (polarization-modulation-infrared reflection-adsorption spectroscopy (PM-IRRAS)/ellipsometry, attenuated-total reflectance Fourier-transform infrared (ATR-FTIR), solid-state nuclear magnetic resonance (NMR), plasmon waveguide resonance (PWR), fluorescence spectroscopy) to elucidate their interactions. Small rubber particle protein (SRPP) shows less affinity than rubber elongation factor (REF) for the membranes but displays a kind of "covering" effect on the lipid headgroups without disturbing the membrane integrity. Its structure is conserved in the presence of lipids. Contrarily, REF demonstrates higher membrane affinity with changes in its aggregation properties, the amyloid nature of REF, which we previously reported, is not favored in the presence of lipids. REF binds and inserts into membranes. The membrane integrity is highly perturbed, and we suspect that REF is even able to remove lipids from the membrane leading to the formation of mixed micelles. These two homologous proteins show affinity to all membrane models tested but neatly differ in their interacting features. This could imply differential roles on the surface of rubber particles. © 2013.

32-Bit-Wide Memory Tolerates Failures

NASA Technical Reports Server (NTRS)

Buskirk, Glenn A.

1990-01-01

Electronic memory system of 32-bit words corrects bit errors caused by some common type of failures - even failure of entire 4-bit-wide random-access-memory (RAM) chip. Detects failure of two such chips, so user warned that ouput of memory may contain errors. Includes eight 4-bit-wide DRAM's configured so each bit of each DRAM assigned to different one of four parallel 8-bit words. Each DRAM contributes only 1 bit to each 8-bit word.

Comparison of Three Surgical Methods in Treatment of Patients with Pilonidal Sinus: Modified Excision and Repair/Wide Excision/Wide Excision and Flap in RASOUL, OMID and SADR Hospitals( 2004-2007).

PubMed

Hosseini, Mostafa; Heidari, Afshin; Jafarnejad, Babak

2013-10-01

This study is a comparison between three methods that are frequently used for the surgical treatment of pilonidal disease all over the world: modified excision and repair, wide excision and secondary repair, and wide excision and flap. The first technique is done by our group for the first time, and has not been described previously in the literature. This is an interventional study performed at Omid, Sadr, and Rasoul Akram hospitals on patients who had undergone operation because of pilonidal sinus disease and met the inclusion criteria between 2004 and 2007. Exclusion criteria were (1) acute pilonidal sinus diseases, (2) history of pilonidal sinus surgery, (3) history of systemic diseases (DM, malignancy, etc.), and (4) pilonidal abscess. Essential information was extracted from complete medical archives. Any data not available in files or during follow-up visits (all patients supposed to be followed at least for 1 year) were gathered by a telephone interview. A total of 194 patients met the criteria and had complete archived files. Longer duration of hospital stay was found in the "wide excision and closing with flap" method comparing with two other methods (P < 0.05). Length of incapacity for work was not different between the "wide excision and modified repair" and "wide excision" (P > 0.5) methods, but longer for "wide excision and flap" in comparison with two others (P < 0.05). Healing time was significantly longer in the "wide excision" method in comparison with two other methods (P < 0.05). However, "wide excision and modified repair" method had the least healing time between all above techniques, except for length of leaving the office. All the three recurrences (1.5 %) occurred in the wide excision and flap method (P < 0.05). The frequency of postoperative complications was 2 (3.3 %) in wide excision and modified repair, 15 (18.5 %) in wide excision, and 17 (32.7 %) in wide excision and flap closure; these differences in

Formation of wide binaries by turbulent fragmentation

NASA Astrophysics Data System (ADS)

Lee, Jeong-Eun; Lee, Seokho; Dunham, Michael M.; Tatematsu, Ken'ichi; Choi, Minho; Bergin, Edwin A.; Evans, Neal J.

2017-08-01

Understanding the formation of wide-binary systems of very low-mass stars (M ≤ 0.1 solar masses, M⊙) is challenging 1,2,3 . The most obvious route is through widely separated low-mass collapsing fragments produced by turbulent fragmentation of a molecular core4,5. However, close binaries or multiples from disk fragmentation can also evolve to wide binaries over a few initial crossing times of the stellar cluster through tidal evolution6. Finding an isolated low-mass wide-binary system in the earliest stage of formation, before tidal evolution could occur, would prove that turbulent fragmentation is a viable mechanism for (very) low-mass wide binaries. Here we report high-resolution ALMA observations of a known wide-separation protostellar binary, showing that each component has a circumstellar disk. The system is too young7 to have evolved from a close binary, and the disk axes are misaligned, providing strong support for the turbulent fragmentation model. Masses of both stars are derived from the Keplerian rotation of the disks; both are very low-mass stars.

Real-life decision making in college students. II: Do individual differences show reliable effects?

PubMed

Galotti, Kathleen M; Tandler, Jane M; Wiener, Hillary J D

2014-01-01

First-year undergraduates participated in a short-term longitudinal study of real-life decision making over their first 14 months of college. They were surveyed about 7 different decisions: choosing courses for upcoming terms (on 3 different occasions), choosing an academic major (twice), planning for the upcoming summer, and planning for sophomore-year housing. They also completed a survey of self-reported decision-making styles and the Need for Cognition survey (Cacioppo & Petty, 1982) to assess their focus on rationality and enjoyment of analytic thinking. Results showed few statistically significant correlations between stylistic measures and behavioral measures of decision making, in either the amount of information considered or the way in which the information integration tracked predictions of linear models of decision making applied to each participant's data. However, there were consistent correlations, across the 7 decisions, between stylistic measures and affective reactions to, or retrospective descriptions of, episodes of decision making. We suggest that decision-making styles instruments may better reflect the construction of narratives of self as a decision maker more than they do actual behavior during decision making.

Leaf traits show different relationships with shade tolerance in moist versus dry tropical forests.

PubMed

Poorter, Lourens

2009-03-01

Shade tolerance is the central paradigm for understanding forest succession and dynamics, but there is considerable debate as to what the salient features of shade tolerance are, whether adult leaves show similar shade adaptations to seedling leaves, and whether the same leaf adaptations are found in forests under different climatic control. Here, adult leaf and metamer traits were measured for 39 tree species from a tropical moist semi-evergreen forest (1580 mm rain yr(-1)) and 41 species from a dry deciduous forest (1160 mm yr(-1)) in Bolivia. Twenty-six functional traits were measured and related to species regeneration light requirements.Adult leaf traits were clearly associated with shade tolerance. Different, rather than stronger, shade adaptations were found for moist compared with dry forest species. Shade adaptations exclusively found in the evergreen moist forest were related to tough and persistent leaves, and shade adaptations in the dry deciduous forest were related to high light interception and water use.These results suggest that, for forests differing in rainfall seasonality, there is a shift in the relative importance of functional leaf traits and performance trade-offs that control light partitioning. In the moist evergreen forest leaf traits underlying the growth-survival trade-off are important, whereas in the seasonally deciduous forest leaf traits underlying the growth trade-off between low and high light might become important.

Comparison of different detection methods for persistent multiple hypothesis tracking in wide area motion imagery

NASA Astrophysics Data System (ADS)

Hartung, Christine; Spraul, Raphael; Schuchert, Tobias

2017-10-01

Wide area motion imagery (WAMI) acquired by an airborne multicamera sensor enables continuous monitoring of large urban areas. Each image can cover regions of several square kilometers and contain thousands of vehicles. Reliable vehicle tracking in this imagery is an important prerequisite for surveillance tasks, but remains challenging due to low frame rate and small object size. Most WAMI tracking approaches rely on moving object detections generated by frame differencing or background subtraction. These detection methods fail when objects slow down or stop. Recent approaches for persistent tracking compensate for missing motion detections by combining a detection-based tracker with a second tracker based on appearance or local context. In order to avoid the additional complexity introduced by combining two trackers, we employ an alternative single tracker framework that is based on multiple hypothesis tracking and recovers missing motion detections with a classifierbased detector. We integrate an appearance-based similarity measure, merge handling, vehicle-collision tests, and clutter handling to adapt the approach to the specific context of WAMI tracking. We apply the tracking framework on a region of interest of the publicly available WPAFB 2009 dataset for quantitative evaluation; a comparison to other persistent WAMI trackers demonstrates state of the art performance of the proposed approach. Furthermore, we analyze in detail the impact of different object detection methods and detector settings on the quality of the output tracking results. For this purpose, we choose four different motion-based detection methods that vary in detection performance and computation time to generate the input detections. As detector parameters can be adjusted to achieve different precision and recall performance, we combine each detection method with different detector settings that yield (1) high precision and low recall, (2) high recall and low precision, and (3) best f

Mitigating fluorescence spectral overlap in wide-field endoscopic imaging

PubMed Central

Hou, Vivian; Nelson, Leonard Y.; Seibel, Eric J.

2013-01-01

Abstract. The number of molecular species suitable for multispectral fluorescence imaging is limited due to the overlap of the emission spectra of indicator fluorophores, e.g., dyes and nanoparticles. To remove fluorophore emission cross-talk in wide-field multispectral fluorescence molecular imaging, we evaluate three different solutions: (1) image stitching, (2) concurrent imaging with cross-talk ratio subtraction algorithm, and (3) frame-sequential imaging. A phantom with fluorophore emission cross-talk is fabricated, and a 1.2-mm ultrathin scanning fiber endoscope (SFE) is used to test and compare these approaches. Results show that fluorophore emission cross-talk could be successfully avoided or significantly reduced. Near term, the concurrent imaging method of wide-field multispectral fluorescence SFE is viable for early stage cancer detection and localization in vivo. Furthermore, a means to enhance exogenous fluorescence target-to-background ratio by the reduction of tissue autofluorescence background is demonstrated. PMID:23966226

Insights learned from teaching pathophysiology on the World Wide Web.

PubMed

Yucha, C; Princen, T

2000-02-01

This article describes a one-credit, graduate level pathophysiology module taught using the World Wide Web. Student outcomes are compared to those of students who took the same module in a traditional classroom setting. Although the majority of the graduate students were not Web literate, they became more comfortable with this instructional medium over time. A comparison of the Web-based instruction with the traditional format, both directed by the same instructor, showed no significant differences in student performance on a multiple choice examination.

Genetic variants in LEKR1 and GALNT10 modulate sex-difference in carotid intima-media thickness: a genome-wide interaction study.

PubMed

Dong, Chuanhui; Della-Morte, David; Beecham, Ashley; Wang, Liyong; Cabral, Digna; Blanton, Susan H; Sacco, Ralph L; Rundek, Tatjana

2015-06-01

There is an established sex-difference in carotid artery intima-media thickness (cIMT), a recognized marker of subclinical atherosclerosis. However, the genetic underpinnings of sex-differences in gene-IMT associations are largely unknown. With a multistage design using 731,037 single nucleotide polymorphisms (SNP), a genome wide interaction study was performed in a discovery sample of 931 unrelated Hispanics, followed by replication in 153 non-Hispanic whites and 257 non-Hispanic blacks. Assuming an additive genetic model, we tested for sex-SNP interactions on cIMT using regression analysis. We did not identify any genome-wide significant SNPs but identified 14 loci with suggestive significance. Specifically, SNP-by-sex interaction was found for rs7616559 within LEKR1 gene (P = 3.5E-06 in Hispanic discovery sample, P = 0.018 in White, and P = 1.3E-06 in combined analysis) and for rs2081015 located within GALNT10 gene (P = 4.5E-06 in Hispanic discovery sample, P = 0.042 in Blacks, and P = 5.3E-07 in combined analysis). For rs7616559 within LEKR1, men had greater cIMT than women in G allele carriers (beta ± SE: 0.044 ± 0.007, P = 4.2E-09 in AG carriers; beta ± SE: 0.064 ± 0.007, P = 6.2E-05 in GG carriers). For rs2081015 within GALNT10, men had greater cIMT than women in C allele carriers (beta ± SE: 0.022 ± 0.007, P = 0.002 in CT carriers; beta ± SE: 0.051 ± 0.008, P = 3.1E-10 in CC carriers). Our genome-wide interaction analysis reveals multiple loci that may modulate sex difference in cIMT. Of them, genetic variants on LEKR1 and GALNT10 genes have been associated with control of adiposity and weight. Given the consistent findings across different-ethnic groups, further studies are warranted to perform investigations of functional genetic variants in these regions. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Sample reproducibility of genetic association using different multimarker TDTs in genome-wide association studies: characterization and a new approach.

PubMed

Abad-Grau, Mara M; Medina-Medina, Nuria; Montes-Soldado, Rosana; Matesanz, Fuencisla; Bafna, Vineet

2012-01-01

Multimarker Transmission/Disequilibrium Tests (TDTs) are very robust association tests to population admixture and structure which may be used to identify susceptibility loci in genome-wide association studies. Multimarker TDTs using several markers may increase power by capturing high-degree associations. However, there is also a risk of spurious associations and power reduction due to the increase in degrees of freedom. In this study we show that associations found by tests built on simple null hypotheses are highly reproducible in a second independent data set regardless the number of markers. As a test exhibiting this feature to its maximum, we introduce the multimarker 2-Groups TDT (mTDT(2G)), a test which under the hypothesis of no linkage, asymptotically follows a χ2 distribution with 1 degree of freedom regardless the number of markers. The statistic requires the division of parental haplotypes into two groups: disease susceptibility and disease protective haplotype groups. We assessed the test behavior by performing an extensive simulation study as well as a real-data study using several data sets of two complex diseases. We show that mTDT(2G) test is highly efficient and it achieves the highest power among all the tests used, even when the null hypothesis is tested in a second independent data set. Therefore, mTDT(2G) turns out to be a very promising multimarker TDT to perform genome-wide searches for disease susceptibility loci that may be used as a preprocessing step in the construction of more accurate genetic models to predict individual susceptibility to complex diseases.

Psychoacoustic Tinnitus Loudness and Tinnitus-Related Distress Show Different Associations with Oscillatory Brain Activity

PubMed Central

Balkenhol, Tobias; Wallhäusser-Franke, Elisabeth; Delb, Wolfgang

2013-01-01

Background The phantom auditory perception of subjective tinnitus is associated with aberrant brain activity as evidenced by magneto- and electroencephalographic studies. We tested the hypotheses (1) that psychoacoustically measured tinnitus loudness is related to gamma oscillatory band power, and (2) that tinnitus loudness and tinnitus-related distress are related to distinct brain activity patterns as suggested by the distinction between loudness and distress experienced by tinnitus patients. Furthermore, we explored (3) how hearing impairment, minimum masking level, and (4) psychological comorbidities are related to spontaneous oscillatory brain activity in tinnitus patients. Methods and Findings Resting state oscillatory brain activity recorded electroencephalographically from 46 male tinnitus patients showed a positive correlation between gamma band oscillations and psychoacoustic tinnitus loudness determined with the reconstructed tinnitus sound, but not with the other psychoacoustic loudness measures that were used. Tinnitus-related distress did also correlate with delta band activity, but at electrode positions different from those associated with tinnitus loudness. Furthermore, highly distressed tinnitus patients exhibited a higher level of theta band activity. Moreover, mean hearing loss between 0.125 kHz and 16 kHz was associated with a decrease in gamma activity, whereas minimum masking levels correlated positively with delta band power. In contrast, psychological comorbidities did not express significant correlations with oscillatory brain activity. Conclusion Different clinically relevant tinnitus characteristics show distinctive associations with spontaneous brain oscillatory power. Results support hypothesis (1), but exclusively for the tinnitus loudness derived from matching to the reconstructed tinnitus sound. This suggests to preferably use the reconstructed tinnitus spectrum to determine psychoacoustic tinnitus loudness. Results also support

Dietary patterns among children aged 6-7 y in four Spanish cities with widely differing cardiovascular mortality.

PubMed

Rodríguez-Artalejo, F; Garcés, C; Gorgojo, L; López García, E; Martín-Moreno, J M; Benavente, M; del Barrio, J L; Rubio, R; Ortega, H; Fernández, O; de Oya, M

2002-02-01

Classic cardiovascular risk factors, such as smoking, arterial hypertension and hypercholesterolaemia, cannot explain a substantial part of the geographic differences in cardiovascular mortality. Anthropometric and nutritional factors in early stages of life may contribute to adult cardiovascular disease. Therefore, this work examines certain anthropometric variables and diet among children aged 6-7 y, living in four Spanish cities with widely differing ischaemic heart disease (IHD) mortality. Cross-sectional anthropometric and dietary survey in four cities in Spain. A total of 1112 children (50.1% males, 49.9% females) attending public and private schools in Cadiz and Murcia, cities with a relatively high IHD mortality, and Madrid and Orense, cities with a relatively low IHD mortality. A standardized method was used to measure anthropometric variables, and a food-frequency questionnaire completed by subjects' mothers, to measure diet. Body mass index (BMI), overweight (BMI>17.6 kg/m(2)), obesity (BMI>20.1 kg/m(2)) and intake of food and nutrients. Children in the four cities showed a high prevalence of overweight (range across cities, 28.9-34.5%) and obesity (8.5-15.7%). They also had a moderately hypercaloric diet (range, 2078-2218 kcal/day), marked by an excessive intake of lipids (45.0-47.3% kcal), particularly saturated fats (16.6-16.9% kcal), proteins (17.0-17.3% kcal), sugars (20.0-21.9% kcal) and cholesterol (161.6-182.9 mg/1000 kcal/day), and a low intake of complex carbohydrates (17.5-18.1% kcal) and fibre (19.6-19.9 g/day). Compared with children in the two low-IHD-mortality cities, those in the two high-IHD-mortality cities had a greater BMI (mean difference, 0.61 kg/m(2); P=0.0001) and ponderal index (0.58 kg/m(3); P=0.0001) and a higher intake of energy (104 kcal/day; P=0.007), cholesterol (16.00 mg/1000 kcal/day; P=0.0001) and sodium (321 mg/day; P=0.0001). Inter-city differences in anthropometric variables remained after adjustment for birthweight

Vive la résistance: genome-wide selection against introduced alleles in invasive hybrid zones

USGS Publications Warehouse

Kovach, Ryan P.; Hand, Brian K.; Hohenlohe, Paul A.; Cosart, Ted F.; Boyer, Matthew C.; Neville, Helen H.; Muhlfeld, Clint C.; Amish, Stephen J.; Carim, Kellie; Narum, Shawn R.; Lowe, Winsor H.; Allendorf, Fred W.; Luikart, Gordon

2016-01-01

Evolutionary and ecological consequences of hybridization between native and invasive species are notoriously complicated because patterns of selection acting on non-native alleles can vary throughout the genome and across environments. Rapid advances in genomics now make it feasible to assess locus-specific and genome-wide patterns of natural selection acting on invasive introgression within and among natural populations occupying diverse environments. We quantified genome-wide patterns of admixture across multiple independent hybrid zones of native westslope cutthroat trout and invasive rainbow trout, the world's most widely introduced fish, by genotyping 339 individuals from 21 populations using 9380 species-diagnostic loci. A significantly greater proportion of the genome appeared to be under selection favouring native cutthroat trout (rather than rainbow trout), and this pattern was pervasive across the genome (detected on most chromosomes). Furthermore, selection against invasive alleles was consistent across populations and environments, even in those where rainbow trout were predicted to have a selective advantage (warm environments). These data corroborate field studies showing that hybrids between these species have lower fitness than the native taxa, and show that these fitness differences are due to selection favouring many native genes distributed widely throughout the genome.

Optimization and quality control of genome-wide Hi-C library preparation.

PubMed

Zhang, Xiang-Yuan; He, Chao; Ye, Bing-Yu; Xie, De-Jian; Shi, Ming-Lei; Zhang, Yan; Shen, Wen-Long; Li, Ping; Zhao, Zhi-Hu

2017-09-20

Highest-throughput chromosome conformation capture (Hi-C) is one of the key assays for genome- wide chromatin interaction studies. It is a time-consuming process that involves many steps and many different kinds of reagents, consumables, and equipments. At present, the reproducibility is unsatisfactory. By optimizing the key steps of the Hi-C experiment, such as crosslinking, pretreatment of digestion, inactivation of restriction enzyme, and in situ ligation etc., we established a robust Hi-C procedure and prepared two biological replicates of Hi-C libraries from the GM12878 cells. After preliminary quality control by Sanger sequencing, the two replicates were high-throughput sequenced. The bioinformatics analysis of the raw sequencing data revealed the mapping-ability and pair-mate rate of the raw data were around 90% and 72%, respectively. Additionally, after removal of self-circular ligations and dangling-end products, more than 96% of the valid pairs were reached. Genome-wide interactome profiling shows clear topological associated domains (TADs), which is consistent with previous reports. Further correlation analysis showed that the two biological replicates strongly correlate with each other in terms of both bin coverage and all bin pairs. All these results indicated that the optimized Hi-C procedure is robust and stable, which will be very helpful for the wide applications of the Hi-C assay.

Guidelines for signal operations at intersections with wide medians.

DOT National Transportation Integrated Search

2010-03-01

The objective of this project is to evaluate the operations at signalized intersections with wide medians in : order to improve safety and efficiency. Intersections with wide medians are characterized by two : intersections and operate differently co...

Genome-wide single nucleotide polymorphisms reveal population history and adaptive divergence in wild guppies.

PubMed

Willing, Eva-Maria; Bentzen, Paul; van Oosterhout, Cock; Hoffmann, Margarete; Cable, Joanne; Breden, Felix; Weigel, Detlef; Dreyer, Christine

2010-03-01

Adaptation of guppies (Poecilia reticulata) to contrasting upland and lowland habitats has been extensively studied with respect to behaviour, morphology and life history traits. Yet population history has not been studied at the whole-genome level. Although single nucleotide polymorphisms (SNPs) are the most abundant form of variation in many genomes and consequently very informative for a genome-wide picture of standing natural variation in populations, genome-wide SNP data are rarely available for wild vertebrates. Here we use genetically mapped SNP markers to comprehensively survey genetic variation within and among naturally occurring guppy populations from a wide geographic range in Trinidad and Venezuela. Results from three different clustering methods, Neighbor-net, principal component analysis (PCA) and Bayesian analysis show that the population substructure agrees with geographic separation and largely with previously hypothesized patterns of historical colonization. Within major drainages (Caroni, Oropouche and Northern), populations are genetically similar, but those in different geographic regions are highly divergent from one another, with some indications of ancient shared polymorphisms. Clear genomic signatures of a previous introduction experiment were seen, and we detected additional potential admixture events. Headwater populations were significantly less heterozygous than downstream populations. Pairwise F(ST) values revealed marked differences in allele frequencies among populations from different regions, and also among populations within the same region. F(ST) outlier methods indicated some regions of the genome as being under directional selection. Overall, this study demonstrates the power of a genome-wide SNP data set to inform for studies on natural variation, adaptation and evolution of wild populations.

Chronic Myeloid Leukemia Patients Sensitive and Resistant to Imatinib Treatment Show Different Metabolic Responses

PubMed Central

Wang, Guangji; Yan, Bei; Zhang, Sujiang; Huang, Qing; Ni, Lingna; Zha, Weibin; Liu, Linsheng; Cao, Bei; Hong, Ming; Wu, Hanxin; Lu, Hua; Shi, Jian; Li, Mengjie; Li, Jianyong

2010-01-01

The BCR-ABL tyrosine kinase inhibitor imatinib is highly effective for chronic myeloid leukemia (CML). However, some patients gradually develop resistance to imatinib, resulting in therapeutic failure. Metabonomic and genomic profiling of patients' responses to drug interventions can provide novel information about the in vivo metabolism of low-molecular-weight compounds and extend our insight into the mechanism of drug resistance. Based on a multi-platform of high-throughput metabonomics, SNP array analysis, karyotype and mutation, the metabolic phenotypes and genomic polymorphisms of CML patients and their diverse responses to imatinib were characterized. The untreated CML patients (UCML) showed different metabolic patterns from those of healthy controls, and the discriminatory metabolites suggested the perturbed metabolism of the urea cycle, tricarboxylic acid cycle, lipid metabolism, and amino acid turnover in UCML. After imatinib treatment, patients sensitive to imatinib (SCML) and patients resistant to imatinib (RCML) had similar metabolic phenotypes to those of healthy controls and UCML, respectively. SCML showed a significant metabolic response to imatinib, with marked restoration of the perturbed metabolism. Most of the metabolites characterizing CML were adjusted to normal levels, including the intermediates of the urea cycle and tricarboxylic acid cycle (TCA). In contrast, neither cytogenetic nor metabonomic analysis indicated any positive response to imatinib in RCML. We report for the first time the associated genetic and metabonomic responses of CML patients to imatinib and show that the perturbed in vivo metabolism of UCML is independent of imatinib treatment in resistant patients. Thus, metabonomics can potentially characterize patients' sensitivity or resistance to drug intervention. PMID:20949032

Ethnic differences in mental health among incarcerated youths: do Moroccan immigrant boys show less psychopathology than native Dutch boys?

PubMed

Veen, Violaine; Stevens, Gonneke; Doreleijers, Theo; van der Ende, Jan; Vollebergh, Wilma

2010-05-01

Psychiatric disorders are highly prevalent among incarcerated youth. However, whereas ethnic minority youths are overrepresented in the juvenile justice system, limited research is available on their mental health. In this study, differences in mental health problems between incarcerated adolescents of native Dutch and Moroccan origin, were examined. Child Behavior Checklist and Youth Self-Report scores were compared between incarcerated adolescents of native Dutch and Moroccan origin. Their scores were also compared to those of native Dutch and Moroccan immigrant youths in the general, non-incarcerated population. Native Dutch incarcerated adolescents showed higher levels of various mental health problems than incarcerated adolescents with a Moroccan background. Compared to the general population, incarcerated youths showed higher levels of mental health problems, but this deviation was much larger for native Dutch than for Moroccan immigrant youths. These ethnic differences in mental health problems could not be explained by ethnic differences in socio-economic background and social desirable answering tendencies. Incarcerated youths of Moroccan origin show less psychopathology than incarcerated native Dutch youths, which might be explained by disparities in sentencing procedures.

Ethnic differences in mental health among incarcerated youths: do Moroccan immigrant boys show less psychopathology than native Dutch boys?

PubMed Central

Stevens, Gonneke; Doreleijers, Theo; van der Ende, Jan; Vollebergh, Wilma

2009-01-01

Psychiatric disorders are highly prevalent among incarcerated youth. However, whereas ethnic minority youths are overrepresented in the juvenile justice system, limited research is available on their mental health. In this study, differences in mental health problems between incarcerated adolescents of native Dutch and Moroccan origin, were examined. Child Behavior Checklist and Youth Self-Report scores were compared between incarcerated adolescents of native Dutch and Moroccan origin. Their scores were also compared to those of native Dutch and Moroccan immigrant youths in the general, non-incarcerated population. Native Dutch incarcerated adolescents showed higher levels of various mental health problems than incarcerated adolescents with a Moroccan background. Compared to the general population, incarcerated youths showed higher levels of mental health problems, but this deviation was much larger for native Dutch than for Moroccan immigrant youths. These ethnic differences in mental health problems could not be explained by ethnic differences in socio-economic background and social desirable answering tendencies. Incarcerated youths of Moroccan origin show less psychopathology than incarcerated native Dutch youths, which might be explained by disparities in sentencing procedures. PMID:20449708

Obesity in show cats.

PubMed

Corbee, R J

2014-12-01

Obesity is an important disease with a high prevalence in cats. Because obesity is related to several other diseases, it is important to identify the population at risk. Several risk factors for obesity have been described in the literature. A higher incidence of obesity in certain cat breeds has been suggested. The aim of this study was to determine whether obesity occurs more often in certain breeds. The second aim was to relate the increased prevalence of obesity in certain breeds to the official standards of that breed. To this end, 268 cats of 22 different breeds investigated by determining their body condition score (BCS) on a nine-point scale by inspection and palpation, at two different cat shows. Overall, 45.5% of the show cats had a BCS > 5, and 4.5% of the show cats had a BCS > 7. There were significant differences between breeds, which could be related to the breed standards. Most overweight and obese cats were in the neutered group. It warrants firm discussions with breeders and cat show judges to come to different interpretations of the standards in order to prevent overweight conditions in certain breeds from being the standard of beauty. Neutering predisposes for obesity and requires early nutritional intervention to prevent obese conditions. Journal of Animal Physiology and Animal Nutrition © 2014 Blackwell Verlag GmbH.

Comparative study of recent wide-pore materials of different stationary phase morphology, applied for the reversed-phase analysis of recombinant monoclonal antibodies.

PubMed

Fekete, Szabolcs; Veuthey, Jean-Luc; Eeltink, Sebastiaan; Guillarme, Davy

2013-04-01

Various recent wide-pore reversed-phase stationary phases were studied for the analysis of intact monoclonal antibodies (mAbs) of 150 kDa and their fragments possessing sizes between 25 and 50 kDa. Different types of column technology were evaluated, namely, a prototype silica-based inorganic monolith containing mesopores of ~250 Å and macropores of ~ 1.1 μm, a column packed with 3.6 μm wide-pore core-shell particles possessing a wide pore size distribution with an average around 200 Å and a column packed with fully porous 1.7 μm particles having pore size of ~300 Å. The performance of these wide-pore materials was compared with that of a poly(styrene-divinyl benzene) organic monolithic column, with a macropore size of approximately 1 μm but without mesopores (stagnant pores). A systematic investigation was carried out using model IgG1 and IgG2 mAbs, namely rituximab, panitumumab, and bevacizumab. Firstly, the recoveries of intact and reduced mAbs were compared on the two monolithic phases, and it appeared that adsorption was less pronounced on the organic monolith, probably due to the difference in chemistry (C18 versus phenyl) and the absence of mesopores (stagnant zones). Secondly, the kinetic performance was investigated in gradient elution mode for all columns. For this purpose, peak capacities per meter as well as peak capacities per time unit and per pressure unit (PPT) were calculated at various flow rates, to compare performance of columns with different dimensions. In terms of peak capacity per meter, the core-shell 3.6 μm and fully porous 1.7 μm columns outperformed the two monolithic phases, at a temperature of 60 °C. However, when considering the PPT values, the core-shell 3.6 μm column remained the best phase while the prototype silica-based monoliths became very interesting, mostly due to a very high permeability compared with the organic monolith. Therefore, these core-shell and silica-based monolith provided the fastest achievable

Simultaneous multicolor imaging of wide-field epi-fluorescence microscopy with four-bucket detection

PubMed Central

Park, Kwan Seob; Kim, Dong Uk; Lee, Jooran; Kim, Geon Hee; Chang, Ki Soo

2016-01-01

We demonstrate simultaneous imaging of multiple fluorophores using wide-field epi-fluorescence microscopy with a monochrome camera. The intensities of the three lasers are modulated by a sinusoidal waveform in order to excite each fluorophore with the same modulation frequency and a different time-delay. Then, the modulated fluorescence emissions are simultaneously detected by a camera operating at four times the excitation frequency. We show that two different fluorescence beads having crosstalk can be clearly separated using digital processing based on the phase information. In addition, multiple organelles within multi-stained single cells are shown with the phase mapping method, demonstrating an improved dynamic range and contrast compared to the conventional fluorescence image. These findings suggest that wide-field epi-fluorescence microscopy with four-bucket detection could be utilized for high-contrast multicolor imaging applications such as drug delivery and fluorescence in situ hybridization. PMID:27375944

Massive, wide binaries as tracers of massive star formation

NASA Astrophysics Data System (ADS)

Griffiths, Daniel W.; Goodwin, Simon P.; Caballero-Nieves, Saida M.

2018-05-01

Massive stars can be found in wide (hundreds to thousands au) binaries with other massive stars. We use N-body simulations to show that any bound cluster should always have approximately one massive wide binary: one will probably form if none are present initially, and probably only one will survive if more than one is present initially. Therefore, any region that contains many massive wide binaries must have been composed of many individual subregions. Observations of Cyg OB2 show that the massive wide binary fraction is at least a half (38/74), which suggests that Cyg OB2 had at least 30 distinct massive star formation sites. This is further evidence that Cyg OB2 has always been a large, low-density association. That Cyg OB2 has a normal high-mass initial mass function (IMF) for its total mass suggests that however massive stars form, they `randomly sample' the IMF (as the massive stars did not `know' about each other).

Effect of screens in wide-angle diffusers

NASA Technical Reports Server (NTRS)

Schubauer, G B; Spangenberg, W G

1949-01-01

An experimental investigation at low airspeeds was made of the filling effect observed when a screen or similar resistance is placed across a diffuser. The filling effect is found to be real in that screens can prevent separation or restore separated flow in diffusers even of extreme divergence and to depend principally on screen location and pressure-drop coefficient of the screen. Results are given for three different diffusers of circular cross section with a variety of screen arrangements. Effects of single screens and multiple screens are shown. The mechanics of the filling effect is explained, and possible efficiencies are discussed. Results of arrangements of multiple screens in wide-angle diffusers are given to show a possible application to damping screens as used in wind tunnels to reduce turbulence. (author)

Chinese and Australians showed difference in mental time travel in emotion and content but not specificity

PubMed Central

Chen, Xing-Jie; Liu, Lu-Lu; Cui, Ji-Fang; Wang, Ya; Shum, David H. K.; Chan, Raymond C. K.

2015-01-01

Mental time travel refers to the ability to recall episodic past and imagine future events. The present study aimed to investigate cultural differences in mental time travel between Chinese and Australian university students. A total of 231 students (108 Chinese and 123 Australians) participated in the study. Their mental time travel abilities were measured by the Sentence Completion for Events from the Past Test (SCEPT) and the Sentence Completion for Events in the Future Test (SCEFT). Results showed that there were no cultural differences in the number of specific events generated for the past or future. Significant differences between the Chinese and Australian participants were found mainly in the emotional valence and content of the events generated. Both Chinese and Australian participants generated more specific positive events compared to negative events when thinking about the future and Chinese participants were more positive about their past than Australian participants when recalling specific events. For content, Chinese participants recalled more events about their interpersonal relationships, while Australian participants imagined more about personal future achievements. These findings shed some lights on cultural differences in episodic past and future thinking. PMID:26167154

Methodology for Wide Band-Gap Device Dynamic Characterization

DOE PAGES

Zhang, Zheyu; Guo, Ben; Wang, Fei Fred; ...

2017-01-19

Here, the double pulse test (DPT) is a widely accepted method to evaluate the dynamic behavior of power devices. Considering the high switching-speed capability of wide band-gap devices, the test results are very sensitive to the alignment of voltage and current (V-I) measurements. Also, because of the shoot-through current induced by Cdv/dt (i.e., cross-talk), the switching losses of the nonoperating switch device in a phase-leg must be considered in addition to the operating device. This paper summarizes the key issues of the DPT, including components and layout design, measurement considerations, grounding effects, and data processing. Additionally, a practical method ismore » proposed for phase-leg switching loss evaluation by calculating the difference between the input energy supplied by a dc capacitor and the output energy stored in a load inductor. Based on a phase-leg power module built with 1200-V/50-A SiC MOSFETs, the test results show that this method can accurately evaluate the switching loss of both the upper and lower switches by detecting only one switching current and voltage, and it is immune to V-I timing misalignment errors.« less

Emotion Knowledge and Attentional Differences in Preschoolers Showing Context-Inappropriate Anger.

PubMed

Locke, Robin L; Lang, Nichole J

2016-08-01

Some children show anger inappropriate for the situation based on the predominant incentives, which is called context-inappropriate anger. Children need to attend to and interpret situational incentives for appropriate emotional responses. We examined associations of context-inappropriate anger with emotion recognition and attention problems in 43 preschoolers (42% male; M age = 55.1 months, SD = 4.1). Parents rated context-inappropriate anger across situations. Teachers rated attention problems using the Child Behavior Checklist-Teacher Report Form. Emotion recognition was ability to recognize emotional faces using the Emotion Matching Test. Anger perception bias was indicated by anger to non-anger situations using an adapted Affect Knowledge Test. 28% of children showed context-inappropriate anger, which correlated with lower emotion recognition (β = -.28) and higher attention problems (β = .36). Higher attention problems correlated with more anger perception bias (β = .32). This cross-sectional, correlational study provides preliminary findings that children with context-inappropriate anger showed more attention problems, which suggests that both "problems" tend to covary and associate with deficits or biases in emotion knowledge. © The Author(s) 2016.

Genome-wide meta-analysis of observational studies shows common genetic variants associated with macronutrient intake.

PubMed

Tanaka, Toshiko; Ngwa, Julius S; van Rooij, Frank J A; Zillikens, M Carola; Wojczynski, Mary K; Frazier-Wood, Alexis C; Houston, Denise K; Kanoni, Stavroula; Lemaitre, Rozenn N; Luan, Jian'an; Mikkilä, Vera; Renstrom, Frida; Sonestedt, Emily; Zhao, Jing Hua; Chu, Audrey Y; Qi, Lu; Chasman, Daniel I; de Oliveira Otto, Marcia C; Dhurandhar, Emily J; Feitosa, Mary F; Johansson, Ingegerd; Khaw, Kay-Tee; Lohman, Kurt K; Manichaikul, Ani; McKeown, Nicola M; Mozaffarian, Dariush; Singleton, Andrew; Stirrups, Kathleen; Viikari, Jorma; Ye, Zheng; Bandinelli, Stefania; Barroso, Inês; Deloukas, Panos; Forouhi, Nita G; Hofman, Albert; Liu, Yongmei; Lyytikäinen, Leo-Pekka; North, Kari E; Dimitriou, Maria; Hallmans, Goran; Kähönen, Mika; Langenberg, Claudia; Ordovas, Jose M; Uitterlinden, André G; Hu, Frank B; Kalafati, Ioanna-Panagiota; Raitakari, Olli; Franco, Oscar H; Johnson, Andrew; Emilsson, Valur; Schrack, Jennifer A; Semba, Richard D; Siscovick, David S; Arnett, Donna K; Borecki, Ingrid B; Franks, Paul W; Kritchevsky, Stephen B; Lehtimäki, Terho; Loos, Ruth J F; Orho-Melander, Marju; Rotter, Jerome I; Wareham, Nicholas J; Witteman, Jacqueline C M; Ferrucci, Luigi; Dedoussis, George; Cupples, L Adrienne; Nettleton, Jennifer A

2013-06-01

Macronutrient intake varies substantially between individuals, and there is evidence that this variation is partly accounted for by genetic variants. The objective of the study was to identify common genetic variants that are associated with macronutrient intake. We performed 2-stage genome-wide association (GWA) meta-analysis of macronutrient intake in populations of European descent. Macronutrients were assessed by using food-frequency questionnaires and analyzed as percentages of total energy consumption from total fat, protein, and carbohydrate. From the discovery GWA (n = 38,360), 35 independent loci associated with macronutrient intake at P < 5 × 10(-6) were identified and taken forward to replication in 3 additional cohorts (n = 33,533) from the DietGen Consortium. For one locus, fat mass obesity-associated protein (FTO), cohorts with Illumina MetaboChip genotype data (n = 7724) provided additional replication data. A variant in the chromosome 19 locus (rs838145) was associated with higher carbohydrate (β ± SE: 0.25 ± 0.04%; P = 1.68 × 10(-8)) and lower fat (β ± SE: -0.21 ± 0.04%; P = 1.57 × 10(-9)) consumption. A candidate gene in this region, fibroblast growth factor 21 (FGF21), encodes a fibroblast growth factor involved in glucose and lipid metabolism. The variants in this locus were associated with circulating FGF21 protein concentrations (P < 0.05) but not mRNA concentrations in blood or brain. The body mass index (BMI)-increasing allele of the FTO variant (rs1421085) was associated with higher protein intake (β ± SE: 0.10 ± 0.02%; P = 9.96 × 10(-10)), independent of BMI (after adjustment for BMI, β ± SE: 0.08 ± 0.02%; P = 3.15 × 10(-7)). Our results indicate that variants in genes involved in nutrient metabolism and obesity are associated with macronutrient consumption in humans. Trials related to this study were registered at clinicaltrials.gov as NCT00005131 (Atherosclerosis Risk in Communities), NCT00005133 (Cardiovascular Health

Wide-angle, polarization-insensitive and broadband absorber based on eight-fold symmetric SRRs metamaterial

NASA Astrophysics Data System (ADS)

Wu, Dong; Liu, Yumin; Yu, Zhongyuan; Chen, Lei; Ma, Rui; Li, Yutong; Li, Ruifang; Ye, Han

2016-12-01

In this paper, we propose a novel three dimensional metamaterial design with eight-fold rotational symmetry that shows a polarization-insensitive, wide-angle and broadband perfect absorption in the microwave band. By simulation, the polarization-insensitive absorption is over 90% between 26.9 GHz to 32.9 GHz, and the broadband absorption remains a good absorption performance to a wide incident angles for both TE and TM polarizations. The magnetic field distribution are investigated to interpret the physical mechanism of broadband absorption. The broadband absorption is based on overlapping the multiple magnetic resonances at the neighboring frequencies by coupling effects of multiple metallic split-ring resonators (SRRs). Moreover, it is demonstrate that the designed structure can be extended to other frequencies by scale down the size of the unit cell, such as the visible frequencies. The simulated results show that the absorption of the smaller absorber is above 90% in the frequency range from 467 THz to 765 THz(392-642 nm), which include orange to purple light in visible region(400-760nm). The wide-angle and polarization-insensitive stabilities of the smaller absorber is also demonstrated at visible region. The proposed work provides a new design of realization of a polarization-insensitive, wide-angle and broadband absorber ranging different frequency bands, and such a structure has potential application in the fields of solar cell, imaging and detection.

Genome-wide association study identifies a locus associated with rotator cuff injury

PubMed Central

Roos, Thomas R.; Roos, Andrew K.; Avins, Andrew L.; Ahmed, Marwa A.; Kleimeyer, John P.; Fredericson, Michael; Ioannidis, John P. A.; Dragoo, Jason L.

2017-01-01

Rotator cuff tears are common, especially in the fifth and sixth decades of life, but can also occur in the competitive athlete. Genetic differences may contribute to overall injury risk. Identifying genetic loci associated with rotator cuff injury could shed light on the etiology of this injury. We performed a genome-wide association screen using publically available data from the Research Program in Genes, Environment and Health including 8,357 cases of rotator cuff injury and 94,622 controls. We found rs71404070 to show a genome-wide significant association with rotator cuff injury with p = 2.31x10-8 and an odds ratio of 1.25 per allele. This SNP is located next to cadherin8, which encodes a protein involved in cell adhesion. We also attempted to validate previous gene association studies that had reported a total of 18 SNPs showing a significant association with rotator cuff injury. However, none of the 18 SNPs were validated in our dataset. rs71404070 may be informative in explaining why some individuals are more susceptible to rotator cuff injury than others. PMID:29228018

Transformation of Cortex-wide Emergent Properties during Motor Learning.

PubMed

Makino, Hiroshi; Ren, Chi; Liu, Haixin; Kim, An Na; Kondapaneni, Neehar; Liu, Xin; Kuzum, Duygu; Komiyama, Takaki

2017-05-17

Learning involves a transformation of brain-wide operation dynamics. However, our understanding of learning-related changes in macroscopic dynamics is limited. Here, we monitored cortex-wide activity of the mouse brain using wide-field calcium imaging while the mouse learned a motor task over weeks. Over learning, the sequential activity across cortical modules became temporally more compressed, and its trial-by-trial variability decreased. Moreover, a new flow of activity emerged during learning, originating from premotor cortex (M2), and M2 became predictive of the activity of many other modules. Inactivation experiments showed that M2 is critical for the post-learning dynamics in the cortex-wide activity. Furthermore, two-photon calcium imaging revealed that M2 ensemble activity also showed earlier activity onset and reduced variability with learning, which was accompanied by changes in the activity-movement relationship. These results reveal newly emergent properties of macroscopic cortical dynamics during motor learning and highlight the importance of M2 in controlling learned movements. Copyright © 2017 Elsevier Inc. All rights reserved.

Sperm whales and killer whales with the largest brains of all toothed whales show extreme differences in cerebellum.

PubMed

Ridgway, Sam H; Hanson, Alicia C

2014-01-01

Among cetaceans, killer whales and sperm whales have the widest distribution in the world's oceans. Both species use echolocation, are long-lived, and have the longest periods of gestation among whales. Sperm whales dive much deeper and much longer than killer whales. It has long been thought that sperm whales have the largest brains of all living things, but our brain mass evidence, from published sources and our own specimens, shows that big males of these two species share this distinction. Despite this, we also find that cerebellum size is very different between killer whales and sperm whales. The sperm whale cerebellum is only about 7% of the total brain mass, while the killer whale cerebellum is almost 14%. These results are significant because they contradict claims that the cerebellum scales proportionally with the rest of the brain in all mammals. They also correct the generalization that all cetaceans have enlarged cerebella. We suggest possible reasons for the existence of such a large cerebellar size difference between these two species. Cerebellar function is not fully understood, and comparing the abilities of animals with differently sized cerebella can help uncover functional roles of the cerebellum in humans and animals. Here we show that the large cerebellar difference likely relates to evolutionary history, diving, sensory capability, and ecology. © 2014 S. Karger AG, Basel.

Genome-wide methylation study of diploid and triploid brown trout (Salmo trutta L.).

PubMed

Covelo-Soto, L; Leunda, P M; Pérez-Figueroa, A; Morán, P

2015-06-01

The induction of triploidization in fish is a very common practice in aquaculture. Although triploidization has been applied successfully in many salmonid species, little is known about the epigenetic mechanisms implicated in the maintenance of the normal functions of the new polyploid genome. By means of methylation-sensitive amplified polymorphism (MSAP) techniques, genome-wide methylation changes associated with triploidization were assessed in DNA samples obtained from diploid and triploid siblings of brown trout (Salmo trutta). Simple comparative body measurements showed that the triploid trout used in the study were statistically bigger, however, not heavier than their diploid counterparts. The statistical analysis of the MSAP data showed no significant differences between diploid and triploid brown trout in respect to brain, gill, heart, liver, kidney or muscle samples. Nonetheless, local analysis pointed to the possibility of differences in connection with concrete loci. This is the first study that has investigated DNA methylation alterations associated with triploidization in brown trout. Our results set the basis for new studies to be undertaken and provide a new approach concerning triploidization effects of the salmonid genome while also contributing to the better understanding of the genome-wide methylation processes. © 2015 Stichting International Foundation for Animal Genetics.

Genome wide approaches to identify protein-DNA interactions.

PubMed

Ma, Tao; Ye, Zhenqing; Wang, Liguo

2018-05-29

Transcription factors are DNA-binding proteins that play key roles in many fundamental biological processes. Unraveling their interactions with DNA is essential to identify their target genes and understand the regulatory network. Genome-wide identification of their binding sites became feasible thanks to recent progress in experimental and computational approaches. ChIP-chip, ChIP-seq, and ChIP-exo are three widely used techniques to demarcate genome-wide transcription factor binding sites. This review aims to provide an overview of these three techniques including their experiment procedures, computational approaches, and popular analytic tools. ChIP-chip, ChIP-seq, and ChIP-exo have been the major techniques to study genome-wide in vivo protein-DNA interaction. Due to the rapid development of next-generation sequencing technology, array-based ChIP-chip is deprecated and ChIP-seq has become the most widely used technique to identify transcription factor binding sites in genome-wide. The newly developed ChIP-exo further improves the spatial resolution to single nucleotide. Numerous tools have been developed to analyze ChIP-chip, ChIP-seq and ChIP-exo data. However, different programs may employ different mechanisms or underlying algorithms thus each will inherently include its own set of statistical assumption and bias. So choosing the most appropriate analytic program for a given experiment needs careful considerations. Moreover, most programs only have command line interface so their installation and usage will require basic computation expertise in Unix/Linux. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Medicago truncatula shows distinct patterns of mycorrhiza-related gene expression after inoculation with three different arbuscular mycorrhizal fungi.

PubMed

Feddermann, Nadja; Boller, Thomas; Salzer, Peter; Elfstrand, Sara; Wiemken, Andres; Elfstrand, Malin

2008-02-01

Different arbuscular mycorrhizal fungi (AMF) alter growth and nutrition of a given plant differently. Plant gene expression patterns in response to fungal colonization show a certain overlap when colonized by fungi of the Glomeraceae. However, little is known of plant responses to fungi of different fungal taxa, e.g. the Gigasporaceae. We therefore compared the impact of colonization by three taxonomically different AMF species (Glomus intraradices, Glomus mosseae and Scutellospora castanea) on Medicago truncatula at the physiological and transcriptional level using quantitative-PCR. Each AMF developed a species-typical colonization pattern, with a colonization degree of 60% for G. intraradices and 30% for G. mosseae. Both species developed appressoria, intraradical hyphae, arbuscules and vesicles. S. castanea showed a colonization degree of 10% and developed appressoria, intraradical hyphae, arbuscules and arbusculate coils. All AMF enhanced the plant biomass accumulation and nutritional status although not in correlation with the colonization degree. The expression of 10 mycorrhiza-specific or mycorrhiza-associated plant genes could be separated into two clusters. The first cluster, containing arbuscule-induced genes, was highly induced in interactions with G. intraradices and G. mosseae but also slightly induced by S. castanea. The second cluster of genes contained genes that were induced primarily by S. castanea. In conclusion, genes that respond to colonization by fungi of the genus Glomus also respond to Scutellospora. However, there is also a group of genes that is significantly induced only by Scutellospora and not by Glomus species in this study. Our data indicate that genes may be differentially regulated in response to the different AM fungi.

5. VIEW SHOWING INCLINED OUTLET GATE WHEEL, STEM AND STEM ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

5. VIEW SHOWING INCLINED OUTLET GATE WHEEL, STEM AND STEM GUIDE (28' WIDE HARDESTY CAST IRON SLIDE HEADGATE), LOOKING NORTHEAST - High Mountain Dams in Bonneville Unit, Duck Lake Dam, Wasatch National Forest, Kamas, Summit County, UT

Holocentromeres in Rhynchospora are associated with genome-wide centromere-specific repeat arrays interspersed among euchromatin.

PubMed

Marques, André; Ribeiro, Tiago; Neumann, Pavel; Macas, Jiří; Novák, Petr; Schubert, Veit; Pellino, Marco; Fuchs, Jörg; Ma, Wei; Kuhlmann, Markus; Brandt, Ronny; Vanzela, André L L; Beseda, Tomáš; Šimková, Hana; Pedrosa-Harand, Andrea; Houben, Andreas

2015-11-03

Holocentric chromosomes lack a primary constriction, in contrast to monocentrics. They form kinetochores distributed along almost the entire poleward surface of the chromatids, to which spindle fibers attach. No centromere-specific DNA sequence has been found for any holocentric organism studied so far. It was proposed that centromeric repeats, typical for many monocentric species, could not occur in holocentrics, most likely because of differences in the centromere organization. Here we show that the holokinetic centromeres of the Cyperaceae Rhynchospora pubera are highly enriched by a centromeric histone H3 variant-interacting centromere-specific satellite family designated "Tyba" and by centromeric retrotransposons (i.e., CRRh) occurring as genome-wide interspersed arrays. Centromeric arrays vary in length from 3 to 16 kb and are intermingled with gene-coding sequences and transposable elements. We show that holocentromeres of metaphase chromosomes are composed of multiple centromeric units rather than possessing a diffuse organization, thus favoring the polycentric model. A cell-cycle-dependent shuffling of multiple centromeric units results in the formation of functional (poly)centromeres during mitosis. The genome-wide distribution of centromeric repeat arrays interspersing the euchromatin provides a previously unidentified type of centromeric chromatin organization among eukaryotes. Thus, different types of holocentromeres exist in different species, namely with and without centromeric repetitive sequences.

Genome-Wide Association Analyses Highlight the Potential for Different Genetic Mechanisms for Litter Size Among Sheep Breeds

PubMed Central

Xu, Song-Song; Gao, Lei; Xie, Xing-Long; Ren, Yan-Ling; Shen, Zhi-Qiang; Wang, Feng; Shen, Min; Eyϸórsdóttir, Emma; Hallsson, Jón H.; Kiseleva, Tatyana; Kantanen, Juha; Li, Meng-Hua

2018-01-01

Reproduction is an important trait in sheep breeding as well as in other livestock. However, despite its importance the genetic mechanisms of litter size in domestic sheep (Ovis aries) are still poorly understood. To explore genetic mechanisms underlying the variation in litter size, we conducted multiple independent genome-wide association studies in five sheep breeds of high prolificacy (Wadi, Hu, Icelandic, Finnsheep, and Romanov) and one low prolificacy (Texel) using the Ovine Infinium HD BeadChip, respectively. We identified different sets of candidate genes associated with litter size in different breeds: BMPR1B, FBN1, and MMP2 in Wadi; GRIA2, SMAD1, and CTNNB1 in Hu; NCOA1 in Icelandic; INHBB, NF1, FLT1, PTGS2, and PLCB3 in Finnsheep; ESR2 in Romanov and ESR1, GHR, ETS1, MMP15, FLI1, and SPP1 in Texel. Further annotation of genes and bioinformatics analyses revealed that different biological pathways could be involved in the variation in litter size of females: hormone secretion (FSH and LH) in Wadi and Hu, placenta and embryonic lethality in Icelandic, folliculogenesis and LH signaling in Finnsheep, ovulation and preovulatory follicle maturation in Romanov, and estrogen and follicular growth in Texel. Taken together, our results provide new insights into the genetic mechanisms underlying the prolificacy trait in sheep and other mammals, suggesting targets for selection where the aim is to increase prolificacy in breeding projects. PMID:29692799

Motor units in vastus lateralis and in different vastus medialis regions show different firing properties during low-level, isometric knee extension contraction.

PubMed

de Souza, Leonardo Mendes Leal; Cabral, Hélio Veiga; de Oliveira, Liliam Fernandes; Vieira, Taian Martins

2018-04-01

Architectural differences along vastus medialis (VM) and between VM and vastus lateralis (VL) are considered functionally important for the patellar tracking, knee joint stability and knee joint extension. Whether these functional differences are associated with a differential activity of motor units between VM and VL is however unknown. In the present study, we, therefore, investigate neuroanatomical differences in the activity of motor units detected proximo-distally from VM and from the VL muscle. Nine healthy volunteers performed low-level isometric knee extension contractions (20% of their maximum voluntary contraction) following a trapezoidal trajectory. Surface electromyograms (EMGs) were recorded from VM proximal and distal regions and from VL using three linear adhesive arrays of eight electrodes. The firing rate and recruitment threshold of motor units decomposed from EMGs were then compared among muscle regions. Results show that VL motor units reached lower mean firing rates in comparison with VM motor units, regardless of their position within VM (P < .040). No significant differences in firing rate were found between proximal and distal, VM motor units (P = .997). Furthermore, no significant differences in the recruitment threshold were observed for all motor units analysed (P = .108). Our findings possibly suggest the greater potential of VL to generate force, due to its fibres arrangement, may account for the lower discharge rate observed for VL then either proximally or distally detected motor units in VM. Additionally, the present study opens new perspectives on the importance of considering muscle architecture in investigations of the neural aspects of motor behaviour. Copyright © 2017 Elsevier B.V. All rights reserved.

Show Us How: A School-Wide Programme for Reluctant Readers.

ERIC Educational Resources Information Center

Maguiness, Colleen

Westerns Springs College in Auckland, New Zealand is an inner city coeducational secondary school of 670 multicultural and diverse students. Achievement test results in reading comprehension and vocabulary grouped students at the top and bottom of the scale. Reading was identified as a significant barrier to learning and in 1997 staff agreed to…

Wide field OCT based microangiography in living human eye (Conference Presentation)

NASA Astrophysics Data System (ADS)

Zhang, Qinqin; Chen, Chieh-Li; Chu, Zhongdi; Zhang, Anqi; An, Lin; Durbin, Mary; Sharma, Utkarsh; Rosenfeld, Philip J.; Wang, Ruikang K.

2016-03-01

To investigate the application of optical microangiography (OMAG) in living human eye. Patients with different macular diseases were recruited, including diabetic retinopathy (DR), geographic atrophy (GA), retinitis pigmentosa (RP), and venous occlusion, et al. Wide field OCT angiography images can be generated by montage scanning protocol based on the tracking system. OMAG algorithm based on complex differentiation was used to extract the blood flow and removed the bulk motion by 2D cross-correlation method. The 3D angiography was segmented into 3 layers in the retina and 2 layers in the choroid. The en-face maximum projection was used to obtain 2-dimensional angiograms of different layers coded with different colors. Flow and structure images were combined for cross-sectional view. En face OMAG images of different macular diseases showed a great agreement with FA. Meanwhile, OMAG gave more distinct vascular network visions that were less affected by hemorrhage and leakage. The MAs were observed in both superficial and middle retinal layers based on OMAG angiograms in different layers of DR patients. The contour line of FAZ was extracted as well, which can be quantitative the retinal diseases. For GA patient, the damage of RPE layer enhanced the penetration of light and enabled the acquisition of choriocapillaries and choroidal vessels. The wide field OMAG angiogram enabled the capability of capturing the entire geographic atrophy. OMAG provides depth-resolved information and detailed vascular images of DR and GA patients, providing a better visualization of vascular network compared to FA.

Base compositions of genes encoding alpha-actin and lactate dehydrogenase-A from differently adapted vertebrates show no temperature-adaptive variation in G + C content.

PubMed

Ream, Rachael A; Johns, Glenn C; Somero, George N

2003-01-01

There is a long-standing debate in molecular evolution concerning the putative importance of GC content in adapting the thermal stabilities of DNA and RNA. Most studies of this relationship have examined broad-scale compositional patterns, for example, total GC percentages in genomes and occurrence of GC-rich isochores. Few studies have systematically examined the GC contents of individual orthologous genes from differently thermally adapted species. When this has been done, the emphasis has been on comparing large numbers of genes in only a few species. We have approached the GC-adaptation temperature hypothesis in a different manner by examining patterns of base composition of genes encoding lactate dehydrogenase-A (ldh-a) and alpha-actin (alpha-actin) from 51 species of vertebrates whose adaptation temperatures ranged from -1.86 degrees C (Antarctic fishes) to approximately 45 degrees C (desert reptile). No significant positive correlation was found between any index of GC content (GC content of the entire sequence, GC content of the third codon position [GC(3)], and GC content at fourfold degenerate sites [GC(4)]) and any index of adaptation temperature (maximal, mean, or minimal body temperature). For alpha-actin, slopes of regression lines for all comparisons did not differ significantly from zero. For ldh-a, negative correlations between adaptation temperature and total GC content, GC(3), and GC(4) were observed but were shown to be due entirely to phylogenetic influences (as revealed by independent contrast analyses). This comparison of GC content across a wide range of ectothermic ("cold-blooded") and endothermic ("warm-blooded") vertebrates revealed that frogs of the genus Xenopus, which have commonly been used as a representative cold-blooded species, in fact are outliers among ectotherms for the alpha-actin analyses, raising concern about the appropriateness of choosing these amphibians as representative of ectothermic vertebrates in general. Our study

Genic rather than genome-wide differences between sexually deceptive Ophrys orchids with different pollinators.

PubMed

Sedeek, Khalid E M; Scopece, Giovanni; Staedler, Yannick M; Schönenberger, Jürg; Cozzolino, Salvatore; Schiestl, Florian P; Schlüter, Philipp M

2014-12-01

High pollinator specificity and the potential for simple genetic changes to affect pollinator attraction make sexually deceptive orchids an ideal system for the study of ecological speciation, in which change of flower odour is likely important. This study surveys reproductive barriers and differences in floral phenotypes in a group of four closely related, coflowering sympatric Ophrys species and uses a genotyping-by-sequencing (GBS) approach to obtain information on the proportion of the genome that is differentiated between species. Ophrys species were found to effectively lack postpollination barriers, but are strongly isolated by their different pollinators (floral isolation) and, to a smaller extent, by shifts in flowering time (temporal isolation). Although flower morphology and perhaps labellum coloration may contribute to floral isolation, reproductive barriers may largely be due to differences in flower odour chemistry. GBS revealed shared polymorphism throughout the Ophrys genome, with very little population structure between species. Genome scans for FST outliers identified few markers that are highly differentiated between species and repeatable in several populations. These genome scans also revealed highly differentiated polymorphisms in genes with putative involvement in floral odour production, including a previously identified candidate gene thought to be involved in the biosynthesis of pseudo-pheromones by the orchid flowers. Taken together, these data suggest that ecological speciation associated with different pollinators in sexually deceptive orchids has a genic rather than a genomic basis, placing these species at an early phase of genomic divergence within the 'speciation continuum'. © 2014 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.

Breeding experiments and genome-wide association analysis elucidate two genetically different forms of non-syndromic congenital cleft lip and jaw in Vorderwald × Montbéliarde cattle.

PubMed

Reinartz, S; Distl, O

2017-10-01

Non-syndromic congenital cleft lip and jaw (CLJ) is a condition reported in Vorderwald × Montbéliarde cattle. The objective of the present study was to perform a genome-wide association study (GWAS) for 10 CLJ-affected and 50 unaffected Vorderwald × Montbéliarde cattle using the bovine Illumina high density bead chip to identify loci for this condition. Phenotypic classification of CLJ was based on a detailed recording of orofacial structures using computed tomography. A breeding experiment among CLJ-affected Vorderwald × Montbéliarde cattle and CLJ-affected Vorderwald × Montbéliarde cattle with unaffected Holsteins confirmed recessive inheritance and different loci for bilateral or left-sided versus right-sided CLJ. The GWAS for the five cases with right-sided CLJ gave a genome-wide signal on bovine chromosome (BTA) 29 at 16 Mb. For the four left-sided and one bilateral CLJ case, a genome-wide significant association was identified on BTA4 at 32 Mb. Two different loci are very likely to be involved in CLJ in Vorderwald × Montbéliarde cattle because experimental matings among affected cows and bulls with different types of CLJ did not result in CLJ-affected progeny, and in addition, two different loci were also found through GWAS and mapped on two different bovine chromosomes. Validation in 346 Vorderwald × Montbéliarde cattle for the highly associated SNPs on BTA4 and 29 gave ratios of 33/346 (0.095, BTA4) and 6/346 (0.017, BTA29) homozygous mutant genotypes. Further studies should elucidate the responsible mutations underlying the different types of CLJ in Vorderwald × Montbéliarde cattle. © 2017 Stichting International Foundation for Animal Genetics.

Nonlinear Analysis of Motor Activity Shows Differences between Schizophrenia and Depression: A Study Using Fourier Analysis and Sample Entropy

PubMed Central

Hauge, Erik R.; Berle, Jan Øystein; Oedegaard, Ketil J.; Holsten, Fred; Fasmer, Ole Bernt

2011-01-01

The purpose of this study has been to describe motor activity data obtained by using wrist-worn actigraphs in patients with schizophrenia and major depression by the use of linear and non-linear methods of analysis. Different time frames were investigated, i.e., activity counts measured every minute for up to five hours and activity counts made hourly for up to two weeks. The results show that motor activity was lower in the schizophrenic patients and in patients with major depression, compared to controls. Using one minute intervals the depressed patients had a higher standard deviation (SD) compared to both the schizophrenic patients and the controls. The ratio between the root mean square successive differences (RMSSD) and SD was higher in the schizophrenic patients compared to controls. The Fourier analysis of the activity counts measured every minute showed that the relation between variance in the low and the high frequency range was lower in the schizophrenic patients compared to the controls. The sample entropy was higher in the schizophrenic patients compared to controls in the time series from the activity counts made every minute. The main conclusions of the study are that schizophrenic and depressive patients have distinctly different profiles of motor activity and that the results differ according to period length analysed. PMID:21297977

Maude: A Wide Spectrum Language for Secure Active Networks

DTIC Science & Technology

2002-08-01

AFRL-IF-RS-TR-2002-197 Final Technical Report August 2002 MAUDE: A WIDE SPECTRUM LANGUAGE FOR SECURE ACTIVE NETWORKS SRI...MAUDE: A WIDE SPECTRUM FORMAL LANGUAGE FOR SECURE ACTIVE NETWORKS 6. AUTHOR(S) Jose Meseguer and Carolyn Talcott 5. FUNDING NUMBERS C...specifications to address this challenge. We also show how, using the Maude rewriting logic language and tools, active network systems, languages , and

Chicken skin virome analyzed by high-throughput sequencing shows a composition highly different from human skin.

PubMed

Denesvre, Caroline; Dumarest, Marine; Rémy, Sylvie; Gourichon, David; Eloit, Marc

2015-10-01

Recent studies show that human skin at homeostasis is a complex ecosystem whose virome include circular DNA viruses, especially papillomaviruses and polyomaviruses. To determine the chicken skin virome in comparison with human skin virome, a chicken swabs pool sample from fifteen indoor healthy chickens of five genetic backgrounds was examined for the presence of DNA viruses by high-throughput sequencing (HTS). The results indicate a predominance of herpesviruses from the Mardivirus genus, coming from either vaccinal origin or presumably asymptomatic infection. Despite the high sensitivity of the HTS method used herein to detect small circular DNA viruses, we did not detect any papillomaviruses, polyomaviruses, or circoviruses, indicating that these viruses may not be resident of the chicken skin. The results suggest that the turkey herpesvirus is a resident of chicken skin in vaccinated chickens. This study indicates major differences between the skin viromes of chickens and humans. The origin of this difference remains to be further studied in relation with skin physiology, environment, or virus population dynamics.

Growth and Characterization of Wide Bandgap Semiconductor Oxide Thin Films

NASA Astrophysics Data System (ADS)

Ghose, Susmita

Wide bandgap semiconductors are receiving extensive attention due to their exceptional physical and chemical properties making them useful for high efficiency and high power electronic devices. Comparing other conventional wide bandgap materials, monoclinic beta-Ga2O3 also represents an outstanding semiconductor oxide for next generation of UV optoelectronics and high temperature sensors due to its wide band gap ( 4.9eV). This new semiconductor material has higher breakdown voltage (8MV/cm) and n-type conductivity which make it more suitable for potential application as high power electronics. The properties and potential applications of these wide bandgap materials have not yet fully explored. In this study, the growth and characterization of single crystal beta-Ga2O3 thin films grown on c-plane sapphire (Al2O3) substrate using two different techniques; molecular beam epitaxy (MBE) and pulsed laser deposition (PLD) techniques has been investigated. The influence of the growth parameters of MBE and PLD on crystalline quality and surface has been explored. Two methods have been used to grow Ga2O3 using MBE; one method is to use elemental Ga and the second is the use of a polycrystalline Ga2O3 compound source with and without an oxygen source. Using the elemental Ga source, growth rate of beta-Ga2O3 thin films was limited due to the formation and desorption of Ga2O molecules. In order to mitigate this problem, a compound Ga2O3 source has been introduced and used for the growth of crystalline beta-Ga2O 3 thin films without the need for additional oxygen since this source produces Ga-O molecules and additional oxygen. Two different alloys (InGa) 2O3 and (AlGa)2O3 has been grown on c-plane sapphire substrate by pulsed laser deposition technique to tune the bandgap of the oxide thin films from 3.5-8.6 eV suitable for applications such as wavelength-tunable optical devices, solid-state lighting and high electron mobility transistors (HEMTs). The crystallinity, chemical

High yielding biomass genotypes of willow (Salix spp.) show differences in below ground biomass allocation

PubMed Central

Cunniff, Jennifer; Purdy, Sarah J.; Barraclough, Tim J.P.; Castle, March; Maddison, Anne L.; Jones, Laurence E.; Shield, Ian F.; Gregory, Andrew S.; Karp, Angela

2015-01-01

Willows (Salix spp.) grown as short rotation coppice (SRC) are viewed as a sustainable source of biomass with a positive greenhouse gas (GHG) balance due to their potential to fix and accumulate carbon (C) below ground. However, exploiting this potential has been limited by the paucity of data available on below ground biomass allocation and the extent to which it varies between genotypes. Furthermore, it is likely that allocation can be altered considerably by environment. To investigate the role of genotype and environment on allocation, four willow genotypes were grown at two replicated field sites in southeast England and west Wales, UK. Above and below ground biomass was intensively measured over two two-year rotations. Significant genotypic differences in biomass allocation were identified, with below ground allocation differing by up to 10% between genotypes. Importantly, the genotype with the highest below ground biomass also had the highest above ground yield. Furthermore, leaf area was found to be a good predictor of below ground biomass. Growth environment significantly impacted allocation; the willow genotypes grown in west Wales had up to 94% more biomass below ground by the end of the second rotation. A single investigation into fine roots showed the same pattern with double the volume of fine roots present. This greater below ground allocation may be attributed primarily to higher wind speeds, plus differences in humidity and soil characteristics. These results demonstrate that the capacity exists to breed plants with both high yields and high potential for C accumulation. PMID:26339128

Quantitative phase imaging by wide field lensless digital holographic microscope

NASA Astrophysics Data System (ADS)

Adinda-Ougba, A.; Koukourakis, N.; Essaidi, A.; Ger­hardt, N. C.; Hofmann, M. R.

2015-05-01

Wide field, lensless microscopes have been developed for telemedicine and for resource limited setting [1]. They are based on in-line digital holography which is capable to provide amplitude and phase information resulting from numerical reconstruction. The phase information enables achieving axial resolution in the nanometer range. Hence, such microscopes provide a powerful tool to determine three-dimensional topologies of microstructures. In this contribution, a compact, low-cost, wide field, lensless microscope is presented, which is capable of providing topological profiles of microstructures in transparent material. Our setup consist only of two main components: a CMOSsensor chip and a laser diode without any need of a pinhole. We use this very simple setup to record holograms of microobjects. A wide field of view of ~24 mm², and a lateral resolution of ~2 μm are achieved. Moreover, amplitude and phase information are obtained from the numerical reconstruction of the holograms using a phase retrieval algorithm together with the angular spectrum propagation method. Topographic information of highly transparent micro-objects is obtained from the phase data. We evaluate our system by recording holograms of lines with different depths written by a focused laser beam. A reliable characterization of laser written microstructures is crucial for their functionality. Our results show that this system is valuable for determination of topological profiles of microstructures in transparent material.

Frontal and Parietal Cortices Show Different Spatiotemporal Dynamics across Problem-solving Stages.

PubMed

Tschentscher, Nadja; Hauk, Olaf

2016-08-01

Arithmetic problem-solving can be conceptualized as a multistage process ranging from task encoding over rule and strategy selection to step-wise task execution. Previous fMRI research suggested a frontal-parietal network involved in the execution of complex numerical and nonnumerical tasks, but evidence is lacking on the particular contributions of frontal and parietal cortices across time. In an arithmetic task paradigm, we evaluated individual participants' "retrieval" and "multistep procedural" strategies on a trial-by-trial basis and contrasted those in time-resolved analyses using combined EEG and MEG. Retrieval strategies relied on direct retrieval of arithmetic facts (e.g., 2 + 3 = 5). Procedural strategies required multiple solution steps (e.g., 12 + 23 = 12 + 20 + 3 or 23 + 10 + 2). Evoked source analyses revealed independent activation dynamics within the first second of problem-solving in brain areas previously described as one network, such as the frontal-parietal cognitive control network: The right frontal cortex showed earliest effects of strategy selection for multistep procedural strategies around 300 msec, before parietal cortex activated around 700 msec. In time-frequency source power analyses, memory retrieval and multistep procedural strategies were differentially reflected in theta, alpha, and beta frequencies: Stronger beta and alpha desynchronizations emerged for procedural strategies in right frontal, parietal, and temporal regions as function of executive demands. Arithmetic fact retrieval was reflected in right prefrontal increases in theta power. Our results demonstrate differential brain dynamics within frontal-parietal networks across the time course of a problem-solving process, and analyses of different frequency bands allowed us to disentangle cortical regions supporting the underlying memory and executive functions.

A mutation in the neurofibromatosis type 2 tumor-suppressor gene, giving rise to widely different clinical phenotypes in two unrelated individuals

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

Bourn, D.; Carter, S.A.; Goodship, J.

The authors have sought mutations in the recently identified neurofibromatosis type 2 (NF2) tumor-suppressor gene in a large panel of NF2 patients, using PCR-based SSCP and heteroduplex analysis, followed by cloning and sequencing of appropriate PCR products. Two unrelated NF2 patients were found to have identical nonsense mutations caused by a C-to-T transition in a CpG dinucleotide that is a potential mutational hot spot in the NF2 tumor-suppressor gene. Unexpectedly, the two individuals had widely different clinical phenotypes, representing the severe Wishart and mild Gardner clinical subtypes. Analysis of DNA samples from different tissues of the mildly affected patient suggestsmore » that he is a somatic mosaic for the mutation. 26 refs., 3 figs.« less

Wide forbidden band induced by the interference of different transverse acoustic standing-wave modes

NASA Astrophysics Data System (ADS)

Tao, Zhiyong; He, Weiyu; Xiao, Yumeng; Wang, Xinlong

2008-03-01

A non-Bragg nature forbidden band is experimentally observed in an axially symmetric hard-walled duct with a periodically varying cross section. Unlike the familiar Bragg ones, the observed bandgap is found to result from the interference of sound wave modes having different transverse standing-wave profiles, the so-called non-Bragg resonance. The experiments also show that the non-Bragg band can be comparably wider than the Bragg one; furthermore, the sound transmission loss within the band can be much more effective, exhibiting the great significance of the non-Bragg resonance in wave propagation in periodic waveguides.

Wide and ultra-wide bandgap oxides: where paradigm-shift photovoltaics meets transparent power electronics

NASA Astrophysics Data System (ADS)

Pérez-Tomás, Amador; Chikoidze, Ekaterine; Jennings, Michael R.; Russell, Stephen A. O.; Teherani, Ferechteh H.; Bove, Philippe; Sandana, Eric V.; Rogers, David J.

2018-03-01

Oxides represent the largest family of wide bandgap (WBG) semiconductors and also offer a huge potential range of complementary magnetic and electronic properties, such as ferromagnetism, ferroelectricity, antiferroelectricity and high-temperature superconductivity. Here, we review our integration of WBG and ultra WBG semiconductor oxides into different solar cells architectures where they have the role of transparent conductive electrodes and/or barriers bringing unique functionalities into the structure such above bandgap voltages or switchable interfaces. We also give an overview of the state-of-the-art and perspectives for the emerging semiconductor β- Ga2O3, which is widely forecast to herald the next generation of power electronic converters because of the combination of an UWBG with the capacity to conduct electricity. This opens unprecedented possibilities for the monolithic integration in solar cells of both self-powered logic and power electronics functionalities. Therefore, WBG and UWBG oxides have enormous promise to become key enabling technologies for the zero emissions smart integration of the internet of things.

Statistical survey of widely spread out solar electron events observed with STEREO and ACE with special attention to anisotropies

NASA Astrophysics Data System (ADS)

Dresing, N.; Gómez-Herrero, R.; Heber, B.; Klassen, A.; Malandraki, O.; Dröge, W.; Kartavykh, Y.

2014-07-01

Context. In February 2011, the two STEREO spacecrafts reached a separation of 180 degrees in longitude, offering a complete view of the Sun for the first time ever. When the full Sun surface is visible, source active regions of solar energetic particle (SEP) events can be identified unambiguously. STEREO, in combination with near-Earth observatories such as ACE or SOHO, provides three well separated viewpoints, which build an unprecedented platform from which to investigate the longitudinal variations of SEP events. Aims: We show an ensemble of SEP events that were observed between 2009 and mid-2013 by at least two spacecrafts and show a remarkably wide particle spread in longitude (wide-spread events). The main selection criterion for these events was a longitudinal separation of at least 80 degrees between active region and spacecraft magnetic footpoint for the widest separated spacecraft. We investigate the events statistically in terms of peak intensities, onset delays, and rise times, and determine the spread of the longitudinal events, which is the range filled by SEPs during the events. Energetic electron anisotropies are investigated to distinguish the source and transport mechanisms that lead to the observed wide particle spreads. Methods: According to the anisotropy distributions, we divided the events into three classes depending on different source and transport scenarios. One potential mechanism for wide-spread events is efficient perpendicular transport in the interplanetary medium that competes with another scenario, which is a wide particle spread that occurs close to the Sun. In the latter case, the observations at 1 AU during the early phase of the events are expected to show significant anisotropies because of the wide injection range at the Sun and particle-focusing during the outward propagation, while in the first case only low anisotropies are anticipated. Results: We find events for both of these scenarios in our sample that match the

Demonstration Show That Promotes and Assesses Conceptual Understanding Using the Structure of Drama

ERIC Educational Resources Information Center

Walter Kerby, Holly; DeKorver, Brittland K.; Cantor, Joanne; Weiland, Marcia J.; Babiarz, Christopher L.

2016-01-01

Demonstration shows are a widely used form of Informal Science Education. While there is evidence that the shows are highly enjoyable, little work has been done to investigate the cognitive impacts of these shows. This article describes the development and production of "The Boiling Point," a show that uses the structure of a play to…

WIDE Research Center as an Incubator for Graduate Student Experience

ERIC Educational Resources Information Center

Turner, Heather Noel; Nguyen, Minh-Tam; Keller, Beth; Sackey, Donnie Johnson; Ridolfo, Jim; Pigg, Stacey; Lauren, Benjamin; Potts, Liza; Hart-Davidson, Bill; Grabill, Jeff

2017-01-01

This article describes graduate mentorship experiences at the Writing, Information, and Digital Experience (WIDE) research center at Michigan State University and offers a stance on graduate student mentorship. It describes WIDE's mentorship model as feminist and inclusive and as a means to invite researchers with different backgrounds to engage…

Different Achilles Tendon Pathologies Show Distinct Histological and Molecular Characteristics

PubMed Central

Minkwitz, Susann; Schmock, Aysha; Bormann, Nicole; Kurtoglu, Alper; Tsitsilonis, Serafeim; Manegold, Sebastian

2018-01-01

Reasons for the development of chronic tendon pathologies are still under debate and more basic knowledge is needed about the different diseases. The aim of the present study was therefore to characterize different acute and chronic Achilles tendon disorders. Achilles tendon samples from patients with chronic tendinopathy (n = 7), chronic ruptures (n = 6), acute ruptures (n = 13), and intact tendons (n = 4) were analyzed. The histological score investigating pathological changes was significantly increased in tendinopathy and chronic ruptures compared to acute ruptures. Inflammatory infiltration was detected by immunohistochemistry in all tendon pathology groups, but was significantly lower in tendinopathy compared to chronic ruptures. Quantitative real-time PCR (qRT-PCR) analysis revealed significantly altered expression of genes related to collagens and matrix modeling/remodeling (matrix metalloproteinases, tissue inhibitors of metalloproteinases) in tendinopathy and chronic ruptures compared to intact tendons and/or acute ruptures. In all three tendon pathology groups markers of inflammation (interleukin (IL) 1β, tumor necrosis factor α, IL6, IL10, IL33, soluble ST2, transforming growth factor β1, cyclooxygenase 2), inflammatory cells (cluster of differentaition (CD) 3, CD68, CD80, CD206), fat metabolism (fatty acid binding protein 4, peroxisome proliferator-activated receptor γ, CCAAT/enhancer-binding protein α, adiponectin), and innervation (protein gene product 9.5, growth associated protein 43, macrophage migration inhibitory factor) were detectable, but only in acute ruptures significantly regulated compared to intact tendons. The study gives an insight into structural and molecular changes of pathological processes in tendons and might be used to identify targets for future therapy of tendon pathologies. PMID:29385715

Obesity in show dogs.

PubMed

Corbee, R J

2013-10-01

Obesity is an important disease with a growing incidence. Because obesity is related to several other diseases, and decreases life span, it is important to identify the population at risk. Several risk factors for obesity have been described in the literature. A higher incidence of obesity in certain breeds is often suggested. The aim of this study was to determine whether obesity occurs more often in certain breeds. The second aim was to relate the increased prevalence of obesity in certain breeds to the official standards of that breed. To this end, we investigated 1379 dogs of 128 different breeds by determining their body condition score (BCS). Overall, 18.6% of the show dogs had a BCS >5, and 1.1% of the show dogs had a BCS>7. There were significant differences between breeds, which could be correlated to the breed standards. It warrants firm discussions with breeders and judges in order to come to different interpretations of the standards to prevent overweight conditions from being the standard of beauty. © 2012 Blackwell Verlag GmbH.

Replication of genome-wide association signals in Asian Indians with early-onset type 2 diabetes.

PubMed

Chidambaram, Manickam; Liju, Samuel; Saboo, Banshi; Sathyavani, Kumpatla; Viswanathan, Vijay; Pankratz, Nathan; Gross, Myron; Mohan, Viswanathan; Radha, Venkatesan

2016-12-01

To evaluate the association of 87 genetic variants previously associated with type 2 diabetes mellitus (T2DM) in genome-wide association studies of populations of European ancestry in an Asian Indian population with early-onset type 2 diabetes mellitus (EOT2DM). The study groups comprised of 877 type 2 diabetes individuals, 436 individuals with EOT2DM (age at diagnosis below 35 years), 441 individuals with older T2DM (diagnosis at 35 years or greater) and controls with normal glucose tolerance (NGT) (n = 400 younger than 35 years; n = 438 older than 35 years). The participants were genotyped for 87 SNPs from 44 genes and 27 intergenic loci. Associations were tested using logistic regression. All the variants in TCF7L2 and CDKN2A/2B showed study-wide significance (p < 1.4 × 10 -4 ) with T2DM, but only rs7903146, rs12243326, rs12255372 of TCF7L2 and rs7020996 of CDKN2A/2B showed study-wide significance (p < 1.4 × 10 -4 ) with EOT2DM in this population. In addition, an intergenic SNP on chromosome 1 (rs10493685) was also shown to be study-wide significant (p = 7.1 × 10 -6 ). Several additional SNPs previously associated with T2DM reached borderline significance in this study, but may have been limited by relatively low sample numbers. Various other SNPs of T2DM were not associated with EOT2DM. Some of the variants in TCF7L2 and CDKN2A/2B associated with T2DM are associated with EOT2DM as well. An intergenic SNP on chromosome 1p31 showed association only with early-onset T2DM in this Asian Indian population. The lack of association with many other SNPs of T2DM may be a reflection of the lack of power of the study, sample size, differences in the frequencies of genetic polymorphisms in different ethnic groups, effect sizes, as well as ancestral differences in pattern of LD between the genetic variants involved in early- and late-onset T2DM.

Synthesis of styrene/isoprene/butadiene integrated rubber with wide glass transition temperature by reactive extrusion

NASA Astrophysics Data System (ADS)

Huang, Tianhua; Zheng, Anna; Zhan, Pengfei; Shi, Han; Li, Xiang; Guan, Yong; Wei, Dafu

2018-05-01

In this work, styrene/isoprene/butadiene integrated rubber (SIBR) was synthesized with n-butyllithium as the initiator and tetrahydrofuran as structure modifier in a co-rotating intermeshing twin-screw extruder. The content of diene in these terpolymers reached a surprising 70 wt% by feeding the monomers in two different sites of the twin-screw extruder. 1H-NMR, GPC and TEM results showed that the molecular structures of terpolymers changed with the variation of feeding site. Dynamic mechanical analysis of the vulcanized SIBR showed that the terpolymer had a wide glass transition region, which assured an excellent combination of high antiskid properties and low rolling resistance. Different from traditional solution polymerization, the present work provides a green approach to prepare the SIBR via bulk polymerization without solvent.

Widely tunable semiconductor lasers with three interferometric arms.

PubMed

Su, Guan-Lin; Wu, Ming C

2017-09-04

We present a comprehensive study for a new three-branch widely tunable semiconductor laser based on a self-imaging, lossless multi-mode interference (MMI) coupler. We have developed a general theoretical framework that is applicable to all types of interferometric lasers. Our analysis showed that the three-branch laser offers high side-mode suppression ratios (SMSRs) while maintaining a wide tuning range and a low threshold modal gain of the lasing mode. We also present the design rules for tuning over the dense-wavelength division multiplexing grid over the C-band.

Genome-wide identification, classification, and analysis of NADP-ME family members from 12 crucifer species.

PubMed

Tao, Peng; Guo, Weiling; Li, Biyuan; Wang, Wuhong; Yue, Zhichen; Lei, Juanli; Zhao, Yanting; Zhong, Xinmin

2016-06-01

NADP-dependent malic enzymes (NADP-MEs) play essential roles in both normal development and stress responses in plants. Here, genome-wide analysis was performed to identify 65 putative NADP-ME genes from 12 crucifer species. These NADP-ME genes were grouped into five categories of syntenic orthologous genes and were divided into three clades of a phylogenic tree. Promoter motif analysis showed that NADP-ME1 genes in Group IV were more conserved with each other than the other NADP-ME genes in Groups I and II. A nucleotide motif involved in ABA responses, desiccation and seed development was found in the promoters of most NADP-ME1 genes. Generally, the NADP-ME genes of Brassica rapa, B. oleracea and B. napus had less introns than their corresponding Arabidopsis orthologs. In these three Brassica species, the NADP-ME genes derived from the least fractionated subgenome have lost less introns than those from the medium fractionated and most fractionated subgenomes. BrNADP-ME1 showed the highest expression in petals and mature embryos. Two paralogous NADP-ME2 genes (BrNADP-ME2a and BrNADP-ME2b) shared similar expression profiles and differential expression levels. BrNADP-ME3 showed down-regulation during embryogenesis and reached its lowest expression in early cotyledonary embryos. BrNADP-ME4 was expressed widely in multiple organs and showed high expression during the whole embryogenesis process. Different NADP-ME genes of B. rapa showed differential gene expression profiles in young leaves after ABA treatment or cold stress. Our genome-wide identification and characterization of NADP-ME genes extend our understanding of the evolution or function of this family in Brassicaceae.

Proton pump inhibitors while belonging to the same family of generic drugs show different anti-tumor effect.

PubMed

Lugini, Luana; Federici, Cristina; Borghi, Martina; Azzarito, Tommaso; Marino, Maria Lucia; Cesolini, Albino; Spugnini, Enrico Pierluigi; Fais, Stefano

2016-08-01

Tumor acidity represents a major cause of chemoresistance. Proton pump inhibitors (PPIs) can neutralize tumor acidity, sensitizing cancer cells to chemotherapy. To compare the anti-tumor efficacy of different PPIs in vitro and in vivo. In vitro experiments PPIs anti-tumor efficacy in terms of cell proliferation and cell death/apoptosis/necrosis evaluation were performed. In vivo PPIs efficacy experiments were carried out using melanoma xenograft model in SCID mice. Lansoprazole showed higher anti-tumor effect when compared to the other PPIs. The lansoprazole effect lasted even upon drug removal from the cell culture medium and it was independent from the lipophilicity of the PPIs formulation. These PPIs have shown different anti-tumoral efficacy, and the most effective at low dose was lansoprazole. The possibility to contrast tumor acidity by off-label using PPIs opens a new field of oncology investigation.

Genus-wide comparison of Pseudovibrio bacterial genomes reveal diverse adaptations to different marine invertebrate hosts.

PubMed

Alex, Anoop; Antunes, Agostinho

2018-01-01

Bacteria belonging to the genus Pseudovibrio have been frequently found in association with a wide variety of marine eukaryotic invertebrate hosts, indicative of their versatile and symbiotic lifestyle. A recent comparison of the sponge-associated Pseudovibrio genomes has shed light on the mechanisms influencing a successful symbiotic association with sponges. In contrast, the genomic architecture of Pseudovibrio bacteria associated with other marine hosts has received less attention. Here, we performed genus-wide comparative analyses of 18 Pseudovibrio isolated from sponges, coral, tunicates, flatworm, and seawater. The analyses revealed a certain degree of commonality among the majority of sponge- and coral-associated bacteria. Isolates from other marine invertebrate host, tunicates, exhibited a genetic repertoire for cold adaptation and specific metabolic abilities including mucin degradation in the Antarctic tunicate-associated bacterium Pseudovibrio sp. Tun.PHSC04_5.I4. Reductive genome evolution was simultaneously detected in the flatworm-associated bacteria and the sponge-associated bacterium P. axinellae AD2, through the loss of major secretion systems (type III/VI) and virulence/symbioses factors such as proteins involved in adhesion and attachment to the host. Our study also unraveled the presence of a CRISPR-Cas system in P. stylochi UST20140214-052 a flatworm-associated bacterium possibly suggesting the role of CRISPR-based adaptive immune system against the invading virus particles. Detection of mobile elements and genomic islands (GIs) in all bacterial members highlighted the role of horizontal gene transfer for the acquisition of novel genetic features, likely enhancing the bacterial ecological fitness. These findings are insightful to understand the role of genome diversity in Pseudovibrio as an evolutionary strategy to increase their colonizing success across a wide range of marine eukaryotic hosts.

Genus-wide comparison of Pseudovibrio bacterial genomes reveal diverse adaptations to different marine invertebrate hosts

PubMed Central

Alex, Anoop

2018-01-01

Bacteria belonging to the genus Pseudovibrio have been frequently found in association with a wide variety of marine eukaryotic invertebrate hosts, indicative of their versatile and symbiotic lifestyle. A recent comparison of the sponge-associated Pseudovibrio genomes has shed light on the mechanisms influencing a successful symbiotic association with sponges. In contrast, the genomic architecture of Pseudovibrio bacteria associated with other marine hosts has received less attention. Here, we performed genus-wide comparative analyses of 18 Pseudovibrio isolated from sponges, coral, tunicates, flatworm, and seawater. The analyses revealed a certain degree of commonality among the majority of sponge- and coral-associated bacteria. Isolates from other marine invertebrate host, tunicates, exhibited a genetic repertoire for cold adaptation and specific metabolic abilities including mucin degradation in the Antarctic tunicate-associated bacterium Pseudovibrio sp. Tun.PHSC04_5.I4. Reductive genome evolution was simultaneously detected in the flatworm-associated bacteria and the sponge-associated bacterium P. axinellae AD2, through the loss of major secretion systems (type III/VI) and virulence/symbioses factors such as proteins involved in adhesion and attachment to the host. Our study also unraveled the presence of a CRISPR-Cas system in P. stylochi UST20140214-052 a flatworm-associated bacterium possibly suggesting the role of CRISPR-based adaptive immune system against the invading virus particles. Detection of mobile elements and genomic islands (GIs) in all bacterial members highlighted the role of horizontal gene transfer for the acquisition of novel genetic features, likely enhancing the bacterial ecological fitness. These findings are insightful to understand the role of genome diversity in Pseudovibrio as an evolutionary strategy to increase their colonizing success across a wide range of marine eukaryotic hosts. PMID:29775460

Different Epidermal Growth Factor (EGF) Receptor Ligands Show Distinct Kinetics and Biased or Partial Agonism for Homodimer and Heterodimer Formation*

PubMed Central

Macdonald-Obermann, Jennifer L.; Pike, Linda J.

2014-01-01

The EGF receptor has seven different cognate ligands. Previous work has shown that these different ligands are capable of inducing different biological effects, even in the same cell. To begin to understand the molecular basis for this variation, we used luciferase fragment complementation to measure ligand-induced dimer formation and radioligand binding to study the effect of the ligands on subunit-subunit interactions in EGF receptor (EGFR) homodimers and EGFR/ErbB2 heterodimers. In luciferase fragment complementation imaging studies, amphiregulin (AREG) functioned as a partial agonist, inducing only about half as much total dimerization as the other three ligands. However, unlike the other ligands, AREG showed biphasic kinetics for dimer formation, suggesting that its path for EGF receptor activation involves binding to both monomers and preformed dimers. EGF, TGFα, and betacellulin (BTC) appear to mainly stimulate receptor activation through binding to and dimerization of receptor monomers. In radioligand binding assays, EGF and TGFα exhibited increased affinity for EGFR/ErbB2 heterodimers compared with EGFR homodimers. By contrast, BTC and AREG showed a similar affinity for both dimers. Thus, EGF and TGFα are biased agonists, whereas BTC and AREG are balanced agonists with respect to selectivity of dimer formation. These data suggest that the differences in biological response to different EGF receptor ligands may result from partial agonism for dimer formation, differences in the kinetic pathway utilized to generate activated receptor dimers, and biases in the formation of heterodimers versus homodimers. PMID:25086039

AβPP/PS1 Transgenic Mice Show Sex Differences in the Cerebellum Associated with Aging.

PubMed

Ordoñez-Gutierrez, Lara; Fernandez-Perez, Ivan; Herrera, Jose Luis; Anton, Marta; Benito-Cuesta, Irene; Wandosell, Francisco

2016-09-06

Cerebellar pathology has been related to presenilin 1 mutations in certain pedigrees of familial Alzheimer's disease. However, cerebellum tissue has not been intensively analyzed in transgenic models of mutant presenilins. Furthermore, the effect of the sex of the mice was not systematically analyzed, despite the fact that important gender differences in the evolution of the disease in the human population have been described. We analyzed whether the progression of amyloidosis in a double transgenic mouse, AβPP/PS1, is susceptible to aging and differentially affects males and females. The accumulation of amyloid in the cerebellum differentially affects males and females of the AβPP/PS1 transgenic line, which was found to be ten-fold higher in 15-month-old females. Amyloid-β accumulation was more evident in the molecular layer of the cerebellum, but glia reaction was only observed in the granular layer of the older mice. The sex divergence was also observed in other neuronal, survival, and autophagic markers. The cerebellum plays an important role in the evolution of the pathology in this transgenic mouse model. Sex differences could be crucial for a complete understanding of this disease. We propose that the human population could be studied in this way. Sex-specific treatment strategies in human populations could show a differential response to the therapeutic approach.

The Oral Antimalarial Drug Tafenoquine Shows Activity against Trypanosoma brucei

PubMed Central

Carvalho, Luis; Martínez-García, Marta; Pérez-Victoria, Ignacio; Manzano, José Ignacio; Yardley, Vanessa

2015-01-01

The protozoan parasite Trypanosoma brucei causes human African trypanosomiasis, or sleeping sickness, a neglected tropical disease that requires new, safer, and more effective treatments. Repurposing oral drugs could reduce both the time and cost involved in sleeping sickness drug discovery. Tafenoquine (TFQ) is an oral antimalarial drug belonging to the 8-aminoquinoline family which is currently in clinical phase III. We show here that TFQ efficiently kills different T. brucei spp. in the submicromolar concentration range. Our results suggest that TFQ accumulates into acidic compartments and induces a necrotic process involving cell membrane disintegration and loss of cytoplasmic content, leading to parasite death. Cell lysis is preceded by a wide and multitarget drug action, affecting the lysosome, mitochondria, and acidocalcisomes and inducing a depolarization of the mitochondrial membrane potential, elevation of intracellular Ca2+, and production of reactive oxygen species. This is the first report of an 8-aminoquinoline demonstrating significant in vitro activity against T. brucei. PMID:26195527

The Oral Antimalarial Drug Tafenoquine Shows Activity against Trypanosoma brucei.

PubMed

Carvalho, Luis; Martínez-García, Marta; Pérez-Victoria, Ignacio; Manzano, José Ignacio; Yardley, Vanessa; Gamarro, Francisco; Pérez-Victoria, José M

2015-10-01

The protozoan parasite Trypanosoma brucei causes human African trypanosomiasis, or sleeping sickness, a neglected tropical disease that requires new, safer, and more effective treatments. Repurposing oral drugs could reduce both the time and cost involved in sleeping sickness drug discovery. Tafenoquine (TFQ) is an oral antimalarial drug belonging to the 8-aminoquinoline family which is currently in clinical phase III. We show here that TFQ efficiently kills different T. brucei spp. in the submicromolar concentration range. Our results suggest that TFQ accumulates into acidic compartments and induces a necrotic process involving cell membrane disintegration and loss of cytoplasmic content, leading to parasite death. Cell lysis is preceded by a wide and multitarget drug action, affecting the lysosome, mitochondria, and acidocalcisomes and inducing a depolarization of the mitochondrial membrane potential, elevation of intracellular Ca(2+), and production of reactive oxygen species. This is the first report of an 8-aminoquinoline demonstrating significant in vitro activity against T. brucei. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Burkholderia, a genus rich in plant-associated nitrogen fixers with wide environmental and geographic distribution.

PubMed

Estrada-De Los Santos, P; Bustillos-Cristales, R; Caballero-Mellado, J

2001-06-01

The genus Burkholderia comprises 19 species, including Burkholderia vietnamiensis which is the only known N(2)-fixing species of this bacterial genus. The first isolates of B. vietnamiensis were recovered from the rhizosphere of rice plants grown in a phytotron, but its existence in natural environments and its geographic distribution were not reported. In the present study, most N(2)-fixing isolates recovered from the environment of field-grown maize and coffee plants cultivated in widely separated regions of Mexico were phenotypically identified as B. cepacia using the API 20NE system. Nevertheless, a number of these isolates recovered from inside of maize roots, as well as from the rhizosphere and rhizoplane of maize and coffee plants, showed similar or identical features to those of B. vietnamiensis TVV75(T). These features include nitrogenase activity with 10 different carbon sources, identical or very similar nifHDK hybridization patterns, very similar protein electrophoregrams, identical amplified 16S rDNA restriction (ARDRA) profiles, and levels of DNA-DNA reassociation higher than 70% with total DNA from strain TVV75(T). Although the ability to fix N(2) is not reported to be a common feature among the known species of the genus Burkholderia, the results obtained show that many diazotrophic Burkholderia isolates analyzed showed phenotypic and genotypic features different from those of the known N(2)-fixing species B. vietnamiensis as well as from those of B. kururiensis, a bacterium identified in the present study as a diazotrophic species. DNA-DNA reassociation assays confirmed the existence of N(2)-fixing Burkholderia species different from B. vietnamiensis. In addition, this study shows the wide geographic distribution and substantial capability of N(2)-fixing Burkholderia spp. for colonizing diverse host plants in distantly separated environments.

Burkholderia, a Genus Rich in Plant-Associated Nitrogen Fixers with Wide Environmental and Geographic Distribution

PubMed Central

Estrada-De Los Santos, Paulina; Bustillos-Cristales, Rocío; Caballero-Mellado, Jesús

2001-01-01

The genus Burkholderia comprises 19 species, including Burkholderia vietnamiensis which is the only known N2-fixing species of this bacterial genus. The first isolates of B. vietnamiensis were recovered from the rhizosphere of rice plants grown in a phytotron, but its existence in natural environments and its geographic distribution were not reported. In the present study, most N2-fixing isolates recovered from the environment of field-grown maize and coffee plants cultivated in widely separated regions of Mexico were phenotypically identified as B. cepacia using the API 20NE system. Nevertheless, a number of these isolates recovered from inside of maize roots, as well as from the rhizosphere and rhizoplane of maize and coffee plants, showed similar or identical features to those of B. vietnamiensis TVV75T. These features include nitrogenase activity with 10 different carbon sources, identical or very similar nifHDK hybridization patterns, very similar protein electrophoregrams, identical amplified 16S rDNA restriction (ARDRA) profiles, and levels of DNA-DNA reassociation higher than 70% with total DNA from strain TVV75T. Although the ability to fix N2 is not reported to be a common feature among the known species of the genus Burkholderia, the results obtained show that many diazotrophic Burkholderia isolates analyzed showed phenotypic and genotypic features different from those of the known N2-fixing species B. vietnamiensis as well as from those of B. kururiensis, a bacterium identified in the present study as a diazotrophic species. DNA-DNA reassociation assays confirmed the existence of N2-fixing Burkholderia species different from B. vietnamiensis. In addition, this study shows the wide geographic distribution and substantial capability of N2-fixing Burkholderia spp. for colonizing diverse host plants in distantly separated environments. PMID:11375196

Clinical and virological heterogeneity of hepatitis delta in different regions world-wide: The Hepatitis Delta International Network (HDIN).

PubMed

Wranke, Anika; Pinheiro Borzacov, Lourdes M; Parana, Raymundo; Lobato, Cirley; Hamid, Saeed; Ceausu, Emanoil; Dalekos, George N; Rizzetto, Mario; Turcanu, Adela; Niro, Grazia A; Lubna, Farheen; Abbas, Minaam; Ingiliz, Patrick; Buti, Maria; Ferenci, Peter; Vanwolleghem, Thomas; Hayden, Tonya; Dashdorj, Naranjargal; Motoc, Adriana; Cornberg, Markus; Abbas, Zaigham; Yurdaydin, Cihan; Manns, Michael P; Wedemeyer, Heiner; Hardtke, Svenja

2018-05-01

Chronic hepatitis D (delta) is a major global health burden. Clinical and virological characteristics of patients with hepatitis D virus (HDV) infection and treatment approaches in different regions world-wide are poorly defined. The Hepatitis Delta International Network (HDIN) registry was established in 2011 with centres in Europe, Asia, North- and South America. Here, we report on clinical/ virological characteristics of the first 1576 patients with ongoing or past HDV infection included in the database until October 2016 and performed a retrospective outcome analysis. The primary aim was to investigate if the region of origin was associated with HDV replication and clinical outcome. The majority of patients was male (n = 979, 62%) and the mean age was 36.7 years (range 1-79, with 9% of patients younger than 20 years). Most patients were HBeAg-negative (77%) and HDV-RNA positive (85%). Cirrhosis was reported in 48.7% of cases which included 13% of patients with previous or ongoing liver decompensation. Hepatocellular carcinoma (HCC) developed in 30 patients (2.5%) and 44 (3.6%) underwent liver transplantation. Regions of origin were independently associated with clinical endpoints and detectability of HDV RNA. Antiviral therapy was administered to 356 patients with different treatment uptakes in different regions. Of these, 264 patients were treated with interferon-a and 92 were treated with HBV-Nucs only. The HDIN registry confirms the severity of hepatitis delta but also highlights the heterogeneity of patient characteristics and clinical outcomes in different regions. There is an urgent need for novel treatment options for HDV infection. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Genome-Wide Screening of Genes Showing Altered Expression in Liver Metastases of Human Colorectal Cancers by cDNA Microarray1

PubMed Central

Yanagawa, Rempei; Furukawa, Yoichi; Tsunoda, Tatsuhiko; Kitahara, Osamu; Kameyama, Masao; Murata, Kohei; Ishikawa, Osamu; Nakamura, Yusuke

2001-01-01

Abstract In spite of intensive and increasingly successful attempts to determine the multiple steps involved in colorectal carcinogenesis, the mechanisms responsible for metastasis of colorectal tumors to the liver remain to be clarified. To identify genes that are candidates for involvement in the metastatic process, we analyzed genome-wide expression profiles of 10 primary colorectal cancers and their corresponding metastatic lesions by means of a cDNA microarray consisting of 9121 human genes. This analysis identified 40 genes whose expression was commonly upregulated in metastatic lesions, and 7 that were commonly downregulated. The upregulated genes encoded proteins involved in cell adhesion, or remodeling of the actin cytoskeleton. Investigation of the functions of more of the altered genes should improve our understanding of metastasis and may identify diagnostic markers and/or novel molecular targets for prevention or therapy of metastatic lesions. PMID:11687950

Akinetic-rigid and tremor-dominant Parkinson's disease patients show different patterns of intrinsic brain activity.

PubMed

Zhang, Jiuquan; Wei, Luqing; Hu, Xiaofei; Xie, Bing; Zhang, Yanling; Wu, Guo-Rong; Wang, Jian

2015-01-01

Parkinson's disease (PD) is a surprisingly heterogeneous neurodegenerative disorder. It is well established that different subtypes of PD present with different clinical courses and prognoses. However, the neural mechanism underlying these disparate presentations is uncertain. Here we used resting-state fMRI (rs-fMRI) and the regional homogeneity (ReHo) method to determine neural activity patterns in the two main clinical subgroups of PD (akinetic-rigid and tremor-dominant). Compared with healthy controls, akinetic-rigid (AR) subjects had increased ReHo mainly in right amygdala, left putamen, bilateral angular gyrus, bilateral medial prefrontal cortex (MPFC), and decreased ReHo in left post cingulate gyrus/precuneus (PCC/PCu) and bilateral thalamus. In contrast, tremor-dominant (TD) patients showed higher ReHo mostly in bilateral angular gyrus, left PCC, cerebellum_crus1, and cerebellum_6, while ReHo was decreased in right putamen, primary sensory cortex (S1), vermis_3, and cerebellum_4_5. These results indicate that AR and TD subgroups both represent altered spontaneous neural activity in default-mode regions and striatum, and AR subjects exhibit more changed neural activity in the mesolimbic cortex (amygdala) but TD in the cerebellar regions. Of note, direct comparison of the two subgroups revealed a distinct ReHo pattern primarily located in the striatal-thalamo-cortical (STC) and cerebello-thalamo-cortical (CTC) loops. Overall, our findings highlight the involvement of default mode network (DMN) and STC circuit both in AR and TD subtypes, but also underscore the importance of integrating mesolimbic-striatal and CTC loops in understanding neural systems of akinesia and rigidity, as well as resting tremor in PD. This study provides improved understanding of the pathophysiological models of different subtypes of PD. Copyright © 2014 Elsevier Ltd. All rights reserved.

Validation of a plant-wide phosphorus modelling approach with minerals precipitation in a full-scale WWTP.

PubMed

Kazadi Mbamba, Christian; Flores-Alsina, Xavier; John Batstone, Damien; Tait, Stephan

2016-09-01

The focus of modelling in wastewater treatment is shifting from single unit to plant-wide scale. Plant-wide modelling approaches provide opportunities to study the dynamics and interactions of different transformations in water and sludge streams. Towards developing more general and robust simulation tools applicable to a broad range of wastewater engineering problems, this paper evaluates a plant-wide model built with sub-models from the Benchmark Simulation Model No. 2-P (BSM2-P) with an improved/expanded physico-chemical framework (PCF). The PCF includes a simple and validated equilibrium approach describing ion speciation and ion pairing with kinetic multiple minerals precipitation. Model performance is evaluated against data sets from a full-scale wastewater treatment plant, assessing capability to describe water and sludge lines across the treatment process under steady-state operation. With default rate kinetic and stoichiometric parameters, a good general agreement is observed between the full-scale datasets and the simulated results under steady-state conditions. Simulation results show differences between measured and modelled phosphorus as little as 4-15% (relative) throughout the entire plant. Dynamic influent profiles were generated using a calibrated influent generator and were used to study the effect of long-term influent dynamics on plant performance. Model-based analysis shows that minerals precipitation strongly influences composition in the anaerobic digesters, but also impacts on nutrient loading across the entire plant. A forecasted implementation of nutrient recovery by struvite crystallization (model scenario only), reduced the phosphorus content in the treatment plant influent (via centrate recycling) considerably and thus decreased phosphorus in the treated outflow by up to 43%. Overall, the evaluated plant-wide model is able to jointly describe the physico-chemical and biological processes, and is advocated for future use as a tool for

A CPW-fed circular wide-slot UWB antenna with wide tunable and flexible reconfigurable dual notch bands.

PubMed

Li, Yingsong; Li, Wenxing; Ye, Qiubo

2013-01-01

A coplanar waveguide (CPW)-fed circular slot antenna with wide tunable dual band-notched function and frequency reconfigurable characteristic is designed, and its performance is verified experimentally for ultra-wideband (UWB) communication applications. The dual band-notched function is achieved by using a T-shaped stepped impedance resonator (T-SIR) inserted inside the circular ring radiation patch and by etching a parallel stub loaded resonator (PSLR) in the CPW transmission line, while the wide tunable bands can be implemented by adjusting the dimensions of the T-SIR and the PSLR. The notch band reconfigurable characteristic is realized by integrating three switches into the T-SIR and the PSLR. The numerical and experimental results show that the proposed antenna has a wide bandwidth ranging from 2.7 GHz to 12 GHz with voltage standing wave ratio (VSWR) less than 2, except for the two notch bands operating at 3.8-5.9 GHz and 7.7-9.2 GHz, respectively. In addition, the proposed antenna has been optimized to a compact size and can provide omnidirectional radiation patterns, which are suitable for UWB communication applications.

A CPW-Fed Circular Wide-Slot UWB Antenna with Wide Tunable and Flexible Reconfigurable Dual Notch Bands

PubMed Central

Li, Yingsong; Li, Wenxing; Ye, Qiubo

2013-01-01

A coplanar waveguide (CPW)-fed circular slot antenna with wide tunable dual band-notched function and frequency reconfigurable characteristic is designed, and its performance is verified experimentally for ultra-wideband (UWB) communication applications. The dual band-notched function is achieved by using a T-shaped stepped impedance resonator (T-SIR) inserted inside the circular ring radiation patch and by etching a parallel stub loaded resonator (PSLR) in the CPW transmission line, while the wide tunable bands can be implemented by adjusting the dimensions of the T-SIR and the PSLR. The notch band reconfigurable characteristic is realized by integrating three switches into the T-SIR and the PSLR. The numerical and experimental results show that the proposed antenna has a wide bandwidth ranging from 2.7 GHz to 12 GHz with voltage standing wave ratio (VSWR) less than 2, except for the two notch bands operating at 3.8–5.9 GHz and 7.7–9.2 GHz, respectively. In addition, the proposed antenna has been optimized to a compact size and can provide omnidirectional radiation patterns, which are suitable for UWB communication applications. PMID:24222733

A genome-wide approach to children's aggressive behavior: The EAGLE consortium.

PubMed

Pappa, Irene; St Pourcain, Beate; Benke, Kelly; Cavadino, Alana; Hakulinen, Christian; Nivard, Michel G; Nolte, Ilja M; Tiesler, Carla M T; Bakermans-Kranenburg, Marian J; Davies, Gareth E; Evans, David M; Geoffroy, Marie-Claude; Grallert, Harald; Groen-Blokhuis, Maria M; Hudziak, James J; Kemp, John P; Keltikangas-Järvinen, Liisa; McMahon, George; Mileva-Seitz, Viara R; Motazedi, Ehsan; Power, Christine; Raitakari, Olli T; Ring, Susan M; Rivadeneira, Fernando; Rodriguez, Alina; Scheet, Paul A; Seppälä, Ilkka; Snieder, Harold; Standl, Marie; Thiering, Elisabeth; Timpson, Nicholas J; Veenstra, René; Velders, Fleur P; Whitehouse, Andrew J O; Smith, George Davey; Heinrich, Joachim; Hypponen, Elina; Lehtimäki, Terho; Middeldorp, Christel M; Oldehinkel, Albertine J; Pennell, Craig E; Boomsma, Dorret I; Tiemeier, Henning

2016-07-01

Individual differences in aggressive behavior emerge in early childhood and predict persisting behavioral problems and disorders. Studies of antisocial and severe aggression in adulthood indicate substantial underlying biology. However, little attention has been given to genome-wide approaches of aggressive behavior in children. We analyzed data from nine population-based studies and assessed aggressive behavior using well-validated parent-reported questionnaires. This is the largest sample exploring children's aggressive behavior to date (N = 18,988), with measures in two developmental stages (N = 15,668 early childhood and N = 16,311 middle childhood/early adolescence). First, we estimated the additive genetic variance of children's aggressive behavior based on genome-wide SNP information, using genome-wide complex trait analysis (GCTA). Second, genetic associations within each study were assessed using a quasi-Poisson regression approach, capturing the highly right-skewed distribution of aggressive behavior. Third, we performed meta-analyses of genome-wide associations for both the total age-mixed sample and the two developmental stages. Finally, we performed a gene-based test using the summary statistics of the total sample. GCTA quantified variance tagged by common SNPs (10-54%). The meta-analysis of the total sample identified one region in chromosome 2 (2p12) at near genome-wide significance (top SNP rs11126630, P = 5.30 × 10(-8) ). The separate meta-analyses of the two developmental stages revealed suggestive evidence of association at the same locus. The gene-based analysis indicated association of variation within AVPR1A with aggressive behavior. We conclude that common variants at 2p12 show suggestive evidence for association with childhood aggression. Replication of these initial findings is needed, and further studies should clarify its biological meaning. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Comparisons between Murine Polyomavirus and Simian Virus 40 Show Significant Differences in Small T Antigen Function ▿

PubMed Central

Andrabi, Shaida; Hwang, Justin H.; Choe, Jennifer Kean; Roberts, Thomas M.; Schaffhausen, Brian S.

2011-01-01

Although members of a virus family produce similar gene products, those products may have quite different functions. Simian virus 40 (SV40) large T antigen (LT), for example, targets p53 directly, but murine polyomavirus LT does not. SV40 small T antigen (SVST) has received considerable attention because of its ability to contribute to transformation of human cells. Here, we show that there are major differences between SVST and polyomavirus small T antigen (POLST) in their effects on differentiation, transformation, and cell survival. Both SVST and POLST induce cell cycle progression. However, POLST also inhibits differentiation of 3T3-L1 preadipocytes and C2C12 myoblasts. Additionally, POLST induces apoptosis of mouse embryo fibroblasts. SVST reduces the proapoptotic transcriptional activity of FOXO1 through phosphorylation. On the other hand, SVST complements large T antigen and Ras for the transformation of human mammary epithelial cells (HMECs), but POLST does not. Mechanistically, the differences between SVST and POLST may lie in utilization of protein phosphatase 2A (PP2A). POLST binds both Aα and Aβ scaffolding subunits of PP2A while SVST binds only Aα. Knockdown of Aβ could mimic POLST-induced apoptosis. The two small T antigens can target different proteins for dephosphorylation. POLST binds and dephosphorylates substrates, such as lipins, that SVST does not. PMID:21835797

Compact ultra wide band microstrip bandpass filter based on multiple-mode resonator and modified complementary split ring resonator.

PubMed

Marcotegui, J Antonio; Illescas, Jesús Miguel; Estevez, Aritz; Falcone, Francisco

2013-01-01

A new class of broadband microstrip filters for Ultra Wide Band (UWB) applications is proposed. In the design, different stages of parallel-coupled microstrip line and other stages with a Modified Complementary Split Ring Resonator (MCSRR)-a concept proposed here for the first time-are adjusted to obtain the desired response with broadband, sharp rejection, low insertion loss, and low return loss. Full wave simulation results as well as measurement results from fabricated prototypes are presented, showing good agreement. The proposed technique offers a new alternative to implement low-cost high-performance filter devices, applicable to a wide range of communication systems.

A Geographically Diverse Collection of Schizosaccharomyces pombe Isolates Shows Limited Phenotypic Variation but Extensive Karyotypic Diversity

PubMed Central

Brown, William R. A.; Liti, Gianni; Rosa, Carlos; James, Steve; Roberts, Ian; Robert, Vincent; Jolly, Neil; Tang, Wen; Baumann, Peter; Green, Carter; Schlegel, Kristina; Young, Jonathan; Hirchaud, Fabienne; Leek, Spencer; Thomas, Geraint; Blomberg, Anders; Warringer, Jonas

2011-01-01

The fission yeast Schizosaccharomyces pombe has been widely used to study eukaryotic cell biology, but almost all of this work has used derivatives of a single strain. We have studied 81 independent natural isolates and 3 designated laboratory strains of Schizosaccharomyces pombe. Schizosaccharomyces pombe varies significantly in size but shows only limited variation in proliferation in different environments compared with Saccharomyces cerevisiae. Nucleotide diversity, π, at a near neutral site, the central core of the centromere of chromosome II is approximately 0.7%. Approximately 20% of the isolates showed karyotypic rearrangements as detected by pulsed field gel electrophoresis and filter hybridization analysis. One translocation, found in 6 different isolates, including the type strain, has a geographically widespread distribution and a unique haplotype and may be a marker of an incipient speciation event. All of the other translocations are unique. Exploitation of this karyotypic diversity may cast new light on both the biology of telomeres and centromeres and on isolating mechanisms in single-celled eukaryotes. PMID:22384373

CHARACTERIZATION OF SEVEN ULTRA-WIDE TRANS-NEPTUNIAN BINARIES

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

Parker, Alex H.; Kavelaars, J. J.; Petit, Jean-Marc

2011-12-10

The low-inclination component of the Classical Kuiper Belt is host to a population of extremely widely separated binaries. These systems are similar to other trans-Neptunian binaries (TNBs) in that the primary and secondary components of each system are of roughly equal size. We have performed an astrometric monitoring campaign of a sample of seven wide-separation, long-period TNBs and present the first-ever well-characterized mutual orbits for each system. The sample contains the most eccentric (2006 CH{sub 69}, e{sub m} = 0.9) and the most widely separated, weakly bound (2001 QW{sub 322}, a/R{sub H} {approx_equal} 0.22) binary minor planets known, and alsomore » contains the system with lowest-measured mass of any TNB (2000 CF{sub 105}, M{sub sys} {approx_equal} 1.85 Multiplication-Sign 10{sup 17} kg). Four systems orbit in a prograde sense, and three in a retrograde sense. They have a different mutual inclination distribution compared to all other TNBs, preferring low mutual-inclination orbits. These systems have geometric r-band albedos in the range of 0.09-0.3, consistent with radiometric albedo estimates for larger solitary low-inclination Classical Kuiper Belt objects, and we limit the plausible distribution of albedos in this region of the Kuiper Belt. We find that gravitational collapse binary formation models produce an orbital distribution similar to that currently observed, which along with a confluence of other factors supports formation of the cold Classical Kuiper Belt in situ through relatively rapid gravitational collapse rather than slow hierarchical accretion. We show that these binary systems are sensitive to disruption via collisions, and their existence suggests that the size distribution of TNOs at small sizes remains relatively shallow.« less

Venomics of New World pit vipers: genus-wide comparisons of venom proteomes across Agkistrodon.

PubMed

Lomonte, Bruno; Tsai, Wan-Chih; Ureña-Diaz, Juan Manuel; Sanz, Libia; Mora-Obando, Diana; Sánchez, Elda E; Fry, Bryan G; Gutiérrez, José María; Gibbs, H Lisle; Sovic, Michael G; Calvete, Juan J

2014-01-16

We report a genus-wide comparison of venom proteome variation across New World pit vipers in the genus Agkistrodon. Despite the wide variety of habitats occupied by this genus and that all its taxa feed on diverse species of vertebrates and invertebrate prey, the venom proteomes of copperheads, cottonmouths, and cantils are remarkably similar, both in the type and relative abundance of their different toxin families. The venoms from all the eleven species and subspecies sampled showed relatively similar proteolytic and PLA2 activities. In contrast, quantitative differences were observed in hemorrhagic and myotoxic activities in mice. The highest myotoxic activity was observed with the venoms of A. b. bilineatus, followed by A. p. piscivorus, whereas the venoms of A. c. contortrix and A. p. leucostoma induced the lowest myotoxic activity. The venoms of Agkistrodon bilineatus subspecies showed the highest hemorrhagic activity and A. c. contortrix the lowest. Compositional and toxicological analyses agree with clinical observations of envenomations by Agkistrodon in the USA and Central America. A comparative analysis of Agkistrodon shows that venom divergence tracks phylogeny of this genus to a greater extent than in Sistrurus rattlesnakes, suggesting that the distinct natural histories of Agkistrodon and Sistrurus clades may have played a key role in molding the patterns of evolution of their venom protein genes. A deep understanding of the structural and functional profiles of venoms and of the principles governing the evolution of venomous systems is a goal of venomics. Isolated proteomics analyses have been conducted on venoms from many species of vipers and pit vipers. However, making sense of these large inventories of data requires the integration of this information across multiple species to identify evolutionary and ecological trends. Our genus-wide venomics study provides a comprehensive overview of the toxic arsenal across Agkistrodon and a ground for

Microfluidic oscillators with widely tunable periods

PubMed Central

Kim, Sung-Jin; Yokokawa, Ryuji; Takayama, Shuichi

2013-01-01

We present experiments and theory of a constant flow-driven microfluidic oscillator with widely tunable oscillation periods. This oscillator converts two constant input-flows from a syringe pump into an alternating, periodic output-flow with oscillation periods that can be adjusted to between 0.3 s to 4.1 h by tuning an external membrane capacitor. This capacitor allows multiple adjustable periods at a given input flow-rate, thus providing great flexibility in device operation. Also, we show that a sufficiently large external capacitance, relative to the internal capacitance of the microfluidic valve itself, is a critical requirement for oscillation. These widely tunable microfluidic oscillators are envisioned to be broadly useful for the study of biological rhythms, as on-chip timing sources for microfluidic logic circuits, and other applications that require variation in timed flow switching. PMID:23429765

Subtypes of breast cancer show different spatial distributions of brain metastases.

PubMed

Kyeong, Sunghyon; Cha, Yoon Jin; Ahn, Sung Gwe; Suh, Sang Hyun; Son, Eun Ju; Ahn, Sung Jun

2017-01-01

The aim of our study was to test the hypothesis that the spatial distribution of breast cancer brain metastases (BM) differ according to their biological subtypes. MR images of 100 patients with BM from primary breast cancer were retrospectively reviewed. Patients were divided according to the biological subtype of the primary tumor, (triple-negative: 24, HER2 positive: 48, luminal: 28). All images marked with BMs were standardized to the human brain MRI atlas provided by the Montreal Neurological Institute 152 database. Distribution pattern of BM was evaluated with intra-group and intergroup analysis. In intra-group analysis, hot spots of metastases from triple-negative are evenly distributed in the brain, meanwhile BMs from HER2 positive and luminal type occur dominantly in occipital lobe and cerebellum. In intergroup analysis, BMs from triple-negative type occurred more often in frontal lobe, limbic region, and parietal lobe, compared with other types (P < .05). Breast cancer subtypes tend to demonstrate different spatial distributions of their BMs. These findings may have direct implications for dose modulation in prophylactic irradiation as well as for differential diagnoses. Thus, this result should be validated in future study with a larger population.

HIV+ Men and Women Show Different Performance Patterns on Procedural Learning Tasks

PubMed Central

Martin, Eileen; Gonzalez, Raul; Vassileva, Jasmin; Maki, Pauline

2010-01-01

The literature suggests that nondeclarative, or nonconscious, learning might be impaired among HIV+ individuals compared with HIV− matched control groups, but these studies have included relatively few women. We administered measures of motor skill and probabilistic learning, tasks with a nondeclarative or procedural learning component that are dependent on integrity of prefrontal-striatal systems, to well-matched groups of 148 men and 65 women with a history of substance dependence that included 45 men and 30 women seropositive for HIV. All participants were abstinent at testing. Compared to HIV− women, HIV+ women performed significantly more poorly on both tasks, but HIV+ men’s performance did not differ significantly compared to HIV− men on either task. These different patterns of performance indicate that features of HIV-associated neurocognitive disorder (HAND) can not always be generalized from men to women. Additional studies are needed to address directly the possibility of sex differences in HIV-associated neurocognitive disorder (HAND) and the possibility that women might be more vulnerable to the effects of HIV and substance dependence on some neurocognitive functions. PMID:20694870

Wide-field microscopy using microcamera arrays

NASA Astrophysics Data System (ADS)

Marks, Daniel L.; Youn, Seo Ho; Son, Hui S.; Kim, Jungsang; Brady, David J.

2013-02-01

A microcamera is a relay lens paired with image sensors. Microcameras are grouped into arrays to relay overlapping views of a single large surface to the sensors to form a continuous synthetic image. The imaged surface may be curved or irregular as each camera may independently be dynamically focused to a different depth. Microcamera arrays are akin to microprocessors in supercomputers in that both join individual processors by an optoelectronic routing fabric to increase capacity and performance. A microcamera may image ten or more megapixels and grouped into an array of several hundred, as has already been demonstrated by the DARPA AWARE Wide-Field program with multiscale gigapixel photography. We adapt gigapixel microcamera array architectures to wide-field microscopy of irregularly shaped surfaces to greatly increase area imaging over 1000 square millimeters at resolutions of 3 microns or better in a single snapshot. The system includes a novel relay design, a sensor electronics package, and a FPGA-based networking fabric. Biomedical applications of this include screening for skin lesions, wide-field and resolution-agile microsurgical imaging, and microscopic cytometry of millions of cells performed in situ.

Word Reading Fluency: Role of Genome-Wide Single-Nucleotide Polymorphisms in Developmental Stability and Correlations with Print Exposure

ERIC Educational Resources Information Center

Harlaar, Nicole; Trzaskowski, Maciej; Dale, Philip S.; Plomin, Robert

2014-01-01

The genetic effects on individual differences in reading development were examined using genome-wide complex trait analysis (GCTA) in a twin sample. In unrelated individuals (one twin per pair, n = 2,942), the GCTA-based heritability of reading fluency was ~20%-29% at ages 7 and 12. GCTA bivariate results showed that the phenotypic stability of…

The two envelope membrane glycoproteins of Tomato spotted wilt virus show differences in lectin-binding properties and sensitivities to glycosidases.

PubMed

Naidu, Rayapati A; Ingle, Caroline J; Deom, Carl M; Sherwood, John L

2004-02-05

Tomato spotted wilt virus (TSWV, Genus: Tospovirus, Family: Bunyaviridae) is a major constraint to the production of several different crops of agronomic and horticultural importance worldwide. The amino acid sequence of the two envelope membrane glycoproteins, designated as G(N) (N-terminal) and G(C) (C-terminal), of TSWV contain several tripeptide sequences, Asn-Xaa-Ser/Thr, suggesting that the proteins are N-glycosylated. In this study, the lectin-binding properties of the viral glycoproteins and their sensitivities to glycosidases were examined to obtain information on the nature of potential oligosaccharide moieties present on G(N) and G(C). The viral proteins were separated by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and probed by affinoblotting using a battery of biotinylated lectins with specificity to different oligosaccharide structures. G(C) showed strong binding with five mannose-binding lectins, four N-acetyllactosamine-binding lectins and one fucose-binding lectin. G(N) was resolved into two molecular masses and only the slow migrating form showed binding, albeit to a lesser extent than G(C), with three of the five mannose-binding lectins. The N-acetyllactosamine- and fucose-specific lectins did not bind to either molecular mass form of G(N). None of the galactose-, N-acetylgalactosamine-, or sialic acid-binding lectins tested showed binding specificity to G(C) or G(N). Treatment of the denatured virions with endoglycosidase H and peptide:N-glycosidase F (PNGase F) resulted in a significant decrease in the binding of G(C) to high mannose- and N-acetyllactosamine-specific lectins. However, no such differences in lectin binding were apparent with G(N). These results indicate the presence of N-linked oligosaccharides of high mannose- and complex-type on G(C) and possibly high mannose-type on G(N). Differences in the extent of binding of the two envelope glycoproteins to different lectins suggest that G(C) is likely to be more

Genome-wide expression profiling of five mouse models identifies similarities and differences with human psoriasis.

PubMed

Swindell, William R; Johnston, Andrew; Carbajal, Steve; Han, Gangwen; Wohn, Christian; Lu, Jun; Xing, Xianying; Nair, Rajan P; Voorhees, John J; Elder, James T; Wang, Xiao-Jing; Sano, Shigetoshi; Prens, Errol P; DiGiovanni, John; Pittelkow, Mark R; Ward, Nicole L; Gudjonsson, Johann E

2011-04-04

Development of a suitable mouse model would facilitate the investigation of pathomechanisms underlying human psoriasis and would also assist in development of therapeutic treatments. However, while many psoriasis mouse models have been proposed, no single model recapitulates all features of the human disease, and standardized validation criteria for psoriasis mouse models have not been widely applied. In this study, whole-genome transcriptional profiling is used to compare gene expression patterns manifested by human psoriatic skin lesions with those that occur in five psoriasis mouse models (K5-Tie2, imiquimod, K14-AREG, K5-Stat3C and K5-TGFbeta1). While the cutaneous gene expression profiles associated with each mouse phenotype exhibited statistically significant similarity to the expression profile of psoriasis in humans, each model displayed distinctive sets of similarities and differences in comparison to human psoriasis. For all five models, correspondence to the human disease was strong with respect to genes involved in epidermal development and keratinization. Immune and inflammation-associated gene expression, in contrast, was more variable between models as compared to the human disease. These findings support the value of all five models as research tools, each with identifiable areas of convergence to and divergence from the human disease. Additionally, the approach used in this paper provides an objective and quantitative method for evaluation of proposed mouse models of psoriasis, which can be strategically applied in future studies to score strengths of mouse phenotypes relative to specific aspects of human psoriasis.

Extracting knowledge from the World Wide Web

PubMed Central

Henzinger, Monika; Lawrence, Steve

2004-01-01

The World Wide Web provides a unprecedented opportunity to automatically analyze a large sample of interests and activity in the world. We discuss methods for extracting knowledge from the web by randomly sampling and analyzing hosts and pages, and by analyzing the link structure of the web and how links accumulate over time. A variety of interesting and valuable information can be extracted, such as the distribution of web pages over domains, the distribution of interest in different areas, communities related to different topics, the nature of competition in different categories of sites, and the degree of communication between different communities or countries. PMID:14745041

Widely tunable long-period waveguide grating couplers

NASA Astrophysics Data System (ADS)

Bai, Y.; Liu, Q.; Lor, K. P.; Chiang, K. S.

2006-12-01

We demonstrate experimentally two widely tunable optical couplers formed with parallel long-period polymer waveguide gratings. One of the couplers consists of two parallel gratings and shows a peak coupling efficiency of ~34%. The resonance wavelength of the coupler can be tuned thermally with a sensitivity of 4.7 nm/°C. The experimental results agree well with the coupled-mode analysis. The other coupler consists of an array of ten widely separated gratings. A peak coupling efficiency of ~11% is obtained between the two best matched gratings in the array and the resonance wavelength can be tuned thermally with a sensitivity of -3.8 nm/°C. These couplers have the potential to be further developed into practical broadband add/drop multiplexers and signal dividers.

Weaving a wide net.

PubMed

Garber, Linda

2002-10-01

SUMMARY Any single approach tostudents' heterosexism and homophobia, however well conceived and executed, is most successful when supported by an integrated campus approach to the problem. Taking as a model the multifaceted efforts at California State University, Fresno-a large public institution located in what can be considered the state's Bible Belt-this essay discusses the strengths and logistics of a campus-wide program to address homophobia and alleviate LGBTQ students' feelings of alienation from the institution and their oppression in society. The efforts of CSUF take place at a number of different levels-classroom, academic department, student services, faculty networking-and can be considered a successful work in progress.

Phylogeography of Asian wild rice, Oryza rufipogon: a genome-wide view.

PubMed

Huang, Pu; Molina, Jeanmaire; Flowers, Jonathan M; Rubinstein, Samara; Jackson, Scott A; Purugganan, Michael D; Schaal, Barbara A

2012-09-01

Asian wild rice (Oryza rufipogon) that ranges widely across the eastern and southern part of Asia is recognized as the direct ancestor of cultivated Asian rice (O. sativa). Studies of the geographic structure of O. rufipogon, based on chloroplast and low-copy nuclear markers, reveal a possible phylogeographic signal of subdivision in O. rufipogon. However, this signal of geographic differentiation is not consistently observed among different markers and studies, with often conflicting results. To more precisely characterize the phylogeography of O. rufipogon populations, a genome-wide survey of unlinked markers, intensively sampled from across the entire range of O. rufipogon is critical. In this study, we surveyed sequence variation at 42 genome-wide sequence tagged sites (STS) in 108 O. rufipogon accessions from throughout the native range of the species. Using Bayesian clustering, principal component analysis and amova, we conclude that there are two genetically distinct O. rufipogon groups, Ruf-I and Ruf-II. The two groups exhibit a clinal variation pattern generally from north-east to south-west. Different from many earlier studies, Ruf-I, which is found mainly in China and the Indochinese Peninsula, shows genetic similarity with one major cultivated rice variety, O. satvia indica, whereas Ruf-II, mainly from South Asia and the Indochinese Peninsula, is not found to be closely related to cultivated rice varieties. The other major cultivated rice variety, O. sativa japonica, is not found to be similar to either O. rufipogon groups. Our results support the hypothesis of a single origin of the domesticated O. sativa in China. The possible role of palaeoclimate, introgression and migration-drift balance in creating this clinal variation pattern is also discussed. © 2012 Blackwell Publishing Ltd.

Quality analysis of patient information about knee arthroscopy on the World Wide Web.

PubMed

Sambandam, Senthil Nathan; Ramasamy, Vijayaraj; Priyanka, Priyanka; Ilango, Balakrishnan

2007-05-01

This study was designed to ascertain the quality of patient information available on the World Wide Web on the topic of knee arthroscopy. For the purpose of quality analysis, we used a pool of 232 search results obtained from 7 different search engines. We used a modified assessment questionnaire to assess the quality of these Web sites. This questionnaire was developed based on similar studies evaluating Web site quality and includes items on illustrations, accessibility, availability, accountability, and content of the Web site. We also compared results obtained with different search engines and tried to establish the best possible search strategy to attain the most relevant, authentic, and adequate information with minimum time consumption. For this purpose, we first compared 100 search results from the single most commonly used search engine (AltaVista) with the pooled sample containing 20 search results from each of the 7 different search engines. The search engines used were metasearch (Copernic and Mamma), general search (Google, AltaVista, and Yahoo), and health topic-related search engines (MedHunt and Healthfinder). The phrase "knee arthroscopy" was used as the search terminology. Excluding the repetitions, there were 117 Web sites available for quality analysis. These sites were analyzed for accessibility, relevance, authenticity, adequacy, and accountability by use of a specially designed questionnaire. Our analysis showed that most of the sites providing patient information on knee arthroscopy contained outdated information, were inadequate, and were not accountable. Only 16 sites were found to be providing reasonably good patient information and hence can be recommended to patients. Understandably, most of these sites were from nonprofit organizations and educational institutions. Furthermore, our study revealed that using multiple search engines increases patients' chances of obtaining more relevant information rather than using a single search

Apigenin shows synergistic anticancer activity with curcumin by binding at different sites of tubulin.

PubMed

Choudhury, Diptiman; Ganguli, Arnab; Dastidar, Debabrata Ghosh; Acharya, Bipul R; Das, Amlan; Chakrabarti, Gopal

2013-06-01

Apigenin, a natural flavone, present in many plants sources, induced apoptosis and cell death in lung epithelium cancer (A549) cells with an IC50 value of 93.7 ± 3.7 μM for 48 h treatment. Target identification investigations using A549 cells and also in cell-free system demonstrated that apigenin depolymerized microtubules and inhibited reassembly of cold depolymerized microtubules of A549 cells. Again apigenin inhibited polymerization of purified tubulin with an IC50 value of 79.8 ± 2.4 μM. It bounds to tubulin in cell-free system and quenched the intrinsic fluorescence of tubulin in a concentration- and time-dependent manner. The interaction was temperature-dependent and kinetics of binding was biphasic in nature with binding rate constants of 11.5 × 10(-7) M(-1) s(-1) and 4.0 × 10(-9) M(-1) s(-1) for fast and slow phases at 37 °C, respectively. The stoichiometry of tubulin-apigenin binding was 1:1 and binding the binding constant (Kd) was 6.08 ± 0.096 μM. Interestingly, apigenin showed synergistic anti-cancer effect with another natural anti-tubulin agent curcumin. Apigenin and curcumin synergistically induced cell death and apoptosis and also blocked cell cycle progression at G2/M phase of A549 cells. The synergistic activity of apigenin and curcumin was also apparent from their strong depolymerizing effects on interphase microtubules and inhibitory effect of reassembly of cold depolymerized microtubules when used in combinations, indicating that these ligands bind to tubulin at different sites. In silico modeling suggested apigenin bounds at the interphase of α-β-subunit of tubulin. The binding site is 19 Å in distance from the previously predicted curcumin binding site. Binding studies with purified protein also showed both apigenin and curcumin can simultaneously bind to purified tubulin. Understanding the mechanism of synergistic effect of apigenin and curcumin could be helped to develop anti-cancer combination drugs from cheap and readily

Different Types of Luciferase Reporters Show Distinct Susceptibility to T3-Evoked Downregulation.

PubMed

Kollár, Anna; Kvárta-Papp, Zsuzsanna; Egri, Péter; Gereben, Balázs

2016-01-01

The firefly luciferase reporter protein is a crucial tool for studies targeting a broad range of biological questions. Importantly, luciferase assays are also widely used to explore mechanisms underlying thyroid hormone dependent regulation of gene expression. However, it was demonstrated that the firefly luciferase reporter is subject to triiodothyronine (T3)-evoked, promoter independent downregulation that is mediated by the thyroid hormone receptor. Since this effect can interfere with readout accuracy, the study aimed to find luciferase reporters that are not susceptible to this phenomenon. Luciferase reporter constructs were generated under the control of a minimal thymidine kinase (TK) promoter and transiently transfected into JEG-3 cells to test their activity upon T3 treatment. Activity of the TK-(dCpG)Luc encoding a synthetic (dCpG)Luciferase and TK-NanoLuc expressing the NanoLuc reporter was not significantly changed by T3 treatment while the firefly luciferase control was suppressed by ∼2.6-fold. T3 also downregulated the activity of Renilla luciferase by ∼30%. Novel types of luciferase reporters, especially the synthetic (dCpG)Luciferase, can be more accurate to study T3-regulated gene expression than the classical firefly luciferase reporter. Renilla luciferase, a popular transfection control of dual luciferase assays, should be used with caution in conditions with T3 treatment.

Satellite Radar Show Complex Set of Faults Moved in 2016 New Zealand Earthquake

NASA Image and Video Library

2017-03-23

NASA and its partners are contributing important observations and expertise to the ongoing response to the Nov. 14, 2016, magnitude 7.8 Kaikoura earthquake in New Zealand. This shallow earthquake was so complex and unusual, it is likely to change how scientists think about earthquake hazards in plate boundary zones around the world. Scientists with the Advanced Rapid Imaging and Analysis project (ARIA), a collaboration between NASA's Jet Propulsion Laboratory, Pasadena, California, and Caltech in Pasadena, analyzed interferometric synthetic aperture radar images from the PALSAR-2 instrument on the ALOS-2 satellite operated by the Japan Aerospace Exploration Agency (JAXA) to calculate maps of the deformation of Earth's surface caused by the quake. Two maps show motion of the surface in two different directions. Each false-color map shows the amount of permanent surface movement caused almost entirely by the earthquake, as viewed by the satellite, during a 28-day interval between two ALOS-2 wide-swath images acquired on Oct. 18 and Nov. 15, 2016. In these two new maps made from the wide-swath images, the colors of the surface displacements are proportional to the surface motion. The wide-swath images cover the entire 106-mile (170-kilometer) length of the complex set of earthquake ruptures. The arrows show the direction of the radar motion measurement. In the left image, the blue and purple tones show the areas where the land around the Kaikoura peninsula in the Marlborough region of New Zealand's South Island has moved toward the satellite by up to 13.2 feet (4 meters), both eastward and upward. In the right image, the blue and purple tones show the areas that moved to the north by up to 30 feet (9 meters) and green tones show the area that moved to the south. The sharp line of color change is across the Kekerengu Fault, which had the largest amount of motion in the earthquake. Field studies found maximum rupture at the surface was measured at 39 feet (12 meters) of

Multilocus microsatellite typing shows three different genetic clusters of Leishmania major in Iran.

PubMed

Mahnaz, Tashakori; Al-Jawabreh, Amer; Kuhls, Katrin; Schönian, Gabriele

2011-10-01

Ten polymorphic microsatellite markers were used to analyse 25 strains of Leishmania major collected from cutaneous leishmaniasis cases in different endemic areas in Iran. Nine of the markers were polymorphic, revealing 21 different genotypes. The data displayed significant microsatellite polymorphism with rare allelic heterozygosity. Bayesian statistic and distance based analyses identified three genetic clusters among the 25 strains analysed. Cluster I represented mainly strains isolated in the west and south-west of Iran, with the exception of four strains originating from central Iran. Cluster II comprised strains from the central part of Iran, and cluster III included only strains from north Iran. The geographical distribution of L. major in Iran was supported by comparing the microsatellite profiles of the 25 Iranian strains to those of 105 strains collected in 19 Asian and African countries. The Iranian clusters I and II were separated from three previously described populations comprising strains from Africa, the Middle East and Central Asia whereas cluster III grouped together with the Central Asian population. The considerable genetic variability of L. major might be related to the existence of different populations of Phlebotomus papatasi and/or to differences in reservoir host abundance in different parts of Iran. Copyright © 2011 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Wide dynamic range enrichment method of semiconducting single-walled carbon nanotubes with weak field centrifugation

NASA Astrophysics Data System (ADS)

Reis, Wieland G.; Tomović, Željko; Weitz, R. Thomas; Krupke, Ralph; Mikhael, Jules

2017-03-01

The potential of single-walled carbon nanotubes (SWCNTs) to outperform silicon in electronic application was finally enabled through selective separation of semiconducting nanotubes from the as-synthesized statistical mix with polymeric dispersants. Such separation methods provide typically high semiconducting purity samples with narrow diameter distribution, i.e. almost single chiralities. But for a wide range of applications high purity mixtures of small and large diameters are sufficient or even required. Here we proof that weak field centrifugation is a diameter independent method for enrichment of semiconducting nanotubes. We show that the non-selective and strong adsorption of polyarylether dispersants on nanostructured carbon surfaces enables simple separation of diverse raw materials with different SWCNT diameter. In addition and for the first time, we demonstrate that increased temperature enables higher purity separation. Furthermore we show that the mode of action behind this electronic enrichment is strongly connected to both colloidal stability and protonation. By giving simple access to electronically sorted SWCNTs of any diameter, the wide dynamic range of weak field centrifugation can provide economical relevance to SWCNTs.

Compact Ultra Wide Band Microstrip Bandpass Filter Based on Multiple-Mode Resonator and Modified Complementary Split Ring Resonator

PubMed Central

Marcotegui, J. Antonio; Illescas, Jesús Miguel; Estevez, Aritz

2013-01-01

A new class of broadband microstrip filters for Ultra Wide Band (UWB) applications is proposed. In the design, different stages of parallel-coupled microstrip line and other stages with a Modified Complementary Split Ring Resonator (MCSRR)—a concept proposed here for the first time—are adjusted to obtain the desired response with broadband, sharp rejection, low insertion loss, and low return loss. Full wave simulation results as well as measurement results from fabricated prototypes are presented, showing good agreement. The proposed technique offers a new alternative to implement low-cost high-performance filter devices, applicable to a wide range of communication systems. PMID:24319366

Meta-Analysis in Genome-Wide Association Datasets: Strategies and Application in Parkinson Disease

PubMed Central

Evangelou, Evangelos; Maraganore, Demetrius M.; Ioannidis, John P.A.

2007-01-01

Background Genome-wide association studies hold substantial promise for identifying common genetic variants that regulate susceptibility to complex diseases. However, for the detection of small genetic effects, single studies may be underpowered. Power may be improved by combining genome-wide datasets with meta-analytic techniques. Methodology/Principal Findings Both single and two-stage genome-wide data may be combined and there are several possible strategies. In the two-stage framework, we considered the options of (1) enhancement of replication data and (2) enhancement of first-stage data, and then, we also considered (3) joint meta-analyses including all first-stage and second-stage data. These strategies were examined empirically using data from two genome-wide association studies (three datasets) on Parkinson disease. In the three strategies, we derived 12, 5, and 49 single nucleotide polymorphisms that show significant associations at conventional levels of statistical significance. None of these remained significant after conservative adjustment for the number of performed analyses in each strategy. However, some may warrant further consideration: 6 SNPs were identified with at least 2 of the 3 strategies and 3 SNPs [rs1000291 on chromosome 3, rs2241743 on chromosome 4 and rs3018626 on chromosome 11] were identified with all 3 strategies and had no or minimal between-dataset heterogeneity (I2 = 0, 0 and 15%, respectively). Analyses were primarily limited by the suboptimal overlap of tested polymorphisms across different datasets (e.g., only 31,192 shared polymorphisms between the two tier 1 datasets). Conclusions/Significance Meta-analysis may be used to improve the power and examine the between-dataset heterogeneity of genome-wide association studies. Prospective designs may be most efficient, if they try to maximize the overlap of genotyping platforms and anticipate the combination of data across many genome-wide association studies. PMID:17332845

Formulated Beta-Cyfluthrin Shows Wide Divergence in Toxicity among Bird Species

PubMed Central

Addy-Orduna, Laura M.; Zaccagnini, María-Elena; Canavelli, Sonia B.; Mineau, Pierre

2011-01-01

It is generally assumed that the toxicity of pyrethroid insecticides to birds is negligible, though few species have been tested. The oral acute toxicity of formulated beta-cyfluthrin was determined for canaries (Serinus sp.), shiny cowbirds (Molothrus bonariensis), and eared doves (Zenaida auriculata). Single doses were administered to adults by gavage. Approximate lethal doses 50 (LD50) and their confidence intervals were determined by approximate D-optimal design. Canaries were found to be substantially more sensitive to formulated beta-cyfluthrin (LD50 = (170 ± 41) mg/kg) than the other two species tested (LD50 = (2234 ± 544) mg/kg and LD50 = (2271 ± 433) mg/kg, resp.). The LD50 obtained for canaries was also considerably lower than typical toxicity values available in the literature for pyrethroids. This study emphasizes the need for testing a broader range of species with potentially toxic insecticides, using modern up and down test designs with minimal numbers of birds. PMID:21584255

Formulated Beta-Cyfluthrin Shows Wide Divergence in Toxicity among Bird Species.

PubMed

Addy-Orduna, Laura M; Zaccagnini, María-Elena; Canavelli, Sonia B; Mineau, Pierre

2011-01-01

It is generally assumed that the toxicity of pyrethroid insecticides to birds is negligible, though few species have been tested. The oral acute toxicity of formulated beta-cyfluthrin was determined for canaries (Serinus sp.), shiny cowbirds (Molothrus bonariensis), and eared doves (Zenaida auriculata). Single doses were administered to adults by gavage. Approximate lethal doses 50 (LD(50)) and their confidence intervals were determined by approximate D-optimal design. Canaries were found to be substantially more sensitive to formulated beta-cyfluthrin (LD(50) = (170 ± 41) mg/kg) than the other two species tested (LD(50) = (2234 ± 544) mg/kg and LD(50) = (2271 ± 433) mg/kg, resp.). The LD(50) obtained for canaries was also considerably lower than typical toxicity values available in the literature for pyrethroids. This study emphasizes the need for testing a broader range of species with potentially toxic insecticides, using modern up and down test designs with minimal numbers of birds.

A wide-band fiber optic frequency distribution system employing thermally controlled phase compensation

NASA Technical Reports Server (NTRS)

Johnson, Dean; Calhoun, Malcolm; Sydnor, Richard; Lutes, George

1993-01-01

An active wide-band fiber optic frequency distribution system employing a thermally controlled phase compensator to stabilize phase variations induced by environmental temperature changes is described. The distribution system utilizes bidirectional dual wavelength transmission to provide optical feedback of induced phase variations of 100 MHz signals propagating along the distribution cable. The phase compensation considered differs from earlier narrow-band phase compensation designs in that it uses a thermally controlled fiber delay coil rather than a VCO or phase modulation to compensate for induced phase variations. Two advantages of the wide-band system over earlier designs are (1) that it provides phase compensation for all transmitted frequencies, and (2) the compensation is applied after the optical interface rather than electronically ahead of it as in earlier schemes. Experimental results on the first prototype shows that the thermal stabilizer reduces phase variations and Allan deviation by a factor of forty over an equivalent uncompensated fiber optic distribution system.

Ultra-wide-field fundus autofluorescence in multiple evanescent white dot syndrome.

PubMed

Hashimoto, Hideaki; Kishi, Shoji

2015-04-01

To observe the progression of affected lesions using ultra-wide-field fundus autofluorescence (FAF) in multiple evanescent white dot syndrome. Retrospective, observational case series. setting: Institutional. 14 eyes of 13 patients (mean age, 35.8 years) with acute disease unilaterally. Patients underwent ultra-wide-field FAF, spectral-domain optical coherence tomography (SD OCT), multifocal electroretinography (mfERG), and Goldmann or automated perimetry; the best-corrected visual acuity (BCVA) and refractive error were measured. Ability of ultra-wide-field FAF to detect lesions with greater sensitivity compared with color fundus photography. Ultra-wide-field FAF imaging enabled improved visualization of the affected lesions and showed that the core lesion was in the posterior fundus involving the peripapillary retina and posterior pole and surrounded by hyper-autofluorescent spots outside the vascular arcade. The posterior lesions expanded rapidly and peripheral spots spread farther peripherally and reached a maximal extent during the acute stage. During follow-up, the peripheral hyper-autofluorescent spots resolved and then hyper-autofluorescence of the posterior fundus gradually faded. SD OCT showed diffuse disruption of the photoreceptor inner segment/outer segment junction (IS/OS) in the posterior fundus during the acute stage. The correlation between the IS/OS abnormality and hyper-autofluorescent areas was unclear. The disrupted IS/OS was restored with normalization of the FAF. Ultra-wide-field FAF showed that the lesions arise from the peripapillary retina and the posterior pole and spread peripherally in a centrifugal manner during the acute stage. The hyper-autofluorescent spots faded from the periphery in a centripetal manner. Copyright © 2015 Elsevier Inc. All rights reserved.

Narcolepsy type 1 and hypersomnia associated with a psychiatric disorder show different slow wave activity dynamics.

PubMed

Walacik-Ufnal, Ewa; Piotrowska, Anna Justyna; Wołyńczyk-Gmaj, Dorota; Januszko, Piotr; Gmaj, Bartłomiej; Ufnal, Marcin; Kabat, Marek; Wojnar, Marcin

2017-01-01

The aim of the study was to compare electrophysiological parameters of night sleep in narcolepsy type 1 and hypersomnia associated with a psychiatric disorder. Fortyfour patients: 15 with narcolepsy type 1, 14 with hypersomnia associated with a psychiatric disorder and 15 age- and sex-matched controls participated in the study. The study subjects filled in the Athens Insomnia Scale (AIS) and the Beck Depression Inventory (BDI). The severity of daytime sleepiness was quantified subjectively using the Epworth Sleepiness Scale (ESS) and the Stanford Sleepiness Scale (SSS), and objectively using the Multiple Sleep Latency Test (MSLT). All subjects underwent polysomnography (PSG) on the two consecutive nights. The data from the second night was analysed. The slow wave activity (SWA, 1-4 Hz) was calculated for the three consecutive sleep cycles, and topographic delta power maps were plotted. In contrast to narcoleptics, psychiatric hypersomniacs had undisturbed nocturnal sleep, high sleep efficiency, normal non-rapid eye movement (NREM) and rapid eye movement (REM) sleep proportions, normal REM latency and sleep latencies on MSLT and PSG. The subjective and objective sleepiness was significantly higher in narcolepsy group than in psychiatric hypersomnia group. In all the study groups SWA was the most prominent in frontal areas, while the greatest between-group differences were found in the central areas. There were significant differences between the groups in SWA in the second NREM episode. The highest SWA was observed in the hypersomnia group, while the lowest in the narcolepsy group. Psychiatric hypersomniacs and controls did not differ in the SWA exponential decline over consecutive NREM episodes, whereas narcoleptics exhibited a steeper dissipation of sleep pressure from the first to the second NREM episode. In conclusion, narcolepsy type1 and hypersomnia associated with psychiatric disorder differ in the SWA dynamics. Narcoleptics presented with the altered

Sex-based Differences in Common Sports Injuries.

PubMed

Carter, Cordelia W; Ireland, Mary Lloyd; Johnson, Anthony E; Levine, William N; Martin, Scott; Bedi, Asheesh; Matzkin, Elizabeth G

2018-05-28

The patient's sex plays an important role in mediating the risk for, and experience of, disease. Injuries of the musculoskeletal system are no exception to this phenomenon. Increasing evidence shows that the incidence, clinical presentation, and treatment outcomes for male and female patients with common sports injuries may vary widely. Stress fracture, which is associated with the female athlete triad, is a sports injury with known sex-based differences. Other common sports-related injuries may also have distinct sex-based differences. Understanding these differences is important to optimize each patient's musculoskeletal care.

Optimal selection of markers for validation or replication from genome-wide association studies.

PubMed

Greenwood, Celia M T; Rangrej, Jagadish; Sun, Lei

2007-07-01

With reductions in genotyping costs and the fast pace of improvements in genotyping technology, it is not uncommon for the individuals in a single study to undergo genotyping using several different platforms, where each platform may contain different numbers of markers selected via different criteria. For example, a set of cases and controls may be genotyped at markers in a small set of carefully selected candidate genes, and shortly thereafter, the same cases and controls may be used for a genome-wide single nucleotide polymorphism (SNP) association study. After such initial investigations, often, a subset of "interesting" markers is selected for validation or replication. Specifically, by validation, we refer to the investigation of associations between the selected subset of markers and the disease in independent data. However, it is not obvious how to choose the best set of markers for this validation. There may be a prior expectation that some sets of genotyping data are more likely to contain real associations. For example, it may be more likely for markers in plausible candidate genes to show disease associations than markers in a genome-wide scan. Hence, it would be desirable to select proportionally more markers from the candidate gene set. When a fixed number of markers are selected for validation, we propose an approach for identifying an optimal marker-selection configuration by basing the approach on minimizing the stratified false discovery rate. We illustrate this approach using a case-control study of colorectal cancer from Ontario, Canada, and we show that this approach leads to substantial reductions in the estimated false discovery rates in the Ontario dataset for the selected markers, as well as reductions in the expected false discovery rates for the proposed validation dataset. Copyright 2007 Wiley-Liss, Inc.

Genome-Wide Expression Profiling of Five Mouse Models Identifies Similarities and Differences with Human Psoriasis

PubMed Central

Swindell, William R.; Johnston, Andrew; Carbajal, Steve; Han, Gangwen; Wohn, Christian; Lu, Jun; Xing, Xianying; Nair, Rajan P.; Voorhees, John J.; Elder, James T.; Wang, Xiao-Jing; Sano, Shigetoshi; Prens, Errol P.; DiGiovanni, John; Pittelkow, Mark R.; Ward, Nicole L.; Gudjonsson, Johann E.

2011-01-01

Development of a suitable mouse model would facilitate the investigation of pathomechanisms underlying human psoriasis and would also assist in development of therapeutic treatments. However, while many psoriasis mouse models have been proposed, no single model recapitulates all features of the human disease, and standardized validation criteria for psoriasis mouse models have not been widely applied. In this study, whole-genome transcriptional profiling is used to compare gene expression patterns manifested by human psoriatic skin lesions with those that occur in five psoriasis mouse models (K5-Tie2, imiquimod, K14-AREG, K5-Stat3C and K5-TGFbeta1). While the cutaneous gene expression profiles associated with each mouse phenotype exhibited statistically significant similarity to the expression profile of psoriasis in humans, each model displayed distinctive sets of similarities and differences in comparison to human psoriasis. For all five models, correspondence to the human disease was strong with respect to genes involved in epidermal development and keratinization. Immune and inflammation-associated gene expression, in contrast, was more variable between models as compared to the human disease. These findings support the value of all five models as research tools, each with identifiable areas of convergence to and divergence from the human disease. Additionally, the approach used in this paper provides an objective and quantitative method for evaluation of proposed mouse models of psoriasis, which can be strategically applied in future studies to score strengths of mouse phenotypes relative to specific aspects of human psoriasis. PMID:21483750

Wide bandwidth phase-locked loop circuit

NASA Technical Reports Server (NTRS)

Koudelka, Robert David (Inventor)

2005-01-01

A PLL circuit uses a multiple frequency range PLL in order to phase lock input signals having a wide range of frequencies. The PLL includes a VCO capable of operating in multiple different frequency ranges and a divider bank independently configurable to divide the output of the VCO. A frequency detector detects a frequency of the input signal and a frequency selector selects an appropriate frequency range for the PLL. The frequency selector automatically switches the PLL to a different frequency range as needed in response to a change in the input signal frequency. Frequency range hysteresis is implemented to avoid operating the PLL near a frequency range boundary.

An integrated approach shows different use of water resources from Mediterranean maquis species in a coastal dune ecosystem

NASA Astrophysics Data System (ADS)

Mereu, S.; Salvatori, E.; Fusaro, L.; Gerosa, G.; Muys, B.; Manes, F.

2009-11-01

An integrated approach has been used to analyse the dependence of three Mediterranean species, A. unedo L., Q. ilex L., and P. latifolia L. co-occurring in a coastal dune ecosystem on two different water resources: groundwater and rainfed upper soil layers. The approach included leaf level gas exchanges, sap flow measurements and structural adaptations between 15 May and 31 July 2007. During this period it was possible to capture different species-specific response patterns to an environment characterized by a sandy soil, with a low water retention capacity, and the presence of a water table. The latter did not completely prevent the development of a drought response and, combined with previous studies in the same area, response differences between species have been partially attributed to different root distributions. Sap flow of A. unedo decreased rapidly with the decline of soil water content, while that of Q. ilex decreased only moderately. Midday leaf water potential of P. latifolia and A. unedo ranged between -2.2 and -2.7 MPa throughout the measuring period, while in Q. ilex it decreased down to -3.4 MPa at the end of the season. A. unedo was the only species that responded to drought with a decrease of its leaf area to sapwood area ratio from 23.9±1.2 (May) to 15.2±1.5 (July). While A. unedo also underwent an almost stepwise loss on hydraulic conductivity, such a loss did not occur for Q. ilex, whereas P. latifolia was able to slightly increase its hydraulic conducitivity. These differences show how different plant compartments coordinate differently between species in their responses to drought. The different responses appear to be mediated by different root distributions of the species and their relative resistances to drought are likely to depend on the duration of the periods in which water remains extractable in the upper soil layers.

Implementing meta-analysis from genome-wide association studies for pork quality traits

USDA-ARS?s Scientific Manuscript database

Pork quality plays an important role in the meat processing industry, thus different methodologies have been implemented to elucidate the genetic architecture of traits affecting meat quality. One of the most common and widely used approaches is to perform genome-wide association (GWA) studies. Howe...

Health status assessment via the World Wide Web.

PubMed Central

Bell, D. S.; Kahn, C. E.

1996-01-01

We explored the use of the World Wide Web to collect health status information for medical outcomes research. The RAND 36-Item Health Survey 1.0 (RAND-36), which contains the 36 multiple-choice questions of the Medical Outcomes Study SF-36 "Short Form" and differs only in its simplified scoring scheme, was made available for anonymous use on the Internet. Participation in the survey was invited through health-related Internet news groups and mailing lists. Participants entered data and received, their scores using the World Wide Web protocol. Entries were recorded from 15 June 1995 to 14 June 1996 (1 year). The survey was completed anonymously by 4876 individuals with access to the World Wide Web. Two-thirds completed the survey within 5 minutes, and 97% did so within 10 minutes. The item-completion rate was 99.28%. Values of Cronbach's alpha of 0.76 to 0.90 for the scoring scales matched the high reliability found in the Medical Outcomes Study. The World Wide Web provides a method of rapidly measuring individual health status and may play an important role in advancing health services research and outcomes-based patient care. PMID:8947684

Realization of an Ultra-thin Metasurface to Facilitate Wide Bandwidth, Wide Angle Beam Scanning.

PubMed

Bah, Alpha O; Qin, Pei-Yuan; Ziolkowski, Richard W; Cheng, Qiang; Guo, Y Jay

2018-03-19

A wide bandwidth, ultra-thin, metasurface is reported that facilitates wide angle beam scanning. Each unit cell of the metasurface contains a multi-resonant, strongly-coupled unequal arm Jerusalem cross element. This element consists of two bent-arm, orthogonal, capacitively loaded strips. The wide bandwidth of the metasurface is achieved by taking advantage of the strong coupling within and between its multi-resonant elements. A prototype of the proposed metasurface has been fabricated and measured. The design concept has been validated by the measured results. The proposed metasurface is able to alleviate the well-known problem of impedance mismatch caused by mutual coupling when the main beam of an array is scanned. In order to validate the wideband and wide scanning ability of the proposed metasurface, it is integrated with a wideband antenna array as a wide angle impedance matching element. The metasurface-array combination facilitates wide angle scanning over a 6:1 impedance bandwidth without the need for bulky dielectrics or multi-layered structures.

Advanced Behavioral Analyses Show that the Presence of Food Causes Subtle Changes in C. elegans Movement.

PubMed

Angstman, Nicholas B; Frank, Hans-Georg; Schmitz, Christoph

2016-01-01

As a widely used and studied model organism, Caenorhabditis elegans worms offer the ability to investigate implications of behavioral change. Although, investigation of C. elegans behavioral traits has been shown, analysis is often narrowed down to measurements based off a single point, and thus cannot pick up on subtle behavioral and morphological changes. In the present study videos were captured of four different C. elegans strains grown in liquid cultures and transferred to NGM-agar plates with an E. coli lawn or with no lawn. Using an advanced software, WormLab, the full skeleton and outline of worms were tracked to determine whether the presence of food affects behavioral traits. In all seven investigated parameters, statistically significant differences were found in worm behavior between those moving on NGM-agar plates with an E. coli lawn and NGM-agar plates with no lawn. Furthermore, multiple test groups showed differences in interaction between variables as the parameters that significantly correlated statistically with speed of locomotion varied. In the present study, we demonstrate the validity of a model to analyze C. elegans behavior beyond simple speed of locomotion. The need to account for a nested design while performing statistical analyses in similar studies is also demonstrated. With extended analyses, C. elegans behavioral change can be investigated with greater sensitivity, which could have wide utility in fields such as, but not limited to, toxicology, drug discovery, and RNAi screening.

Mimas Showing False Colors #1

NASA Technical Reports Server (NTRS)

2005-01-01

False color images of Saturn's moon, Mimas, reveal variation in either the composition or texture across its surface.

During its approach to Mimas on Aug. 2, 2005, the Cassini spacecraft narrow-angle camera obtained multi-spectral views of the moon from a range of 228,000 kilometers (142,500 miles).

The image at the left is a narrow angle clear-filter image, which was separately processed to enhance the contrast in brightness and sharpness of visible features. The image at the right is a color composite of narrow-angle ultraviolet, green, infrared and clear filter images, which have been specially processed to accentuate subtle changes in the spectral properties of Mimas' surface materials. To create this view, three color images (ultraviolet, green and infrared) were combined into a single black and white picture that isolates and maps regional color differences. This 'color map' was then superimposed over the clear-filter image at the left.

The combination of color map and brightness image shows how the color differences across the Mimas surface materials are tied to geological features. Shades of blue and violet in the image at the right are used to identify surface materials that are bluer in color and have a weaker infrared brightness than average Mimas materials, which are represented by green.

Herschel crater, a 140-kilometer-wide (88-mile) impact feature with a prominent central peak, is visible in the upper right of each image. The unusual bluer materials are seen to broadly surround Herschel crater. However, the bluer material is not uniformly distributed in and around the crater. Instead, it appears to be concentrated on the outside of the crater and more to the west than to the north or south. The origin of the color differences is not yet understood. It may represent ejecta material that was excavated from inside Mimas when the Herschel impact occurred. The bluer color of these materials may be caused by subtle differences in

Genome-wide evolutionary dynamics of influenza B viruses on a global scale

PubMed Central

Langat, Pinky; Bowden, Thomas A.; Edwards, Stephanie; Gall, Astrid; Rambaut, Andrew; Daniels, Rodney S.; Russell, Colin A.; Pybus, Oliver G.; McCauley, John

2017-01-01

The global-scale epidemiology and genome-wide evolutionary dynamics of influenza B remain poorly understood compared with influenza A viruses. We compiled a spatio-temporally comprehensive dataset of influenza B viruses, comprising over 2,500 genomes sampled worldwide between 1987 and 2015, including 382 newly-sequenced genomes that fill substantial gaps in previous molecular surveillance studies. Our contributed data increase the number of available influenza B virus genomes in Europe, Africa and Central Asia, improving the global context to study influenza B viruses. We reveal Yamagata-lineage diversity results from co-circulation of two antigenically-distinct groups that also segregate genetically across the entire genome, without evidence of intra-lineage reassortment. In contrast, Victoria-lineage diversity stems from geographic segregation of different genetic clades, with variability in the degree of geographic spread among clades. Differences between the lineages are reflected in their antigenic dynamics, as Yamagata-lineage viruses show alternating dominance between antigenic groups, while Victoria-lineage viruses show antigenic drift of a single lineage. Structural mapping of amino acid substitutions on trunk branches of influenza B gene phylogenies further supports these antigenic differences and highlights two potential mechanisms of adaptation for polymerase activity. Our study provides new insights into the epidemiological and molecular processes shaping influenza B virus evolution globally. PMID:29284042

High-resolution frequency measurement method with a wide-frequency range based on a quantized phase step law.

PubMed

Du, Baoqiang; Dong, Shaofeng; Wang, Yanfeng; Guo, Shuting; Cao, Lingzhi; Zhou, Wei; Zuo, Yandi; Liu, Dan

2013-11-01

A wide-frequency and high-resolution frequency measurement method based on the quantized phase step law is presented in this paper. Utilizing a variation law of the phase differences, the direct different frequency phase processing, and the phase group synchronization phenomenon, combining an A/D converter and the adaptive phase shifting principle, a counter gate is established in the phase coincidences at one-group intervals, which eliminates the ±1 counter error in the traditional frequency measurement method. More importantly, the direct phase comparison, the measurement, and the control between any periodic signals have been realized without frequency normalization in this method. Experimental results show that sub-picosecond resolution can be easily obtained in the frequency measurement, the frequency standard comparison, and the phase-locked control based on the phase quantization processing technique. The method may be widely used in navigation positioning, space techniques, communication, radar, astronomy, atomic frequency standards, and other high-tech fields.

Races of Heliconius erato (Nymphalidae: Heliconiinae) found on different sides of the Andes show wing size differences

USDA-ARS?s Scientific Manuscript database

Differences in wing size in geographical races of Heliconius erato distributed over the western and eastern sides of the Andes are reported on here. Individuals from the eastern side of the Andes are statistically larger in size than the ones on the western side of the Andes. A statistical differenc...

Affiliation, joint venture or PSO? Case studies show why provider strategies differ.

PubMed

1998-03-01

Joint venture, affiliation or PSO? Here are three case studies of providers who chose different paths under Medicare risk, plus some key questions you'll want to ask of your own provider organization. Learn from these examples so you'll make the best contracting decisions.

A Genome-wide Analysis of Admixture in Uyghurs and a High-Density Admixture Map for Disease-Gene Discovery

PubMed Central

Xu, Shuhua; Jin, Li

2008-01-01

Following up on our previous study, we conducted a genome-wide analysis of admixture for two Uyghur population samples (HGDP-UG and PanAsia-UG), collected from the northern and southern regions of Xinjiang in China, respectively. Both HGDP-UG and PanAsia-UG showed a substantial admixture of East-Asian (EAS) and European (EUR) ancestries, with an empirical estimation of ancestry contribution of 53:47 (EAS:EUR) and 48:52 for HGDP-UG and PanAsia-UG, respectively. The effective admixture time under a model with a single pulse of admixture was estimated as 110 generations and 129 generations, or admixture events occurred about 2200 and 2580 years ago for HGDP-UG and PanAsia-UG, respectively, assuming an average of 20 yr per generation. Despite Uyghurs' earlier history compared to other admixture populations, admixture mapping, holds promise for this population, because of its large size and its mixture of ancestry from different continents. We screened multiple databases and identified a genome-wide single-nucleotide polymorphism panel that can distinguish EAS and EUR ancestry of chromosomal segments in Uyghurs. The panel contains 8150 ancestry-informative markers (AIMs) showing large frequency differences between EAS and EUR populations (FST > 0.25, mean FST = 0.43) but small frequency differences (7999 AIMs validated) within both populations (FST < 0.05, mean FST < 0.01). We evaluated the effectiveness of this admixture map for localizing disease genes in two Uyghur populations. To our knowledge, our map constitutes the first practical resource for admixture mapping in Uyghurs, and it will enable studies of diseases showing differences in genetic risk between EUR and EAS populations. PMID:18760393

Combustion Mechanisms of Wide Distribution Propellants

DTIC Science & Technology

1988-06-01

trimodal propellants were formulated. Each set contains an HTPB binder and duplicate formulations were made with either a IPDI or a DDI curative. The...Distinctive Mechanisms Previous studies [12,131 have shown that HTPB * propellants with wide AP distributions burn at rates much different than predictions...propellants. 17 .- = i.= i i i il =.. .l=limim mll ili= =.l i@ w. -’- 87% 400/20/ 3 MICRON,AP/ HTPB PROPELLANT 2.0 Z -1.0 --- 0--.-7- 0 CALCULATIONO0

3-D phononic crystals with ultra-wide band gaps

PubMed Central

Lu, Yan; Yang, Yang; Guest, James K.; Srivastava, Ankit

2017-01-01

In this paper gradient based topology optimization (TO) is used to discover 3-D phononic structures that exhibit ultra-wide normalized all-angle all-mode band gaps. The challenging computational task of repeated 3-D phononic band-structure evaluations is accomplished by a combination of a fast mixed variational eigenvalue solver and distributed Graphic Processing Unit (GPU) parallel computations. The TO algorithm utilizes the material distribution-based approach and a gradient-based optimizer. The design sensitivity for the mixed variational eigenvalue problem is derived using the adjoint method and is implemented through highly efficient vectorization techniques. We present optimized results for two-material simple cubic (SC), body centered cubic (BCC), and face centered cubic (FCC) crystal structures and show that in each of these cases different initial designs converge to single inclusion network topologies within their corresponding primitive cells. The optimized results show that large phononic stop bands for bulk wave propagation can be achieved at lower than close packed spherical configurations leading to lighter unit cells. For tungsten carbide - epoxy crystals we identify all angle all mode normalized stop bands exceeding 100%, which is larger than what is possible with only spherical inclusions. PMID:28233812

3-D phononic crystals with ultra-wide band gaps.

PubMed

Lu, Yan; Yang, Yang; Guest, James K; Srivastava, Ankit

2017-02-24

In this paper gradient based topology optimization (TO) is used to discover 3-D phononic structures that exhibit ultra-wide normalized all-angle all-mode band gaps. The challenging computational task of repeated 3-D phononic band-structure evaluations is accomplished by a combination of a fast mixed variational eigenvalue solver and distributed Graphic Processing Unit (GPU) parallel computations. The TO algorithm utilizes the material distribution-based approach and a gradient-based optimizer. The design sensitivity for the mixed variational eigenvalue problem is derived using the adjoint method and is implemented through highly efficient vectorization techniques. We present optimized results for two-material simple cubic (SC), body centered cubic (BCC), and face centered cubic (FCC) crystal structures and show that in each of these cases different initial designs converge to single inclusion network topologies within their corresponding primitive cells. The optimized results show that large phononic stop bands for bulk wave propagation can be achieved at lower than close packed spherical configurations leading to lighter unit cells. For tungsten carbide - epoxy crystals we identify all angle all mode normalized stop bands exceeding 100%, which is larger than what is possible with only spherical inclusions.

Genome-Wide siRNA Screen Identifies Complementary Signaling Pathways Involved in Listeria Infection and Reveals Different Actin Nucleation Mechanisms during Listeria Cell Invasion and Actin Comet Tail Formation

PubMed Central

Kühbacher, Andreas; Emmenlauer, Mario; Rämo, Pauli; Kafai, Natasha; Dehio, Christoph

2015-01-01

ABSTRACT Listeria monocytogenes enters nonphagocytic cells by a receptor-mediated mechanism that is dependent on a clathrin-based molecular machinery and actin rearrangements. Bacterial intra- and intercellular movements are also actin dependent and rely on the actin nucleating Arp2/3 complex, which is activated by host-derived nucleation-promoting factors downstream of the cell receptor Met during entry and by the bacterial nucleation-promoting factor ActA during comet tail formation. By genome-wide small interfering RNA (siRNA) screening for host factors involved in bacterial infection, we identified diverse cellular signaling networks and protein complexes that support or limit these processes. In addition, we could precise previously described molecular pathways involved in Listeria invasion. In particular our results show that the requirements for actin nucleators during Listeria entry and actin comet tail formation are different. Knockdown of several actin nucleators, including SPIRE2, reduced bacterial invasion while not affecting the generation of comet tails. Most interestingly, we observed that in contrast to our expectations, not all of the seven subunits of the Arp2/3 complex are required for Listeria entry into cells or actin tail formation and that the subunit requirements for each of these processes differ, highlighting a previously unsuspected versatility in Arp2/3 complex composition and function. PMID:25991686

Home on the Wide-Open Range of Gender

ERIC Educational Resources Information Center

Beemyn, Genny

2011-01-01

Kate Bornstein and S. Bear Bergman's "Gender Outlaws: The Next Generation" is a collection of narratives written by individuals with a wide range of gender identities and expressions from around the world. The text shows how gender-nonconforming people are changing how society looks at gender. As many of the individuals who are challenging gender…

World Wide Web Homepages: An Examination of Content and Audience.

ERIC Educational Resources Information Center

Reynolds, Betty; And Others

This paper shows how the content of a World Wide Web page is selected and how an examination of the intended audience influences content. Examples from the New Mexico Tech (NMT) Library homepage show what sources are selected and what level of detail is appropriate for the intended audience. Six fundamental functions of libraries and information…

System-wide lean implementation in health care: A multiple case study.

PubMed

Centauri, Federica; Mazzocato, Pamela; Villa, Stefano; Marsilio, Marta

2018-05-01

Background Lean practices have been widely used by health care organizations to meet efficiency, performance and quality improvement needs. The lean health care literature shows that the effective implementation of lean requires a holistic system-wide approach. However, there is still limited evidence on what drives effective system-wide lean implementation in health care. The existing literature suggests that a deeper understanding of how lean interventions interact with the organizational context is necessary to identify the critical variables to successfully sustain system-wide lean strategies. Purpose and methodology: A multiple case study of three Italian hospitals is conducted with the aim to explore the organizational conditions that are relevant for an effective system-wide lean implementation. A conceptual framework, built on socio-technical system schemas, is used to guide data collection and analysis. The analysis points out the importance to support lean implementation with an integrated and coordinated strategy involving the social, technical, and external components of the overall hospital system.

Genome-wide DNA methylation analysis of pseudohypoparathyroidism patients with GNAS imprinting defects.

PubMed

Rochtus, Anne; Martin-Trujillo, Alejandro; Izzi, Benedetta; Elli, Francesca; Garin, Intza; Linglart, Agnes; Mantovani, Giovanna; Perez de Nanclares, Guiomar; Thiele, Suzanne; Decallonne, Brigitte; Van Geet, Chris; Monk, David; Freson, Kathleen

2016-01-01

Pseudohypoparathyroidism (PHP) is caused by (epi)genetic defects in the imprinted GNAS cluster. Current classification of PHP patients is hampered by clinical and molecular diagnostic overlaps. The European Consortium for the study of PHP designed a genome-wide methylation study to improve molecular diagnosis. The HumanMethylation 450K BeadChip was used to analyze genome-wide methylation in 24 PHP patients with parathyroid hormone resistance and 20 age- and gender-matched controls. Patients were previously diagnosed with GNAS-specific differentially methylated regions (DMRs) and include 6 patients with known STX16 deletion (PHP(Δstx16)) and 18 without deletion (PHP(neg)). The array demonstrated that PHP patients do not show DNA methylation differences at the whole-genome level. Unsupervised clustering of GNAS-specific DMRs divides PHP(Δstx16) versus PHP(neg) patients. Interestingly, in contrast to the notion that all PHP patients share methylation defects in the A/B DMR while only PHP(Δstx16) patients have normal NESP, GNAS-AS1 and XL methylation, we found a novel DMR (named GNAS-AS2) in the GNAS-AS1 region that is significantly different in both PHP(Δstx16) and PHP(neg), as validated by Sequenom EpiTYPER in a larger PHP cohort. The analysis of 58 DMRs revealed that 8/18 PHP(neg) and 1/6 PHP(Δstx16) patients have multi-locus methylation defects. Validation was performed for FANCC and SVOPL DMRs. This is the first genome-wide methylation study for PHP patients that confirmed that GNAS is the most significant DMR, and the presence of STX16 deletion divides PHP patients in two groups. Moreover, a novel GNAS-AS2 DMR affects all PHP patients, and PHP patients seem sensitive to multi-locus methylation defects.

Terahertz wide aperture reflection tomography.

PubMed

Pearce, Jeremy; Choi, Hyeokho; Mittleman, Daniel M; White, Jeff; Zimdars, David

2005-07-01

We describe a powerful imaging modality for terahertz (THz) radiation, THz wide aperture reflection tomography (WART). Edge maps of an object's cross section are reconstructed from a series of time-domain reflection measurements at different viewing angles. Each measurement corresponds to a parallel line projection of the object's cross section. The filtered backprojection algorithm is applied to recover the image from the projection data. To our knowledge, this is the first demonstration of a reflection computed tomography technique using electromagnetic waves. We demonstrate the capabilities of THz WART by imaging the cross sections of two test objects.

Housing conditions influence cortical and behavioural reactions of sheep in response to videos showing social interactions of different valence.

PubMed

Vögeli, Sabine; Wolf, Martin; Wechsler, Beat; Gygax, Lorenz

2015-05-01

Mood, as a long-term affective state, is thought to modulate short-term emotional reactions in animals, but the details of this interplay have hardly been investigated experimentally. Apart from a basic interest in this affective system, mood is likely to have an important impact on animal welfare, as bad mood may taint all emotional experience. In the present study about mood - emotion interaction, 29 sheep were kept under predictable, stimulus-rich or unpredictable, stimulus-poor housing conditions, to induce different mood states. In an experiment, the animals were confronted with video sequences of social interactions of conspecifics showing agonistic interactions, ruminating or tolerantly co-feeding as stimuli of different valences. Emotional reactions were assessed by measuring frontal brain activity using functional near-infrared spectroscopy and by recording behavioral reactions. Attentiveness of the sheep decreased from videos showing agonistic interactions to ruminating sheep to those displaying co-feeding sheep. Seeing agonistic interactions was also associated with a deactivation of the frontal cortex, specifically in animals living under predictable, stimulus-rich housing conditions. These sheep generally showed less attentiveness and locomotor activity and they had their ears in a forward position less often and in a backward position more often than the sheep from the unpredictable, stimulus-poor conditions. Housing conditions influenced how the sheep behaved, which can either be thought to be mediated by mood or by the animals' previous experience with stimulus-richness in their housing conditions. Frontal cortical activity may not depend on valence only, but also on the perceptual channel through which the stimuli were perceived. Copyright © 2015 Elsevier B.V. All rights reserved.

The Gateway from Near into Remote Oceania: New Insights from Genome-Wide Data

PubMed Central

Pugach, Irina; Duggan, Ana T; Merriwether, D Andrew; Friedlaender, Françoise R; Friedlaender, Jonathan S; Stoneking, Mark

2018-01-01

Abstract A widely accepted two-wave scenario of human settlement of Oceania involves the first out-of-Africa migration circa 50,000 years ago (ya), and the more recent Austronesian expansion, which reached the Bismarck Archipelago by 3,450 ya. Whereas earlier genetic studies provided evidence for extensive sex-biased admixture between the incoming and the indigenous populations, some archaeological, linguistic, and genetic evidence indicates a more complicated picture of settlement. To study regional variation in Oceania in more detail, we have compiled a genome-wide data set of 823 individuals from 72 populations (including 50 populations from Oceania) and over 620,000 autosomal single nucleotide polymorphisms (SNPs). We show that the initial dispersal of people from the Bismarck Archipelago into Remote Oceania occurred in a “leapfrog” fashion, completely by-passing the main chain of the Solomon Islands, and that the colonization of the Solomon Islands proceeded in a bidirectional manner. Our results also support a divergence between western and eastern Solomons, in agreement with the sharp linguistic divide known as the Tryon–Hackman line. We also report substantial post-Austronesian gene flow across the Solomons. In particular, Santa Cruz (in Remote Oceania) exhibits extraordinarily high levels of Papuan ancestry that cannot be explained by a simple bottleneck/founder event scenario. Finally, we use simulations to show that discrepancies between different methods for dating admixture likely reflect different sensitivities of the methods to multiple admixture events from the same (or similar) sources. Overall, this study points to the importance of fine-scale sampling to understand the complexities of human population history. PMID:29301001

Genome-wide transcriptome study in wheat identified candidate genes related to processing quality, majority of them showing interaction (quality x development) and having temporal and spatial distributions.

PubMed

Singh, Anuradha; Mantri, Shrikant; Sharma, Monica; Chaudhury, Ashok; Tuli, Rakesh; Roy, Joy

2014-01-16

The cultivated bread wheat (Triticum aestivum L.) possesses unique flour quality, which can be processed into many end-use food products such as bread, pasta, chapatti (unleavened flat bread), biscuit, etc. The present wheat varieties require improvement in processing quality to meet the increasing demand of better quality food products. However, processing quality is very complex and controlled by many genes, which have not been completely explored. To identify the candidate genes whose expressions changed due to variation in processing quality and interaction (quality x development), genome-wide transcriptome studies were performed in two sets of diverse Indian wheat varieties differing for chapatti quality. It is also important to understand the temporal and spatial distributions of their expressions for designing tissue and growth specific functional genomics experiments. Gene-specific two-way ANOVA analysis of expression of about 55 K transcripts in two diverse sets of Indian wheat varieties for chapatti quality at three seed developmental stages identified 236 differentially expressed probe sets (10-fold). Out of 236, 110 probe sets were identified for chapatti quality. Many processing quality related key genes such as glutenin and gliadins, puroindolines, grain softness protein, alpha and beta amylases, proteases, were identified, and many other candidate genes related to cellular and molecular functions were also identified. The ANOVA analysis revealed that the expression of 56 of 110 probe sets was involved in interaction (quality x development). Majority of the probe sets showed differential expression at early stage of seed development i.e. temporal expression. Meta-analysis revealed that the majority of the genes expressed in one or a few growth stages indicating spatial distribution of their expressions. The differential expressions of a few candidate genes such as pre-alpha/beta-gliadin and gamma gliadin were validated by RT-PCR. Therefore, this study

Genome-wide transcriptome study in wheat identified candidate genes related to processing quality, majority of them showing interaction (quality x development) and having temporal and spatial distributions

PubMed Central

2014-01-01

Background The cultivated bread wheat (Triticum aestivum L.) possesses unique flour quality, which can be processed into many end-use food products such as bread, pasta, chapatti (unleavened flat bread), biscuit, etc. The present wheat varieties require improvement in processing quality to meet the increasing demand of better quality food products. However, processing quality is very complex and controlled by many genes, which have not been completely explored. To identify the candidate genes whose expressions changed due to variation in processing quality and interaction (quality x development), genome-wide transcriptome studies were performed in two sets of diverse Indian wheat varieties differing for chapatti quality. It is also important to understand the temporal and spatial distributions of their expressions for designing tissue and growth specific functional genomics experiments. Results Gene-specific two-way ANOVA analysis of expression of about 55 K transcripts in two diverse sets of Indian wheat varieties for chapatti quality at three seed developmental stages identified 236 differentially expressed probe sets (10-fold). Out of 236, 110 probe sets were identified for chapatti quality. Many processing quality related key genes such as glutenin and gliadins, puroindolines, grain softness protein, alpha and beta amylases, proteases, were identified, and many other candidate genes related to cellular and molecular functions were also identified. The ANOVA analysis revealed that the expression of 56 of 110 probe sets was involved in interaction (quality x development). Majority of the probe sets showed differential expression at early stage of seed development i.e. temporal expression. Meta-analysis revealed that the majority of the genes expressed in one or a few growth stages indicating spatial distribution of their expressions. The differential expressions of a few candidate genes such as pre-alpha/beta-gliadin and gamma gliadin were validated by RT

Visible-infrared achromatic imaging by wavefront coding with wide-angle automobile camera

NASA Astrophysics Data System (ADS)

Ohta, Mitsuhiko; Sakita, Koichi; Shimano, Takeshi; Sugiyama, Takashi; Shibasaki, Susumu

2016-09-01

We perform an experiment of achromatic imaging with wavefront coding (WFC) using a wide-angle automobile lens. Our original annular phase mask for WFC was inserted to the lens, for which the difference between the focal positions at 400 nm and at 950 nm is 0.10 mm. We acquired images of objects using a WFC camera with this lens under the conditions of visible and infrared light. As a result, the effect of the removal of the chromatic aberration of the WFC system was successfully determined. Moreover, we fabricated a demonstration set assuming the use of a night vision camera in an automobile and showed the effect of the WFC system.

Material rhetoric: spreading stones and showing bones in the study of prehistory.

PubMed

Van Reybrouck, David; de Bont, Raf; Rock, Jan

2009-06-01

Since the linguistic turn, the role of rhetoric in the circulation and the popular representation of knowledge has been widely accepted in science studies. This article aims to analyze not a textual form of scientific rhetoric, but the crucial role of materiality in scientific debates. It introduces the concept of material rhetoric to understand the promotional regimes in which material objects play an essential argumentative role. It analyzes the phenomenon by looking at two students of prehistory from nineteenth-century Belgium. In the study of human prehistory and evolution, material data are either fairly abundant stone tools or very scarce fossil bones. These two types of material data stand for two different strategies in material rhetoric. In this article, the first strategy is exemplified by Aimé Rutot, who gathered great masses of eoliths (crudely chipped stones which he believed to be prehistoric tools). The second strategy is typified by the example of Julien Fraipont, who based his scientific career on only two Neanderthal skeletons. Rutot sent his "artifacts" to a very wide audience, while Fraipont showed his skeletons to only a few selected scholars. Unlike Rutot, however, Fraipont was able to monitor his audience's interpretation of the finds by means of personal contacts. What an archaeologist gains in reach, he or she apparently loses in control. In this article we argue that only those scholars who find the right balance between the extremes of reach and control will prove to be successful.

Genome-wide meta-analyses of stratified depression in Generation Scotland and UK Biobank.

PubMed

Hall, Lynsey S; Adams, Mark J; Arnau-Soler, Aleix; Clarke, Toni-Kim; Howard, David M; Zeng, Yanni; Davies, Gail; Hagenaars, Saskia P; Maria Fernandez-Pujals, Ana; Gibson, Jude; Wigmore, Eleanor M; Boutin, Thibaud S; Hayward, Caroline; Scotland, Generation; Porteous, David J; Deary, Ian J; Thomson, Pippa A; Haley, Chris S; McIntosh, Andrew M

2018-01-10

Few replicable genetic associations for Major Depressive Disorder (MDD) have been identified. Recent studies of MDD have identified common risk variants by using a broader phenotype definition in very large samples, or by reducing phenotypic and ancestral heterogeneity. We sought to ascertain whether it is more informative to maximize the sample size using data from all available cases and controls, or to use a sex or recurrent stratified subset of affected individuals. To test this, we compared heritability estimates, genetic correlation with other traits, variance explained by MDD polygenic score, and variants identified by genome-wide meta-analysis for broad and narrow MDD classifications in two large British cohorts - Generation Scotland and UK Biobank. Genome-wide meta-analysis of MDD in males yielded one genome-wide significant locus on 3p22.3, with three genes in this region (CRTAP, GLB1, and TMPPE) demonstrating a significant association in gene-based tests. Meta-analyzed MDD, recurrent MDD and female MDD yielded equivalent heritability estimates, showed no detectable difference in association with polygenic scores, and were each genetically correlated with six health-correlated traits (neuroticism, depressive symptoms, subjective well-being, MDD, a cross-disorder phenotype and Bipolar Disorder). Whilst stratified GWAS analysis revealed a genome-wide significant locus for male MDD, the lack of independent replication, and the consistent pattern of results in other MDD classifications suggests that phenotypic stratification using recurrence or sex in currently available sample sizes is currently weakly justified. Based upon existing studies and our findings, the strategy of maximizing sample sizes is likely to provide the greater gain.

SuperDCA for genome-wide epistasis analysis.

PubMed

Puranen, Santeri; Pesonen, Maiju; Pensar, Johan; Xu, Ying Ying; Lees, John A; Bentley, Stephen D; Croucher, Nicholas J; Corander, Jukka

2018-05-29

The potential for genome-wide modelling of epistasis has recently surfaced given the possibility of sequencing densely sampled populations and the emerging families of statistical interaction models. Direct coupling analysis (DCA) has previously been shown to yield valuable predictions for single protein structures, and has recently been extended to genome-wide analysis of bacteria, identifying novel interactions in the co-evolution between resistance, virulence and core genome elements. However, earlier computational DCA methods have not been scalable to enable model fitting simultaneously to 10 4 -10 5 polymorphisms, representing the amount of core genomic variation observed in analyses of many bacterial species. Here, we introduce a novel inference method (SuperDCA) that employs a new scoring principle, efficient parallelization, optimization and filtering on phylogenetic information to achieve scalability for up to 10 5 polymorphisms. Using two large population samples of Streptococcus pneumoniae, we demonstrate the ability of SuperDCA to make additional significant biological findings about this major human pathogen. We also show that our method can uncover signals of selection that are not detectable by genome-wide association analysis, even though our analysis does not require phenotypic measurements. SuperDCA, thus, holds considerable potential in building understanding about numerous organisms at a systems biological level.

Genome-wide association study of alcohol dependence

PubMed Central

Treutlein, Jens; Cichon, Sven; Ridinger, Monika; Wodarz, Norbert; Soyka, Michael; Zill, Peter; Maier, Wolfgang; Moessner, Rainald; Gaebel, Wolfgang; Dahmen, Norbert; Fehr, Christoph; Scherbaum, Norbert; Steffens, Michael; Ludwig, Kerstin U.; Frank, Josef; Wichmann, H.- Erich; Schreiber, Stefan; Dragano, Nico; Sommer, Wolfgang; Leonardi-Essmann, Fernando; Lourdusamy, Anbarasu; Gebicke-Haerter, Peter; Wienker, Thomas F.; Sullivan, Patrick F.; Nöthen, Markus M.; Kiefer, Falk; Spanagel, Rainer; Mann, Karl; Rietschel, Marcella

2014-01-01

Context Identification of genes contributing to alcohol dependence will improve our understanding of the mechanisms underlying this disorder. Objective To identify susceptibility genes for alcohol dependence through a genome-wide association study (GWAS) and follow-up study in a population of German male inpatients with an early age at onset. Design The GWAS included 487 male inpatients with DSM-IV alcohol dependence with an age at onset below 28 years and 1,358 population based control individuals. The follow-up study included 1,024 male inpatients and 996 age-matched male controls. All subjects were of German descent. The GWAS tested 524,396 single nucleotide polymorphisms (SNPs). All SNPs with p<10-4 were subjected to the follow-up study. In addition, nominally significant SNPs from those genes that had also shown expression changes in rat brains after chronic alcohol consumption were selected for the follow-up step. Results The GWAS produced 121 SNPs with nominal p<10-4. These, together with 19 additional SNPs from homologs of rat genes showing differential expression, were genotyped in the follow-up sample. Fifteen SNPs showed significant association with the same allele as in the GWAS. In the combined analysis, two closely linked intergenic SNPs met genome-wide significance (rs7590720 p=9.72×10-9; rs1344694 p=1.69×10-8). They are located on chromosome 2q35, a region which has been implicated in linkage studies for alcohol phenotypes. Nine SNPs were located in genes, including CDH13 and ADH1C genes which have been reported to be associated with alcohol dependence. Conclusion This is the first GWAS and follow-up study to identify a genome-wide significant association in alcohol dependence. Further independent studies are required to confirm these findings. PMID:19581569

Comparative Analyses of the Lipooligosaccharides from Nontypeable Haemophilus influenzae and Haemophilus haemolyticus Show Differences in Sialic Acid and Phosphorylcholine Modifications

PubMed Central

Post, Deborah M. B.; Ketterer, Margaret R.; Coffin, Jeremy E.; Reinders, Lorri M.; Munson, Robert S.; Bair, Thomas; Murphy, Timothy F.; Foster, Eric D.; Gibson, Bradford W.

2016-01-01

Haemophilus haemolyticus and nontypeable Haemophilus influenzae (NTHi) are closely related upper airway commensal bacteria that are difficult to distinguish phenotypically. NTHi causes upper and lower airway tract infections in individuals with compromised airways, while H. haemolyticus rarely causes such infections. The lipooligosaccharide (LOS) is an outer membrane component of both species and plays a role in NTHi pathogenesis. In this study, comparative analyses of the LOS structures and corresponding biosynthesis genes were performed. Mass spectrometric and immunochemical analyses showed that NTHi LOS contained terminal sialic acid more frequently and to a higher extent than H. haemolyticus LOS did. Genomic analyses of 10 strains demonstrated that H. haemolyticus lacked the sialyltransferase genes lic3A and lic3B (9/10) and siaA (10/10), but all strains contained the sialic acid uptake genes siaP and siaT (10/10). However, isothermal titration calorimetry analyses of SiaP from two H. haemolyticus strains showed a 3.4- to 7.3-fold lower affinity for sialic acid compared to that of NTHi SiaP. Additionally, mass spectrometric and immunochemical analyses showed that the LOS from H. haemolyticus contained phosphorylcholine (ChoP) less frequently than the LOS from NTHi strains. These differences observed in the levels of sialic acid and ChoP incorporation in the LOS structures from H. haemolyticus and NTHi may explain some of the differences in their propensities to cause disease. PMID:26729761

Heritability and molecular genetic basis of acoustic startle eye blink and affectively modulated startle response: A genome-wide association study

PubMed Central

VAIDYANATHAN, UMA; MALONE, STEPHEN M.; MILLER, MICHAEL B.; McGUE, MATT; IACONO, WILLIAM G.

2014-01-01

Acoustic startle responses have been studied extensively in relation to individual differences and psychopathology. We examined three indices of the blink response in a picture-viewing paradigm—overall startle magnitude across all picture types, and aversive and pleasant modulation scores—in 3,323 twins and parents. Biometric models and molecular genetic analyses showed that half the variance in overall startle was due to additive genetic effects. No single nucleotide polymorphism was genome-wide significant, but GRIK3 did produce a significant effect when examined as part of a candidate gene set. In contrast, emotion modulation scores showed little evidence of heritability in either biometric or molecular genetic analyses. However, in a genome-wide scan, PARP14 did produce a significant effect for aversive modulation. We conclude that, although overall startle retains potential as an endophenotype, emotion-modulated startle does not. PMID:25387708

Sex and stress: Men and women show different cortisol responses to psychological stress induced by the Trier social stress test and the Iowa singing social stress test.

PubMed

Reschke-Hernández, Alaine E; Okerstrom, Katrina L; Bowles Edwards, Angela; Tranel, Daniel

2017-01-02

Acute psychological stress affects each of us in our daily lives and is increasingly a topic of discussion for its role in mental illness, aging, cognition, and overall health. A better understanding of how such stress affects the body and mind could contribute to the development of more effective clinical interventions and prevention practices. Over the past 3 decades, the Trier Social Stress Test (TSST) has been widely used to induce acute stress in a laboratory setting based on the principles of social evaluative threat, namely, a judged speech-making task. A comparable alternative task may expand options for examining acute stress in a controlled laboratory setting. This study uses a within-subjects design to examine healthy adult participants' (n = 20 men, n = 20 women) subjective stress and salivary cortisol responses to the standard TSST (involving public speaking and math) and the newly created Iowa Singing Social Stress Test (I-SSST). The I-SSST is similar to the TSST but with a new twist: public singing. Results indicated that men and women reported similarly high levels of subjective stress in response to both tasks. However, men and women demonstrated different cortisol responses; men showed a robust response to both tasks, and women displayed a lesser response. These findings are in line with previous literature and further underscore the importance of examining possible sex differences throughout various phases of research, including design, analysis, and interpretation of results. Furthermore, this nascent examination of the I-SSST suggests a possible alternative for inducing stress in the laboratory. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Region-wide and ecotype-specific differences in demographic histories of threespine stickleback populations, estimated from whole genome sequences.

PubMed

Liu, Shenglin; Hansen, Michael M; Jacobsen, Magnus W

2016-10-01

We analysed 81 whole genome sequences of threespine sticklebacks from Pacific North America, Greenland and Northern Europe, representing 16 populations. Principal component analysis of nuclear SNPs grouped populations according to geographical location, with Pacific populations being more divergent from each other relative to European and Greenlandic populations. Analysis of mitogenome sequences showed Northern European populations to represent a single phylogeographical lineage, whereas Greenlandic and particularly Pacific populations showed admixture between lineages. We estimated demographic history using a genomewide coalescence with recombination approach. The Pacific populations showed gradual population expansion starting >100 Kya, possibly reflecting persistence in cryptic refuges near the present distributional range, although we do not rule out possible influence of ancient admixture. Sharp population declines ca. 14-15 Kya were suggested to reflect founding of freshwater populations by marine ancestors. In Greenland and Northern Europe, demographic expansion started ca. 20-25 Kya coinciding with the end of the Last Glacial Maximum. In both regions, marine and freshwater populations started to show different demographic trajectories ca. 8-9 Kya, suggesting that this was the time of recolonization. In Northern Europe, this estimate was surprisingly late, but found support in subfossil evidence for presence of several freshwater fish species but not sticklebacks 12 Kya. The results demonstrate distinctly different demographic histories across geographical regions with potential consequences for adaptive processes. They also provide empirical support for previous assumptions about freshwater populations being founded independently from large, coherent marine populations, a key element in the Transporter Hypothesis invoked to explain the widespread occurrence of parallel evolution across freshwater stickleback populations. © 2016 John Wiley & Sons Ltd.

Nerve compression and pain in human volunteers with narrow vs wide tourniquets

PubMed Central

Kovar, Florian M; Jaindl, Manuela; Oberleitner, Gerhard; Endler, Georg; Breitenseher, Julia; Prayer, Daniela; Kasprian, Gregor; Kutscha-Lissberg, Florian

2015-01-01

AIM: To assess the clinical effects and the morphological grade of nerve compression. METHODS: In a prospective single-center randomized, open study we assessed the clinical effects and the morphological grade of nerve compression during 20 min of either a silicon ring (group A) or pneumatic tourniquet (group B) placement variantly on the upper non-dominant limb in 14 healthy human volunteers. Before and during compression, the median and radial nerves were visualized in both groups by 3 Tesla MR imaging, using high resolutional (2.5 mm slice thickness) axial T2-weighted sequences. RESULTS: In group A, Visual analog pain scale was 5.4 ± 2.2 compared to results of group B, 2.9 ± 2.5, showing a significant difference (P = 0.028). FPS levels in group A were 2.6 ± 0.9 compared to levels in group B 1.6 ± 1, showing a significant difference (P = 0.039). Results related to measureable effect on median and radial nerve function were equal in both groups. No undue pressure signs on the skin, redness or nerve damage occurred in either group. There was no significant difference in the diameters of the nerves without and under compression in either group on T2 weighted images. CONCLUSION: Based on our results, no differences between narrow and wide tourniquets were identified. Silicon ring tourniquets can be regarded as safe for short time application. PMID:25992317

Comparison of Weather Shows in Eastern Europe

NASA Astrophysics Data System (ADS)

Najman, M.

2009-09-01

Comparison of Weather Shows in Eastern Europe Television weather shows in Eastern Europe have in most cases in the high graphical standard. There is though a wast difference in duration and information content in the weather shows. There are few signs and regularities by which we can see the character of the weather show. The main differences are mainly caused by the income structure of the TV station. Either it is a fully privately funded TV relying on the TV commercials income. Or it is a public service TV station funded mainly by the national budget or fixed fee structure/tax. There are wast differences in duration and even a graphical presentation of the weather. Next important aspect is a supplier of the weather information and /or the processor. Shortly we can say, that when the TV show is produced by the national met office, the TV show consists of more scientific terms, synoptic maps, satellite imagery, etc. If the supplier is the private meteorological company, the weather show is more user-friendly, laical with less scientific terms. We are experiencing a massive shift in public weather knowledge and demand for information. In the past, weather shows consisted only of maps with weather icons. In todaýs world, even the laic weather shows consist partly of numerical weather model outputs - they are of course designed to be understandable and graphically attractive. Outputs of the numerical weather models used to be only a part of daily life of a professional meteorologist, today they are common part of life of regular people. Video samples are a part of this presentation.

Compact silicon photonic wavelength-tunable laser diode with ultra-wide wavelength tuning range

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

Kita, Tomohiro, E-mail: tkita@ecei.tohoku.ac.jp; Tang, Rui; Yamada, Hirohito

2015-03-16

We present a wavelength-tunable laser diode with a 99-nm-wide wavelength tuning range. It has a compact wavelength-tunable filter with high wavelength selectivity fabricated using silicon photonics technology. The silicon photonic wavelength-tunable filter with wide wavelength tuning range was realized using two ring resonators and an asymmetric Mach-Zehnder interferometer. The wavelength-tunable laser diode fabricated by butt-joining a silicon photonic filter and semiconductor optical amplifier shows stable single-mode operation over a wide wavelength range.

Seizures and Sleep in the Thalamus: Focal Limbic Seizures Show Divergent Activity Patterns in Different Thalamic Nuclei

PubMed Central

Feng, Li; Motelow, Joshua E.; Ma, Chanthia; Liu, Mengran; Zhan, Qiong; Jia, Ruonan; Xiao, Bo; Duque, Alvaro

2017-01-01

The thalamus plays diverse roles in cortical-subcortical brain activity patterns. Recent work suggests that focal temporal lobe seizures depress subcortical arousal systems and convert cortical activity into a pattern resembling slow-wave sleep. The potential simultaneous and paradoxical role of the thalamus in both limbic seizure propagation, and in sleep-like cortical rhythms has not been investigated. We recorded neuronal activity from the central lateral (CL), anterior (ANT), and ventral posteromedial (VPM) nuclei of the thalamus in an established female rat model of focal limbic seizures. We found that population firing of neurons in CL decreased during seizures while the cortex exhibited slow waves. In contrast, ANT showed a trend toward increased neuronal firing compatible with polyspike seizure discharges seen in the hippocampus. Meanwhile, VPM exhibited a remarkable increase in sleep spindles during focal seizures. Single-unit juxtacellular recordings from CL demonstrated reduced overall firing rates, but a switch in firing pattern from single spikes to burst firing during seizures. These findings suggest that different thalamic nuclei play very different roles in focal limbic seizures. While limbic nuclei, such as ANT, appear to participate directly in seizure propagation, arousal nuclei, such as CL, may contribute to depressed cortical function, whereas sleep spindles in relay nuclei, such as VPM, may interrupt thalamocortical information flow. These combined effects could be critical for controlling both seizure severity and impairment of consciousness. Further understanding of differential effects of seizures on different thalamocortical networks may lead to improved treatments directly targeting these modes of impaired function. SIGNIFICANCE STATEMENT Temporal lobe epilepsy has a major negative impact on quality of life. Previous work suggests that the thalamus plays a critical role in thalamocortical network modulation and subcortical arousal

Using WorldWide Telescope in Observing, Research and Presentation

NASA Astrophysics Data System (ADS)

Roberts, Douglas A.; Fay, J.

2014-01-01

WorldWide Telescope (WWT) is free software that enables researchers to interactively explore observational data using a user-friendly interface. Reference, all-sky datasets and pointed observations are available as layers along with the ability to easily overlay additional FITS images and catalog data. Connections to the Astrophysics Data System (ADS) are included which enable visual investigation using WWT to drive document searches in ADS. WWT can be used to capture and share visual exploration with colleagues during observational planning and analysis. Finally, researchers can use WorldWide Telescope to create videos for professional, education and outreach presentations. I will conclude with an example of how I have used WWT in a research project. Specifically, I will discuss how WorldWide Telescope helped our group to prepare for radio observations and following them, in the analysis of multi-wavelength data taken in the inner parsec of the Galaxy. A concluding video will show how WWT brought together disparate datasets in a unified interactive visualization environment.

Accretion of chemically fractionated material on a wide binary with a blue straggler

NASA Astrophysics Data System (ADS)

Desidera, S.; Gratton, R. G.; Lucatello, S.; Endl, M.; Udry, S.

2007-02-01

Context: The components of the wide binary HIP 64030 = HD 113984 show a large (about 0.25 dex) iron content difference (Desidera et al. 2006). The positions of the components on the color magnitude diagram suggest that the primary is a blue straggler. Aims: We studied the abundance difference of several elements besides iron, and we searched for stellar and substellar companions around the components to unveil the origin of the observed iron difference. Methods: A line-by-line differential abundance analysis for several elements was performed for iron, while suitable spectral synthesis was performed for C, N, and Li. High precision radial velocities obtained with the iodine cell were combined with available literature data. Results: The analysis of additional elements shows that the abundance difference for the elements studied increases with increasing condensation temperature, suggesting that accretion of chemically fractionated material might have occurred in the system. Alteration of C and N likely due to CNO processing is also observed. We also show that the primary is a spectroscopic binary with a period of 445 days and moderate eccentricity. The minimum mass of the companion is 0.17~M⊙. Conclusions: .Two scenarios were explored to explain the observed abundance pattern. In the first, all abundance anomalies arise on the blue straggler. If this is the case, the dust-gas separation may have been occurred in a circumbinary disk around the blue straggler and its expected white dwarf companion, as observed in several RV Tauri and post AGB binaries. In the second scenario, accretion of dust-rich material occurred on the secondary. This would also explain the anomalous carbon isotopic ratio of the secondary. Such a scenario requires that a substantial amount of mass lost by the central binary has been accreted by the wide component. Further studies to compare the two scenarios are proposed. Based on observations collected at the European Southern Observatory

Genome-wide characterization of the WRKY gene family in radish (Raphanus sativus L.) reveals its critical functions under different abiotic stresses.

PubMed

Karanja, Bernard Kinuthia; Fan, Lianxue; Xu, Liang; Wang, Yan; Zhu, Xianwen; Tang, Mingjia; Wang, Ronghua; Zhang, Fei; Muleke, Everlyne M'mbone; Liu, Liwang

2017-11-01

The radish WRKY gene family was genome-widely identified and played critical roles in response to multiple abiotic stresses. The WRKY is among the largest transcription factors (TFs) associated with multiple biological activities for plant survival, including control response mechanisms against abiotic stresses such as heat, salinity, and heavy metals. Radish is an important root vegetable crop and therefore characterization and expression pattern investigation of WRKY transcription factors in radish is imperative. In the present study, 126 putative WRKY genes were retrieved from radish genome database. Protein sequence and annotation scrutiny confirmed that RsWRKY proteins possessed highly conserved domains and zinc finger motif. Based on phylogenetic analysis results, RsWRKYs candidate genes were divided into three groups (Group I, II and III) with the number 31, 74, and 20, respectively. Additionally, gene structure analysis revealed that intron-exon patterns of the WRKY genes are highly conserved in radish. Linkage map analysis indicated that RsWRKY genes were distributed with varying densities over nine linkage groups. Further, RT-qPCR analysis illustrated the significant variation of 36 RsWRKY genes under one or more abiotic stress treatments, implicating that they might be stress-responsive genes. In total, 126 WRKY TFs were identified from the R. sativus genome wherein, 35 of them showed abiotic stress-induced expression patterns. These results provide a genome-wide characterization of RsWRKY TFs and baseline for further functional dissection and molecular evolution investigation, specifically for improving abiotic stress resistances with an ultimate goal of increasing yield and quality of radish.

Logistic regression accuracy across different spatial and temporal scales for a wide-ranging species, the marbled murrelet

Treesearch

Carolyn B. Meyer; Sherri L. Miller; C. John Ralph

2004-01-01

The scale at which habitat variables are measured affects the accuracy of resource selection functions in predicting animal use of sites. We used logistic regression models for a wide-ranging species, the marbled murrelet, (Brachyramphus marmoratus) in a large region in California to address how much changing the spatial or temporal scale of...

Genome-wide identification and characterization of aquaporin gene family in Beta vulgaris

PubMed Central

Kong, Weilong; Yang, Shaozong; Wang, Yulu; Bendahmane, Mohammed

2017-01-01

Aquaporins (AQPs) are essential channel proteins that execute multi-functions throughout plant growth and development, including water transport, uncharged solutes uptake, stress response, and so on. Here, we report the first genome-wide identification and characterization AQP (BvAQP) genes in sugar beet (Beta vulgaris), an important crop widely cultivated for feed, for sugar production and for bioethanol production. Twenty-eight sugar beet AQPs (BvAQPs) were identified and assigned into five subfamilies based on phylogenetic analyses: seven of plasma membrane (PIPs), eight of tonoplast (TIPs), nine of NOD26-like (NIPs), three of small basic (SIPs), and one of x-intrinsic proteins (XIPs). BvAQP genes unevenly mapped on all chromosomes, except on chromosome 4. Gene structure and motifs analyses revealed that BvAQP have conserved exon-intron organization and that they exhibit conserved motifs within each subfamily. Prediction of BvAQPs functions, based on key protein domains conservation, showed a remarkable difference in substrate specificity among the five subfamilies. Analyses of BvAQPs expression, by mean of RNA-seq, in different plant organs and in response to various abiotic stresses revealed that they were ubiquitously expressed and that their expression was induced by heat and salt stresses. These results provide a reference base to address further the function of sugar beet aquaporins and to explore future applications for plants growth and development improvements as well as in response to environmental stresses. PMID:28948097

Upper wide-angle viewing system for ITER.

PubMed

Lasnier, C J; McLean, A G; Gattuso, A; O'Neill, R; Smiley, M; Vasquez, J; Feder, R; Smith, M; Stratton, B; Johnson, D; Verlaan, A L; Heijmans, J A C

2016-11-01

The Upper Wide Angle Viewing System (UWAVS) will be installed on five upper ports of ITER. This paper shows major requirements, gives an overview of the preliminary design with reasons for some design choices, examines self-emitted IR light from UWAVS optics and its effect on accuracy, and shows calculations of signal-to-noise ratios for the two-color temperature output as a function of integration time and divertor temperature. Accurate temperature output requires correction for vacuum window absorption vs. wavelength and for self-emitted IR, which requires good measurement of the temperature of the optical components. The anticipated signal-to-noise ratio using presently available IR cameras is adequate for the required 500 Hz frame rate.

Not All Trees Sleep the Same—High Temporal Resolution Terrestrial Laser Scanning Shows Differences in Nocturnal Plant Movement

PubMed Central

Zlinszky, András; Molnár, Bence; Barfod, Anders S.

2017-01-01

Circadian leaf movements are widely known in plants, but nocturnal movement of tree branches were only recently discovered by using terrestrial laser scanning (TLS), a high resolution three-dimensional surveying technique. TLS uses a pulsed laser emitted in a regular scan pattern for rapid measurement of distances to the targets, thus producing three dimensional point cloud models of sub-centimeter resolution and accuracy in a few minutes. Here, we aim to gain an overview of the variability of circadian movement of small trees across different taxonomic groups, growth forms and leaf anatomies. We surveyed a series of 18 full scans over a 12-h night period to measure nocturnal changes in shape simultaneously for an experimental setup of 22 plants representing different species. Resulting point clouds were evaluated by comparing changes in height percentiles of laser scanning points belonging to the canopy. Changes in crown shape were observed for all studied trees, but clearly distinguishable sleep movements are apparently rare. Ambient light conditions were continuously dark between sunset (7:30 p.m.) and sunrise (6:00 a.m.), but most changes in movement direction occurred during this period, thus most of the recorded changes in crown shape were probably not controlled by ambient light. The highest movement amplitudes, for periodic circadian movement around 2 cm were observed for Aesculus and Acer, compared to non-periodic continuous change in shape of 5 cm for Gleditschia and 2 cm for Fargesia. In several species we detected 2–4 h cycles of minor crown movement of 0.5–1 cm, which is close to the limit of our measurement accuracy. We present a conceptual framework for interpreting observed changes as a combination of circadian rhythm with a period close to 12 h, short-term oscillation repeated every 2–4 h, aperiodic continuous movement in one direction and measurement noise which we assume to be random. Observed movement patterns are interpreted within this

Development and testing of a European Union-wide farm-level carbon calculator

PubMed Central

Tuomisto, Hanna L; De Camillis, Camillo; Leip, Adrian; Nisini, Luigi; Pelletier, Nathan; Haastrup, Palle

2015-01-01

Direct greenhouse gas (GHG) emissions from agriculture accounted for approximately 10% of total European Union (EU) emissions in 2010. To reduce farming-related GHG emissions, appropriate policy measures and supporting tools for promoting low-C farming practices may be efficacious. This article presents the methodology and testing results of a new EU-wide, farm-level C footprint calculator. The Carbon Calculator quantifies GHG emissions based on international standards and technical specifications on Life Cycle Assessment (LCA) and C footprinting. The tool delivers its results both at the farm level and as allocated to up to 5 main products of the farm. In addition to the quantification of GHG emissions, the calculator proposes mitigation options and sequestration actions that may be suitable for individual farms. The results obtained during a survey made on 54 farms from 8 EU Member States are presented. These farms were selected in view of representing the diversity of farm types across different environmental zones in the EU. The results of the C footprint of products in the data set show wide range of variation between minimum and maximum values. The results of the mitigation actions showed that the tool can help identify practices that can lead to substantial emission reductions. To avoid burden-shifting from climate change to other environmental issues, the future improvements of the tool should include incorporation of other environmental impact categories in place of solely focusing on GHG emissions. Integr Environ Assess Manag 2015;11:404–416. © 2015 The Authors. Published by Wiley Periodicals, Inc. on behalf of SETAC. Key Points The methodology and testing results of a new European Union-wide, farm-level carbon calculator are presented. The Carbon Calculator reports life cycle assessment-based greenhouse gas emissions at farm and product levels and recommends farm- specific mitigation actions. Based on the results obtained from testing the tool in 54

Wide-band gas leak imaging detection system using UFPA

NASA Astrophysics Data System (ADS)

Jin, Wei-qi; Li, Jia-kun; Dun, Xiong; Jin, Minglei; Wang, Xia

2014-11-01

plume intuitively and so on. The simulation experiment shows that the gas IR imaging detection has great advantages and widely promotion space compared with the traditional techniques, such as point-contact or line-contactless detection.

Wide coverage biomedical event extraction using multiple partially overlapping corpora

PubMed Central

2013-01-01

Background Biomedical events are key to understanding physiological processes and disease, and wide coverage extraction is required for comprehensive automatic analysis of statements describing biomedical systems in the literature. In turn, the training and evaluation of extraction methods requires manually annotated corpora. However, as manual annotation is time-consuming and expensive, any single event-annotated corpus can only cover a limited number of semantic types. Although combined use of several such corpora could potentially allow an extraction system to achieve broad semantic coverage, there has been little research into learning from multiple corpora with partially overlapping semantic annotation scopes. Results We propose a method for learning from multiple corpora with partial semantic annotation overlap, and implement this method to improve our existing event extraction system, EventMine. An evaluation using seven event annotated corpora, including 65 event types in total, shows that learning from overlapping corpora can produce a single, corpus-independent, wide coverage extraction system that outperforms systems trained on single corpora and exceeds previously reported results on two established event extraction tasks from the BioNLP Shared Task 2011. Conclusions The proposed method allows the training of a wide-coverage, state-of-the-art event extraction system from multiple corpora with partial semantic annotation overlap. The resulting single model makes broad-coverage extraction straightforward in practice by removing the need to either select a subset of compatible corpora or semantic types, or to merge results from several models trained on different individual corpora. Multi-corpus learning also allows annotation efforts to focus on covering additional semantic types, rather than aiming for exhaustive coverage in any single annotation effort, or extending the coverage of semantic types annotated in existing corpora. PMID:23731785

Variability in the measurement of hospital-wide mortality rates.

PubMed

Shahian, David M; Wolf, Robert E; Iezzoni, Lisa I; Kirle, Leslie; Normand, Sharon-Lise T

2010-12-23

Several countries use hospital-wide mortality rates to evaluate the quality of hospital care, although the usefulness of this metric has been questioned. Massachusetts policymakers recently requested an assessment of methods to calculate this aggregate mortality metric for use as a measure of hospital quality. The Massachusetts Division of Health Care Finance and Policy provided four vendors with identical information on 2,528,624 discharges from Massachusetts acute care hospitals from October 1, 2004, through September 30, 2007. Vendors applied their risk-adjustment algorithms and provided predicted probabilities of in-hospital death for each discharge and for hospital-level observed and expected mortality rates. We compared the numbers and characteristics of discharges and hospitals included by each of the four methods. We also compared hospitals' standardized mortality ratios and classification of hospitals with mortality rates that were higher or lower than expected, according to each method. The proportions of discharges that were included by each method ranged from 28% to 95%, and the severity of patients' diagnoses varied widely. Because of their discharge-selection criteria, two methods calculated in-hospital mortality rates (4.0% and 5.9%) that were twice the state average (2.1%). Pairwise associations (Pearson correlation coefficients) of discharge-level predicted mortality probabilities ranged from 0.46 to 0.70. Hospital-performance categorizations varied substantially and were sometimes completely discordant. In 2006, a total of 12 of 28 hospitals that had higher-than-expected hospital-wide mortality when classified by one method had lower-than-expected mortality when classified by one or more of the other methods. Four common methods for calculating hospital-wide mortality produced substantially different results. This may have resulted from a lack of standardized national eligibility and exclusion criteria, different statistical methods, or

Interpreting Meta-Analyses of Genome-Wide Association Studies

PubMed Central

Han, Buhm; Eskin, Eleazar

2012-01-01

Meta-analysis is an increasingly popular tool for combining multiple genome-wide association studies in a single analysis to identify associations with small effect sizes. The effect sizes between studies in a meta-analysis may differ and these differences, or heterogeneity, can be caused by many factors. If heterogeneity is observed in the results of a meta-analysis, interpreting the cause of heterogeneity is important because the correct interpretation can lead to a better understanding of the disease and a more effective design of a replication study. However, interpreting heterogeneous results is difficult. The standard approach of examining the association p-values of the studies does not effectively predict if the effect exists in each study. In this paper, we propose a framework facilitating the interpretation of the results of a meta-analysis. Our framework is based on a new statistic representing the posterior probability that the effect exists in each study, which is estimated utilizing cross-study information. Simulations and application to the real data show that our framework can effectively segregate the studies predicted to have an effect, the studies predicted to not have an effect, and the ambiguous studies that are underpowered. In addition to helping interpretation, the new framework also allows us to develop a new association testing procedure taking into account the existence of effect. PMID:22396665

Surfing the World Wide Web to Education Hot-Spots.

ERIC Educational Resources Information Center

Dyrli, Odvard Egil

1995-01-01

Provides a brief explanation of Web browsers and their use, as well as technical information for those considering access to the WWW (World Wide Web). Curriculum resources and addresses to useful Web sites are included. Sidebars show sample searches using Yahoo and Lycos search engines, and a list of recommended Web resources. (JKP)

Widely tunable chaotic fiber laser for WDM-PON detection

NASA Astrophysics Data System (ADS)

Zhang, Juan; Yang, Ling-zhen; Xu, Nai-jun; Wang, Juan-fen; Zhang, Zhao-xia; Liu, Xiang-lian

2014-05-01

A widely tunable high precision chaotic fiber laser is proposed and experimentally demonstrated. A tunable fiber Bragg grating (TFBG) filter is used as a tuning element to determine the turning range from 1533 nm to 1558 nm with a linewidth of 0.5 nm at any wavelength. The wide tuning range is capable of supporting 32 wavelength-division multiplexing (WDM) channels with 100 GHz channel spacing. All single wavelengths are found to be chaotic with 10 GHz bandwidth. The full width at half maximum (FWHM) of the chaotic correlation curve of the different wavelengths is on a picosecond time scale, thereby offering millimeter spatial resolution in WDM detection.

Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains

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

Lan, Yemin; Rosen, Gail; Hershberg, Ruth

The 16s rRNA gene is so far the most widely used marker for taxonomical classification and separation of prokaryotes. Since it is universally conserved among prokaryotes, it is possible to use this gene to classify a broad range of prokaryotic organisms. At the same time, it has often been noted that the 16s rRNA gene is too conserved to separate between prokaryotes at finer taxonomic levels. In this paper, we examine how well levels of similarity of 16s rRNA and 73 additional universal or nearly universal marker genes correlate with genome-wide levels of gene sequence similarity. We demonstrate that themore » percent identity of 16s rRNA predicts genome-wide levels of similarity very well for distantly related prokaryotes, but not for closely related ones. In closely related prokaryotes, we find that there are many other marker genes for which levels of similarity are much more predictive of genome-wide levels of gene sequence similarity. Finally, we show that the identities of the markers that are most useful for predicting genome-wide levels of similarity within closely related prokaryotic lineages vary greatly between lineages. However, the most useful markers are always those that are least conserved in their sequences within each lineage. In conclusion, our results show that by choosing markers that are less conserved in their sequences within a lineage of interest, it is possible to better predict genome-wide gene sequence similarity between closely related prokaryotes than is possible using the 16s rRNA gene. We point readers towards a database we have created (POGO-DB) that can be used to easily establish which markers show lowest levels of sequence conservation within different prokaryotic lineages.« less

Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains

DOE PAGES

Lan, Yemin; Rosen, Gail; Hershberg, Ruth

2016-05-03

The 16s rRNA gene is so far the most widely used marker for taxonomical classification and separation of prokaryotes. Since it is universally conserved among prokaryotes, it is possible to use this gene to classify a broad range of prokaryotic organisms. At the same time, it has often been noted that the 16s rRNA gene is too conserved to separate between prokaryotes at finer taxonomic levels. In this paper, we examine how well levels of similarity of 16s rRNA and 73 additional universal or nearly universal marker genes correlate with genome-wide levels of gene sequence similarity. We demonstrate that themore » percent identity of 16s rRNA predicts genome-wide levels of similarity very well for distantly related prokaryotes, but not for closely related ones. In closely related prokaryotes, we find that there are many other marker genes for which levels of similarity are much more predictive of genome-wide levels of gene sequence similarity. Finally, we show that the identities of the markers that are most useful for predicting genome-wide levels of similarity within closely related prokaryotic lineages vary greatly between lineages. However, the most useful markers are always those that are least conserved in their sequences within each lineage. In conclusion, our results show that by choosing markers that are less conserved in their sequences within a lineage of interest, it is possible to better predict genome-wide gene sequence similarity between closely related prokaryotes than is possible using the 16s rRNA gene. We point readers towards a database we have created (POGO-DB) that can be used to easily establish which markers show lowest levels of sequence conservation within different prokaryotic lineages.« less

A multi-directional backlight for a wide-angle, glasses-free three-dimensional display.

PubMed

Fattal, David; Peng, Zhen; Tran, Tho; Vo, Sonny; Fiorentino, Marco; Brug, Jim; Beausoleil, Raymond G

2013-03-21

Multiview three-dimensional (3D) displays can project the correct perspectives of a 3D image in many spatial directions simultaneously. They provide a 3D stereoscopic experience to many viewers at the same time with full motion parallax and do not require special glasses or eye tracking. None of the leading multiview 3D solutions is particularly well suited to mobile devices (watches, mobile phones or tablets), which require the combination of a thin, portable form factor, a high spatial resolution and a wide full-parallax view zone (for short viewing distance from potentially steep angles). Here we introduce a multi-directional diffractive backlight technology that permits the rendering of high-resolution, full-parallax 3D images in a very wide view zone (up to 180 degrees in principle) at an observation distance of up to a metre. The key to our design is a guided-wave illumination technique based on light-emitting diodes that produces wide-angle multiview images in colour from a thin planar transparent lightguide. Pixels associated with different views or colours are spatially multiplexed and can be independently addressed and modulated at video rate using an external shutter plane. To illustrate the capabilities of this technology, we use simple ink masks or a high-resolution commercial liquid-crystal display unit to demonstrate passive and active (30 frames per second) modulation of a 64-view backlight, producing 3D images with a spatial resolution of 88 pixels per inch and full-motion parallax in an unprecedented view zone of 90 degrees. We also present several transparent hand-held prototypes showing animated sequences of up to six different 200-view images at a resolution of 127 pixels per inch.

On the Occurrence of Wide Binaries in the Local Disk and Halo Populations

NASA Astrophysics Data System (ADS)

Hartman, Zachary; Lepine, Sebastien

2018-01-01

We present results from our search for wide binaries in the SUPERBLINK+GAIA all-sky catalog of 2.8 million high proper motion stars (μ>40 mas/yr). Through a Bayesian analysis of common proper motion pairs, we have identified highly probable wide binary/multiple systems based on statistics of their proper motion differences and angular separations. Using a reduced proper motion diagram, we determine whether these wide are part of the young disk, old disk, or Galactic halo population. We examine the relative occurrence rate for very wide companions in these respective populations. All groups are found to contain a significant number of wide binary systems, with about 1 percent of the stars in each group having pairs with separations >1,000 AU.

Genome-wide analysis and expression profiling of the Solanum tuberosum aquaporins.

PubMed

Venkatesh, Jelli; Yu, Jae-Woong; Park, Se Won

2013-12-01

Aquaporins belongs to the major intrinsic proteins involved in the transcellular membrane transport of water and other small solutes. A comprehensive genome-wide search for the homologues of Solanum tuberosum major intrinsic protein (MIP) revealed 41 full-length potato aquaporin genes. All potato aquaporins are grouped into five subfamilies; plasma membrane intrinsic proteins (PIPs), tonoplast intrinsic proteins (TIPs), NOD26-like intrinsic proteins (NIPs), small basic intrinsic proteins (SIPs) and x-intrinsic proteins (XIPs). Functional predictions based on the aromatic/arginine (ar/R) selectivity filters and Froger's positions showed a remarkable difference in substrate transport specificity among subfamilies. The expression pattern of potato aquaporins, examined by qPCR analysis, showed distinct expression profiles in various organs and tuber developmental stages. Furthermore, qPCR analysis of potato plantlets, subjected to various abiotic stresses revealed the marked effect of stresses on expression levels of aquaporins. Taken together, the expression profiles of aquaporins imply that aquaporins play important roles in plant growth and development, in addition to maintaining water homeostasis in response to environmental stresses. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Wide-Field Plate Database

NASA Astrophysics Data System (ADS)

Tsvetkov, M. K.; Stavrev, K. Y.; Tsvetkova, K. P.; Semkov, E. H.; Mutatov, A. S.

The Wide-Field Plate Database (WFPDB) and the possibilities for its application as a research tool in observational astronomy are presented. Currently the WFPDB comprises the descriptive data for 400 000 archival wide field photographic plates obtained with 77 instruments, from a total of 1 850 000 photographs stored in 269 astronomical archives all over the world since the end of last century. The WFPDB is already accessible for the astronomical community, now only in batch mode through user requests sent by e-mail. We are working on on-line interactive access to the data via INTERNET from Sofia and parallel from the Centre de Donnees Astronomiques de Strasbourg. (Initial information can be found on World Wide Web homepage URL http://www.wfpa.acad.bg.) The WFPDB may be useful in studies of a variety of astronomical objects and phenomena, andespecially for long-term investigations of variable objects and for multi-wavelength research. We have analysed the data in the WFPDB in order to derive the overall characteristics of the totality of wide-field observations, such as the sky coverage, the distributions by observation time and date, by spectral band, and by object type. We have also examined the totality of wide-field observations from point of view of their quality, availability and digitisation. The usefulness of the WFPDB is demonstrated by the results of identification and investigation of the photometrical behaviour of optical analogues of gamma-ray bursts.

Genome-wide genetic homogeneity between sexes and populations for human height and body mass index.

PubMed

Yang, Jian; Bakshi, Andrew; Zhu, Zhihong; Hemani, Gibran; Vinkhuyzen, Anna A E; Nolte, Ilja M; van Vliet-Ostaptchouk, Jana V; Snieder, Harold; Esko, Tonu; Milani, Lili; Mägi, Reedik; Metspalu, Andres; Hamsten, Anders; Magnusson, Patrik K E; Pedersen, Nancy L; Ingelsson, Erik; Visscher, Peter M

2015-12-20

Sex-specific genetic effects have been proposed to be an important source of variation for human complex traits. Here we use two distinct genome-wide methods to estimate the autosomal genetic correlation (rg) between men and women for human height and body mass index (BMI), using individual-level (n = ∼44 000) and summary-level (n = ∼133 000) data from genome-wide association studies. Results are consistent and show that the between-sex genetic correlation is not significantly different from unity for both traits. In contrast, we find evidence of genetic heterogeneity between sexes for waist-hip ratio (rg = ∼0.7) and between populations for BMI (rg = ∼0.9 between Europe and the USA) but not for height. The lack of evidence for substantial genetic heterogeneity for body size is consistent with empirical findings across traits and species. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Gun Shows and Gun Violence: Fatally Flawed Study Yields Misleading Results

PubMed Central

Hemenway, David; Webster, Daniel; Pierce, Glenn; Braga, Anthony A.

2010-01-01

A widely publicized but unpublished study of the relationship between gun shows and gun violence is being cited in debates about the regulation of gun shows and gun commerce. We believe the study is fatally flawed. A working paper entitled “The Effect of Gun Shows on Gun-Related Deaths: Evidence from California and Texas” outlined this study, which found no association between gun shows and gun-related deaths. We believe the study reflects a limited understanding of gun shows and gun markets and is not statistically powered to detect even an implausibly large effect of gun shows on gun violence. In addition, the research contains serious ascertainment and classification errors, produces results that are sensitive to minor specification changes in key variables and in some cases have no face validity, and is contradicted by 1 of its own authors’ prior research. The study should not be used as evidence in formulating gun policy. PMID:20724672

Gun shows and gun violence: fatally flawed study yields misleading results.

PubMed

Wintemute, Garen J; Hemenway, David; Webster, Daniel; Pierce, Glenn; Braga, Anthony A

2010-10-01

A widely publicized but unpublished study of the relationship between gun shows and gun violence is being cited in debates about the regulation of gun shows and gun commerce. We believe the study is fatally flawed. A working paper entitled "The Effect of Gun Shows on Gun-Related Deaths: Evidence from California and Texas" outlined this study, which found no association between gun shows and gun-related deaths. We believe the study reflects a limited understanding of gun shows and gun markets and is not statistically powered to detect even an implausibly large effect of gun shows on gun violence. In addition, the research contains serious ascertainment and classification errors, produces results that are sensitive to minor specification changes in key variables and in some cases have no face validity, and is contradicted by 1 of its own authors' prior research. The study should not be used as evidence in formulating gun policy.

Genome-Wide Tuning of Protein Expression Levels to Rapidly Engineer Microbial Traits.

PubMed

Freed, Emily F; Winkler, James D; Weiss, Sophie J; Garst, Andrew D; Mutalik, Vivek K; Arkin, Adam P; Knight, Rob; Gill, Ryan T

2015-11-20

The reliable engineering of biological systems requires quantitative mapping of predictable and context-independent expression over a broad range of protein expression levels. However, current techniques for modifying expression levels are cumbersome and are not amenable to high-throughput approaches. Here we present major improvements to current techniques through the design and construction of E. coli genome-wide libraries using synthetic DNA cassettes that can tune expression over a ∼10(4) range. The cassettes also contain molecular barcodes that are optimized for next-generation sequencing, enabling rapid and quantitative tracking of alleles that have the highest fitness advantage. We show these libraries can be used to determine which genes and expression levels confer greater fitness to E. coli under different growth conditions.

Stabilized wide bandgap perovskite solar cells by tin substitution

DOE PAGES

Yang, Zhibin; Rajagopal, Adharsh; Jo, Sae Byeok; ...

2016-11-16

Wide bandgap MAPb(I 1-yBr y) 3 perovskites show promising potential for application in tandem solar cells. However, unstable photovoltaic performance caused by phase segregation has been observed under illumination when y is above 0.2. Herein, we successfully demonstrate stabilization of the I/Br phase by partially replacing Pb 2+ with Sn 2+ and verify this stabilization with X-ray diffractometry and transient absorption spectroscopy. The resulting MAPb 0.75Sn 0.25(I 1-yBr y) 3 perovskite solar cells show stable photovoltaic performance under continuous illumination. Among these cells, the one based on MAPb 0.75Sn 0.25(I 0.4Br 0.6) 3 perovskite shows the highest efficiency of 12.59%more » with a bandgap of 1.73 eV, which make it a promising wide bandgap candidate for application in tandem solar cells. The engineering of internal bonding environment by partial Sn substitution is believed to be the main reason for making MAPb 0.75Sn 0.25(I 1-yBr y) 3 perovskite less vulnerable to phase segregation during the photostriction under illumination. Furthermore, this study establishes composition engineering of the metal site as a promising strategy to impart phase stability in hybrid perovskites under illumination.« less

Seizures and Sleep in the Thalamus: Focal Limbic Seizures Show Divergent Activity Patterns in Different Thalamic Nuclei.

PubMed

Feng, Li; Motelow, Joshua E; Ma, Chanthia; Biche, William; McCafferty, Cian; Smith, Nicholas; Liu, Mengran; Zhan, Qiong; Jia, Ruonan; Xiao, Bo; Duque, Alvaro; Blumenfeld, Hal

2017-11-22

The thalamus plays diverse roles in cortical-subcortical brain activity patterns. Recent work suggests that focal temporal lobe seizures depress subcortical arousal systems and convert cortical activity into a pattern resembling slow-wave sleep. The potential simultaneous and paradoxical role of the thalamus in both limbic seizure propagation, and in sleep-like cortical rhythms has not been investigated. We recorded neuronal activity from the central lateral (CL), anterior (ANT), and ventral posteromedial (VPM) nuclei of the thalamus in an established female rat model of focal limbic seizures. We found that population firing of neurons in CL decreased during seizures while the cortex exhibited slow waves. In contrast, ANT showed a trend toward increased neuronal firing compatible with polyspike seizure discharges seen in the hippocampus. Meanwhile, VPM exhibited a remarkable increase in sleep spindles during focal seizures. Single-unit juxtacellular recordings from CL demonstrated reduced overall firing rates, but a switch in firing pattern from single spikes to burst firing during seizures. These findings suggest that different thalamic nuclei play very different roles in focal limbic seizures. While limbic nuclei, such as ANT, appear to participate directly in seizure propagation, arousal nuclei, such as CL, may contribute to depressed cortical function, whereas sleep spindles in relay nuclei, such as VPM, may interrupt thalamocortical information flow. These combined effects could be critical for controlling both seizure severity and impairment of consciousness. Further understanding of differential effects of seizures on different thalamocortical networks may lead to improved treatments directly targeting these modes of impaired function. SIGNIFICANCE STATEMENT Temporal lobe epilepsy has a major negative impact on quality of life. Previous work suggests that the thalamus plays a critical role in thalamocortical network modulation and subcortical arousal

Meta-analysis of epigenome-wide association studies of cognitive abilities.

PubMed

Marioni, Riccardo E; McRae, Allan F; Bressler, Jan; Colicino, Elena; Hannon, Eilis; Li, Shuo; Prada, Diddier; Smith, Jennifer A; Trevisi, Letizia; Tsai, Pei-Chien; Vojinovic, Dina; Simino, Jeannette; Levy, Daniel; Liu, Chunyu; Mendelson, Michael; Satizabal, Claudia L; Yang, Qiong; Jhun, Min A; Kardia, Sharon L R; Zhao, Wei; Bandinelli, Stefania; Ferrucci, Luigi; Hernandez, Dena G; Singleton, Andrew B; Harris, Sarah E; Starr, John M; Kiel, Douglas P; McLean, Robert R; Just, Allan C; Schwartz, Joel; Spiro, Avron; Vokonas, Pantel; Amin, Najaf; Ikram, M Arfan; Uitterlinden, Andre G; van Meurs, Joyce B J; Spector, Tim D; Steves, Claire; Baccarelli, Andrea A; Bell, Jordana T; van Duijn, Cornelia M; Fornage, Myriam; Hsu, Yi-Hsiang; Mill, Jonathan; Mosley, Thomas H; Seshadri, Sudha; Deary, Ian J

2018-01-08

Cognitive functions are important correlates of health outcomes across the life-course. Individual differences in cognitive functions are partly heritable. Epigenetic modifications, such as DNA methylation, are susceptible to both genetic and environmental factors and may provide insights into individual differences in cognitive functions. Epigenome-wide meta-analyses for blood-based DNA methylation levels at ~420,000 CpG sites were performed for seven measures of cognitive functioning using data from 11 cohorts. CpGs that passed a Bonferroni correction, adjusting for the number of CpGs and cognitive tests, were assessed for: longitudinal change; being under genetic control (methylation QTLs); and associations with brain health (structural MRI), brain methylation and Alzheimer's disease pathology. Across the seven measures of cognitive functioning (meta-analysis n range: 2557-6809), there were epigenome-wide significant (P < 1.7 × 10 -8 ) associations for global cognitive function (cg21450381, P = 1.6 × 10 -8 ), and phonemic verbal fluency (cg12507869, P = 2.5 × 10 -9 ). The CpGs are located in an intergenic region on chromosome 12 and the INPP5A gene on chromosome 10, respectively. Both probes have moderate correlations (~0.4) with brain methylation in Brodmann area 20 (ventral temporal cortex). Neither probe showed evidence of longitudinal change in late-life or associations with white matter brain MRI measures in one cohort with these data. A methylation QTL analysis suggested that rs113565688 was a cis methylation QTL for cg12507869 (P = 5 × 10 -5 and 4 × 10 -13 in two lookup cohorts). We demonstrate a link between blood-based DNA methylation and measures of phonemic verbal fluency and global cognitive ability. Further research is warranted to understand the mechanisms linking genomic regulatory changes with cognitive function to health and disease.

Calibration of Wide-Field Deconvolution Microscopy for Quantitative Fluorescence Imaging

PubMed Central

Lee, Ji-Sook; Wee, Tse-Luen (Erika); Brown, Claire M.

2014-01-01

Deconvolution enhances contrast in fluorescence microscopy images, especially in low-contrast, high-background wide-field microscope images, improving characterization of features within the sample. Deconvolution can also be combined with other imaging modalities, such as confocal microscopy, and most software programs seek to improve resolution as well as contrast. Quantitative image analyses require instrument calibration and with deconvolution, necessitate that this process itself preserves the relative quantitative relationships between fluorescence intensities. To ensure that the quantitative nature of the data remains unaltered, deconvolution algorithms need to be tested thoroughly. This study investigated whether the deconvolution algorithms in AutoQuant X3 preserve relative quantitative intensity data. InSpeck Green calibration microspheres were prepared for imaging, z-stacks were collected using a wide-field microscope, and the images were deconvolved using the iterative deconvolution algorithms with default settings. Afterwards, the mean intensities and volumes of microspheres in the original and the deconvolved images were measured. Deconvolved data sets showed higher average microsphere intensities and smaller volumes than the original wide-field data sets. In original and deconvolved data sets, intensity means showed linear relationships with the relative microsphere intensities given by the manufacturer. Importantly, upon normalization, the trend lines were found to have similar slopes. In original and deconvolved images, the volumes of the microspheres were quite uniform for all relative microsphere intensities. We were able to show that AutoQuant X3 deconvolution software data are quantitative. In general, the protocol presented can be used to calibrate any fluorescence microscope or image processing and analysis procedure. PMID:24688321

Wide-field absolute transverse blood flow velocity mapping in vessel centerline

NASA Astrophysics Data System (ADS)

Wu, Nanshou; Wang, Lei; Zhu, Bifeng; Guan, Caizhong; Wang, Mingyi; Han, Dingan; Tan, Haishu; Zeng, Yaguang

2018-02-01

We propose a wide-field absolute transverse blood flow velocity measurement method in vessel centerline based on absorption intensity fluctuation modulation effect. The difference between the light absorption capacities of red blood cells and background tissue under low-coherence illumination is utilized to realize the instantaneous and average wide-field optical angiography images. The absolute fuzzy connection algorithm is used for vessel centerline extraction from the average wide-field optical angiography. The absolute transverse velocity in the vessel centerline is then measured by a cross-correlation analysis according to instantaneous modulation depth signal. The proposed method promises to contribute to the treatment of diseases, such as those related to anemia or thrombosis.

Multicellular structures developing during maize microspore culture express endosperm and embryo-specific genes and show different embryogenic potentialities.

PubMed

Massonneau, Agnes; Coronado, Maria-José; Audran, Arthur; Bagniewska, Agnieszka; Mòl, Rafal; Testillano, Pilar S; Goralski, Grzegorz; Dumas, Christian; Risueño, Maria-Carmen; Matthys-Rochon, Elisabeth

2005-07-01

During maize pollen embryogenesis, a range of multicellular structures are formed. Using different approaches, the "nature" of these structures has been determined in terms of their embryogenic potential. In situ molecular identification techniques for gene transcripts and products, and a novel cell tracking system indicated the presence of embryogenic (embryo-like structures, ELS) and non-embryogenic (callus-like structures, CLS) structures that occurred for short periods within the cultures. Some multicellular structures with a compact appearance generated embryos. RT-PCR and fluorescence in situ hybridization (FISH) with confocal microscopy techniques using specific gene markers of the endosperm (ZmESR2, ZmAE3) and embryo (LTP2 and ZmOCL1, ZmOCL3) revealed "embryo" and "endosperm" potentialities in these various multicellular structures present in the cultures. The results presented here showed distinct and specific patterns of gene expression. Altogether, the results demonstrate the presence of different molecules on both embryonic and non-embryonic structures. Their possible roles are discussed in the context of a parallel between embryo/endosperm interactions in planta and embryonic and non-embryonic structure interrelations under in vitro conditions.

Wide baseline stereo matching based on double topological relationship consistency

NASA Astrophysics Data System (ADS)

Zou, Xiaohong; Liu, Bin; Song, Xiaoxue; Liu, Yang

2009-07-01

Stereo matching is one of the most important branches in computer vision. In this paper, an algorithm is proposed for wide-baseline stereo vision matching. Here, a novel scheme is presented called double topological relationship consistency (DCTR). The combination of double topological configuration includes the consistency of first topological relationship (CFTR) and the consistency of second topological relationship (CSTR). It not only sets up a more advanced model on matching, but discards mismatches by iteratively computing the fitness of the feature matches and overcomes many problems of traditional methods depending on the powerful invariance to changes in the scale, rotation or illumination across large view changes and even occlusions. Experimental examples are shown where the two cameras have been located in very different orientations. Also, epipolar geometry can be recovered using RANSAC by far the most widely method adopted possibly. By the method, we can obtain correspondences with high precision on wide baseline matching problems. Finally, the effectiveness and reliability of this method are demonstrated in wide-baseline experiments on the image pairs.

A Galaxy Zoo - WorldWide Telescope Mashup: Expanding User Defined Exploration

NASA Astrophysics Data System (ADS)

Luebbert, Jarod; Sands, M.; Fay, J.; Smith, A.; Gay, P. L.; Galaxy Zoo Team

2010-01-01

We present a new way of exploring your favorite Galaxy Zoo galaxies within the context of the sky using Microsoft Research's WorldWide Telescope. Galaxy Zoo has a fantastic community that is eager to learn and contribute to science through morphological classifications of galaxies. WorldWide Telescope is an interactive observatory that allows users to explore the sky. WorldWide Telescope uses images from the world's best telescopes, including the galaxies of the Sloan Digital Sky Survey. WorldWide Telescope provides a fantastic sense of size and distance that is hard to experience in Galaxy Zoo. Creating tours from favorite galaxies directly from Galaxy Zoo aims to solve this dilemma.The incorporation of Galaxy Zoo and WorldWide telescope provides a great resource for users to learn more about the galaxies they are classifying. Users can now explore the areas around certain galaxies and view information about that location from within WorldWide Telescope. Not only does this encourage self-motivated research but after tours are created they can be shared with anyone. We hope this will help spread citizen science to different audiences via email, Facebook, and Twitter.Without the WorldWide Telescope team at Microsoft Research this project would not have been possible. Please go start exploring at http://wwt.galaxyzoo.org. This project was funded through the Microsoft Research Academic Program.

Rapid genome-wide evolution in Brassica rapa populations following drought revealed by sequencing of ancestral and descendant gene pools.

PubMed

Franks, Steven J; Kane, Nolan C; O'Hara, Niamh B; Tittes, Silas; Rest, Joshua S

2016-08-01

There is increasing evidence that evolution can occur rapidly in response to selection. Recent advances in sequencing suggest the possibility of documenting genetic changes as they occur in populations, thus uncovering the genetic basis of evolution, particularly if samples are available from both before and after selection. Here, we had a unique opportunity to directly assess genetic changes in natural populations following an evolutionary response to a fluctuation in climate. We analysed genome-wide differences between ancestors and descendants of natural populations of Brassica rapa plants from two locations that rapidly evolved changes in multiple phenotypic traits, including flowering time, following a multiyear late-season drought in California. These ancestor-descendant comparisons revealed evolutionary shifts in allele frequencies in many genes. Some genes showing evolutionary shifts have functions related to drought stress and flowering time, consistent with an adaptive response to selection. Loci differentiated between ancestors and descendants (FST outliers) were generally different from those showing signatures of selection based on site frequency spectrum analysis (Tajima's D), indicating that the loci that evolved in response to the recent drought and those under historical selection were generally distinct. Very few genes showed similar evolutionary responses between two geographically distinct populations, suggesting independent genetic trajectories of evolution yielding parallel phenotypic changes. The results show that selection can result in rapid genome-wide evolutionary shifts in allele frequencies in natural populations, and highlight the usefulness of combining resurrection experiments in natural populations with genomics for studying the genetic basis of adaptive evolution. © 2016 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Obese subjects show sex-specific differences in right ventricular hypertrophy.

PubMed

Rider, Oliver J; Lewis, Andrew J M; Lewandowski, Adam J; Ntusi, Ntobeko; Nethononda, Richard; Petersen, Steffen E; Francis, Jane M; Pitcher, Alex; Banerjee, Rajarshi; Leeson, Paul; Neubauer, Stefan

2015-01-01

As right ventricular (RV) remodeling in obesity remains underinvestigated, and the impact of left ventricular (LV) diastolic dysfunction on RV hypertrophy is unknown, we aimed to investigate whether (1) sex-specific patterns of RV remodeling exist in obesity and (2) LV diastolic dysfunction in obesity is related to RV hypertrophy. Seven hundred thirty-nine subjects (women, n=345; men, n=394) without identifiable cardiovascular risk factors (body mass index [BMI], 15.3-59.2 kg/m2) underwent cardiovascular magnetic resonance (1.5 T) to measure RV mass (g), RV end-diastolic volume (mL), RV mass/volume ratio, and LV diastolic peak filling rate (mL/s). All subjects were normotensive (average, 119±11/73±8 mm Hg), normoglycaemic (4.8±0.5 mmol/L), and normocholesterolaemic (4.8±0.9 mmol/L) at the time of scanning. Across both sexes, there was a moderately strong positive correlation between BMI and RV mass (men, +0.8 g per BMI point increase; women, +1.0 g per BMI point increase; both P<0.001). Whereas women exhibited RV cavity dilatation (RV end-diastolic volume, +1.0 mL per BMI point increase; P<0.001), BMI was not correlated with RV end-diastolic volume in men (R=0.04; P=0.51). Concentric RV remodeling was present in both sexes, with RV mass/volume ratio being positively correlated to BMI (men, R=0.41; women, R=0.51; both P<0.001). Irrespective of sex, the LV peak filling rate was negatively correlated with both RV mass (men, R=-0.43; women, R=-0.44; both P<0.001) and RV mass/volume ratio (men, R=-0.37; women, R=-0.35; both P<0.001). A sex difference in RV remodeling exists in obesity. Whereas men exhibit concentric RV remodeling, women exhibit a mixed pattern of eccentric and concentric remodeling. Regardless of sex, reduced LV diastolic function is associated with concentric RV remodeling. © 2014 American Heart Association, Inc.

Upper wide-angle viewing system for ITER

DOE PAGES

Lasnier, C. J.; McLean, A. G.; Gattuso, A.; ...

2016-08-15

The Upper Wide Angle Viewing System (UWAVS) will be installed on five upper ports of ITER. Here, this paper shows major requirements, gives an overview of the preliminary design with reasons for some design choices, examines self-emitted IR light from UWAVS optics and its effect on accuracy, and shows calculations of signal-to-noise ratios for the two-color temperature output as a function of integration time and divertor temperature. Accurate temperature output requires correction for vacuum window absorption vs. wavelength and for self-emitted IR, which requires good measurement of the temperature of the optical components. The anticipated signal-to-noise ratio using presently availablemore » IR cameras is adequate for the required 500 Hz frame rate.« less

Wounding response in xylem of Scots pine seedlings shows wide genetic variation and connection with the constitutive defence of heartwood.

PubMed

Harju, Anni M; Venäläinen, Martti; Laakso, Tapio; Saranpää, Pekka

2009-01-01

In this greenhouse experiment, 3-year-old Scots pine (Pinus sylvestris L.) seedlings were wounded by drilling holes through the stem. In the xylem next to the wound, the concentration of resin acids (RAC) increased, and the production of extractives typical for heartwood (stilbenes) and knotwood (stilbenes and lignans) of mature trees was induced. The induced stilbenes were pinosylvin (PS) and pinosylvin monomethyl ether (PSM), and the lignans nortrachelogenin (NTG) and matairesinol (MR). There was positive phenotypic correlation between concentrations of the different extractives. Except for the RAC, the extractive concentrations showed no correlation with the size of the seedlings. The treated seedlings belonged to half-sib families, which enabled the estimation of the genetic parameters for the response variables. The proportion of heritable variation (heritability, h(2)) in the concentration of PS, NTG and MR varied between 0.71 and 1.03, whereas for PSM and RAC the heritability was lower (0.35 and 0.31). Genetic correlation was significant between PS and PSM (r = 0.55, P = 0.018), and between NTG and MR (r = 0.50, P = 0.033). Heritabilities were also estimated on the basis of the regression of the offspring on their mothers h(2)(0P). These estimates were assessed for the concentration of PS, PSM and RAC in the wound response area of the seedlings and correspondingly in the heartwood of their mothers. The heritability was highest for the concentration of PS h(2)(0P). The findings of this study support the suggestion that the wounding of Scots pine seedlings may facilitate the development of an early testing method for breeding heartwood durability.

Epigenetics and sex differences in the brain: A genome-wide comparison of histone-3 lysine-4 trimethylation (H3K4me3) in male and female mice.

PubMed

Shen, Erica Y; Ahern, Todd H; Cheung, Iris; Straubhaar, Juerg; Dincer, Aslihan; Houston, Isaac; de Vries, Geert J; Akbarian, Schahram; Forger, Nancy G

2015-06-01

Many neurological and psychiatric disorders exhibit gender disparities, and sex differences in the brain likely explain some of these effects. Recent work in rodents points to a role for epigenetics in the development or maintenance of neural sex differences, although genome-wide studies have so far been lacking. Here we review the existing literature on epigenetics and brain sexual differentiation and present preliminary analyses on the genome-wide distribution of histone-3 lysine-4 trimethylation in a sexually dimorphic brain region in male and female mice. H3K4me3 is a histone mark primarily organized as 'peaks' surrounding the transcription start site of active genes. We microdissected the bed nucleus of the stria terminalis and preoptic area (BNST/POA) in adult male and female mice and used ChIP-Seq to compare the distribution of H3K4me3 throughout the genome. We found 248 genes and loci with a significant sex difference in H3K4me3. Of these, the majority (71%) had larger H3K4me3 peaks in females. Comparisons with existing databases indicate that genes and loci with increased H3K4me3 in females are associated with synaptic function and with expression atlases from related brain areas. Based on RT-PCR, only a minority of genes with a sex difference in H3K4me3 has detectable sex differences in expression at baseline conditions. Together with previous findings, our data suggest that there may be sex biases in the use of epigenetic marks. Such biases could underlie sex differences in vulnerabilities to drugs or diseases that disrupt specific epigenetic processes. Copyright © 2014 Elsevier Inc. All rights reserved.

Epigenetics and Sex Differences in the Brain: A Genome-Wide Comparison of Histone-3 Lysine-4 Trimethylation (H3K4me3) in Male and Female Mice

PubMed Central

Shen, Erica Y.; Ahern, Todd H.; Cheung, Iris; Straubhaar, Juerg; Dincer, Aslihan; Houston, Isaac; de Vries, Geert J.; Akbarian, Schahram; Forger, Nancy G.

2014-01-01

Many neurological and psychiatric disorders exhibit gender disparities, and sex differences in the brain likely explain some of these effects. Recent work in rodents points to a role for epigenetics in the development or maintenance of neural sex differences, although genome-wide studies have so far been lacking. Here we review the existing literature on epigenetics and brain sexual differentiation and present preliminary analyses on the genome-wide distribution of histone-3 lysine-4 trimethylation in a sexually dimorphic brain region in male and female mice. H3K4me3 is a histone mark primarily organized as ‘peaks’ surrounding the transcription start site of active genes. We microdissected the bed nucleus of the stria terminalis and preoptic area (BNST/POA) in adult male and female mice and used ChIP-Seq to compare the distribution of H3K4me3 throughout the genome. We found 248 genes and loci with a significant sex difference in H3K4me3. Of these, the majority (71%) had larger H3K4me3 peaks in females. Comparisons with existing databases indicate that genes and loci with increased H3K4me3 in females are associated with synaptic function and with expression atlases from related brain areas. Based on RT-PCR, only a minority of genes with a sex difference in H3K4me3 has detectable sex differences in expression at baseline conditions. Together with previous findings, our data suggest there may be sex biases in the use of epigenetic marks. Such biases could underlie sex differences in vulnerabilities to drugs or diseases that disrupt specific epigenetic processes. PMID:25131640

Genome-wide SNP scan in a porcine Large White×Minzhu intercross population reveals a locus influencing muscle mass on chromosome 2.

PubMed

Liu, Xin; Wang, Li Gang; Luo, Wei Zhen; Li, Yong; Liang, Jing; Yan, Hua; Zhao, Ke Bin; Wang, Li Xian; Zhang, Long Chao

2014-12-01

A high-density single nucleotide polymorphism (SNP) array containing 62 163 markers was employed for a genome-wide association study (GWAS) to identify variants associated with lean meat in ham (LMH, %) and lean meat percentage (LMP, %) within a porcine Large White×Minzhu intercross population. For each individual, LMH and LMP were measured after slaughter at the age of 240±7 days. A total of 557 F2 animals were genotyped. The GWAS revealed that 21 SNPs showed significant genome-wide or chromosome-wide associations with LMH and LMP by the Genome-wide Rapid Association using Mixed Model and Regression-Genomic Control approach. Nineteen significant genome-wide SNPs were mapped to the distal end of Sus Scrofa Chromosome (SSC) 2, where a major known gene responsible for muscle mass, IGF2 is located. A conditioned analysis, in which the genotype of the strongest associated SNP is included as a fixed effect in the model, showed that those significant SNPs on SSC2 were derived from a single quantitative trait locus. The two chromosome-wide association SNPs on SSC1 disappeared after conditioned analysis suggested the association signal is a false association derived from using a F2 population. The present result is expected to lead to novel insights into muscle mass in different pig breeds and lays a preliminary foundation for follow-up studies for identification of causal mutations for subsequent application in marker-assisted selection programs for improving muscle mass in pigs. © 2014 Japanese Society of Animal Science.

Genome-wide expression profiling in pediatric septic shock

PubMed Central

Wong, Hector R.

2013-01-01

For nearly a decade, our research group has had the privilege of developing and mining a multi-center, microarray-based, genome-wide expression database of critically ill children (≤ 10 years of age) with septic shock. Using bioinformatic and systems biology approaches, the expression data generated through this discovery-oriented, exploratory approach have been leveraged for a variety of objectives, which will be reviewed. Fundamental observations include wide spread repression of gene programs corresponding to the adaptive immune system, and biologically significant differential patterns of gene expression across developmental age groups. The data have also identified gene expression-based subclasses of pediatric septic shock having clinically relevant phenotypic differences. The data have also been leveraged for the discovery of novel therapeutic targets, and for the discovery and development of novel stratification and diagnostic biomarkers. Almost a decade of genome-wide expression profiling in pediatric septic shock is now demonstrating tangible results. The studies have progressed from an initial discovery-oriented and exploratory phase, to a new phase where the data are being translated and applied to address several areas of clinical need. PMID:23329198

Stability Mechanisms of Laccase Isoforms using a Modified FoldX Protocol Applicable to Widely Different Proteins.

PubMed

Christensen, Niels J; Kepp, Kasper P

2013-07-09

A recent computational protocol that accurately predicts and rationalizes protein multisite mutant stabilities has been extended to handle widely different isoforms of laccases. We apply the protocol to four isoenzymes of Trametes versicolor laccase (TvL) with variable lengths (498-503 residues) and thermostability (Topt ∼ 45-80 °C) and with 67-77% sequence identity. The extended protocol uses (i) statistical averaging, (ii) a molecular-dynamics-validated "compromise" homology model to minimize bias that causes proteins close in sequence to a structural template to be too stable due to having the benefits of the better sampled template (typically from a crystal structure), (iii) correction for hysteresis that favors the input template to overdestabilize, and (iv) a preparative protocol to provide robust input sequences of equal length. The computed ΔΔG values are in good agreement with the major trends in experimental stabilities; that is, the approach may be applicable for fast estimates of the relative stabilities of proteins with as little as 70% identity, something that is currently extremely challenging. The computed stability changes associated with variations are Gaussian-distributed, in good agreement with experimental distributions of stability effects from mutation. The residues causing the differential stability of the four isoforms are consistent with a range of compiled laccase wild type data, suggesting that we may have identified general drivers of laccase stability. Several sites near Cu, notably 79, 241, and 245, or near substrate, mainly 265, are identified that contribute to stability-function trade-offs, of relevance to the search for new proficient and stable variants of these important industrial enzymes.

In-house access to PACS images and related data through World Wide Web

NASA Astrophysics Data System (ADS)

Mascarini, Christian; Ratib, Osman M.; Trayser, Gerhard; Ligier, Yves; Appel, R. D.

1996-05-01

The development of a hospital wide PACS is in progress at the University Hospital of Geneva and several archive modules are operational since 1992. This PACS is intended for wide distribution of images to clinical wards. As the PACS project and the number of archived images grow rapidly in the hospital, it was necessary to provide an easy, more widely accessible and convenient access to the PACS database for the clinicians in the different wards and clinical units of the hospital. An innovative solution has been developed using tools such as Netscape navigator and NCSA World Wide Web server as an alternative to conventional database query and retrieval software. These tools present the advantages of providing an user interface which is the same independently of the platform being used (Mac, Windows, UNIX, ...), and an easy integration of different types of documents (text, images, ...). A strict access control has been added to this interface. It allows user identification and access rights checking, as defined by the in-house hospital information system, before allowing the navigation through patient data records.

Printed wide-slot antenna design with bandwidth and gain enhancement on low-cost substrate.

PubMed

Samsuzzaman, M; Islam, M T; Mandeep, J S; Misran, N

2014-01-01

This paper presents a printed wide-slot antenna design and prototyping on available low-cost polymer resin composite material fed by a microstrip line with a rotated square slot for bandwidth enhancement and defected ground structure for gain enhancement. An I-shaped microstrip line is used to excite the square slot. The rotated square slot is embedded in the middle of the ground plane, and its diagonal points are implanted in the middle of the strip line and ground plane. To increase the gain, four L-shaped slots are etched in the ground plane. The measured results show that the proposed structure retains a wide impedance bandwidth of 88.07%, which is 20% better than the reference antenna. The average gain is also increased, which is about 4.17 dBi with a stable radiation pattern in the entire operating band. Moreover, radiation efficiency, input impedance, current distribution, axial ratio, and parametric studies of S11 for different design parameters are also investigated using the finite element method-based simulation software HFSS.

Printed Wide-Slot Antenna Design with Bandwidth and Gain Enhancement on Low-Cost Substrate

PubMed Central

Samsuzzaman, M.; Islam, M. T.; Mandeep, J. S.; Misran, N.

2014-01-01

This paper presents a printed wide-slot antenna design and prototyping on available low-cost polymer resin composite material fed by a microstrip line with a rotated square slot for bandwidth enhancement and defected ground structure for gain enhancement. An I-shaped microstrip line is used to excite the square slot. The rotated square slot is embedded in the middle of the ground plane, and its diagonal points are implanted in the middle of the strip line and ground plane. To increase the gain, four L-shaped slots are etched in the ground plane. The measured results show that the proposed structure retains a wide impedance bandwidth of 88.07%, which is 20% better than the reference antenna. The average gain is also increased, which is about 4.17 dBi with a stable radiation pattern in the entire operating band. Moreover, radiation efficiency, input impedance, current distribution, axial ratio, and parametric studies of S11 for different design parameters are also investigated using the finite element method-based simulation software HFSS. PMID:24696661

Admiration and adoration: their different ways of showing and shaping who we are.

PubMed

Schindler, Ines; Zink, Veronika; Windrich, Johannes; Menninghaus, Winfried

2013-01-01

Admiration and adoration have been considered as emotions with the power to change people, yet our knowledge of the specific nature and function of these emotions is quite limited. From an interdisciplinary perspective, we present a prototype approach to admiration and what has variously been labelled adoration, worship, or reverence. Both admiration and adoration contribute to the formation of personal and collective ideals, values, and identities, but their workings differ. We offer a detailed theoretical account of commonalities and differences in the appraisal patterns and action tendencies associated with the two emotions. This analysis reveals that admiration motivates the internalisation and emulation of ideals embodied by an outstanding role model. Adoration motivates adherence to the teachings and expectations of a meaning maker and benefactor perceived as superhuman or sacred. Thus, the primary function of admiration is to promote individual learning and change, whereas adoration primarily serves to bind communities together.

Cell Context Dependent p53 Genome-Wide Binding Patterns and Enrichment at Repeats

DOE PAGES

Botcheva, Krassimira; McCorkle, Sean R.

2014-11-21

The p53 ability to elicit stress specific and cell type specific responses is well recognized, but how that specificity is established remains to be defined. Whether upon activation p53 binds to its genomic targets in a cell type and stress type dependent manner is still an open question. Here we show that the p53 binding to the human genome is selective and cell context-dependent. We mapped the genomic binding sites for the endogenous wild type p53 protein in the human cancer cell line HCT116 and compared them to those we previously determined in the normal cell line IMR90. We reportmore » distinct p53 genome-wide binding landscapes in two different cell lines, analyzed under the same treatment and experimental conditions, using the same ChIP-seq approach. This is evidence for cell context dependent p53 genomic binding. The observed differences affect the p53 binding sites distribution with respect to major genomic and epigenomic elements (promoter regions, CpG islands and repeats). We correlated the high-confidence p53 ChIP-seq peaks positions with the annotated human repeats (UCSC Human Genome Browser) and observed both common and cell line specific trends. In HCT116, the p53 binding was specifically enriched at LINE repeats, compared to IMR90 cells. The p53 genome-wide binding patterns in HCT116 and IMR90 likely reflect the different epigenetic landscapes in these two cell lines, resulting from cancer-associated changes (accumulated in HCT116) superimposed on tissue specific differences (HCT116 has epithelial, while IMR90 has mesenchymal origin). In conclusion, our data support the model for p53 binding to the human genome in a highly selective manner, mobilizing distinct sets of genes, contributing to distinct pathways.« less

Development and testing of a European Union-wide farm-level carbon calculator.

PubMed

Tuomisto, Hanna L; De Camillis, Camillo; Leip, Adrian; Nisini, Luigi; Pelletier, Nathan; Haastrup, Palle

2015-07-01

Direct greenhouse gas (GHG) emissions from agriculture accounted for approximately 10% of total European Union (EU) emissions in 2010. To reduce farming-related GHG emissions, appropriate policy measures and supporting tools for promoting low-C farming practices may be efficacious. This article presents the methodology and testing results of a new EU-wide, farm-level C footprint calculator. The Carbon Calculator quantifies GHG emissions based on international standards and technical specifications on Life Cycle Assessment (LCA) and C footprinting. The tool delivers its results both at the farm level and as allocated to up to 5 main products of the farm. In addition to the quantification of GHG emissions, the calculator proposes mitigation options and sequestration actions that may be suitable for individual farms. The results obtained during a survey made on 54 farms from 8 EU Member States are presented. These farms were selected in view of representing the diversity of farm types across different environmental zones in the EU. The results of the C footprint of products in the data set show wide range of variation between minimum and maximum values. The results of the mitigation actions showed that the tool can help identify practices that can lead to substantial emission reductions. To avoid burden-shifting from climate change to other environmental issues, the future improvements of the tool should include incorporation of other environmental impact categories in place of solely focusing on GHG emissions. © 2015 The Authors. Integrated Environmental Assessment and Management Published by Wiley Periodicals, Inc. on behalf of SETAC.

Metagenome-Wide Association Study and Machine Learning Prediction of Bulk Soil Microbiome and Crop Productivity

PubMed Central

Chang, Hao-Xun; Haudenshield, James S.; Bowen, Charles R.; Hartman, Glen L.

2017-01-01

Areas within an agricultural field in the same season often differ in crop productivity despite having the same cropping history, crop genotype, and management practices. One hypothesis is that abiotic or biotic factors in the soils differ between areas resulting in these productivity differences. In this study, bulk soil samples collected from a high and a low productivity area from within six agronomic fields in Illinois were quantified for abiotic and biotic characteristics. Extracted DNA from these bulk soil samples were shotgun sequenced. While logistic regression analyses resulted in no significant association between crop productivity and the 26 soil characteristics, principal coordinate analysis and constrained correspondence analysis showed crop productivity explained a major proportion of the taxa variance in the bulk soil microbiome. Metagenome-wide association studies (MWAS) identified more Bradyrhizodium and Gammaproteobacteria in higher productivity areas and more Actinobacteria, Ascomycota, Planctomycetales, and Streptophyta in lower productivity areas. Machine learning using a random forest method successfully predicted productivity based on the microbiome composition with the best accuracy of 0.79 at the order level. Our study showed that crop productivity differences were associated with bulk soil microbiome composition and highlighted several nitrogen utility-related taxa. We demonstrated the merit of MWAS and machine learning for the first time in a plant-microbiome study. PMID:28421041

Body stability and muscle and motor cortex activity during walking with wide stance

PubMed Central

Farrell, Brad J.; Bulgakova, Margarita A.; Beloozerova, Irina N.; Sirota, Mikhail G.

2014-01-01

Biomechanical and neural mechanisms of balance control during walking are still poorly understood. In this study, we examined the body dynamic stability, activity of limb muscles, and activity of motor cortex neurons [primarily pyramidal tract neurons (PTNs)] in the cat during unconstrained walking and walking with a wide base of support (wide-stance walking). By recording three-dimensional full-body kinematics we found for the first time that during unconstrained walking the cat is dynamically unstable in the forward direction during stride phases when only two diagonal limbs support the body. In contrast to standing, an increased lateral between-paw distance during walking dramatically decreased the cat's body dynamic stability in double-support phases and prompted the cat to spend more time in three-legged support phases. Muscles contributing to abduction-adduction actions had higher activity during stance, while flexor muscles had higher activity during swing of wide-stance walking. The overwhelming majority of neurons in layer V of the motor cortex, 82% and 83% in the forelimb and hindlimb representation areas, respectively, were active differently during wide-stance walking compared with unconstrained condition, most often by having a different depth of stride-related frequency modulation along with a different mean discharge rate and/or preferred activity phase. Upon transition from unconstrained to wide-stance walking, proximal limb-related neuronal groups subtly but statistically significantly shifted their activity toward the swing phase, the stride phase where most of body instability occurs during this task. The data suggest that the motor cortex participates in maintenance of body dynamic stability during locomotion. PMID:24790167

A wide-angle high Mach number modal expansion for infrasound propagation.

PubMed

Assink, Jelle; Waxler, Roger; Velea, Doru

2017-03-01

The use of modal expansions to solve the problem of atmospheric infrasound propagation is revisited. A different form of the associated modal equation is introduced, valid for wide-angle propagation in atmospheres with high Mach number flow. The modal equation can be formulated as a quadratic eigenvalue problem for which there are simple and efficient numerical implementations. A perturbation expansion for the treatment of attenuation, valid for stratified media with background flow, is derived as well. Comparisons are carried out between the proposed algorithm and a modal algorithm assuming an effective sound speed, including a real data case study. The comparisons show that the effective sound speed approximation overestimates the effect of horizontal wind on sound propagation, leading to errors in traveltime, propagation path, trace velocity, and absorption. The error is found to be dependent on propagation angle and Mach number.

One-step multiplex RT-qPCR detects three citrus viroids from different genera in a wide range of hosts.

PubMed

Osman, Fatima; Dang, Tyler; Bodaghi, Sohrab; Vidalakis, Georgios

2017-07-01

A one-step multiplex reverse transcription real-time quantitative polymerase chain reaction (RT-qPCR) based on species-specific minor groove binding (MGB) probes, was developed for the simultaneous detection, identification, and quantification of three citrus viroids belonging to different genera. Citrus exocortis viroid (Pospiviroid), Hop stunt viroid (Hostuviroid), and Citrus bark cracking viroid (Cocadviroid) cause a variety of maladies in agriculturally significant crops. Therefore, reliable assays for their detection are essential tools for various government and industry organizations implementing disease management programs. Singleplex qPCR primers and MGB probes were designed individually for the detection of the three targeted viroids, and subsequently combined in a one-step multiplex RT-qPCR reaction. A wide host range of woody plants, including citrus, grapevines, apricots, plums and herbaceous plants such as tomato, cucumber, eggplant and chrysanthemum different world regions were used to validate the assay. Single, double and triple viroid infections were identified in the tested samples. The developed multiplex RT-qPCR assay was compared with a previously reported SYBR Green I RT-qPCR for the universal detection of citrus viroids. Both assays accurately identified all citrus viroid infected samples. The multiplex assay complemented the SYBR Green I universal detection assay by differentiating among citrus viroid species in the positive samples. The developed multiplex RT-qPCR assay has the potential to simultaneously detect each targeted viroid and could be used in high throughput screenings for citrus viroids in field surveys, germplasm banks, nurseries and other viroid disease management programs. Copyright © 2017. Published by Elsevier B.V.

Design on the wide band absorber with low density based on the particle distribution

NASA Astrophysics Data System (ADS)

Zheng, Dianliang; Liu, Ting; Liu, Longbin; Xu, Yonggang

2018-04-01

In order to widen the absorbing band, an equivalent gradient structure absorber was designed based on the particle distribution. Firstly, the electromagnetic parameter of the absorbent with uniform dispersion was tested using the vector network analyzer in 8-18 GHz. Three different equivalent materials of the spherical, square and hexagon empty shape were designed. The scattering parameters and the monostatic reflection loss (RL) of the periodic structural materials were simulated in the commercial software. Then the effective permittivity and the permeability was derived by the Nicolson-Ross-Weir algorithm and fitted by Maxwell-Garnett mixing rule. The results showed that the simulated reflectance and transmission parameters of equivalent composites with the different shapes were very close. The derived effective permittivity and permeability of the composite with different absorbent content was also close, and the average deviation was about 0.52 + j0.15 and 0.15 + j0.01 respectively. Finally, the wide band absorbing material was designed using the genetic algorithm. The optimized RL result showed that the absorbing composites with thickness 3 mm had an excellent absorbing property (RL <-10 dB) in 8-18 GHz, the equivalent absorber density could be decreased 30.7% compared with the uniform structure.

Wide spectral band beam analysis

NASA Astrophysics Data System (ADS)

Aharon, Oren

2015-03-01

The reality in laser beam profiling is that measurements are performed over a wide spectrum of wavelengths and power ranges. Many applications use multiple laser wavelengths with very different power levels, a fact which dictates a need for a better measuring tool. Rapid progress in the fiber laser area has increased the demand for lasers in the wavelength range of 900 - 1030 nm, while the telecommunication market has increased the demand for wavelength range of 1300nm - 1600 nm, on the other hand the silicone chip manufacturing and mass production requirements tend to lower the laser wavelength towards the 190nm region. In many cases there is a need to combine several lasers together in order to perform a specific task. A typical application is to combine one visible laser for pointing, with a different laser for material processing with a very different wavelength and power level. The visible laser enables accurate pointing before the second laser is operated. The beam profile of the intensity distribution is an important parameter that indicates how a laser beam will behave in an application. Currently a lab, where many different lasers are used, will find itself using various laser beam profilers from several vendors with different specifications and accuracies. It is the propose of this article to present a technological breakthrough in the area of detectors, electronics and optics allowing intricate measurements of lasers with different wavelength and with power levels that vary many orders of magnitude by a single beam profiler.

Integrated data analysis for genome-wide research.

PubMed

Steinfath, Matthias; Repsilber, Dirk; Scholz, Matthias; Walther, Dirk; Selbig, Joachim

2007-01-01

Integrated data analysis is introduced as the intermediate level of a systems biology approach to analyse different 'omics' datasets, i.e., genome-wide measurements of transcripts, protein levels or protein-protein interactions, and metabolite levels aiming at generating a coherent understanding of biological function. In this chapter we focus on different methods of correlation analyses ranging from simple pairwise correlation to kernel canonical correlation which were recently applied in molecular biology. Several examples are presented to illustrate their application. The input data for this analysis frequently originate from different experimental platforms. Therefore, preprocessing steps such as data normalisation and missing value estimation are inherent to this approach. The corresponding procedures, potential pitfalls and biases, and available software solutions are reviewed. The multiplicity of observations obtained in omics-profiling experiments necessitates the application of multiple testing correction techniques.

Transcriptome analysis of the Bombyx mori fat body after constant high temperature treatment shows differences between the sexes.

PubMed

Wang, Hua; Fang, Yan; Wang, Lipeng; Zhu, Wenjuan; Ji, Haipeng; Wang, Haiying; Xu, Shiqing; Sima, Yanghu

2014-09-01

Ambient temperature plays a large role in insect growth, development and even their distribution. The elucidation of the associated molecular mechanism that underlies the effect of constant high temperature will enables us to further understand the stress responses. We constructed four digital gene expression libraries from the fat body of female and male Bombyx mori. Differential gene expression was analyzed after constant high temperature treatment. The results showed that there were significant changes to the gene expression in the fat body after heat treatment, especially in binding, catalytic, cellular and metabolic processes. Constant high temperature may induce more traditional cryoprotectants, such as glycerol, glycogen, sorbitol and lipids, to protect cells from damage, and induce heat oxidative stress in conjunction with the heat shock proteins. The data also indicated a difference between males and females. The heat shock protein-related genes were up-regulated in both sexes but the expression of Hsp25.4 and DnaJ5 were down-regulated in the male fat body of B. mori. This is the first report of such a result. Constant high temperature also affected the expression of other functional genes and differences were observed between male and female fat bodies in the expression of RPS2, RPL37A and MREL. These findings provide abundant data on the effect of high temperature on insects at the molecular level. The data will also be beneficial to the study of differences between the sexes, manifested in variations in gene expression under high temperature.

A robust clustering algorithm for identifying problematic samples in genome-wide association studies.

PubMed

Bellenguez, Céline; Strange, Amy; Freeman, Colin; Donnelly, Peter; Spencer, Chris C A

2012-01-01

High-throughput genotyping arrays provide an efficient way to survey single nucleotide polymorphisms (SNPs) across the genome in large numbers of individuals. Downstream analysis of the data, for example in genome-wide association studies (GWAS), often involves statistical models of genotype frequencies across individuals. The complexities of the sample collection process and the potential for errors in the experimental assay can lead to biases and artefacts in an individual's inferred genotypes. Rather than attempting to model these complications, it has become a standard practice to remove individuals whose genome-wide data differ from the sample at large. Here we describe a simple, but robust, statistical algorithm to identify samples with atypical summaries of genome-wide variation. Its use as a semi-automated quality control tool is demonstrated using several summary statistics, selected to identify different potential problems, and it is applied to two different genotyping platforms and sample collections. The algorithm is written in R and is freely available at www.well.ox.ac.uk/chris-spencer chris.spencer@well.ox.ac.uk Supplementary data are available at Bioinformatics online.

Genome-Wide Detection and Analysis of Multifunctional Genes

PubMed Central

Pritykin, Yuri; Ghersi, Dario; Singh, Mona

2015-01-01

Many genes can play a role in multiple biological processes or molecular functions. Identifying multifunctional genes at the genome-wide level and studying their properties can shed light upon the complexity of molecular events that underpin cellular functioning, thereby leading to a better understanding of the functional landscape of the cell. However, to date, genome-wide analysis of multifunctional genes (and the proteins they encode) has been limited. Here we introduce a computational approach that uses known functional annotations to extract genes playing a role in at least two distinct biological processes. We leverage functional genomics data sets for three organisms—H. sapiens, D. melanogaster, and S. cerevisiae—and show that, as compared to other annotated genes, genes involved in multiple biological processes possess distinct physicochemical properties, are more broadly expressed, tend to be more central in protein interaction networks, tend to be more evolutionarily conserved, and are more likely to be essential. We also find that multifunctional genes are significantly more likely to be involved in human disorders. These same features also hold when multifunctionality is defined with respect to molecular functions instead of biological processes. Our analysis uncovers key features about multifunctional genes, and is a step towards a better genome-wide understanding of gene multifunctionality. PMID:26436655

COLLISIONAL EVOLUTION OF ULTRA-WIDE TRANS-NEPTUNIAN BINARIES

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

Parker, Alex H.; Kavelaars, J. J., E-mail: alexhp@uvic.ca

2012-01-10

The widely separated, near-equal mass binaries hosted by the cold classical Kuiper Belt are delicately bound and subject to disruption by many perturbing processes. We use analytical arguments and numerical simulations to determine their collisional lifetimes given various impactor size distributions and include the effects of mass loss and multiple impacts over the lifetime of each system. These collisional lifetimes constrain the population of small (R {approx}> 1 km) objects currently residing in the Kuiper Belt and confirm that the size distribution slope at small size cannot be excessively steep-likely q {approx}< 3.5. We track mutual semimajor axis, inclination, andmore » eccentricity evolution through our simulations and show that it is unlikely that the wide binary population represents an evolved tail of the primordially tight binary population. We find that if the wide binaries are a collisionally eroded population, their primordial mutual orbit planes must have preferred to lie in the plane of the solar system. Finally, we find that current limits on the size distribution at small radii remain high enough that the prospect of detecting dust-producing collisions in real time in the Kuiper Belt with future optical surveys is feasible.« less

Body-wide anatomy recognition in PET/CT images

NASA Astrophysics Data System (ADS)

Wang, Huiqian; Udupa, Jayaram K.; Odhner, Dewey; Tong, Yubing; Zhao, Liming; Torigian, Drew A.

2015-03-01

With the rapid growth of positron emission tomography/computed tomography (PET/CT)-based medical applications, body-wide anatomy recognition on whole-body PET/CT images becomes crucial for quantifying body-wide disease burden. This, however, is a challenging problem and seldom studied due to unclear anatomy reference frame and low spatial resolution of PET images as well as low contrast and spatial resolution of the associated low-dose CT images. We previously developed an automatic anatomy recognition (AAR) system [15] whose applicability was demonstrated on diagnostic computed tomography (CT) and magnetic resonance (MR) images in different body regions on 35 objects. The aim of the present work is to investigate strategies for adapting the previous AAR system to low-dose CT and PET images toward automated body-wide disease quantification. Our adaptation of the previous AAR methodology to PET/CT images in this paper focuses on 16 objects in three body regions - thorax, abdomen, and pelvis - and consists of the following steps: collecting whole-body PET/CT images from existing patient image databases, delineating all objects in these images, modifying the previous hierarchical models built from diagnostic CT images to account for differences in appearance in low-dose CT and PET images, automatically locating objects in these images following object hierarchy, and evaluating performance. Our preliminary evaluations indicate that the performance of the AAR approach on low-dose CT images achieves object localization accuracy within about 2 voxels, which is comparable to the accuracies achieved on diagnostic contrast-enhanced CT images. Object recognition on low-dose CT images from PET/CT examinations without requiring diagnostic contrast-enhanced CT seems feasible.

VLA's Sharpened Vision Shows Details of Still-Forming Star

NASA Astrophysics Data System (ADS)

2001-01-01

." Made famous in movies, commercials, magazine articles and numerous published photos, the VLA has been one of the world's most versatile and productive astronomical observatories since its dedication in 1980. VLA image and model of system The VLBA is a continent-wide system of 10 radio telescopes distributed across the continental United States, Hawaii and St. Croix in the U.S. Virgin Islands. Dedicated in 1993, the VLBA has made important contributions to the understanding of stars in the Milky Way, the workings of distant galaxies, and to calibrating the distance scale of the universe. Both the VLA and the VLBA use multiple radio-telescope antennas to produce greater resolving power than is possible with an individual antenna. Because of the different sizes of these two arrays of antennas, they produce images showing different levels of detail. NRAO scientists and engineers have developed plans to combine the VLA with the VLBA antennas closest to it, in New Mexico, Texas and Arizona, along with a number of new antennas, to fill in a gap in resolving power that exists between the VLA and VLBA. If this plan is funded, the closer VLBA antennas and the new antennas will be connected to the VLA by fiber-optic links to produce the Expanded VLA (EVLA). "The successful linking of the Pie Town VLBA antenna to the VLA shows that we can connect these radio-telescope antennas with fiber-optic cable over long distances and make them work as a single instrument," said Claussen, who worked extensively on the project. "This has produced a valuable new capability for astronomers to use now -- as shown by our study of this young stellar system -- but it also proves that our concept for expanding the VLA is technically sound," he added. The National Radio Astronomy Observatory is a facility of the National Science Foundation, operated under cooperative agreement by Associated Universities, Inc.

Wide band design on the scaled absorbing material filled with flaky CIPs

NASA Astrophysics Data System (ADS)

Xu, Yonggang; Yuan, Liming; Gao, Wei; Wang, Xiaobing; Liang, Zichang; Liao, Yi

2018-02-01

The scaled target measurement is an important method to get the target characteristic. Radar absorbing materials are widely used in the low detectable target, considering the absorbing material frequency dispersion characteristics, it makes designing and manufacturing scaled radar absorbing materials on the scaled target very difficult. This paper proposed a wide band design method on the scaled absorbing material of the thin absorption coating with added carbonyl iron particles. According to the theoretical radar cross section (RCS) of the plate, the reflection loss determined by the permittivity and permeability was chosen as the main design factor. Then, the parameters of the scaled absorbing materials were designed using the effective medium theory, and the scaled absorbing material was constructed. Finally, the full-size coating plate and scaled coating plates (under three different scale factors) were simulated; the RCSs of the coating plates were numerically calculated and measured at 4 GHz and a scale factor of 2. The results showed that the compensated RCS of the scaled coating plate was close to that of the full-size coating plate, that is, the mean deviation was less than 0.5 dB, and the design method for the scaled material was very effective.

Continuity-based model interfacing for plant-wide simulation: a general approach.

PubMed

Volcke, Eveline I P; van Loosdrecht, Mark C M; Vanrolleghem, Peter A

2006-08-01

In plant-wide simulation studies of wastewater treatment facilities, often existing models from different origin need to be coupled. However, as these submodels are likely to contain different state variables, their coupling is not straightforward. The continuity-based interfacing method (CBIM) provides a general framework to construct model interfaces for models of wastewater systems, taking into account conservation principles. In this contribution, the CBIM approach is applied to study the effect of sludge digestion reject water treatment with a SHARON-Anammox process on a plant-wide scale. Separate models were available for the SHARON process and for the Anammox process. The Benchmark simulation model no. 2 (BSM2) is used to simulate the behaviour of the complete WWTP including sludge digestion. The CBIM approach is followed to develop three different model interfaces. At the same time, the generally applicable CBIM approach was further refined and particular issues when coupling models in which pH is considered as a state variable, are pointed out.

Measurements of 42 Wide CPM Pairs with a CCD

NASA Astrophysics Data System (ADS)

Harshaw, Richard

2015-11-01

This paper addresses the use of a Skyris 618C color CCD camera as a means of obtaining data for analysis in the measurement of wide common proper motion stars. The equipment setup is described and data collection procedure outlined. Results of the measures of 42 CPM stars are presented, showing the Skyris is a reliable device for the measurement of double stars.

Automated MeSH indexing of the World-Wide Web.

PubMed Central

Fowler, J.; Kouramajian, V.; Maram, S.; Devadhar, V.

1995-01-01

To facilitate networked discovery and information retrieval in the biomedical domain, we have designed a system for automatic assignment of Medical Subject Headings to documents retrieved from the World-Wide Web. Our prototype implementations show significant promise. We describe our methods and discuss the further development of a completely automated indexing tool called the "Web-MeSH Medibot." PMID:8563421

Modal Analysis of β -Ga2O3:Cr Widely Tunable Luminescent Optical Microcavities

NASA Astrophysics Data System (ADS)

Alonso-Orts, M.; Nogales, E.; San Juan, J. M.; Nó, M. L.; Piqueras, J.; Méndez, B.

2018-06-01

Optical microcavities are key elements in many photonic devices, and those based on distributed Bragg reflectors (DBRs) enhance dramatically the end reflectivity, allowing for higher quality factors and finesse values. Besides, they allow for wide wavelength tunability, needed for nano- and microscale light sources to be used as photonic building blocks in the micro- and nanoscale. Understanding the complete behavior of light within the cavity is essential to obtaining an optimized design of properties and optical tunability. In this work, focused ion-beam fabrication of high refractive-index contrast DBR-based optical cavities within Ga2O3:Cr microwires grown and doped by the vapor-solid mechanism is reported. Room-temperature microphotoluminescence spectra show strong modulations from about 650 nm up to beyond 800 nm due to the microcavity resonance modes. Selectivity of the peak wavelength is achieved for two different cavities, demonstrating the tunability of this kind of optical system. Analysis of the confined modes is carried out by an analytical approximation and by finite-difference-time-domain simulations. A good agreement is obtained between the reflectivity values of the DBRs calculated from the experimental resonance spectra, and those obtained by finite-difference-time-domain simulations. Experimental reflectivities up to 70% are observed in the studied wavelength range and cavities, and simulations demonstrate that reflectivities up to about 90% could be reached. Therefore, Ga2O3:Cr high-reflectivity optical microcavities are shown as good candidates for single-material-based, widely tunable light emitters for micro- and nanodevices.

A Theoretical Approach to Norm Ecosystems: Two Adaptive Architectures of Indirect Reciprocity Show Different Paths to the Evolution of Cooperation

NASA Astrophysics Data System (ADS)

Uchida, Satoshi; Yamamoto, Hitoshi; Okada, Isamu; Sasaki, Tatsuya

2018-02-01

Indirect reciprocity is one of the basic mechanisms to sustain mutual cooperation, by which beneficial acts are returned, not by the recipient, but by third parties. This mechanism relies on the ability of individuals to know the past actions of others, and to assess those actions. There are many different systems of assessing others, which can be interpreted as rudimentary social norms (i.e., views on what is “good” or “bad”). In this paper, impacts of different adaptive architectures, i.e., ways for individuals to adapt to environments, on indirect reciprocity are investigated. We examine two representative architectures: one based on replicator dynamics and the other on genetic algorithm. Different from the replicator dynamics, the genetic algorithm requires describing the mixture of all possible norms in the norm space under consideration. Therefore, we also propose an analytic method to study norm ecosystems in which all possible second order social norms potentially exist and compete. The analysis reveals that the different adaptive architectures show different paths to the evolution of cooperation. Especially we find that so called Stern-Judging, one of the best studied norms in the literature, exhibits distinct behaviors in both architectures. On one hand, in the replicator dynamics, Stern-Judging remains alive and gets a majority steadily when the population reaches a cooperative state. On the other hand, in the genetic algorithm, it gets a majority only temporarily and becomes extinct in the end.

Managing In-House Development of a Campus-Wide Information System

ERIC Educational Resources Information Center

Shurville, Simon; Williams, John

2005-01-01

Purpose: To show how a combination of hard and soft project and change management methodologies guided successful in-house development of a campus-wide information system. Design/methodology/approach: A case study of the methodologies and management structures that guided the development is presented. Findings: Applying a combination of the…

Epigenome-wide analysis of DNA methylation in lung tissue shows concordance with blood studies and identifies tobacco smoke-inducible enhancers.

PubMed

Stueve, Theresa Ryan; Li, Wen-Qing; Shi, Jianxin; Marconett, Crystal N; Zhang, Tongwu; Yang, Chenchen; Mullen, Daniel; Yan, Chunli; Wheeler, William; Hua, Xing; Zhou, Beiyun; Borok, Zea; Caporaso, Neil E; Pesatori, Angela C; Duan, Jubao; Laird-Offringa, Ite A; Landi, Maria Teresa

2017-08-01

Smoking-associated DNA hypomethylation has been observed in blood cells and linked to lung cancer risk. However, its cause and mechanistic relationship to lung cancer remain unclear. We studied the association between tobacco smoking and epigenome-wide methylation in non-tumor lung (NTL) tissue from 237 lung cancer cases in the Environment And Genetics in Lung cancer Etiology study, using the Infinium HumanMethylation450 BeadChip. We identified seven smoking-associated hypomethylated CpGs (P < 1.0 × 10-7), which were replicated in NTL data from The Cancer Genome Atlas. Five of these loci were previously reported as hypomethylated in smokers' blood, suggesting that blood-based biomarkers can reflect changes in the target tissue for these loci. Four CpGs border sequences carrying aryl hydrocarbon receptor binding sites and enhancer-specific histone modifications in primary alveolar epithelium and A549 lung adenocarcinoma cells. A549 cell exposure to cigarette smoke condensate increased these enhancer marks significantly and stimulated expression of predicted target xenobiotic response-related genes AHRR (P = 1.13 × 10-62) and CYP1B1 (P < 2.49 × 10-61). Expression of both genes was linked to smoking-related transversion mutations in lung tumors. Thus, smoking-associated hypomethylation may be a consequence of enhancer activation, revealing environmentally-induced regulatory elements implicated in lung carcinogenesis. Published by Oxford University Press 2017. This work is written by US Government employees and is in the public domain in the US.

A hierarchical and modular approach to the discovery of robust associations in genome-wide association studies from pooled DNA samples

PubMed Central

Sebastiani, Paola; Zhao, Zhenming; Abad-Grau, Maria M; Riva, Alberto; Hartley, Stephen W; Sedgewick, Amanda E; Doria, Alessandro; Montano, Monty; Melista, Efthymia; Terry, Dellara; Perls, Thomas T; Steinberg, Martin H; Baldwin, Clinton T

2008-01-01

Background One of the challenges of the analysis of pooling-based genome wide association studies is to identify authentic associations among potentially thousands of false positive associations. Results We present a hierarchical and modular approach to the analysis of genome wide genotype data that incorporates quality control, linkage disequilibrium, physical distance and gene ontology to identify authentic associations among those found by statistical association tests. The method is developed for the allelic association analysis of pooled DNA samples, but it can be easily generalized to the analysis of individually genotyped samples. We evaluate the approach using data sets from diverse genome wide association studies including fetal hemoglobin levels in sickle cell anemia and a sample of centenarians and show that the approach is highly reproducible and allows for discovery at different levels of synthesis. Conclusion Results from the integration of Bayesian tests and other machine learning techniques with linkage disequilibrium data suggest that we do not need to use too stringent thresholds to reduce the number of false positive associations. This method yields increased power even with relatively small samples. In fact, our evaluation shows that the method can reach almost 70% sensitivity with samples of only 100 subjects. PMID:18194558

Distributing and Showing Farmer Learning Videos in Bangladesh

ERIC Educational Resources Information Center

Bentley, Jeffery W.; Van Mele, Paul; Harun-ar-Rashid, Md.; Krupnik, Timothy J.

2016-01-01

Purpose: To describe the results of showing farmer learning videos through different types of volunteers. Design/Methodology/Approach: Semi-structured interviews with volunteers from different occupational groups in Bangladesh, and a phone survey with 227 respondents. Findings: Each occupational group acted differently. Shop keepers, tillage…

Absolute Radiometric Calibration of Narrow-Swath Imaging Sensors with Reference to Non-Coincident Wide-Swath Sensors

NASA Technical Reports Server (NTRS)

McCorkel, Joel; Thome, Kurtis; Lockwood, Ronald

2012-01-01

An inter-calibration method is developed to provide absolute radiometric calibration of narrow-swath imaging sensors with reference to non-coincident wide-swath sensors. The method predicts at-sensor radiance using non-coincident imagery from the reference sensor and knowledge of spectral reflectance of the test site. The imagery of the reference sensor is restricted to acquisitions that provide similar view and solar illumination geometry to reduce uncertainties due to directional reflectance effects. Spectral reflectance of the test site is found with a simple iterative radiative transfer method using radiance values of a well-understood wide-swath sensor and spectral shape information based on historical ground-based measurements. At-sensor radiance is calculated for the narrow-swath sensor using this spectral reflectance and atmospheric parameters that are also based on historical in situ measurements. Results of the inter-calibration method show agreement on the 2 5 percent level in most spectral regions with the vicarious calibration technique relying on coincident ground-based measurements referred to as the reflectance-based approach. While the variability of the inter-calibration method based on non-coincident image pairs is significantly larger, results are consistent with techniques relying on in situ measurements. The method is also insensitive to spectral differences between the sensors by transferring to surface spectral reflectance prior to prediction of at-sensor radiance. The utility of this inter-calibration method is made clear by its flexibility to utilize image pairings with acquisition dates differing in excess of 30 days allowing frequent absolute calibration comparisons between wide- and narrow-swath sensors.

Research on Wide-field Imaging Technologies for Low-frequency Radio Array

NASA Astrophysics Data System (ADS)

Lao, B. Q.; An, T.; Chen, X.; Wu, X. C.; Lu, Y.

2017-09-01

Wide-field imaging of low-frequency radio telescopes are subject to a number of difficult problems. One particularly pernicious problem is the non-coplanar baseline effect. It will lead to distortion of the final image when the phase of w direction called w-term is ignored. The image degradation effects are amplified for telescopes with the wide field of view. This paper summarizes and analyzes several w-term correction methods and their technical principles. Their advantages and disadvantages have been analyzed after comparing their computational cost and computational complexity. We conduct simulations with two of these methods, faceting and w-projection, based on the configuration of the first-phase Square Kilometre Array (SKA) low frequency array. The resulted images are also compared with the two-dimensional Fourier transform method. The results show that image quality and correctness derived from both faceting and w-projection are better than the two-dimensional Fourier transform method in wide-field imaging. The image quality and run time affected by the number of facets and w steps have been evaluated. The results indicate that the number of facets and w steps must be reasonable. Finally, we analyze the effect of data size on the run time of faceting and w-projection. The results show that faceting and w-projection need to be optimized before the massive amounts of data processing. The research of the present paper initiates the analysis of wide-field imaging techniques and their application in the existing and future low-frequency array, and fosters the application and promotion to much broader fields.

Genome-wide cloning, identification, classification and functional analysis of cotton heat shock transcription factors in cotton (Gossypium hirsutum).

PubMed

Wang, Jun; Sun, Na; Deng, Ting; Zhang, Lida; Zuo, Kaijing

2014-11-06

Heat shock transcriptional factors (Hsfs) play important roles in the processes of biotic and abiotic stresses as well as in plant development. Cotton (Gossypium hirsutum, 2n=4x=(AD)2=52) is an important crop for natural fiber production. Due to continuous high temperature and intermittent drought, heat stress is becoming a handicap to improve cotton yield and lint quality. Recently, the related wild diploid species Gossypium raimondii genome (2n=2x=(D5)2=26) has been fully sequenced. In order to analyze the functions of different Hsfs at the genome-wide level, detailed characterization and analysis of the Hsf gene family in G. hirsutum is indispensable. EST assembly and genome-wide analyses were applied to clone and identify heat shock transcription factor (Hsf) genes in Upland cotton (GhHsf). Forty GhHsf genes were cloned, identified and classified into three main classes (A, B and C) according to the characteristics of their domains. Analysis of gene duplications showed that GhHsfs have occurred more frequently than reported in plant genomes such as Arabidopsis and Populus. Quantitative real-time PCR (qRT-PCR) showed that all GhHsf transcripts are expressed in most cotton plant tissues including roots, stems, leaves and developing fibers, and abundantly in developing ovules. Three expression patterns were confirmed in GhHsfs when cotton plants were exposed to high temperature for 1 h. GhHsf39 exhibited the most immediate response to heat shock. Comparative analysis of Hsfs expression differences between the wild-type and fiberless mutant suggested that Hsfs are involved in fiber development. Comparative genome analysis showed that Upland cotton D-subgenome contains 40 Hsf members, and that the whole genome of Upland cotton contains more than 80 Hsf genes due to genome duplication. The expression patterns in different tissues in response to heat shock showed that GhHsfs are important for heat stress as well as fiber development. These results provide an improved

Peanut sensitization pattern in Norwegian children and adults with specific IgE to peanut show age related differences.

PubMed

Namork, Ellen; Stensby, Berit A

2015-01-01

Peanuts contain potent food allergens and the prevalence of allergy is reported to increase, especially in children. Since peanut sensitization may differ between different geographical regions, we wanted to investigate the sensitization pattern to the individual peanut allergens in a Norwegian population. Cases reported to the Norwegian Food Allergy Register with sera positive to peanut extract were analyzed for specific IgE (sIgE) to the recombinant peanut allergens Ara h 1, Ara h 2, Ara h 3, Ara h 8 and Ara h 9 and to birch pollen extract. Serum samples negative to the above allergens were analyzed for sIgE to Ara h 6, and sIgE to Pru p 3 in peach were analyzed in sera positive to the cross-reactive allergen Ara h 9. Highest frequency of sIgE to Ara h 2, often co-sensitized to Ara h 1 and 3, were found in the small children up to 6 years of age. From the age of 6 years, sensitization to Ara h 8 was predominant. The sIgE levels to the storage proteins Ara h 1, 2 and 3 were strongly correlated, as was the sIgE levels to Ara h 8 and birch pollen extract. A low sensitization rate of sIgE to Ara h 9 in young adults was observed, which sIgE levels were very strongly correlated to Pru p 3. The sensitization to peanut allergens in a Norwegian population shows a clear age dependent pattern. The results add to the previously published research on the sensitization patterns of peanut sensitized patients in different geographical areas.

Sensor-Aware Recognition and Tracking for Wide-Area Augmented Reality on Mobile Phones

PubMed Central

Chen, Jing; Cao, Ruochen; Wang, Yongtian

2015-01-01

Wide-area registration in outdoor environments on mobile phones is a challenging task in mobile augmented reality fields. We present a sensor-aware large-scale outdoor augmented reality system for recognition and tracking on mobile phones. GPS and gravity information is used to improve the VLAD performance for recognition. A kind of sensor-aware VLAD algorithm, which is self-adaptive to different scale scenes, is utilized to recognize complex scenes. Considering vision-based registration algorithms are too fragile and tend to drift, data coming from inertial sensors and vision are fused together by an extended Kalman filter (EKF) to achieve considerable improvements in tracking stability and robustness. Experimental results show that our method greatly enhances the recognition rate and eliminates the tracking jitters. PMID:26690439

Sensor-Aware Recognition and Tracking for Wide-Area Augmented Reality on Mobile Phones.

PubMed

Chen, Jing; Cao, Ruochen; Wang, Yongtian

2015-12-10

Wide-area registration in outdoor environments on mobile phones is a challenging task in mobile augmented reality fields. We present a sensor-aware large-scale outdoor augmented reality system for recognition and tracking on mobile phones. GPS and gravity information is used to improve the VLAD performance for recognition. A kind of sensor-aware VLAD algorithm, which is self-adaptive to different scale scenes, is utilized to recognize complex scenes. Considering vision-based registration algorithms are too fragile and tend to drift, data coming from inertial sensors and vision are fused together by an extended Kalman filter (EKF) to achieve considerable improvements in tracking stability and robustness. Experimental results show that our method greatly enhances the recognition rate and eliminates the tracking jitters.

Gender differences in the adverse events’ profile registered in seven observational studies of a wide gender-medicine (MetaGeM) project: the MetaGeM safety analysis

PubMed Central

Colombo, Delia; Zagni, Emanuela; Nica, Mihaela; Rizzoli, Sara; Ori, Alessandra; Bellia, Gilberto

2016-01-01

Background MetaGeM is a wide gender-medicine project comprising post hoc and meta-analyses by gender of clinical outcomes, therapeutic approaches, and safety data from previously conducted observational studies to explore possible gender differences in real-life clinical settings. We report the results of the safety meta-analysis of seven MetaGeM studies, evaluating gender differences in adverse event (AE) incidence and severity. Methods Data were collected between February 2002 and July 2013. Male and female patients were compared for the main safety variables, using Student’s t-test, χ2 test, or Fisher’s exact test as appropriate. As supportive analysis, a logistic regression model was estimated to evaluate associations between gender and outcome. Results In total, 4,870 patients (46% females, 54% males) were included in the analysis; age was higher for females (mean ± standard deviation 61.2±18.3 years) than males (56.3±16.6 years). Overall, 264 AEs were reported (59.1% in males). There were no significant gender differences in the percentage of patients with at least one AE: 3.0% for females versus 3.9% for males, χ2 test P>0.05. According to the logistic regression model results, no association between gender and AEs occurrence seems to exist. A statistically significant gender difference in the percentage of drug-related AEs emerged (37.6% in females vs 20.8% in males, χ2 P=0.0039). Slightly significantly more AEs in females were addressed with treatment compared with males (78.1% vs 66.7%, χ2 P=0.0485). Total serious AEs (SAEs) were 47 (72% in males). The frequency of patients with ≥1 SAE was 0.6% in females versus 1.2% in males (χ2 test P=0.0246). Conclusion This safety analysis on a large sample of almost 5,000 patients with different diseases and treated with a wide range of different drugs provides a useful overview on possible gender differences in drug tolerability, which may be helpful in more accurately designing future clinical trials

Widely tunable and monochromatic terahertz difference frequency generation with organic crystal 2-(3-(4-hydroxystyryl)-5,5-dime-thylcyclohex-2-enylidene) malononitrile

NASA Astrophysics Data System (ADS)

Liu, Pengxiang; Zhang, Xinyuan; Yan, Chao; Xu, Degang; Li, Yin; Shi, Wei; Zhang, Guochun; Zhang, Xinzheng; Yao, Jianquan; Wu, Yicheng

2016-01-01

We report an experimental study on widely tunable terahertz (THz) wave difference frequency generation (DFG) with hydrogen-bonded crystals 2-(3-(4-hydroxystyryl)-5,5-dime-thylcyclohex-2-enylidene) malononitrile (OH1). The organic crystals were pumped by a ˜1.3 μm double-pass KTiOPO4 optical parametric oscillator. A tuning range of 0.02-20 THz was achieved. OH1 crystals offer a long effective interaction length (also high output) for the generation below 3 THz, owing to the low absorption and favorable phase-matching. The highest energy of 507 nJ/pulse was generated at 1.92 THz with a 1.89-mm-thick crystal. Comprehensive explanations were provided, on the basis of theoretical calculations. Cascading phenomenon during the DFG process was demonstrated. The photon conversion efficiency could reach 2.9%.

Sex differences in addictive disorders.

PubMed

Fattore, Liana; Melis, Miriam; Fadda, Paola; Fratta, Walter

2014-08-01

Gender-dependent differences in the rate of initiation and frequency of misuse of addicting drugs have been widely described. Yet, men and women also differ in their propensity to become addicted to other rewarding stimuli (e.g., sex, food) or activities (e.g., gambling, exercising). The goal of the present review is to summarize current evidence for gender differences not only in drug addiction, but also in other forms of addictive behaviours. Thus, we first reviewed studies showing gender-dependent differences in drug addiction, food addiction, compulsive sexual activity, pathological gambling, Internet addiction and physical exercise addiction. Potential risk factors and underlying brain mechanisms are also examined, with particular emphasis given to the role of sex hormones in modulating addictive behaviours. Investigations on factors allowing the pursuit of non-drug rewards to become pathological in men and women are crucial for designing gender-appropriate treatments of both substance and non-substance addictions. Copyright © 2014 Elsevier Inc. All rights reserved.

Differences in neural responses to ipsilateral stimuli in wide-view fields between face- and house-selective areas

PubMed Central

Li, Ting; Niu, Yan; Xiang, Jie; Cheng, Junjie; Liu, Bo; Zhang, Hui; Yan, Tianyi; Kanazawa, Susumu; Wu, Jinglong

2018-01-01

Category-selective brain areas exhibit varying levels of neural activity to ipsilaterally presented stimuli. However, in face- and house-selective areas, the neural responses evoked by ipsilateral stimuli in the peripheral visual field remain unclear. In this study, we displayed face and house images using a wide-view visual presentation system while performing functional magnetic resonance imaging (fMRI). The face-selective areas (fusiform face area (FFA) and occipital face area (OFA)) exhibited intense neural responses to ipsilaterally presented images, whereas the house-selective areas (parahippocampal place area (PPA) and transverse occipital sulcus (TOS)) exhibited substantially smaller and even negative neural responses to the ipsilaterally presented images. We also found that the category preferences of the contralateral and ipsilateral neural responses were similar. Interestingly, the face- and house-selective areas exhibited neural responses to ipsilateral images that were smaller than the responses to the contralateral images. Multi-voxel pattern analysis (MVPA) was implemented to evaluate the difference between the contralateral and ipsilateral responses. The classification accuracies were much greater than those expected by chance. The classification accuracies in the FFA were smaller than those in the PPA and TOS. The closer eccentricities elicited greater classification accuracies in the PPA and TOS. We propose that these ipsilateral neural responses might be interpreted by interhemispheric communication through intrahemispheric connectivity of white matter connection and interhemispheric connectivity via the corpus callosum and occipital white matter connection. Furthermore, the PPA and TOS likely have weaker interhemispheric communication than the FFA and OFA, particularly in the peripheral visual field. PMID:29451872

Mare Orientale: Widely Accepted Large Impact or a Regular Tectonic Depression?

NASA Astrophysics Data System (ADS)

Kochemasov, G. G.

2018-04-01

Mare Orientale is one of the critical features on Moon surface explaining its tectonics. The impact origin of it is widely accepted, but an attentive examination shows that this large Mare is a part of endogenous tectonic structure, not a random impact.

A comparison of image restoration approaches applied to three-dimensional confocal and wide-field fluorescence microscopy.

PubMed

Verveer, P. J; Gemkow, M. J; Jovin, T. M

1999-01-01

We have compared different image restoration approaches for fluorescence microscopy. The most widely used algorithms were classified with a Bayesian theory according to the assumed noise model and the type of regularization imposed. We considered both Gaussian and Poisson models for the noise in combination with Tikhonov regularization, entropy regularization, Good's roughness and without regularization (maximum likelihood estimation). Simulations of fluorescence confocal imaging were used to examine the different noise models and regularization approaches using the mean squared error criterion. The assumption of a Gaussian noise model yielded only slightly higher errors than the Poisson model. Good's roughness was the best choice for the regularization. Furthermore, we compared simulated confocal and wide-field data. In general, restored confocal data are superior to restored wide-field data, but given sufficient higher signal level for the wide-field data the restoration result may rival confocal data in quality. Finally, a visual comparison of experimental confocal and wide-field data is presented.

The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape: A Large-Scale Genome-Wide Interaction Study.

PubMed

Winkler, Thomas W; Justice, Anne E; Graff, Mariaelisa; Barata, Llilda; Feitosa, Mary F; Chu, Su; Czajkowski, Jacek; Esko, Tõnu; Fall, Tove; Kilpeläinen, Tuomas O; Lu, Yingchang; Mägi, Reedik; Mihailov, Evelin; Pers, Tune H; Rüeger, Sina; Teumer, Alexander; Ehret, Georg B; Ferreira, Teresa; Heard-Costa, Nancy L; Karjalainen, Juha; Lagou, Vasiliki; Mahajan, Anubha; Neinast, Michael D; Prokopenko, Inga; Simino, Jeannette; Teslovich, Tanya M; Jansen, Rick; Westra, Harm-Jan; White, Charles C; Absher, Devin; Ahluwalia, Tarunveer S; Ahmad, Shafqat; Albrecht, Eva; Alves, Alexessander Couto; Bragg-Gresham, Jennifer L; de Craen, Anton J M; Bis, Joshua C; Bonnefond, Amélie; Boucher, Gabrielle; Cadby, Gemma; Cheng, Yu-Ching; Chiang, Charleston W K; Delgado, Graciela; Demirkan, Ayse; Dueker, Nicole; Eklund, Niina; Eiriksdottir, Gudny; Eriksson, Joel; Feenstra, Bjarke; Fischer, Krista; Frau, Francesca; Galesloot, Tessel E; Geller, Frank; Goel, Anuj; Gorski, Mathias; Grammer, Tanja B; Gustafsson, Stefan; Haitjema, Saskia; Hottenga, Jouke-Jan; Huffman, Jennifer E; Jackson, Anne U; Jacobs, Kevin B; Johansson, Åsa; Kaakinen, Marika; Kleber, Marcus E; Lahti, Jari; Mateo Leach, Irene; Lehne, Benjamin; Liu, Youfang; Lo, Ken Sin; Lorentzon, Mattias; Luan, Jian'an; Madden, Pamela A F; Mangino, Massimo; McKnight, Barbara; Medina-Gomez, Carolina; Monda, Keri L; Montasser, May E; Müller, Gabriele; Müller-Nurasyid, Martina; Nolte, Ilja M; Panoutsopoulou, Kalliope; Pascoe, Laura; Paternoster, Lavinia; Rayner, Nigel W; Renström, Frida; Rizzi, Federica; Rose, Lynda M; Ryan, Kathy A; Salo, Perttu; Sanna, Serena; Scharnagl, Hubert; Shi, Jianxin; Smith, Albert Vernon; Southam, Lorraine; Stančáková, Alena; Steinthorsdottir, Valgerdur; Strawbridge, Rona J; Sung, Yun Ju; Tachmazidou, Ioanna; Tanaka, Toshiko; Thorleifsson, Gudmar; Trompet, Stella; Pervjakova, Natalia; Tyrer, Jonathan P; Vandenput, Liesbeth; van der Laan, Sander W; van der Velde, Nathalie; van Setten, Jessica; van Vliet-Ostaptchouk, Jana V; Verweij, Niek; Vlachopoulou, Efthymia; Waite, Lindsay L; Wang, Sophie R; Wang, Zhaoming; Wild, Sarah H; Willenborg, Christina; Wilson, James F; Wong, Andrew; Yang, Jian; Yengo, Loïc; Yerges-Armstrong, Laura M; Yu, Lei; Zhang, Weihua; Zhao, Jing Hua; Andersson, Ehm A; Bakker, Stephan J L; Baldassarre, Damiano; Banasik, Karina; Barcella, Matteo; Barlassina, Cristina; Bellis, Claire; Benaglio, Paola; Blangero, John; Blüher, Matthias; Bonnet, Fabrice; Bonnycastle, Lori L; Boyd, Heather A; Bruinenberg, Marcel; Buchman, Aron S; Campbell, Harry; Chen, Yii-Der Ida; Chines, Peter S; Claudi-Boehm, Simone; Cole, John; Collins, Francis S; de Geus, Eco J C; de Groot, Lisette C P G M; Dimitriou, Maria; Duan, Jubao; Enroth, Stefan; Eury, Elodie; Farmaki, Aliki-Eleni; Forouhi, Nita G; Friedrich, Nele; Gejman, Pablo V; Gigante, Bruna; Glorioso, Nicola; Go, Alan S; Gottesman, Omri; Gräßler, Jürgen; Grallert, Harald; Grarup, Niels; Gu, Yu-Mei; Broer, Linda; Ham, Annelies C; Hansen, Torben; Harris, Tamara B; Hartman, Catharina A; Hassinen, Maija; Hastie, Nicholas; Hattersley, Andrew T; Heath, Andrew C; Henders, Anjali K; Hernandez, Dena; Hillege, Hans; Holmen, Oddgeir; Hovingh, Kees G; Hui, Jennie; Husemoen, Lise L; Hutri-Kähönen, Nina; Hysi, Pirro G; Illig, Thomas; De Jager, Philip L; Jalilzadeh, Shapour; Jørgensen, Torben; Jukema, J Wouter; Juonala, Markus; Kanoni, Stavroula; Karaleftheri, Maria; Khaw, Kay Tee; Kinnunen, Leena; Kittner, Steven J; Koenig, Wolfgang; Kolcic, Ivana; Kovacs, Peter; Krarup, Nikolaj T; Kratzer, Wolfgang; Krüger, Janine; Kuh, Diana; Kumari, Meena; Kyriakou, Theodosios; Langenberg, Claudia; Lannfelt, Lars; Lanzani, Chiara; Lotay, Vaneet; Launer, Lenore J; Leander, Karin; Lindström, Jaana; Linneberg, Allan; Liu, Yan-Ping; Lobbens, Stéphane; Luben, Robert; Lyssenko, Valeriya; Männistö, Satu; Magnusson, Patrik K; McArdle, Wendy L; Menni, Cristina; Merger, Sigrun; Milani, Lili; Montgomery, Grant W; Morris, Andrew P; Narisu, Narisu; Nelis, Mari; Ong, Ken K; Palotie, Aarno; Pérusse, Louis; Pichler, Irene; Pilia, Maria G; Pouta, Anneli; Rheinberger, Myriam; Ribel-Madsen, Rasmus; Richards, Marcus; Rice, Kenneth M; Rice, Treva K; Rivolta, Carlo; Salomaa, Veikko; Sanders, Alan R; Sarzynski, Mark A; Scholtens, Salome; Scott, Robert A; Scott, William R; Sebert, Sylvain; Sengupta, Sebanti; Sennblad, Bengt; Seufferlein, Thomas; Silveira, Angela; Slagboom, P Eline; Smit, Jan H; Sparsø, Thomas H; Stirrups, Kathleen; Stolk, Ronald P; Stringham, Heather M; Swertz, Morris A; Swift, Amy J; Syvänen, Ann-Christine; Tan, Sian-Tsung; Thorand, Barbara; Tönjes, Anke; Tremblay, Angelo; Tsafantakis, Emmanouil; van der Most, Peter J; Völker, Uwe; Vohl, Marie-Claude; Vonk, Judith M; Waldenberger, Melanie; Walker, Ryan W; Wennauer, Roman; Widén, Elisabeth; Willemsen, Gonneke; Wilsgaard, Tom; Wright, Alan F; Zillikens, M Carola; van Dijk, Suzanne C; van Schoor, Natasja M; Asselbergs, Folkert W; de Bakker, Paul I W; Beckmann, Jacques S; Beilby, John; Bennett, David A; Bergman, Richard N; Bergmann, Sven; Böger, Carsten A; Boehm, Bernhard O; Boerwinkle, Eric; Boomsma, Dorret I; Bornstein, Stefan R; Bottinger, Erwin P; Bouchard, Claude; Chambers, John C; Chanock, Stephen J; Chasman, Daniel I; Cucca, Francesco; Cusi, Daniele; Dedoussis, George; Erdmann, Jeanette; Eriksson, Johan G; Evans, Denis A; de Faire, Ulf; Farrall, Martin; Ferrucci, Luigi; Ford, Ian; Franke, Lude; Franks, Paul W; Froguel, Philippe; Gansevoort, Ron T; Gieger, Christian; Grönberg, Henrik; Gudnason, Vilmundur; Gyllensten, Ulf; Hall, Per; Hamsten, Anders; van der Harst, Pim; Hayward, Caroline; Heliövaara, Markku; Hengstenberg, Christian; Hicks, Andrew A; Hingorani, Aroon; Hofman, Albert; Hu, Frank; Huikuri, Heikki V; Hveem, Kristian; James, Alan L; Jordan, Joanne M; Jula, Antti; Kähönen, Mika; Kajantie, Eero; Kathiresan, Sekar; Kiemeney, Lambertus A L M; Kivimaki, Mika; Knekt, Paul B; Koistinen, Heikki A; Kooner, Jaspal S; Koskinen, Seppo; Kuusisto, Johanna; Maerz, Winfried; Martin, Nicholas G; Laakso, Markku; Lakka, Timo A; Lehtimäki, Terho; Lettre, Guillaume; Levinson, Douglas F; Lind, Lars; Lokki, Marja-Liisa; Mäntyselkä, Pekka; Melbye, Mads; Metspalu, Andres; Mitchell, Braxton D; Moll, Frans L; Murray, Jeffrey C; Musk, Arthur W; Nieminen, Markku S; Njølstad, Inger; Ohlsson, Claes; Oldehinkel, Albertine J; Oostra, Ben A; Palmer, Lyle J; Pankow, James S; Pasterkamp, Gerard; Pedersen, Nancy L; Pedersen, Oluf; Penninx, Brenda W; Perola, Markus; Peters, Annette; Polašek, Ozren; Pramstaller, Peter P; Psaty, Bruce M; Qi, Lu; Quertermous, Thomas; Raitakari, Olli T; Rankinen, Tuomo; Rauramaa, Rainer; Ridker, Paul M; Rioux, John D; Rivadeneira, Fernando; Rotter, Jerome I; Rudan, Igor; den Ruijter, Hester M; Saltevo, Juha; Sattar, Naveed; Schunkert, Heribert; Schwarz, Peter E H; Shuldiner, Alan R; Sinisalo, Juha; Snieder, Harold; Sørensen, Thorkild I A; Spector, Tim D; Staessen, Jan A; Stefania, Bandinelli; Thorsteinsdottir, Unnur; Stumvoll, Michael; Tardif, Jean-Claude; Tremoli, Elena; Tuomilehto, Jaakko; Uitterlinden, André G; Uusitupa, Matti; Verbeek, André L M; Vermeulen, Sita H; Viikari, Jorma S; Vitart, Veronique; Völzke, Henry; Vollenweider, Peter; Waeber, Gérard; Walker, Mark; Wallaschofski, Henri; Wareham, Nicholas J; Watkins, Hugh; Zeggini, Eleftheria; Chakravarti, Aravinda; Clegg, Deborah J; Cupples, L Adrienne; Gordon-Larsen, Penny; Jaquish, Cashell E; Rao, D C; Abecasis, Goncalo R; Assimes, Themistocles L; Barroso, Inês; Berndt, Sonja I; Boehnke, Michael; Deloukas, Panos; Fox, Caroline S; Groop, Leif C; Hunter, David J; Ingelsson, Erik; Kaplan, Robert C; McCarthy, Mark I; Mohlke, Karen L; O'Connell, Jeffrey R; Schlessinger, David; Strachan, David P; Stefansson, Kari; van Duijn, Cornelia M; Hirschhorn, Joel N; Lindgren, Cecilia M; Heid, Iris M; North, Kari E; Borecki, Ingrid B; Kutalik, Zoltán; Loos, Ruth J F

2015-10-01

Genome-wide association studies (GWAS) have identified more than 100 genetic variants contributing to BMI, a measure of body size, or waist-to-hip ratio (adjusted for BMI, WHRadjBMI), a measure of body shape. Body size and shape change as people grow older and these changes differ substantially between men and women. To systematically screen for age- and/or sex-specific effects of genetic variants on BMI and WHRadjBMI, we performed meta-analyses of 114 studies (up to 320,485 individuals of European descent) with genome-wide chip and/or Metabochip data by the Genetic Investigation of Anthropometric Traits (GIANT) Consortium. Each study tested the association of up to ~2.8M SNPs with BMI and WHRadjBMI in four strata (men ≤50y, men >50y, women ≤50y, women >50y) and summary statistics were combined in stratum-specific meta-analyses. We then screened for variants that showed age-specific effects (G x AGE), sex-specific effects (G x SEX) or age-specific effects that differed between men and women (G x AGE x SEX). For BMI, we identified 15 loci (11 previously established for main effects, four novel) that showed significant (FDR<5%) age-specific effects, of which 11 had larger effects in younger (<50y) than in older adults (≥50y). No sex-dependent effects were identified for BMI. For WHRadjBMI, we identified 44 loci (27 previously established for main effects, 17 novel) with sex-specific effects, of which 28 showed larger effects in women than in men, five showed larger effects in men than in women, and 11 showed opposite effects between sexes. No age-dependent effects were identified for WHRadjBMI. This is the first genome-wide interaction meta-analysis to report convincing evidence of age-dependent genetic effects on BMI. In addition, we confirm the sex-specificity of genetic effects on WHRadjBMI. These results may provide further insights into the biology that underlies weight change with age or the sexually dimorphism of body shape.

The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape: A Large-Scale Genome-Wide Interaction Study

PubMed Central

Feitosa, Mary F.; Chu, Su; Czajkowski, Jacek; Esko, Tõnu; Fall, Tove; Kilpeläinen, Tuomas O.; Lu, Yingchang; Mägi, Reedik; Mihailov, Evelin; Pers, Tune H.; Rüeger, Sina; Teumer, Alexander; Ehret, Georg B.; Ferreira, Teresa; Heard-Costa, Nancy L.; Karjalainen, Juha; Lagou, Vasiliki; Mahajan, Anubha; Neinast, Michael D.; Prokopenko, Inga; Simino, Jeannette; Teslovich, Tanya M.; Jansen, Rick; Westra, Harm-Jan; White, Charles C.; Absher, Devin; Ahluwalia, Tarunveer S.; Ahmad, Shafqat; Albrecht, Eva; Alves, Alexessander Couto; Bragg-Gresham, Jennifer L.; de Craen, Anton J. M.; Bis, Joshua C.; Bonnefond, Amélie; Boucher, Gabrielle; Cadby, Gemma; Cheng, Yu-Ching; Chiang, Charleston W. K.; Delgado, Graciela; Demirkan, Ayse; Dueker, Nicole; Eklund, Niina; Eiriksdottir, Gudny; Eriksson, Joel; Feenstra, Bjarke; Fischer, Krista; Frau, Francesca; Galesloot, Tessel E.; Geller, Frank; Goel, Anuj; Gorski, Mathias; Grammer, Tanja B.; Gustafsson, Stefan; Haitjema, Saskia; Hottenga, Jouke-Jan; Huffman, Jennifer E.; Jackson, Anne U.; Jacobs, Kevin B.; Johansson, Åsa; Kaakinen, Marika; Kleber, Marcus E.; Lahti, Jari; Leach, Irene Mateo; Lehne, Benjamin; Liu, Youfang; Lo, Ken Sin; Lorentzon, Mattias; Luan, Jian'an; Madden, Pamela A. F.; Mangino, Massimo; McKnight, Barbara; Medina-Gomez, Carolina; Monda, Keri L.; Montasser, May E.; Müller, Gabriele; Müller-Nurasyid, Martina; Nolte, Ilja M.; Panoutsopoulou, Kalliope; Pascoe, Laura; Paternoster, Lavinia; Rayner, Nigel W.; Renström, Frida; Rizzi, Federica; Rose, Lynda M.; Ryan, Kathy A.; Salo, Perttu; Sanna, Serena; Scharnagl, Hubert; Shi, Jianxin; Smith, Albert Vernon; Southam, Lorraine; Stančáková, Alena; Steinthorsdottir, Valgerdur; Strawbridge, Rona J.; Sung, Yun Ju; Tachmazidou, Ioanna; Tanaka, Toshiko; Thorleifsson, Gudmar; Trompet, Stella; Pervjakova, Natalia; Tyrer, Jonathan P.; Vandenput, Liesbeth; van der Laan, Sander W; van der Velde, Nathalie; van Setten, Jessica; van Vliet-Ostaptchouk, Jana V.; Verweij, Niek; Vlachopoulou, Efthymia; Waite, Lindsay L.; Wang, Sophie R.; Wang, Zhaoming; Wild, Sarah H.; Willenborg, Christina; Wilson, James F.; Wong, Andrew; Yang, Jian; Yengo, Loïc; Yerges-Armstrong, Laura M.; Yu, Lei; Zhang, Weihua; Zhao, Jing Hua; Andersson, Ehm A.; Bakker, Stephan J. L.; Baldassarre, Damiano; Banasik, Karina; Barcella, Matteo; Barlassina, Cristina; Bellis, Claire; Benaglio, Paola; Blangero, John; Blüher, Matthias; Bonnet, Fabrice; Bonnycastle, Lori L.; Boyd, Heather A.; Bruinenberg, Marcel; Buchman, Aron S; Campbell, Harry; Chen, Yii-Der Ida; Chines, Peter S.; Claudi-Boehm, Simone; Cole, John; Collins, Francis S.; de Geus, Eco J. C.; de Groot, Lisette C. P. G. M.; Dimitriou, Maria; Duan, Jubao; Enroth, Stefan; Eury, Elodie; Farmaki, Aliki-Eleni; Forouhi, Nita G.; Friedrich, Nele; Gejman, Pablo V.; Gigante, Bruna; Glorioso, Nicola; Go, Alan S.; Gottesman, Omri; Gräßler, Jürgen; Grallert, Harald; Grarup, Niels; Gu, Yu-Mei; Broer, Linda; Ham, Annelies C.; Hansen, Torben; Harris, Tamara B.; Hartman, Catharina A.; Hassinen, Maija; Hastie, Nicholas; Hattersley, Andrew T.; Heath, Andrew C.; Henders, Anjali K.; Hernandez, Dena; Hillege, Hans; Holmen, Oddgeir; Hovingh, Kees G; Hui, Jennie; Husemoen, Lise L.; Hutri-Kähönen, Nina; Hysi, Pirro G.; Illig, Thomas; De Jager, Philip L.; Jalilzadeh, Shapour; Jørgensen, Torben; Jukema, J. Wouter; Juonala, Markus; Kanoni, Stavroula; Karaleftheri, Maria; Khaw, Kay Tee; Kinnunen, Leena; Kittner, Steven J.; Koenig, Wolfgang; Kolcic, Ivana; Kovacs, Peter; Krarup, Nikolaj T.; Kratzer, Wolfgang; Krüger, Janine; Kuh, Diana; Kumari, Meena; Kyriakou, Theodosios; Langenberg, Claudia; Lannfelt, Lars; Lanzani, Chiara; Lotay, Vaneet; Launer, Lenore J.; Leander, Karin; Lindström, Jaana; Linneberg, Allan; Liu, Yan-Ping; Lobbens, Stéphane; Luben, Robert; Lyssenko, Valeriya; Männistö, Satu; Magnusson, Patrik K.; McArdle, Wendy L.; Menni, Cristina; Merger, Sigrun; Milani, Lili; Montgomery, Grant W.; Morris, Andrew P.; Narisu, Narisu; Nelis, Mari; Ong, Ken K.; Palotie, Aarno; Pérusse, Louis; Pichler, Irene; Pilia, Maria G.; Pouta, Anneli; Rheinberger, Myriam; Ribel-Madsen, Rasmus; Richards, Marcus; Rice, Kenneth M.; Rice, Treva K.; Rivolta, Carlo; Salomaa, Veikko; Sanders, Alan R.; Sarzynski, Mark A.; Scholtens, Salome; Scott, Robert A.; Scott, William R.; Sebert, Sylvain; Sengupta, Sebanti; Sennblad, Bengt; Seufferlein, Thomas; Silveira, Angela; Slagboom, P. Eline; Smit, Jan H.; Sparsø, Thomas H.; Stirrups, Kathleen; Stolk, Ronald P.; Stringham, Heather M.; Swertz, Morris A; Swift, Amy J.; Syvänen, Ann-Christine; Tan, Sian-Tsung; Thorand, Barbara; Tönjes, Anke; Tremblay, Angelo; Tsafantakis, Emmanouil; van der Most, Peter J.; Völker, Uwe; Vohl, Marie-Claude; Vonk, Judith M.; Waldenberger, Melanie; Walker, Ryan W.; Wennauer, Roman; Widén, Elisabeth; Willemsen, Gonneke; Wilsgaard, Tom; Wright, Alan F.; Zillikens, M. Carola; van Dijk, Suzanne C.; van Schoor, Natasja M.; Asselbergs, Folkert W.; de Bakker, Paul I. W.; Beckmann, Jacques S.; Beilby, John; Bennett, David A.; Bergman, Richard N.; Bergmann, Sven; Böger, Carsten A.; Boehm, Bernhard O.; Boerwinkle, Eric; Boomsma, Dorret I.; Bornstein, Stefan R.; Bottinger, Erwin P.; Bouchard, Claude; Chambers, John C.; Chanock, Stephen J.; Chasman, Daniel I.; Cucca, Francesco; Cusi, Daniele; Dedoussis, George; Erdmann, Jeanette; Eriksson, Johan G.; Evans, Denis A.; de Faire, Ulf; Farrall, Martin; Ferrucci, Luigi; Ford, Ian; Franke, Lude; Franks, Paul W.; Froguel, Philippe; Gansevoort, Ron T.; Gieger, Christian; Grönberg, Henrik; Gudnason, Vilmundur; Gyllensten, Ulf; Hall, Per; Hamsten, Anders; van der Harst, Pim; Hayward, Caroline; Heliövaara, Markku; Hengstenberg, Christian; Hicks, Andrew A; Hingorani, Aroon; Hofman, Albert; Hu, Frank; Huikuri, Heikki V.; Hveem, Kristian; James, Alan L.; Jordan, Joanne M.; Jula, Antti; Kähönen, Mika; Kajantie, Eero; Kathiresan, Sekar; Kiemeney, Lambertus A. L. M.; Kivimaki, Mika; Knekt, Paul B.; Koistinen, Heikki A.; Kooner, Jaspal S.; Koskinen, Seppo; Kuusisto, Johanna; Maerz, Winfried; Martin, Nicholas G; Laakso, Markku; Lakka, Timo A.; Lehtimäki, Terho; Lettre, Guillaume; Levinson, Douglas F.; Lind, Lars; Lokki, Marja-Liisa; Mäntyselkä, Pekka; Melbye, Mads; Metspalu, Andres; Mitchell, Braxton D.; Moll, Frans L.; Murray, Jeffrey C.; Musk, Arthur W.; Nieminen, Markku S.; Njølstad, Inger; Ohlsson, Claes; Oldehinkel, Albertine J.; Oostra, Ben A.; Palmer, Lyle J; Pankow, James S.; Pasterkamp, Gerard; Pedersen, Nancy L.; Pedersen, Oluf; Penninx, Brenda W.; Perola, Markus; Peters, Annette; Polašek, Ozren; Pramstaller, Peter P.; Psaty, Bruce M.; Qi, Lu; Quertermous, Thomas; Raitakari, Olli T.; Rankinen, Tuomo; Rauramaa, Rainer; Ridker, Paul M.; Rioux, John D.; Rivadeneira, Fernando; Rotter, Jerome I.; Rudan, Igor; den Ruijter, Hester M.; Saltevo, Juha; Sattar, Naveed; Schunkert, Heribert; Schwarz, Peter E. H.; Shuldiner, Alan R.; Sinisalo, Juha; Snieder, Harold; Sørensen, Thorkild I. A.; Spector, Tim D.; Staessen, Jan A.; Stefania, Bandinelli; Thorsteinsdottir, Unnur; Stumvoll, Michael; Tardif, Jean-Claude; Tremoli, Elena; Tuomilehto, Jaakko; Uitterlinden, André G.; Uusitupa, Matti; Verbeek, André L. M.; Vermeulen, Sita H.; Viikari, Jorma S.; Vitart, Veronique; Völzke, Henry; Vollenweider, Peter; Waeber, Gérard; Walker, Mark; Wallaschofski, Henri; Wareham, Nicholas J.; Watkins, Hugh; Zeggini, Eleftheria; Chakravarti, Aravinda; Clegg, Deborah J.; Cupples, L. Adrienne; Gordon-Larsen, Penny; Jaquish, Cashell E.; Rao, D. C.; Abecasis, Goncalo R.; Assimes, Themistocles L.; Barroso, Inês; Berndt, Sonja I.; Boehnke, Michael; Deloukas, Panos; Fox, Caroline S.; Groop, Leif C.; Hunter, David J.; Ingelsson, Erik; Kaplan, Robert C.; McCarthy, Mark I.; Mohlke, Karen L.; O'Connell, Jeffrey R.; Schlessinger, David; Strachan, David P.; Stefansson, Kari; van Duijn, Cornelia M.; Hirschhorn, Joel N.; Lindgren, Cecilia M.; Heid, Iris M.; North, Kari E.; Borecki, Ingrid B.; Kutalik, Zoltán; Loos, Ruth J. F.

2015-01-01

Genome-wide association studies (GWAS) have identified more than 100 genetic variants contributing to BMI, a measure of body size, or waist-to-hip ratio (adjusted for BMI, WHRadjBMI), a measure of body shape. Body size and shape change as people grow older and these changes differ substantially between men and women. To systematically screen for age- and/or sex-specific effects of genetic variants on BMI and WHRadjBMI, we performed meta-analyses of 114 studies (up to 320,485 individuals of European descent) with genome-wide chip and/or Metabochip data by the Genetic Investigation of Anthropometric Traits (GIANT) Consortium. Each study tested the association of up to ~2.8M SNPs with BMI and WHRadjBMI in four strata (men ≤50y, men >50y, women ≤50y, women >50y) and summary statistics were combined in stratum-specific meta-analyses. We then screened for variants that showed age-specific effects (G x AGE), sex-specific effects (G x SEX) or age-specific effects that differed between men and women (G x AGE x SEX). For BMI, we identified 15 loci (11 previously established for main effects, four novel) that showed significant (FDR<5%) age-specific effects, of which 11 had larger effects in younger (<50y) than in older adults (≥50y). No sex-dependent effects were identified for BMI. For WHRadjBMI, we identified 44 loci (27 previously established for main effects, 17 novel) with sex-specific effects, of which 28 showed larger effects in women than in men, five showed larger effects in men than in women, and 11 showed opposite effects between sexes. No age-dependent effects were identified for WHRadjBMI. This is the first genome-wide interaction meta-analysis to report convincing evidence of age-dependent genetic effects on BMI. In addition, we confirm the sex-specificity of genetic effects on WHRadjBMI. These results may provide further insights into the biology that underlies weight change with age or the sexually dimorphism of body shape. PMID:26426971

Highly Safe Ionic Liquid Electrolytes for Sodium-Ion Battery: Wide Electrochemical Window and Good Thermal Stability.

PubMed

Wu, Feng; Zhu, Na; Bai, Ying; Liu, Libin; Zhou, Hang; Wu, Chuan

2016-08-24

Novel ionic liquid (IL) electrolytes are prepared by mixing 1-ethyl-3-methylimidazolium-bis-tetrafluoroborate (EMIBF4) with different concentrations of sodium salt (NaBF4). The as-prepared IL electrolytes display wide electrochemical windows of ∼4 V (1-5 V), which are consistent with the quantum chemical theoretical calculation. The IL electrolyte with 0.1 M NaBF4 shows excellent ionic conductivity, namely, 9.833 × 10(-3) S cm(-1) at 20 °C. In addition, nonflammability and good thermal stability are exhibited by combustion test and thermogravimetric analysis (TGA), which indicate the high safety of the IL electrolyte.

Wide-angle vision for road views

NASA Astrophysics Data System (ADS)

Huang, F.; Fehrs, K.-K.; Hartmann, G.; Klette, R.

2013-03-01

The field-of-view of a wide-angle image is greater than (say) 90 degrees, and so contains more information than available in a standard image. A wide field-of-view is more advantageous than standard input for understanding the geometry of 3D scenes, and for estimating the poses of panoramic sensors within such scenes. Thus, wide-angle imaging sensors and methodologies are commonly used in various road-safety, street surveillance, street virtual touring, or street 3D modelling applications. The paper reviews related wide-angle vision technologies by focusing on mathematical issues rather than on hardware.

Germany wide seasonal flood risk analysis for agricultural crops

NASA Astrophysics Data System (ADS)

Klaus, Stefan; Kreibich, Heidi; Kuhlmann, Bernd; Merz, Bruno; Schröter, Kai

2016-04-01

In recent years, large-scale flood risk analysis and mapping has gained attention. Regional to national risk assessments are needed, for example, for national risk policy developments, for large-scale disaster management planning and in the (re-)insurance industry. Despite increasing requests for comprehensive risk assessments some sectors have not received much scientific attention, one of these is the agricultural sector. In contrast to other sectors, agricultural crop losses depend strongly on the season. Also flood probability shows seasonal variation. Thus, the temporal superposition of high flood susceptibility of crops and high flood probability plays an important role for agricultural flood risk. To investigate this interrelation and provide a large-scale overview of agricultural flood risk in Germany, an agricultural crop loss model is used for crop susceptibility analyses and Germany wide seasonal flood-frequency analyses are undertaken to derive seasonal flood patterns. As a result, a Germany wide map of agricultural flood risk is shown as well as the crop type most at risk in a specific region. The risk maps may provide guidance for federal state-wide coordinated designation of retention areas.

Mantle dynamics of continent-wide tilting of Australia

NASA Astrophysics Data System (ADS)

Dicaprio, L.; Gurnis, M.; Muller, R. D.

2009-12-01

Australia is distinctive in that during the Cenozoic it experienced first order, broad-scale vertical motions unrelated to normal orogenic processes. The progressive continent-wide tilting down to the northeast is attributed to the horizontal motion of the continent over subducted slabs. We use plate tectonic reconstructions and a model of mantle convection to quantitatively link the geological evolution of the continent to mantle convection. The passage of slabs beneath the Southwest Pacific since 50 Ma is modeled numerically, and the results are compared to geologic observations of anomalous topography. Models show that Australia undergoes a 300 m northeast downward tilt as it approaches and overrides subducted slabs between Melanesia and the active margin along the Loyalty and proto-Tonga Kermadec subduction systems. This pattern of dynamic subsidence is consistent with observations of continent wide tilting and may indicate that during the Cenozoic Australia moved northward away from a relatively hot mantle anomaly presently located beneath Antarctica.

A genome-wide 20 K citrus microarray for gene expression analysis

PubMed Central

Martinez-Godoy, M Angeles; Mauri, Nuria; Juarez, Jose; Marques, M Carmen; Santiago, Julia; Forment, Javier; Gadea, Jose

2008-01-01

Background Understanding of genetic elements that contribute to key aspects of citrus biology will impact future improvements in this economically important crop. Global gene expression analysis demands microarray platforms with a high genome coverage. In the last years, genome-wide EST collections have been generated in citrus, opening the possibility to create new tools for functional genomics in this crop plant. Results We have designed and constructed a publicly available genome-wide cDNA microarray that include 21,081 putative unigenes of citrus. As a functional companion to the microarray, a web-browsable database [1] was created and populated with information about the unigenes represented in the microarray, including cDNA libraries, isolated clones, raw and processed nucleotide and protein sequences, and results of all the structural and functional annotation of the unigenes, like general description, BLAST hits, putative Arabidopsis orthologs, microsatellites, putative SNPs, GO classification and PFAM domains. We have performed a Gene Ontology comparison with the full set of Arabidopsis proteins to estimate the genome coverage of the microarray. We have also performed microarray hybridizations to check its usability. Conclusion This new cDNA microarray replaces the first 7K microarray generated two years ago and allows gene expression analysis at a more global scale. We have followed a rational design to minimize cross-hybridization while maintaining its utility for different citrus species. Furthermore, we also provide access to a website with full structural and functional annotation of the unigenes represented in the microarray, along with the ability to use this site to directly perform gene expression analysis using standard tools at different publicly available servers. Furthermore, we show how this microarray offers a good representation of the citrus genome and present the usefulness of this genomic tool for global studies in citrus by using it to

Bandgap engineering in semiconductor alloy nanomaterials with widely tunable compositions

NASA Astrophysics Data System (ADS)

Ning, Cun-Zheng; Dou, Letian; Yang, Peidong

2017-12-01

Over the past decade, tremendous progress has been achieved in the development of nanoscale semiconductor materials with a wide range of bandgaps by alloying different individual semiconductors. These materials include traditional II-VI and III-V semiconductors and their alloys, inorganic and hybrid perovskites, and the newly emerging 2D materials. One important common feature of these materials is that their nanoscale dimensions result in a large tolerance to lattice mismatches within a monolithic structure of varying composition or between the substrate and target material, which enables us to achieve almost arbitrary control of the variation of the alloy composition. As a result, the bandgaps of these alloys can be widely tuned without the detrimental defects that are often unavoidable in bulk materials, which have a much more limited tolerance to lattice mismatches. This class of nanomaterials could have a far-reaching impact on a wide range of photonic applications, including tunable lasers, solid-state lighting, artificial photosynthesis and new solar cells.

Women show a higher level of anxiety during IVF treatment than men and hold different concerns: a cohort study.

PubMed

Schaller, Martin Alexander; Griesinger, Georg; Banz-Jansen, Constanze

2016-05-01

The aim of the present study was to determine levels of anxiety during the course of IVF treatment and gender differences in treatment anxiety. This was a prospective cohort study set in a university affiliated, tertiary care IVF program. 119 women and 82 men entering the clinic to undergo IVF treatment filled out questionnaires containing the Spielberger state-trait-anxiety-inventory (STAI) as well as further items on specific stress triggers. Women and men undergoing IVF have higher levels of anxiety than the average population in Germany. Overall, female patients show significantly higher values (mean ± SD) for state and trait anxiety (47.4 ± 11.0 and 40.1 ± 9.85) than their male partners (41.4 ± 9.66 and 35.3 ± 8.57, p < 0.01). Over the course of several IVF cycles, average STAI scores increased for both genders. When asked about specific stress factors on a 4-point scale from 'not at all' to 'very much so', women report as their main anxiety the failure to achieve a successful pregnancy, scoring significantly higher on questions like 'obtaining a negative pregnancy test' (3.24 ± 0.82, p < 0.01) and 'disclosure of infertility' (3.02 ± 1.10, p < 0.001). Their male partners are more concerned about the health risks the women have to take such as 'side effects of ovarian stimulation' (2.55 ± 0.77, p = 0.002) and 'bleeding or infection after the oocyte aspiration' (2.58 ± 0.84, p = 0.007). Both genders indicated to be very little worried about multiple pregnancies after IVF. Women show a higher level of anxiety during IVF treatment and hold different concerns. Neither of the sexes appears to be familiar with the risks associated with multiple pregnancies, a matter that should better be addressed.

Large differences in proportions of harmful and benign amino acid substitutions between proteins and diseases.

PubMed

Schaafsma, Gerard C P; Vihinen, Mauno

2017-07-01

Genes and proteins are known to have differences in their sensitivity to alterations. Despite numerous sequencing studies, proportions of harmful and harmless substitutions are not known for proteins and groups of proteins. To address this question, we predicted the outcome for all possible single amino acid substitutions (AASs) in nine representative protein groups by using the PON-P2 method. The effects on 996 proteins were studied and vast differences were noticed. Proteins in the cancer group harbor the largest proportion of harmful variants (42.1%), whereas the non-disease group of proteins not known to have a disease association and not involved in the housekeeping functions had the lowest number of harmful variants (4.2%). Differences in the proportions of the harmful and benign variants are wide within each group, but they still show clear differences between the groups. Frequently appearing protein domains show a wide spectrum of variant frequencies, whereas no major protein structural class-specific differences were noticed. AAS types in the original and variant residues showed distinctive patterns, which are shared by all the protein groups. The observations are relevant for understanding genetic bases of diseases, variation interpretation, and for the development of methods for that purpose. © 2017 Wiley Periodicals, Inc.

Wide field and highly sensitive angiography based on optical coherence tomography with akinetic swept source.

PubMed

Xu, Jingjiang; Song, Shaozhen; Wei, Wei; Wang, Ruikang K

2017-01-01

Wide-field vascular visualization in bulk tissue that is of uneven surface is challenging due to the relatively short ranging distance and significant sensitivity fall-off for most current optical coherence tomography angiography (OCTA) systems. We report a long ranging and ultra-wide-field OCTA (UW-OCTA) system based on an akinetic swept laser. The narrow instantaneous linewidth of the swept source with its high phase stability, combined with high-speed detection in the system enable us to achieve long ranging (up to 46 mm) and almost negligible system sensitivity fall-off. To illustrate these advantages, we compare the basic system performances between conventional spectral domain OCTA and UW-OCTA systems and their functional imaging of microvascular networks in living tissues. In addition, we show that the UW-OCTA is capable of different depth-ranging of cerebral blood flow within entire brain in mice, and providing unprecedented blood perfusion map of human finger in vivo . We believe that the UW-OCTA system has promises to augment the existing clinical practice and explore new biomedical applications for OCT imaging.

Wide field and highly sensitive angiography based on optical coherence tomography with akinetic swept source

PubMed Central

Xu, Jingjiang; Song, Shaozhen; Wei, Wei; Wang, Ruikang K.

2016-01-01

Wide-field vascular visualization in bulk tissue that is of uneven surface is challenging due to the relatively short ranging distance and significant sensitivity fall-off for most current optical coherence tomography angiography (OCTA) systems. We report a long ranging and ultra-wide-field OCTA (UW-OCTA) system based on an akinetic swept laser. The narrow instantaneous linewidth of the swept source with its high phase stability, combined with high-speed detection in the system enable us to achieve long ranging (up to 46 mm) and almost negligible system sensitivity fall-off. To illustrate these advantages, we compare the basic system performances between conventional spectral domain OCTA and UW-OCTA systems and their functional imaging of microvascular networks in living tissues. In addition, we show that the UW-OCTA is capable of different depth-ranging of cerebral blood flow within entire brain in mice, and providing unprecedented blood perfusion map of human finger in vivo. We believe that the UW-OCTA system has promises to augment the existing clinical practice and explore new biomedical applications for OCT imaging. PMID:28101428

Accumulation characteristics and correlation analysis of five ginsenosides with different cultivation ages from different regions.

PubMed

Xiao, Dan; Yue, Hao; Xiu, Yang; Sun, Xiuli; Wang, YiBo; Liu, ShuYing

2015-10-01

Ginseng (the roots of Panax ginseng Meyer) is a well-known traditional Oriental medicine and is now widely used as a health food. It contains several types of ginsenosides, which are considered the major active medicinal components of ginseng. It has recently been reported that the qualitative and quantitative properties of ginsenosides found in ginseng may differ, depending on cultivation regions, ages, species, and so on. Therefore, it is necessary to study these variations with respect to cultivation ages and regions. In this study, 3-6-yr-old roots of P. ginseng were collected from three different cultivation regions. The contents of five ginsenosides (Rb1, Rd, Rc, Re, and Rgl) were measured by rapid resolution liquid chromatography coupled with quadruple-time-of-flight mass spectrometry. The Kruskal-Wallis Rank sum test and multiple t test were used for comparative analysis of the data to evaluate the dynamic changes in the accumulation of these ginsenosides affected by cultivation regions and ages. The content and composition of ginsenosides varied significantly among specimens collected from different cultivation regions and having different cultivation ages. For all samples, the content of Rg1 and Re ginsenosides increases with age and this rate of increase is different for each sample. The contents of Rb1, Rc, and Rd varied with cultivation ages in samples from different cultivation regions; especially, Rb1 from a 6-yr-old root showed approximately twofold variation among the samples from three cultivation regions. Furthermore, the content of Rb1 highly correlated with that of Rd (r = 0.89 across all locations and ages). In our study, only the contents of ginsenosides Rg1 and Re were affected by the root age. Ginsenosides Rb1, Rc, and Rd varied widely with ages in samples from different cultivation regions.

Identifying Pleiotropic Genes in Genome-Wide Association Studies for Multivariate Phenotypes with Mixed Measurement Scales

PubMed Central

Williams, L. Keoki; Buu, Anne

2017-01-01

We propose a multivariate genome-wide association test for mixed continuous, binary, and ordinal phenotypes. A latent response model is used to estimate the correlation between phenotypes with different measurement scales so that the empirical distribution of the Fisher’s combination statistic under the null hypothesis is estimated efficiently. The simulation study shows that our proposed correlation estimation methods have high levels of accuracy. More importantly, our approach conservatively estimates the variance of the test statistic so that the type I error rate is controlled. The simulation also shows that the proposed test maintains the power at the level very close to that of the ideal analysis based on known latent phenotypes while controlling the type I error. In contrast, conventional approaches–dichotomizing all observed phenotypes or treating them as continuous variables–could either reduce the power or employ a linear regression model unfit for the data. Furthermore, the statistical analysis on the database of the Study of Addiction: Genetics and Environment (SAGE) demonstrates that conducting a multivariate test on multiple phenotypes can increase the power of identifying markers that may not be, otherwise, chosen using marginal tests. The proposed method also offers a new approach to analyzing the Fagerström Test for Nicotine Dependence as multivariate phenotypes in genome-wide association studies. PMID:28081206

Anthropometric indices for non-pregnant women of childbearing age differ widely among four low-middle income populations.

PubMed

Hambidge, K Michael; Krebs, Nancy F; Garcés, Ana; Westcott, Jamie E; Figueroa, Lester; Goudar, Shivaprasad S; Dhaded, Sangappa; Pasha, Omrana; Aziz Ali, Sumera; Tshefu, Antoinette; Lokangaka, Adrien; Thorsten, Vanessa R; Das, Abhik; Stolka, Kristen; McClure, Elizabeth M; Lander, Rebecca L; Bose, Carl L; Derman, Richard J; Goldenberg, Robert L; Bauserman, Melissa

2017-07-24

Maternal stature and body mass indices (BMI) of non-pregnant women (NPW) of child bearing age are relevant to maternal and offspring health. The objective was to compare anthropometric indices of NPW in four rural communities in low- to low-middle income countries (LMIC). Anthropometry and maternal characteristics/household wealth questionnaires were obtained for NPW enrolled in the Women First Preconception Maternal Nutrition Trial. Body mass index (BMI, kg/m 2 ) was calculated. Z-scores were determined using WHO reference data. A total of 7268 NPW participated in Equateur, DRC (n = 1741); Chimaltenango, Guatemala (n = 1695); North Karnataka, India (n = 1823); and Thatta, Sindh, Pakistan (n = 2009). Mean age was 23 y and mean parity 1.5. Median (P25-P75) height (cm) ranged from 145.5 (142.2-148.9) in Guatemala to 156.0 (152.0-160.0) in DRC. Median weight (kg) ranged from 44.7 (39.9-50.3) in India to 52.7 (46.9-59.8) in Guatemala. Median BMI ranged from 19.4 (17.6-21.9) in India to 24.9 (22.3-28.0) in Guatemala. Percent stunted (<-2SD height for age z-score) ranged from 13.9% in DRC to 80.5% in Guatemala; % underweight (BMI <18.5) ranged from 1.2% in Guatemala to 37.1% in India; % overweight/obese (OW, BMI ≥25.0) ranged from 5.7% in DRC to 49.3% in Guatemala. For all sites, indicators for higher SES and higher age were associated with BMI. Lower SES women were underweight more frequently and higher SES women were OW more frequently at all sites. Younger women tended to be underweight, while older women tended to be OW. Anthropometric data for NPW varied widely among low-income rural populations in four countries located on three different continents. Global comparisons of anthropometric measurements across sites using standard reference data serve to highlight major differences among populations of low-income rural NPW and assist in evaluating the rationale for and the design of optimal intervention trials. ClinicalTrials.gov # NCT01883193 (18 June 2013

A Six Months Exercise Intervention Influences the Genome-wide DNA Methylation Pattern in Human Adipose Tissue

PubMed Central

Rönn, Tina; Volkov, Petr; Davegårdh, Cajsa; Dayeh, Tasnim; Hall, Elin; Olsson, Anders H.; Nilsson, Emma; Tornberg, Åsa; Dekker Nitert, Marloes; Eriksson, Karl-Fredrik; Jones, Helena A.; Groop, Leif; Ling, Charlotte

2013-01-01

Epigenetic mechanisms are implicated in gene regulation and the development of different diseases. The epigenome differs between cell types and has until now only been characterized for a few human tissues. Environmental factors potentially alter the epigenome. Here we describe the genome-wide pattern of DNA methylation in human adipose tissue from 23 healthy men, with a previous low level of physical activity, before and after a six months exercise intervention. We also investigate the differences in adipose tissue DNA methylation between 31 individuals with or without a family history of type 2 diabetes. DNA methylation was analyzed using Infinium HumanMethylation450 BeadChip, an array containing 485,577 probes covering 99% RefSeq genes. Global DNA methylation changed and 17,975 individual CpG sites in 7,663 unique genes showed altered levels of DNA methylation after the exercise intervention (q<0.05). Differential mRNA expression was present in 1/3 of gene regions with altered DNA methylation, including RALBP1, HDAC4 and NCOR2 (q<0.05). Using a luciferase assay, we could show that increased DNA methylation in vitro of the RALBP1 promoter suppressed the transcriptional activity (p = 0.03). Moreover, 18 obesity and 21 type 2 diabetes candidate genes had CpG sites with differences in adipose tissue DNA methylation in response to exercise (q<0.05), including TCF7L2 (6 CpG sites) and KCNQ1 (10 CpG sites). A simultaneous change in mRNA expression was seen for 6 of those genes. To understand if genes that exhibit differential DNA methylation and mRNA expression in human adipose tissue in vivo affect adipocyte metabolism, we silenced Hdac4 and Ncor2 respectively in 3T3-L1 adipocytes, which resulted in increased lipogenesis both in the basal and insulin stimulated state. In conclusion, exercise induces genome-wide changes in DNA methylation in human adipose tissue, potentially affecting adipocyte metabolism. PMID:23825961

Variation in the susceptibility of Drosophila to different entomopathogenic nematodes.

PubMed

Peña, Jennifer M; Carrillo, Mayra A; Hallem, Elissa A

2015-03-01

Entomopathogenic nematodes (EPNs) in the genera Heterorhabditis and Steinernema are lethal parasites of insects that are of interest as models for understanding parasite-host interactions and as biocontrol agents for insect pests. EPNs harbor a bacterial endosymbiont in their gut that assists in insect killing. EPNs are capable of infecting and killing a wide range of insects, yet how the nematodes and their bacterial endosymbionts interact with the insect immune system is poorly understood. Here, we develop a versatile model system for understanding the insect immune response to parasitic nematode infection that consists of seven species of EPNs as model parasites and five species of Drosophila fruit flies as model hosts. We show that the EPN Steinernema carpocapsae, which is widely used for insect control, is capable of infecting and killing D. melanogaster larvae. S. carpocapsae is associated with the bacterium Xenorhabdus nematophila, and we show that X. nematophila induces expression of a subset of antimicrobial peptide genes and suppresses the melanization response to the nematode. We further show that EPNs vary in their virulence toward D. melanogaster and that Drosophila species vary in their susceptibilities to EPN infection. Differences in virulence among different EPN-host combinations result from differences in both rates of infection and rates of postinfection survival. Our results establish a powerful model system for understanding mechanisms of host-parasite interactions and the insect immune response to parasitic nematode infection. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Wide-Field Imaging Using Nitrogen Vacancies

NASA Technical Reports Server (NTRS)

Englund, Dirk Robert (Inventor); Trusheim, Matthew Edwin (Inventor)

2017-01-01

Nitrogen vacancies in bulk diamonds and nanodiamonds can be used to sense temperature, pressure, electromagnetic fields, and pH. Unfortunately, conventional sensing techniques use gated detection and confocal imaging, limiting the measurement sensitivity and precluding wide-field imaging. Conversely, the present sensing techniques do not require gated detection or confocal imaging and can therefore be used to image temperature, pressure, electromagnetic fields, and pH over wide fields of view. In some cases, wide-field imaging supports spatial localization of the NVs to precisions at or below the diffraction limit. Moreover, the measurement range can extend over extremely wide dynamic range at very high sensitivity.

Local and Widely Distributed EEG Activity in Schizophrenia With Prevalence of Negative Symptoms.

PubMed

Grin-Yatsenko, Vera A; Ponomarev, Valery A; Pronina, Marina V; Poliakov, Yury I; Plotnikova, Irina V; Kropotov, Juri D

2017-09-01

We evaluated EEG frequency abnormalities in resting state (eyes closed and eyes open) EEG in a group of chronic schizophrenia patients as compared with healthy subjects. The study included 3 methods of analysis of deviation of EEG characteristics: genuine EEG, current source density (CSD), and group independent component (gIC). All 3 methods have shown that the EEG in schizophrenia patients is characterized by enhanced low-frequency (delta and theta) and high-frequency (beta) activity in comparison with the control group. However, the spatial pattern of differences was dependent on the type of method used. Comparative analysis has shown that increased EEG power in schizophrenia patients apparently concerns both widely spatially distributed components and local components of signal. Furthermore, the observed differences in the delta and theta range can be described mainly by the local components, and those in the beta range mostly by spatially widely distributed ones. The possible nature of the widely distributed activity is discussed.

[Differences of vegetation phenology monitoring by remote sensing based on different spectral vegetation indices.

PubMed

Zuo, Lu; Wang, Huan Jiong; Liu, Rong Gao; Liu, Yang; Shang, Rong

2018-02-01

Vegetation phenology is a comprehensive indictor for the responses of terrestrial ecosystem to climatic and environmental changes. Remote sensing spectrum has been widely used in the extraction of vegetation phenology information. However, there are many differences between phenology extracted by remote sensing and site observations, with their physical meaning remaining unclear. We selected one tile of MODIS data in northeastern China (2000-2014) to examine the SOS and EOS differences derived from the normalized difference vegetation index (NDVI) and the simple ratio vegetation index (SR) based on both the red and near-infrared bands. The results showed that there were significant differences between NDVI-phenology and SR-phenology. SOS derived from NDVI averaged 18.9 days earlier than that from SR. EOS derived from NDVI averaged 19.0 days later than from SR. NDVI-phenology had a longer growing season. There were significant differences in the inter-annual variation of phenology from NDVI and SR. More than 20% of the pixel SOS and EOS derived from NDVI and SR showed the opposite temporal trend. These results caused by the seasonal curve characteristics and noise resistance differences of NDVI and SR. The observed data source of NDVI and SR were completely consistent, only the mathematical expressions were different, but phenology results were significantly different. Our results indicated that vegetation phenology monitoring by remote sensing is highly dependent on the mathematical expression of vegetation index. How to establish a reliable method for extracting vegetation phenology by remote sensing needs further research.

Ultra-widely tunable long-period holey-fiber grating by the use of mechanical pressure.

PubMed

Ceballos-Herrera, D E; Torres-Gómez, I; Martínez-Ríos, A; Anzueto-Sánchez, G; Alvarez-Chávez, J A; Selvas-Aguilar, R; Sánchez-Mondragón, J J

2007-01-20

We report an ultra-widely tunable long-period holey-fiber grating, which combines the wide-range single-mode behavior and transverse strain sensitivity of the holey fibers with the advantages of mechanically induced long-period fiber gratings. We obtain a versatile widely tunable long-period holey-fiber grating with attractive transmission spectral characteristics for optical communications, fiber-based amplifiers, and lasers. The mechanically induced long-period holey-fiber grating shows a continuous tuning range over 500 nm, more than 12 dB depth notches with less than 0.75 dB out-of-band losses, and bandwidth control from 10 to 40 nm.

Genome-Wide Association Studies of 11 Agronomic Traits in Cassava (Manihot esculenta Crantz)

PubMed Central

Zhang, Shengkui; Chen, Xin; Lu, Cheng; Ye, Jianqiu; Zou, Meiling; Lu, Kundian; Feng, Subin; Pei, Jinli; Liu, Chen; Zhou, Xincheng; Ma, Ping’an; Li, Zhaogui; Liu, Cuijuan; Liao, Qi; Xia, Zhiqiang; Wang, Wenquan

2018-01-01

Cassava (Manihot esculenta Crantz) is a major tuberous crop produced worldwide. In this study, we sequenced 158 diverse cassava varieties and identified 349,827 single-nucleotide polymorphisms (SNPs) and indels. In each chromosome, the number of SNPs and the physical length of the respective chromosome were in agreement. Population structure analysis indicated that this panel can be divided into three subgroups. Genetic diversity analysis indicated that the average nucleotide diversity of the panel was 1.21 × 10-4 for all sampled landraces. This average nucleotide diversity was 1.97 × 10-4, 1.01 × 10-4, and 1.89 × 10-4 for subgroups 1, 2, and 3, respectively. Genome-wide linkage disequilibrium (LD) analysis demonstrated that the average LD was about ∼8 kb. We evaluated 158 cassava varieties under 11 different environments. Finally, we identified 36 loci that were related to 11 agronomic traits by genome-wide association analyses. Four loci were associated with two traits, and 62 candidate genes were identified in the peak SNP sites. We found that 40 of these genes showed different expression profiles in different tissues. Of the candidate genes related to storage roots, Manes.13G023300, Manes.16G000800, Manes.02G154700, Manes.02G192500, and Manes.09G099100 had higher expression levels in storage roots than in leaf and stem; on the other hand, of the candidate genes related to leaves, Manes.05G164500, Manes.05G164600, Manes.04G057300, Manes.01G202000, and Manes.03G186500 had higher expression levels in leaves than in storage roots and stem. This study provides basis for research on genetics and the genetic improvement of cassava. PMID:29725343

Genome-Wide Association Studies of 11 Agronomic Traits in Cassava (Manihot esculenta Crantz).

PubMed

Zhang, Shengkui; Chen, Xin; Lu, Cheng; Ye, Jianqiu; Zou, Meiling; Lu, Kundian; Feng, Subin; Pei, Jinli; Liu, Chen; Zhou, Xincheng; Ma, Ping'an; Li, Zhaogui; Liu, Cuijuan; Liao, Qi; Xia, Zhiqiang; Wang, Wenquan

2018-01-01

Cassava ( Manihot esculenta Crantz) is a major tuberous crop produced worldwide. In this study, we sequenced 158 diverse cassava varieties and identified 349,827 single-nucleotide polymorphisms (SNPs) and indels. In each chromosome, the number of SNPs and the physical length of the respective chromosome were in agreement. Population structure analysis indicated that this panel can be divided into three subgroups. Genetic diversity analysis indicated that the average nucleotide diversity of the panel was 1.21 × 10 -4 for all sampled landraces. This average nucleotide diversity was 1.97 × 10 -4 , 1.01 × 10 -4 , and 1.89 × 10 -4 for subgroups 1, 2, and 3, respectively. Genome-wide linkage disequilibrium (LD) analysis demonstrated that the average LD was about ∼8 kb. We evaluated 158 cassava varieties under 11 different environments. Finally, we identified 36 loci that were related to 11 agronomic traits by genome-wide association analyses. Four loci were associated with two traits, and 62 candidate genes were identified in the peak SNP sites. We found that 40 of these genes showed different expression profiles in different tissues. Of the candidate genes related to storage roots, Manes.13G023300, Manes.16G000800, Manes.02G154700, Manes.02G192500, and Manes.09G099100 had higher expression levels in storage roots than in leaf and stem; on the other hand, of the candidate genes related to leaves, Manes.05G164500, Manes.05G164600, Manes.04G057300, Manes.01G202000, and Manes.03G186500 had higher expression levels in leaves than in storage roots and stem. This study provides basis for research on genetics and the genetic improvement of cassava.

Differences in exam performance between pupils attending selective and non-selective schools mirror the genetic differences between them

NASA Astrophysics Data System (ADS)

Smith-Woolley, Emily; Pingault, Jean-Baptiste; Selzam, Saskia; Rimfeld, Kaili; Krapohl, Eva; von Stumm, Sophie; Asbury, Kathryn; Dale, Philip S.; Young, Toby; Allen, Rebecca; Kovas, Yulia; Plomin, Robert

2018-03-01

On average, students attending selective schools outperform their non-selective counterparts in national exams. These differences are often attributed to value added by the school, as well as factors schools use to select pupils, including ability, achievement and, in cases where schools charge tuition fees or are located in affluent areas, socioeconomic status. However, the possible role of DNA differences between students of different schools types has not yet been considered. We used a UK-representative sample of 4814 genotyped students to investigate exam performance at age 16 and genetic differences between students in three school types: state-funded, non-selective schools (`non-selective'), state-funded, selective schools (`grammar') and private schools, which are selective (`private'). We created a genome-wide polygenic score (GPS) derived from a genome-wide association study of years of education (EduYears). We found substantial mean genetic differences between students of different school types: students in non-selective schools had lower EduYears GPS compared to those in grammar (d = 0.41) and private schools (d = 0.37). Three times as many students in the top EduYears GPS decile went to a selective school compared to the bottom decile. These results were mirrored in the exam differences between school types. However, once we controlled for factors involved in pupil selection, there were no significant genetic differences between school types, and the variance in exam scores at age 16 explained by school type dropped from 7% to <1%. These results show that genetic and exam differences between school types are primarily due to the heritable characteristics involved in pupil admission.

Genome-wide differences in hepatitis C- vs alcoholism-associated hepatocellular carcinoma

PubMed Central

Derambure, Céline; Coulouarn, Cédric; Caillot, Frédérique; Daveau, Romain; Hiron, Martine; Scotte, Michel; François, Arnaud; Duclos, Celia; Goria, Odile; Gueudin, Marie; Cavard, Catherine; Terris, Benoit; Daveau, Maryvonne; Salier, Jean-Philippe

2008-01-01

AIM: To look at a comprehensive picture of etiology-dependent gene abnormalities in hepatocellular carcinoma in Western Europe. METHODS: With a liver-oriented microarray, transcript levels were compared in nodules and cirrhosis from a training set of patients with hepatocellular carcinoma (alcoholism, 12; hepatitis C, 10) and 5 controls. Loose or tight selection of informative transcripts with an abnormal abundance was statistically valid and the tightly selected transcripts were next quantified by qRTPCR in the nodules from our training set (12 + 10) and a test set (6 + 7). RESULTS: A selection of 475 transcripts pointed to significant gene over-representation on chromosome 8 (alcoholism) or -2 (hepatitis C) and ontology indicated a predominant inflammatory response (alcoholism) or changes in cell cycle regulation, transcription factors and interferon responsiveness (hepatitis C). A stringent selection of 23 transcripts whose differences between etiologies were significant in nodules but not in cirrhotic tissue indicated that the above dysregulations take place in tumor but not in the surrounding cirrhosis. These 23 transcripts separated our test set according to etiologies. The inflammation-associated transcripts pointed to limited alterations of free iron metabolism in alcoholic vs hepatitis C tumors. CONCLUSION: Etiology-specific abnormalities (chromosome preference; differences in transcriptomes and related functions) have been identified in hepatocellular carcinoma driven by alcoholism or hepatitis C. This may open novel avenues for differential therapies in this disease. PMID:18350606

Meta-analysis of genome-wide association from genomic prediction models

USDA-ARS?s Scientific Manuscript database

A limitation of many genome-wide association studies (GWA) in animal breeding is that there are many loci with small effect sizes; thus, larger sample sizes (N) are required to guarantee suitable power of detection. To increase sample size, results from different GWA can be combined in a meta-analys...

Development of a Piezoelectric Vacuum Sensing Component for a Wide Pressure Range

PubMed Central

Wang, Bing-Yu; Hsieh, Fan-Chun; Lin, Che-Yu; Chen, Shao-En; Chen, Fong-Zhi; Wu, Chia-Che

2014-01-01

In this study, we develop a clamped–clamped beam-type piezoelectric vacuum pressure sensing element. The clamped–clamped piezoelectric beam is composed of a PZT layer and a copper substrate. A pair of electrodes is set near each end. An input voltage is applied to a pair of electrodes to vibrate the piezoelectric beam, and the output voltage is measured at the other pair. Because the viscous forces on the piezoelectric beam vary at different air pressures, the vibration of the beam depends on the vacuum pressure. The developed pressure sensor can sense a wide range of pressure, from 6.5 × 10−6 to 760 Torr. The experimental results showed that the output voltage is inversely proportional to the gas damping ratio, and thus, the vacuum pressure was estimated from the output voltage. PMID:25421736

Generalized weighted ratio method for accurate turbidity measurement over a wide range.

PubMed

Liu, Hongbo; Yang, Ping; Song, Hong; Guo, Yilu; Zhan, Shuyue; Huang, Hui; Wang, Hangzhou; Tao, Bangyi; Mu, Quanquan; Xu, Jing; Li, Dejun; Chen, Ying

2015-12-14

Turbidity measurement is important for water quality assessment, food safety, medicine, ocean monitoring, etc. In this paper, a method that accurately estimates the turbidity over a wide range is proposed, where the turbidity of the sample is represented as a weighted ratio of the scattered light intensities at a series of angles. An improvement in the accuracy is achieved by expanding the structure of the ratio function, thus adding more flexibility to the turbidity-intensity fitting. Experiments have been carried out with an 850 nm laser and a power meter fixed on a turntable to measure the light intensity at different angles. The results show that the relative estimation error of the proposed method is 0.58% on average for a four-angle intensity combination for all test samples with a turbidity ranging from 160 NTU to 4000 NTU.

Wide Field Camera 3 Accommodations for HST Robotics Servicing Mission

NASA Technical Reports Server (NTRS)

Ginyard, Amani

2005-01-01

This slide presentation discusses the objectives of the Hubble Space Telescope (HST) Robotics Servicing and Deorbit Mission (HRSDM), reviews the Wide Field Camera 3 (WFC3), and also reviews the contamination accomodations for the WFC3. The objectives of the HRSDM are (1) to provide a disposal capability at the end of HST's useful life, (2) to upgrade the hardware by installing two new scientific instruments: replace the Corrective Optics Space Telescope Axial Replacement (COSTAR) with the Cosmic Origins Spectrograph (COS), and to replace the Wide Field/Planetary Camera-2 (WFPC2) with Wide Field Camera-3, and (3) Extend the Scientific life of HST for a minimum of 5 years after servicing. Included are slides showing the Hubble Robotic Vehicle (HRV) and slides describing what the HRV contains. There are also slides describing the WFC3. One of the mechanisms of the WFC3 is to serve partially as replacement gyroscopes for HST. There are also slides that discuss the contamination requirements for the Rate Sensor Units (RSUs), that are part of the Rate Gyroscope Assembly on the WFC3.

Design of a polarization-independent, wide-angle, broadband visible absorber

NASA Astrophysics Data System (ADS)

Jia, Xiuli; Wang, Xiaoou

2018-01-01

Many optical systems benefit from elements that can absorb a broad range of wavelengths over a wide range of angles, independent of polarization. In this paper, we present a polarization-independent, wide-angle, broadband absorber in the visible regime that exploits strong symmetric and asymmetric resonance modes of electromagnetic dipoles. It makes use of a bilayer cross-pattern structure which is simple, having five layers that include two stacks of metal ribbon in cross-patterns, two dielectric spacers and a metal reflecting layer. Simulations show that the design exhibits a significantly enhanced absorption property when compared to a device with a bilayer metal film structure or any other complex structure of cross-patterns that have no intersection angle. The maximum absorption efficiency of the device is 100% at resonances, and its absorption characteristics can be maintained over a wide range of angles of incidence - up to ± 60° - regardless of the incident polarization. This strategy can, in principle, be applied to other material systems and could be useful in diverse applications, including thermal emitters, photovoltaics and photodetectors.

Widely tunable and monochromatic terahertz difference frequency generation with organic crystal 2-(3-(4-hydroxystyryl)-5,5-dime-thylcyclohex-2-enylidene) malononitrile

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

Liu, Pengxiang; The Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics and TEDA Applied Physics Institute, Nankai University, Tianjin 300071; Zhang, Xinyuan

2016-01-04

We report an experimental study on widely tunable terahertz (THz) wave difference frequency generation (DFG) with hydrogen-bonded crystals 2-(3-(4-hydroxystyryl)-5,5-dime-thylcyclohex-2-enylidene) malononitrile (OH1). The organic crystals were pumped by a ∼1.3 μm double-pass KTiOPO{sub 4} optical parametric oscillator. A tuning range of 0.02–20 THz was achieved. OH1 crystals offer a long effective interaction length (also high output) for the generation below 3 THz, owing to the low absorption and favorable phase-matching. The highest energy of 507 nJ/pulse was generated at 1.92 THz with a 1.89-mm-thick crystal. Comprehensive explanations were provided, on the basis of theoretical calculations. Cascading phenomenon during the DFG process wasmore » demonstrated. The photon conversion efficiency could reach 2.9%.« less

Differential wide temperature range CMOS interface circuit for capacitive MEMS pressure sensors.

PubMed

Wang, Yucai; Chodavarapu, Vamsy P

2015-02-12

We describe a Complementary Metal-Oxide Semiconductor (CMOS) differential interface circuit for capacitive Micro-Electro-Mechanical Systems (MEMS) pressure sensors that is functional over a wide temperature range between -55 °C and 225 °C. The circuit is implemented using IBM 0.13 μm CMOS technology with 2.5 V power supply. A constant-gm biasing technique is used to mitigate performance degradation at high temperatures. The circuit offers the flexibility to interface with MEMS sensors with a wide range of the steady-state capacitance values from 0.5 pF to 10 pF. Simulation results show that the circuitry has excellent linearity and stability over the wide temperature range. Experimental results confirm that the temperature effects on the circuitry are small, with an overall linearity error around 2%.

Differential Wide Temperature Range CMOS Interface Circuit for Capacitive MEMS Pressure Sensors

PubMed Central

Wang, Yucai; Chodavarapu, Vamsy P.

2015-01-01

We describe a Complementary Metal-Oxide Semiconductor (CMOS) differential interface circuit for capacitive Micro-Electro-Mechanical Systems (MEMS) pressure sensors that is functional over a wide temperature range between −55 °C and 225 °C. The circuit is implemented using IBM 0.13 μm CMOS technology with 2.5 V power supply. A constant-gm biasing technique is used to mitigate performance degradation at high temperatures. The circuit offers the flexibility to interface with MEMS sensors with a wide range of the steady-state capacitance values from 0.5 pF to 10 pF. Simulation results show that the circuitry has excellent linearity and stability over the wide temperature range. Experimental results confirm that the temperature effects on the circuitry are small, with an overall linearity error around 2%. PMID:25686312

Gastrointestinal Simulation Model TWIN-SHIME Shows Differences between Human Urolithin-Metabotypes in Gut Microbiota Composition, Pomegranate Polyphenol Metabolism, and Transport along the Intestinal Tract.

PubMed

García-Villalba, Rocío; Vissenaekens, Hanne; Pitart, Judit; Romo-Vaquero, María; Espín, Juan C; Grootaert, Charlotte; Selma, María V; Raes, Katleen; Smagghe, Guy; Possemiers, Sam; Van Camp, John; Tomas-Barberan, Francisco A

2017-07-12

A TWIN-SHIME system was used to compare the metabolism of pomegranate polyphenols by the gut microbiota from two individuals with different urolithin metabotypes. Gut microbiota, ellagitannin metabolism, short-chain fatty acids (SCFA), transport of metabolites, and phase II metabolism using Caco-2 cells were explored. The simulation reproduced the in vivo metabolic profiles for each metabotype. The study shows for the first time that microbial composition, metabolism of ellagitannins, and SCFA differ between metabotypes and along the large intestine. The assay also showed that pomegranate phenolics preserved intestinal cell integrity. Pomegranate polyphenols enhanced urolithin and propionate production, as well as Akkermansia and Gordonibacter prevalence with the highest effect in the descending colon. The system provides an insight into the mechanisms of pomegranate polyphenol gut microbiota metabolism and absorption through intestinal cells. The results obtained by the combined SHIME/Caco-2 cell system are consistent with previous human and animal studies and show that although urolithin metabolites are present along the gastrointestinal tract due to enterohepatic circulation, they are predominantly produced in the distal colon region.

Differences in the API 20E biochemical patterns of clinical and environmental Vibrio parahaemolyticus isolates.

PubMed

Martinez-Urtaza, Jaime; Lozano-Leon, Antonio; Viña-Feas, Alejandro; de Novoa, Jacobo; Garcia-Martin, Oscar

2006-02-01

Genetic differences in clinical and environmental strains of Vibrio parahaemolyticus have been widely used as criteria in identifying pathogenic isolates. However, few studies have been carried out to assess the differences in biochemical characteristics of V. parahaemolyticus isolates from human and environmental sources. We compared the biochemical profiles obtained by the characterization of V. parahaemolyticus isolates from human infections and the marine environment using the API 20E system. Environmental and clinical isolates showed significant differences in the gelatin and arabinose tests. Additionally, clinical isolates were correctly identified according to the API 20E profile using 0.85% NaCl diluent, but they presented nonspecific profiles with 2% NaCl diluent. In contrast, use of 2% NaCl diluent facilitated correct identification of the environmental isolates. Clinical isolates showed significant differences in up to five biochemical tests with respect to the API 20E database. The API 20E system is widely used in routine identification of bacteria in clinical laboratories, and this discrepancy in an important number of biochemical tests may lead to misidentification of V. parahaemolyticus infection.

Improving Hospital-wide Patient Scheduling Decisions by Clinical Pathway Mining.

PubMed

Gartner, Daniel; Arnolds, Ines V; Nickel, Stefan

2015-01-01

Recent research has highlighted the need for solving hospital-wide patient scheduling problems. Inpatient scheduling, patient activities have to be scheduled on scarce hospital resources such that temporal relations between activities (e.g. for recovery times) are ensured. Common objectives are, among others, the minimization of the length of stay (LOS). In this paper, we consider a hospital-wide patient scheduling problem with LOS minimization based on uncertain clinical pathways. We approach the problem in three stages: First, we learn most likely clinical pathways using a sequential pattern mining approach. Second, we provide a mathematical model for patient scheduling and finally, we combine the two approaches. In an experimental study carried out using real-world data, we show that our approach outperforms baseline approaches on two metrics.

Genome-wide analysis of the DNA-binding with one zinc finger (Dof) transcription factor family in bananas.

PubMed

Dong, Chen; Hu, Huigang; Xie, Jianghui

2016-12-01

DNA-binding with one finger (Dof) domain proteins are a multigene family of plant-specific transcription factors involved in numerous aspects of plant growth and development. In this study, we report a genome-wide search for Musa acuminata Dof (MaDof) genes and their expression profiles at different developmental stages and in response to various abiotic stresses. In addition, a complete overview of the Dof gene family in bananas is presented, including the gene structures, chromosomal locations, cis-regulatory elements, conserved protein domains, and phylogenetic inferences. Based on the genome-wide analysis, we identified 74 full-length protein-coding MaDof genes unevenly distributed on 11 chromosomes. Phylogenetic analysis with Dof members from diverse plant species showed that MaDof genes can be classified into four subgroups (StDof I, II, III, and IV). The detailed genomic information of the MaDof gene homologs in the present study provides opportunities for functional analyses to unravel the exact role of the genes in plant growth and development.

Wide-bandwidth, wide-beamwidth, high-resolution, millimeter-wave imaging for concealed weapon detection

NASA Astrophysics Data System (ADS)

Sheen, David M.; Fernandes, Justin L.; Tedeschi, Jonathan R.; McMakin, Douglas L.; Jones, A. Mark; Lechelt, Wayne M.; Severtsen, Ronald H.

2013-05-01

Active millimeter-wave imaging is currently being used for personnel screening at airports and other high-security facilities. The cylindrical imaging techniques used in the deployed systems are based on licensed technology developed at the Pacific Northwest National Laboratory. The cylindrical and a related planar imaging technique form three-dimensional images by scanning a diverging beam swept frequency transceiver over a two-dimensional aperture and mathematically focusing or reconstructing the data into three-dimensional images of the person being screened. The resolution, clothing penetration, and image illumination quality obtained with these techniques can be significantly enhanced through the selection of the aperture size, antenna beamwidth, center frequency, and bandwidth. The lateral resolution can be improved by increasing the center frequency, or it can be increased with a larger antenna beamwidth. The wide beamwidth approach can significantly improve illumination quality relative to a higher frequency system. Additionally, a wide antenna beamwidth allows for operation at a lower center frequency resulting in less scattering and attenuation from the clothing. The depth resolution of the system can be improved by increasing the bandwidth. Utilization of extremely wide bandwidths of up to 30 GHz can result in depth resolution as fine as 5 mm. This wider bandwidth operation may allow for improved detection techniques based on high range resolution. In this paper, the results of an extensive imaging study that explored the advantages of using extremely wide beamwidth and bandwidth are presented, primarily for 10-40 GHz frequency band.

Genome-wide association study of the four-constitution medicine.

PubMed

Yin, Chang Shik; Park, Hi Joon; Chung, Joo-Ho; Lee, Hye-Jung; Lee, Byung-Cheol

2009-12-01

Four-constitution medicine (FCM), also known as Sasang constitutional medicine, and the heritage of the long history of individualized acupuncture medicine tradition, is one of the holistic and traditional systems of constitution to appraise and categorize individual differences into four major types. This study first reports a genome-wide association study on FCM, to explore the genetic basis of FCM and facilitate the integration of FCM with conventional individual differences research. Healthy individuals of the Korean population were classified into the four constitutional types (FCTs). A total of 353,202 single nucleotide polymorphisms (SNPs) were typed using whole genome amplified samples, and six-way comparison of FCM types provided lists of significantly differential SNPs. In one-to-one FCT comparisons, 15,944 SNPs were significantly differential, and 5 SNPs were commonly significant in all of the three comparisons. In one-to-two FCT comparisons, 22,616 SNPs were significantly differential, and 20 SNPs were commonly significant in all of the three comparison groups. This study presents the association between genome-wide SNP profiles and the categorization of the FCM, and it could further provide a starting point of genome-based identification and research of the constitutions of FCM.

Tobacco Smoking Leads to Extensive Genome-Wide Changes in DNA Methylation

PubMed Central

Zeilinger, Sonja; Kühnel, Brigitte; Klopp, Norman; Baurecht, Hansjörg; Kleinschmidt, Anja; Gieger, Christian; Weidinger, Stephan; Lattka, Eva; Adamski, Jerzy; Peters, Annette; Strauch, Konstantin

2013-01-01

Environmental factors such as tobacco smoking may have long-lasting effects on DNA methylation patterns, which might lead to changes in gene expression and in a broader context to the development or progression of various diseases. We conducted an epigenome-wide association study (EWAs) comparing current, former and never smokers from 1793 participants of the population-based KORA F4 panel, with replication in 479 participants from the KORA F3 panel, carried out by the 450K BeadChip with genomic DNA obtained from whole blood. We observed wide-spread differences in the degree of site-specific methylation (with p-values ranging from 9.31E-08 to 2.54E-182) as a function of tobacco smoking in each of the 22 autosomes, with the percent of variance explained by smoking ranging from 1.31 to 41.02. Depending on cessation time and pack-years, methylation levels in former smokers were found to be close to the ones seen in never smokers. In addition, methylation-specific protein binding patterns were observed for cg05575921 within AHRR, which had the highest level of detectable changes in DNA methylation associated with tobacco smoking (–24.40% methylation; p = 2.54E-182), suggesting a regulatory role for gene expression. The results of our study confirm the broad effect of tobacco smoking on the human organism, but also show that quitting tobacco smoking presumably allows regaining the DNA methylation state of never smokers. PMID:23691101

Tobacco smoking leads to extensive genome-wide changes in DNA methylation.

PubMed

Zeilinger, Sonja; Kühnel, Brigitte; Klopp, Norman; Baurecht, Hansjörg; Kleinschmidt, Anja; Gieger, Christian; Weidinger, Stephan; Lattka, Eva; Adamski, Jerzy; Peters, Annette; Strauch, Konstantin; Waldenberger, Melanie; Illig, Thomas

2013-01-01

Environmental factors such as tobacco smoking may have long-lasting effects on DNA methylation patterns, which might lead to changes in gene expression and in a broader context to the development or progression of various diseases. We conducted an epigenome-wide association study (EWAs) comparing current, former and never smokers from 1793 participants of the population-based KORA F4 panel, with replication in 479 participants from the KORA F3 panel, carried out by the 450K BeadChip with genomic DNA obtained from whole blood. We observed wide-spread differences in the degree of site-specific methylation (with p-values ranging from 9.31E-08 to 2.54E-182) as a function of tobacco smoking in each of the 22 autosomes, with the percent of variance explained by smoking ranging from 1.31 to 41.02. Depending on cessation time and pack-years, methylation levels in former smokers were found to be close to the ones seen in never smokers. In addition, methylation-specific protein binding patterns were observed for cg05575921 within AHRR, which had the highest level of detectable changes in DNA methylation associated with tobacco smoking (-24.40% methylation; p = 2.54E-182), suggesting a regulatory role for gene expression. The results of our study confirm the broad effect of tobacco smoking on the human organism, but also show that quitting tobacco smoking presumably allows regaining the DNA methylation state of never smokers.

Genetically encoded ratiometric fluorescent thermometer with wide range and rapid response

PubMed Central

Nakano, Masahiro; Arai, Yoshiyuki; Kotera, Ippei; Okabe, Kohki; Kamei, Yasuhiro; Nagai, Takeharu

2017-01-01

Temperature is a fundamental physical parameter that plays an important role in biological reactions and events. Although thermometers developed previously have been used to investigate several important phenomena, such as heterogeneous temperature distribution in a single living cell and heat generation in mitochondria, the development of a thermometer with a sensitivity over a wide temperature range and rapid response is still desired to quantify temperature change in not only homeotherms but also poikilotherms from the cellular level to in vivo. To overcome the weaknesses of the conventional thermometers, such as a limitation of applicable species and a low temporal resolution, owing to the narrow temperature range of sensitivity and the thermometry method, respectively, we developed a genetically encoded ratiometric fluorescent temperature indicator, gTEMP, by using two fluorescent proteins with different temperature sensitivities. Our thermometric method enabled a fast tracking of the temperature change with a time resolution of 50 ms. We used this method to observe the spatiotemporal temperature change between the cytoplasm and nucleus in cells, and quantified thermogenesis from the mitochondria matrix in a single living cell after stimulation with carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone, which was an uncoupler of oxidative phosphorylation. Moreover, exploiting the wide temperature range of sensitivity from 5°C to 50°C of gTEMP, we monitored the temperature in a living medaka embryo for 15 hours and showed the feasibility of in vivo thermometry in various living species. PMID:28212432

Using genome wide association studies to identify common QTL regions in three different genetic backgrounds based on Iberian pig breed.

PubMed

Martínez-Montes, Ángel M; Fernández, Almudena; Muñoz, María; Noguera, Jose Luis; Folch, Josep M; Fernández, Ana I

2018-01-01

One of the major limitation for the application of QTL results in pig breeding and QTN identification has been the limited number of QTL effects validated in different animal material. The aim of the current work was to validate QTL regions through joint and specific genome wide association and haplotype analyses for growth, fatness and premier cut weights in three different genetic backgrounds, backcrosses based on Iberian pigs, which has a major role in the analysis due to its high productive relevance. The results revealed nine common QTL regions, three segregating in all three backcrosses on SSC1, 0-3 Mb, for body weight, on SSC2, 3-9 Mb, for loin bone-in weight, and on SSC7, 3 Mb, for shoulder weight, and six segregating in two of the three backcrosses, on SSC2, SSC4, SSC6 and SSC10 for backfat thickness, shoulder and ham weights. Besides, 18 QTL regions were specifically identified in one of the three backcrosses, five identified only in BC_LD, seven in BC_DU and six in BC_PI. Beyond identifying and validating QTL, candidate genes and gene variants within the most interesting regions have been explored using functional annotation, gene expression data and SNP identification from RNA-Seq data. The results allowed us to propose a promising list of candidate mutations, those identified in PDE10A, DHCR7, MFN2 and CCNY genes located within the common QTL regions and those identified near ssc-mir-103-1 considered PANK3 regulators to be further analysed.

Using genome wide association studies to identify common QTL regions in three different genetic backgrounds based on Iberian pig breed

PubMed Central

Martínez-Montes, Ángel M.; Fernández, Almudena; Muñoz, María; Noguera, Jose Luis; Folch, Josep M.

2018-01-01

One of the major limitation for the application of QTL results in pig breeding and QTN identification has been the limited number of QTL effects validated in different animal material. The aim of the current work was to validate QTL regions through joint and specific genome wide association and haplotype analyses for growth, fatness and premier cut weights in three different genetic backgrounds, backcrosses based on Iberian pigs, which has a major role in the analysis due to its high productive relevance. The results revealed nine common QTL regions, three segregating in all three backcrosses on SSC1, 0–3 Mb, for body weight, on SSC2, 3–9 Mb, for loin bone-in weight, and on SSC7, 3 Mb, for shoulder weight, and six segregating in two of the three backcrosses, on SSC2, SSC4, SSC6 and SSC10 for backfat thickness, shoulder and ham weights. Besides, 18 QTL regions were specifically identified in one of the three backcrosses, five identified only in BC_LD, seven in BC_DU and six in BC_PI. Beyond identifying and validating QTL, candidate genes and gene variants within the most interesting regions have been explored using functional annotation, gene expression data and SNP identification from RNA-Seq data. The results allowed us to propose a promising list of candidate mutations, those identified in PDE10A, DHCR7, MFN2 and CCNY genes located within the common QTL regions and those identified near ssc-mir-103-1 considered PANK3 regulators to be further analysed. PMID:29522525

FGWAS: Functional genome wide association analysis.

PubMed

Huang, Chao; Thompson, Paul; Wang, Yalin; Yu, Yang; Zhang, Jingwen; Kong, Dehan; Colen, Rivka R; Knickmeyer, Rebecca C; Zhu, Hongtu

2017-10-01

Functional phenotypes (e.g., subcortical surface representation), which commonly arise in imaging genetic studies, have been used to detect putative genes for complexly inherited neuropsychiatric and neurodegenerative disorders. However, existing statistical methods largely ignore the functional features (e.g., functional smoothness and correlation). The aim of this paper is to develop a functional genome-wide association analysis (FGWAS) framework to efficiently carry out whole-genome analyses of functional phenotypes. FGWAS consists of three components: a multivariate varying coefficient model, a global sure independence screening procedure, and a test procedure. Compared with the standard multivariate regression model, the multivariate varying coefficient model explicitly models the functional features of functional phenotypes through the integration of smooth coefficient functions and functional principal component analysis. Statistically, compared with existing methods for genome-wide association studies (GWAS), FGWAS can substantially boost the detection power for discovering important genetic variants influencing brain structure and function. Simulation studies show that FGWAS outperforms existing GWAS methods for searching sparse signals in an extremely large search space, while controlling for the family-wise error rate. We have successfully applied FGWAS to large-scale analysis of data from the Alzheimer's Disease Neuroimaging Initiative for 708 subjects, 30,000 vertices on the left and right hippocampal surfaces, and 501,584 SNPs. Copyright © 2017 Elsevier Inc. All rights reserved.

Genome-Wide Gene Expression Analysis Shows AKAP13-Mediated PKD1 Signaling Regulates the Transcriptional Response to Cardiac Hypertrophy.

PubMed

Johnson, Keven R; Nicodemus-Johnson, Jessie; Spindler, Mathew J; Carnegie, Graeme K

2015-01-01

In the heart, scaffolding proteins such as A-Kinase Anchoring Proteins (AKAPs) play a crucial role in normal cellular function by serving as a signaling hub for multiple protein kinases including protein kinase D1 (PKD1). Under cardiac hypertrophic conditions AKAP13 anchored PKD1 activates the transcription factor MEF2 leading to subsequent fetal gene activation and hypertrophic response. We used an expression microarray to identify the global transcriptional response in the hearts of wild-type mice expressing the native form of AKAP13 compared to a gene-trap mouse model expressing a truncated form of AKAP13 that is unable to bind PKD1 (AKAP13-ΔPKD1). Microarray analysis showed that AKAP13-ΔPKD1 mice broadly failed to exhibit the transcriptional profile normally associated with compensatory cardiac hypertrophy following trans-aortic constriction (TAC). The identified differentially expressed genes in WT and AKAP13-ΔPKD1 hearts are vital for the compensatory hypertrophic response to pressure-overload and include myofilament, apoptotic, and cell growth/differentiation genes in addition to genes not previously identified as affected by AKAP13-anchored PKD1. Our results show that AKAP13-PKD1 signaling is critical for transcriptional regulation of key contractile, cell death, and metabolic pathways during the development of compensatory hypertrophy in vivo.

Genome-Wide Gene Expression Analysis Shows AKAP13-Mediated PKD1 Signaling Regulates the Transcriptional Response to Cardiac Hypertrophy

PubMed Central

Johnson, Keven R.; Nicodemus-Johnson, Jessie; Spindler, Mathew J.

2015-01-01

In the heart, scaffolding proteins such as A-Kinase Anchoring Proteins (AKAPs) play a crucial role in normal cellular function by serving as a signaling hub for multiple protein kinases including protein kinase D1 (PKD1). Under cardiac hypertrophic conditions AKAP13 anchored PKD1 activates the transcription factor MEF2 leading to subsequent fetal gene activation and hypertrophic response. We used an expression microarray to identify the global transcriptional response in the hearts of wild-type mice expressing the native form of AKAP13 compared to a gene-trap mouse model expressing a truncated form of AKAP13 that is unable to bind PKD1 (AKAP13-ΔPKD1). Microarray analysis showed that AKAP13-ΔPKD1 mice broadly failed to exhibit the transcriptional profile normally associated with compensatory cardiac hypertrophy following trans-aortic constriction (TAC). The identified differentially expressed genes in WT and AKAP13-ΔPKD1 hearts are vital for the compensatory hypertrophic response to pressure-overload and include myofilament, apoptotic, and cell growth/differentiation genes in addition to genes not previously identified as affected by AKAP13-anchored PKD1. Our results show that AKAP13-PKD1 signaling is critical for transcriptional regulation of key contractile, cell death, and metabolic pathways during the development of compensatory hypertrophy in vivo. PMID:26192751

Origin of African Physacanthus (Acanthaceae) via wide hybridization.

PubMed

Tripp, Erin A; Fatimah, Siti; Darbyshire, Iain; McDade, Lucinda A

2013-01-01

Gene flow between closely related species is a frequent phenomenon that is known to play important roles in organismal evolution. Less clear, however, is the importance of hybridization between distant relatives. We present molecular and morphological evidence that support origin of the plant genus Physacanthus via "wide hybridization" between members of two distantly related lineages in the large family Acanthaceae. These two lineages are well characterized by very different morphologies yet, remarkably, Physacanthus shares features of both. Chloroplast sequences from six loci indicate that all three species of Physacanthus contain haplotypes from both lineages, suggesting that heteroplasmy likely predated speciation in the genus. Although heteroplasmy is thought to be unstable and thus transient, multiple haplotypes have been maintained through time in Physacanthus. The most likely scenario to explain these data is that Physacanthus originated via an ancient hybridization event that involved phylogenetically distant parents. This wide hybridization has resulted in the establishment of an independently evolving clade of flowering plants.

Origin of African Physacanthus (Acanthaceae) via Wide Hybridization

PubMed Central

Tripp, Erin A.; Fatimah, Siti; Darbyshire, Iain; McDade, Lucinda A.

2013-01-01

Gene flow between closely related species is a frequent phenomenon that is known to play important roles in organismal evolution. Less clear, however, is the importance of hybridization between distant relatives. We present molecular and morphological evidence that support origin of the plant genus Physacanthus via “wide hybridization” between members of two distantly related lineages in the large family Acanthaceae. These two lineages are well characterized by very different morphologies yet, remarkably, Physacanthus shares features of both. Chloroplast sequences from six loci indicate that all three species of Physacanthus contain haplotypes from both lineages, suggesting that heteroplasmy likely predated speciation in the genus. Although heteroplasmy is thought to be unstable and thus transient, multiple haplotypes have been maintained through time in Physacanthus. The most likely scenario to explain these data is that Physacanthus originated via an ancient hybridization event that involved phylogenetically distant parents. This wide hybridization has resulted in the establishment of an independently evolving clade of flowering plants. PMID:23383261

Wide-Field Imaging Interferometry Spatial-Spectral Image Synthesis Algorithms

NASA Technical Reports Server (NTRS)

Lyon, Richard G.; Leisawitz, David T.; Rinehart, Stephen A.; Memarsadeghi, Nargess; Sinukoff, Evan J.

2012-01-01

Developed is an algorithmic approach for wide field of view interferometric spatial-spectral image synthesis. The data collected from the interferometer consists of a set of double-Fourier image data cubes, one cube per baseline. These cubes are each three-dimensional consisting of arrays of two-dimensional detector counts versus delay line position. For each baseline a moving delay line allows collection of a large set of interferograms over the 2D wide field detector grid; one sampled interferogram per detector pixel per baseline. This aggregate set of interferograms, is algorithmically processed to construct a single spatial-spectral cube with angular resolution approaching the ratio of the wavelength to longest baseline. The wide field imaging is accomplished by insuring that the range of motion of the delay line encompasses the zero optical path difference fringe for each detector pixel in the desired field-of-view. Each baseline cube is incoherent relative to all other baseline cubes and thus has only phase information relative to itself. This lost phase information is recovered by having point, or otherwise known, sources within the field-of-view. The reference source phase is known and utilized as a constraint to recover the coherent phase relation between the baseline cubes and is key to the image synthesis. Described will be the mathematical formalism, with phase referencing and results will be shown using data collected from NASA/GSFC Wide-Field Imaging Interferometry Testbed (WIIT).

Blind deconvolution with principal components analysis for wide-field and small-aperture telescopes

NASA Astrophysics Data System (ADS)

Jia, Peng; Sun, Rongyu; Wang, Weinan; Cai, Dongmei; Liu, Huigen

2017-09-01

Telescopes with a wide field of view (greater than 1°) and small apertures (less than 2 m) are workhorses for observations such as sky surveys and fast-moving object detection, and play an important role in time-domain astronomy. However, images captured by these telescopes are contaminated by optical system aberrations, atmospheric turbulence, tracking errors and wind shear. To increase the quality of images and maximize their scientific output, we propose a new blind deconvolution algorithm based on statistical properties of the point spread functions (PSFs) of these telescopes. In this new algorithm, we first construct the PSF feature space through principal component analysis, and then classify PSFs from a different position and time using a self-organizing map. According to the classification results, we divide images of the same PSF types and select these PSFs to construct a prior PSF. The prior PSF is then used to restore these images. To investigate the improvement that this algorithm provides for data reduction, we process images of space debris captured by our small-aperture wide-field telescopes. Comparing the reduced results of the original images and the images processed with the standard Richardson-Lucy method, our method shows a promising improvement in astrometry accuracy.

Wide wavelength range tunable one-dimensional silicon nitride nano-grating guided mode resonance filter based on azimuthal rotation

NASA Astrophysics Data System (ADS)

Yukino, Ryoji; Sahoo, Pankaj K.; Sharma, Jaiyam; Takamura, Tsukasa; Joseph, Joby; Sandhu, Adarsh

2017-01-01

We describe wavelength tuning in a one dimensional (1D) silicon nitride nano-grating guided mode resonance (GMR) structure under conical mounting configuration of the device. When the GMR structure is rotated about the axis perpendicular to the surface of the device (azimuthal rotation) for light incident at oblique angles, the conditions for resonance are different than for conventional GMR structures under classical mounting. These resonance conditions enable tuning of the GMR peak position over a wide range of wavelengths. We experimental demonstrate tuning over a range of 375 nm between 500 nm˜875 nm. We present a theoretical model to explain the resonance conditions observed in our experiments and predict the peak positions with show excellent agreement with experiments. Our method for tuning wavelengths is simpler and more efficient than conventional procedures that employ variations in the design parameters of structures or conical mounting of two-dimensional (2D) GMR structures and enables a single 1D GMR device to function as a high efficiency wavelength filter over a wide range of wavelengths. We expect tunable filters based on this technique to be applicable in a wide range of fields including astronomy and biomedical imaging.

Genome-Wide Prediction of the Performance of Three-Way Hybrids in Barley.

PubMed

Li, Zuo; Philipp, Norman; Spiller, Monika; Stiewe, Gunther; Reif, Jochen C; Zhao, Yusheng

2017-03-01

Predicting the grain yield performance of three-way hybrids is challenging. Three-way crosses are relevant for hybrid breeding in barley ( L.) and maize ( L.) adapted to East Africa. The main goal of our study was to implement and evaluate genome-wide prediction approaches of the performance of three-way hybrids using data of single-cross hybrids for a scenario in which parental lines of the three-way hybrids originate from three genetically distinct subpopulations. We extended the ridge regression best linear unbiased prediction (RRBLUP) and devised a genomic selection model allowing for subpopulation-specific marker effects (GSA-RRBLUP: general and subpopulation-specific additive RRBLUP). Using an empirical barley data set, we showed that applying GSA-RRBLUP tripled the prediction ability of three-way hybrids from 0.095 to 0.308 compared with RRBLUP, modeling one additive effect for all three subpopulations. The experimental findings were further substantiated with computer simulations. Our results emphasize the potential of GSA-RRBLUP to improve genome-wide hybrid prediction of three-way hybrids for scenarios of genetically diverse parental populations. Because of the advantages of the GSA-RRBLUP model in dealing with hybrids from different parental populations, it may also be a promising approach to boost the prediction ability for hybrid breeding programs based on genetically diverse heterotic groups. Copyright © 2017 Crop Science Society of America.

Modifications to JLab 12 GeV Refrigerator and Wide Range Mix Mode Performance Testing Results

NASA Astrophysics Data System (ADS)

Knudsen, P.; Ganni, V.; Hasan, N.; Dixon, K.; Norton, R.; Creel, J.

2017-02-01

Analysis of data obtained during the spring 2013 commissioning of the new 4.5 K refrigeration system at Jefferson Lab (JLab) for the 12 GeV upgrade indicated a wide capacity range with good efficiency and minimal operator interaction. Testing also showed that the refrigerator required higher liquid nitrogen (LN) consumption for its pre-cooler than anticipated by the design. This does not affect the capacity of the refrigerator, but it does result in an increased LN utility cost. During the summer of 2015 the modifications were implemented by the cold box manufacturer, according to a design similar to the JLab 12 GeV cold box specification. Subsequently, JLab recommissioned the cold box and performed extensive performance testing, ranging from 20% to 100% of the design maximum capacity, and in various modes of operation, ranging from pure refrigeration, pure liquefaction, half-and-half mix mode and at selected design modes using the Floating Pressure - Ganni Cycle. The testing demonstrated that the refrigerator system has a good and fairly constant performance over a wide capacity range and different modes of operation. It also demonstrated the modifications resulted in a LN consumption that met the design for the pure refrigeration mode (which is the most demanding) and was lower than the design for the nominal and maximum capacity modes. In addition, a pulsed-load test, similar to what is expected for cryogenic systems supporting fusion experiments, was conducted to observe the response using the Floating Pressure - Ganni Cycle, which was stable and robust. This paper will discuss the results and analysis of this testing pertaining to the LN consumption, the system efficiency over a wide range of capacity and different modes and the behaviour of the system to a pulsed load.

Genome-wide oxidative bisulfite sequencing identifies sex-specific methylation differences in the human placenta

PubMed Central

Johnson, Michelle D; Dopierala, Justyna

2018-01-01

ABSTRACT DNA methylation is an important regulator of gene function. Fetal sex is associated with the risk of several specific pregnancy complications related to placental function. However, the association between fetal sex and placental DNA methylation remains poorly understood. We carried out whole-genome oxidative bisulfite sequencing in the placentas of two healthy female and two healthy male pregnancies generating an average genome depth of coverage of 25x. Most highly ranked differentially methylated regions (DMRs) were located on the X chromosome but we identified a 225 kb sex-specific DMR in the body of the CUB and Sushi Multiple Domains 1 (CSMD1) gene on chromosome 8. The sex-specific differential methylation pattern observed in this region was validated in additional placentas using in-solution target capture. In a new RNA-seq data set from 64 female and 67 male placentas, CSMD1 mRNA was 1.8-fold higher in male than in female placentas (P value = 8.5 × 10−7, Mann-Whitney test). Exon-level quantification of CSMD1 mRNA from these 131 placentas suggested a likely placenta-specific CSMD1 isoform not detected in the 21 somatic tissues analyzed. We show that the gene body of an autosomal gene, CSMD1, is differentially methylated in a sex- and placental-specific manner, displaying sex-specific differences in placental transcript abundance. PMID:29376485

High-efficiency non-uniformity correction for wide dynamic linear infrared radiometry system

NASA Astrophysics Data System (ADS)

Li, Zhou; Yu, Yi; Tian, Qi-Jie; Chang, Song-Tao; He, Feng-Yun; Yin, Yan-He; Qiao, Yan-Feng

2017-09-01

Several different integration times are always set for a wide dynamic linear and continuous variable integration time infrared radiometry system, therefore, traditional calibration-based non-uniformity correction (NUC) are usually conducted one by one, and furthermore, several calibration sources required, consequently makes calibration and process of NUC time-consuming. In this paper, the difference of NUC coefficients between different integration times have been discussed, and then a novel NUC method called high-efficiency NUC, which combines the traditional calibration-based non-uniformity correction, has been proposed. It obtains the correction coefficients of all integration times in whole linear dynamic rangesonly by recording three different images of a standard blackbody. Firstly, mathematical procedure of the proposed non-uniformity correction method is validated and then its performance is demonstrated by a 400 mm diameter ground-based infrared radiometry system. Experimental results show that the mean value of Normalized Root Mean Square (NRMS) is reduced from 3.78% to 0.24% by the proposed method. In addition, the results at 4 ms and 70 °C prove that this method has a higher accuracy compared with traditional calibration-based NUC. In the meantime, at other integration time and temperature there is still a good correction effect. Moreover, it greatly reduces the number of correction time and temperature sampling point, and is characterized by good real-time performance and suitable for field measurement.

Point symmetric design approach to a wide-field wide-wavelength cat's eye retro-reflector anastigmat

NASA Astrophysics Data System (ADS)

Liepmann, Till W.

2009-08-01

A point symmetric design approach for creating a practical cat's eye retro-reflector (CERR) anastigmat lens with a wide field of regard (FOR), uniform reflectance and wide wavelength range is described. An anastigmat design is presented that demonstrates the performance capability of the design approach. The lens design is diffraction limited in double pass at F/3, has a "working distance" between lens and reflector, wide wavelength range of operation, and uniform reflectivity over a 120 deg FOR. An anastigmat fabricated from the design is presented; however, the design approach is generally useful for any application requiring a high performance retro-reflector. The design uses only spherical surfaces, thereby avoiding the fabrication expense of aspheric surfaces.

Wide area Hyperspectral Motion Imaging

DTIC Science & Technology

2017-02-03

LEXINGTON, MASSACHUSETTS 02420-9108 (781) 981-1343 3 February 2017 TO: FROM: Dr. Joseph Lin (joseph.lin@ll.mit.edu), Advanced Imager ...Technology SUBJECT: Wide-area Hyperspectral Motion Imaging Introduction Wide-area motion imaging (WAMI) has received increased attention in...fielded imaging spectrometers use either dispersive or interferometric techniques. A dispersive spectrometer uses a grating or prism to disperse the

Designing Phononic Crystals with Wide and Robust Band Gaps

NASA Astrophysics Data System (ADS)

Jia, Zian; Chen, Yanyu; Yang, Haoxiang; Wang, Lifeng

2018-04-01

Phononic crystals (PnCs) engineered to manipulate and control the propagation of mechanical waves have enabled the design of a range of novel devices, such as waveguides, frequency modulators, and acoustic cloaks, for which wide and robust phononic band gaps are highly preferable. While numerous PnCs have been designed in recent decades, to the best of our knowledge, PnCs that possess simultaneous wide and robust band gaps (to randomness and deformations) have not yet been reported. Here, we demonstrate that by combining the band-gap formation mechanisms of Bragg scattering and local resonances (the latter one is dominating), PnCs with wide and robust phononic band gaps can be established. The robustness of the phononic band gaps are then discussed from two aspects: robustness to geometric randomness (manufacture defects) and robustness to deformations (mechanical stimuli). Analytical formulations further predict the optimal design parameters, and an uncertainty analysis quantifies the randomness effect of each designing parameter. Moreover, we show that the deformation robustness originates from a local resonance-dominant mechanism together with the suppression of structural instability. Importantly, the proposed PnCs require only a small number of layers of elements (three unit cells) to obtain broad, robust, and strong attenuation bands, which offer great potential in designing flexible and deformable phononic devices.

Genome-wide association study of rice grain width variation.

PubMed

Zheng, Xiao-Ming; Gong, Tingting; Ou, Hong-Ling; Xue, Dayuan; Qiao, Weihua; Wang, Junrui; Liu, Sha; Yang, Qingwen; Olsen, Kenneth M

2018-04-01

Seed size is variable within many plant species, and understanding the underlying genetic factors can provide insights into mechanisms of local environmental adaptation. Here we make use of the abundant genomic and germplasm resources available for rice (Oryza sativa) to perform a large-scale genome-wide association study (GWAS) of grain width. Grain width varies widely within the crop and is also known to show climate-associated variation across populations of its wild progenitor. Using a filtered dataset of >1.9 million genome-wide SNPs in a sample of 570 cultivated and wild rice accessions, we performed GWAS with two complementary models, GLM and MLM. The models yielded 10 and 33 significant associations, respectively, and jointly yielded seven candidate locus regions, two of which have been previously identified. Analyses of nucleotide diversity and haplotype distributions at these loci revealed signatures of selection and patterns consistent with adaptive introgression of grain width alleles across rice variety groups. The results provide a 50% increase in the total number of rice grain width loci mapped to date and support a polygenic model whereby grain width is shaped by gene-by-environment interactions. These loci can potentially serve as candidates for studies of adaptive seed size variation in wild grass species.

Genome-Wide Expression Profiling of Complex Regional Pain Syndrome

PubMed Central

Jin, Eun-Heui; Zhang, Enji; Ko, Youngkwon; Sim, Woo Seog; Moon, Dong Eon; Yoon, Keon Jung; Hong, Jang Hee; Lee, Won Hyung

2013-01-01

Complex regional pain syndrome (CRPS) is a chronic, progressive, and devastating pain syndrome characterized by spontaneous pain, hyperalgesia, allodynia, altered skin temperature, and motor dysfunction. Although previous gene expression profiling studies have been conducted in animal pain models, there genome-wide expression profiling in the whole blood of CRPS patients has not been reported yet. Here, we successfully identified certain pain-related genes through genome-wide expression profiling in the blood from CRPS patients. We found that 80 genes were differentially expressed between 4 CRPS patients (2 CRPS I and 2 CRPS II) and 5 controls (cut-off value: 1.5-fold change and p<0.05). Most of those genes were associated with signal transduction, developmental processes, cell structure and motility, and immunity and defense. The expression levels of major histocompatibility complex class I A subtype (HLA-A29.1), matrix metalloproteinase 9 (MMP9), alanine aminopeptidase N (ANPEP), l-histidine decarboxylase (HDC), granulocyte colony-stimulating factor 3 receptor (G-CSF3R), and signal transducer and activator of transcription 3 (STAT3) genes selected from the microarray were confirmed in 24 CRPS patients and 18 controls by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). We focused on the MMP9 gene that, by qRT-PCR, showed a statistically significant difference in expression in CRPS patients compared to controls with the highest relative fold change (4.0±1.23 times and p = 1.4×10−4). The up-regulation of MMP9 gene in the blood may be related to the pain progression in CRPS patients. Our findings, which offer a valuable contribution to the understanding of the differential gene expression in CRPS may help in the understanding of the pathophysiology of CRPS pain progression. PMID:24244504

Wide Angle of Incidence-Insensitive Polarization-Independent THz Metamaterial Absorber for Both TE and TM Mode Based on Plasmon Hybridizations.

PubMed

Huang, Xiu Tao; Lu, Cong Hui; Rong, Can Can; Wang, Sheng Ming; Liu, Ming Hai

2018-04-25

An ultra-wide-angle THz metamaterial absorber (MA) utilizing sixteen-circular-sector (SCR) resonator for both transverse electric (TE) and transverse magnetic (TM) mode is designed and investigated numerically. At normal incidence, the absorptivity of the proposed MA is higher than 93.7% at 9.05 THz for different polarization angles, due to the rotational symmetry structure of the unit cell. Under oblique incidence, the absorptivity can still exceed 90%, even when the incident angle is up to 70° for both TE and TM mode. Especially, the frequency variation in TE mode is less than 0.25% for different incident angles from 0° to 70°. The electric field (E z ) distributions are used to explain the absorption mechanism. Numerical simulation results show that the high absorption with wide-angle independence stems from fundamental dipole resonance and gap surface plasmons. The broadband deep-infrared MA is also obtained by stacking three metal-dielectric layers. The designed MA has great potential in bolometric pixel elements, biomedical sensors, THz imaging, and solar cells.

Very Wide Binaries

NASA Astrophysics Data System (ADS)

Olling, Robert; Shaya, E.

2011-01-01

We develop Bayesian statistical methods for discovering and assigning probabilities to physical stellar companions. The probabilities depend on similarities in "corrected" proper motion, parallax, and the phase-space density of field stars. Very wide binaries with separations over 10,000 AU have recently been predicted to form during the dissolution process of low-mass star clusters. In this case, these wide systems would still carry information about the density and size of the star cluster in which they formed. Alternatively, Galactic tides and weak interactions with passing stars peel off stars from such very wide binaries in less than 1/2 of a Hubble time. In the past, these systems have been used to rule in/out MACHOs or less compact dark (matter) objects. Ours is the first all-sky survey to locate escaped companions that are still drifting along with each other, long after their binary bond has been broken. We test stars for companionship up to an apparent separation of 8 parsec: 10 to 100 times wider than previous searches. Among Hipparcos stars within 100 pc, we find about 260 systems with separations between 0.01 and 1 pc, and another 190 with separation from 1 to 8 parsec. We find a number of previously unnoticed naked-eye companions, among which: Capella & 50 Per; Alioth, Megrez & Alcor; gamma & tau Cen; phi Eri & eta Hor; 62 & 63 Cnc; gamma & tau Per; zeta & delta Hya; beta01, beta02 & beta03 Tuc; 44 & 58 Oph and pi & rho Cep. At least 15 of our candidates are exoplanet host stars.

Wide Angle Movie

NASA Technical Reports Server (NTRS)

1999-01-01

This brief movie illustrates the passage of the Moon through the Saturn-bound Cassini spacecraft's wide-angle camera field of view as the spacecraft passed by the Moon on the way to its closest approach with Earth on August 17, 1999. From beginning to end of the sequence, 25 wide-angle images (with a spatial image scale of about 14 miles per pixel (about 23 kilometers)were taken over the course of 7 and 1/2 minutes through a series of narrow and broadband spectral filters and polarizers, ranging from the violet to the near-infrared regions of the spectrum, to calibrate the spectral response of the wide-angle camera. The exposure times range from 5 milliseconds to 1.5 seconds. Two of the exposures were smeared and have been discarded and replaced with nearby images to make a smooth movie sequence. All images were scaled so that the brightness of Crisium basin, the dark circular region in the upper right, is approximately the same in every image. The imaging data were processed and released by the Cassini Imaging Central Laboratory for Operations (CICLOPS)at the University of Arizona's Lunar and Planetary Laboratory, Tucson, AZ.

Photo Credit: NASA/JPL/Cassini Imaging Team/University of Arizona

Cassini, launched in 1997, is a joint mission of NASA, the European Space Agency and Italian Space Agency. The mission is managed by NASA's Jet Propulsion Laboratory, Pasadena, CA, for NASA's Office of Space Science, Washington DC. JPL is a division of the California Institute of Technology, Pasadena, CA.

Introduction to the world wide web.

PubMed

Downes, P K

2007-05-12

The World Wide Web used to be nicknamed the 'World Wide Wait'. Now, thanks to high speed broadband connections, browsing the web has become a much more enjoyable and productive activity. Computers need to know where web pages are stored on the Internet, in just the same way as we need to know where someone lives in order to post them a letter. This section explains how the World Wide Web works and how web pages can be viewed using a web browser.

Advance directives in english and French law: different concepts, different values, different societies.

PubMed

Horn, Ruth Judith

2014-03-01

In Western societies advance directives are widely recognised as important means to extend patient self-determination under circumstances of incapacity. Following other countries, England and France have adopted legislation aiming to clarify the legal status of advance directives. In this paper, I will explore similarities and differences in both sets of legislation, the arguments employed in the respective debates and the socio-political structures on which these differences are based. The comparison highlights how different legislations express different concepts emphasising different values accorded to the duty to respect autonomy and to protect life, and how these differences are informed by different socio-political contexts. Furthermore each country associates different ethical concerns with ADs which raise doubts about whether these directives are a theoretical idea which is hardly applicable in practice.

Genome-wide transcriptome analysis in the ovaries of two goats identifies differentially expressed genes related to fecundity.

PubMed

Miao, Xiangyang; Luo, Qingmiao; Qin, Xiaoyu

2016-05-10

The goats are widely kept as livestock throughout the world. Two excellent domestic breeds in China, the Laiwu Black and Jining Grey goats, have different fecundities and prolificacies. Although the goat genome sequences have been resolved recently, little is known about the gene regulations at the transcriptional level in goat. To understand the molecular and genetic mechanisms related to the fecundities and prolificacies, we performed genome-wide sequencing of the mRNAs from two breeds of goat using the next-generation RNA-Seq technology and used functional annotation to identify pathways of interest. Digital gene expression analysis showed 338 genes were up-regulated in the Jining Grey goats and 404 were up-regulated in the Laiwu Black goats. Quantitative real-time PCR verified the reliability of the RNA-Seq data. This study suggests that multiple genes responsible for various biological functions and signaling pathways are differentially expressed in the two different goat breeds, and these genes might be involved in the regulation of goat fecundity and prolificacy. Taken together, our study provides insight into the transcriptional regulation in the ovaries of 2 species of goats that might serve as a key resource for understanding goat fecundity, prolificacy and genetic diversity between species. Copyright © 2016 Elsevier B.V. All rights reserved.

Statistical correction of the Winner’s Curse explains replication variability in quantitative trait genome-wide association studies

PubMed Central

Pe’er, Itsik

2017-01-01

Genome-wide association studies (GWAS) have identified hundreds of SNPs responsible for variation in human quantitative traits. However, genome-wide-significant associations often fail to replicate across independent cohorts, in apparent inconsistency with their apparent strong effects in discovery cohorts. This limited success of replication raises pervasive questions about the utility of the GWAS field. We identify all 332 studies of quantitative traits from the NHGRI-EBI GWAS Database with attempted replication. We find that the majority of studies provide insufficient data to evaluate replication rates. The remaining papers replicate significantly worse than expected (p < 10−14), even when adjusting for regression-to-the-mean of effect size between discovery- and replication-cohorts termed the Winner’s Curse (p < 10−16). We show this is due in part to misreporting replication cohort-size as a maximum number, rather than per-locus one. In 39 studies accurately reporting per-locus cohort-size for attempted replication of 707 loci in samples with similar ancestry, replication rate matched expectation (predicted 458, observed 457, p = 0.94). In contrast, ancestry differences between replication and discovery (13 studies, 385 loci) cause the most highly-powered decile of loci to replicate worse than expected, due to difference in linkage disequilibrium. PMID:28715421

Subdigital setae of chameleon feet: friction-enhancing microstructures for a wide range of substrate roughness.

PubMed

Spinner, Marlene; Westhoff, Guido; Gorb, Stanislav N

2014-06-27

Hairy adhesive systems of microscopic setae with triangular flattened tips have evolved convergently in spiders, insects and arboreal lizards. The ventral sides of the feet and tails in chameleons are also covered with setae. However, chameleon setae feature strongly elongated narrow spatulae or fibrous tips. The friction enhancing function of these microstructures has so far only been demonstrated in contact with glass spheres. In the present study, the frictional properties of subdigital setae of Chamaeleo calyptratus were measured under normal forces in the physical range on plane substrates having different roughness. We showed that chameleon setae maximize friction on a wide range of substrate roughness. The highest friction was measured on asperities of 1 μm. However, our observations of the climbing ability of Ch. calyptratus on rods of different diameters revealed that also claws and grasping feet are additionally responsible for the force generation on various substrates during locomotion.

Subdigital setae of chameleon feet: Friction-enhancing microstructures for a wide range of substrate roughness

NASA Astrophysics Data System (ADS)

Spinner, Marlene; Westhoff, Guido; Gorb, Stanislav N.

2014-06-01

Hairy adhesive systems of microscopic setae with triangular flattened tips have evolved convergently in spiders, insects and arboreal lizards. The ventral sides of the feet and tails in chameleons are also covered with setae. However, chameleon setae feature strongly elongated narrow spatulae or fibrous tips. The friction enhancing function of these microstructures has so far only been demonstrated in contact with glass spheres. In the present study, the frictional properties of subdigital setae of Chamaeleo calyptratus were measured under normal forces in the physical range on plane substrates having different roughness. We showed that chameleon setae maximize friction on a wide range of substrate roughness. The highest friction was measured on asperities of 1 μm. However, our observations of the climbing ability of Ch. calyptratus on rods of different diameters revealed that also claws and grasping feet are additionally responsible for the force generation on various substrates during locomotion.

Genome-Wide Specific Selection in Three Domestic Sheep Breeds.

PubMed

Wang, Huihua; Zhang, Li; Cao, Jiaxve; Wu, Mingming; Ma, Xiaomeng; Liu, Zhen; Liu, Ruizao; Zhao, Fuping; Wei, Caihong; Du, Lixin

2015-01-01

Commercial sheep raised for mutton grow faster than traditional Chinese sheep breeds. Here, we aimed to evaluate genetic selection among three different types of sheep breed: two well-known commercial mutton breeds and one indigenous Chinese breed. We first combined locus-specific branch lengths and di statistical methods to detect candidate regions targeted by selection in the three different populations. The results showed that the genetic distances reached at least medium divergence for each pairwise combination. We found these two methods were highly correlated, and identified many growth-related candidate genes undergoing artificial selection. For production traits, APOBR and FTO are associated with body mass index. For meat traits, ALDOA, STK32B and FAM190A are related to marbling. For reproduction traits, CCNB2 and SLC8A3 affect oocyte development. We also found two well-known genes, GHR (which affects meat production and quality) and EDAR (associated with hair thickness) were associated with German mutton merino sheep. Furthermore, four genes (POL, RPL7, MSL1 and SHISA9) were associated with pre-weaning gain in our previous genome-wide association study. Our results indicated that combine locus-specific branch lengths and di statistical approaches can reduce the searching ranges for specific selection. And we got many credible candidate genes which not only confirm the results of previous reports, but also provide a suite of novel candidate genes in defined breeds to guide hybridization breeding.

MAGNAMWAR: an R package for genome-wide association studies of bacterial orthologs.

PubMed

Sexton, Corinne E; Smith, Hayden Z; Newell, Peter D; Douglas, Angela E; Chaston, John M

2018-06-01

Here we report on an R package for genome-wide association studies of orthologous genes in bacteria. Before using the software, orthologs from bacterial genomes or metagenomes are defined using local or online implementations of OrthoMCL. These presence-absence patterns are statistically associated with variation in user-collected phenotypes using the Mono-Associated GNotobiotic Animals Metagenome-Wide Association R package (MAGNAMWAR). Genotype-phenotype associations can be performed with several different statistical tests based on the type and distribution of the data. MAGNAMWAR is available on CRAN. john_chaston@byu.edu.

Manganese- and 1-methyl-4-phenylpyridinium-induced neurotoxicity display differences in morphological, electrophysiological and genome-wide alterations: implications for idiopathic Parkinson's disease.

PubMed

Mythri, Rajeswara Babu; Raghunath, Narayana Reddy; Narwade, Santosh Chandrakant; Pandareesh, Mirazkar Dasharatha Rao; Sabitha, Kollarkandi Rajesh; Aiyaz, Mohamad; Chand, Bipin; Sule, Manas; Ghosh, Krittika; Kumar, Senthil; Shankarappa, Bhagyalakshmi; Soundararajan, Soundarya; Alladi, Phalguni Anand; Purushottam, Meera; Gayathri, Narayanappa; Deobagkar, Deepti Dileep; Laxmi, Thenkanidiyoor Rao; Srinivas Bharath, Muchukunte Mukunda

2017-11-01

Idiopathic Parkinson's disease and manganese-induced atypical parkinsonism are characterized by movement disorder and nigrostriatal pathology. Although clinical features, brain region involved and responsiveness to levodopa distinguish both, differences at the neuronal level are largely unknown. We studied the morphological, neurophysiological and molecular differences in dopaminergic neurons exposed to the Parkinson's disease toxin 1-methyl-4-phenylpyridinium ion (MPP + ) and manganese (Mn), followed by validation in the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine and Mn mouse models. Morphological analysis highlighted loss of neuronal processes in the MPP + and not the Mn model. Cellular network dynamics of dopaminergic neurons characterized by spike frequency and inter-spike intervals indicated major neuronal population (~ 93%) with slow discharge rates (0-5 Hz). While MPP + exposure suppressed the firing of these neurons, Mn neither suppressed nor elevated the neuronal activity. High-throughput transcriptomic analysis revealed up-regulation of 694 and 603 genes and down-regulation of 428 and 255 genes in the MPP + and Mn models respectively. Many differentially expressed genes were unique to either models and contributed to neuroinflammation, metabolic/mitochondrial function, apoptosis and nuclear function, synaptic plasticity, neurotransmission and cytoskeleton. Analysis of the Janus kinase-signal transducer and activator of transcription pathway with implications for neuritogenesis and neuronal proliferation revealed contrasting profile in both models. Genome-wide DNA methylomics revealed differences between both models and substantiated the epigenetic basis of the difference in the Janus kinase-signal transducer and activator of transcription pathway. We conclude that idiopathic Parkinson's disease and atypical parkinsonism have divergent neurotoxicological manifestation at the dopaminergic neuronal level with implications for pathobiology and evolution

Strong Showing for AGU Journals in 2009 Impact Factors

NASA Astrophysics Data System (ADS)

Cook, Bill

2010-06-01

AGU publishes great science, which is recognized in several ways. One of the most widely recognized is from Thomson Reuters, which provides the Journal Citation Report (JCR) each year as a component of the Web of Science®. JCR reports on several measures of journal usage, including a journal's Eigenfactor score, its Article Influence score, its Impact Factor, and its rank within a cohort of similar journals. According to the 2009 statistics released last week, AGU again has outperformed its larger competitors. For the twelfth time, two different AGU titles hold the top rank in their categories, and AGU titles hold the second spot in two other categories and third in two more.

Development of high frequency and wide bandwidth Johnson noise thermometry

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

Crossno, Jesse; Liu, Xiaomeng; Kim, Philip

We develop a high frequency, wide bandwidth radiometer operating at room temperature, which augments the traditional technique of Johnson noise thermometry for nanoscale thermal transport studies. Employing low noise amplifiers and an analog multiplier operating at 2 GHz, auto- and cross-correlated Johnson noise measurements are performed in the temperature range of 3 to 300 K, achieving a sensitivity of 5.5 mK (110 ppm) in 1 s of integration time. This setup allows us to measure the thermal conductance of a boron nitride encapsulated monolayer graphene device over a wide temperature range. Our data show a high power law (T ∼ 4) deviation from the Wiedemann-Franz law abovemore » T ∼ 100 K.« less

Micro-Viscometer for Measuring Shear-Varying Blood Viscosity over a Wide-Ranging Shear Rate.

PubMed

Kim, Byung Jun; Lee, Seung Yeob; Jee, Solkeun; Atajanov, Arslan; Yang, Sung

2017-06-20

In this study, a micro-viscometer is developed for measuring shear-varying blood viscosity over a wide-ranging shear rate. The micro-viscometer consists of 10 microfluidic channel arrays, each of which has a different micro-channel width. The proposed design enables the retrieval of 10 different shear rates from a single flow rate, thereby enabling the measurement of shear-varying blood viscosity with a fixed flow rate condition. For this purpose, an optimal design that guarantees accurate viscosity measurement is selected from a parametric study. The functionality of the micro-viscometer is verified by both numerical and experimental studies. The proposed micro-viscometer shows 6.8% (numerical) and 5.3% (experimental) in relative error when compared to the result from a standard rotational viscometer. Moreover, a reliability test is performed by repeated measurement (N = 7), and the result shows 2.69 ± 2.19% for the mean relative error. Accurate viscosity measurements are performed on blood samples with variations in the hematocrit (35%, 45%, and 55%), which significantly influences blood viscosity. Since the blood viscosity correlated with various physical parameters of the blood, the micro-viscometer is anticipated to be a significant advancement for realization of blood on a chip.

Micro-Viscometer for Measuring Shear-Varying Blood Viscosity over a Wide-Ranging Shear Rate

PubMed Central

Kim, Byung Jun; Lee, Seung Yeob; Jee, Solkeun; Atajanov, Arslan; Yang, Sung

2017-01-01

In this study, a micro-viscometer is developed for measuring shear-varying blood viscosity over a wide-ranging shear rate. The micro-viscometer consists of 10 microfluidic channel arrays, each of which has a different micro-channel width. The proposed design enables the retrieval of 10 different shear rates from a single flow rate, thereby enabling the measurement of shear-varying blood viscosity with a fixed flow rate condition. For this purpose, an optimal design that guarantees accurate viscosity measurement is selected from a parametric study. The functionality of the micro-viscometer is verified by both numerical and experimental studies. The proposed micro-viscometer shows 6.8% (numerical) and 5.3% (experimental) in relative error when compared to the result from a standard rotational viscometer. Moreover, a reliability test is performed by repeated measurement (N = 7), and the result shows 2.69 ± 2.19% for the mean relative error. Accurate viscosity measurements are performed on blood samples with variations in the hematocrit (35%, 45%, and 55%), which significantly influences blood viscosity. Since the blood viscosity correlated with various physical parameters of the blood, the micro-viscometer is anticipated to be a significant advancement for realization of blood on a chip. PMID:28632151

Ultra-wide-field angiography improves the detection and classification of diabetic retinopathy.

PubMed

Wessel, Matthew M; Aaker, Grant D; Parlitsis, George; Cho, Minhee; D'Amico, Donald J; Kiss, Szilárd

2012-04-01

To evaluate patients with diabetic retinopathy using ultra-wide-field fluorescein angiography and to compare the visualized retinal pathology with that seen on an overly of conventional 7 standard field (7SF) imaging. Two hundred and eighteen eyes of 118 diabetic patients who underwent diagnostic fluorescein angiography using the Optos Optomap Panoramic 200A imaging system were included. The visualized area of the retina, retinal nonperfusion, retinal neovascularization, and panretinal photocoagulation were quantified by two independent masked graders. The respective areas identified on the ultra-wide-field fluorescein angiography image were compared with an overly of a modified 7SF image as outlined in the Early Treatment Diabetic Retinopathy Study. Ultra-wide-field fluorescein angiograms imaging, on average, demonstrated 3.2 times more total retinal surface area than 7SF. When compared with 7SF, ultra-wide-field fluorescein angiography showed 3.9 times more nonperfusion (P < 0.001), 1.9 times more neovascularization (P = 0.036), and 3.8 times more panretinal photocoagulation (P < 0.001). In 22 eyes (10%), ultra-wide-field fluorescein angiography demonstrated retinal pathology (including nonperfusion and neovascularization) not evident in an 7SF overly. Compared with conventional 7SF imaging, ultra-wide-field fluorescein angiography reveals significantly more retinal vascular pathology in patients with diabetic retinopathy. Improved retinal visualization may alter the classification of diabetic retinopathy and may therefore influence follow-up and treatment of these patients.

A genome-wide analysis of gene–caffeine consumption interaction on basal cell carcinoma

PubMed Central

Li, Xin; Cornelis, Marilyn C.; Liang, Liming; Song, Fengju; De Vivo, Immaculata; Giovannucci, Edward; Tang, Jean Y.; Han, Jiali

2016-01-01

Animal models have suggested that oral or topical administration of caffeine could inhibit ultraviolet-induced carcinogenesis via the ataxia telangiectasia and rad3 (ATR)-related apoptosis. Previous epidemiological studies have demonstrated that increased caffeine consumption is associated with reduced risk of basal cell carcinoma (BCC). To identify common genetic markers that may modify this association, we tested gene–caffeine intake interaction on BCC risk in a genome-wide analysis. We included 3383 BCC cases and 8528 controls of European ancestry from the Nurses’ Health Study and Health Professionals Follow-up Study. Single nucleotide polymorphism (SNP) rs142310826 near the NEIL3 gene showed a genome-wide significant interaction with caffeine consumption (P = 1.78 × 10–8 for interaction) on BCC risk. There was no gender difference for this interaction (P = 0.64 for heterogeneity). NEIL3, a gene belonging to the base excision DNA repair pathway, encodes a DNA glycosylase that recognizes and removes lesions produced by oxidative stress. In addition, we identified several loci with P value for interaction <5 × 10–7 in gender-specific analyses (P for heterogeneity between genders < 0.001) including those mapping to the genes LRRTM4, ATF3 and DCLRE1C in women and POTEA in men. Finally, we tested the associations between caffeine consumption-related SNPs reported by previous genome-wide association studies and risk of BCC, both individually and jointly, but found no significant association. In sum, we identified a DNA repair gene that could be involved in caffeine-mediated skin tumor inhibition. Further studies are warranted to confirm these findings. PMID:27797824

Genome-Wide Identification, Characterization and Expression Analysis of the TCP Gene Family in Prunus mume

PubMed Central

Zhou, Yuzhen; Xu, Zongda; Zhao, Kai; Yang, Weiru; Cheng, Tangren; Wang, Jia; Zhang, Qixiang

2016-01-01

TCP proteins, belonging to a plant-specific transcription factors family, are known to have great functions in plant development, especially flower and leaf development. However, there is little information about this gene family in Prunus mume, which is widely cultivated in China as an ornamental and fruit tree. Here a genome-wide analysis of TCP genes was performed to explore their evolution in P. mume. Nineteen PmTCPs were identified and three of them contained putative miR319 target sites. Phylogenetic and comprehensive bioinformatics analyses of these genes revealed that different types of TCP genes had undergone different evolutionary processes and the genes in the same clade had similar chromosomal location, gene structure, and conserved domains. Expression analysis of these PmTCPs indicated that there were diverse expression patterns among different clades. Most TCP genes were predominantly expressed in flower, leaf, and stem, and showed high expression levels in the different stages of flower bud differentiation, especially in petal formation stage and gametophyte development. Genes in TCP-P subfamily had main roles in both flower development and gametophyte development. The CIN genes in double petal cultivars might have key roles in the formation of petal, while they were correlated with gametophyte development in the single petal cultivar. The CYC/TB1 type genes were highly detected in the formation of petal and pistil. The less-complex flower types of P. mume might result from the fact that there were only two CYC type genes present in P. mume and a lack of CYC2 genes to control the identity of flower types. These results lay the foundation for further study on the functions of TCP genes during flower development. PMID:27630648

Genome-Wide Identification, Characterization and Expression Analysis of the TCP Gene Family in Prunus mume.

PubMed

Zhou, Yuzhen; Xu, Zongda; Zhao, Kai; Yang, Weiru; Cheng, Tangren; Wang, Jia; Zhang, Qixiang

2016-01-01

TCP proteins, belonging to a plant-specific transcription factors family, are known to have great functions in plant development, especially flower and leaf development. However, there is little information about this gene family in Prunus mume, which is widely cultivated in China as an ornamental and fruit tree. Here a genome-wide analysis of TCP genes was performed to explore their evolution in P. mume. Nineteen PmTCPs were identified and three of them contained putative miR319 target sites. Phylogenetic and comprehensive bioinformatics analyses of these genes revealed that different types of TCP genes had undergone different evolutionary processes and the genes in the same clade had similar chromosomal location, gene structure, and conserved domains. Expression analysis of these PmTCPs indicated that there were diverse expression patterns among different clades. Most TCP genes were predominantly expressed in flower, leaf, and stem, and showed high expression levels in the different stages of flower bud differentiation, especially in petal formation stage and gametophyte development. Genes in TCP-P subfamily had main roles in both flower development and gametophyte development. The CIN genes in double petal cultivars might have key roles in the formation of petal, while they were correlated with gametophyte development in the single petal cultivar. The CYC/TB1 type genes were highly detected in the formation of petal and pistil. The less-complex flower types of P. mume might result from the fact that there were only two CYC type genes present in P. mume and a lack of CYC2 genes to control the identity of flower types. These results lay the foundation for further study on the functions of TCP genes during flower development.

Cryptic Plutella species show deep divergence despite the capacity to hybridize.

PubMed

Perry, Kym D; Baker, Gregory J; Powis, Kevin J; Kent, Joanne K; Ward, Christopher M; Baxter, Simon W

2018-05-29

Understanding genomic and phenotypic diversity among cryptic pest taxa has important implications for the management of pests and diseases. The diamondback moth, Plutella xylostella L., has been intensively studied due to its ability to evolve insecticide resistance and status as the world's most destructive pest of brassicaceous crops. The surprise discovery of a cryptic species endemic to Australia, Plutella australiana Landry & Hebert, raised questions regarding the distribution, ecological traits and pest status of the two species, the capacity for gene flow and whether specific management was required. Here, we collected Plutella from wild and cultivated brassicaceous plants from 75 locations throughout Australia and screened 1447 individuals to identify mtDNA lineages and Wolbachia infections. We genotyped genome-wide SNP markers using RADseq in coexisting populations of each species. In addition, we assessed reproductive compatibility in crossing experiments and insecticide susceptibility phenotypes using bioassays. The two Plutella species coexisted on wild brassicas and canola crops, but only 10% of Plutella individuals were P. australiana. This species was not found on commercial Brassica vegetable crops, which are routinely sprayed with insecticides. Bioassays found that P. australiana was 19-306 fold more susceptible to four commonly-used insecticides than P. xylostella. Laboratory crosses revealed that reproductive isolation was incomplete but directionally asymmetric between the species. However, genome-wide nuclear SNPs revealed striking differences in genetic diversity and strong population structure between coexisting wild populations of each species. Nuclear diversity was 1.5-fold higher in P. australiana, yet both species showed limited variation in mtDNA. Infection with a single Wolbachia subgroup B strain was fixed in P. australiana, suggesting that a selective sweep contributed to low mtDNA diversity, while a subgroup A strain infected just 1

A School Wide Approach to Leading Pedagogical Enhancement: An Australian Perspective

ERIC Educational Resources Information Center

Conway, Joan M.; Andrews, Dorothy

2016-01-01

This paper presents how some Australian schools are changing their approaches to leading the teaching and learning in their diverse and multi-characteristic contexts. Experiences of these schools shows that the development of a school wide approach to pedagogy and its implementation needs to be firmly embedded in the leadership of learning.…

The VLT Interferometer and its AMBER Instrument: Simulations of Interferometric Imaging in the Wide-Field Mode

NASA Astrophysics Data System (ADS)

Blöcker, T.; Hofmann, K.-H.; Przygodda, F.; Weigelt, G.

We present computer simulations of interferometric imaging with the VLT interferometer and the AMBER instrument. These simulations include both the astrophysical modelling of a stellar object by radiative transfer calculations and the simulation of light propagation from the object to the detector (through atmosphere, telescopes, and the AMBER instrument), simulation of photon noise and detector read-out noise, and finally data processing of the interferograms. The results show the dependence of the visibility error bars on the following observational parameters: different seeing during the observation of object and reference star (Fried parameters r0,object and r0,ref. ranging between 0.9 m and 1.2 m), different residual tip-tilt error (δtt,object and δtt,ref. ranging between 0.1% and 20% of the Airy disk diameter), and object brightness (Kobject=3.5 mag to 13 mag, Kref.=3.5 mag). Exemplarily, we focus on stars in late stages of stellar evolution and study one of its key objects, the dusty supergiant IRC +10 420 that is rapidly evolving on human timescales. We show computer simulations of VLT interferometry of IRC +10 420 with two ATs (wide-field mode, i.e. without fiber optics spatial filters) and discuss whether the visibility accuracy is sufficient to distinguish between different theoretical model predictions.

A NARROW SHORT-DURATION GRB JET FROM A WIDE CENTRAL ENGINE

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

Duffell, Paul C.; Quataert, Eliot; MacFadyen, Andrew I., E-mail: duffell@berkeley.edu

2015-11-01

We use two-dimensional relativistic hydrodynamic numerical calculations to show that highly collimated relativistic jets can be produced in neutron star merger models of short-duration gamma-ray bursts (GRBs) without the need for a highly directed engine or a large net magnetic flux. Even a hydrodynamic engine generating a very wide sustained outflow on small scales can, in principle, produce a highly collimated relativistic jet, facilitated by a dense surrounding medium that provides a cocoon surrounding the jet core. An oblate geometry to the surrounding gas significantly enhances the collimation process. Previous numerical simulations have shown that the merger of two neutronmore » stars produces an oblate, expanding cloud of dynamical ejecta. We show that this gas can efficiently collimate the central engine power much like the surrounding star does in long-duration GRB models. For typical short-duration GRB central engine parameters, we find jets with opening angles of an order of 10° in which a large fraction of the total outflow power of the central engine resides in highly relativistic material. These results predict large differences in the opening angles of outflows from binary neutron star mergers versus neutron star–black hole mergers.« less

Theory and simulation of multi-channel interference (MCI) widely tunable lasers.

PubMed

Chen, Quanan; Lu, Qiaoyin; Guo, Weihua

2015-07-13

A novel design of an InP-based monolithic widely tunable laser, multi-channel interference (MCI) laser, is proposed and presented for the first time. The device is comprised of a gain section, a common phase section and a multi-channel interference section. The multi-channel interference section contains a 1x8 splitter based on cascaded 1 × 2 multi-mode interferometers (MMIs) and eight arms with unequal length difference. The rear part of each arm is integrated with a one-port multi-mode interference reflector (MIR). Mode selection of the MCI laser is realized by the constructive interference of the lights reflected back by the eight arms. Through optimizing the arm length difference, a tuning range of more than 40 nm covering the whole C band, a threshold current around 11.5 mA and an side-mode-suppression-ratio (SMSR) up to 48 dB have been predicted for this widely tunable laser. Detailed design principle and numerical simulation results are presented.

Natural CMT2 Variation Is Associated With Genome-Wide Methylation Changes and Temperature Seasonality

PubMed Central

Shen, Xia; De Jonge, Jennifer; Forsberg, Simon K. G.; Pettersson, Mats E.; Sheng, Zheya; Hennig, Lars; Carlborg, Örjan

2014-01-01

As Arabidopsis thaliana has colonized a wide range of habitats across the world it is an attractive model for studying the genetic mechanisms underlying environmental adaptation. Here, we used public data from two collections of A. thaliana accessions to associate genetic variability at individual loci with differences in climates at the sampling sites. We use a novel method to screen the genome for plastic alleles that tolerate a broader climate range than the major allele. This approach reduces confounding with population structure and increases power compared to standard genome-wide association methods. Sixteen novel loci were found, including an association between Chromomethylase 2 (CMT2) and temperature seasonality where the genome-wide CHH methylation was different for the group of accessions carrying the plastic allele. Cmt2 mutants were shown to be more tolerant to heat-stress, suggesting genetic regulation of epigenetic modifications as a likely mechanism underlying natural adaptation to variable temperatures, potentially through differential allelic plasticity to temperature-stress. PMID:25503602

Water metamaterial for ultra-broadband and wide-angle absorption.

PubMed

Xie, Jianwen; Zhu, Weiren; Rukhlenko, Ivan D; Xiao, Fajun; He, Chong; Geng, Junping; Liang, Xianling; Jin, Ronghong; Premaratne, Malin

2018-02-19

A subwavelength water metamaterial is proposed and analyzed for ultra-broadband perfect absorption at microwave frequencies. We experimentally demonstrate that this metamaterial shows over 90% absorption within almost the entire frequency band of 12-29.6 GHz. It is also shown that the proposed metamaterial exhibits a good thermal stability with its absorption performance almost unchanged for the temperature range from 0 to 100°C. The study of the angular tolerance of the metamaterial absorber shows its ability of working at wide angles of incidence. Given that the proposed water metamaterial absorber is low-cost and easy for manufacture, we envision it may find numerous applications in electromagnetics such as broadband scattering reduction and electromagnetic energy harvesting.

A Wide Field of View Plasma Spectrometer

DOE PAGES

Skoug, Ruth M.; Funsten, Herbert O.; Moebius, Eberhard; ...

2016-07-01

Here we present a fundamentally new type of space plasma spectrometer, the wide field of view plasma spectrometer, whose field of view is >1.25π ster using fewer resources than traditional methods. The enabling component is analogous to a pinhole camera with an electrostatic energy-angle filter at the image plane. Particle energy-per-charge is selected with a tunable bias voltage applied to the filter plate relative to the pinhole aperture plate. For a given bias voltage, charged particles from different directions are focused by different angles to different locations. Particles with appropriate locations and angles can transit the filter plate and aremore » measured using a microchannel plate detector with a position-sensitive anode. Full energy and angle coverage are obtained using a single high-voltage power supply, resulting in considerable resource savings and allowing measurements at fast timescales. Lastly, we present laboratory prototype measurements and simulations demonstrating the instrument concept and discuss optimizations of the instrument design for application to space measurements.« less

Pooled genome wide association detects association upstream of FCRL3 with Graves' disease.

PubMed

Khong, Jwu Jin; Burdon, Kathryn P; Lu, Yi; Laurie, Kate; Leonardos, Lefta; Baird, Paul N; Sahebjada, Srujana; Walsh, John P; Gajdatsy, Adam; Ebeling, Peter R; Hamblin, Peter Shane; Wong, Rosemary; Forehan, Simon P; Fourlanos, Spiros; Roberts, Anthony P; Doogue, Matthew; Selva, Dinesh; Montgomery, Grant W; Macgregor, Stuart; Craig, Jamie E

2016-11-18

Graves' disease is an autoimmune thyroid disease of complex inheritance. Multiple genetic susceptibility loci are thought to be involved in Graves' disease and it is therefore likely that these can be identified by genome wide association studies. This study aimed to determine if a genome wide association study, using a pooling methodology, could detect genomic loci associated with Graves' disease. Nineteen of the top ranking single nucleotide polymorphisms including HLA-DQA1 and C6orf10, were clustered within the Major Histo-compatibility Complex region on chromosome 6p21, with rs1613056 reaching genome wide significance (p = 5 × 10 -8 ). Technical validation of top ranking non-Major Histo-compatablity complex single nucleotide polymorphisms with individual genotyping in the discovery cohort revealed four single nucleotide polymorphisms with p ≤ 10 -4 . Rs17676303 on chromosome 1q23.1, located upstream of FCRL3, showed evidence of association with Graves' disease across the discovery, replication and combined cohorts. A second single nucleotide polymorphism rs9644119 downstream of DPYSL2 showed some evidence of association supported by finding in the replication cohort that warrants further study. Pooled genome wide association study identified a genetic variant upstream of FCRL3 as a susceptibility locus for Graves' disease in addition to those identified in the Major Histo-compatibility Complex. A second locus downstream of DPYSL2 is potentially a novel genetic variant in Graves' disease that requires further confirmation.

Wide distribution of cysteine-rich secretory proteins in snake venoms: isolation and cloning of novel snake venom cysteine-rich secretory proteins.

PubMed

Yamazaki, Yasuo; Hyodo, Fumiko; Morita, Takashi

2003-04-01

Cysteine-rich secretory proteins (CRISPs) are found in epididymis and granules of mammals, and they are thought to function in sperm maturation and in the immune system. Recently, we isolated and obtained clones for novel snake venom proteins that are classified as CRISP family proteins. To elucidate the distribution of snake venom CRISP family proteins, we evaluated a wide range of venoms for immuno-cross-reactivity. Then we isolated, characterized, and cloned genes for three novel CRISP family proteins (piscivorin, ophanin, and catrin) from the venom of eastern cottonmouth (Agkistrodon piscivorus piscivorus), king cobra (Ophiophagus hannah), and western diamondback rattlesnake (Crotalus atrox). Our results show the wide distribution of snake venom CRISP family proteins among Viperidae and Elapidae from different continents, indicating that CRISP family proteins compose a new group of snake venom proteins.

Snake venomics of Lachesis muta rhombeata and genus-wide antivenomics assessment of the paraspecific immunoreactivity of two antivenoms evidence the high compositional and immunological conservation across Lachesis.

PubMed

Pla, Davinia; Sanz, Libia; Molina-Sánchez, Pedro; Zorita, Virginia; Madrigal, Marvin; Flores-Díaz, Marietta; Alape-Girón, Alberto; Núñez, Vitelbina; Andrés, Vicente; Gutiérrez, José María; Calvete, Juan J

2013-08-26

We report the proteomic analysis of the Atlantic bushmaster, Lachesis muta rhombeata, from Brazil. Along with previous characterization of the venom proteomes of L. stenophrys (Costa Rica), L. melanocephala (Costa Rica), L. acrochorda (Colombia), and L. muta muta (Bolivia), the present study provides the first overview of the composition and distribution of venom proteins across this wide-ranging genus, and highlights the remarkable similar compositional and pharmacological profiles across Lachesis venoms. The paraspecificity of two antivenoms, produced at Instituto Vital Brazil (Brazil) and Instituto Clodomiro Picado (Costa Rica) using different conspecific taxa in the immunization mixtures, was assessed using genus-wide comparative antivenomics. This study confirms that the proteomic similarity among Lachesis sp. venoms is mirrored in their high immunological conservation across the genus. The clinical and therapeutic consequences of genus-wide venomics and antivenomics investigations of Lachesis venoms are discussed. The proteomics characterization of L. m. rhombeata venom completes the overview of Lachesis venom proteomes and confirms the remarkable toxin profile conservation across the five clades of this wide-ranging genus. Genus-wide antivenomics showed that two antivenoms, produced against L. stenophrys or L. m. rhombeata, exhibit paraspecificity towards all other congeneric venoms. Our venomics study shows that, despite the broad geographic distribution of the genus, monospecific antivenoms may achieve clinical coverage for any Lachesis sp. envenoming. Copyright © 2013 Elsevier B.V. All rights reserved.

Genome-wide study of methotrexate clearance replicates SLCO1B1

PubMed Central

Ramsey, Laura B.; Panetta, John C.; Smith, Colton; Yang, Wenjian; Fan, Yiping; Winick, Naomi J.; Martin, Paul L.; Cheng, Cheng; Devidas, Meenakshi; Pui, Ching-Hon; Evans, William E.; Hunger, Stephen P.; Loh, Mignon

2013-01-01

Methotrexate clearance can influence the cure of and toxicity in children with acute lymphoblastic leukemia (ALL). We estimated methotrexate plasma clearance for 1279 patients with ALL treated with methotrexate (24-hour infusion of a 1 g/m2 dose or 4-hour infusion of a 2 g/m2 dose) on the Children's Oncology Group P9904 and P9905 protocols. Methotrexate clearance was lower in older children (P = 7 × 10−7), girls (P = 2.7 × 10−4), and those who received a delayed-intensification phase (P = .0022). A genome-wide analysis showed that methotrexate clearance was associated with polymorphisms in the organic anion transporter gene SLCO1B1 (P = 2.1 × 10−11). This replicates findings using different schedules of high-dose methotrexate in St Jude ALL treatment protocols; a combined meta-analysis yields a P value of 5.7 × 10−19 for the association of methotrexate clearance with SLCO1B1 SNP rs4149056. Validation of this variant with 5 different treatment regimens of methotrexate solidifies the robustness of this pharmacogenomic determinant of methotrexate clearance. This study is registered at http://www.clinicaltrials.gov as NCT00005585 and NCT00005596. PMID:23233662

Investigation on wide-band scattering of a 2-D target above 1-D randomly rough surface by FDTD method.

PubMed

Li, Juan; Guo, Li-Xin; Jiao, Yong-Chang; Li, Ke

2011-01-17

Finite-difference time-domain (FDTD) algorithm with a pulse wave excitation is used to investigate the wide-band composite scattering from a two-dimensional(2-D) infinitely long target with arbitrary cross section located above a one-dimensional(1-D) randomly rough surface. The FDTD calculation is performed with a pulse wave incidence, and the 2-D representative time-domain scattered field in the far zone is obtained directly by extrapolating the currently calculated data on the output boundary. Then the 2-D wide-band scattering result is acquired by transforming the representative time-domain field to the frequency domain with a Fourier transform. Taking the composite scattering of an infinitely long cylinder above rough surface as an example, the wide-band response in the far zone by FDTD with the pulsed excitation is computed and it shows a good agreement with the numerical result by FDTD with the sinusoidal illumination. Finally, the normalized radar cross section (NRCS) from a 2-D target above 1-D rough surface versus the incident frequency, and the representative scattered fields in the far zone versus the time are analyzed in detail.

Mapping wide row crops with video sequences acquired from a tractor moving at treatment speed.

PubMed

Sainz-Costa, Nadir; Ribeiro, Angela; Burgos-Artizzu, Xavier P; Guijarro, María; Pajares, Gonzalo

2011-01-01

This paper presents a mapping method for wide row crop fields. The resulting map shows the crop rows and weeds present in the inter-row spacing. Because field videos are acquired with a camera mounted on top of an agricultural vehicle, a method for image sequence stabilization was needed and consequently designed and developed. The proposed stabilization method uses the centers of some crop rows in the image sequence as features to be tracked, which compensates for the lateral movement (sway) of the camera and leaves the pitch unchanged. A region of interest is selected using the tracked features, and an inverse perspective technique transforms the selected region into a bird's-eye view that is centered on the image and that enables map generation. The algorithm developed has been tested on several video sequences of different fields recorded at different times and under different lighting conditions, with good initial results. Indeed, lateral displacements of up to 66% of the inter-row spacing were suppressed through the stabilization process, and crop rows in the resulting maps appear straight.

Genome-wide patterns of selection in 230 ancient Eurasians

PubMed Central

Mathieson, Iain; Lazaridis, Iosif; Rohland, Nadin; Mallick, Swapan; Patterson, Nick; Roodenberg, Songül Alpaslan; Harney, Eadaoin; Stewardson, Kristin; Fernandes, Daniel; Novak, Mario; Sirak, Kendra; Gamba, Cristina; Jones, Eppie R.; Llamas, Bastien; Dryomov, Stanislav; Pickrel, Joseph; Arsuaga, Juan Luís; de Castro, José María Bermúdez; Carbonell, Eudald; Gerritsen, Fokke; Khokhlov, Aleksandr; Kuznetsov, Pavel; Lozano, Marina; Meller, Harald; Mochalov, Oleg; Moiseyev, Vayacheslav; Rojo Guerra, Manuel A.; Roodenberg, Jacob; Vergès, Josep Maria; Krause, Johannes; Cooper, Alan; Alt, Kurt W.; Brown, Dorcas; Anthony, David; Lalueza-Fox, Carles; Haak, Wolfgang; Pinhasi, Ron; Reich, David

2016-01-01

Ancient DNA makes it possible to directly witness natural selection by analyzing samples from populations before, during and after adaptation events. Here we report the first scan for selection using ancient DNA, capitalizing on the largest genome-wide dataset yet assembled: 230 West Eurasians dating to between 6500 and 1000 BCE, including 163 with newly reported data. The new samples include the first genome-wide data from the Anatolian Neolithic culture whose genetic material we extracted from the DNA-rich petrous bone and who we show were members of the population that was the source of Europe’s first farmers. We also report a complete transect of the steppe region in Samara between 5500 and 1200 BCE that allows us to recognize admixture from at least two external sources into steppe populations during this period. We detect selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height. PMID:26595274

Implementation of a School-wide Clinical Intervention Documentation System

PubMed Central

Stevenson, T. Lynn; Fox, Brent I.; Andrus, Miranda; Carroll, Dana

2011-01-01

Objective. To evaluate the effectiveness and impact of a customized Web-based software program implemented in 2006 for school-wide documentation of clinical interventions by pharmacy practice faculty members, pharmacy residents, and student pharmacists. Methods. The implementation process, directed by a committee of faculty members and school administrators, included preparation and refinement of the software, user training, development of forms and reports, and integration of the documentation process within the curriculum. Results. Use of the documentation tool consistently increased from May 2007 to December 2010. Over 187,000 interventions were documented with over $6.2 million in associated cost avoidance. Conclusions. Successful implementation of a school-wide documentation tool required considerable time from the oversight committee and a comprehensive training program for all users, with ongoing monitoring of data collection practices. Data collected proved to be useful to show the impact of faculty members, residents, and student pharmacists at affiliated training sites. PMID:21829264

Investigating Faculty Technology Mentoring as a University-Wide Professional Development Model

ERIC Educational Resources Information Center

Baran, Evrim

2016-01-01

A growing and increasingly important area of research in higher education is the investigation of how different forms of support and training programs facilitate faculty adoption of technology into pedagogical practices. This study explored the implementation of a faculty technology mentoring (FTM) program as a university-wide professional…

ASD Is Not DLI: Individuals With Autism and Individuals With Syntactic DLI Show Similar Performance Level in Syntactic Tasks, but Different Error Patterns.

PubMed

Sukenik, Nufar; Friedmann, Naama

2018-01-01

Do individuals with autism have a developmental syntactic impairment, DLI (formerly known as SLI)? In this study we directly compared the performance of 18 individuals with Autism Spectrum Disorder (ASD) aged 9;0-18;0 years with that of 93 individuals with Syntactic-Developmental Language Impairment (SyDLI) aged 8;8-14;6 (and with 166 typically-developing children aged 5;2-18;1). We tested them using three syntactic tests assessing the comprehension and production of syntactic structures that are known to be sensitive to syntactic impairment: elicitation of subject and object relative clauses, reading and paraphrasing of object relatives, and repetition of complex syntactic structures including Wh questions, relative clauses, topicalized sentences, sentences with verb movement, sentences with A-movement, and embedded sentences. The results were consistent across the three tasks: the overall rate of correct performance on the syntactic tasks is similar for the children with ASD and those with SyDLI. However, once we look closer, they are very different. The types of errors of the ASD group differ from those of the SyDLI group-the children with ASD provide various types of pragmatically infelicitous responses that are not evinced in the SyDLI or in the age equivalent typically-developing groups. The two groups (ASD and SyDLI) also differ in the pattern of performance-the children with SyDLI show a syntactically-principled pattern of impairment, with selective difficulty in specific sentence types (such as sentences derived by movement of the object across the subject), and normal performance on other structures (such as simple sentences). In contrast, the ASD participants showed generalized low performance on the various sentence structures. Syntactic performance was far from consistent within the ASD group. Whereas all ASD participants had errors that can originate in pragmatic/discourse difficulties, seven of them had completely normal syntax in the structures we

ASD Is Not DLI: Individuals With Autism and Individuals With Syntactic DLI Show Similar Performance Level in Syntactic Tasks, but Different Error Patterns

PubMed Central

Sukenik, Nufar; Friedmann, Naama

2018-01-01

Do individuals with autism have a developmental syntactic impairment, DLI (formerly known as SLI)? In this study we directly compared the performance of 18 individuals with Autism Spectrum Disorder (ASD) aged 9;0–18;0 years with that of 93 individuals with Syntactic-Developmental Language Impairment (SyDLI) aged 8;8–14;6 (and with 166 typically-developing children aged 5;2–18;1). We tested them using three syntactic tests assessing the comprehension and production of syntactic structures that are known to be sensitive to syntactic impairment: elicitation of subject and object relative clauses, reading and paraphrasing of object relatives, and repetition of complex syntactic structures including Wh questions, relative clauses, topicalized sentences, sentences with verb movement, sentences with A-movement, and embedded sentences. The results were consistent across the three tasks: the overall rate of correct performance on the syntactic tasks is similar for the children with ASD and those with SyDLI. However, once we look closer, they are very different. The types of errors of the ASD group differ from those of the SyDLI group—the children with ASD provide various types of pragmatically infelicitous responses that are not evinced in the SyDLI or in the age equivalent typically-developing groups. The two groups (ASD and SyDLI) also differ in the pattern of performance—the children with SyDLI show a syntactically-principled pattern of impairment, with selective difficulty in specific sentence types (such as sentences derived by movement of the object across the subject), and normal performance on other structures (such as simple sentences). In contrast, the ASD participants showed generalized low performance on the various sentence structures. Syntactic performance was far from consistent within the ASD group. Whereas all ASD participants had errors that can originate in pragmatic/discourse difficulties, seven of them had completely normal syntax in the

Genome-Wide Spectra of Transcription Insertions and Deletions Reveal That Slippage Depends on RNA:DNA Hybrid Complementarity.

PubMed

Traverse, Charles C; Ochman, Howard

2017-08-29

Advances in sequencing technologies have enabled direct quantification of genome-wide errors that occur during RNA transcription. These errors occur at rates that are orders of magnitude higher than rates during DNA replication, but due to technical difficulties such measurements have been limited to single-base substitutions and have not yet quantified the scope of transcription insertions and deletions. Previous reporter gene assay findings suggested that transcription indels are produced exclusively by elongation complex slippage at homopolymeric runs, so we enumerated indels across the protein-coding transcriptomes of Escherichia coli and Buchnera aphidicola , which differ widely in their genomic base compositions and incidence of repeat regions. As anticipated from prior assays, transcription insertions prevailed in homopolymeric runs of A and T; however, transcription deletions arose in much more complex sequences and were rarely associated with homopolymeric runs. By reconstructing the relocated positions of the elongation complex as inferred from the sequences inserted or deleted during transcription, we show that continuation of transcription after slippage hinges on the degree of nucleotide complementarity within the RNA:DNA hybrid at the new DNA template location. IMPORTANCE The high level of mistakes generated during transcription can result in the accumulation of malfunctioning and misfolded proteins which can alter global gene regulation and in the expenditure of energy to degrade these nonfunctional proteins. The transcriptome-wide occurrence of base substitutions has been elucidated in bacteria, but information on transcription insertions and deletions-errors that potentially have more dire effects on protein function-is limited to reporter gene constructs. Here, we capture the transcriptome-wide spectrum of insertions and deletions in Escherichia coli and Buchnera aphidicola and show that they occur at rates approaching those of base substitutions

Only multi-taxon studies show the full range of arthropod responses to fire

PubMed Central

Pryke, James S.; Gaigher, René; Samways, Michael J.

2018-01-01

Fire is a major driver in many ecosystems. Yet, little is known about how different ground-living arthropods survive fire. Using three sampling methods, and time-since-fire (last fire event: 3 months, 1 year, and 7 years), we investigate how ground-living arthropod diversity responds to fire, and how species richness, diversity, abundance, and composition of the four dominant taxa: ants, beetles, cockroaches and mites, respond. We did this in the naturally fire-prone Mediterranean-type scrubland vegetation (fynbos) of the Cape Floristic Region. Surprisingly, overall species richness and diversity was the same for all time-since-fire categories. However, when each dominant taxon was analysed separately, effect of fire on species richness and abundance varied among taxa. This emphasizes that many taxa must be investigated to really understand fire-driven events. We also highlight the importance of using different diversity measures, as fire did not influence species richness and abundance of particular taxa, while it affected others, overall greatly affecting assemblages of all taxa. Rockiness affected species richness, abundance and composition of a few taxa. We found that all time-since-fire categories supported distinctive assemblages. Some indicator species occurred across all time-since-fire categories, while others were restricted to a single time-since-fire category, showing that there is a wide range of responses to fire between taxa. Details of local landscape structure, abiotic and biotic, and frequency and intensity of fire add complexity to the fire-arthropod interaction. Overall, we show that the relationship between fire and arthropods is phylogenetically constrained, having been honed by many millennia of fire events, and highly complex. Present-day species manifest a variety of adaptations for surviving the great natural selective force of fire. PMID:29614132

Low cost and thin metasurface for ultra wide band and wide angle polarization insensitive radar cross section reduction

NASA Astrophysics Data System (ADS)

Ameri, Edris; Esmaeli, Seyed Hassan; Sedighy, Seyed Hassan

2018-05-01

A planar low cost and thin metasurface is proposed to achieve ultra-wideband radar cross section (RCS) reduction with stable performance with respect to polarization and incident angles. This metasurface is composed of two different artificial magnetic conductor unit cells arranged in a chessboard like configuration. These unit cells have a Jerusalem cross pattern with different thicknesses, which results in wideband out-phase reflection and RCS reduction, consequently. The designed metasurface reduces RCS more than 10-dB from 13.6 GHz to 45.5 GHz (108% bandwidth) and more than 20-dB RCS from 15.2 GHz to 43.6 GHz (96.6%). Moreover, the 10-dB RCS reduction bandwidth is very stable (more than 107%) for both TE and TM polarizations. The good agreement between simulations and measurement results proves the design, properly. The ultra-wide bandwidth, low cost, low profile, and stable performance of this metasurface prove its high capability compared with the state-of-the-art references.

Plasma DNA tissue mapping by genome-wide methylation sequencing for noninvasive prenatal, cancer, and transplantation assessments

PubMed Central

Sun, Kun; Jiang, Peiyong; Chan, K. C. Allen; Wong, John; Cheng, Yvonne K. Y.; Liang, Raymond H. S.; Chan, Wai-kong; Ma, Edmond S. K.; Chan, Stephen L.; Cheng, Suk Hang; Chan, Rebecca W. Y.; Tong, Yu K.; Ng, Simon S. M.; Wong, Raymond S. M.; Hui, David S. C.; Leung, Tse Ngong; Leung, Tak Y.; Lai, Paul B. S.; Chiu, Rossa W. K.; Lo, Yuk Ming Dennis

2015-01-01

Plasma consists of DNA released from multiple tissues within the body. Using genome-wide bisulfite sequencing of plasma DNA and deconvolution of the sequencing data with reference to methylation profiles of different tissues, we developed a general approach for studying the major tissue contributors to the circulating DNA pool. We tested this method in pregnant women, patients with hepatocellular carcinoma, and subjects following bone marrow and liver transplantation. In most subjects, white blood cells were the predominant contributors to the circulating DNA pool. The placental contributions in the plasma of pregnant women correlated with the proportional contributions as revealed by fetal-specific genetic markers. The graft-derived contributions to the plasma in the transplant recipients correlated with those determined using donor-specific genetic markers. Patients with hepatocellular carcinoma showed elevated plasma DNA contributions from the liver, which correlated with measurements made using tumor-associated copy number aberrations. In hepatocellular carcinoma patients and in pregnant women exhibiting copy number aberrations in plasma, comparison of methylation deconvolution results using genomic regions with different copy number status pinpointed the tissue type responsible for the aberrations. In a pregnant woman diagnosed as having follicular lymphoma during pregnancy, methylation deconvolution indicated a grossly elevated contribution from B cells into the plasma DNA pool and localized B cells as the origin of the copy number aberrations observed in plasma. This method may serve as a powerful tool for assessing a wide range of physiological and pathological conditions based on the identification of perturbed proportional contributions of different tissues into plasma. PMID:26392541

A micromixer with consistent mixing performance for a wide range of flow rates.

PubMed

Goovaerts, Robert; Van Assche, Tom; Sonck, Marc; Denayer, Joeri; Desmet, Gert

2015-02-01

A micromixer with consistent mixing performance for a wide range of flow rates is presented. The mixer makes use of internally moving elements, i.e. steel balls that are located in dedicated mixing chambers. Movement is induced by a rotating magnetic field. To get better insight in differences between active and passive mixing, we studied a mixer that can operate in both regimes. A mixing performance study for a range of flow rates along with pressure drop data is presented. The response of the moving elements in regard to the magnetic field is shown experimentally and shows the limitations of earlier modeling studies. Lastly, the estimated power input on the fluids was calculated and allows for a comparison with more well-known convective-type mixers. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Apparent competition drives community-wide parasitism rates and changes in host abundance across ecosystem boundaries

PubMed Central

Frost, Carol M.; Peralta, Guadalupe; Rand, Tatyana A.; Didham, Raphael K.; Varsani, Arvind; Tylianakis, Jason M.

2016-01-01

Species have strong indirect effects on others, and predicting these effects is a central challenge in ecology. Prey species sharing an enemy (predator or parasitoid) can be linked by apparent competition, but it is unknown whether this process is strong enough to be a community-wide structuring mechanism that could be used to predict future states of diverse food webs. Whether species abundances are spatially coupled by enemy movement across different habitats is also untested. Here, using a field experiment, we show that predicted apparent competitive effects between species, mediated via shared parasitoids, can significantly explain future parasitism rates and herbivore abundances. These predictions are successful even across edges between natural and managed forests, following experimental reduction of herbivore densities by aerial spraying of insecticide over 20 hectares. This result shows that trophic indirect effects propagate across networks and habitats in important, predictable ways, with implications for landscape planning, invasion biology and biological control. PMID:27577948

Improvements in Empirical Modelling of the World-Wide Ionosphere

DTIC Science & Technology

1986-10-31

The fact that the world-wide distribution of the basic inputs is far from being uniform forced Gallet and Jones to develop . a special procedure for...made the result more reasonable, it had a disappointing effect on the latitudinal variation over the oceans. Feeling that shifting along circles of...range. Ano- ther vertical profile model is used in the Bent-model4 which is applied in NASA practice for computing the different effects of

Wide binaries in Tycho-Gaia II: metallicities, abundances and prospects for chemical tagging

NASA Astrophysics Data System (ADS)

Andrews, Jeff J.; Chanamé, Julio; Agüeros, Marcel A.

2018-02-01

From our recent catalogue based on the first Gaia data release (TGAS), we select wide binaries in which both stars have been observed by the Radial Velocity Experiment (RAVE) or the Large Sky Area Multi-Object Fiber Spectroscopic Telescope (LAMOST). Using RAVE and LAMOST metallicities and RAVE Mg, Al, Si, Ti and Fe abundances, we find that the differences in the metallicities and elemental abundances of components of wide binaries are consistent with being due to observational uncertainties, in agreement with previous results for smaller and more restricted samples. The metallicity and elemental abundance consistency between wide binary components presented in this work confirms their common origin and bolsters the status of wide binaries as 'mini-open clusters'. Furthermore, this is evident that wide binaries are effectively co-eval and co-chemical, supporting their use for, e.g. constraining age-activity-rotation relations, the initial-final mass relation for white dwarfs and M-dwarf metallicity indicators. Additionally, we demonstrate that the common proper motion, common parallax pairs in TGAS with the most extreme separations (s ≳ 0.1 pc) typically have inconsistent metallicities, radial velocities or both and are therefore likely to be predominantly comprised of random alignments of unassociated stars with similar astrometry, in agreement with our previous results. Finally, we propose that wide binaries form an ideal data set with which we can test chemical tagging as a method to identify stars of common origin, particularly because the stars in wide binaries span a wide range of metallicities, much wider than that spanned by nearby open clusters.

IOT Overview: Wide-Field Imaging

NASA Astrophysics Data System (ADS)

Selman, F. J.

The Wide Field Imager (WFI) instrument at La Silla has been the workhorse of wide-field imaging instruments at ESO for several years. In this contribution I will summarize the issues relating to its productivity for the community both in terms of the quality and quantity of data that has come out of it. Although only surveys of limited scope have been completed using WFI, it is ESO's stepping-stone to the new generation of survey telescopes.

TEAM: efficient two-locus epistasis tests in human genome-wide association study.

PubMed

Zhang, Xiang; Huang, Shunping; Zou, Fei; Wang, Wei

2010-06-15

As a promising tool for identifying genetic markers underlying phenotypic differences, genome-wide association study (GWAS) has been extensively investigated in recent years. In GWAS, detecting epistasis (or gene-gene interaction) is preferable over single locus study since many diseases are known to be complex traits. A brute force search is infeasible for epistasis detection in the genome-wide scale because of the intensive computational burden. Existing epistasis detection algorithms are designed for dataset consisting of homozygous markers and small sample size. In human study, however, the genotype may be heterozygous, and number of individuals can be up to thousands. Thus, existing methods are not readily applicable to human datasets. In this article, we propose an efficient algorithm, TEAM, which significantly speeds up epistasis detection for human GWAS. Our algorithm is exhaustive, i.e. it does not ignore any epistatic interaction. Utilizing the minimum spanning tree structure, the algorithm incrementally updates the contingency tables for epistatic tests without scanning all individuals. Our algorithm has broader applicability and is more efficient than existing methods for large sample study. It supports any statistical test that is based on contingency tables, and enables both family-wise error rate and false discovery rate controlling. Extensive experiments show that our algorithm only needs to examine a small portion of the individuals to update the contingency tables, and it achieves at least an order of magnitude speed up over the brute force approach.

Genome-Wide DNA Methylation Indicates Silencing of Tumor Suppressor Genes in Uterine Leiomyoma

PubMed Central

Navarro, Antonia; Yin, Ping; Monsivais, Diana; Lin, Simon M.; Du, Pan; Wei, Jian-Jun; Bulun, Serdar E.

2012-01-01

Background Uterine leiomyomas, or fibroids, represent the most common benign tumor of the female reproductive tract. Fibroids become symptomatic in 30% of all women and up to 70% of African American women of reproductive age. Epigenetic dysregulation of individual genes has been demonstrated in leiomyoma cells; however, the in vivo genome-wide distribution of such epigenetic abnormalities remains unknown. Principal Findings We characterized and compared genome-wide DNA methylation and mRNA expression profiles in uterine leiomyoma and matched adjacent normal myometrial tissues from 18 African American women. We found 55 genes with differential promoter methylation and concominant differences in mRNA expression in uterine leiomyoma versus normal myometrium. Eighty percent of the identified genes showed an inverse relationship between DNA methylation status and mRNA expression in uterine leiomyoma tissues, and the majority of genes (62%) displayed hypermethylation associated with gene silencing. We selected three genes, the known tumor suppressors KLF11, DLEC1, and KRT19 and verified promoter hypermethylation, mRNA repression and protein expression using bisulfite sequencing, real-time PCR and western blot. Incubation of primary leiomyoma smooth muscle cells with a DNA methyltransferase inhibitor restored KLF11, DLEC1 and KRT19 mRNA levels. Conclusions These results suggest a possible functional role of promoter DNA methylation-mediated gene silencing in the pathogenesis of uterine leiomyoma in African American women. PMID:22428009

Single linearly polarized, widely and freely tunable two wavelengths Yb3+-doped fiber laser

NASA Astrophysics Data System (ADS)

Liu, Dongfeng; Wang, Chinhua

2010-01-01

We report a novel single linearly polarized, widely, freely and continuously tunable two wavelengths Yb3+-doped fiber laser. The laser generates stable arbitrary two wavelengths output between 1003.1 and 1080.7 nm peak wavelengths simultaneously with a 346.0 mW CW power by using polarization beam splitting (PBS) for separation of two wavelengths. Each lasing line shows a single polarization with a polarization extinction ratio of >20 dB under different pump levels. The central and the interval of the two wavelengths can be tuned smoothly and independently in the entire gain region of >70 nm of PM Yb3+-doped single mode fiber. Strongly enhanced polarization-hole burning (PHB) phenomena in polarization maintain (PM) Yb3+-doped fiber was observed in the tunable two wavelengths Yb3+-doped fiber laser.

Subdigital setae of chameleon feet: Friction-enhancing microstructures for a wide range of substrate roughness

PubMed Central

Spinner, Marlene; Westhoff, Guido; Gorb, Stanislav N.

2014-01-01

Hairy adhesive systems of microscopic setae with triangular flattened tips have evolved convergently in spiders, insects and arboreal lizards. The ventral sides of the feet and tails in chameleons are also covered with setae. However, chameleon setae feature strongly elongated narrow spatulae or fibrous tips. The friction enhancing function of these microstructures has so far only been demonstrated in contact with glass spheres. In the present study, the frictional properties of subdigital setae of Chamaeleo calyptratus were measured under normal forces in the physical range on plane substrates having different roughness. We showed that chameleon setae maximize friction on a wide range of substrate roughness. The highest friction was measured on asperities of 1 μm. However, our observations of the climbing ability of Ch. calyptratus on rods of different diameters revealed that also claws and grasping feet are additionally responsible for the force generation on various substrates during locomotion. PMID:24970387

Wide speed range turboshaft study

NASA Technical Reports Server (NTRS)

Dangelo, Martin

1995-01-01

NASA-Lewis and NASA-Ames have sponsored a series of studies over the last few years to identify key high speed rotorcraft propulsion and airframe technologies. NASA concluded from these studies that for near term aircraft with cruise speeds up to 450 kt, tilting rotor rotorcraft concepts are the most economical and technologically viable. The propulsion issues critical to tilting rotor rotorcraft are: (1) high speed cruise propulsion system efficiency and (2) adequate power to hover safely with one engine inoperative. High speed cruise propeller efficiency can be dramatically improved by reducing rotor speed, yet high rotor speed is critical for good hover performance. With a conventional turboshaft, this wide range of power turbine operating speeds would result in poor engine performance at one or more of these critical operating conditions. This study identifies several wide speed range turboshaft concepts, and analyzes their potential to improve performance at the diverse cruise and hover operating conditions. Many unique concepts were examined, and the selected concepts are simple, low cost, relatively low risk, and entirely contained within the power turbine. These power turbine concepts contain unique, incidence tolerant airfoil designs that allow the engine to cruise efficiently at 51 percent of the hover rotor speed. Overall propulsion system efficiency in cruise is improved as much as 14 percent, with similar improvements in engine weight and cost. The study is composed of a propulsion requirement survey, a concept screening study, a preliminary definition and evaluation of selected concepts, and identification of key technologies and development needs. In addition, a civil transport tilting rotor rotorcraft mission analysis was performed to show the benefit of these concepts versus a conventional turboshaft. Other potential applications for this technology are discussed.

Multi-trait analysis of genome-wide association summary statistics using MTAG.

PubMed

Turley, Patrick; Walters, Raymond K; Maghzian, Omeed; Okbay, Aysu; Lee, James J; Fontana, Mark Alan; Nguyen-Viet, Tuan Anh; Wedow, Robbee; Zacher, Meghan; Furlotte, Nicholas A; Magnusson, Patrik; Oskarsson, Sven; Johannesson, Magnus; Visscher, Peter M; Laibson, David; Cesarini, David; Neale, Benjamin M; Benjamin, Daniel J

2018-02-01

We introduce multi-trait analysis of GWAS (MTAG), a method for joint analysis of summary statistics from genome-wide association studies (GWAS) of different traits, possibly from overlapping samples. We apply MTAG to summary statistics for depressive symptoms (N eff  = 354,862), neuroticism (N = 168,105), and subjective well-being (N = 388,538). As compared to the 32, 9, and 13 genome-wide significant loci identified in the single-trait GWAS (most of which are themselves novel), MTAG increases the number of associated loci to 64, 37, and 49, respectively. Moreover, association statistics from MTAG yield more informative bioinformatics analyses and increase the variance explained by polygenic scores by approximately 25%, matching theoretical expectations.

Wide distribution of virulence genes among Enterococcus faecium and Enterococcus faecalis clinical isolates.

PubMed

Soheili, Sara; Ghafourian, Sobhan; Sekawi, Zamberi; Neela, Vasanthakumari; Sadeghifard, Nourkhoda; Ramli, Ramliza; Hamat, Rukman Awang

2014-01-01

Enterococcus, a Gram-positive facultative anaerobic cocci belonging to the lactic acid bacteria of the phylum Firmicutes, is known to be able to resist a wide range of hostile conditions such as different pH levels, high concentration of NaCl (6.5%), and the extended temperatures between 5(°)C and 65(°)C. Despite being the third most common nosocomial pathogen, our understanding on its virulence factors is still poorly understood. The current study was aimed to determine the prevalence of different virulence genes in Enterococcus faecalis and Enterococcus faecium. For this purpose, 79 clinical isolates of Malaysian enterococci were evaluated for the presence of virulence genes. pilB, fms8, efaAfm, and sgrA genes are prevalent in all clinical isolates. In conclusion, the pathogenicity of E. faecalis and E. faecium could be associated with different virulence factors and these genes are widely distributed among the enterococcal species.

Wide Distribution of Virulence Genes among Enterococcus faecium and Enterococcus faecalis Clinical Isolates

PubMed Central

Soheili, Sara; Ghafourian, Sobhan; Sekawi, Zamberi; Neela, Vasanthakumari; Sadeghifard, Nourkhoda; Ramli, Ramliza; Hamat, Rukman Awang

2014-01-01

Enterococcus, a Gram-positive facultative anaerobic cocci belonging to the lactic acid bacteria of the phylum Firmicutes, is known to be able to resist a wide range of hostile conditions such as different pH levels, high concentration of NaCl (6.5%), and the extended temperatures between 5°C and 65°C. Despite being the third most common nosocomial pathogen, our understanding on its virulence factors is still poorly understood. The current study was aimed to determine the prevalence of different virulence genes in Enterococcus faecalis and Enterococcus faecium. For this purpose, 79 clinical isolates of Malaysian enterococci were evaluated for the presence of virulence genes. pilB, fms8, efaAfm, and sgrA genes are prevalent in all clinical isolates. In conclusion, the pathogenicity of E. faecalis and E. faecium could be associated with different virulence factors and these genes are widely distributed among the enterococcal species. PMID:25147855

Silk gland-specific proteinase inhibitor serpin16 from the Bombyx mori shows cysteine proteinase inhibitory activity.

PubMed

Guo, Peng-Chao; Dong, Zhaoming; Xiao, Li; Li, Tao; Zhang, Yan; He, Huawei; Xia, Qingyou; Zhao, Ping

2015-01-30

Serpins (serine proteinase inhibitors) are widely distributed in different species and are well known for their inhibitory activities towards serine proteinases. Here, we report the functional characterization of Bombyx mori serpin16. Expression analysis showed that serpin16 was specifically expressed at high levels in the silk gland at both the transcriptional and translational levels. Moreover, homology modeling and multi-sequence alignment suggested that serpin16 had a canonical serpin fold, but it contained a unique reactive center loop, which was obviously shorter than that of typical serpins. Inhibitory activity analyses revealed that the target proteinase of serpin18 is a cysteine proteinase, rather than a serine proteinase. Furthermore, a Michaelis complex model of serpin16 with its target proteinase was constructed to explain the structural basis of how serpin16 recognizes the cysteine proteinase and its target specificity. Copyright © 2014 Elsevier Inc. All rights reserved.

[The investigation of formant on different artistic voice].

PubMed

Wang, Jianqun; Gao, Xia; Liu, Xiaozhou; Feng, Yulin; Shen, Xiaohui; Yu, Chenjie; Yang, Ye

2008-08-01

To explore the characteristic of formant-a very important parameter in the spectrogram of three types of artistic voice (western mode; Chinese mode; Beijing opera). We used MATLAB software to make the short-time Fourier transform and spectrogram analysis on the homeostasis vowel examples of the three types. The western mode had different representation "singer formant" (Fs) based on the voice part; the Chinese mode's notable features were that F1, F2, F3, were continuous and the energy of them changed softly; the Beijing opera had the common representation which was a very wide formant and there was soft transition between formants and various harmonic, besides it showed a similar component like the "Fs" (two formants connected normally). Different artistic voice showed their own characteristics of the formant parameter in the spectrogram, which had important value on the identification, objective evaluation and prediction.

Simulation studies of a wide area health care network.

PubMed Central

McDaniel, J. G.

1994-01-01

There is an increasing number of efforts to install wide area health care networks. Some of these networks are being built to support several applications over a wide user base consisting primarily of medical practices, hospitals, pharmacies, medical laboratories, payors, and suppliers. Although on-line, multi-media telecommunication is desirable for some purposes such as cardiac monitoring, store-and-forward messaging is adequate for many common, high-volume applications. Laboratory test results and payment claims, for example, can be distributed using electronic messaging networks. Several network prototypes have been constructed to determine the technical problems and to assess the effectiveness of electronic messaging in wide area health care networks. Our project, Health Link, developed prototype software that was able to use the public switched telephone network to exchange messages automatically, reliably and securely. The network could be configured to accommodate the many different traffic patterns and cost constraints of its users. Discrete event simulations were performed on several network models. Canonical star and mesh networks, that were composed of nodes operating at steady state under equal loads, were modeled. Both topologies were found to support the throughput of a generic wide area health care network. The mean message delivery time of the mesh network was found to be less than that of the star network. Further simulations were conducted for a realistic large-scale health care network consisting of 1,553 doctors, 26 hospitals, four medical labs, one provincial lab and one insurer. Two network topologies were investigated: one using predominantly peer-to-peer communication, the other using client-server communication.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7949966

New Inspiring Planetarium Show Introduces ALMA to the Public

NASA Astrophysics Data System (ADS)

2009-03-01

As part of a wide range of education and public outreach activities for the International Year of Astronomy 2009 (IYA2009), ESO, together with the Association of French Language Planetariums (APLF), has produced a 30-minute planetarium show, In Search of our Cosmic Origins. It is centred on the global ground-based astronomical Atacama Large Millimeter/submillimeter Array (ALMA) project and represents a unique chance for planetariums to be associated with the IYA2009. ESO PR Photo 09a/09 Logo of the ALMA Planetarium Show ESO PR Photo 09b/09 Galileo's first observations with a telescope ESO PR Photo 09c/09 The ALMA Observatory ESO PR Photo 09d/09 The Milky Way band ESO PR Video 09a/09 Trailer in English ALMA is the leading telescope for observing the cool Universe -- the relic radiation of the Big Bang, and the molecular gas and dust that constitute the building blocks of stars, planetary systems, galaxies and life itself. It is currently being built in the extremely arid environment of the Chajnantor plateau, at 5000 metres altitude in the Chilean Andes, and will start scientific observations around 2011. ALMA, the largest current astronomical project, is a revolutionary telescope, comprising a state-of-the-art array of 66 giant 12-metre and 7-metre diameter antennas observing at millimetre and submillimetre wavelengths. In Search of our Cosmic Origins highlights the unprecedented window on the Universe that this facility will open for astronomers. "The show gives viewers a fascinating tour of the highest observatory on Earth, and takes them from there out into our Milky Way, and beyond," says Douglas Pierce-Price, the ALMA Public Information Officer at ESO. Edited by world fulldome experts Mirage3D, the emphasis of the new planetarium show is on the incomparable scientific adventure of the ALMA project. A young female astronomer guides the audience through a story that includes unique animations and footage, leading the viewer from the first observations by Galileo

Genome-wide analyses of four major histone modifications in Arabidopsis hybrids at the germinating seed stage.

PubMed

Zhu, Anyu; Greaves, Ian K; Dennis, Elizabeth S; Peacock, W James

2017-02-07

Hybrid vigour (heterosis) has been used for decades in cropping agriculture, especially in the production of maize and rice, because hybrid varieties exceed their parents in plant biomass and seed yield. The molecular basis of hybrid vigour is not fully understood. Previous studies have suggested that epigenetic systems could play a role in heterosis. In this project, we investigated genome-wide patterns of four histone modifications in Arabidopsis hybrids in germinating seeds. We found that although hybrids have similar histone modification patterns to the parents in most regions of the genome, they have altered patterns at specific loci. A small subset of genes show changes in histone modifications in the hybrids that correlate with changes in gene expression. Our results also show that genome-wide patterns of histone modifications in geminating seeds parallel those at later developmental stages of seedlings. Ler/C24 hybrids showed similar genome-wide patterns of histone modifications as the parents at an early germination stage. However, a small subset of genes, such as FLC, showed correlated changes in histone modification and in gene expression in the hybrids. The altered patterns of histone modifications for those genes in hybrids could be related to some heterotic traits in Arabidopsis, such as flowering time, and could play a role in hybrid vigour establishment.

WIDE BAND REGENERATIVE FREQUENCY DIVIDER AND MULTIPLIER

DOEpatents

Laine, E.F.

1959-11-17

A regenerative frequency divider and multiplier having wide band input characteristics is presented. The circuit produces output oscillations having frequencies related by a fixed ratio to input oscillations over a wide band of frequencies. In accomplishing this end, the divider-multiplier includes a wide band input circuit coupled by mixer means to a wide band output circuit having a pass band related by a fixed ratio to that of the input circuit. A regenerative feedback circuit derives a fixed frequency ratio feedback signal from the output circuit and applies same to the mixer means in proper phase relation to sustain fixed frequency ratio oscillations in the output circuit.

Image Maps in the World-Wide Web: The Uses and Limitations.

ERIC Educational Resources Information Center

Cochenour, John J.; And Others

A study of nine different image maps from World Wide Web home pages was conducted to evaluate their effectiveness in information display and access, relative to visual, navigational, and practical characteristics. Nine independent viewers completed 20-question surveys on the image maps, in which they evaluated the characteristics of the maps on a…

Wide Bandgap Extrinsic Photoconductive Switches

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

Sullivan, James S.

2013-07-03

Semi-insulating Gallium Nitride, 4H and 6H Silicon Carbide are attractive materials for compact, high voltage, extrinsic, photoconductive switches due to their wide bandgap, high dark resistance, high critical electric field strength and high electron saturation velocity. These wide bandgap semiconductors are made semi-insulating by the addition of vanadium (4H and 6HSiC) and iron (2H-GaN) impurities that form deep acceptors. These deep acceptors trap electrons donated from shallow donor impurities. The electrons can be optically excited from these deep acceptor levels into the conduction band to transition the wide bandgap semiconductor materials from a semi-insulating to a conducting state. Extrinsic photoconductivemore » switches with opposing electrodes have been constructed using vanadium compensated 6H-SiC and iron compensated 2H-GaN. These extrinsic photoconductive switches were tested at high voltage and high power to determine if they could be successfully used as the closing switch in compact medical accelerators.« less

Vibration Sensitivity of a Wide-Temperature Electronically Scanned Pressure Measurement (ESP) Module

NASA Technical Reports Server (NTRS)

Zuckerwar, Allan J.; Garza, Frederico R.

2001-01-01

A vibration sensitivity test was conducted on a Wide-Temperature ESP module. The test object was Module "M4," a 16-channel, 4 psi unit scheduled for installation in the Arc Sector of NTF. The module was installed on a vibration exciter and loaded to positive then negative full-scale pressures (+/-2.5 psid). Test variables were the following: Vibration frequencies: 20, 55, 75 Hz. Vibration level: 1 g. Vibration axes: X, Y, Z. The pressure response was measured on each channel, first without and then with the vibration turned on, and the difference analyzed by means of the statistical t-test. The results show that the vibration sensitivity does not exceed 0.01% Full Scale Output per g (with the exception of one channel on one axis) to a 95 percent confidence level. This specification, limited by the resolution of the pressure source, lies well below the total uncertainty specification of 0.1 percent Full Scale Output.

Feature-Based Visual Short-Term Memory Is Widely Distributed and Hierarchically Organized.

PubMed

Dotson, Nicholas M; Hoffman, Steven J; Goodell, Baldwin; Gray, Charles M

2018-06-15

Feature-based visual short-term memory is known to engage both sensory and association cortices. However, the extent of the participating circuit and the neural mechanisms underlying memory maintenance is still a matter of vigorous debate. To address these questions, we recorded neuronal activity from 42 cortical areas in monkeys performing a feature-based visual short-term memory task and an interleaved fixation task. We find that task-dependent differences in firing rates are widely distributed throughout the cortex, while stimulus-specific changes in firing rates are more restricted and hierarchically organized. We also show that microsaccades during the memory delay encode the stimuli held in memory and that units modulated by microsaccades are more likely to exhibit stimulus specificity, suggesting that eye movements contribute to visual short-term memory processes. These results support a framework in which most cortical areas, within a modality, contribute to mnemonic representations at timescales that increase along the cortical hierarchy. Copyright © 2018 Elsevier Inc. All rights reserved.

Genome-wide admixture and ecological niche modelling reveal the maintenance of species boundaries despite long history of interspecific gene flow

PubMed Central

De La Torre, Amanda R; Roberts, David R; Aitken, Sally N

2014-01-01

The maintenance of species boundaries despite interspecific gene flow has been a continuous source of interest in evolutionary biology. Many hybridizing species have porous genomes with regions impermeable to introgression, conferring reproductive barriers between species. We used ecological niche modelling to study the glacial and postglacial recolonization patterns between the widely hybridizing spruce species Picea glauca and P. engelmannii in western North America. Genome-wide estimates of admixture based on a panel of 311 candidate gene single nucleotide polymorphisms (SNP) from 290 genes were used to assess levels of admixture and introgression and to identify loci putatively involved in adaptive differences or reproductive barriers between species. Our palaeoclimatic modelling suggests that these two closely related species have a long history of hybridization and introgression, dating to at least 21 000 years ago, yet species integrity is maintained by a combination of strong environmental selection and reduced current interspecific gene flow. Twenty loci showed evidence of divergent selection, including six loci that were both Fst outliers and associated with climatic gradients, and fourteen loci that were either outliers or showed associations with climate. These included genes responsible for carbohydrate metabolism, signal transduction and transcription factors. PMID:24597663

Different approaches to acute organophosphorus poison treatment.

PubMed

Nurulain, Syed Muhammad

2012-07-01

Organophosphorus compounds (OPCs) have a wide variety of applications and are a serious threat for self-poisoning, unintentional misuse, terrorist attack, occupational hazard and warfare attack. The present standard treatment has been reported to be unsatisfactory. Many novel approaches are being used and tested for acute organophosphorus (OP) poison treatment. The bioscavenger concept captured high attention among the scientific community during the last few decades. Other approaches like alkalinisation of blood plasma/serum and use of weak inhibitors against strong inhibitors, though it showed promising results, did not get such wide attention. The introduction of a novel broad-spectrum oxime has also been in focus. In this mini-review, an update of the overview of four different approaches has been discussed. The standard therapy that is atropine+oxime+benzodiazepine along with supportive measures will continue to be the best option with only the replacement of a single oxime to improve its broad-spectrum efficacy.

Wide-Band Heterodyne Submillimetre Wave Spectrometer for Planetary Atmospheres

NASA Technical Reports Server (NTRS)

Schlecht, Erich

2010-01-01

We present calculations and measurements on a passive submillimetre wave spectroscopic sounder to gather data on the thermal structure, dynamics and composition of the upper atmosphere of a planet, e.g. the stratosphere of Jupiter, or the entire thickness of the atmosphere of Mars. The instrument will be capable of measuring wind speeds, temperature, pressure, and key constituent concentrations in the stratosphere of the target planet. This instrument consists of a Schottky diode based front end and a digital back-end spectrometer. It differs from previous space-based spectrometers in its combination of wide tunability (520-590 GHz), and rapid frequency switching between widely spaced lines within that range. This will enable near simultaneous observation of multiple lines, which is critical to the reconstruction of atmospheric pressure and density versus altitude profiles. At the same time frequency accuracy must be high to enable wind speeds to be determined directly by measurement of the line's Doppler shift.

System-wide versus component-specific trust using multiple aids.

PubMed

Keller, David; Rice, Stephen

2010-01-01

Previous research in operator trust toward automated aids has focused primarily on single aids. The current study focuses on how operator trust is affected by the presence of multiple aids. Two competing theories of multiple-trust are presented. A component-specific trust theory predicts that operators will differentially place their trust in automated aids that vary in reliability. A system-wide trust theory predicts that operators will treat multiple imperfect aids as one "system" and merge their trust across aids despite differences in the aids' reliability. A simulated flight task was used to test these theories, whereby operators performed a pursuit tracking task while concurrently monitoring multiple system gauges that were augmented with perfect or imperfect automated aids. The data revealed that a system-wide trust theory best predicted the data; operators merged their trust across both aids, behaving toward a perfectly reliable aid in the same manner as they did towards unreliable aids.

Large differences in the genome organization of different plant Trypanosomatid parasites (Phytomonas spp.) reveal wide evolutionary divergences between taxa.

PubMed

Marín, C; Dollet, M; Pagès, M; Bastien, P

2009-03-01

All currently known plant trypanosomes have been grouped in the genus Phytomonas spp., although they can differ greatly in terms of both their biological properties and effects upon the host. Those parasitizing the phloem sap are specifically associated with lethal syndromes in Latin America, such as, phloem necrosis of coffee, 'Hartrot' of coconut and 'Marchitez sorpresiva' of oil palm, that inflict considerable economic losses in endemic countries. The genomic organization of one group of Phytomonas (D) considered as representative of the genus has been published previously. The present work presents the genomic structure of two representative isolates from the pathogenic phloem-restricted group (H) of Phytomonas, analyzed by pulsed field gel electrophoresis followed by hybridization with chromosome-specific DNA markers. It came as a surprise to observe an extremely different genomic organization in this group as compared with that of group D. Most notably, the chromosome number is 7 in this group (with a genome size of 10 Mb) versus 21 in the group D (totalling 25 Mb). These data unravel an unsuspected genomic diversity within plant trypanosomatids, that may justify a further debate about their division into different genera.

Seedlings of subtropical rainforest species from similar successional guild show different photosynthetic and morphological responses to varying light levels.

PubMed

Lestari, D Puji; Nichols, J Doland

2017-02-01

Restoration using rainforest species in Australia and elsewhere has been limited to a small number of widely known species, mainly pioneer or early successional species, Using the presumed successional status as a guideline for species selection in reforestation should be taken with a caveat since a species' capacity to adjust to light gradients is not easily predicted. This study examined the photosynthetic and growth responses of four Australian subtropical rainforest species in the context of using late successional species in restoration programs. Since the selected species [Sloanea australis ((Benth.) F. Muell.), Cinnamomum oliveri (F. M. Bailey),Caldcluvia paniculosa ((F. Muell.) Hoogland) and Geissois benthamiana (F. Muell.)] are considered late-successional species, this study also discussed the possibility of separating these species according to their acclimation level towards light gradients. Seedlings of four species were grown under four light treatments using neutral density shade cloth (5, 33, 64 and 80% irradiance) during summer November 2014 to February 2015. All species demonstrated a narrow range of photosynthetic acclimation to different light levels, experienced photoinhibition and photodamage in 80% irradiance and allocated more biomass to leaves in 5% irradiance, supporting their classification as late successional species. Cinnamomum oliveri was the only species able to utilize higher irradiance, with a higher light saturated rate of photosynthesis than the other species. Canonical analysis of principal coordinates revealed that the degree of plasticity of each species in response to contrasting irradiance levels varied. This analysis separated the species into three light tolerance classes: obligate shade-adapted species (S. australis and G. benthamiana), high light-adapted species (C. paniculosa) and the generalist (C. oliveri). Overall, this study suggests that the four species can be planted and will grow well under 33-64% irradiance

Maximum likelihood estimators for truncated and censored power-law distributions show how neuronal avalanches may be misevaluated

NASA Astrophysics Data System (ADS)

Langlois, Dominic; Cousineau, Denis; Thivierge, J. P.

2014-01-01

The coordination of activity amongst populations of neurons in the brain is critical to cognition and behavior. One form of coordinated activity that has been widely studied in recent years is the so-called neuronal avalanche, whereby ongoing bursts of activity follow a power-law distribution. Avalanches that follow a power law are not unique to neuroscience, but arise in a broad range of natural systems, including earthquakes, magnetic fields, biological extinctions, fluid dynamics, and superconductors. Here, we show that common techniques that estimate this distribution fail to take into account important characteristics of the data and may lead to a sizable misestimation of the slope of power laws. We develop an alternative series of maximum likelihood estimators for discrete, continuous, bounded, and censored data. Using numerical simulations, we show that these estimators lead to accurate evaluations of power-law distributions, improving on common approaches. Next, we apply these estimators to recordings of in vitro rat neocortical activity. We show that different estimators lead to marked discrepancies in the evaluation of power-law distributions. These results call into question a broad range of findings that may misestimate the slope of power laws by failing to take into account key aspects of the observed data.

Maximum likelihood estimators for truncated and censored power-law distributions show how neuronal avalanches may be misevaluated.

PubMed

Langlois, Dominic; Cousineau, Denis; Thivierge, J P

2014-01-01

The coordination of activity amongst populations of neurons in the brain is critical to cognition and behavior. One form of coordinated activity that has been widely studied in recent years is the so-called neuronal avalanche, whereby ongoing bursts of activity follow a power-law distribution. Avalanches that follow a power law are not unique to neuroscience, but arise in a broad range of natural systems, including earthquakes, magnetic fields, biological extinctions, fluid dynamics, and superconductors. Here, we show that common techniques that estimate this distribution fail to take into account important characteristics of the data and may lead to a sizable misestimation of the slope of power laws. We develop an alternative series of maximum likelihood estimators for discrete, continuous, bounded, and censored data. Using numerical simulations, we show that these estimators lead to accurate evaluations of power-law distributions, improving on common approaches. Next, we apply these estimators to recordings of in vitro rat neocortical activity. We show that different estimators lead to marked discrepancies in the evaluation of power-law distributions. These results call into question a broad range of findings that may misestimate the slope of power laws by failing to take into account key aspects of the observed data.

Liquid Lens module with wide field-of-view and variable focal length

NASA Astrophysics Data System (ADS)

Seo, Sang Won; Han, Seungoh; Seo, Jun Ho; Choi, Woo Bum; Sung, Man Young

2010-12-01

A novel wide angle and variable-focus imaging module based on a miniaturized liquid lens is presented for capsule endoscopy applications. For these applications, it is desirable to have features such as a wide field of view (FOV), variable focus, small size, and low power consumption, thereby taking full advantage of the miniaturized liquid lens. The proposed imaging module has three aspheric plastic lenses for a wide FOV, and one liquid lens that can change the focal length by as much as 24.5 cm with a bias voltage difference of 23 Vrms for variable focusing. The assembled lens module has an overall length of 8.4 mm and a FOV of 120.5°. The realized imaging module including the proposed lenses is small enough to be inserted into a capsule endoscope, and it is expected to improve the diagnostic capability of capsule endoscopes.

Genome-wide association studies to identify rice salt-tolerance markers.

PubMed

Patishtan, Juan; Hartley, Tom N; Fonseca de Carvalho, Raquel; Maathuis, Frans J M

2018-05-01

Salinity is an ever increasing menace that affects agriculture worldwide. Crops such as rice are salt sensitive, but its degree of susceptibility varies widely between cultivars pointing to extensive genetic diversity that can be exploited to identify genes and proteins that are relevant in the response of rice to salt stress. We used a diversity panel of 306 rice accessions and collected phenotypic data after short (6 h), medium (7 d) and long (30 d) salinity treatment (50 mm NaCl). A genome-wide association study (GWAS) was subsequently performed, which identified around 1200 candidate genes from many functional categories, but this was treatment period dependent. Further analysis showed the presence of cation transporters and transcription factors with a known role in salinity tolerance and those that hitherto were not known to be involved in salt stress. Localization analysis of single nucleotide polymorphisms (SNPs) showed the presence of several hundred non-synonymous SNPs (nsSNPs) in coding regions and earmarked specific genomic regions with increased numbers of nsSNPs. It points to components of the ubiquitination pathway as important sources of genetic diversity that could underpin phenotypic variation in stress tolerance. © 2017 John Wiley & Sons Ltd.

Genome-Wide Association Study of Seed Dormancy and the Genomic Consequences of Improvement Footprints in Rice (Oryza sativa L.)

PubMed Central

Lu, Qing; Niu, Xiaojun; Zhang, Mengchen; Wang, Caihong; Xu, Qun; Feng, Yue; Yang, Yaolong; Wang, Shan; Yuan, Xiaoping; Yu, Hanyong; Wang, Yiping; Chen, Xiaoping; Liang, Xuanqiang; Wei, Xinghua

2018-01-01

Seed dormancy is an important agronomic trait affecting grain yield and quality because of pre-harvest germination and is influenced by both environmental and genetic factors. However, our knowledge of the factors controlling seed dormancy remains limited. To better reveal the molecular mechanism underlying this trait, a genome-wide association study was conducted in an indica-only population consisting of 453 accessions genotyped using 5,291 SNPs. Nine known and new significant SNPs were identified on eight chromosomes. These lead SNPs explained 34.9% of the phenotypic variation, and four of them were designed as dCAPS markers in the hope of accelerating molecular breeding. Moreover, a total of 212 candidate genes was predicted and eight candidate genes showed plant tissue-specific expression in expression profile data from different public bioinformatics databases. In particular, LOC_Os03g10110, which had a maize homolog involved in embryo development, was identified as a candidate regulator for further biological function investigations. Additionally, a polymorphism information content ratio method was used to screen improvement footprints and 27 selective sweeps were identified, most of which harbored domestication-related genes. Further studies suggested that three significant SNPs were adjacent to the candidate selection signals, supporting the accuracy of our genome-wide association study (GWAS) results. These findings show that genome-wide screening for selective sweeps can be used to identify new improvement-related DNA regions, although the phenotypes are unknown. This study enhances our knowledge of the genetic variation in seed dormancy, and the new dormancy-associated SNPs will provide real benefits in molecular breeding. PMID:29354150

Investigating gender differences in alcohol problems: a latent trait modeling approach.

PubMed

Nichol, Penny E; Krueger, Robert F; Iacono, William G

2007-05-01

Inconsistent results have been found in research investigating gender differences in alcohol problems. Previous studies of gender differences used a wide range of methodological techniques, as well as limited assortments of alcohol problems. Parents (1,348 men and 1,402 women) of twins enrolled in the Minnesota Twin Family Study answered questions about a wide range of alcohol problems. A latent trait modeling technique was used to evaluate gender differences in the probability of endorsement at the problem level and for the overall 105-problem scale. Of the 34 problems that showed significant gender differences, 29 were more likely to be endorsed by men than women with equivalent overall alcohol problem levels. These male-oriented symptoms included measures of heavy drinking, duration of drinking, tolerance, and acting out behaviors. Nineteen symptoms were denoted for removal to create a scale that favored neither gender in assessment. Significant gender differences were found in approximately one-third of the symptoms assessed and in the overall scale. Further examination of the nature of gender differences in alcohol problem symptoms should be undertaken to investigate whether a gender-neutral scale should be created or if men and women should be assessed with separate criteria for alcohol dependence and abuse.

Weighted south-wide average pulpwood prices

Treesearch

James E. Granskog; Kevin D. Growther

1991-01-01

Weighted average prices provide a more accurate representation of regional pulpwood price trends when production volumes valy widely by state. Unweighted South-wide average delivered prices for pulpwood, as reported by Timber Mart-South, were compared to average annual prices weighted by each state's pulpwood production from 1977 to 1986. Weighted average prices...

Innovation in Science Education - World-Wide.

ERIC Educational Resources Information Center

Baez, Albert V.

The purpose of this book is to promote improvements in science education, world-wide, but particularly in developing countries. It is addressed to those in positions to make effective contributions to the improvement of science education. The world-wide role of science education, the goals of innovative activities, past experience in efforts to…

Application of Economic Analysis to School-Wide Positive Behavior Support (SWPBS) Programs

ERIC Educational Resources Information Center

Blonigen, Bruce A.; Harbaugh, William T.; Singell, Larry D.; Horner, Robert H.; Irvin, Larry K.; Smolkowski, Keith S.

2008-01-01

The authors discuss how to use economic techniques to evaluate educational programs and show how to apply basic cost analysis to implementation of school-wide positive behavior support (SWPBS). A description of cost analysis concepts used for economic program evaluation is provided, emphasizing the suitability of these concepts for evaluating…

Wide-undermining neck liposuction: tips and tricks for good results.

PubMed

Innocenti, Alessandro; Andretto Amodeo, Chiara; Ciancio, Francesco

2014-08-01

Neck rejuvenation is one of the most sought after procedures in the restoration of the facial contour. Numerous techniques to improve the aesthetic outcome and reduce downtime have been described. In our experience, wide undermining and local anesthesia are key to obtaining good results in selected patients who want a quick recovery. This article presents our experience with liposuction of the neck and proposes some tips and tricks to master wide-undermining neck liposuction. From January 2005 to September 2012, a total of 118 patients (34 males, 84 females) underwent neck liposuction. Patient selection was based mainly on age and neck-aging features. The procedure was performed with the patients under local anesthesia. A wide rhomboid-shaped skin undermining of the submandibular and neck area was performed and a very thin fat layer was preserved. Dressing was applied for 3 days. Improvement of the neck's contour was observed in all patients. Redefinition of the cervicomandibular angle and skin redraping of the cervical area occurred in all cases. No further touch-ups were needed. Edema and ecchymosis resolved in a few days. No major complications were observed. Our results show that wide-undermining neck liposuction performed under local anesthesia is an effective and safe procedure. Patient selection based on age and anatomical features was fundamental to obtain impressive improvement of neck contour. This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

Different Duck Species Infected Intramuscularly with Duck-Origin Genotype IX APMV-1 Show Discrepant Mortality and Indicate Another Fatal Genotype APMV-1 to Ducks.

PubMed

Fu, Guanghua; Cheng, Longfei; Fu, Qiuling; Qi, Baomin; Chen, Cuiteng; Shi, Shaohua; Chen, Hongmei; Wan, Chunhe; Liu, Rongchang; Huang, Yu

2017-03-01

Isolations of genotype IX (gIX) avian paramyxovirus type 1 (APMV-1) from various bird species have been more common recently, with isolates showing variable pathogenicity in different species of poultry. Here we sequenced the genome of a Muscovy duck origin gIX virus strain XBT14 and characterized the virulence and pathogenicity of this isolate in chickens and ducks. The genome sequence of strain XBT14 is 15,192 nt in length, containing multiple basic amino acids at the fusion protein cleavage site. The XBT14 strain shared 91.6%-91.9% nucleotide identities with early-genotype viruses (such as genotype III and IV) and shared 85.3%-85.9% nucleotide homologies with later genotype viruses (such as genotype VII). Pathogenicity tests showed that strain XBT14 could cause death in different duck breeds with a mortality rate of 44.4% in Muscovy duck, 25.9% in Sheldrake, and 11.1% in Cherry Valley duck, respectively. Similar mortality discrepancies were also observed in different ducks when infected with chicken-origin gIX virus strain F48E8. These results indicate that XBT14-like velogenic gIX APMV-1 (such as XBT14, F48E8, and GD09-2) could cause fatal infection in duck, and genotype IX is another genotype velogenic to duck as well as genotype VII. Accompanied by genetic differences in the vaccine strains or dominant strains prevailing in poultry, the virulent XBT14-like gIX viruses might become potentially endemic strains in poultry in the future.

Video game players show higher performance but no difference in speed of attention shifts.

PubMed

Mack, David J; Wiesmann, Helene; Ilg, Uwe J

2016-09-01

Video games have become both a widespread leisure activity and a substantial field of research. In a variety of tasks, video game players (VGPs) perform better than non-video game players (NVGPs). This difference is most likely explained by an alteration of the basic mechanisms underlying visuospatial attention. More specifically, the present study hypothesizes that VGPs are able to shift attention faster than NVGPs. Such alterations in attention cannot be disentangled from changes in stimulus-response mappings in reaction time based measurements. Therefore, we used a spatial cueing task with varying cue lead times (CLTs) to investigate the speed of covert attention shifts of 98 male participants divided into 36 NVGPs and 62 VGPs based on their weekly gaming time. VGPs exhibited higher peak and mean performance than NVGPs. However, we did not find any differences in the speed of covert attention shifts as measured by the CLT needed to achieve peak performance. Thus, our results clearly rule out faster stimulus-response mappings as an explanation for the higher performance of VGPs in line with previous studies. More importantly, our data do not support the notion of faster attention shifts in VGPs as another possible explanation. Copyright © 2016 Elsevier B.V. All rights reserved.

The Land of Confusion? High School Students and Their Use of the World Wide Web for Research.

ERIC Educational Resources Information Center

Lorenzen, Michael

2002-01-01

Examines high school students' use of the World Wide Web to complete assignments. Findings showed the students used a good variety of resources, including libraries and the World Wide Web, to find information for assignments. However, students were weak at determining the quality of the information found on web sites. Students did poorly at…

Modelling seasonal habitat suitability for wide-ranging species: Invasive wild pigs in northern Australia.